Query 025493
Match_columns 252
No_of_seqs 131 out of 234
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 06:24:36 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025493.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025493hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05158 RNA_pol_Rpc34: RNA po 100.0 3.3E-78 7.1E-83 562.3 7.6 236 8-251 54-327 (327)
2 KOG3233 RNA polymerase III, su 100.0 1.2E-73 2.5E-78 513.7 16.6 224 8-250 54-296 (297)
3 COG5111 RPC34 DNA-directed RNA 100.0 4.2E-63 9.2E-68 436.8 15.9 226 7-251 54-301 (301)
4 PF04182 B-block_TFIIIC: B-blo 98.3 2.5E-06 5.4E-11 63.7 7.7 65 35-102 1-68 (75)
5 COG2512 Predicted membrane-ass 98.0 2E-05 4.4E-10 72.0 7.9 56 31-90 190-245 (258)
6 PF12802 MarR_2: MarR family; 97.9 7.2E-05 1.6E-09 52.5 7.9 58 33-93 2-59 (62)
7 TIGR01889 Staph_reg_Sar staphy 97.9 0.00014 2.9E-09 57.6 10.2 85 33-137 22-108 (109)
8 PF01978 TrmB: Sugar-specific 97.8 5E-05 1.1E-09 55.0 5.6 62 33-103 5-66 (68)
9 PF13412 HTH_24: Winged helix- 97.8 8.9E-05 1.9E-09 50.1 6.4 48 34-86 1-48 (48)
10 PF13730 HTH_36: Helix-turn-he 97.8 0.00011 2.3E-09 50.9 6.7 52 32-85 1-55 (55)
11 PF01047 MarR: MarR family; I 97.6 0.00035 7.6E-09 48.7 7.1 55 34-93 1-55 (59)
12 PRK03573 transcriptional regul 97.6 0.0015 3.3E-08 53.4 11.9 66 32-101 27-92 (144)
13 PF13463 HTH_27: Winged helix 97.5 0.00051 1.1E-08 48.9 7.5 64 34-101 1-64 (68)
14 smart00550 Zalpha Z-DNA-bindin 97.5 0.00041 8.8E-09 50.9 6.6 51 35-88 5-55 (68)
15 COG1846 MarR Transcriptional r 97.5 0.00061 1.3E-08 52.4 7.6 63 34-101 20-82 (126)
16 TIGR02337 HpaR homoprotocatech 97.5 0.00069 1.5E-08 53.8 8.0 65 32-101 24-88 (118)
17 PRK10870 transcriptional repre 97.4 0.00071 1.5E-08 58.0 8.3 61 31-94 50-110 (176)
18 TIGR02698 CopY_TcrY copper tra 97.4 0.0063 1.4E-07 50.0 13.4 53 33-88 1-55 (130)
19 smart00347 HTH_MARR helix_turn 97.4 0.0012 2.6E-08 49.3 8.1 57 32-93 6-62 (101)
20 PRK11512 DNA-binding transcrip 97.2 0.0018 3.9E-08 53.2 8.2 59 32-95 36-94 (144)
21 PF03965 Penicillinase_R: Peni 97.1 0.014 3.1E-07 46.4 11.8 111 34-174 1-113 (115)
22 PRK13777 transcriptional regul 97.1 0.0027 5.9E-08 55.4 8.2 57 32-93 41-97 (185)
23 PF01726 LexA_DNA_bind: LexA D 96.9 0.0015 3.3E-08 47.8 4.5 58 31-90 1-61 (65)
24 PF05158 RNA_pol_Rpc34: RNA po 96.8 0.018 3.9E-07 54.4 12.1 133 33-205 6-148 (327)
25 COG1522 Lrp Transcriptional re 96.5 0.015 3.1E-07 47.7 7.7 71 31-106 3-78 (154)
26 TIGR02702 SufR_cyano iron-sulf 96.3 0.014 3E-07 50.9 7.3 64 38-107 3-66 (203)
27 TIGR01884 cas_HTH CRISPR locus 96.3 0.018 4E-07 50.1 8.1 55 31-90 138-192 (203)
28 PF08784 RPA_C: Replication pr 96.3 0.01 2.2E-07 46.2 5.8 53 33-87 44-97 (102)
29 COG3355 Predicted transcriptio 96.3 0.023 5E-07 47.0 7.9 71 32-107 23-93 (126)
30 TIGR00498 lexA SOS regulatory 96.2 0.014 3E-07 50.3 6.8 56 32-89 2-60 (199)
31 cd00090 HTH_ARSR Arsenical Res 96.2 0.041 8.9E-07 38.2 7.9 58 35-101 6-63 (78)
32 PF02082 Rrf2: Transcriptional 96.1 0.034 7.4E-07 41.7 7.6 62 41-111 13-75 (83)
33 PF09012 FeoC: FeoC like trans 95.9 0.019 4.1E-07 41.9 5.2 47 131-185 3-49 (69)
34 PRK00215 LexA repressor; Valid 95.9 0.023 4.9E-07 49.3 6.5 54 34-89 2-58 (205)
35 smart00344 HTH_ASNC helix_turn 95.9 0.022 4.7E-07 44.2 5.8 53 34-91 1-53 (108)
36 PF13601 HTH_34: Winged helix 95.8 0.015 3.3E-07 44.0 4.2 43 51-95 12-54 (80)
37 TIGR01610 phage_O_Nterm phage 95.5 0.058 1.3E-06 41.8 6.7 58 30-89 19-81 (95)
38 COG3888 Predicted transcriptio 95.5 0.042 9.1E-07 50.9 6.7 62 35-101 4-65 (321)
39 PF02295 z-alpha: Adenosine de 95.5 0.037 8.1E-07 40.6 5.2 51 35-88 3-53 (66)
40 smart00420 HTH_DEOR helix_turn 95.5 0.079 1.7E-06 35.0 6.5 46 39-89 3-48 (53)
41 PF12840 HTH_20: Helix-turn-he 95.2 0.12 2.7E-06 36.4 7.2 50 36-90 10-59 (61)
42 PF09339 HTH_IclR: IclR helix- 94.9 0.055 1.2E-06 37.1 4.6 43 41-87 8-50 (52)
43 COG1725 Predicted transcriptio 94.9 0.2 4.4E-06 41.3 8.5 86 49-154 31-118 (125)
44 PF14947 HTH_45: Winged helix- 94.7 0.046 9.9E-07 40.8 4.0 55 39-103 6-60 (77)
45 PF00325 Crp: Bacterial regula 94.7 0.064 1.4E-06 34.2 3.9 30 54-85 3-32 (32)
46 PRK06474 hypothetical protein; 94.4 0.54 1.2E-05 40.5 10.5 130 36-175 11-149 (178)
47 PHA02943 hypothetical protein; 94.3 0.29 6.3E-06 42.0 8.3 113 40-177 15-137 (165)
48 PRK04172 pheS phenylalanyl-tRN 94.2 0.18 4E-06 49.8 8.1 62 33-103 3-64 (489)
49 PF04703 FaeA: FaeA-like prote 94.2 0.28 6.1E-06 35.7 7.0 49 40-92 4-52 (62)
50 PF01638 HxlR: HxlR-like helix 94.1 0.15 3.4E-06 38.8 5.8 53 50-103 15-67 (90)
51 smart00529 HTH_DTXR Helix-turn 94.1 0.55 1.2E-05 35.4 8.9 33 56-90 2-34 (96)
52 PRK14165 winged helix-turn-hel 94.0 0.2 4.4E-06 44.8 7.3 130 49-204 17-170 (217)
53 PF01325 Fe_dep_repress: Iron 94.0 0.27 5.9E-06 35.2 6.5 45 39-88 11-55 (60)
54 TIGR03433 padR_acidobact trans 94.0 0.19 4.1E-06 39.1 6.2 63 38-101 6-73 (100)
55 TIGR02944 suf_reg_Xantho FeS a 93.8 0.19 4.2E-06 40.4 6.2 52 35-89 8-59 (130)
56 PF01475 FUR: Ferric uptake re 93.7 0.38 8.3E-06 38.1 7.6 57 127-186 7-64 (120)
57 cd00092 HTH_CRP helix_turn_hel 93.7 0.2 4.3E-06 35.1 5.3 36 51-88 23-58 (67)
58 COG3398 Uncharacterized protei 93.7 0.94 2E-05 41.1 10.7 124 34-184 99-222 (240)
59 PF10007 DUF2250: Uncharacteri 93.6 0.23 5E-06 39.0 6.0 72 34-116 5-79 (92)
60 PF08672 APC2: Anaphase promot 93.6 0.13 2.9E-06 37.1 4.3 51 133-183 2-54 (60)
61 smart00418 HTH_ARSR helix_turn 93.5 0.33 7.1E-06 32.7 6.0 37 51-89 8-44 (66)
62 TIGR00738 rrf2_super rrf2 fami 93.3 1.1 2.3E-05 35.9 9.6 39 49-89 21-59 (132)
63 PRK11169 leucine-responsive tr 93.2 0.19 4.1E-06 42.5 5.4 58 31-93 9-66 (164)
64 PF04703 FaeA: FaeA-like prote 92.9 0.2 4.4E-06 36.5 4.4 49 129-185 1-50 (62)
65 PRK09334 30S ribosomal protein 92.8 0.28 6.1E-06 38.1 5.3 57 40-100 27-84 (86)
66 smart00346 HTH_ICLR helix_turn 92.7 0.42 9E-06 35.5 6.1 46 39-88 8-53 (91)
67 smart00345 HTH_GNTR helix_turn 92.4 0.58 1.3E-05 31.6 6.0 34 53-88 19-53 (60)
68 PF01022 HTH_5: Bacterial regu 92.3 0.5 1.1E-05 31.7 5.5 34 52-87 14-47 (47)
69 COG1378 Predicted transcriptio 92.3 0.49 1.1E-05 43.1 7.0 62 32-102 12-73 (247)
70 KOG2165 Anaphase-promoting com 92.2 1.7 3.7E-05 45.1 11.4 142 32-183 598-757 (765)
71 PRK12423 LexA repressor; Provi 92.1 0.4 8.6E-06 41.9 6.1 56 33-90 3-61 (202)
72 COG1733 Predicted transcriptio 92.1 0.36 7.9E-06 39.3 5.5 48 56-104 39-86 (120)
73 PRK11014 transcriptional repre 92.1 0.48 1E-05 38.9 6.3 52 37-91 7-61 (141)
74 PF03297 Ribosomal_S25: S25 ri 92.1 0.39 8.4E-06 38.6 5.5 57 40-100 45-102 (105)
75 smart00419 HTH_CRP helix_turn_ 91.9 0.39 8.4E-06 31.3 4.5 32 54-87 9-40 (48)
76 PF06224 HTH_42: Winged helix 91.6 6.1 0.00013 36.3 13.7 124 38-186 87-217 (327)
77 cd00131 PAX Paired Box domain 91.6 5.2 0.00011 32.7 11.8 109 32-173 16-126 (128)
78 PF03551 PadR: Transcriptional 91.6 0.3 6.5E-06 35.7 4.0 38 66-103 28-67 (75)
79 cd07153 Fur_like Ferric uptake 91.5 1 2.3E-05 35.1 7.3 55 130-187 3-58 (116)
80 PRK09462 fur ferric uptake reg 91.1 1.7 3.6E-05 36.0 8.5 55 129-186 18-74 (148)
81 TIGR02010 IscR iron-sulfur clu 91.0 0.75 1.6E-05 37.5 6.3 48 42-91 14-61 (135)
82 PRK10857 DNA-binding transcrip 90.9 0.66 1.4E-05 39.6 6.1 48 49-102 21-68 (164)
83 PRK10402 DNA-binding transcrip 90.9 1 2.2E-05 39.2 7.5 60 33-101 148-209 (226)
84 PRK11179 DNA-binding transcrip 90.8 0.76 1.6E-05 38.2 6.2 54 33-91 6-59 (153)
85 PRK06266 transcription initiat 90.6 2.6 5.6E-05 36.6 9.6 50 35-89 21-70 (178)
86 cd07153 Fur_like Ferric uptake 90.5 1.7 3.8E-05 33.8 7.7 59 39-101 4-65 (116)
87 PRK03902 manganese transport t 90.4 0.84 1.8E-05 37.4 6.1 47 37-88 9-55 (142)
88 PHA00738 putative HTH transcri 90.3 1.1 2.3E-05 36.3 6.3 50 35-89 11-60 (108)
89 smart00351 PAX Paired Box doma 90.2 4.5 9.8E-05 32.8 10.1 93 33-158 17-109 (125)
90 PF05732 RepL: Firmicute plasm 90.1 0.59 1.3E-05 40.1 5.1 60 38-108 57-119 (165)
91 smart00550 Zalpha Z-DNA-bindin 90.1 1.2 2.6E-05 32.4 6.0 50 127-184 5-56 (68)
92 TIGR02719 repress_PhaQ poly-be 89.9 1.1 2.3E-05 37.6 6.3 64 38-102 26-92 (138)
93 PRK09954 putative kinase; Prov 89.8 1.2 2.6E-05 41.6 7.4 50 34-88 1-50 (362)
94 PF08279 HTH_11: HTH domain; 89.7 1.7 3.6E-05 29.6 6.2 41 39-83 3-43 (55)
95 smart00420 HTH_DEOR helix_turn 89.4 2.2 4.9E-05 27.8 6.6 46 131-184 3-48 (53)
96 TIGR03697 NtcA_cyano global ni 89.4 1.2 2.6E-05 37.0 6.4 61 32-101 111-183 (193)
97 PRK09391 fixK transcriptional 89.1 0.91 2E-05 39.8 5.6 55 31-87 150-211 (230)
98 PF09202 Rio2_N: Rio2, N-termi 89.0 2.2 4.8E-05 32.6 6.9 59 32-93 2-61 (82)
99 PRK11050 manganese transport r 88.9 1.2 2.6E-05 37.2 6.1 45 39-88 40-84 (152)
100 cd07377 WHTH_GntR Winged helix 88.9 0.78 1.7E-05 31.5 4.2 32 55-88 27-58 (66)
101 PF09012 FeoC: FeoC like trans 88.8 1.5 3.2E-05 31.7 5.7 47 40-91 4-50 (69)
102 COG1654 BirA Biotin operon rep 88.7 1.5 3.4E-05 33.3 5.9 69 38-111 5-73 (79)
103 PF08220 HTH_DeoR: DeoR-like h 88.6 2.2 4.8E-05 29.9 6.3 46 39-89 3-48 (57)
104 PF01978 TrmB: Sugar-specific 88.5 1.4 3.1E-05 31.4 5.4 50 128-185 8-57 (68)
105 smart00421 HTH_LUXR helix_turn 88.4 2 4.4E-05 28.2 5.8 43 32-81 2-44 (58)
106 PRK13918 CRP/FNR family transc 88.3 1.6 3.4E-05 36.8 6.4 60 33-101 118-189 (202)
107 PRK11161 fumarate/nitrate redu 88.3 1.2 2.7E-05 38.6 5.9 53 32-87 152-216 (235)
108 PRK10411 DNA-binding transcrip 87.3 8.8 0.00019 34.5 10.9 121 36-170 4-130 (240)
109 PF01475 FUR: Ferric uptake re 87.2 2.1 4.6E-05 33.8 6.2 66 34-103 6-74 (120)
110 PF13412 HTH_24: Winged helix- 87.2 2.9 6.2E-05 27.8 5.9 47 127-181 2-48 (48)
111 COG3432 Predicted transcriptio 87.2 0.87 1.9E-05 36.0 3.8 60 39-104 18-77 (95)
112 PRK10430 DNA-binding transcrip 87.1 3.4 7.4E-05 35.9 8.0 58 32-92 157-216 (239)
113 PRK11920 rirA iron-responsive 86.9 2.3 5E-05 35.7 6.5 42 50-93 21-62 (153)
114 PRK09462 fur ferric uptake reg 86.7 5.3 0.00011 33.0 8.6 65 33-100 14-81 (148)
115 PRK10141 DNA-binding transcrip 86.7 4.5 9.8E-05 32.9 7.9 56 30-90 9-65 (117)
116 PRK15431 ferrous iron transpor 86.6 4.5 9.8E-05 30.9 7.3 45 132-184 6-50 (78)
117 PRK11753 DNA-binding transcrip 86.4 2.9 6.2E-05 35.4 7.0 54 31-87 136-200 (211)
118 PF13034 DUF3895: Protein of u 86.3 3.7 8.1E-05 31.4 6.7 61 128-188 4-71 (78)
119 PF07106 TBPIP: Tat binding pr 86.1 18 0.00038 30.6 11.6 109 38-156 3-122 (169)
120 PRK05638 threonine synthase; V 85.6 2.9 6.3E-05 40.8 7.4 61 34-102 369-431 (442)
121 PF08784 RPA_C: Replication pr 85.5 1.6 3.5E-05 33.7 4.6 50 126-183 45-98 (102)
122 PRK11920 rirA iron-responsive 85.5 5.2 0.00011 33.6 7.9 37 141-185 23-59 (153)
123 PF05584 Sulfolobus_pRN: Sulfo 85.2 3.6 7.7E-05 31.0 6.0 34 53-88 18-51 (72)
124 PRK10434 srlR DNA-bindng trans 85.1 9.4 0.0002 34.5 10.0 112 37-165 6-124 (256)
125 PHA02943 hypothetical protein; 84.8 4.4 9.5E-05 34.9 7.1 51 126-185 9-59 (165)
126 COG1321 TroR Mn-dependent tran 84.7 3.5 7.7E-05 34.9 6.6 110 39-176 13-122 (154)
127 PHA02701 ORF020 dsRNA-binding 84.5 2.7 5.8E-05 37.0 5.9 50 36-89 4-53 (183)
128 PRK13509 transcriptional repre 84.3 12 0.00027 33.6 10.4 111 38-165 7-125 (251)
129 PF13545 HTH_Crp_2: Crp-like h 84.1 2.1 4.5E-05 30.7 4.4 33 53-87 28-60 (76)
130 COG1777 Predicted transcriptio 84.0 1.4 3.1E-05 39.5 4.0 48 54-103 29-78 (217)
131 COG0735 Fur Fe2+/Zn2+ uptake r 83.9 5.3 0.00012 33.3 7.3 55 130-187 23-78 (145)
132 TIGR00373 conserved hypothetic 83.8 11 0.00023 32.0 9.2 49 36-89 14-62 (158)
133 COG1959 Predicted transcriptio 83.7 3.4 7.3E-05 34.7 6.0 42 50-93 22-63 (150)
134 COG0735 Fur Fe2+/Zn2+ uptake r 83.6 5.5 0.00012 33.2 7.3 59 32-92 17-78 (145)
135 PRK09834 DNA-binding transcrip 83.6 3.6 7.8E-05 37.1 6.6 45 40-88 15-59 (263)
136 PRK09416 lstR lineage-specific 83.4 1.5 3.3E-05 36.7 3.7 68 31-102 38-108 (135)
137 PRK10163 DNA-binding transcrip 83.4 2.7 5.8E-05 38.2 5.8 44 40-87 29-72 (271)
138 PF13551 HTH_29: Winged helix- 82.8 15 0.00033 27.7 9.0 98 52-173 10-110 (112)
139 TIGR02431 pcaR_pcaU beta-ketoa 82.7 2.8 6.1E-05 37.2 5.5 43 41-87 14-56 (248)
140 PF13936 HTH_38: Helix-turn-he 82.4 2.6 5.6E-05 28.1 3.9 41 32-78 3-43 (44)
141 PF08220 HTH_DeoR: DeoR-like h 81.7 4.4 9.5E-05 28.4 5.1 47 130-184 2-48 (57)
142 PF02002 TFIIE_alpha: TFIIE al 81.7 3.2 6.8E-05 32.3 4.8 50 35-89 12-61 (105)
143 PF08461 HTH_12: Ribonuclease 81.5 4.8 0.0001 29.3 5.4 49 132-183 2-51 (66)
144 COG3682 Predicted transcriptio 80.9 4 8.7E-05 33.7 5.3 55 128-186 6-60 (123)
145 PF04492 Phage_rep_O: Bacterio 80.7 6.7 0.00015 31.0 6.4 55 31-87 27-86 (100)
146 TIGR02147 Fsuc_second hypothet 80.4 15 0.00032 34.0 9.5 146 5-174 77-239 (271)
147 PRK15090 DNA-binding transcrip 80.4 4.5 9.8E-05 36.2 6.0 45 42-88 17-61 (257)
148 PRK11569 transcriptional repre 80.1 4.1 8.9E-05 37.0 5.7 43 41-87 33-75 (274)
149 PRK11639 zinc uptake transcrip 80.1 6.6 0.00014 33.5 6.6 53 130-185 28-81 (169)
150 PF14394 DUF4423: Domain of un 79.9 20 0.00043 30.8 9.5 124 30-175 9-142 (171)
151 PF00538 Linker_histone: linke 79.3 13 0.00027 27.5 7.2 57 35-91 3-67 (77)
152 PF01726 LexA_DNA_bind: LexA D 79.3 6.1 0.00013 28.7 5.3 49 129-184 11-60 (65)
153 PRK10906 DNA-binding transcrip 79.3 29 0.00063 31.4 10.9 118 36-170 5-129 (252)
154 PRK09802 DNA-binding transcrip 78.6 28 0.0006 31.8 10.7 119 37-170 18-144 (269)
155 PF12802 MarR_2: MarR family; 77.8 9.9 0.00022 26.0 5.9 49 130-186 7-57 (62)
156 PF10264 Stork_head: Winged he 77.3 11 0.00025 28.8 6.4 58 125-182 12-69 (80)
157 PRK00135 scpB segregation and 77.2 12 0.00025 32.9 7.4 52 31-90 85-136 (188)
158 PF03444 HrcA_DNA-bdg: Winged 77.1 12 0.00026 28.6 6.5 55 34-90 2-58 (78)
159 PRK10512 selenocysteinyl-tRNA- 76.6 40 0.00087 34.6 12.2 107 49-185 435-541 (614)
160 COG1414 IclR Transcriptional r 76.3 6.4 0.00014 35.4 5.8 45 40-88 8-52 (246)
161 cd04781 HTH_MerR-like_sg6 Heli 76.3 35 0.00077 27.1 9.5 69 55-156 2-70 (120)
162 PRK10046 dpiA two-component re 76.1 9.6 0.00021 32.8 6.6 53 33-91 161-213 (225)
163 PRK09392 ftrB transcriptional 75.9 12 0.00025 32.5 7.2 50 32-84 145-202 (236)
164 PF10007 DUF2250: Uncharacteri 75.5 9.8 0.00021 29.8 5.8 49 129-185 8-56 (92)
165 PF00392 GntR: Bacterial regul 75.3 6 0.00013 27.9 4.3 36 52-89 22-58 (64)
166 cd06170 LuxR_C_like C-terminal 75.0 11 0.00024 24.7 5.4 41 34-81 1-41 (57)
167 PF00196 GerE: Bacterial regul 73.9 8.4 0.00018 26.6 4.7 44 32-82 2-45 (58)
168 COG4189 Predicted transcriptio 73.9 6.9 0.00015 36.2 5.2 45 38-87 25-69 (308)
169 PRK13719 conjugal transfer tra 73.7 9 0.0002 34.5 5.9 47 28-81 138-184 (217)
170 PRK00411 cdc6 cell division co 73.6 12 0.00026 35.1 7.0 58 30-90 290-360 (394)
171 PF04545 Sigma70_r4: Sigma-70, 73.6 12 0.00026 25.0 5.2 43 31-79 2-44 (50)
172 PF13404 HTH_AsnC-type: AsnC-t 73.0 16 0.00034 24.3 5.5 42 34-80 1-42 (42)
173 COG5647 Cullin, a subunit of E 72.3 20 0.00043 37.7 8.6 143 34-183 606-763 (773)
174 COG2345 Predicted transcriptio 72.1 48 0.001 29.9 10.1 84 40-133 15-100 (218)
175 PF03965 Penicillinase_R: Peni 71.7 12 0.00027 29.4 5.7 54 129-186 4-57 (115)
176 PF04967 HTH_10: HTH DNA bindi 71.2 20 0.00043 25.2 6.0 46 34-82 1-50 (53)
177 PF03551 PadR: Transcriptional 70.7 20 0.00043 25.9 6.3 66 134-205 2-67 (75)
178 KOG0121 Nuclear cap-binding pr 70.6 1.8 3.9E-05 36.5 0.7 44 113-156 14-61 (153)
179 COG1693 Repressor of nif and g 70.6 5.5 0.00012 37.6 3.9 55 33-89 3-60 (325)
180 COG1695 Predicted transcriptio 70.1 9.5 0.0002 30.8 4.8 66 37-103 10-80 (138)
181 PF01047 MarR: MarR family; I 69.5 12 0.00025 25.5 4.6 48 131-186 6-53 (59)
182 COG4738 Predicted transcriptio 69.4 20 0.00043 29.5 6.4 64 34-101 9-90 (124)
183 TIGR03879 near_KaiC_dom probab 69.1 5.7 0.00012 29.9 3.0 53 28-85 10-62 (73)
184 PF08222 HTH_CodY: CodY helix- 68.8 21 0.00046 26.0 5.7 38 56-96 7-44 (61)
185 smart00418 HTH_ARSR helix_turn 68.6 17 0.00036 24.0 5.1 43 133-184 2-44 (66)
186 KOG3233 RNA polymerase III, su 68.5 40 0.00087 31.7 9.0 140 33-205 7-148 (297)
187 PF10557 Cullin_Nedd8: Cullin 67.9 25 0.00054 25.4 6.2 61 124-184 4-64 (68)
188 PRK10840 transcriptional regul 67.8 14 0.0003 31.4 5.6 44 32-82 149-192 (216)
189 PRK04217 hypothetical protein; 67.8 18 0.00038 29.2 5.8 44 30-79 39-82 (110)
190 PRK11083 DNA-binding response 67.4 19 0.00041 29.7 6.3 57 32-91 153-222 (228)
191 smart00531 TFIIE Transcription 67.4 8 0.00017 32.2 3.9 45 39-88 4-48 (147)
192 PF08461 HTH_12: Ribonuclease 67.2 16 0.00034 26.5 5.0 47 40-88 2-51 (66)
193 PF09397 Ftsk_gamma: Ftsk gamm 67.1 20 0.00043 26.3 5.5 53 41-100 11-63 (65)
194 PF04157 EAP30: EAP30/Vps36 fa 67.0 29 0.00062 30.7 7.6 100 54-181 114-221 (223)
195 PTZ00326 phenylalanyl-tRNA syn 67.0 23 0.00051 35.6 7.7 61 35-103 5-65 (494)
196 TIGR02277 PaaX_trns_reg phenyl 66.8 12 0.00026 34.5 5.4 51 50-103 14-65 (280)
197 PRK09483 response regulator; P 66.6 19 0.00042 29.7 6.2 45 31-82 146-190 (217)
198 cd06171 Sigma70_r4 Sigma70, re 66.4 26 0.00055 22.1 5.5 44 31-80 8-51 (55)
199 PF02082 Rrf2: Transcriptional 66.1 37 0.00081 25.1 7.0 35 142-184 25-59 (83)
200 cd01105 HTH_GlnR-like Helix-Tu 66.1 55 0.0012 24.7 8.4 84 54-178 2-85 (88)
201 PRK15411 rcsA colanic acid cap 65.6 14 0.0003 32.1 5.2 43 33-82 137-179 (207)
202 PF08281 Sigma70_r4_2: Sigma-7 65.5 20 0.00044 24.0 5.0 42 31-78 8-49 (54)
203 COG4189 Predicted transcriptio 65.4 36 0.00079 31.5 8.0 52 124-183 19-70 (308)
204 TIGR02702 SufR_cyano iron-sulf 65.4 21 0.00046 30.9 6.4 47 130-184 3-49 (203)
205 PRK00135 scpB segregation and 65.4 95 0.0021 27.2 11.0 126 37-183 5-134 (188)
206 PF08221 HTH_9: RNA polymerase 65.3 25 0.00055 25.1 5.7 44 40-88 17-60 (62)
207 COG2188 PhnF Transcriptional r 65.3 18 0.00039 32.1 6.0 56 40-103 11-74 (236)
208 PRK06266 transcription initiat 65.1 24 0.00052 30.6 6.6 44 131-182 25-68 (178)
209 PHA03103 double-strand RNA-bin 64.4 19 0.00042 31.6 5.9 49 40-90 14-62 (183)
210 smart00346 HTH_ICLR helix_turn 64.4 25 0.00055 25.7 5.9 44 132-183 9-53 (91)
211 PRK10512 selenocysteinyl-tRNA- 64.2 1.8E+02 0.0039 29.9 15.4 115 31-182 484-598 (614)
212 PF07574 SMC_Nse1: Nse1 non-SM 64.2 20 0.00043 31.2 6.0 94 85-184 64-186 (200)
213 PRK15201 fimbriae regulatory p 63.9 19 0.00042 31.9 5.7 46 30-82 130-175 (198)
214 PLN02853 Probable phenylalanyl 63.7 21 0.00046 35.9 6.7 59 37-103 4-62 (492)
215 TIGR03433 padR_acidobact trans 63.6 42 0.0009 25.9 7.1 72 129-206 5-76 (100)
216 COG1349 GlpR Transcriptional r 63.3 1E+02 0.0022 27.8 10.6 119 37-172 6-131 (253)
217 PRK10336 DNA-binding transcrip 62.8 22 0.00048 29.2 5.8 56 33-91 149-212 (219)
218 PRK11886 bifunctional biotin-- 62.4 22 0.00047 32.9 6.2 46 38-88 6-52 (319)
219 PRK10906 DNA-binding transcrip 62.2 20 0.00043 32.4 5.8 49 128-184 5-53 (252)
220 PF13463 HTH_27: Winged helix 61.6 43 0.00093 23.1 6.3 49 130-186 5-54 (68)
221 PF00538 Linker_histone: linke 61.4 49 0.0011 24.3 6.9 49 137-187 16-68 (77)
222 PRK10736 hypothetical protein; 61.2 16 0.00035 35.4 5.3 50 33-88 305-354 (374)
223 TIGR02325 C_P_lyase_phnF phosp 60.8 13 0.00029 32.3 4.3 40 55-101 34-73 (238)
224 PRK11402 DNA-binding transcrip 60.8 16 0.00035 32.2 4.8 54 40-101 13-74 (241)
225 COG3355 Predicted transcriptio 60.6 37 0.00081 28.1 6.6 44 135-186 35-78 (126)
226 PRK11475 DNA-binding transcrip 60.3 23 0.0005 31.0 5.7 45 31-82 132-176 (207)
227 cd07377 WHTH_GntR Winged helix 60.3 41 0.0009 22.6 6.0 53 123-183 4-58 (66)
228 PRK09416 lstR lineage-specific 60.0 37 0.00079 28.5 6.5 68 128-206 43-110 (135)
229 PF10576 EndIII_4Fe-2S: Iron-s 59.7 3.6 7.8E-05 22.6 0.3 11 222-232 7-17 (17)
230 cd04787 HTH_HMRTR_unk Helix-Tu 59.7 93 0.002 25.2 9.9 69 55-155 2-70 (133)
231 cd00090 HTH_ARSR Arsenical Res 59.3 51 0.0011 22.1 6.4 47 129-184 8-54 (78)
232 PF14502 HTH_41: Helix-turn-he 59.1 24 0.00051 24.6 4.4 40 50-91 3-42 (48)
233 KOG3095 Transcription initiati 58.4 65 0.0014 30.2 8.4 102 40-170 143-250 (284)
234 PRK10857 DNA-binding transcrip 58.0 35 0.00076 29.0 6.3 37 140-184 23-59 (164)
235 COG0640 ArsR Predicted transcr 57.8 64 0.0014 22.7 7.0 43 40-87 29-71 (110)
236 PRK14137 recX recombination re 57.8 41 0.00089 29.6 6.8 54 122-181 35-88 (195)
237 TIGR00122 birA_repr_reg BirA b 57.8 27 0.00058 24.8 4.8 43 40-88 4-46 (69)
238 smart00345 HTH_GNTR helix_turn 57.7 43 0.00094 22.0 5.6 35 142-184 20-54 (60)
239 COG1959 Predicted transcriptio 57.7 60 0.0013 27.1 7.6 92 133-250 13-112 (150)
240 PF03444 HrcA_DNA-bdg: Winged 56.8 41 0.00088 25.7 5.7 69 125-205 6-74 (78)
241 TIGR02944 suf_reg_Xantho FeS a 56.6 33 0.00071 27.4 5.6 36 141-184 24-59 (130)
242 KOG2587 RNA polymerase III (C) 56.6 1.3E+02 0.0027 30.8 10.6 96 56-156 37-133 (551)
243 PRK10411 DNA-binding transcrip 56.6 35 0.00077 30.6 6.4 47 130-184 6-52 (240)
244 PF04157 EAP30: EAP30/Vps36 fa 56.3 11 0.00024 33.3 3.1 65 119-183 89-154 (223)
245 TIGR00721 tfx DNA-binding prot 56.0 35 0.00075 28.6 5.8 43 31-80 4-50 (137)
246 PRK10651 transcriptional regul 56.0 30 0.00065 28.1 5.4 45 31-82 153-197 (216)
247 TIGR02404 trehalos_R_Bsub treh 55.9 18 0.00039 31.6 4.3 40 55-101 26-65 (233)
248 TIGR02787 codY_Gpos GTP-sensin 55.0 41 0.00089 31.0 6.5 57 30-88 173-231 (251)
249 smart00344 HTH_ASNC helix_turn 54.8 40 0.00086 25.7 5.6 49 128-184 3-51 (108)
250 COG1695 Predicted transcriptio 54.6 66 0.0014 25.8 7.1 73 128-206 9-81 (138)
251 PF09106 SelB-wing_2: Elongati 54.5 15 0.00031 25.8 2.8 41 49-89 13-54 (59)
252 PRK06474 hypothetical protein; 54.5 44 0.00096 28.7 6.4 52 127-185 10-62 (178)
253 PF05402 PqqD: Coenzyme PQQ sy 54.4 29 0.00062 24.3 4.4 54 125-181 14-68 (68)
254 PF13565 HTH_32: Homeodomain-l 54.2 37 0.0008 24.2 5.1 44 128-171 34-77 (77)
255 PRK11639 zinc uptake transcrip 53.8 52 0.0011 27.9 6.7 56 33-90 23-81 (169)
256 PRK04424 fatty acid biosynthes 53.5 11 0.00024 32.6 2.5 51 37-92 8-58 (185)
257 PRK03975 tfx putative transcri 53.4 42 0.0009 28.2 5.9 41 31-78 4-44 (141)
258 PRK14999 histidine utilization 53.4 21 0.00045 31.5 4.3 40 55-101 38-77 (241)
259 PF06969 HemN_C: HemN C-termin 53.3 31 0.00068 24.1 4.5 52 34-87 1-53 (66)
260 PF04539 Sigma70_r3: Sigma-70 53.3 35 0.00076 24.5 4.8 43 124-174 1-44 (78)
261 PF01454 MAGE: MAGE family; I 52.9 44 0.00096 28.5 6.2 137 44-184 6-166 (195)
262 COG4465 CodY Pleiotropic trans 52.9 27 0.00057 32.0 4.8 61 30-93 179-241 (261)
263 KOG1767 40S ribosomal protein 52.6 11 0.00025 30.3 2.2 65 31-99 37-102 (110)
264 COG1522 Lrp Transcriptional re 52.6 48 0.001 26.7 6.1 52 126-185 6-57 (154)
265 PRK04214 rbn ribonuclease BN/u 52.6 31 0.00067 33.4 5.7 37 49-87 306-342 (412)
266 smart00753 PAM PCI/PINT associ 52.6 34 0.00074 25.1 4.8 50 125-182 6-56 (88)
267 smart00088 PINT motif in prote 52.6 34 0.00074 25.1 4.8 50 125-182 6-56 (88)
268 PRK15481 transcriptional regul 52.4 28 0.00061 33.2 5.3 32 55-88 31-62 (431)
269 smart00526 H15 Domain in histo 52.4 69 0.0015 22.7 6.2 54 36-89 6-65 (66)
270 TIGR02018 his_ut_repres histid 52.3 22 0.00048 31.0 4.3 40 55-101 27-66 (230)
271 COG2771 CsgD DNA-binding HTH d 52.2 58 0.0013 21.9 5.6 44 32-82 3-46 (65)
272 KOG4603 TBP-1 interacting prot 52.2 83 0.0018 27.8 7.6 62 35-101 6-68 (201)
273 PRK09764 DNA-binding transcrip 52.1 22 0.00049 31.3 4.3 39 56-101 32-70 (240)
274 PF03979 Sigma70_r1_1: Sigma-7 52.0 28 0.00061 26.1 4.2 37 137-178 16-52 (82)
275 PRK10100 DNA-binding transcrip 51.9 38 0.00082 29.8 5.7 45 31-82 153-197 (216)
276 TIGR03826 YvyF flagellar opero 51.6 37 0.00081 28.4 5.3 43 129-183 31-75 (137)
277 TIGR02698 CopY_TcrY copper tra 51.0 73 0.0016 25.9 6.9 49 132-184 8-56 (130)
278 PF07106 TBPIP: Tat binding pr 51.0 48 0.001 27.9 6.0 47 130-182 3-50 (169)
279 PF13744 HTH_37: Helix-turn-he 50.3 22 0.00047 26.4 3.4 35 40-77 19-53 (80)
280 TIGR00373 conserved hypothetic 50.3 38 0.00082 28.7 5.2 53 124-184 10-62 (158)
281 smart00049 DEP Domain found in 50.1 63 0.0014 23.2 5.8 56 142-203 20-75 (77)
282 TIGR02928 orc1/cdc6 family rep 50.0 68 0.0015 29.6 7.4 60 30-90 282-352 (365)
283 PF06479 Ribonuc_2-5A: Ribonuc 50.0 7.5 0.00016 32.1 0.9 57 107-171 32-88 (129)
284 smart00347 HTH_MARR helix_turn 49.9 57 0.0012 23.6 5.7 48 130-185 12-59 (101)
285 PRK13509 transcriptional repre 49.9 49 0.0011 29.8 6.2 51 127-185 4-54 (251)
286 PRK03902 manganese transport t 49.9 59 0.0013 26.4 6.2 51 126-184 6-56 (142)
287 PF00292 PAX: 'Paired box' dom 49.7 1.3E+02 0.0029 24.8 8.1 107 33-172 17-125 (125)
288 cd08767 Cdt1_c The C-terminal 49.3 64 0.0014 26.3 6.3 48 124-175 45-92 (126)
289 TIGR02337 HpaR homoprotocatech 49.3 46 0.001 25.9 5.3 47 132-186 32-78 (118)
290 cd00073 H15 linker histone 1 a 49.0 88 0.0019 23.7 6.6 66 35-102 5-76 (88)
291 cd04783 HTH_MerR1 Helix-Turn-H 49.0 1.4E+02 0.003 23.9 9.5 70 55-156 2-71 (126)
292 PRK10360 DNA-binding transcrip 48.6 48 0.001 26.8 5.5 44 32-82 136-179 (196)
293 cd04780 HTH_MerR-like_sg5 Heli 48.5 1.2E+02 0.0027 23.2 9.4 69 55-154 2-70 (95)
294 PRK03837 transcriptional regul 48.2 36 0.00079 29.6 5.0 40 55-101 39-78 (241)
295 PF13411 MerR_1: MerR HTH fami 48.0 91 0.002 21.6 7.5 66 55-153 2-67 (69)
296 TIGR01321 TrpR trp operon repr 47.9 31 0.00068 27.2 4.0 44 33-79 32-79 (94)
297 COG5625 Predicted transcriptio 47.8 20 0.00043 28.9 2.9 70 32-107 17-86 (113)
298 TIGR01884 cas_HTH CRISPR locus 47.5 94 0.002 26.8 7.4 47 130-184 145-191 (203)
299 TIGR00738 rrf2_super rrf2 fami 47.5 61 0.0013 25.6 5.8 36 141-184 24-59 (132)
300 cd05029 S-100A6 S-100A6: S-100 47.2 74 0.0016 24.1 5.9 52 124-178 7-64 (88)
301 COG1386 scpB Chromosome segreg 47.1 70 0.0015 28.0 6.5 57 32-96 88-144 (184)
302 COG2197 CitB Response regulato 47.0 47 0.001 29.0 5.5 44 32-82 147-190 (211)
303 PF10711 DUF2513: Hypothetical 46.8 56 0.0012 25.4 5.3 75 39-131 8-82 (102)
304 TIGR02010 IscR iron-sulfur clu 46.3 1.1E+02 0.0025 24.6 7.3 36 141-184 24-59 (135)
305 PF03672 UPF0154: Uncharacteri 45.8 83 0.0018 23.2 5.7 44 129-175 18-61 (64)
306 PF09382 RQC: RQC domain; Int 45.8 98 0.0021 23.5 6.6 54 131-184 7-76 (106)
307 COG2186 FadR Transcriptional r 45.5 56 0.0012 29.2 5.8 85 40-132 18-106 (241)
308 PF13384 HTH_23: Homeodomain-l 45.4 22 0.00047 23.4 2.5 30 53-84 17-46 (50)
309 PRK10079 phosphonate metabolis 45.4 33 0.00071 30.2 4.3 45 50-101 32-76 (241)
310 COG4742 Predicted transcriptio 45.3 37 0.0008 31.4 4.7 53 39-104 16-68 (260)
311 PF12840 HTH_20: Helix-turn-he 45.1 99 0.0021 21.3 5.9 51 127-185 9-59 (61)
312 PF00126 HTH_1: Bacterial regu 44.8 67 0.0014 22.2 5.0 35 40-81 5-39 (60)
313 cd04784 HTH_CadR-PbrR Helix-Tu 44.7 1.2E+02 0.0026 24.1 7.2 69 55-155 2-70 (127)
314 PRK04984 fatty acid metabolism 44.6 35 0.00075 29.8 4.3 32 55-88 33-64 (239)
315 COG1167 ARO8 Transcriptional r 44.6 3.1E+02 0.0068 26.8 12.1 141 40-183 8-184 (459)
316 PF13443 HTH_26: Cro/C1-type H 44.5 22 0.00048 24.4 2.5 25 51-77 8-32 (63)
317 COG5340 Predicted transcriptio 44.4 26 0.00056 32.2 3.5 53 33-90 13-65 (269)
318 COG1339 Transcriptional regula 44.4 45 0.00098 30.0 4.9 37 50-88 16-52 (214)
319 PF08100 Dimerisation: Dimeris 44.4 34 0.00074 23.8 3.4 40 38-79 8-50 (51)
320 PF04695 Pex14_N: Peroxisomal 44.1 70 0.0015 26.3 5.8 47 127-178 3-51 (136)
321 PRK04158 transcriptional repre 44.1 34 0.00073 31.7 4.2 62 31-95 177-240 (256)
322 PF13613 HTH_Tnp_4: Helix-turn 44.0 70 0.0015 21.8 4.9 44 33-81 2-45 (53)
323 COG2390 DeoR Transcriptional r 43.7 32 0.00069 32.7 4.1 37 49-87 22-58 (321)
324 PRK15369 two component system 43.6 86 0.0019 24.9 6.2 45 31-82 147-191 (211)
325 PF01399 PCI: PCI domain; Int 43.5 43 0.00093 24.7 4.1 39 137-183 55-93 (105)
326 PF13833 EF-hand_8: EF-hand do 43.4 40 0.00088 22.3 3.6 37 140-178 2-38 (54)
327 PF13601 HTH_34: Winged helix 43.2 57 0.0012 24.3 4.7 62 130-205 2-63 (80)
328 COG1675 TFA1 Transcription ini 43.0 1E+02 0.0022 26.9 6.8 52 37-93 19-70 (176)
329 PF06648 DUF1160: Protein of u 42.9 44 0.00095 27.6 4.3 65 115-183 25-89 (122)
330 cd04764 HTH_MlrA-like_sg1 Heli 42.9 88 0.0019 21.8 5.5 26 55-86 2-27 (67)
331 PRK14135 recX recombination re 42.8 90 0.002 27.9 6.8 59 118-182 39-106 (263)
332 PRK10710 DNA-binding transcrip 42.7 50 0.0011 27.5 4.9 48 32-82 159-215 (240)
333 PF13182 DUF4007: Protein of u 42.6 56 0.0012 30.2 5.5 90 5-102 173-273 (286)
334 cd04774 HTH_YfmP Helix-Turn-He 42.2 1.6E+02 0.0034 22.6 8.0 70 55-156 2-71 (96)
335 COG1510 Predicted transcriptio 42.1 1.7E+02 0.0036 25.7 8.0 52 41-99 31-83 (177)
336 TIGR02063 RNase_R ribonuclease 42.1 64 0.0014 33.5 6.4 48 38-88 4-55 (709)
337 TIGR03338 phnR_burk phosphonat 42.0 44 0.00095 28.5 4.5 46 40-88 15-67 (212)
338 PF03962 Mnd1: Mnd1 family; I 42.0 28 0.00061 30.4 3.3 43 139-186 8-51 (188)
339 smart00843 Ftsk_gamma This dom 41.8 63 0.0014 23.6 4.6 53 41-100 10-62 (63)
340 PRK14134 recX recombination re 41.8 97 0.0021 28.7 6.9 59 117-181 42-109 (283)
341 PF08679 DsrD: Dissimilatory s 41.7 61 0.0013 24.1 4.4 50 129-185 2-55 (67)
342 PRK10188 DNA-binding transcrip 41.6 62 0.0013 28.9 5.5 44 32-82 178-221 (240)
343 TIGR00475 selB selenocysteine- 41.5 2E+02 0.0042 29.4 9.6 102 31-178 467-568 (581)
344 PRK15320 transcriptional activ 41.4 59 0.0013 29.5 5.2 48 32-86 163-210 (251)
345 PRK11482 putative DNA-binding 41.4 36 0.00079 31.0 4.1 51 30-87 25-78 (317)
346 PF01090 Ribosomal_S19e: Ribos 41.3 32 0.00069 29.0 3.3 46 41-89 57-114 (139)
347 PRK10225 DNA-binding transcrip 41.3 42 0.0009 29.7 4.3 48 40-89 13-67 (257)
348 PRK00523 hypothetical protein; 41.3 1E+02 0.0022 23.3 5.6 43 129-174 26-68 (72)
349 COG1542 Uncharacterized conser 41.1 24 0.00052 35.6 2.9 56 32-89 421-476 (593)
350 PRK04424 fatty acid biosynthes 41.1 17 0.00038 31.3 1.8 49 129-185 8-56 (185)
351 cd04789 HTH_Cfa Helix-Turn-Hel 41.0 1.7E+02 0.0036 22.6 7.8 68 54-154 2-69 (102)
352 TIGR00637 ModE_repress ModE mo 40.9 53 0.0012 25.6 4.4 41 34-81 2-42 (99)
353 COG1867 TRM1 N2,N2-dimethylgua 40.6 3.3E+02 0.0072 26.7 10.5 54 74-133 229-291 (380)
354 PRK09333 30S ribosomal protein 40.5 47 0.001 28.4 4.2 45 40-89 57-115 (150)
355 TIGR00635 ruvB Holliday juncti 40.5 73 0.0016 28.7 5.9 54 31-87 233-288 (305)
356 PRK11512 DNA-binding transcrip 40.5 80 0.0017 25.5 5.6 48 132-187 44-91 (144)
357 PRK09990 DNA-binding transcrip 40.4 93 0.002 27.3 6.4 36 52-89 29-65 (251)
358 cd04776 HTH_GnyR Helix-Turn-He 40.3 1.9E+02 0.0041 23.0 9.7 67 56-156 3-69 (118)
359 PRK10955 DNA-binding transcrip 40.1 18 0.00038 30.2 1.6 57 33-91 156-224 (232)
360 PRK00117 recX recombination re 39.7 82 0.0018 25.9 5.6 54 123-182 7-60 (157)
361 COG2996 Predicted RNA-bindinin 39.6 55 0.0012 30.7 4.9 53 33-87 222-278 (287)
362 TIGR02392 rpoH_proteo alternat 39.6 60 0.0013 29.3 5.1 47 30-80 215-265 (270)
363 TIGR02154 PhoB phosphate regul 39.5 37 0.0008 27.8 3.5 46 33-81 154-208 (226)
364 COG3413 Predicted DNA binding 39.4 1.4E+02 0.003 26.0 7.2 48 32-82 154-205 (215)
365 PF13814 Replic_Relax: Replica 39.3 74 0.0016 26.6 5.4 48 54-103 10-64 (191)
366 TIGR03020 EpsA transcriptional 39.3 72 0.0016 29.0 5.6 45 31-82 188-232 (247)
367 PRK09508 leuO leucine transcri 39.2 78 0.0017 28.5 5.8 45 31-82 19-63 (314)
368 COG3388 Predicted transcriptio 39.1 29 0.00062 27.7 2.5 44 39-87 17-60 (101)
369 PF09279 EF-hand_like: Phospho 39.0 68 0.0015 23.4 4.5 48 129-177 2-49 (83)
370 TIGR03337 phnR transcriptional 39.0 47 0.001 28.7 4.2 33 55-89 27-59 (231)
371 PRK00082 hrcA heat-inducible t 39.0 76 0.0017 30.1 5.9 53 32-89 2-61 (339)
372 PRK11367 hypothetical protein; 38.7 15 0.00033 36.6 1.2 26 110-135 17-45 (476)
373 COG2865 Predicted transcriptio 38.7 64 0.0014 32.3 5.5 66 33-105 399-464 (467)
374 PRK10216 DNA-binding transcrip 38.7 82 0.0018 28.4 5.9 45 30-81 4-48 (319)
375 TIGR02812 fadR_gamma fatty aci 38.5 50 0.0011 28.8 4.3 35 53-89 29-64 (235)
376 PF07524 Bromo_TP: Bromodomain 38.3 1E+02 0.0023 22.4 5.4 37 121-157 24-73 (77)
377 PRK01844 hypothetical protein; 37.9 1.2E+02 0.0027 22.8 5.7 43 129-174 25-67 (72)
378 COG1542 Uncharacterized conser 37.9 47 0.001 33.6 4.4 147 28-186 276-478 (593)
379 PF06971 Put_DNA-bind_N: Putat 37.9 72 0.0016 22.2 4.1 33 41-76 17-49 (50)
380 COG5309 Exo-beta-1,3-glucanase 37.9 44 0.00096 31.5 4.0 71 101-184 89-178 (305)
381 cd01108 HTH_CueR Helix-Turn-He 37.8 2.1E+02 0.0046 22.9 9.7 68 55-154 2-69 (127)
382 cd04775 HTH_Cfa-like Helix-Tur 37.6 1.9E+02 0.0041 22.3 8.0 69 54-155 2-70 (102)
383 PRK10086 DNA-binding transcrip 36.7 56 0.0012 29.4 4.5 45 31-82 11-55 (311)
384 PRK11523 DNA-binding transcrip 36.6 55 0.0012 29.0 4.3 33 55-89 34-66 (253)
385 COG4901 Ribosomal protein S25 36.5 1.1E+02 0.0025 24.6 5.6 59 37-100 43-102 (107)
386 PRK10421 DNA-binding transcrip 36.4 55 0.0012 28.9 4.3 32 55-88 28-59 (253)
387 PRK00118 putative DNA-binding 36.4 1.1E+02 0.0023 24.5 5.4 43 30-78 14-56 (104)
388 PRK10403 transcriptional regul 36.3 92 0.002 25.1 5.3 45 31-82 151-195 (215)
389 COG5051 RPL36A Ribosomal prote 36.2 50 0.0011 25.9 3.4 40 31-74 47-86 (97)
390 TIGR00308 TRM1 tRNA(guanine-26 36.2 1.5E+02 0.0032 28.7 7.5 23 110-132 263-285 (374)
391 PF03501 S10_plectin: Plectin/ 36.1 40 0.00086 26.7 2.9 26 66-91 34-59 (95)
392 PF09079 Cdc6_C: CDC6, C termi 36.1 1E+02 0.0023 22.6 5.2 41 66-106 36-76 (85)
393 COG3398 Uncharacterized protei 36.0 80 0.0017 28.9 5.2 46 38-88 176-221 (240)
394 TIGR02044 CueR Cu(I)-responsiv 35.8 2.3E+02 0.0049 22.6 9.9 68 55-154 2-69 (127)
395 PRK11534 DNA-binding transcrip 35.4 65 0.0014 27.8 4.5 47 40-88 11-63 (224)
396 PF07537 CamS: CamS sex pherom 35.3 14 0.00031 35.1 0.4 76 11-118 114-189 (319)
397 PF04218 CENP-B_N: CENP-B N-te 35.3 1.2E+02 0.0026 20.8 5.0 41 31-78 4-45 (53)
398 cd01107 HTH_BmrR Helix-Turn-He 35.2 2.1E+02 0.0046 22.2 9.3 71 55-156 2-72 (108)
399 cd04770 HTH_HMRTR Helix-Turn-H 35.2 2.2E+02 0.0048 22.3 9.6 69 55-155 2-70 (123)
400 COG5126 FRQ1 Ca2+-binding prot 35.1 80 0.0017 27.1 4.9 111 28-177 8-140 (160)
401 PF06163 DUF977: Bacterial pro 35.1 1E+02 0.0022 25.7 5.3 53 33-87 4-58 (127)
402 cd00073 H15 linker histone 1 a 35.1 1.9E+02 0.004 21.8 6.5 51 137-187 18-68 (88)
403 TIGR02607 antidote_HigA addict 35.0 1.1E+02 0.0025 21.6 5.1 37 35-77 4-40 (78)
404 PRK11169 leucine-responsive tr 35.0 1.6E+02 0.0034 24.6 6.7 51 126-184 12-62 (164)
405 COG2345 Predicted transcriptio 35.0 1.6E+02 0.0034 26.6 6.9 63 130-206 13-76 (218)
406 PF01418 HTH_6: Helix-turn-hel 34.9 33 0.00072 25.2 2.3 50 32-83 12-62 (77)
407 COG1349 GlpR Transcriptional r 34.9 85 0.0018 28.3 5.3 48 130-185 7-54 (253)
408 PRK09464 pdhR transcriptional 34.4 62 0.0013 28.5 4.3 40 55-101 36-75 (254)
409 TIGR03303 OM_YaeT outer membra 34.2 2.3E+02 0.0051 28.6 8.9 102 41-143 70-211 (741)
410 PF06207 DUF1002: Protein of u 34.1 2.1E+02 0.0046 25.9 7.6 116 49-175 88-205 (225)
411 COG4109 Predicted transcriptio 33.9 79 0.0017 31.0 5.1 144 35-181 2-184 (432)
412 PRK11642 exoribonuclease R; Pr 33.9 1.1E+02 0.0025 32.6 6.7 51 32-87 16-70 (813)
413 COG0478 RIO-like serine/threon 33.5 1.3E+02 0.0027 28.6 6.3 62 30-95 7-70 (304)
414 PF09756 DDRGK: DDRGK domain; 33.4 88 0.0019 27.5 5.0 58 129-195 100-157 (188)
415 TIGR02356 adenyl_thiF thiazole 33.4 1.7E+02 0.0037 25.3 6.8 72 109-180 60-137 (202)
416 PRK09645 RNA polymerase sigma 33.4 99 0.0021 25.2 5.1 46 30-81 115-164 (173)
417 PRK04338 N(2),N(2)-dimethylgua 32.9 2.2E+02 0.0047 27.5 8.0 24 110-133 272-295 (382)
418 COG3132 Uncharacterized protei 32.6 22 0.00048 31.5 1.1 94 66-178 49-142 (215)
419 TIGR02719 repress_PhaQ poly-be 32.6 3E+02 0.0064 23.0 8.2 67 132-206 28-94 (138)
420 TIGR02937 sigma70-ECF RNA poly 32.4 91 0.002 23.7 4.5 46 30-81 107-152 (158)
421 COG0150 PurM Phosphoribosylami 32.3 50 0.0011 31.8 3.5 90 58-178 216-323 (345)
422 PF13518 HTH_28: Helix-turn-he 32.2 94 0.002 20.2 4.0 30 53-84 12-41 (52)
423 TIGR01610 phage_O_Nterm phage 32.2 1.7E+02 0.0038 22.3 6.0 36 140-183 45-80 (95)
424 TIGR00475 selB selenocysteine- 32.2 5.6E+02 0.012 26.1 11.6 100 50-185 424-523 (581)
425 PRK11302 DNA-binding transcrip 32.2 62 0.0013 28.9 4.0 52 31-84 11-63 (284)
426 PRK07670 RNA polymerase sigma 32.1 1.5E+02 0.0032 26.3 6.4 110 31-173 1-148 (251)
427 PRK09958 DNA-binding transcrip 32.1 1.2E+02 0.0026 24.6 5.4 47 31-84 141-187 (204)
428 PRK09642 RNA polymerase sigma 32.0 97 0.0021 24.9 4.8 43 31-79 104-150 (160)
429 PRK09802 DNA-binding transcrip 31.9 1.3E+02 0.0028 27.4 6.1 49 128-184 17-65 (269)
430 PRK09935 transcriptional regul 31.7 1.3E+02 0.0027 24.3 5.5 44 32-82 148-191 (210)
431 COG0664 Crp cAMP-binding prote 31.7 1.4E+02 0.0029 24.4 5.7 53 33-88 140-204 (214)
432 PRK09791 putative DNA-binding 31.6 77 0.0017 28.2 4.5 43 33-82 4-46 (302)
433 COG3763 Uncharacterized protei 31.3 1.8E+02 0.0039 21.9 5.6 44 129-175 25-68 (71)
434 cd04773 HTH_TioE_rpt2 Second H 31.1 2.6E+02 0.0055 21.8 10.2 69 55-155 2-70 (108)
435 TIGR02531 yecD_yerC TrpR-relat 31.0 91 0.002 24.0 4.2 37 33-77 36-72 (88)
436 PRK00215 LexA repressor; Valid 30.9 2.3E+02 0.005 24.2 7.2 37 140-184 21-58 (205)
437 PRK11062 nhaR transcriptional 30.9 78 0.0017 28.2 4.4 43 33-82 3-45 (296)
438 cd04767 HTH_HspR-like_MBC Heli 30.9 2.8E+02 0.006 22.6 7.2 29 54-88 2-30 (120)
439 PF03801 Ndc80_HEC: HEC/Ndc80p 30.6 2E+02 0.0044 24.2 6.6 60 122-181 34-112 (157)
440 PTZ00095 40S ribosomal protein 30.5 58 0.0012 28.4 3.3 28 68-97 118-145 (169)
441 PF08097 Toxin_26: Conotoxin T 30.5 21 0.00046 17.4 0.4 9 224-232 1-9 (11)
442 cd04782 HTH_BltR Helix-Turn-He 30.4 2.5E+02 0.0053 21.4 8.2 70 55-156 2-71 (97)
443 TIGR02036 dsdC D-serine deamin 30.3 90 0.0019 28.0 4.7 51 30-87 4-57 (302)
444 PF01381 HTH_3: Helix-turn-hel 30.2 57 0.0012 21.6 2.6 26 51-78 7-32 (55)
445 PRK13752 putative transcriptio 30.2 3.2E+02 0.0069 22.6 8.7 69 54-154 8-76 (144)
446 PRK05803 sporulation sigma fac 30.1 1E+02 0.0022 27.0 4.9 44 30-76 172-216 (233)
447 cd08768 Cdc6_C Winged-helix do 29.8 1.1E+02 0.0024 22.2 4.4 25 66-90 43-67 (87)
448 COG5174 TFA2 Transcription ini 29.8 1.8E+02 0.0039 26.9 6.4 98 41-167 149-250 (285)
449 COG3743 Uncharacterized conser 29.7 38 0.00083 28.4 2.0 48 125-183 71-118 (133)
450 PRK11414 colanic acid/biofilm 29.7 80 0.0017 27.2 4.1 47 40-88 15-67 (221)
451 cd00052 EH Eps15 homology doma 29.6 1.2E+02 0.0026 20.3 4.3 34 139-177 12-45 (67)
452 PRK10082 cell density-dependen 29.5 1.4E+02 0.003 26.7 5.7 44 31-81 8-51 (303)
453 PRK15418 transcriptional regul 29.3 79 0.0017 29.7 4.3 37 49-87 25-61 (318)
454 TIGR03541 reg_near_HchA LuxR f 29.0 1.3E+02 0.0029 26.4 5.5 45 31-82 169-213 (232)
455 PRK11151 DNA-binding transcrip 28.9 1.3E+02 0.0029 26.7 5.6 40 35-81 2-41 (305)
456 PF04079 DUF387: Putative tran 28.8 90 0.0019 26.6 4.2 62 31-100 77-139 (159)
457 PF13099 DUF3944: Domain of un 28.6 81 0.0018 20.6 2.9 18 161-178 12-29 (35)
458 PRK09986 DNA-binding transcrip 28.6 65 0.0014 28.3 3.5 50 31-87 4-56 (294)
459 COG2865 Predicted transcriptio 28.4 2.3E+02 0.0049 28.5 7.4 104 72-187 350-453 (467)
460 PRK15479 transcriptional regul 28.3 1.9E+02 0.0041 23.5 6.0 56 33-91 148-213 (221)
461 PRK13413 mpi multiple promoter 28.2 1.5E+02 0.0032 25.4 5.5 38 34-78 158-195 (200)
462 PF11784 DUF3320: Protein of u 28.2 1.7E+02 0.0036 20.2 4.8 43 118-160 2-45 (52)
463 PF08870 DUF1832: Domain of un 28.2 2.8E+02 0.0061 22.3 6.7 61 57-133 13-76 (113)
464 COG4190 Predicted transcriptio 28.1 2E+02 0.0043 24.4 5.9 57 33-94 61-117 (144)
465 PF10931 DUF2735: Protein of u 28.1 18 0.00039 25.4 -0.2 14 106-119 31-44 (51)
466 PRK01177 hypothetical protein; 28.0 36 0.00078 28.7 1.6 26 220-245 94-119 (140)
467 PRK11013 DNA-binding transcrip 27.9 94 0.002 27.9 4.4 48 33-87 3-53 (309)
468 COG3611 DnaB Replication initi 27.9 2E+02 0.0043 28.5 6.8 90 40-135 38-131 (417)
469 PRK10094 DNA-binding transcrip 27.8 1.5E+02 0.0032 26.7 5.7 42 34-82 2-43 (308)
470 PRK06811 RNA polymerase factor 27.7 1.4E+02 0.0031 24.9 5.3 49 30-84 128-180 (189)
471 PRK10434 srlR DNA-bindng trans 27.5 1.4E+02 0.0031 26.8 5.5 48 129-184 6-53 (256)
472 TIGR01529 argR_whole arginine 27.4 1.6E+02 0.0034 24.6 5.4 40 131-173 5-44 (146)
473 PF08671 SinI: Anti-repressor 27.4 1.5E+02 0.0033 18.5 3.9 28 121-154 1-28 (30)
474 COG1497 Predicted transcriptio 27.4 84 0.0018 29.1 3.9 41 53-101 25-65 (260)
475 PF08221 HTH_9: RNA polymerase 27.3 2.3E+02 0.005 20.1 5.7 48 126-181 11-58 (62)
476 PF01316 Arg_repressor: Argini 27.1 2.6E+02 0.0056 20.7 5.8 49 129-184 6-54 (70)
477 KOG1276 Protoporphyrinogen oxi 27.1 1.2E+02 0.0026 30.5 5.2 68 110-179 388-459 (491)
478 PF06897 DUF1269: Protein of u 27.1 1.7E+02 0.0036 23.1 5.2 59 116-174 35-99 (102)
479 PRK11557 putative DNA-binding 27.0 76 0.0016 28.4 3.6 52 31-84 7-59 (278)
480 PRK13777 transcriptional regul 27.0 2E+02 0.0044 25.0 6.1 47 132-186 49-95 (185)
481 PLN00034 mitogen-activated pro 26.9 2.1E+02 0.0045 26.0 6.5 75 75-167 125-199 (353)
482 PRK13919 putative RNA polymera 26.9 1.4E+02 0.0029 24.7 4.9 44 30-79 132-179 (186)
483 TIGR03787 marine_sort_RR prote 26.9 1.6E+02 0.0035 24.3 5.4 59 32-91 155-221 (227)
484 PF09494 Slx4: Slx4 endonuclea 26.7 2.1E+02 0.0046 20.3 5.3 35 139-173 21-56 (64)
485 cd04786 HTH_MerR-like_sg7 Heli 26.7 3.5E+02 0.0076 22.0 9.9 69 55-155 2-70 (131)
486 PRK07037 extracytoplasmic-func 26.5 1.3E+02 0.0029 24.1 4.7 42 30-77 106-147 (163)
487 smart00526 H15 Domain in histo 26.5 2.3E+02 0.0051 19.9 6.1 48 137-184 18-65 (66)
488 PRK02302 hypothetical protein; 26.4 83 0.0018 24.6 3.2 23 67-89 43-65 (89)
489 PRK03573 transcriptional regul 26.4 2E+02 0.0044 22.9 5.7 46 133-186 36-82 (144)
490 PF13453 zf-TFIIB: Transcripti 26.3 11 0.00023 24.7 -1.5 14 110-123 24-37 (41)
491 PF01853 MOZ_SAS: MOZ/SAS fami 26.3 1.4E+02 0.0031 26.3 5.1 53 32-89 120-181 (188)
492 PF02295 z-alpha: Adenosine de 26.2 1.3E+02 0.0028 21.8 4.1 48 128-183 4-53 (66)
493 PRK05473 hypothetical protein; 26.1 92 0.002 24.3 3.4 68 116-184 10-77 (86)
494 PHA00738 putative HTH transcri 26.0 3.3E+02 0.0071 22.1 6.6 51 127-185 11-61 (108)
495 TIGR02846 spore_sigmaK RNA pol 25.9 1.5E+02 0.0032 25.9 5.2 47 31-80 172-223 (227)
496 PRK15090 DNA-binding transcrip 25.8 1.8E+02 0.0039 25.8 5.8 51 126-184 10-62 (257)
497 PRK15421 DNA-binding transcrip 25.7 1E+02 0.0023 28.0 4.3 42 34-82 2-43 (317)
498 PRK15431 ferrous iron transpor 25.6 1.5E+02 0.0032 22.6 4.4 44 41-89 7-50 (78)
499 PRK11242 DNA-binding transcrip 25.6 1E+02 0.0022 27.1 4.1 41 35-82 2-42 (296)
500 PF07508 Recombinase: Recombin 25.6 2.8E+02 0.006 20.5 6.5 53 127-182 5-60 (102)
No 1
>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=100.00 E-value=3.3e-78 Score=562.33 Aligned_cols=236 Identities=42% Similarity=0.771 Sum_probs=69.4
Q ss_pred hHHHhhccCCC-cccc-cCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493 8 LYLLGLAKGSG-MSKR-KRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI 85 (252)
Q Consensus 8 ~~~~~~~~~~~-~~~~-~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI 85 (252)
..++.+.++++ ..++ +.++.++++++|+++|++||++|++ |||+|||++|||++| |||+++|+|+||+||+|+||
T Consensus 54 ~~~~~~~~~~~~l~~~~~~~~~a~k~~~l~~~e~lvy~~I~~-ag~~GIw~~~i~~~t--~l~~~~~~k~lk~Le~k~lI 130 (327)
T PF05158_consen 54 SGLLKLLKKGGGLSYKAVSEEEAKKLKGLSDEERLVYQLIEE-AGNKGIWTKDIKKKT--NLHQTQLTKILKSLESKKLI 130 (327)
T ss_dssp HTSEEEEE-SSSEEEEE--SSS-----SSSCCHHHHHHHHHH-HTTT-EEHHHHHHHC--T--HHHHHHHHHHHHHTTSE
T ss_pred CCCEEEEEcCCEEEEEEeCHHHHhhhcCCCHHHHHHHHHHHH-hCCCCCcHHHHHHHc--CCCHHHHHHHHHHHHhCCCE
Confidence 34444444433 3444 6678889999999999999999999 999999999999999 99999999999999999999
Q ss_pred eeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhCCC-----------------------
Q 025493 86 KEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKV----------------------- 142 (252)
Q Consensus 86 K~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~----------------------- 142 (252)
|+||||++++|||||||||+||+|||||+||+|||||+|||+.|+++|++||++++.
T Consensus 131 K~vksv~~~~rK~Yml~~l~Ps~eiTGG~wy~d~e~D~efi~~l~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 210 (327)
T PF05158_consen 131 KSVKSVKNPNRKVYMLYDLEPSEEITGGPWYTDGEFDTEFIDVLREQCLRFIQQKSFPSSEQISQKTSSSSADPQALPYP 210 (327)
T ss_dssp EEE--SS-SS--EEEESSS-------------------------------------------------------------
T ss_pred EEecCcCCCCeEEEEEccCCcCcccCCCCcccCCcccHHHHHHHHHHHHHHHHhCcCccccccccccccccccccccccc
Confidence 999999999999999999999999999999999999999999999999999986544
Q ss_pred ------CCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCccee-------ecccCCCC
Q 025493 143 ------ATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCY-------KNVSKGGG 209 (252)
Q Consensus 143 ------~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~Y-------R~~~~~~~ 209 (252)
||++||++||+++||++++|+++||++||++|||||+||++.+++..++...+....++ |....
T Consensus 211 ~~~~~~~T~~eI~~fI~~sgIs~v~Ls~eDI~~LL~tLVyDgkIE~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--- 287 (327)
T PF05158_consen 211 AGYASYPTLEEIAEFINKSGISNVELSEEDIESLLDTLVYDGKIEEVRSGDGYEYYRAPGQSVLYCSKRRYYRAVGP--- 287 (327)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred cccCCCCCHHHHHHHHHHcCCCceecCHHHHHHHHHHHhhCceeEEEeccCCceeeeeecccceeeecccccccccc---
Confidence 99999999999999999999999999999999999999999977444443333333332 22222
Q ss_pred CCCCCCCCcccCCCCCCCccccCCCCCccCcccccchHhhhc
Q 025493 210 GGEPKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWLD 251 (252)
Q Consensus 210 ~~~~~~~~l~~vPCg~CPv~~~C~~gG~IsP~tC~Y~~eWL~ 251 (252)
.+..++++++|||+||||+.|.+||+|||++|+||++||+
T Consensus 288 --~~~~~~~~~~PCg~CPVf~~C~~~G~IsP~~C~Yf~~WL~ 327 (327)
T PF05158_consen 288 --EPSASGLTEVPCGVCPVFDQCSPGGPISPKTCVYFDEWLD 327 (327)
T ss_dssp ------------------------------------------
T ss_pred --ccCCCCccCCCCCCCCccceeCCCCCCCchhchHHHHhhC
Confidence 2446789999999999999999999999999999999996
No 2
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=100.00 E-value=1.2e-73 Score=513.71 Aligned_cols=224 Identities=36% Similarity=0.744 Sum_probs=205.3
Q ss_pred hHHHhhccCC-C-cccccCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493 8 LYLLGLAKGS-G-MSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI 85 (252)
Q Consensus 8 ~~~~~~~~~~-~-~~~~~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI 85 (252)
..+|++.+.+ + .+++++++.+...+++++||++||++|++ +||+|||.++||.++ |||+++|+|+||+||+|+||
T Consensus 54 ~~~l~llr~~~~l~yr~~d~~~a~~~~~~e~eEk~vy~lIe~-sg~~GIW~k~ik~ks--nLp~~~v~K~LkSLEsKkLI 130 (297)
T KOG3233|consen 54 RGLLDLLRQNTGLVYRAKDPKSASKGKGMENEEKLVYSLIEE-SGNEGIWSKEIKRKS--NLPQTVVNKILKSLESKKLI 130 (297)
T ss_pred cCcchhhccCCcceEeccCchhhcccccCChHHHHHHHHHHH-cCCCceeeehhhhcc--CCCHHHHHHHHHHHHHHHHH
Confidence 4567777666 3 34457888888899999999999999999 999999999999999 99999999999999999999
Q ss_pred eeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhh-----------------CCCCCHHHH
Q 025493 86 KEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIK-----------------LKVATLEGI 148 (252)
Q Consensus 86 K~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~-----------------~~~~T~~~I 148 (252)
|+||||++++||+||||+|+||.|+|||+||+||+||.|||+.|.++|++|+++ .+++|++||
T Consensus 131 KsVKsv~n~~~KvYmLy~leP~~elTGG~WytDqdlDvEfIe~L~~~c~~fl~~~~~~~~~~~~gp~~~~~~~~~t~~ei 210 (297)
T KOG3233|consen 131 KSVKSVKNSRKKVYMLYDLEPDSELTGGTWYTDQDLDVEFIEVLKQICVRFLESKRFPAEKNVEGPMFVRNESYPTVQEI 210 (297)
T ss_pred HHHHhhcCCCceEEEEecccccccccCCcccccccccHHHHHHHHHHHHHHHHhcccchhhccccchhhhhccCCCHHHH
Confidence 999999999999999999999999999999999999999999999999999973 479999999
Q ss_pred HHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccCCCCCCCCCCCCcccCCCCCCCc
Q 025493 149 SDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCGVCPQ 228 (252)
Q Consensus 149 ~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~~~~~~~~~~~~l~~vPCg~CPv 228 (252)
++||++.+|++|.|+.+|++.|+++|||||+||+.. +| .+||+..... |..+.+.++|||.|||
T Consensus 211 ~~~i~~l~I~nV~Lsl~dleti~~vlvyDGkvE~r~-dG-----------~~yra~~~~~----~~~~~~~~~Pcg~cPv 274 (297)
T KOG3233|consen 211 KEFIRNLNILNVELSLEDLETILDVLVYDGKVEKRH-DG-----------PRYRAFGPNI----PRAGLVAGIPCGICPV 274 (297)
T ss_pred HHHHHHcCcccccccHHHHHHHhHHheecceeeeee-cC-----------ceeeecCCCC----CCcCccCCCcccCCcc
Confidence 999999999999999999999999999999999833 33 3799887764 3456778899999999
Q ss_pred cccCCCCCccCcccccchHhhh
Q 025493 229 INFCTPDGVISPKTCVYYTKWL 250 (252)
Q Consensus 229 ~~~C~~gG~IsP~tC~Y~~eWL 250 (252)
++.|+|||.|||.||+||++||
T Consensus 275 ~~dC~~~g~isP~tC~Ym~~WL 296 (297)
T KOG3233|consen 275 IDDCSPGGVISPITCVYMDKWL 296 (297)
T ss_pred hhccCCCCccCchhhHHHHhhc
Confidence 9999999999999999999999
No 3
>COG5111 RPC34 DNA-directed RNA polymerase III, subunit C34 [Transcription]
Probab=100.00 E-value=4.2e-63 Score=436.83 Aligned_cols=226 Identities=24% Similarity=0.411 Sum_probs=208.7
Q ss_pred hhHHHhhccCCCcccc--cCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCC
Q 025493 7 DLYLLGLAKGSGMSKR--KRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL 84 (252)
Q Consensus 7 ~~~~~~~~~~~~~~~~--~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l 84 (252)
+.+||+|.+++++.+. +..+++...+.|+++|.+||++|++ +|++|||.+.|+.+| |||++.+-||||+||+|++
T Consensus 54 ~r~li~l~rq~~vL~y~~v~~~ea~~~~tm~~~E~~vYs~i~~-SG~EGiW~Ktik~rT--Nlh~~vV~kcLkSlESkr~ 130 (301)
T COG5111 54 KRQLISLFRQKGVLYYKGVLESEASPINTMDDYELTVYSLISQ-SGGEGIWLKTIKDRT--NLHHNVVGKCLKSLESKRI 130 (301)
T ss_pred HHhhhhHHhcCCEEEEeeeecccCCcccccchHHHHHHHHHHh-cCCCceehhhhhhhc--cCcHHHHHHHHHHHHHHHH
Confidence 4689999999999886 5778888899999999999999999 999999999999999 9999999999999999999
Q ss_pred eeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhh--------------------CCCCC
Q 025493 85 IKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIK--------------------LKVAT 144 (252)
Q Consensus 85 IK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~--------------------~~~~T 144 (252)
||+||||++|+||+||||+|.||+||||||||||||+|.|||+.|.+++.+||.. .+|||
T Consensus 131 vKSvKsvKnptRKiYmLYdlvPS~eiTGGpWFtD~elDvEfi~~ll~ii~rf~~~n~fp~kn~~~gpnv~~~P~y~~ypT 210 (301)
T COG5111 131 VKSVKSVKNPTRKIYMLYDLVPSEEITGGPWFTDNELDVEFIARLLEIIERFLEKNLFPRKNFEEGPNVFYAPKYEDYPT 210 (301)
T ss_pred HHHhhhhcCCCceEEEEecccccccccCCCccccCcccHHHHHHHHHHHHHHHHhccCCccchhcCCccccCCccCCCcc
Confidence 9999999999999999999999999999999999999999999999999999983 37999
Q ss_pred HHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccCCCCCCCCCCCCcccCCCC
Q 025493 145 LEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGGGGEPKTGSSASVPCG 224 (252)
Q Consensus 145 ~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~~~~~~~~~~~~l~~vPCg 224 (252)
++||++||++.+|.+|+|+.++++++.++|||||++|++.++. .||...-.. -..+..++-|||
T Consensus 211 ~~~I~n~vr~~ni~~v~L~l~n~~sL~dvLvyDgKvEK~~~g~------------~yR~~~~~~----~~~nq~~~ep~g 274 (301)
T COG5111 211 LEDIMNYVRNVNILSVPLRLDNLESLADVLVYDGKVEKLHSGP------------IYRYRAFKP----YAKNQGEGEPAG 274 (301)
T ss_pred HHHHHHHHHhceeeeccccHHHHHHHhHheeecCeeeeeccCc------------ceeeeecCh----hhhcccCCCCCC
Confidence 9999999999999999999999999999999999999987542 366544332 125778999999
Q ss_pred CCCccccCCCCCccCcccccchHhhhc
Q 025493 225 VCPQINFCTPDGVISPKTCVYYTKWLD 251 (252)
Q Consensus 225 ~CPv~~~C~~gG~IsP~tC~Y~~eWL~ 251 (252)
.||+-+.|.....+.|.+|+||++|+.
T Consensus 275 n~~led~~e~s~km~p~s~~y~dew~~ 301 (301)
T COG5111 275 NKALEDEEEFSFKMFPASVVYFDEWTI 301 (301)
T ss_pred CCcccchHhhhcccCceeEEeehhhcC
Confidence 999999999999999999999999973
No 4
>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=98.33 E-value=2.5e-06 Score=63.75 Aligned_cols=65 Identities=23% Similarity=0.299 Sum_probs=56.7
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc---ccCCeeeEEec
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI---HNKGKKHLMAV 102 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv---~~~~rK~YmL~ 102 (252)
|+.+..|+..|-. |+..|||+.||.+.+ ++.++.+...+|.|+.+|||.....+ ..++...++|+
T Consensus 1 t~~~~~~Le~I~r-sR~~Gi~q~~L~~~~--~~D~r~i~~~~k~L~~~gLI~k~~~~~~~~~~~~~t~ll~ 68 (75)
T PF04182_consen 1 TDIQYCLLERIAR-SRYNGITQSDLSKLL--GIDPRSIFYRLKKLEKKGLIVKQSVISSSNSKGTRTNLLH 68 (75)
T ss_pred CchHHHHHHHHHh-cCCCCEehhHHHHHh--CCCchHHHHHHHHHHHCCCEEEEEeccccCCCceEEEEEE
Confidence 5678999999999 999999999999999 99999999999999999999996552 34456666664
No 5
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=98.00 E-value=2e-05 Score=72.00 Aligned_cols=56 Identities=25% Similarity=0.470 Sum_probs=51.1
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
.-.|+++|+.|..+|.+ .|+. |-|+||++++ |++.+.+.|+|+.||++|+|+..|.
T Consensus 190 ~~~L~~~e~~il~~i~~-~GGr-i~Q~eL~r~l--glsktTvsR~L~~LEk~GlIe~~K~ 245 (258)
T COG2512 190 EYDLNEDEKEILDLIRE-RGGR-ITQAELRRAL--GLSKTTVSRILRRLEKRGLIEKEKK 245 (258)
T ss_pred cCCCCHHHHHHHHHHHH-hCCE-EeHHHHHHhh--CCChHHHHHHHHHHHhCCceEEEEe
Confidence 35899999999999999 5532 9999999999 9999999999999999999999875
No 6
>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=97.92 E-value=7.2e-05 Score=52.45 Aligned_cols=58 Identities=14% Similarity=0.248 Sum_probs=52.6
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
+|+..|..|+..|.. .+..++-..+|...+ ++++..++++++.||++|||...++-+.
T Consensus 2 glt~~q~~vL~~l~~-~~~~~~t~~~la~~l--~~~~~~vs~~v~~L~~~Glv~r~~~~~D 59 (62)
T PF12802_consen 2 GLTPSQFRVLMALAR-HPGEELTQSELAERL--GISKSTVSRIVKRLEKKGLVERERDPGD 59 (62)
T ss_dssp TSTHHHHHHHHHHHH-STTSGEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEE-SSS
T ss_pred ccCHHHHHHHHHHHH-CCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEeCCCCC
Confidence 689999999999999 999999999999999 9999999999999999999999876553
No 7
>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=97.91 E-value=0.00014 Score=57.56 Aligned_cols=85 Identities=16% Similarity=0.234 Sum_probs=69.1
Q ss_pred CCChHHHHHHHHHH--hhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCc
Q 025493 33 SLTDHERLIYDVIR--SNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDI 110 (252)
Q Consensus 33 ~l~~~e~~vy~~I~--~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~ei 110 (252)
+|+..|..|+..|. + +.+.|+..++|...+ +++...++++++.||++|+|+.+++.+. .|++|+- |+|.
T Consensus 22 ~ls~~q~~vL~~l~~~~-~~~~~~t~~eL~~~l--~~~~stvs~~i~~Le~kg~I~r~~~~~D-~R~~~i~--lT~~--- 92 (109)
T TIGR01889 22 NLSLEELLILYYLGKLE-NNEGKLTLKEIIKEI--LIKQSALVKIIKKLSKKGYLSKERSEDD-ERKVIIS--INKE--- 92 (109)
T ss_pred CCCHHHHHHHHHHHhhh-ccCCcCcHHHHHHHH--CCCHHHHHHHHHHHHHCCCEeccCCccc-CCeEEEE--ECHH---
Confidence 79999999999998 6 667889999999999 9999999999999999999999999887 4444432 3333
Q ss_pred cCCccccCCcCCHHHHHHHHHHHHHHh
Q 025493 111 SGGAWYSEGSLDTEFIKVVKSQCLKQI 137 (252)
Q Consensus 111 TGG~wy~d~e~D~efV~~l~~~~~~~i 137 (252)
-.+.++.+...+.+++
T Consensus 93 -----------G~~~~~~~~~~~~~~~ 108 (109)
T TIGR01889 93 -----------QRSKIESLISEIEQII 108 (109)
T ss_pred -----------HHHHHHHHHHHHHHHh
Confidence 2456677777766664
No 8
>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=97.81 E-value=5e-05 Score=54.99 Aligned_cols=62 Identities=23% Similarity=0.328 Sum_probs=52.8
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE 103 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~ 103 (252)
+|++.|..||..+-+ +.+.-.++|...+ +++.+.+.++|+.|+.+|+|...+. +.++|-..+
T Consensus 5 gLs~~E~~vy~~Ll~---~~~~t~~eIa~~l--~i~~~~v~~~L~~L~~~GlV~~~~~----~~~~Y~a~~ 66 (68)
T PF01978_consen 5 GLSENEAKVYLALLK---NGPATAEEIAEEL--GISRSTVYRALKSLEEKGLVEREEG----RPKVYRAVP 66 (68)
T ss_dssp CHHHHHHHHHHHHHH---HCHEEHHHHHHHH--TSSHHHHHHHHHHHHHTTSEEEEEE----CCEEEEEE-
T ss_pred CcCHHHHHHHHHHHH---cCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEcC----ceEEEEEeC
Confidence 688999999999876 4678899999999 9999999999999999999999762 266776643
No 9
>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=97.80 E-value=8.9e-05 Score=50.13 Aligned_cols=48 Identities=25% Similarity=0.487 Sum_probs=41.1
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCee
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIK 86 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK 86 (252)
||+.++.|+.+|.+ +.++.+++|..++ |++...+++.|+.|+++|+|+
T Consensus 1 l~~~~~~Il~~l~~---~~~~t~~ela~~~--~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 1 LDETQRKILNYLRE---NPRITQKELAEKL--GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp --HHHHHHHHHHHH---CTTS-HHHHHHHH--TS-HHHHHHHHHHHHHTTSEE
T ss_pred CCHHHHHHHHHHHH---cCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCcCcC
Confidence 67889999999999 4459999999999 999999999999999999996
No 10
>PF13730 HTH_36: Helix-turn-helix domain
Probab=97.78 E-value=0.00011 Score=50.93 Aligned_cols=52 Identities=25% Similarity=0.489 Sum_probs=45.8
Q ss_pred CCCChHHHHHHHHHHhhcCCCc-cc--HHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493 32 DSLTDHERLIYDVIRSNKQDMG-IW--TRDMKRELKVNLPDNIVTKSIKSLQNKSLI 85 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~G-Iw--~~dik~~~~~~l~~~~l~k~lK~Le~k~lI 85 (252)
++|++.|++||-.|...+++.| .| .+.|.+.+ ++..++|.|+|+.||++|+|
T Consensus 1 ~~Ls~~~~~v~~~l~~~~~~~~~~~pS~~~la~~~--g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 1 KNLSPTAKLVYLYLASYANKNGGCFPSQETLAKDL--GVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CCCCHHHHHHHHHHHHhcCCCCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCcCC
Confidence 3799999999999998664444 44 79999999 99999999999999999997
No 11
>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=97.59 E-value=0.00035 Score=48.71 Aligned_cols=55 Identities=24% Similarity=0.342 Sum_probs=49.4
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
||..|..++..|.+ .|+ +-..+|...+ +++...++++++.||++|+|....+-+.
T Consensus 1 lt~~q~~iL~~l~~-~~~--~~~~~la~~~--~~~~~~~t~~i~~L~~~g~I~r~~~~~D 55 (59)
T PF01047_consen 1 LTPSQFRILRILYE-NGG--ITQSELAEKL--GISRSTVTRIIKRLEKKGLIERERDPDD 55 (59)
T ss_dssp STHHHHHHHHHHHH-HSS--EEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEEETTE
T ss_pred CCHHHHHHHHHHHH-cCC--CCHHHHHHHH--CCChhHHHHHHHHHHHCCCEEeccCCCC
Confidence 57789999999999 665 9999999999 9999999999999999999999888765
No 12
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=97.59 E-value=0.0015 Score=53.41 Aligned_cols=66 Identities=12% Similarity=0.175 Sum_probs=55.8
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
-+|+..+..|+..|.+ .+ .|+.+++|...+ ++..+.++++++.||++|||...++-+.+..+..-|
T Consensus 27 ~glt~~q~~vL~~l~~-~~-~~~t~~eLa~~l--~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~l~L 92 (144)
T PRK03573 27 LELTQTHWVTLHNIHQ-LP-PEQSQIQLAKAI--GIEQPSLVRTLDQLEEKGLISRQTCASDRRAKRIKL 92 (144)
T ss_pred cCCCHHHHHHHHHHHH-cC-CCCCHHHHHHHh--CCChhhHHHHHHHHHHCCCEeeecCCCCcCeeeeEE
Confidence 4799999999999987 53 468899999999 999999999999999999999999887644444333
No 13
>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=97.53 E-value=0.00051 Score=48.88 Aligned_cols=64 Identities=22% Similarity=0.335 Sum_probs=49.8
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
||..|..|+..|. ..+..+-.++|...+ ++++..++++|++|+.+|||....+-+.+..+.|-|
T Consensus 1 lt~~q~~vL~~l~--~~~~~~t~~~l~~~~--~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~L 64 (68)
T PF13463_consen 1 LTRPQWQVLRALA--HSDGPMTQSDLAERL--GISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYRL 64 (68)
T ss_dssp --HHHHHHHHHHT----TS-BEHHHHHHHT--T--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEEE
T ss_pred CCHHHHHHHHHHH--ccCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEEe
Confidence 5778888888887 246778889999999 999999999999999999999999888755566655
No 14
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=97.49 E-value=0.00041 Score=50.88 Aligned_cols=51 Identities=20% Similarity=0.284 Sum_probs=47.2
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
++.+..|+.++.+ +|.+|+-.++|.+++ +|+...++|+|.+|+++|+|...
T Consensus 5 ~~~~~~IL~~L~~-~g~~~~ta~eLa~~l--gl~~~~v~r~L~~L~~~G~V~~~ 55 (68)
T smart00550 5 DSLEEKILEFLEN-SGDETSTALQLAKNL--GLPKKEVNRVLYSLEKKGKVCKQ 55 (68)
T ss_pred hHHHHHHHHHHHH-CCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEec
Confidence 4567899999999 999999999999999 99999999999999999999763
No 15
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=97.46 E-value=0.00061 Score=52.43 Aligned_cols=63 Identities=17% Similarity=0.292 Sum_probs=55.8
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
|+..|..|+..|.. .+..+. .+|..++ +++...+++.|+.||.+|||+..++-..+.++++.|
T Consensus 20 lt~~q~~~L~~l~~-~~~~~~--~~la~~l--~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~l 82 (126)
T COG1846 20 LTPPQYQVLLALYE-AGGITV--KELAERL--GLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRL 82 (126)
T ss_pred CCHHHHHHHHHHHH-hCCCcH--HHHHHHH--CCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEE
Confidence 89999999999999 888777 9999999 999999999999999999999999887744444444
No 16
>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=97.45 E-value=0.00069 Score=53.77 Aligned_cols=65 Identities=9% Similarity=0.175 Sum_probs=57.0
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
.+|+..+..|+..|.. .| |+-.++|.+.+ ++..+.+++.|+.||++|||...++-..+.++.|-|
T Consensus 24 ~~lt~~q~~iL~~l~~-~~--~~t~~ela~~~--~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~L 88 (118)
T TIGR02337 24 HGLTEQQWRILRILAE-QG--SMEFTQLANQA--CILRPSLTGILARLERDGLVTRLKASNDQRRVYISL 88 (118)
T ss_pred cCCCHHHHHHHHHHHH-cC--CcCHHHHHHHh--CCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEE
Confidence 4789999999999987 54 78899999999 999999999999999999999998888766666555
No 17
>PRK10870 transcriptional repressor MprA; Provisional
Probab=97.42 E-value=0.00071 Score=58.05 Aligned_cols=61 Identities=10% Similarity=0.177 Sum_probs=56.7
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK 94 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~ 94 (252)
.-+|+..+..|+..|.+ .++.++-.++|...+ +++...++++++.||++|||...++-..+
T Consensus 50 ~~gLt~~q~~iL~~L~~-~~~~~it~~eLa~~l--~l~~~tvsr~v~rLe~kGlV~R~~~~~Dr 110 (176)
T PRK10870 50 AQGINETLFMALITLES-QENHSIQPSELSCAL--GSSRTNATRIADELEKRGWIERRESDNDR 110 (176)
T ss_pred HCCCCHHHHHHHHHHhc-CCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEecCCCCCC
Confidence 35799999999999998 999999999999999 99999999999999999999999887763
No 18
>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=97.41 E-value=0.0063 Score=49.99 Aligned_cols=53 Identities=21% Similarity=0.272 Sum_probs=44.2
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeee
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.|++-|..|.++|=+ .| ++..++|....+. ++..+++...|+.|+.||+|...
T Consensus 1 ~Lt~~E~~VM~vlW~-~~--~~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~ 55 (130)
T TIGR02698 1 SISDAEWEVMRVVWT-LG--ETTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE 55 (130)
T ss_pred CCCHHHHHHHHHHHc-CC--CCCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee
Confidence 378899999999988 76 4678996665421 78999999999999999999875
No 19
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=97.36 E-value=0.0012 Score=49.33 Aligned_cols=57 Identities=18% Similarity=0.332 Sum_probs=50.9
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
-+|+..|..|+.+|.. .| ++-.++|...+ ++++..+++.|+.|+++|+|...+.-..
T Consensus 6 ~~l~~~~~~il~~l~~-~~--~~~~~~la~~~--~~s~~~i~~~l~~L~~~g~v~~~~~~~~ 62 (101)
T smart00347 6 LGLTPTQFLVLRILYE-EG--PLSVSELAKRL--GVSPSTVTRVLDRLEKKGLIRRLPSPED 62 (101)
T ss_pred cCCCHHHHHHHHHHHH-cC--CcCHHHHHHHH--CCCchhHHHHHHHHHHCCCeEecCCCCC
Confidence 4789999999999998 66 68899999999 9999999999999999999998766433
No 20
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=97.22 E-value=0.0018 Score=53.18 Aligned_cols=59 Identities=19% Similarity=0.201 Sum_probs=53.1
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG 95 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~ 95 (252)
.+|+..|..|+..|.. . .|+-+++|...+ ++....++++|+.||++|||....+-+.+.
T Consensus 36 ~glt~~q~~vL~~l~~-~--~~~t~~eLa~~l--~i~~~tvsr~l~~Le~~GlI~R~~~~~DrR 94 (144)
T PRK11512 36 LDITAAQFKVLCSIRC-A--ACITPVELKKVL--SVDLGALTRMLDRLVCKGWVERLPNPNDKR 94 (144)
T ss_pred cCCCHHHHHHHHHHHH-c--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEeccCcccCC
Confidence 4899999999999976 4 579999999999 999999999999999999999998887633
No 21
>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=97.08 E-value=0.014 Score=46.39 Aligned_cols=111 Identities=13% Similarity=0.187 Sum_probs=71.3
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhc--CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS 111 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT 111 (252)
|++-|..|.++|=+ .|. +..++|....+- +++.+++...|+.|+.||+|..-+. .+..+|-. +.+-
T Consensus 1 Ls~~E~~IM~~lW~-~~~--~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~~---gr~~~Y~p--~is~---- 68 (115)
T PF03965_consen 1 LSDLELEIMEILWE-SGE--ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREKI---GRAYVYSP--LISR---- 68 (115)
T ss_dssp --HHHHHHHHHHHH-HSS--EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEE---TTCEEEEE--SSSH----
T ss_pred CCHHHHHHHHHHHh-CCC--CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEeec---CCceEEEe--CCcH----
Confidence 67889999999999 888 999999998743 5789999999999999999999654 22333421 1111
Q ss_pred CCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHH
Q 025493 112 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAV 174 (252)
Q Consensus 112 GG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tL 174 (252)
. +.+...+.+++.+--.-+...+..++-+.. .||.+|+++|-+.|
T Consensus 69 -----------~---e~~~~~~~~~l~~~~~gs~~~l~~~l~~~~----~ls~~el~~L~~li 113 (115)
T PF03965_consen 69 -----------E---EYLAQELRQFLDRLFDGSIPQLVAALVESE----ELSPEELEELRKLI 113 (115)
T ss_dssp -----------H---HHHHHHHHHHHHHHSTTHHHHHHHHHHHCT-----S-HHHHHHHHHHH
T ss_pred -----------H---HHHHHHHHHHHHHHhCCCHHHHHHHHHhcC----CCCHHHHHHHHHHH
Confidence 1 233334444444332335555555555444 68899998887765
No 22
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=97.07 E-value=0.0027 Score=55.41 Aligned_cols=57 Identities=11% Similarity=-0.001 Sum_probs=52.0
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
-+|+..|..|+..|.. . .|+.+++|.+.+ +++.++++++|+.||++|||...++-..
T Consensus 41 ~gLt~~q~~iL~~L~~-~--~~itq~eLa~~l--~l~~sTvtr~l~rLE~kGlI~R~~~~~D 97 (185)
T PRK13777 41 YDLNINEHHILWIAYH-L--KGASISEIAKFG--VMHVSTAFNFSKKLEERGYLTFSKKEDD 97 (185)
T ss_pred CCCCHHHHHHHHHHHh-C--CCcCHHHHHHHH--CCCHhhHHHHHHHHHHCCCEEecCCCCC
Confidence 5899999999999887 4 489999999999 9999999999999999999999888665
No 23
>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=96.92 E-value=0.0015 Score=47.77 Aligned_cols=58 Identities=22% Similarity=0.404 Sum_probs=45.9
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcc--cHHHHHHHhhcCCC-hHHHHHHHHHHHhcCCeeeeec
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGI--WTRDMKRELKVNLP-DNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GI--w~~dik~~~~~~l~-~~~l~k~lK~Le~k~lIK~vks 90 (252)
++.||+-|+.||..|.+.--..|. ..++|.... |+. .+.+.+.|+.||.||+|+..+.
T Consensus 1 M~~LT~rQ~~vL~~I~~~~~~~G~~Pt~rEIa~~~--g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 1 MKELTERQKEVLEFIREYIEENGYPPTVREIAEAL--GLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp -----HHHHHHHHHHHHHHHHHSS---HHHHHHHH--TSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCcCccCCCC
Confidence 357999999999999885555666 468999999 998 8999999999999999998654
No 24
>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=96.83 E-value=0.018 Score=54.41 Aligned_cols=133 Identities=21% Similarity=0.291 Sum_probs=85.1
Q ss_pred CCChHHHHHHHHHHhhc-CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493 33 SLTDHERLIYDVIRSNK-QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS 111 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~a-g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT 111 (252)
.+.+-|..||+++.+ + +.+|+..+||....+ +++...+-.+|..|.++++|+-++ ..++-+|-+-+-+=...+.
T Consensus 6 ~~~~~~~~l~~~~~~-~~~~~~~~~~~L~~~~~-~~~~~~~~~~in~Ll~~~~~~~~~---~~~~l~~~~~~~~~a~k~~ 80 (327)
T PF05158_consen 6 KLSELEKKLLELCRE-NPSPKGFSQEDLQQLIP-GLDLQELVKAINELLSSGLLKLLK---KGGGLSYKAVSEEEAKKLK 80 (327)
T ss_dssp -HHHHHHHHHHHHHH----SS-EEHHHHHHH-T-TS-HHHHHHHHHHHHHHTSEEEEE----SSSEEEEE--SSS-----
T ss_pred hHHHHHHHHHHHHHH-hcCCCCcCHHHHHhhcC-CCCHHHHHHHHHHHHhCCCEEEEE---cCCEEEEEEeCHHHHhhhc
Confidence 567789999999999 6 999999999999942 899999999999999999999998 4456566654333222222
Q ss_pred CCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcC---Cc------ceecCHHHHHHHHHHHhhcCeeEE
Q 025493 112 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSG---AF------KVDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 112 GG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~---i~------~~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
|= ...-.-|.+.|.++| |- +..|....|..+|++|+-.+.|-+
T Consensus 81 ~l----------------------------~~~e~lvy~~I~~ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~ 132 (327)
T PF05158_consen 81 GL----------------------------SDEERLVYQLIEEAGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKS 132 (327)
T ss_dssp SS----------------------------SCCHHHHHHHHHHHTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEE
T ss_pred CC----------------------------CHHHHHHHHHHHHhCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEE
Confidence 22 122233444444443 21 356888999999999999999999
Q ss_pred EeeCCCCCcccccCCcceeeccc
Q 025493 183 VKSNGSGEFTNIPVGKVCYKNVS 205 (252)
Q Consensus 183 v~~~g~~~f~~~~~g~~~YR~~~ 205 (252)
|++... .+++.|-+..
T Consensus 133 vksv~~-------~~rK~Yml~~ 148 (327)
T PF05158_consen 133 VKSVKN-------PNRKVYMLYD 148 (327)
T ss_dssp E--SS--------SS--EEEESS
T ss_pred ecCcCC-------CCeEEEEEcc
Confidence 987542 3567776653
No 25
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=96.45 E-value=0.015 Score=47.67 Aligned_cols=71 Identities=21% Similarity=0.361 Sum_probs=59.5
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC---Cee--eEEecccc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK---GKK--HLMAVEFE 105 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~---~rK--~YmL~~le 105 (252)
...|++-++.|++++++ -|. +..++|.++. |++.+.+.+.+|.||..|+|+....+-++ +.. +++....+
T Consensus 3 ~~~lD~~D~~IL~~L~~-d~r--~~~~eia~~l--glS~~~v~~Ri~~L~~~GiI~~~~~~v~~~~lg~~~~a~v~v~~~ 77 (154)
T COG1522 3 MMKLDDIDRRILRLLQE-DAR--ISNAELAERV--GLSPSTVLRRIKRLEEEGVIKGYTAVLDPEKLGLDLTAFVEVKLE 77 (154)
T ss_pred cccccHHHHHHHHHHHH-hCC--CCHHHHHHHH--CCCHHHHHHHHHHHHHCCceeeEEEEECHHHcCCCEEEEEEEEec
Confidence 34689999999999999 444 9999999999 99999999999999999999999987665 444 55555555
Q ss_pred c
Q 025493 106 P 106 (252)
Q Consensus 106 P 106 (252)
|
T Consensus 78 ~ 78 (154)
T COG1522 78 R 78 (154)
T ss_pred C
Confidence 5
No 26
>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=96.34 E-value=0.014 Score=50.93 Aligned_cols=64 Identities=13% Similarity=0.232 Sum_probs=49.7
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS 107 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs 107 (252)
...|+..+.. .|. +..++|...+ +++.+.+++.|+.||++|||.........+|.. .+|.|+|.
T Consensus 3 r~~IL~~L~~-~~~--~t~~eLA~~l--gis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~-~~y~LT~~ 66 (203)
T TIGR02702 3 KEDILSYLLK-QGQ--ATAAALAEAL--AISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQ-YHYQLSRQ 66 (203)
T ss_pred HHHHHHHHHH-cCC--CCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEeecccCCCCCc-eEEEECcc
Confidence 3567888887 654 9999999999 999999999999999999999876543344443 34455655
No 27
>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=96.33 E-value=0.018 Score=50.11 Aligned_cols=55 Identities=13% Similarity=0.309 Sum_probs=49.8
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
..++++.+..|+..|.+ .| ++-.++|.+.+ +++++.+++.|+.||++|+|...+.
T Consensus 138 ~~~ls~~~~~IL~~l~~-~g--~~s~~eia~~l--~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 138 LAGLSREELKVLEVLKA-EG--EKSVKNIAKKL--GKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred hcCCCHHHHHHHHHHHH-cC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 45789999999999988 54 68999999999 9999999999999999999999863
No 28
>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=96.33 E-value=0.01 Score=46.18 Aligned_cols=53 Identities=19% Similarity=0.388 Sum_probs=44.9
Q ss_pred CCChHHHHHHHHHHh-hcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 33 SLTDHERLIYDVIRS-NKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~-~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
+|++-.+.||++|++ ...+.||-..+|.+++ +|+..+|.++|..|...|+|=+
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--~~~~~~v~~al~~L~~eG~IYs 97 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--GMSENEVRKALDFLSNEGHIYS 97 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHS--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--CcCHHHHHHHHHHHHhCCeEec
Confidence 799999999999999 7899999999999999 9999999999999999999843
No 29
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=96.29 E-value=0.023 Score=46.97 Aligned_cols=71 Identities=13% Similarity=0.128 Sum_probs=57.2
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS 107 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs 107 (252)
-+|++.|.-||.++-+ -|.+...-+|..++ |+..++++|+|++|...|||.+.|----.++-.| +|.--|.
T Consensus 23 ~GLs~~Dv~v~~~LL~--~~~~~tvdelae~l--nr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~y-iY~~i~~ 93 (126)
T COG3355 23 YGLSELDVEVYKALLE--ENGPLTVDELAEIL--NRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYY-LYKPIDP 93 (126)
T ss_pred hCCcHHHHHHHHHHHh--hcCCcCHHHHHHHH--CccHHHHHHHHHHHHHcCCeeeeeeccCCCceeE-EEecCCH
Confidence 4799999999999985 36788899999999 9999999999999999999999885444455444 4443333
No 30
>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=96.23 E-value=0.014 Score=50.35 Aligned_cols=56 Identities=21% Similarity=0.347 Sum_probs=49.5
Q ss_pred CCCChHHHHHHHHHHhh--cCCCcccHHHHHHHhhcCCC-hHHHHHHHHHHHhcCCeeeee
Q 025493 32 DSLTDHERLIYDVIRSN--KQDMGIWTRDMKRELKVNLP-DNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~--ag~~GIw~~dik~~~~~~l~-~~~l~k~lK~Le~k~lIK~vk 89 (252)
++||+.|..|+..|.++ .+..+...++|...+ ++. .+.+.+.|++||++|+|+...
T Consensus 2 ~~lt~~q~~iL~~l~~~~~~~~~~~~~~ela~~~--~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 2 KPLTARQQEVLDLIRAHIESTGYPPSIREIARAV--GLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred CccCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHh--CCCChHHHHHHHHHHHHCCCEecCC
Confidence 56999999999999962 356667889999999 999 999999999999999999864
No 31
>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=96.20 E-value=0.041 Score=38.22 Aligned_cols=58 Identities=12% Similarity=0.181 Sum_probs=48.1
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
+..+..|+..|.. .+ +-.++|...+ +++.+.+.+.|+.|+++++|....+- .++.|.+
T Consensus 6 ~~~~~~il~~l~~-~~---~~~~ei~~~~--~i~~~~i~~~l~~L~~~g~i~~~~~~---~~~~~~~ 63 (78)
T cd00090 6 DPTRLRILRLLLE-GP---LTVSELAERL--GLSQSTVSRHLKKLEEAGLVESRREG---RRVYYSL 63 (78)
T ss_pred ChHHHHHHHHHHH-CC---cCHHHHHHHH--CcCHhHHHHHHHHHHHCCCeEEEEec---cEEEEEe
Confidence 3567788888887 54 8899999999 99999999999999999999986543 4566655
No 32
>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=96.12 E-value=0.034 Score=41.73 Aligned_cols=62 Identities=15% Similarity=0.256 Sum_probs=45.1
Q ss_pred HHHHHHhhcCCCc-ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493 41 IYDVIRSNKQDMG-IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS 111 (252)
Q Consensus 41 vy~~I~~~ag~~G-Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT 111 (252)
+.-.+.. .++.+ +..++|..++ +++...+.|+++.|++.|+|++.+..+ -=|.|.. |.++||
T Consensus 13 ~l~~la~-~~~~~~~s~~eiA~~~--~i~~~~l~kil~~L~~~Gli~s~~G~~----GGy~L~~--~~~~It 75 (83)
T PF02082_consen 13 ILLYLAR-HPDGKPVSSKEIAERL--GISPSYLRKILQKLKKAGLIESSRGRG----GGYRLAR--PPEEIT 75 (83)
T ss_dssp HHHHHHC-TTTSC-BEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEETSTT----SEEEESS---CCGSB
T ss_pred HHHHHHh-CCCCCCCCHHHHHHHH--CcCHHHHHHHHHHHhhCCeeEecCCCC----CceeecC--CHHHCC
Confidence 3344555 55555 9999999999 999999999999999999998875332 3566643 555554
No 33
>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=95.92 E-value=0.019 Score=41.87 Aligned_cols=47 Identities=9% Similarity=0.198 Sum_probs=37.1
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
..+.+||+.++.+|+.||+..+ .++.+.|+.+|+.|+--|+|+++..
T Consensus 3 ~~i~~~l~~~~~~S~~eLa~~~--------~~s~~~ve~mL~~l~~kG~I~~~~~ 49 (69)
T PF09012_consen 3 QEIRDYLRERGRVSLAELAREF--------GISPEAVEAMLEQLIRKGYIRKVDM 49 (69)
T ss_dssp HHHHHHHHHS-SEEHHHHHHHT--------T--HHHHHHHHHHHHCCTSCEEEEE
T ss_pred HHHHHHHHHcCCcCHHHHHHHH--------CcCHHHHHHHHHHHHHCCcEEEecC
Confidence 4577788888888888888765 4789999999999999999998864
No 34
>PRK00215 LexA repressor; Validated
Probab=95.90 E-value=0.023 Score=49.28 Aligned_cols=54 Identities=26% Similarity=0.391 Sum_probs=48.2
Q ss_pred CChHHHHHHHHHHhh--cCCCcccHHHHHHHhhcCC-ChHHHHHHHHHHHhcCCeeeee
Q 025493 34 LTDHERLIYDVIRSN--KQDMGIWTRDMKRELKVNL-PDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 34 l~~~e~~vy~~I~~~--ag~~GIw~~dik~~~~~~l-~~~~l~k~lK~Le~k~lIK~vk 89 (252)
||+.|..|+..|.+. .++.++..++|.+.+ ++ +.+.+++.|++||++|+|....
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~~s~~ela~~~--~~~~~~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYPPSRREIADAL--GLRSPSAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCCCEEeCC
Confidence 688999999999841 467788999999999 99 9999999999999999998864
No 35
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=95.90 E-value=0.022 Score=44.20 Aligned_cols=53 Identities=19% Similarity=0.380 Sum_probs=47.1
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI 91 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv 91 (252)
|++.++.|+.++.+ .| .+..++|..++ |++...+.+.++.|+++|+|+.+..+
T Consensus 1 ld~~D~~il~~L~~-~~--~~~~~~la~~l--~~s~~tv~~~l~~L~~~g~i~~~~~~ 53 (108)
T smart00344 1 LDEIDRKILEELQK-DA--RISLAELAKKV--GLSPSTVHNRVKRLEEEGVIKGYTAV 53 (108)
T ss_pred CCHHHHHHHHHHHH-hC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeceEEE
Confidence 57788999999999 54 58899999999 99999999999999999999965544
No 36
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=95.76 E-value=0.015 Score=43.95 Aligned_cols=43 Identities=19% Similarity=0.299 Sum_probs=35.9
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC
Q 025493 51 DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG 95 (252)
Q Consensus 51 ~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~ 95 (252)
+..+.-++|+..+ ++++..+++.|+.||+.|+|+.-|....+.
T Consensus 12 ~~~~~f~~L~~~l--~lt~g~Ls~hL~~Le~~GyV~~~k~~~~~~ 54 (80)
T PF13601_consen 12 NEEATFSELKEEL--GLTDGNLSKHLKKLEEAGYVEVEKEFEGRR 54 (80)
T ss_dssp HSEEEHHHHHHHT--T--HHHHHHHHHHHHHTTSEEEEEE-SSS-
T ss_pred cCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCEEEEEeccCCC
Confidence 5679999999999 999999999999999999999988876543
No 37
>TIGR01610 phage_O_Nterm phage replication protein O, N-terminal domain. This model represents the N-terminal region of the phage lambda replication protein O and homologous regions of other phage proteins.
Probab=95.48 E-value=0.058 Score=41.83 Aligned_cols=58 Identities=19% Similarity=0.166 Sum_probs=47.5
Q ss_pred CCCCCChHHHHHHHHHHhhc-----CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 30 PSDSLTDHERLIYDVIRSNK-----QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~a-----g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
...+++..+..++-.|.... ...+|.+++|-..+ ++....++|+|+.||++|+|+...
T Consensus 19 ~~~~l~~r~~~vLl~L~~~~~G~~~~~~~is~~eLa~~~--g~sr~tVsr~L~~Le~~GlI~r~~ 81 (95)
T TIGR01610 19 PGADLSGREFRVLLAIIRLTYGWNKKQDRVTATVIAELT--GLSRTHVSDAIKSLARRRIIFRQG 81 (95)
T ss_pred HhCCCCHHHHHHHHHHHHHHhCccccCCccCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeec
Confidence 35678888877777554201 47899999999999 999999999999999999999643
No 38
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=95.47 E-value=0.042 Score=50.93 Aligned_cols=62 Identities=16% Similarity=0.327 Sum_probs=53.9
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
+.-| .+...+++ ||..||.|-+|-.=+ |+...+++-+|+.||.+|.||+ +-|..+++.||+.
T Consensus 4 ~~re-klir~Lk~-a~~~GI~Q~eIeel~--GlSKStvSEaLs~LE~~giv~R-rkvsGKs~rVwLa 65 (321)
T COG3888 4 SLRE-KLIRELKR-AGPEGIDQTEIEELM--GLSKSTVSEALSELEKQGIVKR-RKVSGKSKRVWLA 65 (321)
T ss_pred cHHH-HHHHHHHh-cCCCCccHHHHHHHh--CcchhHHHHHHHHHHhcCeeee-eeecCcceEEeec
Confidence 3344 45567888 999999999999999 9999999999999999999999 6677788999865
No 39
>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=95.46 E-value=0.037 Score=40.61 Aligned_cols=51 Identities=16% Similarity=0.181 Sum_probs=45.6
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
++.|..|++++++ +|..++....+.... +.+...||++|=.|+.+|.|...
T Consensus 3 ~~~ee~Il~~L~~-~g~~~a~~ia~~~~L--~~~kk~VN~~LY~L~k~g~v~k~ 53 (66)
T PF02295_consen 3 QDLEEKILDFLKE-LGGSTATAIAKALGL--SVPKKEVNRVLYRLEKQGKVCKE 53 (66)
T ss_dssp HHHHHHHHHHHHH-HTSSEEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred hhHHHHHHHHHHh-cCCccHHHHHHHhCc--chhHHHHHHHHHHHHHCCCEeeC
Confidence 4568899999999 999999999999999 89999999999999999999764
No 40
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.45 E-value=0.079 Score=35.04 Aligned_cols=46 Identities=11% Similarity=0.321 Sum_probs=40.2
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
..|++.+.+ . .++-..+|.... +++.+.+.+.|+.|+.+|+|....
T Consensus 3 ~~il~~l~~-~--~~~s~~~l~~~l--~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 3 QQILELLAQ-Q--GKVSVEELAELL--GVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHH-c--CCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEee
Confidence 457888877 4 369999999999 999999999999999999998754
No 41
>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=95.23 E-value=0.12 Score=36.41 Aligned_cols=50 Identities=16% Similarity=0.245 Sum_probs=41.7
Q ss_pred hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
+.=..|+.++ +++.+....+|...+ +++++.+.+.|+.|+..|||+.++.
T Consensus 10 p~R~~Il~~L---~~~~~~t~~ela~~l--~~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 10 PTRLRILRLL---ASNGPMTVSELAEEL--GISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HHHHHHHHHH---HHCSTBEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHH---hcCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEecc
Confidence 3445677777 347899999999999 9999999999999999999998753
No 42
>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=94.95 E-value=0.055 Score=37.12 Aligned_cols=43 Identities=16% Similarity=0.370 Sum_probs=35.3
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
|++++.+ + ..++-..+|-+++ ++|.+.+.|.|++|+..|+|..
T Consensus 8 iL~~l~~-~-~~~~t~~eia~~~--gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 8 ILEALAE-S-GGPLTLSEIARAL--GLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp HHHCHHC-T-BSCEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHc-C-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCcCeec
Confidence 4555555 3 3447999999999 9999999999999999999986
No 43
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=94.87 E-value=0.2 Score=41.34 Aligned_cols=86 Identities=17% Similarity=0.237 Sum_probs=58.7
Q ss_pred cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHH
Q 025493 49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKV 128 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~ 128 (252)
-|.+==..|+|...+ +++.++++|+.+.||..|+|... +++-+|+-.+-.+ .+|...-..
T Consensus 31 pGdkLPSvRelA~~~--~VNpnTv~raY~eLE~eG~i~t~-----rg~G~fV~~~~~~-------------~~~~~~~~~ 90 (125)
T COG1725 31 PGDKLPSVRELAKDL--GVNPNTVQRAYQELEREGIVETK-----RGKGTFVTEDAKE-------------ILDQLKREL 90 (125)
T ss_pred CCCCCCcHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEe-----cCeeEEEcCCchh-------------hHHHHHHHH
Confidence 466666789999999 99999999999999999999986 3454554422100 455555555
Q ss_pred HHHHHHHHhhh--CCCCCHHHHHHHHHH
Q 025493 129 VKSQCLKQIIK--LKVATLEGISDSIKR 154 (252)
Q Consensus 129 l~~~~~~~i~~--~~~~T~~~I~~~i~~ 154 (252)
+.+.+..||.. .-..|.++|+++++.
T Consensus 91 ~~~~l~~~I~~~~~~G~s~eei~~~~~~ 118 (125)
T COG1725 91 AEEELEEFIEEAKALGLSLEEILELLKE 118 (125)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 55556666653 345666666666653
No 44
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=94.74 E-value=0.046 Score=40.82 Aligned_cols=55 Identities=24% Similarity=0.360 Sum_probs=41.6
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE 103 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~ 103 (252)
.+|+++++. ..+.|.-..+|-.++ ||+...+.+.|+.|+++|||+. ....|.+.+
T Consensus 6 ~Ii~~IL~~-l~~~~~~~t~i~~~~--~L~~~~~~~yL~~L~~~gLI~~-------~~~~Y~lTe 60 (77)
T PF14947_consen 6 EIIFDILKI-LSKGGAKKTEIMYKA--NLNYSTLKKYLKELEEKGLIKK-------KDGKYRLTE 60 (77)
T ss_dssp HHHHHHHHH-H-TT-B-HHHHHTTS--T--HHHHHHHHHHHHHTTSEEE-------ETTEEEE-H
T ss_pred HHHHHHHHH-HHcCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCcCeeC-------CCCEEEECc
Confidence 378888888 658888899999999 9999999999999999999943 456777643
No 45
>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=94.67 E-value=0.064 Score=34.22 Aligned_cols=30 Identities=27% Similarity=0.450 Sum_probs=25.8
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493 54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI 85 (252)
Q Consensus 54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI 85 (252)
+...||-.-+ |+...+++|+|+.|+++|+|
T Consensus 3 mtr~diA~~l--G~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYL--GLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHH--TS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHh--CCcHHHHHHHHHHHHHcCCC
Confidence 4578999999 99999999999999999998
No 46
>PRK06474 hypothetical protein; Provisional
Probab=94.41 E-value=0.54 Score=40.55 Aligned_cols=130 Identities=13% Similarity=0.219 Sum_probs=80.4
Q ss_pred hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEecccccCCCccCC
Q 025493 36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAVEFEPSKDISGG 113 (252)
Q Consensus 36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~~lePs~eiTGG 113 (252)
+.=..|++.+.. .+. +....+|-..++ ++++.+|.+.|+.|+..|||..++.= +....|.|-+-.- .-.+.+.
T Consensus 11 p~R~~Il~~L~~-~~~-~~ta~el~~~l~-~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~~--~~~~~~~ 85 (178)
T PRK06474 11 PVRMKICQVLMR-NKE-GLTPLELVKILK-DVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINEE--DAKIEGS 85 (178)
T ss_pred HHHHHHHHHHHh-CCC-CCCHHHHHHHhc-CCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEeccc--eeeeCHH
Confidence 344578888877 654 499999998884 79999999999999999999998753 3333466755331 1123333
Q ss_pred ccccCC-----cCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc--ceecCHHHHHHHHHHHh
Q 025493 114 AWYSEG-----SLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRAVV 175 (252)
Q Consensus 114 ~wy~d~-----e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~--~~~Ls~~di~~IL~tLV 175 (252)
.|..+. .+-+.|...+.+...+|+.+.+. .-.+-...+.+ ...||+++.+++.+-|.
T Consensus 86 ~~~~~~~e~~~~~~~~~~~~~~~~~~~yl~~~~~-----~~~~~d~~~~s~~~L~Lt~ee~~el~~el~ 149 (178)
T PRK06474 86 EWTGLSDDEKLNYISYYQLSLLQQYQSYLKSLEE-----QNSKEDKATFSVVELKLDEEEFEEFQSELN 149 (178)
T ss_pred HHHHhCHHHHHHHHHHHHHHHHHHHHHHHHhCcc-----cchhccccceeeeeEecCHHHHHHHHHHHH
Confidence 333211 12234555566666677765321 11122333333 46799999888765543
No 47
>PHA02943 hypothetical protein; Provisional
Probab=94.31 E-value=0.29 Score=41.96 Aligned_cols=113 Identities=12% Similarity=0.131 Sum_probs=82.0
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCC
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEG 119 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~ 119 (252)
.|+.+| . .| +-.+.+|-+.+ ++...++.=+|+.||+.|.|++|+ -...-+|++-+ .
T Consensus 15 eILE~L-k-~G--~~TtseIAkaL--GlS~~qa~~~LyvLErEG~VkrV~---~G~~tyw~l~~---------------d 70 (165)
T PHA02943 15 KTLRLL-A-DG--CKTTSRIANKL--GVSHSMARNALYQLAKEGMVLKVE---IGRAAIWCLDE---------------D 70 (165)
T ss_pred HHHHHH-h-cC--CccHHHHHHHH--CCCHHHHHHHHHHHHHcCceEEEe---ecceEEEEECh---------------H
Confidence 466666 3 23 35689999999 999999999999999999999976 32344555522 1
Q ss_pred cCCHHHHHHHHHHHHHHhhh--CCCCCHHHHHHHHHHc--------CCcceecCHHHHHHHHHHHhhc
Q 025493 120 SLDTEFIKVVKSQCLKQIIK--LKVATLEGISDSIKRS--------GAFKVDLTKQQIEEIVRAVVLD 177 (252)
Q Consensus 120 e~D~efV~~l~~~~~~~i~~--~~~~T~~~I~~~i~~~--------~i~~~~Ls~~di~~IL~tLVyD 177 (252)
.+ ...|+.+.+-+..++.+ ..++|+..+++.|.+- .+..|.-....|-+.|+-+.-+
T Consensus 71 ay-~~~v~~~~Relwrlv~s~~~kfi~p~~l~~li~kd~~a~~~~ak~v~v~~r~a~il~fln~~l~~ 137 (165)
T PHA02943 71 AY-TNLVFEIKRELWRLVCNSRLKFITPSRLLRLIAKDTEAHNIFAKYVPVNSRHAHILSFLNSALEM 137 (165)
T ss_pred HH-HHHHHHHHHHHHHHHHhccccccChHHHHHHHHhCHHHHHHHHHhcCcccchHHHHHHHHHHHHH
Confidence 11 12377778888888874 5799999999999864 2345677777888887766544
No 48
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=94.23 E-value=0.18 Score=49.83 Aligned_cols=62 Identities=18% Similarity=0.289 Sum_probs=51.8
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE 103 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~ 103 (252)
+|+..|..|+..|.+ .| ++-+.+|..++ ++....|+++++.||++|||..... .++.|-|.+
T Consensus 3 ~Lt~~e~~vL~~L~~-~~--~~s~~eLA~~l--~l~~~tVt~~i~~Le~kGlV~~~~~----~~~~i~LTe 64 (489)
T PRK04172 3 ELHPNEKKVLKALKE-LK--EATLEELAEKL--GLPPEAVMRAAEWLEEKGLVKVEER----VEEVYVLTE 64 (489)
T ss_pred CCCHHHHHHHHHHHh-CC--CCCHHHHHHHh--CcCHHHHHHHHHHHHhCCCEEEEee----eEEEEEECH
Confidence 689999999999977 55 78999999999 9999999999999999999998532 234555543
No 49
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=94.18 E-value=0.28 Score=35.69 Aligned_cols=49 Identities=14% Similarity=0.176 Sum_probs=40.8
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH 92 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~ 92 (252)
.|++.|.+ . +.++-++||...+ +|...++.+.|..||+.|.|+.++.=+
T Consensus 4 ~Il~~i~~-~-~~p~~T~eiA~~~--gls~~~aR~yL~~Le~eG~V~~~~~~r 52 (62)
T PF04703_consen 4 KILEYIKE-Q-NGPLKTREIADAL--GLSIYQARYYLEKLEKEGKVERSPVRR 52 (62)
T ss_dssp CHHHHHHH-H-TS-EEHHHHHHHH--TS-HHHHHHHHHHHHHCTSEEEES-SS
T ss_pred HHHHHHHH-c-CCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEecCCC
Confidence 47778888 5 7889999999999 999999999999999999999865433
No 50
>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=94.11 E-value=0.15 Score=38.78 Aligned_cols=53 Identities=13% Similarity=0.228 Sum_probs=41.2
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493 50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE 103 (252)
Q Consensus 50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~ 103 (252)
...-.=-.+|+++++ +++++.|++.||.||..|||.....-..|.+.-|.|.+
T Consensus 15 ~~g~~rf~el~~~l~-~is~~~L~~~L~~L~~~GLv~r~~~~~~p~~v~Y~LT~ 67 (90)
T PF01638_consen 15 FQGPMRFSELQRRLP-GISPKVLSQRLKELEEAGLVERRVYPEVPPRVEYSLTE 67 (90)
T ss_dssp TTSSEEHHHHHHHST-TS-HHHHHHHHHHHHHTTSEEEEEESSSSSEEEEEE-H
T ss_pred HhCCCcHHHHHHhcc-hhHHHHHHHHHHHHHHcchhhcccccCCCCCCccCCCc
Confidence 334455678988885 89999999999999999999887765667777787744
No 51
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=94.10 E-value=0.55 Score=35.35 Aligned_cols=33 Identities=24% Similarity=0.362 Sum_probs=29.6
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
.++|...+ +++++.++++|+.||++|||...++
T Consensus 2 ~~ela~~l--~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 2 TSEIAERL--NVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHHh--CCChHHHHHHHHHHHHCCCEEEcCC
Confidence 46788999 9999999999999999999999653
No 52
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=94.04 E-value=0.2 Score=44.85 Aligned_cols=130 Identities=11% Similarity=0.163 Sum_probs=76.5
Q ss_pred cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHH
Q 025493 49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKV 128 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~ 128 (252)
.++.+|.+++|.+.+ ++.+..++|.|+.||++|||....+= .++.++ |++. . .++.+.
T Consensus 17 ~~~~~IS~~eLA~~L--~iS~~Tvsr~Lk~LEe~GlI~R~~~~--r~~~v~----LTek------------G--~~ll~~ 74 (217)
T PRK14165 17 NNTVKISSSEFANHT--GTSSKTAARILKQLEDEGYITRTIVP--RGQLIT----ITEK------------G--LDVLYN 74 (217)
T ss_pred CCCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEEcC--CceEEE----ECHH------------H--HHHHHH
Confidence 445579999999999 99999999999999999999886541 222222 2222 0 111122
Q ss_pred HHHHHHHHhh-----------------hCCCCCHHHHH-HHHHHcCCc------ceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 129 VKSQCLKQII-----------------KLKVATLEGIS-DSIKRSGAF------KVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 129 l~~~~~~~i~-----------------~~~~~T~~~I~-~~i~~~~i~------~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+-....+.+. -+-|.+.+--. +|-+..|+. ++.|..+.++...+..-+++....=-
T Consensus 75 ~~~d~~~if~~~~ei~l~G~v~sGlGeG~~y~~~~~Y~~~f~~~lGf~PypGTLNv~l~~~~~~~~~~~~~~~~i~i~g~ 154 (217)
T PRK14165 75 EYADYSRIFSIKDNLELEGNVVKGLGEGKYYINIKGYKIQFEEKLGFIPYPGTLNVKLDNSSSPLLRKLRESPGIRIEGF 154 (217)
T ss_pred HHHHHHHHhcccccceehhhhhhccCCccEEEeCHHHHHHHHHHhCCcCCCCcEEEEecchhHHHHHHHhcCCCEecCCC
Confidence 2211122111 12366765544 455566765 47787776666666666676443211
Q ss_pred eCCCCCcccccCCcceeecc
Q 025493 185 SNGSGEFTNIPVGKVCYKNV 204 (252)
Q Consensus 185 ~~g~~~f~~~~~g~~~YR~~ 204 (252)
.++...|..+ .||++.
T Consensus 155 ~~~~r~~g~~----~~~~~~ 170 (217)
T PRK14165 155 TDGERTFGGV----KCYPVK 170 (217)
T ss_pred cCCCceeEEE----EEEEEE
Confidence 2334455555 677654
No 53
>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=93.99 E-value=0.27 Score=35.19 Aligned_cols=45 Identities=24% Similarity=0.411 Sum_probs=37.9
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
+.||.+-+ ++..+-.++|..++ |+.+..++..||.|+.+|||.-.
T Consensus 11 ~~Iy~l~~---~~~~v~~~~iA~~L--~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 11 KAIYELSE---EGGPVRTKDIAERL--GVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp HHHHHHHH---CTSSBBHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHc---CCCCccHHHHHHHH--CCChHHHHHHHHHHHHCCCEEec
Confidence 34565554 57889999999999 99999999999999999999864
No 54
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=93.95 E-value=0.19 Score=39.14 Aligned_cols=63 Identities=11% Similarity=0.109 Sum_probs=43.3
Q ss_pred HHHHHHHHHhhcCCCcccHHHHH-HHhh--cCCChHHHHHHHHHHHhcCCeeee--eccccCCeeeEEe
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMK-RELK--VNLPDNIVTKSIKSLQNKSLIKEV--VNIHNKGKKHLMA 101 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik-~~~~--~~l~~~~l~k~lK~Le~k~lIK~v--ksv~~~~rK~YmL 101 (252)
+.+|+.++.+ ....|-+..+.= ..++ ..+.+.+|..+|+.||++|+|.+. .+-..+.||+|-+
T Consensus 6 ~~~iL~~L~~-~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~i 73 (100)
T TIGR03433 6 DLLILKTLSL-GPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRL 73 (100)
T ss_pred HHHHHHHHhc-CCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEE
Confidence 4566666665 555555544332 2221 168899999999999999999994 5556667888876
No 55
>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=93.82 E-value=0.19 Score=40.44 Aligned_cols=52 Identities=15% Similarity=0.216 Sum_probs=43.9
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
++.--.+..++.. +++..+..++|..++ +++.+.+.|+|+.|++.|+|.+.+
T Consensus 8 ~~yal~~l~~la~-~~~~~~s~~eia~~l--~is~~~v~~~l~~L~~~Gli~~~~ 59 (130)
T TIGR02944 8 TDYATLVLTTLAQ-NDSQPYSAAEIAEQT--GLNAPTVSKILKQLSLAGIVTSKR 59 (130)
T ss_pred HhHHHHHHHHHHh-CCCCCccHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEecC
Confidence 3344456667777 777889999999999 999999999999999999998754
No 56
>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=93.70 E-value=0.38 Score=38.12 Aligned_cols=57 Identities=12% Similarity=0.147 Sum_probs=47.4
Q ss_pred HHHHHHHHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 127 KVVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 127 ~~l~~~~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
..-|.+++++|... ..+|++||.+.+++.+ ..++..-|-+.|+.|+-.|.|.++...
T Consensus 7 T~~R~~Il~~l~~~~~~~ta~ei~~~l~~~~---~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 7 TPQRLAILELLKESPEHLTAEEIYDKLRKKG---PRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHHHHHHSSSEEHHHHHHHHHHTT---TT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred CHHHHHHHHHHHcCCCCCCHHHHHHHhhhcc---CCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 34678899999864 5999999999999876 467889999999999999999998765
No 57
>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=93.68 E-value=0.2 Score=35.05 Aligned_cols=36 Identities=19% Similarity=0.399 Sum_probs=33.1
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 51 DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 51 ~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
+..+..++|...+ +++...++|+|+.|+++|+|...
T Consensus 23 ~~~~s~~ela~~~--g~s~~tv~r~l~~L~~~g~i~~~ 58 (67)
T cd00092 23 QLPLTRQEIADYL--GLTRETVSRTLKELEEEGLISRR 58 (67)
T ss_pred cCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEec
Confidence 4568899999999 99999999999999999999875
No 58
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.67 E-value=0.94 Score=41.09 Aligned_cols=124 Identities=15% Similarity=0.206 Sum_probs=93.7
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCC
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGG 113 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG 113 (252)
+++--..||+.|.. |-|....++++.. +++-.+++=.|+.||+.++|++. ...++-.|.-+++.
T Consensus 99 ~ns~R~~Iy~~i~~---nPG~~lsEl~~nl--~i~R~TlRyhlriLe~~~li~a~---~~~g~~~yfpa~~t-------- 162 (240)
T COG3398 99 LNSKRDGIYNYIKP---NPGFSLSELRANL--YINRSTLRYHLRILESNPLIEAG---RVGGALRYFPADMT-------- 162 (240)
T ss_pred hhhhHHHHHHHhcc---CCCccHHHHHHhc--CCChHHHHHHHHHHHhCcchhhh---ccCCceEEccCCCC--------
Confidence 34445679999988 6789999999999 99999999999999999999985 33456667655542
Q ss_pred ccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 114 AWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 114 ~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
|.+.| =.++-+..++.+..+|+..+..|.-+|+.-+ .+|.+-|.==+..|.-=|.|.+-+
T Consensus 163 --~~~~e-~~~Lkn~~~k~I~~eiq~~~~~t~~~ia~~l--------~ls~aTV~~~lk~l~~~Gii~~~~ 222 (240)
T COG3398 163 --YGEAE-VLSLKNETSKAIIYEIQENKCNTNLLIAYEL--------NLSVATVAYHLKKLEELGIIPEDR 222 (240)
T ss_pred --cccch-HHHhhchhHHHHHHHHhcCCcchHHHHHHHc--------CccHHHHHHHHHHHHHcCCCcccc
Confidence 22222 1456667778888888888888888887654 366777777788888888887654
No 59
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=93.60 E-value=0.23 Score=38.95 Aligned_cols=72 Identities=19% Similarity=0.363 Sum_probs=55.7
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec--cccCCeeeEEecccccCCCcc
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN--IHNKGKKHLMAVEFEPSKDIS 111 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks--v~~~~rK~YmL~~lePs~eiT 111 (252)
+++.+..|+..+.. +|.+=.|. |.+.+ +++...+..+|+.||+.|||..+.+ ++...+ .+.|+.|+-
T Consensus 5 ~~~l~~~IL~hl~~-~~~Dy~k~--ia~~l--~~~~~~v~~~l~~Le~~GLler~~g~~iK~~~~------k~K~~~e~~ 73 (92)
T PF10007_consen 5 LDPLDLKILQHLKK-AGPDYAKS--IARRL--KIPLEEVREALEKLEEMGLLERVEGKTIKRSEA------KFKPKKEVH 73 (92)
T ss_pred cChhHHHHHHHHHH-HCCCcHHH--HHHHH--CCCHHHHHHHHHHHHHCCCeEEecCcccchhhh------hcccchhhh
Confidence 57788999999999 99987664 66788 9999999999999999999999985 444322 346666643
Q ss_pred C-Cccc
Q 025493 112 G-GAWY 116 (252)
Q Consensus 112 G-G~wy 116 (252)
. ++.|
T Consensus 74 ~hHtYY 79 (92)
T PF10007_consen 74 KHHTYY 79 (92)
T ss_pred cCCcee
Confidence 3 3444
No 60
>PF08672 APC2: Anaphase promoting complex (APC) subunit 2; InterPro: IPR014786 The anaphase-promoting complex (APC) or cyclosome is a multi-subunit E3 protein ubiquitin ligase that regulates important events in mitosis such as the initiation of anaphase and exit from telophase. The APC, in conjunction with other enzymes, assembles multi-ubiquitin chains on a variety of regulatory proteins, thereby targeting them for proteolysis by the 26S proteasome. Anaphase is initiated when the APC triggers the destruction of securin, thereby allowing the protease, separase, to disrupt sister-chromatid cohesion. Securin ubiquitination by the APC is inhibited by cyclin-dependent kinase 1 (Cdk1)-dependent phosphorylation []. Forkhead Box M1 (FoxM1), which is a transcription factor that is over-expressed in many cancers, is degraded in late mitosis and early G1 phase by the APC/cyclosome (APC/C) E3 ubiquitin ligase []. The APC/C targets mitotic cyclins for destruction in mitosis and G1 phase and is then inactivated at S phase. It thereby generates alternating states of high and low cyclin-Cdk activity, which is required for the alternation of mitosis and DNA replication []. The APC/C is composed of at least 13 subunits that stay tightly associated throughout the cell cycle: APC1, APC2, APC4, APC5, APC9, APC11, CDC16, CDC23, CDC26, CDC27, DOC1, MND2 and SWM1[], []. In fission yeast the 13 subunits are known as: Apc1, Apc2, Nuc2, Apc4, Apc5, Cut9, Apc8, Apc10, Apc11, Hcn1, Apc13, Apc14 and Apc15 []. This entry represents a C-terminal domain found in APC subunit 2. ; PDB: 1LDD_A.
Probab=93.59 E-value=0.13 Score=37.13 Aligned_cols=51 Identities=14% Similarity=0.195 Sum_probs=38.1
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHc--CCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 133 CLKQIIKLKVATLEGISDSIKRS--GAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 133 ~~~~i~~~~~~T~~~I~~~i~~~--~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
|.-.|.+.+..+++.||..++-- +-...+.|.+++++.|+.||-||+++..
T Consensus 2 I~gMLtN~gsl~l~RIh~mLkmf~~~~~~~~~s~~eL~~fL~~lv~e~~L~~~ 54 (60)
T PF08672_consen 2 IVGMLTNLGSLPLDRIHSMLKMFPKDPGGYDISLEELQEFLDRLVEEGKLECS 54 (60)
T ss_dssp HHHHHHHH-SEEHHHHHHHHHHH-GGG--TT--HHHHHHHHHHHHHTTSEE--
T ss_pred HhHHhhcCCCCCHHHHHHHHHhccCCCCCCCCCHHHHHHHHHHHHHCCcEEec
Confidence 44566788889999999999977 3344689999999999999999999975
No 61
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=93.47 E-value=0.33 Score=32.67 Aligned_cols=37 Identities=16% Similarity=0.300 Sum_probs=33.1
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 51 DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 51 ~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
+..+-..+|...+ +++.+.++++|+.|+++|+|....
T Consensus 8 ~~~~~~~~i~~~l--~is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 8 EGELCVCELAEIL--GLSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred cCCccHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeeee
Confidence 4567889999999 999999999999999999998653
No 62
>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=93.26 E-value=1.1 Score=35.89 Aligned_cols=39 Identities=10% Similarity=0.290 Sum_probs=35.2
Q ss_pred cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
.|...+..++|...+ ++|.+.+.++|..|+..|+|.+..
T Consensus 21 ~~~~~~s~~eia~~~--~i~~~~v~~il~~L~~~gli~~~~ 59 (132)
T TIGR00738 21 PDEGPVSVKEIAERQ--GISRSYLEKILRTLRRAGLVESVR 59 (132)
T ss_pred CCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEecc
Confidence 455689999999999 999999999999999999998754
No 63
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=93.22 E-value=0.19 Score=42.45 Aligned_cols=58 Identities=14% Similarity=0.285 Sum_probs=49.3
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
...|++-++.|+.++.+ -| -+..++|.+++ |+..+.+.+-++.||+.|.|+....+-+
T Consensus 9 ~~~lD~~D~~IL~~Lq~-d~--R~s~~eiA~~l--glS~~tv~~Ri~rL~~~GvI~~~~~~v~ 66 (164)
T PRK11169 9 GKDLDRIDRNILNELQK-DG--RISNVELSKRV--GLSPTPCLERVRRLERQGFIQGYTALLN 66 (164)
T ss_pred hhhHHHHHHHHHHHhcc-CC--CCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEEEEEEEC
Confidence 45689999999999888 44 45569999999 9999999999999999999998665443
No 64
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=92.91 E-value=0.2 Score=36.47 Aligned_cols=49 Identities=14% Similarity=0.144 Sum_probs=38.8
Q ss_pred HHHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 129 VKSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 129 l~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
+++.|+.||.. ++.+|..||++-+ .+|.-.++.+|+.|+-+|+|++++.
T Consensus 1 ~ke~Il~~i~~~~~p~~T~eiA~~~--------gls~~~aR~yL~~Le~eG~V~~~~~ 50 (62)
T PF04703_consen 1 MKEKILEYIKEQNGPLKTREIADAL--------GLSIYQARYYLEKLEKEGKVERSPV 50 (62)
T ss_dssp -HHCHHHHHHHHTS-EEHHHHHHHH--------TS-HHHHHHHHHHHHHCTSEEEES-
T ss_pred CcHHHHHHHHHcCCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEecC
Confidence 35678888887 7888888988764 4788999999999999999998764
No 65
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=92.84 E-value=0.28 Score=38.06 Aligned_cols=57 Identities=7% Similarity=0.145 Sum_probs=46.0
Q ss_pred HHHHHHH-hhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493 40 LIYDVIR-SNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM 100 (252)
Q Consensus 40 ~vy~~I~-~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym 100 (252)
..|+-|. +...-+=|....|..+. ++.-+.-.++|+.||++|+||.| +++....+|.
T Consensus 27 ~t~dkl~kEV~~~K~ITps~lserl--kI~~SlAr~~Lr~L~~kG~Ik~V--~~~~~q~IYt 84 (86)
T PRK09334 27 ELLKRVAKEVKKEKIVTPYTLASKY--GIKISVAKKVLRELEKRGVLVLY--SKNRRTPIYV 84 (86)
T ss_pred HHHHHHHHHhccCcEEcHHHHHHHh--cchHHHHHHHHHHHHHCCCEEEE--ecCCCeEEec
Confidence 4455443 53556778888999999 99999999999999999999999 5666778884
No 66
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.73 E-value=0.42 Score=35.53 Aligned_cols=46 Identities=11% Similarity=0.244 Sum_probs=39.0
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
..|+.+|.+ .+ .++-..+|-..+ +++.+.+.+.|+.|++.|+|...
T Consensus 8 ~~Il~~l~~-~~-~~~t~~~ia~~l--~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 8 LAVLRALAE-EP-GGLTLAELAERL--GLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHHh-CC-CCcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCeeec
Confidence 346666766 42 379999999999 99999999999999999999873
No 67
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=92.38 E-value=0.58 Score=31.57 Aligned_cols=34 Identities=15% Similarity=0.370 Sum_probs=31.3
Q ss_pred cc-cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 53 GI-WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 53 GI-w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
-+ ..++|.... +++...+.++|+.|++.|+|..+
T Consensus 19 ~l~s~~~la~~~--~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 19 KLPSERELAAQL--GVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred cCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe
Confidence 46 699999999 99999999999999999999875
No 68
>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=92.31 E-value=0.5 Score=31.73 Aligned_cols=34 Identities=21% Similarity=0.397 Sum_probs=30.2
Q ss_pred CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 52 MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 52 ~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
.-.-..+|...+ ++++..+++.|+.|++.|+|++
T Consensus 14 ~~~~~~el~~~l--~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 14 GPLTVSELAEEL--GLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp SSEEHHHHHHHH--TS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCCchhhHHHhc--cccchHHHHHHHHHHHCcCeeC
Confidence 457788999999 9999999999999999999974
No 69
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=92.27 E-value=0.49 Score=43.05 Aligned_cols=62 Identities=21% Similarity=0.298 Sum_probs=52.5
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV 102 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~ 102 (252)
-+||+.|..||-.+-. -|. .-.++|...+ |+|++.|-.+|++||.||+|... ....+.|-..
T Consensus 12 lGlt~yEa~vY~aLl~-~g~--~tA~eis~~s--gvP~~kvY~vl~sLe~kG~v~~~----~g~P~~y~av 73 (247)
T COG1378 12 LGLTEYEAKVYLALLC-LGE--ATAKEISEAS--GVPRPKVYDVLRSLEKKGLVEVI----EGRPKKYRAV 73 (247)
T ss_pred cCCCHHHHHHHHHHHH-hCC--ccHHHHHHHc--CCCchhHHHHHHHHHHCCCEEee----CCCCceEEeC
Confidence 3799999999999988 665 4678999999 99999999999999999999986 3355667663
No 70
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=92.21 E-value=1.7 Score=45.13 Aligned_cols=142 Identities=16% Similarity=0.227 Sum_probs=95.3
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc-------
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF------- 104 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l------- 104 (252)
...++++..|..+-.+ -.. -...++...+ |+|...++|.|+-..++|+|-+...+..++ +|-+-+=
T Consensus 598 ~tVsp~qA~iI~~Fqe-k~t--wt~eelse~l--~ip~~~lrrrL~fWi~~GvL~e~~~~s~tg--t~T~iEse~d~~q~ 670 (765)
T KOG2165|consen 598 LTVSPEQAAIINLFQE-KNT--WTLEELSESL--GIPVPALRRRLSFWIQKGVLREEPIISDTG--TLTVIESEMDFDQA 670 (765)
T ss_pred EeeCHHHHHHHHHhcC-ccc--ccHHHHHHHh--CCCHHHHHHHHHHHHHcCeeecCCCCCCCc--eeeecccccccccc
Confidence 3567788777777666 332 4457899999 999999999999999999999987553322 3333221
Q ss_pred ------ccCCC--ccCCccccCC-cCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcc--eecCHHHHHHHHHH
Q 025493 105 ------EPSKD--ISGGAWYSEG-SLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFK--VDLTKQQIEEIVRA 173 (252)
Q Consensus 105 ------ePs~e--iTGG~wy~d~-e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~--~~Ls~~di~~IL~t 173 (252)
|-.+| =++.+|+.|+ +. |+. .-+..|...+.+.+...++-||++++=-.... ...+.++++.-|+.
T Consensus 671 ~~~~~~e~eee~~e~~~as~vdqle~--el~-~~~~fI~gMLTNlgsm~leRIHnmLkmF~~~~~~~~~TlqeL~~fLq~ 747 (765)
T KOG2165|consen 671 EGTVLLEAEEENYESHNASEVDQLEE--ELT-LFRSFIVGMLTNLGSMKLERIHNMLKMFVPPDGSAEITLQELQGFLQR 747 (765)
T ss_pred CCCcccccccccchhhhhhHHHHHHH--HHH-HHHHHHHHHhcCcccchHHHHHHHHeeeecCCCCCcccHHHHHHHHHH
Confidence 11111 2344444333 11 110 11123334444679999999999998655443 68999999999999
Q ss_pred HhhcCeeEEE
Q 025493 174 VVLDNQIMEV 183 (252)
Q Consensus 174 LVyDgkIE~v 183 (252)
+|-+|+++-+
T Consensus 748 kV~e~kL~f~ 757 (765)
T KOG2165|consen 748 KVREGKLEFI 757 (765)
T ss_pred HhhccceEEe
Confidence 9999999865
No 71
>PRK12423 LexA repressor; Provisional
Probab=92.14 E-value=0.4 Score=41.86 Aligned_cols=56 Identities=21% Similarity=0.345 Sum_probs=47.3
Q ss_pred CCChHHHHHHHHHHhhcCCCcc--cHHHHHHHhhcCC-ChHHHHHHHHHHHhcCCeeeeec
Q 025493 33 SLTDHERLIYDVIRSNKQDMGI--WTRDMKRELKVNL-PDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GI--w~~dik~~~~~~l-~~~~l~k~lK~Le~k~lIK~vks 90 (252)
.||+-++.||+.|.+.-...|+ ..++|.... ++ ..+.+.+.|+.|+++|+|..-+.
T Consensus 3 ~lt~~q~~il~~l~~~i~~~g~~Ps~~eia~~~--g~~s~~~v~~~l~~L~~~G~l~~~~~ 61 (202)
T PRK12423 3 TLTPKRAAILAFIRERIAQAGQPPSLAEIAQAF--GFASRSVARKHVQALAEAGLIEVVPN 61 (202)
T ss_pred cCCHHHHHHHHHHHHHHHHcCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHCCCEEecCC
Confidence 4899999999999983344455 899999999 96 78899999999999999987544
No 72
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=92.14 E-value=0.36 Score=39.28 Aligned_cols=48 Identities=15% Similarity=0.335 Sum_probs=41.0
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc
Q 025493 56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF 104 (252)
Q Consensus 56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l 104 (252)
-.+|++.++ ++++++|++.||.||+.|+|....-=..|-|--|=|.++
T Consensus 39 F~eL~r~i~-~Is~k~Ls~~Lk~Le~~Glv~R~~~~~~PprveY~LT~~ 86 (120)
T COG1733 39 FNELRRSIG-GISPKMLSRRLKELEEDGLVERVVYPEEPPRVEYRLTEK 86 (120)
T ss_pred HHHHHHHcc-ccCHHHHHHHHHHHHHCCCEEeeecCCCCceeEEEEhhh
Confidence 478899983 599999999999999999999987666688888888665
No 73
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=92.10 E-value=0.48 Score=38.89 Aligned_cols=52 Identities=12% Similarity=0.077 Sum_probs=41.4
Q ss_pred HHHHHHHHHHhhcC---CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493 37 HERLIYDVIRSNKQ---DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI 91 (252)
Q Consensus 37 ~e~~vy~~I~~~ag---~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv 91 (252)
.+..|..+|.. |- +.=+..++|..+. |++.+.|.|+|+.|++.|||++.+..
T Consensus 7 ~~YAl~~~i~l-a~~~~g~~~s~~~ia~~~--~is~~~vrk~l~~L~~~Glv~s~~G~ 61 (141)
T PRK11014 7 TDYGLRALIYM-ASLPEGRMTSISEVTEVY--GVSRNHMVKIINQLSRAGYVTAVRGK 61 (141)
T ss_pred HhHHHHHHHHH-hcCCCCCccCHHHHHHHH--CcCHHHHHHHHHHHHhCCEEEEecCC
Confidence 35556666655 42 2236779999999 99999999999999999999998654
No 74
>PF03297 Ribosomal_S25: S25 ribosomal protein; InterPro: IPR004977 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The S25 ribosomal protein is a component of the 40S ribosomal subunit.; PDB: 2XZM_8 2XZN_8 3O30_Q 3U5G_Z 3IZB_V 3U5C_Z 3O2Z_Q 3IZ6_V.
Probab=92.09 E-value=0.39 Score=38.56 Aligned_cols=57 Identities=19% Similarity=0.293 Sum_probs=46.6
Q ss_pred HHHHHH-HhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493 40 LIYDVI-RSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM 100 (252)
Q Consensus 40 ~vy~~I-~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym 100 (252)
-.|+-| .+.-+-+=|....|..+. ++.-+.-.++|+.|+++|+|+.| +++....+|-
T Consensus 45 ~~~~kl~kEV~~~K~ITp~~lserl--kI~~SlAr~~Lr~L~~kG~Ik~V--~k~~~~~IYt 102 (105)
T PF03297_consen 45 ETYDKLLKEVPKMKLITPSVLSERL--KINGSLARKALRELESKGLIKPV--SKHHRQRIYT 102 (105)
T ss_dssp HHHHHHHHHCTTSSCECHHHHHHHH--CCSCHHHHHHHHHHHHCCSSEEE--ECCTTCEEEE
T ss_pred HHHHHHHHHhccCcEeeHHHHHHhH--hhHHHHHHHHHHHHHHCCCEEEE--eccCCeEEEe
Confidence 445544 453566778999999999 99999999999999999999999 5666777884
No 75
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=91.88 E-value=0.39 Score=31.31 Aligned_cols=32 Identities=22% Similarity=0.449 Sum_probs=29.7
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
+..++|...+ +++...+++.|+.|+++|+|..
T Consensus 9 ~s~~~la~~l--~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 9 LTRQEIAELL--GLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred cCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence 5678999999 9999999999999999999975
No 76
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=91.62 E-value=6.1 Score=36.29 Aligned_cols=124 Identities=16% Similarity=0.124 Sum_probs=93.1
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcC------CChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccc-cCCCc
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVN------LPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFE-PSKDI 110 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~------l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~le-Ps~ei 110 (252)
...|...|+. ...+..++|....... .+.+....+|..|...|.|-...... ...+.|-+.+-- |...
T Consensus 87 ~~~v~~~L~~---~gplt~~eL~~~l~~~~~~~~~~~~~~~~~~l~~l~~~G~l~~~~~~~-g~~~~y~l~~~~lP~~~- 161 (327)
T PF06224_consen 87 AEAVLDALRA---DGPLTRAELREALAEAGWWGWGGPSSPWKHLLEYLWYRGLLCVGPRPR-GRWRTYDLTERWLPAPD- 161 (327)
T ss_pred HHHHHHHHHh---cCCCCHHHHHHHhhhccccCCCCCCchHHHHHHHHHhCCeEEEeccCC-CceEEEechHHhCCCCc-
Confidence 3445555544 5578899999876322 45568999999999999998876442 245888876632 3311
Q ss_pred cCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 111 SGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 111 TGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
.| --+.+.+.+.+|++.++.+|++++..|.. |+..+++..++.|+-.|.++++...
T Consensus 162 ----------~~--~~ea~~~Lv~Ryl~~~GPat~~d~a~w~g--------l~~~~~r~~l~~l~~~~~L~~v~~~ 217 (327)
T PF06224_consen 162 ----------DD--REEALAELVRRYLRAYGPATLADFAWWSG--------LPKTQARRALAQLVEEGELVEVEVE 217 (327)
T ss_pred ----------CC--HHHHHHHHHHHHHHHcCCccHHHHHHHhc--------cCHHHHHHHHHhhccCCcEEEEEEc
Confidence 11 44568888999999999999999999954 7788999999999999999988765
No 77
>cd00131 PAX Paired Box domain
Probab=91.61 E-value=5.2 Score=32.68 Aligned_cols=109 Identities=18% Similarity=0.167 Sum_probs=74.3
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS 111 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT 111 (252)
+.||.+++. .+|.. + ..|...++|.+++ ++..+.|.|.++...+.|-++..+.= ++ .|+
T Consensus 16 ~~lS~d~R~--rIv~~-~-~~G~s~~~iA~~~--~Vs~~tV~r~i~r~~e~G~v~pk~~g---g~--------rpr---- 74 (128)
T cd00131 16 RPLPDSIRQ--RIVEL-A-QSGIRPCDISRQL--RVSHGCVSKILNRYYETGSIRPGAIG---GS--------KPR---- 74 (128)
T ss_pred CcCCHHHHH--HHHHH-H-HcCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcCCCCCC---CC--------CCC----
Confidence 456766543 23333 3 3699999999999 99999999999999998865542211 11 011
Q ss_pred CCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc--ceecCHHHHHHHHHH
Q 025493 112 GGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRA 173 (252)
Q Consensus 112 GG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~--~~~Ls~~di~~IL~t 173 (252)
.. .+.....+..++..++..|+.|+.+.+...|+. .+.+|..-|-.+|+.
T Consensus 75 --------~~----~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 75 --------VA----TPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred --------cC----CHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 00 012233445578889999999999998777764 367788888887764
No 78
>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=91.57 E-value=0.3 Score=35.74 Aligned_cols=38 Identities=16% Similarity=0.237 Sum_probs=33.2
Q ss_pred CCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEecc
Q 025493 66 NLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAVE 103 (252)
Q Consensus 66 ~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~~ 103 (252)
++....|-.+|+.||.+|+|.+.... +.+.||+|-+.+
T Consensus 28 ~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~iT~ 67 (75)
T PF03551_consen 28 KISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRITE 67 (75)
T ss_dssp ETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEESH
T ss_pred ccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEECH
Confidence 68899999999999999999998876 677899998743
No 79
>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=91.49 E-value=1 Score=35.11 Aligned_cols=55 Identities=11% Similarity=0.186 Sum_probs=46.8
Q ss_pred HHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCC
Q 025493 130 KSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNG 187 (252)
Q Consensus 130 ~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g 187 (252)
|..++++|.. ...+|++||++.+++.+ -.++..-|.+.|+.|+-.|.|.++...+
T Consensus 3 R~~Il~~l~~~~~~~sa~ei~~~l~~~~---~~i~~~TVYR~L~~L~~~Gli~~~~~~~ 58 (116)
T cd07153 3 RLAILEVLLESDGHLTAEEIYERLRKKG---PSISLATVYRTLELLEEAGLVREIELGD 58 (116)
T ss_pred HHHHHHHHHhCCCCCCHHHHHHHHHhcC---CCCCHHHHHHHHHHHHhCCCEEEEEeCC
Confidence 5678888876 46899999999999886 3578899999999999999999987543
No 80
>PRK09462 fur ferric uptake regulator; Provisional
Probab=91.09 E-value=1.7 Score=35.99 Aligned_cols=55 Identities=5% Similarity=0.059 Sum_probs=47.4
Q ss_pred HHHHHHHHhhhC--CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 129 VKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 129 l~~~~~~~i~~~--~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
-|..|+++|... ..+|++||++.+++.+ ..++..-|-+.|+.|+-.|.|.++...
T Consensus 18 qR~~Il~~l~~~~~~h~sa~eI~~~l~~~~---~~i~~aTVYR~L~~L~e~Gli~~~~~~ 74 (148)
T PRK09462 18 PRLKILEVLQEPDNHHVSAEDLYKRLIDMG---EEIGLATVYRVLNQFDDAGIVTRHNFE 74 (148)
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHhhC---CCCCHHHHHHHHHHHHHCCCEEEEEcC
Confidence 467889999863 5999999999999888 357889999999999999999998743
No 81
>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=91.02 E-value=0.75 Score=37.54 Aligned_cols=48 Identities=13% Similarity=0.105 Sum_probs=38.6
Q ss_pred HHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493 42 YDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI 91 (252)
Q Consensus 42 y~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv 91 (252)
.-.+..+.++.-+..++|..++ ++|.+.+.|+|..|.+.|||.+++..
T Consensus 14 l~~La~~~~~~~~s~~~ia~~~--~ip~~~l~kil~~L~~~glv~s~~G~ 61 (135)
T TIGR02010 14 MLDLALNAETGPVTLADISERQ--GISLSYLEQLFAKLRKAGLVKSVRGP 61 (135)
T ss_pred HHHHHhCCCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEeCC
Confidence 3344431455568889999999 99999999999999999999986554
No 82
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=90.94 E-value=0.66 Score=39.63 Aligned_cols=48 Identities=8% Similarity=0.078 Sum_probs=40.7
Q ss_pred cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493 49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV 102 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~ 102 (252)
.+...+..++|..+. ++|.+.+.|+|..|.+.|||.+.+..+- =|.|.
T Consensus 21 ~~~~~vs~~eIA~~~--~ip~~~l~kIl~~L~~aGLv~s~rG~~G----Gy~La 68 (164)
T PRK10857 21 SEAGPVPLADISERQ--GISLSYLEQLFSRLRKNGLVSSVRGPGG----GYLLG 68 (164)
T ss_pred CCCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeCCCCCC----Ceecc
Confidence 455678999999999 9999999999999999999998665543 37774
No 83
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=90.93 E-value=1 Score=39.21 Aligned_cols=60 Identities=10% Similarity=0.052 Sum_probs=47.5
Q ss_pred CCChHHHHHHHHHHhhcCCCc--ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 33 SLTDHERLIYDVIRSNKQDMG--IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~G--Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
.++.++|+..-+... ++... .-+.+|...+ |++...|+|+|++|+++|+|+.- ++++.++
T Consensus 148 ~~~~~~Rla~~L~~~-~~~~~~~~t~~~lA~~l--G~sretvsR~L~~L~~~G~I~~~------~~~i~I~ 209 (226)
T PRK10402 148 SFPLENRLAAFILLT-QEGDLYHEKHTQAAEYL--GVSYRHLLYVLAQFIQDGYLKKS------KRGYLIK 209 (226)
T ss_pred cChHHHHHHHHHHhc-ccCCcccchHHHHHHHH--CCcHHHHHHHHHHHHHCCCEEee------CCEEEEe
Confidence 457788888877765 54332 4679999999 99999999999999999999873 4667765
No 84
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=90.76 E-value=0.76 Score=38.24 Aligned_cols=54 Identities=6% Similarity=0.169 Sum_probs=47.9
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI 91 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv 91 (252)
.|++.++.|+.++.. - --+..++|.+++ |++...+.+-++.|+..|.|+....+
T Consensus 6 ~lD~~D~~Il~~Lq~-d--~R~s~~eiA~~l--glS~~tV~~Ri~rL~~~GvI~~~~~~ 59 (153)
T PRK11179 6 QIDNLDRGILEALME-N--ARTPYAELAKQF--GVSPGTIHVRVEKMKQAGIITGTRVD 59 (153)
T ss_pred ccCHHHHHHHHHHHH-c--CCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCeeeEEEE
Confidence 589999999999998 3 457899999999 99999999999999999999976543
No 85
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=90.65 E-value=2.6 Score=36.55 Aligned_cols=50 Identities=12% Similarity=0.131 Sum_probs=42.2
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
++....|..++.. .|. +...+|...+ +|+.+.|.|+|..|+..|||...+
T Consensus 21 ~~~~~~Vl~~L~~-~g~--~tdeeLA~~L--gi~~~~VRk~L~~L~e~gLv~~~r 70 (178)
T PRK06266 21 DEEGFEVLKALIK-KGE--VTDEEIAEQT--GIKLNTVRKILYKLYDARLADYKR 70 (178)
T ss_pred CccHhHHHHHHHH-cCC--cCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEee
Confidence 4445677787777 663 8899999999 999999999999999999999644
No 86
>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=90.50 E-value=1.7 Score=33.83 Aligned_cols=59 Identities=17% Similarity=0.251 Sum_probs=45.4
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
..|++++.+ + +.-+...+|-.+++ +++...+|-|+|+.|++.|+|+++..-. ++..|.+
T Consensus 4 ~~Il~~l~~-~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~--~~~~y~~ 65 (116)
T cd07153 4 LAILEVLLE-S-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGD--GKARYEL 65 (116)
T ss_pred HHHHHHHHh-C-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCC--CceEEEe
Confidence 468888888 6 56678888877663 2689999999999999999999986554 2455544
No 87
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=90.43 E-value=0.84 Score=37.39 Aligned_cols=47 Identities=21% Similarity=0.213 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.=..||.+++. .| .+-.++|...+ ++.+..+++.|+.|+.+|+|...
T Consensus 9 yL~~I~~l~~~-~~--~~~~~ela~~l--~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 9 YIEQIYLLIEE-KG--YARVSDIAEAL--SVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred HHHHHHHHHhc-CC--CcCHHHHHHHh--CCChhHHHHHHHHHHHCCCEEEe
Confidence 33467777766 43 55789999999 99999999999999999999854
No 88
>PHA00738 putative HTH transcription regulator
Probab=90.32 E-value=1.1 Score=36.31 Aligned_cols=50 Identities=18% Similarity=0.145 Sum_probs=40.3
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
++-=+.|+..+.+ .+ +.-..+|...+ +|.+..|++.||.|+.-|||.+-+
T Consensus 11 dptRr~IL~lL~~-~e--~~~V~eLae~l--~lSQptVS~HLKvLreAGLV~srK 60 (108)
T PHA00738 11 KILRRKILELIAE-NY--ILSASLISHTL--LLSYTTVLRHLKILNEQGYIELYK 60 (108)
T ss_pred CHHHHHHHHHHHH-cC--CccHHHHHHhh--CCCHHHHHHHHHHHHHCCceEEEE
Confidence 3344566666655 32 47888999999 999999999999999999999854
No 89
>smart00351 PAX Paired Box domain.
Probab=90.16 E-value=4.5 Score=32.75 Aligned_cols=93 Identities=19% Similarity=0.167 Sum_probs=64.2
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccC
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISG 112 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTG 112 (252)
.++.+++. .+|.. .. .|...++|.+++ ++....|.|.++...+.|.++..+. |
T Consensus 17 ~~s~~~R~--riv~~-~~-~G~s~~~iA~~~--gvs~~tV~kwi~r~~~~G~~~pk~~---------------------g 69 (125)
T smart00351 17 PLPDEERQ--RIVEL-AQ-NGVRPCDISRQL--CVSHGCVSKILGRYYETGSIRPGAI---------------------G 69 (125)
T ss_pred CCCHHHHH--HHHHH-HH-cCCCHHHHHHHH--CcCHHHHHHHHHHHHHcCCcCCcCC---------------------C
Confidence 36776654 23443 32 588999999999 9999999999999998887554221 1
Q ss_pred CccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc
Q 025493 113 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF 158 (252)
Q Consensus 113 G~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~ 158 (252)
|..- .. ..+.....+..++..+...|+.||.+.+.+.||.
T Consensus 70 g~rp--~~----~~~~~~~~I~~~~~~~p~~t~~el~~~L~~~gv~ 109 (125)
T smart00351 70 GSKP--KV----ATPKVVKKIADYKQENPGIFAWEIRDRLLSEGVC 109 (125)
T ss_pred CCCC--Cc----cCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCC
Confidence 1111 00 1123344566678889999999999999887753
No 90
>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=90.09 E-value=0.59 Score=40.06 Aligned_cols=60 Identities=20% Similarity=0.311 Sum_probs=45.2
Q ss_pred HHHHHHHHHhhcCCCcc---cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCC
Q 025493 38 ERLIYDVIRSNKQDMGI---WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSK 108 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GI---w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~ 108 (252)
...|+..|-++....+. .+++|..++ ++..+++.|++|.|+.+++|+.++ ..+||+ -|..
T Consensus 57 ~~~Vl~~il~~~d~~N~v~~t~~~ia~~l--~iS~~Tv~r~ik~L~e~~iI~k~~------~G~Y~i---NP~~ 119 (165)
T PF05732_consen 57 AFRVLMYILENMDKDNAVVATQKEIAEKL--GISKPTVSRAIKELEEKNIIKKIR------NGAYMI---NPNF 119 (165)
T ss_pred HHHHHHHHHHhcCCCCeEEeeHHHHHHHh--CCCHHHHHHHHHHHHhCCcEEEcc------CCeEEE---CcHH
Confidence 34444444443666653 578899999 999999999999999999999862 347887 6663
No 91
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=90.05 E-value=1.2 Score=32.37 Aligned_cols=50 Identities=8% Similarity=0.185 Sum_probs=41.8
Q ss_pred HHHHHHHHHHhhhCCC--CCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 127 KVVKSQCLKQIIKLKV--ATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 127 ~~l~~~~~~~i~~~~~--~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+...+.++.+|..++. .|+.||++-+ .++...|.++|.+|.-+|.|++..
T Consensus 5 ~~~~~~IL~~L~~~g~~~~ta~eLa~~l--------gl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 5 DSLEEKILEFLENSGDETSTALQLAKNL--------GLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred hHHHHHHHHHHHHCCCCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEecC
Confidence 3567889999998877 8999998755 467789999999999999998753
No 92
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=89.85 E-value=1.1 Score=37.61 Aligned_cols=64 Identities=11% Similarity=0.143 Sum_probs=40.6
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhc-CCChHHHHHHHHHHHhcCCeeeeecc--ccCCeeeEEec
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKV-NLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGKKHLMAV 102 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~-~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~rK~YmL~ 102 (252)
+..|+.++.+ .---|=.....-.+.+. .+.+.+|..+|+.||+.|+|.+.... ..|.||+|-|.
T Consensus 26 ~~~IL~~L~~-~p~hGYeI~q~l~~~g~~~v~~GtLYp~L~RLE~~GlI~~~~~~~~~gp~RK~Y~LT 92 (138)
T TIGR02719 26 VPFLLLCLKD-WNLHGYKLIQMLMDFGFSSVDQGNVYRTLRKLEKDNLISSQWDTSAEGPAKRIYSLT 92 (138)
T ss_pred HHHHHHHHcc-CCCCHHHHHHHHHHcCCCCCCcChHHHHHHHHHHCCCEEEEeeecCCCCCcEEEEEC
Confidence 4455555544 43344333222222211 68889999999999999999975433 34668999873
No 93
>PRK09954 putative kinase; Provisional
Probab=89.82 E-value=1.2 Score=41.62 Aligned_cols=50 Identities=22% Similarity=0.303 Sum_probs=44.4
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
|++-++.|+.++.+ .+ =|..++|.+++ ++..+.+.+.|++|+++|+|+.-
T Consensus 1 ~~~~~~~il~~l~~-~~--~~s~~~la~~l--~~s~~~v~~~i~~L~~~g~i~~~ 50 (362)
T PRK09954 1 MNNREKEILAILRR-NP--LIQQNEIADIL--QISRSRVAAHIMDLMRKGRIKGK 50 (362)
T ss_pred CChHHHHHHHHHHH-CC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCcCCc
Confidence 56778889999999 44 59999999999 99999999999999999999643
No 94
>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=89.72 E-value=1.7 Score=29.61 Aligned_cols=41 Identities=17% Similarity=0.374 Sum_probs=34.2
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcC
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKS 83 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~ 83 (252)
..|..++.+ +++. +...+|..++ ++..++|.+-|+.|+..+
T Consensus 3 ~~il~~L~~-~~~~-it~~eLa~~l--~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLE-SKEP-ITAKELAEEL--GVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHH-TTTS-BEHHHHHHHC--TS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHH-cCCC-cCHHHHHHHh--CCCHHHHHHHHHHHHHCC
Confidence 456667766 5555 9999999999 999999999999999988
No 95
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=89.45 E-value=2.2 Score=27.81 Aligned_cols=46 Identities=11% Similarity=0.203 Sum_probs=38.9
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
..+++++.+++.+|..+|++.+ .++..-+...|+.|+-+|.|++..
T Consensus 3 ~~il~~l~~~~~~s~~~l~~~l--------~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 3 QQILELLAQQGKVSVEELAELL--------GVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHHcCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEEee
Confidence 3466777777889999999987 578999999999999999998754
No 96
>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=89.39 E-value=1.2 Score=37.05 Aligned_cols=61 Identities=16% Similarity=0.153 Sum_probs=45.0
Q ss_pred CCCChHHHHHHHHHH---hhcC---CCc------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493 32 DSLTDHERLIYDVIR---SNKQ---DMG------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL 99 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~---~~ag---~~G------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y 99 (252)
...+.++|+..-++. . .| +.| +.+.+|..-+ |++...|+|+|+.|+++|+|+.- .+++.
T Consensus 111 ~~~~~~~Rla~~L~~l~~~-~~~~~~~~~~~~~~~t~~~iA~~l--G~tretvsR~l~~l~~~g~I~~~------~~~i~ 181 (193)
T TIGR03697 111 AHRDMGSRLVSFLLILCRD-FGVPGQRGVTIDLRLSHQAIAEAI--GSTRVTITRLLGDLRKKKLISIH------KKKIT 181 (193)
T ss_pred HhCCHHHHHHHHHHHHHHH-hCCCCCCeEEecCCCCHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEec------CCEEE
Confidence 345667776655443 3 33 233 5799999999 99999999999999999999862 45566
Q ss_pred Ee
Q 025493 100 MA 101 (252)
Q Consensus 100 mL 101 (252)
++
T Consensus 182 I~ 183 (193)
T TIGR03697 182 VH 183 (193)
T ss_pred Ee
Confidence 54
No 97
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=89.06 E-value=0.91 Score=39.80 Aligned_cols=55 Identities=24% Similarity=0.283 Sum_probs=42.1
Q ss_pred CCCCChHHHHHHHHHHh--hcCCCc-----ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 31 SDSLTDHERLIYDVIRS--NKQDMG-----IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~--~ag~~G-----Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
....+.++|++.-+++. ..|..+ +-+++|..-+ |++...|+|+||.|+++|+|+.
T Consensus 150 l~~~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~l--GisretlsR~L~~L~~~GlI~~ 211 (230)
T PRK09391 150 LGRKTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADYL--GLTIETVSRALSQLQDRGLIGL 211 (230)
T ss_pred HcCCCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHHH--CCCHHHHHHHHHHHHHCCcEEe
Confidence 34567788887666553 033322 4578999999 9999999999999999999974
No 98
>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=88.95 E-value=2.2 Score=32.61 Aligned_cols=59 Identities=15% Similarity=0.128 Sum_probs=43.4
Q ss_pred CCCChHHHHHHHHHHhhcCC-CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 32 DSLTDHERLIYDVIRSNKQD-MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~-~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
+.|+.+|..|+..||....| +=+-...|.+.+ +|....+.++|+.|-..+||.. +....
T Consensus 2 r~L~~~d~rvL~aiE~gmk~hE~VP~~~I~~~s--~l~~~~~~~~L~~L~~~kLv~~-~~~~Y 61 (82)
T PF09202_consen 2 RYLSKEDFRVLRAIEMGMKNHEWVPLELIEKIS--GLSEGEVEKRLKRLVKLKLVSR-RNKPY 61 (82)
T ss_dssp -T--HHHHHHHHHHHTTTTT-SSEEHHHHHHHH--T--HHHHHHHHHHHHHTTSEEE-E-SSS
T ss_pred CcCCHHHHHHHHHHHHcccCCccCCHHHHHHHh--CcCHHHHHHHHHHHHhcCCccc-cCCCc
Confidence 57899999999999983222 224567899999 9999999999999999999998 44443
No 99
>PRK11050 manganese transport regulator MntR; Provisional
Probab=88.94 E-value=1.2 Score=37.23 Aligned_cols=45 Identities=24% Similarity=0.293 Sum_probs=37.9
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
..|+.+|.+ - .++-.++|...+ ++.++.+++.|+.||.+|+|...
T Consensus 40 ~~I~~~l~~-~--~~~t~~eLA~~l--~is~stVsr~l~~Le~~GlI~r~ 84 (152)
T PRK11050 40 ELIADLIAE-V--GEARQVDIAARL--GVSQPTVAKMLKRLARDGLVEMR 84 (152)
T ss_pred HHHHHHHHh-c--CCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe
Confidence 355666655 3 478899999999 99999999999999999999763
No 100
>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=88.94 E-value=0.78 Score=31.52 Aligned_cols=32 Identities=19% Similarity=0.433 Sum_probs=29.6
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
-.++|.... +++...++++|+.|+.+|+|...
T Consensus 27 ~~~~la~~~--~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 27 SERELAEEL--GVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEec
Confidence 489999999 99999999999999999999764
No 101
>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=88.79 E-value=1.5 Score=31.75 Aligned_cols=47 Identities=21% Similarity=0.273 Sum_probs=37.9
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI 91 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv 91 (252)
.|.++|++ +.-+..++|..+. +++...|.-.|..|+.+|.|+++..-
T Consensus 4 ~i~~~l~~---~~~~S~~eLa~~~--~~s~~~ve~mL~~l~~kG~I~~~~~~ 50 (69)
T PF09012_consen 4 EIRDYLRE---RGRVSLAELAREF--GISPEAVEAMLEQLIRKGYIRKVDMS 50 (69)
T ss_dssp HHHHHHHH---S-SEEHHHHHHHT--T--HHHHHHHHHHHHCCTSCEEEEEE
T ss_pred HHHHHHHH---cCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCcEEEecCC
Confidence 35667777 4568899999999 99999999999999999999987643
No 102
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=88.66 E-value=1.5 Score=33.35 Aligned_cols=69 Identities=14% Similarity=0.211 Sum_probs=54.4
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCcc
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDIS 111 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiT 111 (252)
...++.+... +++.=+.-.+|..++ ++..+.|.|++++|+..|+ .|.++++++.++=++-++=|...+.
T Consensus 5 ~~~~~~ll~~-~~~~~~SGe~La~~L--giSRtaVwK~Iq~Lr~~G~--~I~s~~~kGY~L~~~~~ll~~~~i~ 73 (79)
T COG1654 5 SQMLLLLLLL-LTGNFVSGEKLAEEL--GISRTAVWKHIQQLREEGV--DIESVRGKGYLLPQLPDLLPQEIIQ 73 (79)
T ss_pred HHHHHHHHHH-cCCCcccHHHHHHHH--CccHHHHHHHHHHHHHhCC--ceEecCCCceeccCccccCcHHHHH
Confidence 3466777777 888889999999999 9999999999999999997 5677777777766665555544443
No 103
>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=88.61 E-value=2.2 Score=29.92 Aligned_cols=46 Identities=15% Similarity=0.411 Sum_probs=40.8
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
..|+++|.+ . .-+..++|.... +....++.|=|..|+++|+|+.+.
T Consensus 3 ~~Il~~l~~-~--~~~s~~ela~~~--~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKE-K--GKVSVKELAEEF--GVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHH-c--CCEEHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEEc
Confidence 467888888 4 468999999999 999999999999999999998864
No 104
>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=88.48 E-value=1.4 Score=31.44 Aligned_cols=50 Identities=10% Similarity=0.189 Sum_probs=42.2
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
.....++.+|-.++..|++||++.+ .++...|..+|+.|+-.|.|++...
T Consensus 8 ~~E~~vy~~Ll~~~~~t~~eIa~~l--------~i~~~~v~~~L~~L~~~GlV~~~~~ 57 (68)
T PF01978_consen 8 ENEAKVYLALLKNGPATAEEIAEEL--------GISRSTVYRALKSLEEKGLVEREEG 57 (68)
T ss_dssp HHHHHHHHHHHHHCHEEHHHHHHHH--------TSSHHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 3456678888888999999999865 4788999999999999999998863
No 105
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=88.36 E-value=2 Score=28.21 Aligned_cols=43 Identities=19% Similarity=0.430 Sum_probs=35.9
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
..|++.|+.++.++.+ |...++|-..+ +++...+.+.++.+..
T Consensus 2 ~~l~~~e~~i~~~~~~-----g~s~~eia~~l--~is~~tv~~~~~~~~~ 44 (58)
T smart00421 2 ASLTPREREVLRLLAE-----GLTNKEIAERL--GISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCCHHHHHHHHHHHc-----CCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence 4588999888877643 68999999999 9999999999988743
No 106
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=88.35 E-value=1.6 Score=36.81 Aligned_cols=60 Identities=15% Similarity=0.102 Sum_probs=44.7
Q ss_pred CCChHHHHHHHHHHhhc---C----CC-----cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493 33 SLTDHERLIYDVIRSNK---Q----DM-----GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM 100 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~a---g----~~-----GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym 100 (252)
..+.++|+..-+++- + | +. =+.+.+|..-+ |+....|+|+|+.|+++|+|+. .++++.+
T Consensus 118 ~~~~~~Rla~~Ll~l-~~~~~~~~~~~~~~~~~~t~~~iA~~l--G~tretvsR~l~~l~~~g~I~~------~~~~i~I 188 (202)
T PRK13918 118 GQRLKNRIAAALLEL-SDTPLATQEDSGETMIYATHDELAAAV--GSVRETVTKVIGELSREGYIRS------GYGKIQL 188 (202)
T ss_pred hCchHHHHHHHHHHH-HHHhCCCCCCCCeEEecCCHHHHHHHh--CccHHHHHHHHHHHHHCCCEEc------CCCEEEE
Confidence 456678887766543 3 2 11 25689999999 9999999999999999999974 2355665
Q ss_pred e
Q 025493 101 A 101 (252)
Q Consensus 101 L 101 (252)
+
T Consensus 189 ~ 189 (202)
T PRK13918 189 L 189 (202)
T ss_pred E
Confidence 4
No 107
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=88.34 E-value=1.2 Score=38.55 Aligned_cols=53 Identities=13% Similarity=0.133 Sum_probs=41.5
Q ss_pred CCCChHHHHHHHHHHhhc---C---CC------cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 32 DSLTDHERLIYDVIRSNK---Q---DM------GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~a---g---~~------GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
...+.++|+..-+.+- + | .. -+.+++|..-+ |++...|+|+|+.|+++|+|+-
T Consensus 152 ~~~~~~~Rla~~L~~l-~~~~~~~~~~~~~~~~~lt~~~iA~~l--G~sr~tvsR~l~~l~~~g~I~~ 216 (235)
T PRK11161 152 SKKNAEERLAAFIYNL-SRRFAQRGFSPREFRLTMTRGDIGNYL--GLTVETISRLLGRFQKSGMLAV 216 (235)
T ss_pred hCCCHHHHHHHHHHHH-HHHHhhcCCCCceeEccccHHHHHHHh--CCcHHHHHHHHHHHHHCCCEEe
Confidence 3456778776655543 3 2 12 26789999999 9999999999999999999996
No 108
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=87.31 E-value=8.8 Score=34.46 Aligned_cols=121 Identities=11% Similarity=0.132 Sum_probs=81.7
Q ss_pred hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCcc
Q 025493 36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAW 115 (252)
Q Consensus 36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~w 115 (252)
+-+..|++++.+ . ..+-.++|...+ ++...++.|-|+.|+.+++|+.+ .+.-+|.... .+..+ -+|
T Consensus 4 ~R~~~Il~~l~~-~--~~~~~~eLa~~l--~VS~~TiRRdL~~L~~~~~l~r~-----~Gga~~~~~~-~~~~~---~~~ 69 (240)
T PRK10411 4 ARQQAIVDLLLN-H--TSLTTEALAEQL--NVSKETIRRDLNELQTQGKILRN-----HGRAKYIHRQ-NQDSG---DPF 69 (240)
T ss_pred HHHHHHHHHHHH-c--CCCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe-----cCeEEEecCC-CcccC---CCH
Confidence 345678888887 4 479999999999 99999999999999999999873 2343443211 11101 122
Q ss_pred ccCCcCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHcCCcceecCHHHHHHH
Q 025493 116 YSEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQQIEEI 170 (252)
Q Consensus 116 y~d~e~D~efV~~l~~~~~~~i~~~------~~~T~~~I~~~i~~~~i~~~~Ls~~di~~I 170 (252)
..-...+.+.=..|-+.+..+|+.. +..|+.++.++|...+++=+.=+..-.+.+
T Consensus 70 ~~r~~~~~~~K~~IA~~Aa~lI~~gd~Ifld~GtT~~~l~~~L~~~~ltVvTNs~~ia~~l 130 (240)
T PRK10411 70 HIRLKSHYAHKADIAREALAWIEEGMVIALDASSTCWYLARQLPDINIQVFTNSHPICQEL 130 (240)
T ss_pred HHHHHhHHHHHHHHHHHHHHhCCCCCEEEEcCcHHHHHHHHhhCCCCeEEEeCCHHHHHHH
Confidence 2223345566677888888888854 578899999999866655555455444443
No 109
>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=87.23 E-value=2.1 Score=33.81 Aligned_cols=66 Identities=14% Similarity=0.259 Sum_probs=50.3
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE 103 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~ 103 (252)
+|..-..|+++|.+ ++. -+...+|..+.. +++..++|-|+|+.|++.|+|..+..- .+...|=+..
T Consensus 6 ~T~~R~~Il~~l~~-~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~--~~~~~Y~~~~ 74 (120)
T PF01475_consen 6 LTPQRLAILELLKE-SPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG--DGESRYELST 74 (120)
T ss_dssp HHHHHHHHHHHHHH-HSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET--TSEEEEEESS
T ss_pred CCHHHHHHHHHHHc-CCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC--CCcceEeecC
Confidence 46677899999999 777 788888887653 378889999999999999999998655 2455664443
No 110
>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=87.22 E-value=2.9 Score=27.77 Aligned_cols=47 Identities=6% Similarity=0.164 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeE
Q 025493 127 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIM 181 (252)
Q Consensus 127 ~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE 181 (252)
+..+..++.+|..++.+|..||++-+ .+|..-+.+.|+.|+-+|.|+
T Consensus 2 ~~~~~~Il~~l~~~~~~t~~ela~~~--------~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 2 DETQRKILNYLRENPRITQKELAEKL--------GISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp -HHHHHHHHHHHHCTTS-HHHHHHHH--------TS-HHHHHHHHHHHHHTTSEE
T ss_pred CHHHHHHHHHHHHcCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCcCcC
Confidence 45677899999999999999999865 478899999999999999885
No 111
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=87.15 E-value=0.87 Score=35.97 Aligned_cols=60 Identities=25% Similarity=0.277 Sum_probs=47.8
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF 104 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l 104 (252)
.+|+++++. .-+.|+-...|--.. ||+-....+.++.|+.+|+|+.- +++.|+.|++.+.
T Consensus 18 eIi~dIL~~-~~~~~~~~Tri~y~a--Nlny~~~~~yi~~L~~~Gli~~~---~~~~~~~y~lT~K 77 (95)
T COG3432 18 EIIFDILKA-ISEGGIGITRIIYGA--NLNYKRAQKYIEMLVEKGLIIKQ---DNGRRKVYELTEK 77 (95)
T ss_pred HHHHHHHHH-hcCCCCCceeeeeec--CcCHHHHHHHHHHHHhCCCEEec---cCCccceEEEChh
Confidence 388889886 556666666777778 99999999999999999977763 4556779999553
No 112
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=87.13 E-value=3.4 Score=35.91 Aligned_cols=58 Identities=17% Similarity=0.159 Sum_probs=49.6
Q ss_pred CCCChHHH-HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe-eeeeccc
Q 025493 32 DSLTDHER-LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI-KEVVNIH 92 (252)
Q Consensus 32 ~~l~~~e~-~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI-K~vksv~ 92 (252)
..|++.|. .+..+|.+ .-+.|...++|-.++ ++..++|.+.+..|-+.++. +++|..+
T Consensus 157 ~~Lt~re~~~l~~~i~~-~~~~g~s~~eIA~~l--~iS~~Tv~~~~~~~~~~~~~~~~~~~~~ 216 (239)
T PRK10430 157 KGLTPQTLRTLCQWIDA-HQDYEFSTDELANAV--NISRVSCRKYLIWLVNCHILFTSIHYGV 216 (239)
T ss_pred CCCCHHHHHHHHHHHHh-CCCCCcCHHHHHHHh--CchHHHHHHHHHHHHhCCEEEEEeeccC
Confidence 35888774 56678888 688999999999999 99999999999999999999 5666544
No 113
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=86.93 E-value=2.3 Score=35.75 Aligned_cols=42 Identities=12% Similarity=0.172 Sum_probs=36.9
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
.+.-+..++|..+. +++.+-|.|+|..|...|+|++++..+-
T Consensus 21 ~~~~~s~~eIA~~~--~is~~~L~kIl~~L~~aGlv~S~rG~~G 62 (153)
T PRK11920 21 DGKLSRIPEIARAY--GVSELFLFKILQPLVEAGLVETVRGRNG 62 (153)
T ss_pred CCCcCcHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEeecCCCC
Confidence 33457899999999 9999999999999999999999886543
No 114
>PRK09462 fur ferric uptake regulator; Provisional
Probab=86.75 E-value=5.3 Score=32.97 Aligned_cols=65 Identities=12% Similarity=0.162 Sum_probs=52.6
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM 100 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym 100 (252)
.+|..=..|++++.+ +.+.-+...+|-.++. +++...+|-|+|+.|++.|+|.++..-. ++..|-
T Consensus 14 r~T~qR~~Il~~l~~-~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~--~~~~y~ 81 (148)
T PRK09462 14 KVTLPRLKILEVLQE-PDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEG--GKSVFE 81 (148)
T ss_pred CCCHHHHHHHHHHHh-CCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCC--CcEEEE
Confidence 478899999999999 8778899988877652 3678899999999999999999986433 344553
No 115
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=86.73 E-value=4.5 Score=32.85 Aligned_cols=56 Identities=16% Similarity=0.221 Sum_probs=44.7
Q ss_pred CCCCCChHHH-HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 30 PSDSLTDHER-LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 30 ~~~~l~~~e~-~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
.++.|.+.-| .|+.++.+ .| +.-..+|-..+ +++++.+++.|+.|++-|||...+.
T Consensus 9 ~fkaLadptRl~IL~~L~~-~~--~~~v~ela~~l--~lsqstvS~HL~~L~~AGLV~~~r~ 65 (117)
T PRK10141 9 LFKILSDETRLGIVLLLRE-SG--ELCVCDLCTAL--DQSQPKISRHLALLRESGLLLDRKQ 65 (117)
T ss_pred HHHHhCCHHHHHHHHHHHH-cC--CcCHHHHHHHH--CcCHHHHHHHHHHHHHCCceEEEEE
Confidence 3445665544 67777776 54 47788999999 9999999999999999999988643
No 116
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=86.59 E-value=4.5 Score=30.89 Aligned_cols=45 Identities=9% Similarity=0.126 Sum_probs=34.4
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 132 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 132 ~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
++-+||..++-+++.++...+ ..+..=|+..|+.|+--|+||++.
T Consensus 6 qlRd~l~~~gr~s~~~Ls~~~--------~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 6 QVRDLLALRGRMEAAQISQTL--------NTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHHHcCcccHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEeec
Confidence 455666666666666666544 467888999999999999999986
No 117
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=86.42 E-value=2.9 Score=35.37 Aligned_cols=54 Identities=19% Similarity=0.307 Sum_probs=40.4
Q ss_pred CCCCChHHHHHHHHH---HhhcCC----Cc----ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 31 SDSLTDHERLIYDVI---RSNKQD----MG----IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I---~~~ag~----~G----Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
....+..+|+..-+. +. .|. .| +.+++|...+ |++...++|+|+.|++.|+|+.
T Consensus 136 ~~~~~~~~Rl~~~L~~l~~~-~~~~~~~~~~~~~~t~~~lA~~l--G~tr~tvsR~l~~l~~~gii~~ 200 (211)
T PRK11753 136 LAFLDVTGRIAQTLLDLAKQ-PDAMTHPDGMQIKITRQEIGRIV--GCSREMVGRVLKMLEDQGLISA 200 (211)
T ss_pred HHhcChhhHHHHHHHHHHHh-cCCcCCCCceecCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEe
Confidence 344566777765443 32 221 23 5579999999 9999999999999999999986
No 118
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=86.34 E-value=3.7 Score=31.35 Aligned_cols=61 Identities=8% Similarity=0.104 Sum_probs=50.0
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc-ceecCHH------HHHHHHHHHhhcCeeEEEeeCCC
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAF-KVDLTKQ------QIEEIVRAVVLDNQIMEVKSNGS 188 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~-~~~Ls~~------di~~IL~tLVyDgkIE~v~~~g~ 188 (252)
..++.+..||++..-.|+.|+++|+-+.+-+ +-..+.. +|-..|+-|+..|+|.=+.+.|.
T Consensus 4 ~e~~~i~~yi~n~~~Isa~elcE~LI~~~~~~~~rysTgKpkiY~~Vc~yLe~L~~eg~l~~i~~~~~ 71 (78)
T PF13034_consen 4 LEKEFINWYIQNEEEISARELCEYLIENGGSPNKRYSTGKPKIYPYVCNYLEYLVKEGKLSFIENDGT 71 (78)
T ss_pred HHHHHHHHHHhccccccHHHHHHHHHHcCCCccccccCCCceeHHHHHHHHHHHHHCCeEEEEecCcc
Confidence 3467788899999999999999999988754 4444443 99999999999999998876653
No 119
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=86.12 E-value=18 Score=30.55 Aligned_cols=109 Identities=21% Similarity=0.178 Sum_probs=74.3
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCcccc
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYS 117 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~ 117 (252)
|..|++++.+ .|.--...||-..++..++.+.+.|+|..|..+|.|.. |.. ...|||..-.-.. ...+.. .
T Consensus 3 e~~Il~y~~~--qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~-K~~--GKqkiY~~~Q~~~-~~~s~e---e 73 (169)
T PF07106_consen 3 EDAILEYMKE--QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVE-KEY--GKQKIYFANQDEL-EVPSPE---E 73 (169)
T ss_pred HHHHHHHHHH--cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeee-eee--cceEEEeeCcccc-CCCCch---h
Confidence 5678888876 78888999999977546888999999999999999987 433 4568887643221 112211 1
Q ss_pred CCcCCHHHHHHHHHHHHHHhh-----------hCCCCCHHHHHHHHHHcC
Q 025493 118 EGSLDTEFIKVVKSQCLKQII-----------KLKVATLEGISDSIKRSG 156 (252)
Q Consensus 118 d~e~D~efV~~l~~~~~~~i~-----------~~~~~T~~~I~~~i~~~~ 156 (252)
..++|.+ |..|+..+...=. -.+.||.+++..-|.+..
T Consensus 74 l~~ld~e-i~~L~~el~~l~~~~k~l~~eL~~L~~~~t~~el~~~i~~l~ 122 (169)
T PF07106_consen 74 LAELDAE-IKELREELAELKKEVKSLEAELASLSSEPTNEELREEIEELE 122 (169)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHH
Confidence 2356666 7777666553311 146888888888776553
No 120
>PRK05638 threonine synthase; Validated
Probab=85.58 E-value=2.9 Score=40.75 Aligned_cols=61 Identities=16% Similarity=0.250 Sum_probs=46.8
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcC--CChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVN--LPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV 102 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~--l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~ 102 (252)
+++-...|+.++.+ . -+--.+|.+++ + +++..|.++|+.||+.|||.+-. +...|+.|-|.
T Consensus 369 ~~~~r~~IL~~L~~-~---~~~~~el~~~l--~~~~s~~~v~~hL~~Le~~GLV~~~~--~~g~~~~Y~Lt 431 (442)
T PRK05638 369 IGGTKLEILKILSE-R---EMYGYEIWKAL--GKPLKYQAVYQHIKELEELGLIEEAY--RKGRRVYYKLT 431 (442)
T ss_pred ccchHHHHHHHHhh-C---CccHHHHHHHH--cccCCcchHHHHHHHHHHCCCEEEee--cCCCcEEEEEC
Confidence 44567888888876 3 37788999999 7 89999999999999999998742 22345556553
No 121
>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=85.54 E-value=1.6 Score=33.71 Aligned_cols=50 Identities=8% Similarity=0.247 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHhhh----CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 126 IKVVKSQCLKQIIK----LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 126 V~~l~~~~~~~i~~----~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
...+++.|+.||+. ...+++++|++-+ .+++++|+..|+.|+-+|.|...
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l--------~~~~~~v~~al~~L~~eG~IYsT 98 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQL--------GMSENEVRKALDFLSNEGHIYST 98 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHS--------TS-HHHHHHHHHHHHHTTSEEES
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHh--------CcCHHHHHHHHHHHHhCCeEecc
Confidence 57889999999987 3578899999776 36799999999999999999753
No 122
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=85.47 E-value=5.2 Score=33.60 Aligned_cols=37 Identities=14% Similarity=0.264 Sum_probs=30.9
Q ss_pred CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 141 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 141 ~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
..+|.++|++.+ .++..-+++|+..|+-.|.|+..+.
T Consensus 23 ~~~s~~eIA~~~--------~is~~~L~kIl~~L~~aGlv~S~rG 59 (153)
T PRK11920 23 KLSRIPEIARAY--------GVSELFLFKILQPLVEAGLVETVRG 59 (153)
T ss_pred CcCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEeecC
Confidence 457888888754 4778999999999999999998873
No 123
>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=85.20 E-value=3.6 Score=31.00 Aligned_cols=34 Identities=9% Similarity=0.206 Sum_probs=32.9
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 53 GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 53 GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.+...+|-.+| |++.+.+...|..|..+|+|.+=
T Consensus 18 c~TLeeL~ekT--gi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 18 CCTLEELEEKT--GISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred cCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeeee
Confidence 99999999999 99999999999999999999984
No 124
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=85.05 E-value=9.4 Score=34.52 Aligned_cols=112 Identities=9% Similarity=0.096 Sum_probs=78.2
Q ss_pred HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccc
Q 025493 37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWY 116 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy 116 (252)
-...|++++.+ .|. +-.+||-..+ +....++.|=|+.||++|+|+++.. +- ++ . .++.+. ++.
T Consensus 6 R~~~Il~~L~~-~~~--v~v~eLa~~l--~VS~~TIRRDL~~Le~~g~l~r~~G----ga-~~--~--~~~~~~---~~~ 68 (256)
T PRK10434 6 RQAAILEYLQK-QGK--TSVEELAQYF--DTTGTTIRKDLVILEHAGTVIRTYG----GV-VL--N--KEESDP---PID 68 (256)
T ss_pred HHHHHHHHHHH-cCC--EEHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEEEC----CE-Ec--C--CCCCCC---CHH
Confidence 35578888888 554 9999999999 9999999999999999999999742 11 11 0 111111 222
Q ss_pred cCCcCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHc-CCcceecCHH
Q 025493 117 SEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTKQ 165 (252)
Q Consensus 117 ~d~e~D~efV~~l~~~~~~~i~~~------~~~T~~~I~~~i~~~-~i~~~~Ls~~ 165 (252)
.-...+.+.=+.|-+....+|... +..|+-+++++|... +++=+.=|..
T Consensus 69 ~r~~~~~~~K~~IA~~Aa~~I~~g~tIfld~GtT~~~la~~L~~~~~ltVvTnsl~ 124 (256)
T PRK10434 69 HKTLINTHKKELIAEAAVSLIHDGDSIILDAGSTVLQMVPLLSRFNNITVMTNSLH 124 (256)
T ss_pred HHHHhhHHHHHHHHHHHHhhCCCCCEEEEcCcHHHHHHHHHhccCCCeEEEECCHH
Confidence 233456666777888888888754 578899999999764 4544444443
No 125
>PHA02943 hypothetical protein; Provisional
Probab=84.83 E-value=4.4 Score=34.90 Aligned_cols=51 Identities=8% Similarity=0.176 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 126 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 126 V~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
|..=...++.|| +.|..|..||++.+ .+|..+++=+|.+|+-+|+|++|+-
T Consensus 9 v~~R~~eILE~L-k~G~~TtseIAkaL--------GlS~~qa~~~LyvLErEG~VkrV~~ 59 (165)
T PHA02943 9 VHTRMIKTLRLL-ADGCKTTSRIANKL--------GVSHSMARNALYQLAKEGMVLKVEI 59 (165)
T ss_pred HHHHHHHHHHHH-hcCCccHHHHHHHH--------CCCHHHHHHHHHHHHHcCceEEEee
Confidence 333445677777 78888899998765 4789999999999999999999873
No 126
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=84.71 E-value=3.5 Score=34.91 Aligned_cols=110 Identities=14% Similarity=0.143 Sum_probs=69.1
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccC
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSE 118 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d 118 (252)
..||.++++ ..-+-++||...+ +..+..+++.|+.|+++|||.-++ .+-|.|.+ .
T Consensus 13 ~~Iy~l~~~---~~~~~~~diA~~L--~Vsp~sVt~ml~rL~~~GlV~~~~------y~gi~LT~--------------~ 67 (154)
T COG1321 13 ETIYELLEE---KGFARTKDIAERL--KVSPPSVTEMLKRLERLGLVEYEP------YGGVTLTE--------------K 67 (154)
T ss_pred HHHHHHHhc---cCcccHHHHHHHh--CCCcHHHHHHHHHHHHCCCeEEec------CCCeEECh--------------h
Confidence 345655553 3348899999999 999999999999999999998863 22233321 1
Q ss_pred CcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhh
Q 025493 119 GSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVL 176 (252)
Q Consensus 119 ~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVy 176 (252)
|+==...+=...+.+..|+.+.-....+++++--.... -.++.+.++.|-+.|-+
T Consensus 68 G~~~a~~~~r~hrlle~fL~~~lg~~~~~~~~ea~~le---h~~s~~~~~rl~~~l~~ 122 (154)
T COG1321 68 GREKAKELLRKHRLLERFLVDVLGLDWEEAHEEAEGLE---HALSDETAERLDELLGF 122 (154)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHh---hcCCHHHHHHHHHHhCC
Confidence 22112222223334556666655566666664433322 35778888888777765
No 127
>PHA02701 ORF020 dsRNA-binding PKR inhibitor; Provisional
Probab=84.50 E-value=2.7 Score=36.98 Aligned_cols=50 Identities=16% Similarity=0.255 Sum_probs=46.0
Q ss_pred hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
+-|++|..++.. .|.+ +-..+|.+++ ||..+.++|.|=.|...+.|..+.
T Consensus 4 ~~~~~i~~~l~~-~~~~-~~a~~i~k~l--~i~k~~vNr~LY~L~~~~~v~~~~ 53 (183)
T PHA02701 4 DCASLILTLLSS-SGDK-LPAKRIAKEL--GISKHEANRCLYRLLESDAVSCED 53 (183)
T ss_pred hHHHHHHHHHHh-cCCC-CcHHHHHHHh--CccHHHHHHHHHHHhhcCcEecCC
Confidence 458899999999 9977 9999999999 999999999999999999998763
No 128
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=84.27 E-value=12 Score=33.65 Aligned_cols=111 Identities=6% Similarity=-0.042 Sum_probs=77.2
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC--CCccCCcc
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS--KDISGGAW 115 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs--~eiTGG~w 115 (252)
...|+.++++ +.-+-.++|..++ ++...++.|=|+.||++|+|+.+..-. ..+ +++ .+. ++
T Consensus 7 ~~~Il~~l~~---~~~~~~~ela~~l--~vS~~TirRdL~~Le~~g~i~r~~gga---~~~------~~~~~~~~---~~ 69 (251)
T PRK13509 7 HQILLELLAQ---LGFVTVEKVIERL--GISPATARRDINKLDESGKLKKVRNGA---EAI------TQQRPRWT---PM 69 (251)
T ss_pred HHHHHHHHHH---cCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEecCCc---ccc------CCCcccCC---CH
Confidence 4567777777 4568899999999 999999999999999999998854321 110 111 011 12
Q ss_pred ccCCcCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHcCCcceecCHH
Q 025493 116 YSEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSGAFKVDLTKQ 165 (252)
Q Consensus 116 y~d~e~D~efV~~l~~~~~~~i~~~------~~~T~~~I~~~i~~~~i~~~~Ls~~ 165 (252)
..-...+.+--..|-+.+..+|... +..|+-+++++|...+++=+.=+..
T Consensus 70 ~~r~~~~~~~K~~IA~~Aa~~I~~g~~Ifld~GsT~~~la~~L~~~~ltVvTnsl~ 125 (251)
T PRK13509 70 NIHQAQNHDEKVRIAKAASQLCNPGESVVINCGSTAFLLGRELCGKPVQIITNYLP 125 (251)
T ss_pred HHHHHhCHHHHHHHHHHHHHhCCCCCEEEECCcHHHHHHHHHhCCCCeEEEeCCHH
Confidence 2233456677778888888888754 5788899999997656554554443
No 129
>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=84.08 E-value=2.1 Score=30.70 Aligned_cols=33 Identities=15% Similarity=0.347 Sum_probs=30.6
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 53 GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 53 GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
.+.+.+|..-+ |++...++|+|+.|+.+|+|..
T Consensus 28 ~lt~~~iA~~~--g~sr~tv~r~l~~l~~~g~I~~ 60 (76)
T PF13545_consen 28 PLTQEEIADML--GVSRETVSRILKRLKDEGIIEV 60 (76)
T ss_dssp ESSHHHHHHHH--TSCHHHHHHHHHHHHHTTSEEE
T ss_pred cCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEE
Confidence 46789999999 9999999999999999999984
No 130
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=83.98 E-value=1.4 Score=39.50 Aligned_cols=48 Identities=21% Similarity=0.419 Sum_probs=39.8
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee-eeccc-cCCeeeEEecc
Q 025493 54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE-VVNIH-NKGKKHLMAVE 103 (252)
Q Consensus 54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~-vksv~-~~~rK~YmL~~ 103 (252)
=+..+|.... ++.|..|-++|+.||..|||-+ +--+. .+.||.|+...
T Consensus 29 ~yvsEiS~~l--gvsqkAVl~HL~~LE~AGlveS~ie~~~Rg~~rKYY~Is~ 78 (217)
T COG1777 29 CYVSEISREL--GVSQKAVLKHLRILERAGLVESRIEKIPRGRPRKYYMISR 78 (217)
T ss_pred hHHHHHHhhc--CcCHHHHHHHHHHHHHcCCchhhccccccCCCcceeeccC
Confidence 4556778889 9999999999999999999998 54443 57789999875
No 131
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=83.87 E-value=5.3 Score=33.26 Aligned_cols=55 Identities=7% Similarity=0.209 Sum_probs=47.7
Q ss_pred HHHHHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCC
Q 025493 130 KSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNG 187 (252)
Q Consensus 130 ~~~~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g 187 (252)
|..++++|... +.+|+++|++.+++.+ ..+|..-|.+.|+.|+--|.|.++...+
T Consensus 23 R~~vl~~L~~~~~~~sAeei~~~l~~~~---p~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 23 RLAVLELLLEADGHLSAEELYEELREEG---PGISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHHhC---CCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 56688888854 6799999999999977 5678999999999999999999988654
No 132
>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=83.81 E-value=11 Score=32.02 Aligned_cols=49 Identities=18% Similarity=0.156 Sum_probs=40.2
Q ss_pred hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
++...|..++-. .| .+.-.+|...+ +|+.+.|.|+|..|...|||...+
T Consensus 14 ~~~v~Vl~aL~~-~~--~~tdEeLa~~L--gi~~~~VRk~L~~L~e~~Lv~~~r 62 (158)
T TIGR00373 14 EEVGLVLFSLGI-KG--EFTDEEISLEL--GIKLNEVRKALYALYDAGLADYKR 62 (158)
T ss_pred hhHHHHHHHHhc-cC--CCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCceeee
Confidence 345667776665 45 48899999999 999999999999999999996544
No 133
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=83.71 E-value=3.4 Score=34.70 Aligned_cols=42 Identities=12% Similarity=0.188 Sum_probs=36.7
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
++.-+..++|..+. |++..-+.|++..|.+.|||++++-.+-
T Consensus 22 ~~~~~s~~~IA~~~--~is~~~L~kil~~L~kaGlV~S~rG~~G 63 (150)
T COG1959 22 GGGPVSSAEIAERQ--GISPSYLEKILSKLRKAGLVKSVRGKGG 63 (150)
T ss_pred CCCcccHHHHHHHh--CcCHHHHHHHHHHHHHcCCEEeecCCCC
Confidence 33346789999999 9999999999999999999999987654
No 134
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=83.64 E-value=5.5 Score=33.17 Aligned_cols=59 Identities=14% Similarity=0.205 Sum_probs=49.9
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVNIH 92 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vksv~ 92 (252)
-.+|+.-..|++++.+ +++. +...+|=.+.. +++...+|-|+|+.|+..|+|.++..-.
T Consensus 17 lr~T~qR~~vl~~L~~-~~~~-~sAeei~~~l~~~~p~islaTVYr~L~~l~e~Glv~~~~~~~ 78 (145)
T COG0735 17 LRLTPQRLAVLELLLE-ADGH-LSAEELYEELREEGPGISLATVYRTLKLLEEAGLVHRLEFEG 78 (145)
T ss_pred CCcCHHHHHHHHHHHh-cCCC-CCHHHHHHHHHHhCCCCCHhHHHHHHHHHHHCCCEEEEEeCC
Confidence 3579999999999999 8777 88888877653 3788999999999999999999986654
No 135
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=83.64 E-value=3.6 Score=37.06 Aligned_cols=45 Identities=13% Similarity=0.226 Sum_probs=37.8
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.|+..+.+ . +.++-.++|-+++ +++.+.+.|+|++|+..|+|...
T Consensus 15 ~iL~~l~~-~-~~~ls~~eia~~l--gl~kstv~RlL~tL~~~g~v~~~ 59 (263)
T PRK09834 15 MVLRALNR-L-DGGATVGLLAELT--GLHRTTVRRLLETLQEEGYVRRS 59 (263)
T ss_pred HHHHHHHh-c-CCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEe
Confidence 34555554 3 3469999999999 99999999999999999999875
No 136
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=83.45 E-value=1.5 Score=36.73 Aligned_cols=68 Identities=12% Similarity=0.134 Sum_probs=49.8
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHH-HHHhh--cCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDM-KRELK--VNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV 102 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~di-k~~~~--~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~ 102 (252)
...+++-...|+.++.+ . .-|-..... ...+. ..+...+|-.+|+.||.+|+|.+-.. .++||+|-+.
T Consensus 38 ~~~~~~~~l~IL~lL~~-~-~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~--~~~RK~Y~IT 108 (135)
T PRK09416 38 SEKEEDILLAILQLLMN-E-KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWD--HEGAKYYQLT 108 (135)
T ss_pred hcccccHHHHHHHHHhC-C-CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeec--CCCceEEEEC
Confidence 44677888899998888 6 677665544 33331 14678999999999999999988543 4578998763
No 137
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=83.45 E-value=2.7 Score=38.17 Aligned_cols=44 Identities=18% Similarity=0.239 Sum_probs=37.6
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
.|++++.+ .+ .++-..+|-+++ +||.+.+.|.|++|+..|++..
T Consensus 29 ~IL~~~~~-~~-~~~tl~eIa~~l--glpkStv~RlL~tL~~~G~l~~ 72 (271)
T PRK10163 29 AILQYLEK-SG-GSSSVSDISLNL--DLPLSTTFRLLKVLQAADFVYQ 72 (271)
T ss_pred HHHHHHHh-CC-CCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence 45666655 43 578899999999 9999999999999999999966
No 138
>PF13551 HTH_29: Winged helix-turn helix
Probab=82.81 E-value=15 Score=27.68 Aligned_cols=98 Identities=16% Similarity=0.226 Sum_probs=64.6
Q ss_pred Cccc-HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHH
Q 025493 52 MGIW-TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVK 130 (252)
Q Consensus 52 ~GIw-~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~ 130 (252)
+|.. .+++.+.+ +++..++.+.++..++.|+-. +.+-+. .||....- ++.+-.+.|.
T Consensus 10 ~g~~~~~~ia~~l--g~s~~Tv~r~~~~~~~~G~~~-l~~~~~-----------------~~g~~~~~--l~~~~~~~l~ 67 (112)
T PF13551_consen 10 EGVSTIAEIARRL--GISRRTVYRWLKRYREGGIEG-LLPRKP-----------------RGGRPRKR--LSEEQRAQLI 67 (112)
T ss_pred cCCCcHHHHHHHH--CcCHHHHHHHHHHHHcccHHH-HHhccc-----------------cCCCCCCC--CCHHHHHHHH
Confidence 3665 99999999 999999999999999988322 222110 02211111 5666666555
Q ss_pred HHHHHHhhh-CCCCCHHHHHHHH-HHcCCcceecCHHHHHHHHHH
Q 025493 131 SQCLKQIIK-LKVATLEGISDSI-KRSGAFKVDLTKQQIEEIVRA 173 (252)
Q Consensus 131 ~~~~~~i~~-~~~~T~~~I~~~i-~~~~i~~~~Ls~~di~~IL~t 173 (252)
+.+...-.. ....|+++|.+++ .+. ..+.+|..-|..+|..
T Consensus 68 ~~~~~~p~~g~~~~t~~~l~~~l~~~~--~~~~~s~~ti~r~L~~ 110 (112)
T PF13551_consen 68 ELLRENPPEGRSRWTLEELAEWLIEEE--FGIDVSPSTIRRILKR 110 (112)
T ss_pred HHHHHCCCCCCCcccHHHHHHHHHHhc--cCccCCHHHHHHHHHH
Confidence 544432222 1368999999998 444 3578899999999874
No 139
>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=82.66 E-value=2.8 Score=37.24 Aligned_cols=43 Identities=7% Similarity=0.136 Sum_probs=36.8
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
|++++.+ .+.++-.+||-+++ +||.+++.|.|++|+..|++..
T Consensus 14 IL~~l~~--~~~~~~l~eia~~l--glpksT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 14 VIEAFGA--ERPRLTLTDVAEAT--GLTRAAARRFLLTLVELGYVTS 56 (248)
T ss_pred HHHHHhc--CCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEe
Confidence 4555544 35789999999999 9999999999999999999975
No 140
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=82.39 E-value=2.6 Score=28.13 Aligned_cols=41 Identities=22% Similarity=0.394 Sum_probs=22.3
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKS 78 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~ 78 (252)
+-||.+|+....... +.|...++|.+.+ |.+.++|.+.||.
T Consensus 3 ~~Lt~~eR~~I~~l~----~~G~s~~~IA~~l--g~s~sTV~relkR 43 (44)
T PF13936_consen 3 KHLTPEERNQIEALL----EQGMSIREIAKRL--GRSRSTVSRELKR 43 (44)
T ss_dssp ---------HHHHHH----CS---HHHHHHHT--T--HHHHHHHHHH
T ss_pred cchhhhHHHHHHHHH----HcCCCHHHHHHHH--CcCcHHHHHHHhc
Confidence 458888887755444 4789999999999 9999999999874
No 141
>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=81.74 E-value=4.4 Score=28.38 Aligned_cols=47 Identities=9% Similarity=0.156 Sum_probs=40.5
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
++.++.+|..++.+|.+|+++.+. .|..-|+.=|+.|+-.|.|.++.
T Consensus 2 ~~~Il~~l~~~~~~s~~ela~~~~--------VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 2 QQQILELLKEKGKVSVKELAEEFG--------VSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHHcCCEEHHHHHHHHC--------cCHHHHHHHHHHHHHCCCEEEEc
Confidence 357888999999999999998763 57888999999999999999875
No 142
>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=81.72 E-value=3.2 Score=32.30 Aligned_cols=50 Identities=20% Similarity=0.230 Sum_probs=37.6
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
.++...|..++-. .| .+--.||...+ +|+.+.+.|+|-.|...+||+..+
T Consensus 12 g~~~~~Il~~L~~-~~--~l~de~la~~~--~l~~~~vRkiL~~L~~~~lv~~~~ 61 (105)
T PF02002_consen 12 GEEAVRILDALLR-KG--ELTDEDLAKKL--GLKPKEVRKILYKLYEDGLVSYRR 61 (105)
T ss_dssp -STTHHHHHHHHH-H----B-HHHHHHTT---S-HHHHHHHHHHHHHHSS-EEEE
T ss_pred CchHHHHHHHHHH-cC--CcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCeEEEE
Confidence 3566788888887 55 58899999999 999999999999999999997654
No 143
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=81.49 E-value=4.8 Score=29.28 Aligned_cols=49 Identities=18% Similarity=0.267 Sum_probs=41.5
Q ss_pred HHHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 132 QCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 132 ~~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
.|+++|..+ .+++..+|.+.+...| .++|++-|..-|+.|.-||.++++
T Consensus 2 ~IL~~L~~~~~P~g~~~l~~~L~~~g---~~~se~avRrrLr~me~~Glt~~~ 51 (66)
T PF08461_consen 2 FILRILAESDKPLGRKQLAEELKLRG---EELSEEAVRRRLRAMERDGLTRKV 51 (66)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHhcC---hhhhHHHHHHHHHHHHHCCCcccc
Confidence 467777755 5789999999999887 689999999999999999976653
No 144
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=80.95 E-value=4 Score=33.70 Aligned_cols=55 Identities=9% Similarity=0.165 Sum_probs=48.2
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
.+-..+.+.|=.++.+|++||+++|.+. -+++..-|..+|+.|+--|.|-+.+.+
T Consensus 6 ~aE~eVM~ilW~~~~~t~~eI~~~l~~~----~ews~sTV~TLl~RL~KKg~l~~~kdg 60 (123)
T COG3682 6 AAEWEVMEILWSRGPATVREIIEELPAD----REWSYSTVKTLLNRLVKKGLLTRKKDG 60 (123)
T ss_pred HHHHHHHHHHHHcCCccHHHHHHHHhhc----ccccHHHHHHHHHHHHhccchhhhhcC
Confidence 4566788888899999999999999976 479999999999999999999887754
No 145
>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=80.73 E-value=6.7 Score=31.04 Aligned_cols=55 Identities=20% Similarity=0.213 Sum_probs=45.8
Q ss_pred CCCCChHHHHHHHHHHh-----hcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 31 SDSLTDHERLIYDVIRS-----NKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~-----~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
..+|+.-|..|+..|-. |...+-|....+...| +++.+.++++++.|+.+++|..
T Consensus 27 ~~dls~rq~ki~~ai~RkTyG~nKk~d~Is~sq~~e~t--g~~~~~V~~al~~Li~~~vI~~ 86 (100)
T PF04492_consen 27 RADLSGRQLKILLAIIRKTYGWNKKMDRISNSQIAEMT--GLSRDHVSKALNELIRRGVIIR 86 (100)
T ss_pred hccccHHHHHHHHHHHHHccCCCCccceeeHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEe
Confidence 35788888888877765 2355678889999999 9999999999999999999954
No 146
>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=80.44 E-value=15 Score=34.04 Aligned_cols=146 Identities=15% Similarity=0.155 Sum_probs=84.5
Q ss_pred cchhHHHhhccCCCcccc-----cCCCCCCCCCCCChHHHHHH-----HHHHhhcCC-Cccc-HHHHHHHhhcCCChHHH
Q 025493 5 FTDLYLLGLAKGSGMSKR-----KRPDSNAPSDSLTDHERLIY-----DVIRSNKQD-MGIW-TRDMKRELKVNLPDNIV 72 (252)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~~~e~~vy-----~~I~~~ag~-~GIw-~~dik~~~~~~l~~~~l 72 (252)
|..++..+.++....++. .......+.+-|+.++...| -.|++.+.- .|-| ...|.+++++.++..++
T Consensus 77 F~~lV~f~~ak~~~~k~~~~~~~~~~~~~~~~~~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev 156 (271)
T TIGR02147 77 FEAMVNFGQAKTDTEKQQFFEEMQALKPRPRLRVLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQV 156 (271)
T ss_pred HHHHHHHhccCCHHHHHHHHHHHHHHhhhchheeccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHH
Confidence 445555566665544332 11111234456788776643 456663332 2442 44599999445999999
Q ss_pred HHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhC---CCCCHHHHH
Q 025493 73 TKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKL---KVATLEGIS 149 (252)
Q Consensus 73 ~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~---~~~T~~~I~ 149 (252)
+.+|..|++-||||.-.+- .|...+ ..+||| .+.-.+.|-.+..+++.+-... -.+.
T Consensus 157 ~~sL~~L~~~glikk~~~g------~y~~t~----~~l~~~-----~~~~~~avr~~h~q~l~lA~~al~~~p~~----- 216 (271)
T TIGR02147 157 KESLDLLERLGLIKKNEDG------FYKQTD----KAVSTG-----DEVIPLAVRQYQKQMIDLAKEALDALPPS----- 216 (271)
T ss_pred HHHHHHHHHCCCeeECCCC------cEEeec----ceeecC-----CccchHHHHHHHHHHHHHHHHHHHhCCcc-----
Confidence 9999999999999985332 233222 234433 4555677777777777665432 1111
Q ss_pred HHHHHcCCcc--eecCHHHHHHHHHHH
Q 025493 150 DSIKRSGAFK--VDLTKQQIEEIVRAV 174 (252)
Q Consensus 150 ~~i~~~~i~~--~~Ls~~di~~IL~tL 174 (252)
...++. ..++.++.++|.+.|
T Consensus 217 ----eR~~S~lT~~i~~~~~~~i~~~i 239 (271)
T TIGR02147 217 ----ERDVSTVTFGISEEAYKEIVKKI 239 (271)
T ss_pred ----ccccceeeEecCHHHHHHHHHHH
Confidence 112333 467788888886655
No 147
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=80.44 E-value=4.5 Score=36.18 Aligned_cols=45 Identities=4% Similarity=0.258 Sum_probs=36.5
Q ss_pred HHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 42 YDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 42 y~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.++++..+...++-.++|-+++ +||.+.+.|.|++|+..|++..-
T Consensus 17 l~IL~~l~~~~~l~l~eia~~l--gl~kstv~Rll~tL~~~G~l~~~ 61 (257)
T PRK15090 17 FGILQALGEEREIGITELSQRV--MMSKSTVYRFLQTMKTLGYVAQE 61 (257)
T ss_pred HHHHHHhhcCCCCCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEc
Confidence 3344443334578899999999 99999999999999999999773
No 148
>PRK11569 transcriptional repressor IclR; Provisional
Probab=80.13 E-value=4.1 Score=36.99 Aligned_cols=43 Identities=9% Similarity=0.371 Sum_probs=36.9
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
|++++.+ .+.++-.++|-+.+ +||.+++.|.|.+|+..|++..
T Consensus 33 IL~~l~~--~~~~~~lseia~~l--glpksTv~RlL~tL~~~G~l~~ 75 (274)
T PRK11569 33 LLEWIAE--SNGSVALTELAQQA--GLPNSTTHRLLTTMQQQGFVRQ 75 (274)
T ss_pred HHHHHHh--CCCCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEE
Confidence 4555544 35778999999999 9999999999999999999975
No 149
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=80.06 E-value=6.6 Score=33.46 Aligned_cols=53 Identities=8% Similarity=0.095 Sum_probs=44.5
Q ss_pred HHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 130 KSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 130 ~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
|..|+.+|.. .+.+|+++|.+.+++.+ ..++..-|-+.|+.|+-.|.|.++..
T Consensus 28 R~~IL~~l~~~~~hlSa~eI~~~L~~~~---~~is~aTVYRtL~~L~e~Glv~~~~~ 81 (169)
T PRK11639 28 RLEVLRLMSLQPGAISAYDLLDLLREAE---PQAKPPTVYRALDFLLEQGFVHKVES 81 (169)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHHHhhC---CCCCcchHHHHHHHHHHCCCEEEEec
Confidence 5567777764 46899999999999988 35677899999999999999999864
No 150
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=79.86 E-value=20 Score=30.77 Aligned_cols=124 Identities=15% Similarity=0.203 Sum_probs=74.4
Q ss_pred CCCCCChHHHHHHH-----HHHhh---cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 30 PSDSLTDHERLIYD-----VIRSN---KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 30 ~~~~l~~~e~~vy~-----~I~~~---ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
+.+.|+.++...|. .|++. .+..+ -...|.+++.++++..++.++|..|++-||||.-.+ -.|..
T Consensus 9 ~~~~l~~~~~~~~~~W~~~~ir~l~~l~~~~~-d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~------g~y~~ 81 (171)
T PF14394_consen 9 KVRVLDEDEFEYYSSWYHPAIRELLPLMPFAP-DPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD------GKYVQ 81 (171)
T ss_pred ceeeccHHHHHHHhhhHHHHHHHHhhcCCCCC-CHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC------CcEEE
Confidence 45566666655443 34442 33333 567888888779999999999999999999999654 12332
Q ss_pred cccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCc--ceecCHHHHHHHHHHHh
Q 025493 102 VEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAF--KVDLTKQQIEEIVRAVV 175 (252)
Q Consensus 102 ~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~--~~~Ls~~di~~IL~tLV 175 (252)
. +..+||| .+.-.+.|-.+..++...-... ++.+- .....++ +..++.++.++|.+.+.
T Consensus 82 t----~~~l~~~-----~~~~~~avr~~h~q~~~lA~~a----l~~~p--~~~R~~s~~T~~vs~~~~~ki~~~i~ 142 (171)
T PF14394_consen 82 T----DKSLTTS-----SEIPSEAVRSYHKQMLELAQEA----LDRVP--PEERDFSGLTMSVSREDYEKIKKEIR 142 (171)
T ss_pred e----cceeeCC-----CCCcHHHHHHHHHHHHHHHHHH----HHhCC--ccccceeeeEEEeCHHHHHHHHHHHH
Confidence 2 2234433 5667777777777777664321 00000 0011233 34677888887766553
No 151
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=79.33 E-value=13 Score=27.50 Aligned_cols=57 Identities=18% Similarity=0.246 Sum_probs=45.0
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhc----CCCh----HHHHHHHHHHHhcCCeeeeecc
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKV----NLPD----NIVTKSIKSLQNKSLIKEVVNI 91 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~----~l~~----~~l~k~lK~Le~k~lIK~vksv 91 (252)
++...+|...|.+....+|.....|++-... +++. ..|.++||.+..+|.+..++..
T Consensus 3 P~y~~mI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~ 67 (77)
T PF00538_consen 3 PPYSDMILEAIKALKERKGSSLQAIKKYIKAKYKVDLNPANFKSRLKRALKRGVEKGKLVQVKGK 67 (77)
T ss_dssp SCHHHHHHHHHHHCCSSSSEEHHHHHHHHHHHSSCCCCHTTHHHHHHHHHHHHHHCTSEEECSCS
T ss_pred CCHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhcCcCCChHHHHHHHHHHHHHHHHCCcEEeeccc
Confidence 3457799999999555699999999884322 3443 6899999999999999999843
No 152
>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=79.32 E-value=6.1 Score=28.72 Aligned_cols=49 Identities=12% Similarity=0.085 Sum_probs=33.9
Q ss_pred HHHHHHHHhhhCC-CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 129 VKSQCLKQIIKLK-VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 129 l~~~~~~~i~~~~-~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+-+.+..|+..++ .||+.||++.+.=+ |..-|..-|+.|+-.|.|.+..
T Consensus 11 vL~~I~~~~~~~G~~Pt~rEIa~~~g~~-------S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 11 VLEFIREYIEENGYPPTVREIAEALGLK-------STSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHHHHHHHHHSS---HHHHHHHHTSS-------SHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHHHHHHHHHHcCCCCCHHHHHHHhCCC-------ChHHHHHHHHHHHHCcCccCCC
Confidence 3344445555544 68999999987522 4888999999999999998754
No 153
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=79.28 E-value=29 Score=31.36 Aligned_cols=118 Identities=12% Similarity=0.164 Sum_probs=79.0
Q ss_pred hHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCcc
Q 025493 36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAW 115 (252)
Q Consensus 36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~w 115 (252)
+-...|..++++ .| -+-..+|.... ++...++.|=|+.||++|+|+++.. +- + +. .+..+ -++
T Consensus 5 ~R~~~Il~~l~~-~~--~~~~~ela~~l--~vS~~TiRRdL~~Le~~g~l~r~~G----Ga-~--~~--~~~~~---~~~ 67 (252)
T PRK10906 5 QRHDAIIELVKQ-QG--YVSTEELVEHF--SVSPQTIRRDLNDLAEQNKILRHHG----GA-A--LP--SSSVN---TPW 67 (252)
T ss_pred HHHHHHHHHHHH-cC--CEeHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEecC----CE-E--ec--CCCCC---CCH
Confidence 345678888877 54 49999999999 9999999999999999999988532 21 1 11 11111 123
Q ss_pred ccCCcCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHc-CCcceecCHHHHHHH
Q 025493 116 YSEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTKQQIEEI 170 (252)
Q Consensus 116 y~d~e~D~efV~~l~~~~~~~i~~~------~~~T~~~I~~~i~~~-~i~~~~Ls~~di~~I 170 (252)
..-...+.+-=..|-+....+|... +..|+.+++++|... +++=+.=+..=+..+
T Consensus 68 ~~r~~~~~~~K~~IA~~Aa~~I~~g~tIflD~GtT~~~la~~L~~~~~ltVvTNsl~ia~~l 129 (252)
T PRK10906 68 HDRKATQTEEKERIARKVASQIPNGATLFIDIGTTPEAVAHALLNHSNLRIVTNNLNVANTL 129 (252)
T ss_pred HHHhhhcHHHHHHHHHHHHhhCCCCCEEEEcCcHHHHHHHHHhcCCCCcEEEECcHHHHHHH
Confidence 2223445566677777778888754 578899999999753 555455444433333
No 154
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=78.65 E-value=28 Score=31.79 Aligned_cols=119 Identities=11% Similarity=0.147 Sum_probs=80.6
Q ss_pred HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc-ccCCCccCCcc
Q 025493 37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF-EPSKDISGGAW 115 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l-ePs~eiTGG~w 115 (252)
-...|.+++.+ .|. +-..+|...+ +....++.|=|..||+.|+++.+. .+. + +.+. .|..+. ++
T Consensus 18 R~~~Il~~L~~-~~~--vtv~eLa~~l--~VS~~TIRRDL~~Le~~G~l~r~~----GGa-~--~~~~~~~~~~~---~~ 82 (269)
T PRK09802 18 RREQIIQRLRQ-QGS--VQVNDLSALY--GVSTVTIRNDLAFLEKQGIAVRAY----GGA-L--ICDSTTPSVEP---SV 82 (269)
T ss_pred HHHHHHHHHHH-cCC--EeHHHHHHHH--CCCHHHHHHHHHHHHhCCCeEEEe----CCE-E--ecCcCCCccCC---CH
Confidence 45678888888 665 9999999999 999999999999999999999753 121 1 1110 011111 11
Q ss_pred ccCCcCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHc-CCcceecCHHHHHHH
Q 025493 116 YSEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRS-GAFKVDLTKQQIEEI 170 (252)
Q Consensus 116 y~d~e~D~efV~~l~~~~~~~i~~~------~~~T~~~I~~~i~~~-~i~~~~Ls~~di~~I 170 (252)
..-...+.+.-..|-+.+..||... +..|+.+++++|... +++=+.=+..-+..+
T Consensus 83 ~~r~~~~~~~K~~IA~~Aa~~I~dgd~Ifld~GtT~~~la~~L~~~~~ltVvTnsl~ia~~l 144 (269)
T PRK09802 83 EDKSALNTAMKRSVAKAAVELIQPGHRVILDSGTTTFEIARLMRKHTDVIAMTNGMNVANAL 144 (269)
T ss_pred HHHHHhCHHHHHHHHHHHHhhCCCCCEEEECCchHHHHHHHhcCcCCCeEEEeCCHHHHHHH
Confidence 1122455666777888888888754 578999999999654 455555555444444
No 155
>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=77.80 E-value=9.9 Score=25.96 Aligned_cols=49 Identities=10% Similarity=0.196 Sum_probs=40.2
Q ss_pred HHHHHHHhhhCCC--CCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 130 KSQCLKQIIKLKV--ATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 130 ~~~~~~~i~~~~~--~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
.-.++.+|..++. .|..||++.+. ++..-+..+|+.|+-.|.|++..+.
T Consensus 7 q~~vL~~l~~~~~~~~t~~~la~~l~--------~~~~~vs~~v~~L~~~Glv~r~~~~ 57 (62)
T PF12802_consen 7 QFRVLMALARHPGEELTQSELAERLG--------ISKSTVSRIVKRLEKKGLVERERDP 57 (62)
T ss_dssp HHHHHHHHHHSTTSGEEHHHHHHHHT--------S-HHHHHHHHHHHHHTTSEEEEE-S
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHC--------cCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 4567888888877 89999998764 6788999999999999999998754
No 156
>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=77.26 E-value=11 Score=28.84 Aligned_cols=58 Identities=9% Similarity=0.023 Sum_probs=47.0
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEE
Q 025493 125 FIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 125 fV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
+=|.|+.+|.+.=.....+|.+.|.+++.+.==.=..=|.+-+..-|.+|+-++||..
T Consensus 12 L~EvlC~~I~dln~~~~~at~E~l~~~L~~~yp~i~~Ps~e~l~~~L~~Li~erkIY~ 69 (80)
T PF10264_consen 12 LPEVLCWVISDLNAAGQPATQETLREHLRKHYPGIAIPSQEVLYNTLGTLIKERKIYH 69 (80)
T ss_pred HHHHHHHHHHHHhccCCcchHHHHHHHHHHhCCCCCCCCHHHHHHHHHHHHHcCceee
Confidence 3467777777777778899999999999987321235789999999999999999986
No 157
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=77.18 E-value=12 Score=32.89 Aligned_cols=52 Identities=21% Similarity=0.237 Sum_probs=45.4
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
...||.-...++.+|.- +..|.+.+|.+.. |... +.+|+.|..+|||+++.-
T Consensus 85 ~~~LS~aaLEtLaiIay---~qPiTr~eI~~ir--Gv~~---~~ii~~L~~~gLI~e~gr 136 (188)
T PRK00135 85 KQSLSQAALEVLAIIAY---KQPITRIEIDEIR--GVNS---DGALQTLLAKGLIKEVGR 136 (188)
T ss_pred cCCCCHHHHHHHHHHHH---cCCcCHHHHHHHH--CCCH---HHHHHHHHHCCCeEEcCc
Confidence 34799999999999976 6799999999999 7875 899999999999998643
No 158
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=77.07 E-value=12 Score=28.58 Aligned_cols=55 Identities=15% Similarity=0.257 Sum_probs=43.9
Q ss_pred CChHHHHHHHHHHh--hcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 34 LTDHERLIYDVIRS--NKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 34 l~~~e~~vy~~I~~--~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
||+-++.|+..|-+ ...+.=|=.++|..+. +....+|...+..||.-|||.++..
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgSk~ia~~l--~~s~aTIRN~M~~Le~lGlve~~p~ 58 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGSKTIAEEL--GRSPATIRNEMADLEELGLVESQPH 58 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCHHHHHHHH--CCChHHHHHHHHHHHHCCCccCCCC
Confidence 67767777666543 1345668899999999 9999999999999999999987643
No 159
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=76.61 E-value=40 Score=34.59 Aligned_cols=107 Identities=9% Similarity=0.063 Sum_probs=76.7
Q ss_pred cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHH
Q 025493 49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKV 128 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~ 128 (252)
--..|+-..+++.+..+.++.......|..|..+|.|+.... .+-+.+..|+ ++.+ -..
T Consensus 435 p~~~g~~~~~l~~~~~~~~~~~~~~~~l~~l~~~~~i~~~~~-------~~~~~~~~~~-------------~~~~-~~~ 493 (614)
T PRK10512 435 RDEPGPGRERLRRMALPMEDEALVLLLIEKMRESGDIHSHHG-------WLHLPDHKAG-------------FSEE-QQA 493 (614)
T ss_pred CcccCCCHHHHHhhcccCCCHHHHHHHHHHHHhCCCEEEeCC-------EEECCCCCCC-------------CCHH-HHH
Confidence 345799999999987447999999999999999999988533 2333333332 2222 234
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
+.+.+...+. ...|++.|+.+.+ .+..++.+++|..|+-.|++.++..
T Consensus 494 ~~~~l~~~~~-~~p~~~~~~~~~l--------~~~~~~~~~~l~~l~~~g~lv~l~~ 541 (614)
T PRK10512 494 LWQKAEPLFG-DEPWWVRDLAKET--------GTDEQAMRLTLRQAAQQGIITAIVK 541 (614)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4455555554 5688888887654 2568889999999999999998863
No 160
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=76.33 E-value=6.4 Score=35.41 Aligned_cols=45 Identities=18% Similarity=0.355 Sum_probs=38.4
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.|++++.+ +..|+-..+|-+++ |||.+.+.|.|.+|+..|++..-
T Consensus 8 ~iL~~l~~--~~~~l~l~ela~~~--glpksT~~RlL~tL~~~G~v~~d 52 (246)
T COG1414 8 AILDLLAE--GPGGLSLAELAERL--GLPKSTVHRLLQTLVELGYVEQD 52 (246)
T ss_pred HHHHHHHh--CCCCCCHHHHHHHh--CcCHHHHHHHHHHHHHCCCEEEc
Confidence 35566655 55568899999999 99999999999999999999984
No 161
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=76.27 E-value=35 Score=27.12 Aligned_cols=69 Identities=14% Similarity=0.227 Sum_probs=47.9
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.++++.+.+ |++..+ |.--|++||+.+++.- + |.+.| |.+-|+.|+ ..
T Consensus 2 ~IgevA~~~--gvs~~t----lRyYe~~GLl~p~~~~-~-gyR~Y----------------------~~~~l~~l~--~I 49 (120)
T cd04781 2 DIAEVARQS--GLPAST----LRYYEEKGLIASIGRR-G-LRRQY----------------------DPQVLDRLA--LI 49 (120)
T ss_pred CHHHHHHHH--CcCHHH----HHHHHHCCCCCCCcCC-C-Cceec----------------------CHHHHHHHH--HH
Confidence 567888889 888765 4678999999986542 2 44333 445566665 33
Q ss_pred HHhhhCCCCCHHHHHHHHHHcC
Q 025493 135 KQIIKLKVATLEGISDSIKRSG 156 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~~ 156 (252)
.+++.. ..|+++|.+++...+
T Consensus 50 ~~lr~~-G~~L~eI~~~l~~~~ 70 (120)
T cd04781 50 ALGRAA-GFSLDEIQAMLSHDG 70 (120)
T ss_pred HHHHHc-CCCHHHHHHHHhccC
Confidence 556665 458999999998764
No 162
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=76.07 E-value=9.6 Score=32.82 Aligned_cols=53 Identities=9% Similarity=0.144 Sum_probs=45.0
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI 91 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv 91 (252)
.||. +.|+++|.+ |..|...++|-.++ ++..+++.+.+..|+..|++..--.-
T Consensus 161 ~Lt~--r~Vl~~~~~--g~~g~s~~eIa~~l--~iS~~Tv~~~~~~~~~~~~~~~~~~~ 213 (225)
T PRK10046 161 PLTL--NAVRKLFKE--PGVQHTAETVAQAL--TISRTTARRYLEYCASRHLIIAEIVH 213 (225)
T ss_pred HHHH--HHHHHHHHc--CCCCcCHHHHHHHh--CccHHHHHHHHHHHHhCCeEEEEeec
Confidence 3554 478888865 67789999999999 99999999999999999999886543
No 163
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=75.89 E-value=12 Score=32.45 Aligned_cols=50 Identities=14% Similarity=0.224 Sum_probs=39.6
Q ss_pred CCCChHHHHHHHHHHhhcCCCc--------ccHHHHHHHhhcCCChHHHHHHHHHHHhcCC
Q 025493 32 DSLTDHERLIYDVIRSNKQDMG--------IWTRDMKRELKVNLPDNIVTKSIKSLQNKSL 84 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~G--------Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~l 84 (252)
...+.++++.+-+.+. +-..| +-+++|-.-+ |++...|+|+|+.|+++|+
T Consensus 145 ~~~~~~~Rla~~Ll~~-~~~~~~~~~~~i~~t~~~iA~~l--G~tretvsR~l~~L~~~gl 202 (236)
T PRK09392 145 KLRSSAERLANYLLKQ-SLRQGGADVVTLPYEKRVLASYL--GMTPENLSRAFAALASHGV 202 (236)
T ss_pred hcCCHHHHHHHHHHHh-ccccCCCcEEEeeCCHHHHHHHh--CCChhHHHHHHHHHHhCCe
Confidence 3457788877766665 54433 3368999999 9999999999999999996
No 164
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=75.52 E-value=9.8 Score=29.80 Aligned_cols=49 Identities=10% Similarity=0.169 Sum_probs=39.1
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
+.-.|+.++...+.-.+.-|+..+ .++.++|+.+++.|+--|.||++..
T Consensus 8 l~~~IL~hl~~~~~Dy~k~ia~~l--------~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 8 LDLKILQHLKKAGPDYAKSIARRL--------KIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred hHHHHHHHHHHHCCCcHHHHHHHH--------CCCHHHHHHHHHHHHHCCCeEEecC
Confidence 445567777777777777776654 7889999999999999999999873
No 165
>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=75.28 E-value=6 Score=27.89 Aligned_cols=36 Identities=14% Similarity=0.296 Sum_probs=30.6
Q ss_pred Ccc-cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 52 MGI-WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 52 ~GI-w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
+=+ ..++|..+. +.+.+.+.++|+.|++.|+|...+
T Consensus 22 ~~lps~~~la~~~--~vsr~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 22 DRLPSERELAERY--GVSRTTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp SBE--HHHHHHHH--TS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CEeCCHHHHHHHh--ccCCcHHHHHHHHHHHCCcEEEEC
Confidence 446 788999999 999999999999999999998863
No 166
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=75.03 E-value=11 Score=24.68 Aligned_cols=41 Identities=17% Similarity=0.368 Sum_probs=33.6
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
|++.|+.++.++. .|+..++|...+ +++.+.+.+.++.+..
T Consensus 1 l~~~e~~i~~~~~-----~~~s~~eia~~l--~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 1 LTPREREVLRLLA-----EGKTNKEIADIL--GISEKTVKTHLRNIMR 41 (57)
T ss_pred CCHHHHHHHHHHH-----cCCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence 5677888887764 378999999999 9999999999887643
No 167
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=73.88 E-value=8.4 Score=26.57 Aligned_cols=44 Identities=20% Similarity=0.414 Sum_probs=37.4
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
..||+.|..|..++-+ |--.++|-... ++...+|...++.+-.|
T Consensus 2 ~~LT~~E~~vl~~l~~-----G~~~~eIA~~l--~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 2 PSLTERELEVLRLLAQ-----GMSNKEIAEEL--GISEKTVKSHRRRIMKK 45 (58)
T ss_dssp GSS-HHHHHHHHHHHT-----TS-HHHHHHHH--TSHHHHHHHHHHHHHHH
T ss_pred CccCHHHHHHHHHHHh-----cCCcchhHHhc--CcchhhHHHHHHHHHHH
Confidence 4799999999999998 88999999999 99999999888887554
No 168
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=73.85 E-value=6.9 Score=36.16 Aligned_cols=45 Identities=22% Similarity=0.426 Sum_probs=38.2
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
-..|++++.. +|. .=.++|.... +|||.+++--+|.||.-|||..
T Consensus 25 Rv~Il~lL~~-k~p--lNvneiAe~l--gLpqst~s~~ik~Le~aGlirT 69 (308)
T COG4189 25 RVAILQLLHR-KGP--LNVNEIAEAL--GLPQSTMSANIKVLEKAGLIRT 69 (308)
T ss_pred HHHHHHHHHH-hCC--CCHHHHHHHh--CCchhhhhhhHHHHHhcCceee
Confidence 3457788888 664 4468999999 9999999999999999999976
No 169
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=73.71 E-value=9 Score=34.54 Aligned_cols=47 Identities=11% Similarity=0.129 Sum_probs=41.5
Q ss_pred CCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 28 NAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 28 ~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
.+....||+-|+.|+.+|.+ |...++|..++ ++..+++.+.++.+-+
T Consensus 138 ~~~~~~LS~RE~eVL~Lia~-----G~SnkEIA~~L--~IS~~TVk~hvs~I~~ 184 (217)
T PRK13719 138 LEAKNKVTKYQNDVFILYSF-----GFSHEYIAQLL--NITVGSSKNKISEILK 184 (217)
T ss_pred hhccCCCCHHHHHHHHHHHC-----CCCHHHHHHHh--CCCHHHHHHHHHHHHH
Confidence 45567899999999999998 99999999999 9999999888877744
No 170
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=73.61 E-value=12 Score=35.06 Aligned_cols=58 Identities=19% Similarity=0.165 Sum_probs=47.3
Q ss_pred CCCCCChHHHHHHHHHHhhcCC---CcccHHHHHHH-------hhcCCCh---HHHHHHHHHHHhcCCeeeeec
Q 025493 30 PSDSLTDHERLIYDVIRSNKQD---MGIWTRDMKRE-------LKVNLPD---NIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~---~GIw~~dik~~-------~~~~l~~---~~l~k~lK~Le~k~lIK~vks 90 (252)
...+|+..|++++..|.. .+. ..+-..++-.+ . ++.+ +.+...|..|+..|||....+
T Consensus 290 ~~~~L~~~~k~~L~ai~~-~~~~~~~~~~~~~i~~~y~~l~~~~--~~~~~~~~~~~~~l~~L~~~glI~~~~~ 360 (394)
T PRK00411 290 VLRTLPLHEKLLLRAIVR-LLKKGGDEVTTGEVYEEYKELCEEL--GYEPRTHTRFYEYINKLDMLGIINTRYS 360 (394)
T ss_pred HHhcCCHHHHHHHHHHHH-HHhcCCCcccHHHHHHHHHHHHHHc--CCCcCcHHHHHHHHHHHHhcCCeEEEEe
Confidence 467999999999999987 543 56888888754 5 6644 999999999999999998664
No 171
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=73.59 E-value=12 Score=24.99 Aligned_cols=43 Identities=19% Similarity=0.266 Sum_probs=34.7
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHH
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSL 79 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~L 79 (252)
+..|++.|+.|..+.-- .|....+|.... |++...|.++++.-
T Consensus 2 l~~L~~~er~vi~~~y~----~~~t~~eIa~~l--g~s~~~V~~~~~~a 44 (50)
T PF04545_consen 2 LDQLPPREREVIRLRYF----EGLTLEEIAERL--GISRSTVRRILKRA 44 (50)
T ss_dssp HCTS-HHHHHHHHHHHT----ST-SHHHHHHHH--TSCHHHHHHHHHHH
T ss_pred hhhCCHHHHHHHHHHhc----CCCCHHHHHHHH--CCcHHHHHHHHHHH
Confidence 35799999999888874 788899999999 99999988877654
No 172
>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=72.97 E-value=16 Score=24.28 Aligned_cols=42 Identities=21% Similarity=0.392 Sum_probs=33.1
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQ 80 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le 80 (252)
|++-++.|++.+.+ -| -+.-++|-.++ |+....+.+-++.||
T Consensus 1 lD~~D~~Il~~Lq~-d~--r~s~~~la~~l--glS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 1 LDELDRKILRLLQE-DG--RRSYAELAEEL--GLSESTVRRRIRRLE 42 (42)
T ss_dssp --HHHHHHHHHHHH--T--TS-HHHHHHHH--TS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-cC--CccHHHHHHHH--CcCHHHHHHHHHHhC
Confidence 57778899999999 44 46778999999 999999999999986
No 173
>COG5647 Cullin, a subunit of E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.29 E-value=20 Score=37.72 Aligned_cols=143 Identities=6% Similarity=0.099 Sum_probs=104.3
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec--cccCCeeeEEeccc-------
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN--IHNKGKKHLMAVEF------- 104 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks--v~~~~rK~YmL~~l------- 104 (252)
.+.-+.+|+.+- -++++|.-.+|...| +|+...++++|.+|-.-+++.-++. --+|+-|-|.=.++
T Consensus 606 ~s~~q~~vfll~---n~~e~lt~eei~e~T--~l~~~dl~~~L~sl~~ak~~~l~~~~~~~~p~~~fy~ne~f~~~~~rI 680 (773)
T COG5647 606 FSVYQLLVFLLF---NDHEELTFEEILELT--KLSTDDLKRVLQSLSCAKLVVLLKDDKLVSPNTKFYVNENFSSKLERI 680 (773)
T ss_pred HHHHHHHHHHHh---cCccceeHHHHHhhc--CCChhhHHHHHHHHHhhheeeeccccccCCCCceEEEcccccccccee
Confidence 455566666554 458999999999999 9999999999999999999888876 22344555544332
Q ss_pred ------ccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcC
Q 025493 105 ------EPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 105 ------ePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDg 178 (252)
+|-..- +| -=+-..+|.+=.-.|+..|.+-+..++...-.++.+.+-+.-=++...++.+|.+-+++|+--|
T Consensus 681 ki~~~~~~~~~q-~~-~~~h~~v~edR~~~lqA~IVRIMK~rk~l~H~~Lv~e~i~q~~~Rf~p~vsmvKr~Ie~LiEKe 758 (773)
T COG5647 681 KINYIAESECMQ-DN-LDTHETVEEDRQAELQACIVRIMKARKKLKHGDLVKEVIAQHKSRFEPKVSMVKRAIETLIEKE 758 (773)
T ss_pred eecccccchhhc-cc-hhhHHHHHHHHHHHHHHHHHHHHHHhccCcHHHHHHHHHHHhhccCCCCHHHHHHHHHHHHHHH
Confidence 111111 11 0111344555666777788888888888888888888776665788999999999999999999
Q ss_pred eeEEE
Q 025493 179 QIMEV 183 (252)
Q Consensus 179 kIE~v 183 (252)
-||+.
T Consensus 759 YLeR~ 763 (773)
T COG5647 759 YLERQ 763 (773)
T ss_pred HHHhc
Confidence 99875
No 174
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=72.12 E-value=48 Score=29.92 Aligned_cols=84 Identities=12% Similarity=0.199 Sum_probs=54.7
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccc--cCCeeeEEecccccCCCccCCcccc
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH--NKGKKHLMAVEFEPSKDISGGAWYS 117 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~--~~~rK~YmL~~lePs~eiTGG~wy~ 117 (252)
.|.-++.. ..++...||.+++ +++...+.+.|+.||.+|+|-..-.=. -+-.|+|-|. ++..+.-+ +.
T Consensus 15 ~il~lL~~---~g~~sa~elA~~L--gis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt--~~g~~~f~---~~ 84 (218)
T COG2345 15 RILELLKK---SGPVSADELAEEL--GISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLT--EKGREQFP---KR 84 (218)
T ss_pred HHHHHHhc---cCCccHHHHHHHh--CCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeec--ccchhhcc---hh
Confidence 44445544 3578899999999 999999999999999999998873222 2224566664 33333100 13
Q ss_pred CCcCCHHHHHHHHHHH
Q 025493 118 EGSLDTEFIKVVKSQC 133 (252)
Q Consensus 118 d~e~D~efV~~l~~~~ 133 (252)
.++|=..+++.|.+..
T Consensus 85 y~~l~~~~l~~l~~~~ 100 (218)
T COG2345 85 YGELALALLDALEETG 100 (218)
T ss_pred hHHHHHHHHHHHHHhc
Confidence 3455566666666554
No 175
>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=71.66 E-value=12 Score=29.39 Aligned_cols=54 Identities=9% Similarity=0.163 Sum_probs=44.1
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
+...++++|-.++.+|+.||++.+.+. -.++..-|..+|+.|+--|.|.+.+.+
T Consensus 4 ~E~~IM~~lW~~~~~t~~eI~~~l~~~----~~~~~sTv~t~L~rL~~Kg~l~~~~~g 57 (115)
T PF03965_consen 4 LELEIMEILWESGEATVREIHEALPEE----RSWAYSTVQTLLNRLVEKGFLTREKIG 57 (115)
T ss_dssp HHHHHHHHHHHHSSEEHHHHHHHHCTT----SS--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHHhc----cccchhHHHHHHHHHHhCCceeEeecC
Confidence 445678888888889999999999877 246889999999999999999987653
No 176
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=71.22 E-value=20 Score=25.22 Aligned_cols=46 Identities=22% Similarity=0.316 Sum_probs=40.4
Q ss_pred CChHHHHHHHHHHhhcC----CCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 34 LTDHERLIYDVIRSNKQ----DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag----~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
||+.|+.++..--+ .| ..++...||..++ |+..+.++..|+.-|+|
T Consensus 1 LT~~Q~e~L~~A~~-~GYfd~PR~~tl~elA~~l--gis~st~~~~LRrae~k 50 (53)
T PF04967_consen 1 LTDRQREILKAAYE-LGYFDVPRRITLEELAEEL--GISKSTVSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHHHHHHH-cCCCCCCCcCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 67888888888888 77 7899999999999 99999999999987764
No 177
>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=70.75 E-value=20 Score=25.93 Aligned_cols=66 Identities=6% Similarity=-0.038 Sum_probs=47.0
Q ss_pred HHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeeccc
Q 025493 134 LKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVS 205 (252)
Q Consensus 134 ~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~ 205 (252)
+..|.. +..+--+|.+.|...--.-..++...|-..|+.|+-+|.|+....... -...++.|+++.
T Consensus 2 L~~L~~-~~~~Gyei~~~l~~~~~~~~~i~~g~lY~~L~~Le~~gli~~~~~~~~-----~~~~rk~Y~iT~ 67 (75)
T PF03551_consen 2 LGLLSE-GPMHGYEIKQELEERTGGFWKISPGSLYPALKRLEEEGLIESRWEEEG-----NGRPRKYYRITE 67 (75)
T ss_dssp HHHHHH-S-EEHHHHHHHHHHCSTTTEETTHHHHHHHHHHHHHTTSEEEEEEEET-----TSSEEEEEEESH
T ss_pred hhhhcc-CCCcHHHHHHHHHHHhCCCcccChhHHHHHHHHHHhCCCEEEeeeccC-----CCCCCEEEEECH
Confidence 344544 567888999999987222368899999999999999999997664311 123467787653
No 178
>KOG0121 consensus Nuclear cap-binding protein complex, subunit CBP20 (RRM superfamily) [RNA processing and modification]
Probab=70.61 E-value=1.8 Score=36.46 Aligned_cols=44 Identities=20% Similarity=0.335 Sum_probs=35.0
Q ss_pred CccccCCcC---CHHHHHHHHHHHHHHhhhCC-CCCHHHHHHHHHHcC
Q 025493 113 GAWYSEGSL---DTEFIKVVKSQCLKQIIKLK-VATLEGISDSIKRSG 156 (252)
Q Consensus 113 G~wy~d~e~---D~efV~~l~~~~~~~i~~~~-~~T~~~I~~~i~~~~ 156 (252)
++.|-|+.| |.|+.+.++..|.-|+.+.+ |.|-++|++...++|
T Consensus 14 ~s~Yr~~~f~gt~~e~~~a~r~S~tvyVgNlSfyttEEqiyELFs~cG 61 (153)
T KOG0121|consen 14 LSAYRDRRFRGTDEEQLEALRKSCTVYVGNLSFYTTEEQIYELFSKCG 61 (153)
T ss_pred hhHHHHHHhcCchHHHHHHHhhcceEEEeeeeeeecHHHHHHHHHhcc
Confidence 446777655 68889999999998988876 566788888888887
No 179
>COG1693 Repressor of nif and glnA expression [Transcription]
Probab=70.60 E-value=5.5 Score=37.57 Aligned_cols=55 Identities=16% Similarity=0.283 Sum_probs=46.7
Q ss_pred CCChHHHHHHHHHHhhcC---CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 33 SLTDHERLIYDVIRSNKQ---DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag---~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
+|+.-+..|+.++++ |+ ..++-..+|+++ |-|+..+.+.=.||.|+.+||+++|.
T Consensus 3 ~~~rk~ieIl~il~e-sd~plgak~Ia~el~kR-Gy~igeRavRYhlk~lderglt~kvg 60 (325)
T COG1693 3 NLNRKLIEILRILAE-SDEPLGAKIIALELRKR-GYNIGERAVRYHLKKLDERGLTRKVG 60 (325)
T ss_pred hHHHHHHHHHHHHHh-cCCccchHHHHHHHHhc-ccchhHHHHHHHHHHHhhccchhhcc
Confidence 455667789999999 88 456777788887 56999999999999999999999986
No 180
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=70.10 E-value=9.5 Score=30.80 Aligned_cols=66 Identities=17% Similarity=0.128 Sum_probs=42.8
Q ss_pred HHHHHHHHHHhhcCCCcccHHH-HHHHhhc--CCChHHHHHHHHHHHhcCCeeeeeccc--cCCeeeEEecc
Q 025493 37 HERLIYDVIRSNKQDMGIWTRD-MKRELKV--NLPDNIVTKSIKSLQNKSLIKEVVNIH--NKGKKHLMAVE 103 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GIw~~d-ik~~~~~--~l~~~~l~k~lK~Le~k~lIK~vksv~--~~~rK~YmL~~ 103 (252)
-+..|+.++.. .-..|-.... +...++. ..+..+|-.+|+.||..|+|....-.. -+.||+|-+.+
T Consensus 10 l~~~iL~~L~~-~~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~g~~rk~Y~lTe 80 (138)
T COG1695 10 LELLILSLLSE-KPSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGGGPPRKYYRLTE 80 (138)
T ss_pred HHHHHHHHHhc-CCchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCCCCCceEEEECH
Confidence 45556666655 4444443322 3333310 277889999999999999999865433 35699998743
No 181
>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=69.50 E-value=12 Score=25.51 Aligned_cols=48 Identities=8% Similarity=0.182 Sum_probs=39.7
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
-.++.+|..++..|..+|.+++. ++..-+-.+++.|+-.|.|++....
T Consensus 6 ~~iL~~l~~~~~~~~~~la~~~~--------~~~~~~t~~i~~L~~~g~I~r~~~~ 53 (59)
T PF01047_consen 6 FRILRILYENGGITQSELAEKLG--------ISRSTVTRIIKRLEKKGLIERERDP 53 (59)
T ss_dssp HHHHHHHHHHSSEEHHHHHHHHT--------S-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHHcCCCCHHHHHHHHC--------CChhHHHHHHHHHHHCCCEEeccCC
Confidence 35677788888899999998875 5678899999999999999988753
No 182
>COG4738 Predicted transcriptional regulator [Transcription]
Probab=69.38 E-value=20 Score=29.52 Aligned_cols=64 Identities=22% Similarity=0.288 Sum_probs=47.7
Q ss_pred CChHHHHHHHHHHhhcC--------------CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc--ccCCe-
Q 025493 34 LTDHERLIYDVIRSNKQ--------------DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI--HNKGK- 96 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag--------------~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv--~~~~r- 96 (252)
|++.|..+-++... .| .+-+.+++|-..+ ||-|..|+=+.+-|-.+|.|.. .+- +.++|
T Consensus 9 l~E~e~~~ie~L~~-lgi~R~vA~tlv~L~~~~E~sS~~IE~~s--gLRQPEVSiAMr~Lre~gWV~~-R~eKKkGKGRP 84 (124)
T COG4738 9 LTEKEYEIIELLRI-LGIPRNVATTLVCLAKGDEASSREIERVS--GLRQPEVSIAMRYLRENGWVDE-REEKKKGKGRP 84 (124)
T ss_pred cchhHHHHHHHHHH-cCCCchHHHHHHHHhcCcchhhhhhHHhh--cCCCchhHHHHHHHHHccccch-HHhcccCCCCC
Confidence 66666666666555 43 4668899999999 9999999999999999999976 333 23333
Q ss_pred -eeEEe
Q 025493 97 -KHLMA 101 (252)
Q Consensus 97 -K~YmL 101 (252)
|.|-|
T Consensus 85 ik~Y~L 90 (124)
T COG4738 85 IKLYRL 90 (124)
T ss_pred ceEEEe
Confidence 66766
No 183
>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=69.11 E-value=5.7 Score=29.89 Aligned_cols=53 Identities=11% Similarity=0.125 Sum_probs=45.0
Q ss_pred CCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCe
Q 025493 28 NAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLI 85 (252)
Q Consensus 28 ~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lI 85 (252)
++....|++..+.+|.+-+. .+|...++|...+ +++.+.|...++.+++.+..
T Consensus 10 ~~~l~~l~~~~r~af~L~R~---~eGlS~kEIAe~L--GIS~~TVk~~l~~~~~~~~~ 62 (73)
T TIGR03879 10 AERLTWVDSLAEAAAALARE---EAGKTASEIAEEL--GRTEQTVRNHLKGETKAGGL 62 (73)
T ss_pred HHHHhcCCHHHHHHHHHHHH---HcCCCHHHHHHHH--CcCHHHHHHHHhcCcccchH
Confidence 34566899999999988765 4799999999999 99999999999998887643
No 184
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=68.81 E-value=21 Score=25.96 Aligned_cols=38 Identities=11% Similarity=0.390 Sum_probs=28.5
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCe
Q 025493 56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGK 96 (252)
Q Consensus 56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~r 96 (252)
...|..+. +++.+.+-.+|++||+-|+|-+ +|.--++-
T Consensus 7 as~iAd~~--GiTRSvIVNALRKleSaGvIes-rSlGmKGT 44 (61)
T PF08222_consen 7 ASKIADRV--GITRSVIVNALRKLESAGVIES-RSLGMKGT 44 (61)
T ss_dssp HHHHHHHH--T--HHHHHHHHHHHHHTTSEEE-EETTSS-E
T ss_pred HHHHHHHh--CccHHHHHHHHHHHHhcCceee-cccCCCce
Confidence 35677888 9999999999999999999997 55544443
No 185
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=68.64 E-value=17 Score=24.01 Aligned_cols=43 Identities=7% Similarity=0.109 Sum_probs=34.7
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 133 CLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 133 ~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
++.+|. .+..|..+|.+.+. ++...+..+|+.|+-+|.|+...
T Consensus 2 il~~l~-~~~~~~~~i~~~l~--------is~~~v~~~l~~L~~~g~i~~~~ 44 (66)
T smart00418 2 ILKLLA-EGELCVCELAEILG--------LSQSTVSHHLKKLREAGLVESRR 44 (66)
T ss_pred HHHHhh-cCCccHHHHHHHHC--------CCHHHHHHHHHHHHHCCCeeeee
Confidence 345565 67789999998873 67788999999999999998654
No 186
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=68.52 E-value=40 Score=31.69 Aligned_cols=140 Identities=17% Similarity=0.149 Sum_probs=88.8
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccC
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISG 112 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTG 112 (252)
.|..+-+-++..|.. +=-.||.+.+|.+.+| .++.+.+..+|..|-++++|+-+++ ++.-+|-.-+ |. +..+
T Consensus 7 ~~~~e~~~~~~~~~~-~~p~git~q~L~~~~p-~~~~~~~~salN~lLs~~~l~llr~---~~~l~yr~~d--~~-~a~~ 78 (297)
T KOG3233|consen 7 ALPVEIENILIQIVK-QIPEGITQQELQSEMP-QISATDRASALNILLSRGLLDLLRQ---NTGLVYRAKD--PK-SASK 78 (297)
T ss_pred cChHHHHHHHHHHHH-hccccccHHHHHHHcC-CCcHHHHHHHHHHHHhcCcchhhcc---CCcceEeccC--ch-hhcc
Confidence 355555556666667 7889999999999997 7999999999999999999988754 3333444322 22 2222
Q ss_pred CccccCCcCCHHHHHHHHHHHHHHhhhCC--CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCC
Q 025493 113 GAWYSEGSLDTEFIKVVKSQCLKQIIKLK--VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGE 190 (252)
Q Consensus 113 G~wy~d~e~D~efV~~l~~~~~~~i~~~~--~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~ 190 (252)
+. =.++ =.+.++.+|+..+ .+...+|.. +..|-...|..+|..|.--..|..|++.+.
T Consensus 79 ~~-~~e~---------eEk~vy~lIe~sg~~GIW~k~ik~--------ksnLp~~~v~K~LkSLEsKkLIKsVKsv~n-- 138 (297)
T KOG3233|consen 79 GK-GMEN---------EEKLVYSLIEESGNEGIWSKEIKR--------KSNLPQTVVNKILKSLESKKLIKSVKSVKN-- 138 (297)
T ss_pred cc-cCCh---------HHHHHHHHHHHcCCCceeeehhhh--------ccCCCHHHHHHHHHHHHHHHHHHHHHhhcC--
Confidence 21 0111 0123444554322 222222211 245777899999999999999988876542
Q ss_pred cccccCCcceeeccc
Q 025493 191 FTNIPVGKVCYKNVS 205 (252)
Q Consensus 191 f~~~~~g~~~YR~~~ 205 (252)
.++++|-+..
T Consensus 139 -----~~~KvYmLy~ 148 (297)
T KOG3233|consen 139 -----SRKKVYMLYD 148 (297)
T ss_pred -----CCceEEEEec
Confidence 2347776654
No 187
>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=67.90 E-value=25 Score=25.39 Aligned_cols=61 Identities=5% Similarity=0.054 Sum_probs=50.3
Q ss_pred HHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 124 EFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 124 efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+-...+..+|.+.+....-.+.+++...+.+.=-.....+..+|.+-|+.|+-.+-|++-.
T Consensus 4 ~R~~~I~AaIVrimK~~k~~~~~~L~~~v~~~l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~ 64 (68)
T PF10557_consen 4 DRKYQIDAAIVRIMKQEKKLSHDELINEVIEELKKRFPPSVSDIKKRIESLIEKEYIERDE 64 (68)
T ss_dssp HHHHHHHHHHHHHHHHSSEEEHHHHHHHHHHHTTTTS---HHHHHHHHHHHHHTTSEEEES
T ss_pred hhhhhhhhheehhhhhcCceeHHHHHHHHHHHhcCCcCCCHHHHHHHHHHHHHhhhhhcCC
Confidence 3446788899999999999999999999988765577899999999999999999999754
No 188
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=67.82 E-value=14 Score=31.39 Aligned_cols=44 Identities=18% Similarity=0.277 Sum_probs=39.5
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
..||+-|+.|+.++.+ |...++|-.++ ++..++|...++.+-.|
T Consensus 149 ~~Lt~rE~evl~~~~~-----G~s~~eIA~~l--~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 149 KRLSPKESEVLRLFAE-----GFLVTEIAKKL--NRSIKTISSQKKSAMMK 192 (216)
T ss_pred ccCCHHHHHHHHHHHC-----CCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence 4699999999999987 99999999999 99999998888877554
No 189
>PRK04217 hypothetical protein; Provisional
Probab=67.76 E-value=18 Score=29.23 Aligned_cols=44 Identities=14% Similarity=0.186 Sum_probs=36.6
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHH
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSL 79 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~L 79 (252)
....|+++|+.++.+... +|+..++|.+.+ +++.++|.+.|+..
T Consensus 39 p~~~Lt~eereai~l~~~----eGlS~~EIAk~L--GIS~sTV~r~L~RA 82 (110)
T PRK04217 39 PPIFMTYEEFEALRLVDY----EGLTQEEAGKRM--GVSRGTVWRALTSA 82 (110)
T ss_pred CcccCCHHHHHHHHHHHH----cCCCHHHHHHHH--CcCHHHHHHHHHHH
Confidence 367899999877666554 788999999999 99999999888764
No 190
>PRK11083 DNA-binding response regulator CreB; Provisional
Probab=67.44 E-value=19 Score=29.73 Aligned_cols=57 Identities=14% Similarity=0.025 Sum_probs=43.4
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCC---------hHHHHHHHHHHHhc----CCeeeeecc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLP---------DNIVTKSIKSLQNK----SLIKEVVNI 91 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~---------~~~l~k~lK~Le~k----~lIK~vksv 91 (252)
..||.-|..|+.++-+ ..++|...++|.... ... ...+.++.++|... ++|+.|..+
T Consensus 153 ~~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l--~~~~~~~~~~tv~~~i~~l~~Kl~~~~~~~~~i~t~~g~ 222 (228)
T PRK11083 153 LTLTRYEFLLLKTLLL-SPGRVFSRQQLMDIV--WEDAQDSYDRTVDTHIKTLRAKLRAINPDLSPINTHRGM 222 (228)
T ss_pred eecCHHHHHHHHHHHh-CCCceECHHHHHHHh--cCCCCCCCccCHHHHHHHHHHHhccCCCCCCeEEEeCce
Confidence 4699999999999999 889999999999998 654 44566677777532 346665443
No 191
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=67.39 E-value=8 Score=32.19 Aligned_cols=45 Identities=20% Similarity=0.234 Sum_probs=35.3
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
..|...+-. .| -+--.||...+ +|+.++|.|+|-.|...++|+..
T Consensus 4 ~~v~d~L~~-~~--~~~dedLa~~l--~i~~n~vRkiL~~L~ed~~~~~~ 48 (147)
T smart00531 4 FLVLDALMR-NG--CVTEEDLAELL--GIKQKQLRKILYLLYDEKLIKID 48 (147)
T ss_pred EeehHHHHh-cC--CcCHHHHHHHh--CCCHHHHHHHHHHHHhhhcchhh
Confidence 345555544 44 47788999999 99999999999999998887653
No 192
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=67.25 E-value=16 Score=26.52 Aligned_cols=47 Identities=17% Similarity=0.426 Sum_probs=34.4
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeee
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.|+.++.+ ++ .-+-.+.|...++ .++...+|.+.|+.||..|+++.+
T Consensus 2 ~IL~~L~~-~~-~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~ 51 (66)
T PF08461_consen 2 FILRILAE-SD-KPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKV 51 (66)
T ss_pred HHHHHHHH-cC-CCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCcccc
Confidence 46777777 54 3466667766652 256678999999999999998863
No 193
>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=67.08 E-value=20 Score=26.30 Aligned_cols=53 Identities=11% Similarity=0.190 Sum_probs=38.1
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM 100 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym 100 (252)
+-++|.+ .| .+.+.-|.++. .+.-+.-.+++..||..|+|-+-... +.|+|++
T Consensus 11 a~~~V~~-~~--~~S~S~lQR~~--rIGynrAariid~LE~~GiVs~~~~~--~~R~Vl~ 63 (65)
T PF09397_consen 11 AVEFVIE-EG--KASISLLQRKF--RIGYNRAARIIDQLEEEGIVSPANGS--KPREVLV 63 (65)
T ss_dssp HHHHHHH-CT--CECHHHHHHHH--T--HHHHHHHHHHHHHCTSBE---TT--SEEEB-S
T ss_pred HHHHHHH-cC--CccHHHHHHHh--CCCHHHHHHHHHHHHHCCCCCCCCCC--CCCeecc
Confidence 4445556 44 58999999999 99999999999999999999987655 4577764
No 194
>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=67.00 E-value=29 Score=30.70 Aligned_cols=100 Identities=11% Similarity=0.079 Sum_probs=67.0
Q ss_pred ccHHHHHH-----Hhhc-CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHH
Q 025493 54 IWTRDMKR-----ELKV-NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIK 127 (252)
Q Consensus 54 Iw~~dik~-----~~~~-~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~ 127 (252)
|--.|+.. +.|+ .+++..+-++++.|+..|+==.+..+.. ++ .|+- ..|..| .+
T Consensus 114 i~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~g~~l~~~~s-g~-~vv~--s~~~~e----------------~~ 173 (223)
T PF04157_consen 114 ISLSDLYCRYNRARGGSELISPEDILRACKLLEVLGLGFRLRKFGS-GV-KVVQ--SVPYSE----------------LS 173 (223)
T ss_dssp EEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTSSEEEEEETT-TE-EEEE--CST-CH----------------H-
T ss_pred EEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCCCeEEEEeCC-Cc-EEEE--eCCchh----------------hh
Confidence 45555544 3233 5799999999999999998655555542 33 3332 133111 13
Q ss_pred HHHHHHHHHh--hhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeE
Q 025493 128 VVKSQCLKQI--IKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIM 181 (252)
Q Consensus 128 ~l~~~~~~~i--~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE 181 (252)
.....++.++ ...+++|+.++.+.+. .+..=.++.|+.|+-+|.+-
T Consensus 174 ~~~~~il~~~~~~~~g~vt~~~l~~~~~--------ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 174 KDQSRILELAEEENGGGVTASELAEKLG--------WSVERAKEALEELEREGLLW 221 (223)
T ss_dssp HHHHHHHHHH--TTTSEEEHHHHHHHHT--------B-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHhhcCCCCCHHHHHHHhC--------CCHHHHHHHHHHHHhCCCEe
Confidence 6677888888 8889999999998765 77888899999999999764
No 195
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=66.96 E-value=23 Score=35.59 Aligned_cols=61 Identities=20% Similarity=0.217 Sum_probs=48.0
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE 103 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~ 103 (252)
-..|..|+..+++ . +..+-+.+|..++ ++....|..++++|+++++|+.-.. ..+.|-|.+
T Consensus 5 ~~~e~~iL~~l~~-~-~~~~~~~~la~~~--~~~~~~v~~~~~~L~~kg~v~~~~~----~~~~~~LT~ 65 (494)
T PTZ00326 5 ELEENTILSKLES-E-NEIVNSLALAESL--NIDHQKVVGAIKSLESANYITTEMK----KSNTWTLTE 65 (494)
T ss_pred hHHHHHHHHHHHh-c-CCCCCHHHHHHHc--CCCHHHHHHHHHHHHhCCCEEEEEE----EEEEEEECH
Confidence 3467788888876 4 3458888999999 9999999999999999999887543 355676654
No 196
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator 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.
Probab=66.80 E-value=12 Score=34.54 Aligned_cols=51 Identities=10% Similarity=0.221 Sum_probs=41.5
Q ss_pred CCCcccHHHHHHHhhc-CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493 50 QDMGIWTRDMKRELKV-NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE 103 (252)
Q Consensus 50 g~~GIw~~dik~~~~~-~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~ 103 (252)
.+.-||.++|-.=... ++....+.-+|..|+++|+|.+.+ ...|+.|-|.+
T Consensus 14 ~gg~i~~~~Li~l~~~~gi~~~~vr~al~RL~~~G~l~~~~---~grr~~Y~LT~ 65 (280)
T TIGR02277 14 RGGAIWLGSLIEFLAGLGINERLVRTAVSRLVAQGWLQSER---KGRRSFYSLTD 65 (280)
T ss_pred CCCceeHHHHHHHHHhcCCCcchHHHHHHHHHHCCCEEeee---cCCCCEEEECH
Confidence 3447999999886544 999999999999999999999963 35678887754
No 197
>PRK09483 response regulator; Provisional
Probab=66.55 E-value=19 Score=29.66 Aligned_cols=45 Identities=24% Similarity=0.263 Sum_probs=39.7
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
...||+-|+.|+.++.+ |.-.++|..++ ++..++|...++.+-.|
T Consensus 146 ~~~Lt~rE~~vl~~~~~-----G~~~~~Ia~~l--~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 146 FASLSERELQIMLMITK-----GQKVNEISEQL--NLSPKTVNSYRYRMFSK 190 (217)
T ss_pred ccccCHHHHHHHHHHHC-----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 46799999999999865 88999999999 99999999999888655
No 198
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=66.37 E-value=26 Score=22.11 Aligned_cols=44 Identities=16% Similarity=0.215 Sum_probs=35.8
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHH
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQ 80 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le 80 (252)
...|+++++.++.+..- .|.-.++|..++ |++...+.+.++...
T Consensus 8 ~~~l~~~~~~~~~~~~~----~~~~~~~ia~~~--~~s~~~i~~~~~~~~ 51 (55)
T cd06171 8 LDKLPEREREVILLRFG----EGLSYEEIAEIL--GISRSTVRQRLHRAL 51 (55)
T ss_pred HHhCCHHHHHHHHHHHh----cCCCHHHHHHHH--CcCHHHHHHHHHHHH
Confidence 44688888888766653 568899999999 999999999988754
No 199
>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=66.13 E-value=37 Score=25.08 Aligned_cols=35 Identities=9% Similarity=0.216 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 142 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 142 ~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
.+|.++|++.+ .++...+++|++.|+-.|.|+..+
T Consensus 25 ~~s~~eiA~~~--------~i~~~~l~kil~~L~~~Gli~s~~ 59 (83)
T PF02082_consen 25 PVSSKEIAERL--------GISPSYLRKILQKLKKAGLIESSR 59 (83)
T ss_dssp -BEHHHHHHHH--------TS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CCCHHHHHHHH--------CcCHHHHHHHHHHHhhCCeeEecC
Confidence 48999999854 477899999999999999998765
No 200
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=66.09 E-value=55 Score=24.68 Aligned_cols=84 Identities=15% Similarity=0.227 Sum_probs=50.2
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHH
Q 025493 54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQC 133 (252)
Q Consensus 54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~ 133 (252)
....++.+.+ +++.++| +..|.+|+|.+...-. .+.+.| +.+=|..|+.+
T Consensus 2 ~ti~evA~~~--gvs~~tL----R~ye~~Gll~p~r~~~-~g~R~Y----------------------s~~dv~~l~~I- 51 (88)
T cd01105 2 IGIGEVSKLT--GVSPRQL----RYWEEKGLIKSIRSDG-GGQRKY----------------------SLADVDRLLVI- 51 (88)
T ss_pred cCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCccCC-CCceec----------------------CHHHHHHHHHH-
Confidence 4567888888 8887765 4669999988643322 144444 22333333332
Q ss_pred HHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcC
Q 025493 134 LKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 134 ~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDg 178 (252)
..++. ...|+++|.+.+...+ +...++..|+.+|
T Consensus 52 -~~Lr~-~G~sl~~i~~~l~~~~---------~~~~~~~~~~~~~ 85 (88)
T cd01105 52 -KELLD-EGFTLAAAVEKLRRRR---------VQAEVRRRLMKDG 85 (88)
T ss_pred -HHHHH-CCCCHHHHHHHHHHcc---------CHHHHHHHHHHHh
Confidence 23344 5678999999998554 4444555555443
No 201
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=65.61 E-value=14 Score=32.13 Aligned_cols=43 Identities=19% Similarity=0.269 Sum_probs=39.1
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
.||+-|+.|++++.+ |...++|..++ ++..++|...++.+-.|
T Consensus 137 ~LT~RE~eVL~lla~-----G~snkeIA~~L--~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 137 SLSRTESSMLRMWMA-----GQGTIQISDQM--NIKAKTVSSHKGNIKRK 179 (207)
T ss_pred cCCHHHHHHHHHHHc-----CCCHHHHHHHc--CCCHHHHHHHHHHHHHH
Confidence 499999999999999 99999999999 99999999888887544
No 202
>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=65.51 E-value=20 Score=24.01 Aligned_cols=42 Identities=14% Similarity=0.282 Sum_probs=31.9
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKS 78 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~ 78 (252)
+..|++.++.|+.+..- .|...++|...+ |++.+.+.+.|..
T Consensus 8 l~~L~~~~r~i~~l~~~----~g~s~~eIa~~l--~~s~~~v~~~l~r 49 (54)
T PF08281_consen 8 LAQLPERQREIFLLRYF----QGMSYAEIAEIL--GISESTVKRRLRR 49 (54)
T ss_dssp HHCS-HHHHHHHHHHHT----S---HHHHHHHC--TS-HHHHHHHHHH
T ss_pred HHCCCHHHHHHHHHHHH----HCcCHHHHHHHH--CcCHHHHHHHHHH
Confidence 45799999999999888 789999999999 9999988877654
No 203
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=65.44 E-value=36 Score=31.55 Aligned_cols=52 Identities=10% Similarity=0.174 Sum_probs=40.8
Q ss_pred HHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 124 EFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 124 efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
.+-..+|-++++.|.+++...+.||++.+ .|...-+..=+++|+--|.|+..
T Consensus 19 alaS~vRv~Il~lL~~k~plNvneiAe~l--------gLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 19 ALASKVRVAILQLLHRKGPLNVNEIAEAL--------GLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHHhCCCCHHHHHHHh--------CCchhhhhhhHHHHHhcCceeee
Confidence 44556777899999999999999999865 35555666668899999999754
No 204
>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=65.40 E-value=21 Score=30.89 Aligned_cols=47 Identities=15% Similarity=0.242 Sum_probs=41.1
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
++.++.+|..++.+|..+|++.+ .++..-|.+.|+.|+-+|.|++..
T Consensus 3 r~~IL~~L~~~~~~t~~eLA~~l--------gis~~tV~~~L~~Le~~GlV~r~~ 49 (203)
T TIGR02702 3 KEDILSYLLKQGQATAAALAEAL--------AISPQAVRRHLKDLETEGLIEYEA 49 (203)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEEee
Confidence 56788889888889999999987 367889999999999999999874
No 205
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=65.39 E-value=95 Score=27.18 Aligned_cols=126 Identities=16% Similarity=0.103 Sum_probs=71.7
Q ss_pred HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc----CCeeeeeccccCCeeeEEecccccCCCccC
Q 025493 37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK----SLIKEVVNIHNKGKKHLMAVEFEPSKDISG 112 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k----~lIK~vksv~~~~rK~YmL~~lePs~eiTG 112 (252)
-...|-.++.. ||.-|+..++|.+-+ ++....+.++|..|..+ +--=++..+.. +=+++.-.++.+-..--.
T Consensus 5 ~~~~iEA~LF~-sg~pgls~~~La~~l--~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~-~y~l~tk~e~~~~v~~~~ 80 (188)
T PRK00135 5 YKSIIEALLFV-SGEEGLSLEQLAEIL--ELEPTEVQQLLEELQEKYEGDDRGLKLIEFND-VYKLVTKEENADYLQKLV 80 (188)
T ss_pred HHHHHHHHHHH-cCCCCCCHHHHHHHH--CCCHHHHHHHHHHHHHHHhhCCCCEEEEEECC-EEEEEEcHHHHHHHHHHh
Confidence 45678888888 999999999999999 99999999999999442 22122222221 111111111111100000
Q ss_pred CccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 113 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 113 G~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
+.. ....+.....+ ++..|..++.+|-.||.+-- |++ ...+|+.|+-.|.|++.
T Consensus 81 ~~~-~~~~LS~aaLE-----tLaiIay~qPiTr~eI~~ir---Gv~--------~~~ii~~L~~~gLI~e~ 134 (188)
T PRK00135 81 KTP-IKQSLSQAALE-----VLAIIAYKQPITRIEIDEIR---GVN--------SDGALQTLLAKGLIKEV 134 (188)
T ss_pred ccc-ccCCCCHHHHH-----HHHHHHHcCCcCHHHHHHHH---CCC--------HHHHHHHHHHCCCeEEc
Confidence 000 00122222222 23445556777777776533 322 17889999999999875
No 206
>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=65.30 E-value=25 Score=25.10 Aligned_cols=44 Identities=20% Similarity=0.288 Sum_probs=33.7
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.|+..+-+ .| ....++|-+.+ +|+.+++.++|-.|.+.+++.=.
T Consensus 17 ~V~~~Ll~-~G--~ltl~~i~~~t--~l~~~~Vk~~L~~LiQh~~v~y~ 60 (62)
T PF08221_consen 17 KVGEVLLS-RG--RLTLREIVRRT--GLSPKQVKKALVVLIQHNLVQYF 60 (62)
T ss_dssp HHHHHHHH-C---SEEHHHHHHHH--T--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHH-cC--CcCHHHHHHHh--CCCHHHHHHHHHHHHHcCCeeee
Confidence 45666666 55 45689999999 99999999999999999998643
No 207
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=65.28 E-value=18 Score=32.15 Aligned_cols=56 Identities=23% Similarity=0.375 Sum_probs=44.6
Q ss_pred HHHHHHHhhcCCCcccH--------HHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493 40 LIYDVIRSNKQDMGIWT--------RDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE 103 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~--------~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~ 103 (252)
.|++.|++ .=..|.|. ++|..+. |....+|.|+|+.|++.|+|... .++=.|+...
T Consensus 11 qI~~~i~~-~I~~G~~~~G~~LPsE~eLa~~f--~VSR~TvRkAL~~L~~eGli~r~-----~G~GtfV~~~ 74 (236)
T COG2188 11 QIAEDIRQ-RIESGELPPGDKLPSERELAEQF--GVSRMTVRKALDELVEEGLIVRR-----QGKGTFVASP 74 (236)
T ss_pred HHHHHHHH-HHHhCCCCCCCCCCCHHHHHHHH--CCcHHHHHHHHHHHHHCCcEEEE-----ecCeeEEcCc
Confidence 56666666 66667775 6899999 99999999999999999999997 3566676644
No 208
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=65.12 E-value=24 Score=30.56 Aligned_cols=44 Identities=18% Similarity=0.139 Sum_probs=34.6
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEE
Q 025493 131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
..++..|.+++..|.++++.-+ .++..+|+++|..|.-||.|..
T Consensus 25 ~~Vl~~L~~~g~~tdeeLA~~L--------gi~~~~VRk~L~~L~e~gLv~~ 68 (178)
T PRK06266 25 FEVLKALIKKGEVTDEEIAEQT--------GIKLNTVRKILYKLYDARLADY 68 (178)
T ss_pred hHHHHHHHHcCCcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCeEE
Confidence 3455556667777777777765 4789999999999999999983
No 209
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=64.39 E-value=19 Score=31.61 Aligned_cols=49 Identities=20% Similarity=0.298 Sum_probs=41.3
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
+|-++|....-++++-..+|.+++ ||..+.++|+|=+|...+.|..+.+
T Consensus 14 lv~~~~~~l~~~~~~~a~~i~~~l--~~~k~~vNr~LY~l~~~~~v~~~~~ 62 (183)
T PHA03103 14 LVKKEVKNLGLGEGITAIEISRKL--NIEKSEVNKQLYKLQREGMVYMSDS 62 (183)
T ss_pred HHHHHHHHhccCCCccHHHHHHHh--CCCHHHHHHHHHHHHhcCceecCCC
Confidence 566667773345999999999999 9999999999999999998877643
No 210
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=64.39 E-value=25 Score=25.71 Aligned_cols=44 Identities=11% Similarity=0.173 Sum_probs=36.7
Q ss_pred HHHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 132 QCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 132 ~~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
.++.+|... +..|+.||++.+ .++..-+.++|+.|+-.|.|++.
T Consensus 9 ~Il~~l~~~~~~~t~~~ia~~l--------~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 9 AVLRALAEEPGGLTLAELAERL--------GLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred HHHHHHHhCCCCcCHHHHHHHh--------CCCHHHHHHHHHHHHHCCCeeec
Confidence 356677665 789999999887 46789999999999999999875
No 211
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=64.21 E-value=1.8e+02 Score=29.95 Aligned_cols=115 Identities=10% Similarity=0.151 Sum_probs=89.8
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDI 110 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~ei 110 (252)
...+++++..+.+.|++...-.=-|.+||-..+ +++...+..+|+.|...|.+-++. ..+|
T Consensus 484 ~~~~~~~~~~~~~~l~~~~~~~p~~~~~~~~~l--~~~~~~~~~~l~~l~~~g~lv~l~------~~~~----------- 544 (614)
T PRK10512 484 KAGFSEEQQALWQKAEPLFGDEPWWVRDLAKET--GTDEQAMRLTLRQAAQQGIITAIV------KDRY----------- 544 (614)
T ss_pred CCCCCHHHHHHHHHHHHHHhcCCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec------CCEE-----------
Confidence 345788888888877774556678899999999 999999999999999988777663 2344
Q ss_pred cCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEE
Q 025493 111 SGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 111 TGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
|+.+.++.+.+.+..+++.++..|+.+..+.+. +|-.-.-.+|+-|=..|...+
T Consensus 545 ----------~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~g--------~sRK~~i~lLE~~D~~~~T~r 598 (614)
T PRK10512 545 ----------YRNDRIVQFANMIRELDQECGSTCAADFRDRLG--------VGRKLAIQILEYFDRIGFTRR 598 (614)
T ss_pred ----------ECHHHHHHHHHHHHHHHhhCCcEeHHHHHHHhC--------ccHHHHHHHHHHhccCCCEEE
Confidence 356788999999999999999999999888773 445666677777766665544
No 212
>PF07574 SMC_Nse1: Nse1 non-SMC component of SMC5-6 complex; InterPro: IPR011513 Saccharomyces cerevisiae Nse1 (Q07913 from SWISSPROT) forms part of a complex with SMC5-SMC6. This non-structural maintenance of chromosomes (SMC) complex plays an essential role in genomic stability, being involved in DNA repair and DNA metabolism [, ]. It is conserved in eukaryotes from yeast to human.; PDB: 3NW0_A.
Probab=64.18 E-value=20 Score=31.25 Aligned_cols=94 Identities=14% Similarity=0.145 Sum_probs=50.1
Q ss_pred eeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCC-H--HHHHHHHHHcCCc---
Q 025493 85 IKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVAT-L--EGISDSIKRSGAF--- 158 (252)
Q Consensus 85 IK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T-~--~~I~~~i~~~~i~--- 158 (252)
|+.++.=...++.+|.+.++.+++..--++=|+..| |+-++..+-..+...+..- . .+ ...++...-.
T Consensus 64 Ir~~~~~q~~g~~~y~lVN~~~D~~sklaT~ys~~E-----i~ffK~lle~I~~~~~~~~~~~~~~-~~~~~~~~~i~~~ 137 (200)
T PF07574_consen 64 IRRIRDGQPDGERYYALVNTSSDEISKLATTYSPNE-----IAFFKKLLEEIVESENTSRSESASS-IMALNEVQAIKLK 137 (200)
T ss_dssp EEEEE--TTT--EEEEEEESSS-TTHHHHTTS-HHH-----HHHHHHHHHHHHHSSSS-EEH-----HHHHGGGTT-SSS
T ss_pred EEEEeccCCCCCEEEEEEeCCCCHHHHhcCCCCHHH-----HHHHHHHHHHHHhCCCCceehhhHH-HHHHHHHHHHHHh
Confidence 444444122689999999999998877776666555 4555555555555443321 1 11 2222222111
Q ss_pred -----------------------ceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 159 -----------------------KVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 159 -----------------------~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
...|+..+++++|+.||-||=+++.+
T Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~~~~L~~~eae~lL~~lv~~gWl~~s~ 186 (200)
T PF07574_consen 138 RPGDPSQWTQGVSYAGGSTQLAQDKGLSKSEAESLLDRLVEDGWLYRSR 186 (200)
T ss_dssp ---H-------------------------HHHHHHHHHHHHTTSE-EEE
T ss_pred ccCcccccccccccccccccccccccchHHHHHHHHHHHHHCCCceeCC
Confidence 13588899999999999999887754
No 213
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=63.90 E-value=19 Score=31.92 Aligned_cols=46 Identities=20% Similarity=0.272 Sum_probs=39.5
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
..+.||+-|+.|+.+|.+ |...++|..++ ++..++|...++.+-.|
T Consensus 130 ~~~~LSpRErEVLrLLAq-----GkTnKEIAe~L--~IS~rTVkth~srImkK 175 (198)
T PRK15201 130 TTRHFSVTERHLLKLIAS-----GYHLSETAALL--SLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCCCCHHHHHHHHHHHC-----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 345699999999999998 99999999999 99999998877766443
No 214
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=63.74 E-value=21 Score=35.90 Aligned_cols=59 Identities=15% Similarity=0.130 Sum_probs=45.6
Q ss_pred HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecc
Q 025493 37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVE 103 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~ 103 (252)
.|..|+..+.+ .+. .+-+.+|..++ ++....|..++++|+++++|+--.. ..+.|-|.+
T Consensus 4 ~e~~iL~~l~~-~~~-~~~~~~la~~~--g~~~~~v~~~~~~L~~kg~v~~~~~----~~~~~~LT~ 62 (492)
T PLN02853 4 AEEALLGALSN-NEE-ISDSGQFAASH--GLDHNEVVGVIKSLHGFRYVDAQDI----KRETWVLTE 62 (492)
T ss_pred HHHHHHHHHHh-cCC-CCCHHHHHHHc--CCCHHHHHHHHHHHHhCCCEEEEEE----EEEEEEECH
Confidence 46777777766 432 26888999999 9999999999999999999887533 355676654
No 215
>TIGR03433 padR_acidobact transcriptional regulator, Acidobacterial, PadR-family. Members of this protein family are putative transcriptional regulators of the PadR family, as found in species of the Acidobacteria. This family of proteins has expanded greatly in this lineage, and where it regularly is found in the vicinity of a putative transporter protein
Probab=63.57 E-value=42 Score=25.87 Aligned_cols=72 Identities=11% Similarity=0.058 Sum_probs=51.4
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccC
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSK 206 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~ 206 (252)
+.-.++..|. .+..+--||.+.|.+..-....++...|-.+|+.|+-+|.|+.......+ ...++.|.++..
T Consensus 5 l~~~iL~~L~-~~~~~GYei~~~l~~~~~~~~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~-----~~~rk~y~iT~~ 76 (100)
T TIGR03433 5 LDLLILKTLS-LGPLHGYGIAQRIQQISEDVLQVEEGSLYPALHRLERRGWIAAEWGESEN-----NRRAKFYRLTAA 76 (100)
T ss_pred HHHHHHHHHh-cCCCCHHHHHHHHHHHcCCccccCCCcHHHHHHHHHHCCCeEEEeeecCC-----CCCceEEEECHH
Confidence 4456677776 45678899999999876445788899999999999999999984221110 123467876543
No 216
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=63.26 E-value=1e+02 Score=27.85 Aligned_cols=119 Identities=9% Similarity=0.145 Sum_probs=81.4
Q ss_pred HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccc
Q 025493 37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWY 116 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy 116 (252)
-.+.|++++.+ . .=+-..||-..+ +....+|.|=|..||++|+++++-.--. -|+....- ++-
T Consensus 6 R~~~Il~~l~~-~--g~v~v~eLa~~~--~VS~~TIRRDL~~Le~~g~l~R~hGGa~-----------~~~~~~~~-~~~ 68 (253)
T COG1349 6 RHQKILELLKE-K--GKVSVEELAELF--GVSEMTIRRDLNELEEQGLLLRVHGGAV-----------LPDSESEY-PFS 68 (253)
T ss_pred HHHHHHHHHHH-c--CcEEHHHHHHHh--CCCHHHHHHhHHHHHHCCcEEEEeCCEe-----------cCCCcccc-cHH
Confidence 35678888888 4 458899999999 9999999999999999999999642211 01100000 333
Q ss_pred cCCcCCHHHHHHHHHHHHHHhhhC------CCCCHHHHHHHHHHcC-CcceecCHHHHHHHHH
Q 025493 117 SEGSLDTEFIKVVKSQCLKQIIKL------KVATLEGISDSIKRSG-AFKVDLTKQQIEEIVR 172 (252)
Q Consensus 117 ~d~e~D~efV~~l~~~~~~~i~~~------~~~T~~~I~~~i~~~~-i~~~~Ls~~di~~IL~ 172 (252)
.......+-=..+.+....+|... ...|..+++++|.+.. ++=+.-+..-+..+.+
T Consensus 69 ~r~~~~~~eK~~IA~~Aa~lI~~g~~ifld~GTT~~~la~~L~~~~~ltviTNsl~ia~~l~~ 131 (253)
T COG1349 69 ERKALNTEEKRAIAKAAATLIEDGDTIFLDAGTTTLALARALPDDNNLTVITNSLNIAAALLE 131 (253)
T ss_pred HHHHhhHHHHHHHHHHHHhhCCCCCEEEECCCcHHHHHHHHhCcCCCeEEEeCCHHHHHHHHh
Confidence 444555555666666777777643 5789999999999665 5555555554544443
No 217
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=62.79 E-value=22 Score=29.18 Aligned_cols=56 Identities=18% Similarity=0.281 Sum_probs=43.3
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcC-----CChHHHHHHHHHHHhc---CCeeeeecc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVN-----LPDNIVTKSIKSLQNK---SLIKEVVNI 91 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~-----l~~~~l~k~lK~Le~k---~lIK~vksv 91 (252)
.||+-|..|+.++.+ ..+++...++|..+. . ...++|...++.|-+| .+|+.|..+
T Consensus 149 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~l--~~~~~~~~~~tv~~~i~~lr~Kl~~~~i~t~~g~ 212 (219)
T PRK10336 149 TLKPKEFALLELLMR-NAGRVLPRKLIEEKL--YTWDEEVTSNAVEVHVHHLRRKLGSDFIRTVHGI 212 (219)
T ss_pred ecCHHHHHHHHHHHh-CCCccCcHHHHHHHh--cCCCCCCCccCHHHHHHHHHHhcCCCcEEEecCc
Confidence 599999999999999 899999999999998 5 6666666666555433 456666554
No 218
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=62.45 E-value=22 Score=32.94 Aligned_cols=46 Identities=17% Similarity=0.161 Sum_probs=38.1
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCC-eeee
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL-IKEV 88 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l-IK~v 88 (252)
++.|+.++.+ +..+...+|..+. +++.+.|.|.|+.|++.|+ |.+.
T Consensus 6 ~~~il~~L~~---~~~~s~~~LA~~l--gvsr~tV~~~l~~L~~~G~~i~~~ 52 (319)
T PRK11886 6 MLQLLSLLAD---GDFHSGEQLGEEL--GISRAAIWKHIQTLEEWGLDIFSV 52 (319)
T ss_pred HHHHHHHHHc---CCCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCceEEe
Confidence 4456666654 4677888999999 9999999999999999999 7765
No 219
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=62.20 E-value=20 Score=32.39 Aligned_cols=49 Identities=10% Similarity=0.176 Sum_probs=43.6
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
.=++.++.+|.+++.+|+.|+.+.+ .+|.+-|++=|+.|.-.|+|.++.
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l--------~vS~~TiRRdL~~Le~~g~l~r~~ 53 (252)
T PRK10906 5 QRHDAIIELVKQQGYVSTEELVEHF--------SVSPQTIRRDLNDLAEQNKILRHH 53 (252)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHh--------CCCHHHHHHHHHHHHHCCCEEEec
Confidence 4567899999999999999999966 578999999999999999999875
No 220
>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=61.61 E-value=43 Score=23.07 Aligned_cols=49 Identities=10% Similarity=0.213 Sum_probs=36.8
Q ss_pred HHHHHHHhh-hCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 130 KSQCLKQII-KLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 130 ~~~~~~~i~-~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
.-.++.+|. ..+.+|..+|.+.+. ++...+..+|+.|+-.|.|++....
T Consensus 5 q~~vL~~l~~~~~~~t~~~l~~~~~--------~~~~~vs~~i~~L~~~glv~~~~~~ 54 (68)
T PF13463_consen 5 QWQVLRALAHSDGPMTQSDLAERLG--------ISKSTVSRIIKKLEEKGLVEKERDP 54 (68)
T ss_dssp HHHHHHHHT--TS-BEHHHHHHHTT----------HHHHHHHHHHHHHTTSEEEEEES
T ss_pred HHHHHHHHHccCCCcCHHHHHHHHC--------cCHHHHHHHHHHHHHCCCEEecCCC
Confidence 345677777 778889999988754 5678899999999999999988754
No 221
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=61.43 E-value=49 Score=24.28 Aligned_cols=49 Identities=27% Similarity=0.398 Sum_probs=38.6
Q ss_pred hhhCCCCCHHHHHHHHHHcCCcceecCH----HHHHHHHHHHhhcCeeEEEeeCC
Q 025493 137 IIKLKVATLEGISDSIKRSGAFKVDLTK----QQIEEIVRAVVLDNQIMEVKSNG 187 (252)
Q Consensus 137 i~~~~~~T~~~I~~~i~~~~i~~~~Ls~----~di~~IL~tLVyDgkIE~v~~~g 187 (252)
+.....+|...|..||...- .+.+.. ..+..-|..+|-.|.++++...|
T Consensus 16 l~er~GsS~~aI~kyI~~~y--~~~~~~~~~~~~l~~aLk~~v~~G~l~~~kg~G 68 (77)
T PF00538_consen 16 LKERKGSSLQAIKKYIKAKY--KVDLNPANFKSRLKRALKRGVEKGKLVQVKGKG 68 (77)
T ss_dssp CCSSSSEEHHHHHHHHHHHS--SCCCCHTTHHHHHHHHHHHHHHCTSEEECSCST
T ss_pred cCCCCCCCHHHHHHHHHHhc--CcCCChHHHHHHHHHHHHHHHHCCcEEeecccC
Confidence 34567899999999999865 344554 46888899999999999988554
No 222
>PRK10736 hypothetical protein; Provisional
Probab=61.20 E-value=16 Score=35.38 Aligned_cols=50 Identities=10% Similarity=-0.044 Sum_probs=43.0
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.++.++..||+.+.. .++-..+|-.++ +|+..++.-+|-.||-+|+|.+.
T Consensus 305 ~~~~~~~~v~~~l~~----~~~~iD~L~~~~--~l~~~~v~~~L~~LEl~G~v~~~ 354 (374)
T PRK10736 305 EVALPFPELLANVGD----EVTPVDVVAERA--GQPVPEVVTQLLELELAGWIAAV 354 (374)
T ss_pred cccchHHHHHHhcCC----CCCCHHHHHHHH--CcCHHHHHHHHHHHHhCCcEEEc
Confidence 466677788887754 356789999999 99999999999999999999986
No 223
>TIGR02325 C_P_lyase_phnF phosphonates metabolism transcriptional regulator PhnF. All members of the seed alignment for this family are predicted helix-turn-helix transcriptional regulatory proteins of the broader gntR and are found associated with genes for the import and degradation of phosphonates and/or related compounds (e.g. phosphonites) with a direct C-P bond.
Probab=60.84 E-value=13 Score=32.29 Aligned_cols=40 Identities=15% Similarity=0.339 Sum_probs=34.0
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
.-++|..+. |....+|.|+|..|++.|+|.+.+ ++=.|+.
T Consensus 34 sE~eLa~~~--~VSR~TvR~Al~~L~~eGli~r~~-----G~GtfV~ 73 (238)
T TIGR02325 34 AEMQLAERF--GVNRHTVRRAIAALVERGLLRAEQ-----GRGTFVA 73 (238)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec-----CCEEEEC
Confidence 357999999 999999999999999999999973 4555654
No 224
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=60.76 E-value=16 Score=32.15 Aligned_cols=54 Identities=13% Similarity=0.288 Sum_probs=42.1
Q ss_pred HHHHHHHhhcCCCcccH--------HHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 40 LIYDVIRSNKQDMGIWT--------RDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~--------~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
.|++.|++ .=..|.|. ++|..+. |....+|.++|..|++.|||.+. ++|=.|+.
T Consensus 13 qI~~~i~~-~I~~G~~~~g~kLPsE~eLa~~~--~VSR~TvR~Al~~L~~eGli~r~-----~G~GTfV~ 74 (241)
T PRK11402 13 TVRQRLLD-DIAQGVYQAGQQIPTENELCTQY--NVSRITIRKAISDLVADGVLIRW-----QGKGTFVQ 74 (241)
T ss_pred HHHHHHHH-HHHcCCCCCCCcCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe-----cCceeEEC
Confidence 45666666 54456664 7899999 99999999999999999999986 35555653
No 225
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=60.62 E-value=37 Score=28.12 Aligned_cols=44 Identities=7% Similarity=0.123 Sum_probs=36.3
Q ss_pred HHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 135 KQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
..|+.++..|+++|++-++ ++..-|+.-|+.|+.=|.|++.+.+
T Consensus 35 ~LL~~~~~~tvdelae~ln--------r~rStv~rsl~~L~~~GlV~Rek~~ 78 (126)
T COG3355 35 ALLEENGPLTVDELAEILN--------RSRSTVYRSLQNLLEAGLVEREKVN 78 (126)
T ss_pred HHHhhcCCcCHHHHHHHHC--------ccHHHHHHHHHHHHHcCCeeeeeec
Confidence 3444789999999998766 4567789999999999999998865
No 226
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=60.31 E-value=23 Score=31.00 Aligned_cols=45 Identities=18% Similarity=0.176 Sum_probs=40.4
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
...||+-|+.|+.+|.+ |-..++|-.++ ++..++|...++++-+|
T Consensus 132 ~~~LT~RE~eVL~ll~~-----G~snkeIA~~L--~iS~~TV~~h~~~I~~K 176 (207)
T PRK11475 132 SRMLSPTEREILRFMSR-----GYSMPQIAEQL--ERNIKTIRAHKFNVMSK 176 (207)
T ss_pred cCCCCHHHHHHHHHHHC-----CCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence 34699999999999998 99999999999 99999999988888554
No 227
>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=60.28 E-value=41 Score=22.63 Aligned_cols=53 Identities=8% Similarity=0.251 Sum_probs=37.5
Q ss_pred HHHHHHHHHHHHHHhhhC--CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 123 TEFIKVVKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 123 ~efV~~l~~~~~~~i~~~--~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
.++.+.|.+.+....... ..+|..+|++.+ .+|..-|.+.|..|.-.|.|+..
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~--------~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEEL--------GVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEec
Confidence 345555555555543322 246799998877 35788999999999999998765
No 228
>PRK09416 lstR lineage-specific thermal regulator protein; Provisional
Probab=60.04 E-value=37 Score=28.50 Aligned_cols=68 Identities=10% Similarity=0.112 Sum_probs=52.2
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccC
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSK 206 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~ 206 (252)
.+.-.++..|... ..-=+|.+.|.+.+.....++...|-.+|+.|+-+|.|+.... + ..++.|+++..
T Consensus 43 ~~~l~IL~lL~~~--~yGYeI~k~I~e~~~g~~~~s~GtIYp~L~RLE~~GlI~s~~~-~--------~~RK~Y~ITe~ 110 (135)
T PRK09416 43 DILLAILQLLMNE--KTGYELLQLLRQRGILTFEGNEGSLYTLLHRLEQNRFIQSSWD-H--------EGAKYYQLTDK 110 (135)
T ss_pred cHHHHHHHHHhCC--CCHHHHHHHHHHhcCCcccCCCccHHHHHHHHHHCCCeEEeec-C--------CCceEEEECHH
Confidence 4455566666654 7888999999988766678899999999999999999986432 1 24678887643
No 229
>PF10576 EndIII_4Fe-2S: Iron-sulfur binding domain of endonuclease III; InterPro: IPR003651 Endonuclease III (4.2.99.18 from EC) is a DNA repair enzyme which removes a number of damaged pyrimidines from DNA via its glycosylase activity and also cleaves the phosphodiester backbone at apurinic / apyrimidinic sites via a beta-elimination mechanism [, ]. The structurally related DNA glycosylase MutY recognises and excises the mutational intermediate 8-oxoguanine-adenine mispair []. The 3-D structures of Escherichia coli endonuclease III [] and catalytic domain of MutY [] have been determined. The structures contain two all-alpha domains: a sequence-continuous, six-helix domain (residues 22-132) and a Greek-key, four-helix domain formed by one N-terminal and three C-terminal helices (residues 1-21 and 133-211) together with the [Fe4S4] cluster. The cluster is bound entirely within the C-terminal loop by four cysteine residues with a ligation pattern Cys-(Xaa)6-Cys-(Xaa)2-Cys-(Xaa)5-Cys which is distinct from all other known Fe4S4 proteins. This structural motif is referred to as a [Fe4S4] cluster loop (FCL) []. Two DNA-binding motifs have been proposed, one at either end of the interdomain groove: the helix-hairpin-helix (HhH) and FCL motifs. The primary role of the iron-sulphur cluster appears to involve positioning conserved basic residues for interaction with the DNA phosphate backbone by forming the loop of the FCL motif [, ]. The iron-sulphur cluster loop (FCL) is also found in DNA-(apurinic or apyrimidinic site) lyase, a subfamily of endonuclease III. The enzyme has both apurinic and apyrimidinic endonuclease activity and a DNA N-glycosylase activity. It cuts damaged DNA at cytosines, thymines and guanines, and acts on the damaged strand 5' of the damaged site. The enzyme binds a 4Fe-4S cluster which is not important for the catalytic activity, but is probably involved in the alignment of the enzyme along the DNA strand.; GO: 0004519 endonuclease activity, 0051539 4 iron, 4 sulfur cluster binding; PDB: 1VRL_A 1RRQ_A 3G0Q_A 3FSQ_A 1RRS_A 3FSP_A 2ABK_A 1KG7_A 1KG2_A 1MUN_A ....
Probab=59.73 E-value=3.6 Score=22.62 Aligned_cols=11 Identities=36% Similarity=1.322 Sum_probs=7.4
Q ss_pred CCCCCCccccC
Q 025493 222 PCGVCPQINFC 232 (252)
Q Consensus 222 PCg~CPv~~~C 232 (252)
-|+.||+.+.|
T Consensus 7 ~C~~Cpl~~~C 17 (17)
T PF10576_consen 7 KCEECPLADYC 17 (17)
T ss_dssp -GGG-TTGGG-
T ss_pred ccccCCCcccC
Confidence 49999999887
No 230
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=59.71 E-value=93 Score=25.19 Aligned_cols=69 Identities=7% Similarity=0.109 Sum_probs=43.8
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.+.++.+.+ |++.++| +--|+.|||++.+.-. .|.+.| |.+-++.|+.+
T Consensus 2 ~IgE~A~~~--gvs~~TL----RyYE~~GLl~p~r~~~-~gyR~Y----------------------~~~~~~~l~~I-- 50 (133)
T cd04787 2 KVKELANAA--GVTPDTV----RFYTRIGLLRPTRDPV-NGYRLY----------------------SEKDLSRLRFI-- 50 (133)
T ss_pred CHHHHHHHH--CcCHHHH----HHHHHCCCCCCCcCCC-CCeeeC----------------------CHHHHHHHHHH--
Confidence 467888899 8988765 6679999999853221 233333 44444444322
Q ss_pred HHhhhCCCCCHHHHHHHHHHc
Q 025493 135 KQIIKLKVATLEGISDSIKRS 155 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~ 155 (252)
.+++. -..|++||.+++...
T Consensus 51 ~~lr~-~G~sL~eI~~~l~~~ 70 (133)
T cd04787 51 LSARQ-LGFSLKDIKEILSHA 70 (133)
T ss_pred HHHHH-cCCCHHHHHHHHhhh
Confidence 22333 467899999998754
No 231
>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=59.27 E-value=51 Score=22.11 Aligned_cols=47 Identities=6% Similarity=0.215 Sum_probs=37.5
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
.+..++.++...+ .+..||.+.+ .++...+...|+.|+-.|.|....
T Consensus 8 ~~~~il~~l~~~~-~~~~ei~~~~--------~i~~~~i~~~l~~L~~~g~i~~~~ 54 (78)
T cd00090 8 TRLRILRLLLEGP-LTVSELAERL--------GLSQSTVSRHLKKLEEAGLVESRR 54 (78)
T ss_pred HHHHHHHHHHHCC-cCHHHHHHHH--------CcCHhHHHHHHHHHHHCCCeEEEE
Confidence 3456677777776 9999998866 357889999999999999998765
No 232
>PF14502 HTH_41: Helix-turn-helix domain
Probab=59.09 E-value=24 Score=24.62 Aligned_cols=40 Identities=13% Similarity=0.094 Sum_probs=32.4
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc
Q 025493 50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI 91 (252)
Q Consensus 50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv 91 (252)
|++=--..++..+. ++.-..|+++||.||..+-|+=.+.=
T Consensus 3 GdRi~tI~e~~~~~--~vs~GtiQ~Alk~Le~~gaI~Le~rG 42 (48)
T PF14502_consen 3 GDRIPTISEYSEKF--GVSRGTIQNALKFLEENGAIKLESRG 42 (48)
T ss_pred CcccCCHHHHHHHh--CcchhHHHHHHHHHHHCCcEEeeecC
Confidence 44444567888999 99999999999999999999875543
No 233
>KOG3095 consensus Transcription initiation factor IIE, beta subunit [Transcription]
Probab=58.38 E-value=65 Score=30.24 Aligned_cols=102 Identities=18% Similarity=0.291 Sum_probs=70.8
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCC
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEG 119 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~ 119 (252)
-+..+++..-+-.||-..||+... ..+...||+||+-+=|=-+.+....+.+ =.||.|.
T Consensus 143 ~Ll~llr~~~~~~GI~v~DL~d~~------pNv~~~lk~L~~s~eIl~l~t~~d~k~k---------------ivf~ND~ 201 (284)
T KOG3095|consen 143 QLLKLLRKHDTLGGILVSDLKDAW------PNVDEDLKELEKSGEILVLRTPKDDKPK---------------IVFYNDK 201 (284)
T ss_pred HHHHHHHhcCccCceehHHhhhcc------cchHHHHHHHhcCCcEEEEeccCCCCCc---------------eEEecCC
Confidence 456677773444799999999965 3567889999887766655544332232 3589886
Q ss_pred ----cCCHHHHHHHHHHHHHHhhhCCCCC-HHHHHHHHHHcCCccee-cCHHHHHHH
Q 025493 120 ----SLDTEFIKVVKSQCLKQIIKLKVAT-LEGISDSIKRSGAFKVD-LTKQQIEEI 170 (252)
Q Consensus 120 ----e~D~efV~~l~~~~~~~i~~~~~~T-~~~I~~~i~~~~i~~~~-Ls~~di~~I 170 (252)
.+|.||....+++ ..++ ..+|.+++.+.|+.... +.+.-+...
T Consensus 202 ~~~~~VDdEFk~LWr~V--------~Ip~~~~dle~eL~k~GLkp~~~v~p~~~~~~ 250 (284)
T KOG3095|consen 202 SCSFSVDDEFKKLWRSV--------TIPSMELDLEEELQKQGLKPMKDVDPKKAAPQ 250 (284)
T ss_pred CCCcccCHHHHHHHHhC--------CCChHHHHHHHHHHHhCCCcccccchHHhhhh
Confidence 4678998877665 2355 67889999999987765 666655554
No 234
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=58.05 E-value=35 Score=29.03 Aligned_cols=37 Identities=14% Similarity=0.224 Sum_probs=31.5
Q ss_pred CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 140 LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 140 ~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
.+.+|.++|++.+ .++..-+++||+.|.-.|.|+..+
T Consensus 23 ~~~vs~~eIA~~~--------~ip~~~l~kIl~~L~~aGLv~s~r 59 (164)
T PRK10857 23 AGPVPLADISERQ--------GISLSYLEQLFSRLRKNGLVSSVR 59 (164)
T ss_pred CCcCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEeCC
Confidence 4578999998765 478899999999999999999754
No 235
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=57.82 E-value=64 Score=22.73 Aligned_cols=43 Identities=16% Similarity=0.285 Sum_probs=35.5
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
.|+..+.+ . ...-..+|...+ ++.+..++..|+.|+..|+|..
T Consensus 29 ~il~~l~~-~--~~~~~~~l~~~~--~~~~~~v~~hL~~L~~~glv~~ 71 (110)
T COG0640 29 EILSLLAE-G--GELTVGELAEAL--GLSQSTVSHHLKVLREAGLVEL 71 (110)
T ss_pred HHHHHHHh-c--CCccHHHHHHHH--CCChhHHHHHHHHHHHCCCeEE
Confidence 44555555 3 456688999999 9999999999999999999999
No 236
>PRK14137 recX recombination regulator RecX; Provisional
Probab=57.82 E-value=41 Score=29.61 Aligned_cols=54 Identities=9% Similarity=0.070 Sum_probs=46.9
Q ss_pred CHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeE
Q 025493 122 DTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIM 181 (252)
Q Consensus 122 D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE 181 (252)
+.|+-+.+...++.||.++ .=|..|+.+++.+.| ++.+.|+.+|+.|.-.|.|-
T Consensus 35 ~~e~~~~~~~~Al~~Ls~R-~rS~~ELr~KL~~kg-----~~~e~Ie~vI~rL~e~gyLD 88 (195)
T PRK14137 35 PDEAREALLAYAFRALAAR-AMTAAELRAKLERRS-----EDEALVTEVLERVQELGYQD 88 (195)
T ss_pred HHHHHHHHHHHHHHHHhcc-hhhHHHHHHHHHhcC-----CCHHHHHHHHHHHHHcCCCC
Confidence 4589999999999999887 446789999999887 57899999999999998874
No 237
>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=57.80 E-value=27 Score=24.80 Aligned_cols=43 Identities=12% Similarity=0.167 Sum_probs=34.2
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.|..++.+ + -+..++|..++ ++..+.+.+.|+.|++.|+.-..
T Consensus 4 ~il~~L~~-~---~~~~~eLa~~l--~vS~~tv~~~l~~L~~~g~~i~~ 46 (69)
T TIGR00122 4 RLLALLAD-N---PFSGEKLGEAL--GMSRTAVNKHIQTLREWGVDVLT 46 (69)
T ss_pred HHHHHHHc-C---CcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCeEEe
Confidence 45555554 3 25589999999 99999999999999999996554
No 238
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=57.72 E-value=43 Score=22.05 Aligned_cols=35 Identities=3% Similarity=0.197 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 142 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 142 ~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
.||..++++.+ .+|..-|.+.|+.|+-+|.|+..+
T Consensus 20 l~s~~~la~~~--------~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 20 LPSERELAAQL--------GVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CcCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEEec
Confidence 45888888877 467899999999999999998764
No 239
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=57.71 E-value=60 Score=27.13 Aligned_cols=92 Identities=20% Similarity=0.307 Sum_probs=55.7
Q ss_pred HHHHhhhCC---CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccCCCC
Q 025493 133 CLKQIIKLK---VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSKGGG 209 (252)
Q Consensus 133 ~~~~i~~~~---~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~~~~ 209 (252)
++-||..+. .+|.++|++.. .++..-+++|+..|.-.|.|+.++..+ -.|++.+.+..
T Consensus 13 ~L~~LA~~~~~~~~s~~~IA~~~--------~is~~~L~kil~~L~kaGlV~S~rG~~-----------GGy~Lar~~~~ 73 (150)
T COG1959 13 ALLYLALLPGGGPVSSAEIAERQ--------GISPSYLEKILSKLRKAGLVKSVRGKG-----------GGYRLARPPEE 73 (150)
T ss_pred HHHHHHhCCCCCcccHHHHHHHh--------CcCHHHHHHHHHHHHHcCCEEeecCCC-----------CCccCCCChHH
Confidence 344554432 57799998753 478899999999999999999987422 13777665421
Q ss_pred C--CC---CCCCCcccCCCCCCCccccCCCCCccCcccccchHhhh
Q 025493 210 G--GE---PKTGSSASVPCGVCPQINFCTPDGVISPKTCVYYTKWL 250 (252)
Q Consensus 210 ~--~~---~~~~~l~~vPCg~CPv~~~C~~gG~IsP~tC~Y~~eWL 250 (252)
= ++ .--.++.-++|...+-.. |. ..+|.--.-|.
T Consensus 74 Isl~dVv~ave~~~~~~~c~~~~~~~-~~------~~~C~i~~~~~ 112 (150)
T COG1959 74 ITLGDVVRALEGPLALVECFSITNNE-CN------TPTCGIRAAWL 112 (150)
T ss_pred CcHHHHHHHhcCCCCccccCCCCCCC-CC------CCcchHHHHHH
Confidence 0 00 001223335666544433 43 46687776664
No 240
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=56.76 E-value=41 Score=25.70 Aligned_cols=69 Identities=9% Similarity=0.027 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecc
Q 025493 125 FIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNV 204 (252)
Q Consensus 125 fV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~ 204 (252)
=-+.|+..|..|++....+...+|++-+ ..|..-|+-.+..|.--|.||..+...+| ..+....||+.
T Consensus 6 q~~IL~alV~~Y~~~~~PVgSk~ia~~l--------~~s~aTIRN~M~~Le~lGlve~~p~~s~G----riPT~~aYr~~ 73 (78)
T PF03444_consen 6 QREILKALVELYIETGEPVGSKTIAEEL--------GRSPATIRNEMADLEELGLVESQPHPSGG----RIPTDKAYRAL 73 (78)
T ss_pred HHHHHHHHHHHHHhcCCCcCHHHHHHHH--------CCChHHHHHHHHHHHHCCCccCCCCCCCC----CCcCHHHHHHH
Confidence 3578899999999999999999999853 35678999999999999999976522111 22445677765
Q ss_pred c
Q 025493 205 S 205 (252)
Q Consensus 205 ~ 205 (252)
.
T Consensus 74 ~ 74 (78)
T PF03444_consen 74 N 74 (78)
T ss_pred c
Confidence 3
No 241
>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=56.64 E-value=33 Score=27.35 Aligned_cols=36 Identities=11% Similarity=0.260 Sum_probs=30.4
Q ss_pred CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 141 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 141 ~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+.+|..||++.+ .++..-+.++|+.|+-.|.|+..+
T Consensus 24 ~~~s~~eia~~l--------~is~~~v~~~l~~L~~~Gli~~~~ 59 (130)
T TIGR02944 24 QPYSAAEIAEQT--------GLNAPTVSKILKQLSLAGIVTSKR 59 (130)
T ss_pred CCccHHHHHHHH--------CcCHHHHHHHHHHHHHCCcEEecC
Confidence 468999998765 478899999999999999998754
No 242
>KOG2587 consensus RNA polymerase III (C) subunit [Transcription]
Probab=56.62 E-value=1.3e+02 Score=30.78 Aligned_cols=96 Identities=13% Similarity=0.132 Sum_probs=71.5
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccc-cCCcCCHHHHHHHHHHHH
Q 025493 56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWY-SEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy-~d~e~D~efV~~l~~~~~ 134 (252)
+.-+.+++ +|+-+.|.++|=+|.+.++++-+....+.++++|--+..+ +|--=--| .+--.+.+.-+.....|+
T Consensus 37 ~~~~~~~t--~i~~~kVk~aL~sLiQh~~V~y~~~~~~~g~vt~Y~~~~~---ei~hilry~r~~~i~~~~~~q~~~sIv 111 (551)
T KOG2587|consen 37 LRVIAKDT--GISLDKVKKALVSLIQHNCVSYQVHTRNSGKVTTYEAQCS---EILHILRYPRYIYITKTLYSQTAESIV 111 (551)
T ss_pred hHHHHhhc--CCChHHHHHHHHHHHHhcceEEEEecCCCCceEEEEehhh---HHHHHHhcccceeeHHHHhhhHHHHHH
Confidence 55667788 9999999999999999999999988877777776554321 11000011 223455666777888888
Q ss_pred HHhhhCCCCCHHHHHHHHHHcC
Q 025493 135 KQIIKLKVATLEGISDSIKRSG 156 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~~ 156 (252)
.+|-.+|..|+.|+.+-+.+.+
T Consensus 112 ~~Lls~GrLTv~e~i~rv~~~~ 133 (551)
T KOG2587|consen 112 EELLSNGRLTVSEVIKRVADRL 133 (551)
T ss_pred HHHHhcCceeHHHHHHHHHhcc
Confidence 9999999999999999998876
No 243
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=56.55 E-value=35 Score=30.56 Aligned_cols=47 Identities=11% Similarity=0.280 Sum_probs=41.3
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+..++.+|.+++.+|.+|+++.+ .+|+.-|++-|+.|.-.|+|.+..
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l--------~VS~~TiRRdL~~L~~~~~l~r~~ 52 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQL--------NVSKETIRRDLNELQTQGKILRNH 52 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEec
Confidence 45689999999999999999998 378899999999999999998753
No 244
>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=56.34 E-value=11 Score=33.31 Aligned_cols=65 Identities=12% Similarity=0.114 Sum_probs=46.1
Q ss_pred CcCCHHHHHHHHHHHHHHhhhCC-CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 119 GSLDTEFIKVVKSQCLKQIIKLK-VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 119 ~e~D~efV~~l~~~~~~~i~~~~-~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
++|-.|+--.|-++|......++ ..++.|+...+++.......+|++||.+-++.|.--|.=.++
T Consensus 89 ~~f~~ELa~qi~e~c~~~~~~~GGii~L~dl~~~~nr~R~g~~lISp~Di~~A~~~l~~lg~g~~l 154 (223)
T PF04157_consen 89 GDFYYELAVQIAEVCLATRSKNGGIISLSDLYCRYNRARGGSELISPEDILRACKLLEVLGLGFRL 154 (223)
T ss_dssp HHHHHHHHHHHHHHHHHHCCTTTSEEEHHHHHHHHHHCTTTSST--HHHHHHHHHHHCCCTSSEEE
T ss_pred hhHHHHHHHHHHHHHHHHHhcCCCEEEHHHHHHHHHHhcccCCCcCHHHHHHHHHHHHHcCCCeEE
Confidence 34555666666666666665554 899999999999987555589999999999999776643333
No 245
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=55.99 E-value=35 Score=28.57 Aligned_cols=43 Identities=14% Similarity=0.361 Sum_probs=35.4
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHH----HHHHHHH
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVT----KSIKSLQ 80 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~----k~lK~Le 80 (252)
...||+.|+.|+.+.. +|..+++|..++ +++...|. ++++.|.
T Consensus 4 ~~~Lte~qr~VL~Lr~-----~GlTq~EIAe~L--giS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-----KGLSQKEIAKEL--KTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCCHHHHHHHHHHH-----cCCCHHHHHHHH--CcCHHHHHHHHHhHHHHHH
Confidence 3579999999999953 589999999999 99999888 5555554
No 246
>PRK10651 transcriptional regulator NarL; Provisional
Probab=55.96 E-value=30 Score=28.07 Aligned_cols=45 Identities=27% Similarity=0.437 Sum_probs=39.0
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
...||+.|+.|+.++.+ |.-.++|..++ +++.++|...++.|-.|
T Consensus 153 ~~~Lt~rE~~vl~~l~~-----g~~~~~ia~~l--~is~~tV~~~~~~l~~K 197 (216)
T PRK10651 153 VNQLTPRERDILKLIAQ-----GLPNKMIARRL--DITESTVKVHVKHMLKK 197 (216)
T ss_pred cccCCHHHHHHHHHHHc-----CCCHHHHHHHc--CCCHHHHHHHHHHHHHH
Confidence 34699999999999876 67899999999 99999999999988554
No 247
>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=55.89 E-value=18 Score=31.60 Aligned_cols=40 Identities=15% Similarity=0.303 Sum_probs=33.8
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
.-++|..+. |....+|.++|..|++.|+|.+.+ ++=.|+.
T Consensus 26 sE~eLa~~~--gVSR~TVR~Al~~L~~eGli~r~~-----G~GTfV~ 65 (233)
T TIGR02404 26 SEHELMDQY--GASRETVRKALNLLTEAGYIQKIQ-----GKGSIVL 65 (233)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEeC-----CceEEEe
Confidence 358899999 999999999999999999999974 4445553
No 248
>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=55.01 E-value=41 Score=31.01 Aligned_cols=57 Identities=7% Similarity=0.226 Sum_probs=44.8
Q ss_pred CCCCCChHH-HHHHHHHHhhcCC-CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 30 PSDSLTDHE-RLIYDVIRSNKQD-MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 30 ~~~~l~~~e-~~vy~~I~~~ag~-~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
+++.||=-| ..|=.+++...|+ --+..++|..+. |+..+.+..+++.||+.|+|+..
T Consensus 173 Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerl--GVSRs~ireAlrkLE~aGvIe~r 231 (251)
T TIGR02787 173 AINTLSYSELEAVEHIFEELDGNEGLLVASKIADRV--GITRSVIVNALRKLESAGVIESR 231 (251)
T ss_pred HHHhccHhHHHHHHHHHHHhccccccccHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEec
Confidence 355666533 3555566665563 568889999999 99999999999999999999985
No 249
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=54.83 E-value=40 Score=25.67 Aligned_cols=49 Identities=12% Similarity=0.207 Sum_probs=41.3
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
.+-..++..++..+..|..+|++.+ .++...+.+.++.|+-+|.|.+..
T Consensus 3 ~~D~~il~~L~~~~~~~~~~la~~l--------~~s~~tv~~~l~~L~~~g~i~~~~ 51 (108)
T smart00344 3 EIDRKILEELQKDARISLAELAKKV--------GLSPSTVHNRVKRLEEEGVIKGYT 51 (108)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeeceE
Confidence 3456788888888889999999876 588999999999999999998554
No 250
>COG1695 Predicted transcriptional regulators [Transcription]
Probab=54.60 E-value=66 Score=25.81 Aligned_cols=73 Identities=10% Similarity=0.029 Sum_probs=55.4
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccC
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSK 206 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~ 206 (252)
.|.-.++..|... ..+--+|.+.+......--..+..-|..+|+.|+-+|.|+.......+ .+.++.|+++..
T Consensus 9 ~l~~~iL~~L~~~-~~~Gyei~k~~~~~~~~~~~~s~gtiYp~L~~Le~~Gli~~~~~~~~~-----g~~rk~Y~lTe~ 81 (138)
T COG1695 9 SLELLILSLLSEK-PSHGYEIIKELEELSGGLWEPSPGTIYPLLKRLEKEGLIESRWEESGG-----GPPRKYYRLTEK 81 (138)
T ss_pred hHHHHHHHHHhcC-CchHHHHHHHHHHHcCCCCcCCCCcHHHHHHHHHHCCCeEEEecccCC-----CCCceEEEECHH
Confidence 4666777777777 888999999999887555678999999999999999999876432211 234678887643
No 251
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 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 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=54.49 E-value=15 Score=25.78 Aligned_cols=41 Identities=15% Similarity=0.210 Sum_probs=33.8
Q ss_pred cCCCcccHHHHHHHhhc-CCChHHHHHHHHHHHhcCCeeeee
Q 025493 49 KQDMGIWTRDMKRELKV-NLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~-~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
-=..|+-..+|+.+... ++++...+..|..|+++|.|+.-.
T Consensus 13 Plr~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~~g 54 (59)
T PF09106_consen 13 PLRPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKVEG 54 (59)
T ss_dssp TTSS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEEES
T ss_pred cCccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeeeEC
Confidence 45679999999988755 789999999999999999998753
No 252
>PRK06474 hypothetical protein; Provisional
Probab=54.47 E-value=44 Score=28.69 Aligned_cols=52 Identities=15% Similarity=0.176 Sum_probs=43.8
Q ss_pred HHHHHHHHHHhhhCCC-CCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 127 KVVKSQCLKQIIKLKV-ATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 127 ~~l~~~~~~~i~~~~~-~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
+..|..|+.+|..++. .|+.+|++.+. .++..-|-.-|+.|+-.|.|+.+..
T Consensus 10 ~p~R~~Il~~L~~~~~~~ta~el~~~l~-------~is~aTvYrhL~~L~e~GLI~~~~~ 62 (178)
T PRK06474 10 HPVRMKICQVLMRNKEGLTPLELVKILK-------DVPQATLYRHLQTMVDSGILHVVKE 62 (178)
T ss_pred CHHHHHHHHHHHhCCCCCCHHHHHHHhc-------CCCHHHHHHHHHHHHHCCCEEEeec
Confidence 4568889999987654 99999999874 3667889999999999999998874
No 253
>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=54.38 E-value=29 Score=24.34 Aligned_cols=54 Identities=13% Similarity=0.125 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHc-CCcceecCHHHHHHHHHHHhhcCeeE
Q 025493 125 FIKVVKSQCLKQIIKLKVATLEGISDSIKRS-GAFKVDLTKQQIEEIVRAVVLDNQIM 181 (252)
Q Consensus 125 fV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~-~i~~~~Ls~~di~~IL~tLVyDgkIE 181 (252)
-++..-..+++.+. +..|+++|.+.+.+. ++..-.+ .+||.+.|+.|.-.|.||
T Consensus 14 ~Ln~~a~~Iw~~~~--g~~t~~ei~~~l~~~y~~~~~~~-~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 14 TLNETAAFIWELLD--GPRTVEEIVDALAEEYDVDPEEA-EEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp ---THHHHHHHH----SSS-HHHHHHHHHHHTT--HHHH-HHHHHHHHHHHHHTT---
T ss_pred cccHHHHHHHHHcc--CCCCHHHHHHHHHHHcCCCHHHH-HHHHHHHHHHHHHCcCcC
Confidence 45566667777773 568999999999865 5554445 889999999999888775
No 254
>PF13565 HTH_32: Homeodomain-like domain
Probab=54.16 E-value=37 Score=24.24 Aligned_cols=44 Identities=11% Similarity=0.136 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHH
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIV 171 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL 171 (252)
.+.+.+...+..+..-|+.+|+++|....-.++.+|..-|.++|
T Consensus 34 e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~L 77 (77)
T PF13565_consen 34 EQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRIL 77 (77)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHhC
Confidence 34455566666777899999999999874334466887777664
No 255
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=53.78 E-value=52 Score=27.95 Aligned_cols=56 Identities=14% Similarity=0.172 Sum_probs=46.4
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhh---cCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELK---VNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~---~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
.+|..=..|++++.+ . ..-+...+|-.+++ +++.-.+|-|.|+.|++.|||.++..
T Consensus 23 R~T~qR~~IL~~l~~-~-~~hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~ 81 (169)
T PRK11639 23 RLTPQRLEVLRLMSL-Q-PGAISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVES 81 (169)
T ss_pred CCCHHHHHHHHHHHh-c-CCCCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEec
Confidence 468888899999998 7 45788888877653 26788999999999999999999853
No 256
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=53.54 E-value=11 Score=32.57 Aligned_cols=51 Identities=8% Similarity=0.160 Sum_probs=44.3
Q ss_pred HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccc
Q 025493 37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIH 92 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~ 92 (252)
-+..|+.++.+ .|- +-..+|.... +....++.|=|..|+..|++.++..+.
T Consensus 8 R~~~Il~~l~~-~~~--~~~~~La~~~--~vS~~TiRRDl~~L~~~g~~~r~~~~~ 58 (185)
T PRK04424 8 RQKALQELIEE-NPF--ITDEELAEKF--GVSIQTIRLDRMELGIPELRERIKHVA 58 (185)
T ss_pred HHHHHHHHHHH-CCC--EEHHHHHHHH--CcCHHHHHHHHHHHhcchHHHHHHHHH
Confidence 45678888888 554 7899999999 999999999999999999998876643
No 257
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=53.45 E-value=42 Score=28.24 Aligned_cols=41 Identities=15% Similarity=0.148 Sum_probs=34.1
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKS 78 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~ 78 (252)
...||+.|+.|+.+.. +|..+++|...+ +++...|.+..+.
T Consensus 4 ~~~Lt~rqreVL~lr~-----~GlTq~EIAe~L--GiS~~tVs~ie~r 44 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-----RGLTQQEIADIL--GTSRANVSSIEKR 44 (141)
T ss_pred ccCCCHHHHHHHHHHH-----cCCCHHHHHHHH--CCCHHHHHHHHHH
Confidence 4579999999999843 589999999999 9999877766654
No 258
>PRK14999 histidine utilization repressor; Provisional
Probab=53.40 E-value=21 Score=31.48 Aligned_cols=40 Identities=8% Similarity=0.294 Sum_probs=34.5
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
.-++|..+. |....+|.++|..|++.|+|... ++|=.|+.
T Consensus 38 sE~eLa~~~--gVSR~TVR~Al~~L~~eGli~r~-----~GkGTfV~ 77 (241)
T PRK14999 38 SEAELVAQY--GFSRMTINRALRELTDEGWLVRL-----QGVGTFVA 77 (241)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe-----cCcEEEEC
Confidence 578999999 99999999999999999999986 35556653
No 259
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=53.30 E-value=31 Score=24.06 Aligned_cols=52 Identities=17% Similarity=0.265 Sum_probs=33.1
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCCh-HHHHHHHHHHHhcCCeee
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPD-NIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~-~~l~k~lK~Le~k~lIK~ 87 (252)
||++|++-=.+|...-=+.||...+++.+. +.+- ....+.|+.|++.|++.-
T Consensus 1 Ls~~d~~~e~i~~~LR~~~Gi~~~~~~~~~--g~~~~~~~~~~l~~l~~~Gll~~ 53 (66)
T PF06969_consen 1 LSPEDRLREYIMLGLRCNEGIDLSEFEQRF--GIDFAEEFQKELEELQEDGLLEI 53 (66)
T ss_dssp --HHHHHHHHHHHHHHHHSEEEHHHHHHHT--T--THHH-HHHHHHHHHTTSEEE
T ss_pred CCHHHHHHHHHHHHHHhHCCcCHHHHHHHH--CcCHHHHHHHHHHHHHHCCCEEE
Confidence 344443333333332235899999999999 7764 344889999999999965
No 260
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=53.27 E-value=35 Score=24.52 Aligned_cols=43 Identities=16% Similarity=0.294 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHH
Q 025493 124 EFIKVVKSQCLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAV 174 (252)
Q Consensus 124 efV~~l~~~~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tL 174 (252)
|-+..|.++...+-++. ..||.+||++++ .++.++|+.++...
T Consensus 1 E~l~~i~~a~~~L~~~lgr~Pt~eEiA~~l--------gis~~~v~~~l~~~ 44 (78)
T PF04539_consen 1 EKLRKIERARRELEQELGREPTDEEIAEEL--------GISVEEVRELLQAS 44 (78)
T ss_dssp HHHHHHHHHHHHHHHHHSS--BHHHHHHHH--------TS-HHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHhCCCCCHHHHHHHH--------cccHHHHHHHHHhC
Confidence 34566777777777655 689999999998 47899999998754
No 261
>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=52.93 E-value=44 Score=28.53 Aligned_cols=137 Identities=12% Similarity=0.138 Sum_probs=71.4
Q ss_pred HHHhhcCCCcccHHHHHHHhhc---CCChHHHHHHHHHHHh-cCC-eeeeeccc------------cCCeeeEEeccccc
Q 025493 44 VIRSNKQDMGIWTRDMKRELKV---NLPDNIVTKSIKSLQN-KSL-IKEVVNIH------------NKGKKHLMAVEFEP 106 (252)
Q Consensus 44 ~I~~~ag~~GIw~~dik~~~~~---~l~~~~l~k~lK~Le~-k~l-IK~vksv~------------~~~rK~YmL~~leP 106 (252)
+..+ .-..-|..+||.+.... .--...+.++=+.|+. =|+ ++++++-. +...+.|+|.+.-|
T Consensus 6 L~~~-~~k~pI~r~~i~k~v~~~~~~~f~~v~~~a~~~L~~vFG~eL~ev~~~~~~~~~~~~~~~~~~~~~~yiL~n~L~ 84 (195)
T PF01454_consen 6 LFKE-QKKQPIRRSDILKKVLKEYRRKFPEVFERANEILEDVFGFELVEVPPKKKDKKRASKKSKKSSSSKSYILVNTLP 84 (195)
T ss_dssp HHHH-HCT--EEHHHHHHHTTCCGGGGHHHHHHHHHHHHHHHH-EEEEESSTT-----------------SEEEEEEGCG
T ss_pred HHHH-hCCCCccHHHHHHHHhHHHHHHhHHHHHHHHHHHHHHhceEEEEeCCcccccccccccccccccCCEEEEEecCC
Confidence 3444 56668888888887511 1123455555555644 233 33333321 22378999998777
Q ss_pred CCCccCCcccc-CCcCCH-HHHHHHHHHHHHHhh-hCCCCCHHHHHHHHHHcCCcc---eecCHHHHHHHH-HHHhhcCe
Q 025493 107 SKDISGGAWYS-EGSLDT-EFIKVVKSQCLKQII-KLKVATLEGISDSIKRSGAFK---VDLTKQQIEEIV-RAVVLDNQ 179 (252)
Q Consensus 107 s~eiTGG~wy~-d~e~D~-efV~~l~~~~~~~i~-~~~~~T~~~I~~~i~~~~i~~---~~Ls~~di~~IL-~tLVyDgk 179 (252)
.+.... +. +.+... ---..|...++.+|. +.+.++-+++.+++++.||.. ...-..++..++ +.||-.+-
T Consensus 85 ~~~~~~---~~~~~~~~~~~~~~Gll~~IL~lI~~~g~~i~E~~L~~~L~~lgi~~~~~~~~~g~~~~~~i~~~~vkq~Y 161 (195)
T PF01454_consen 85 PEYRNE---LSDDSETPSNLAKTGLLMLILSLIFMSGNSISEDDLWKFLRRLGIDEDEKHPILGMDIKKLILKEFVKQGY 161 (195)
T ss_dssp -S------------SSH----HHHHHHHHHHHHHHCTT-EEHHHHHHHHHHTT--TTS-BTTTB--HHHHHHCHHHHCTS
T ss_pred Ccccee---ecCCCCCchhHhHhhHHHHHHHHHHhcCCccCHHHHHHHHHhcCCCccccCccCCCCHHHHHHHHHHHhcC
Confidence 765322 21 122221 112344455555554 567888999999999999873 333344888888 99999999
Q ss_pred eEEEe
Q 025493 180 IMEVK 184 (252)
Q Consensus 180 IE~v~ 184 (252)
|++.+
T Consensus 162 L~~~k 166 (195)
T PF01454_consen 162 LVRYK 166 (195)
T ss_dssp E-EEE
T ss_pred HHhee
Confidence 97765
No 262
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=52.91 E-value=27 Score=31.95 Aligned_cols=61 Identities=8% Similarity=0.261 Sum_probs=48.5
Q ss_pred CCCCCChHHH-HHHHHHHhhcCCCcccHH-HHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 30 PSDSLTDHER-LIYDVIRSNKQDMGIWTR-DMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 30 ~~~~l~~~e~-~vy~~I~~~ag~~GIw~~-dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
..+.|+=.|. .|=.++++.-||+|...+ -|..+. |++.+++-.+|++||+.|.|.+ +|.--
T Consensus 179 Ai~tLSYSEleAve~I~eELdG~EG~lvASkiADrv--GITRSVIVNALRKlESAGvIeS-RSLGM 241 (261)
T COG4465 179 AISTLSYSELEAVEHIFEELDGNEGLLVASKIADRV--GITRSVIVNALRKLESAGVIES-RSLGM 241 (261)
T ss_pred HHhhccHHHHHHHHHHHHhcCCccceeeehhhhhhh--CchHHHHHHHHHHhhhcCceee-cccCc
Confidence 4556776444 566677777899998875 477788 9999999999999999999998 66654
No 263
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=52.62 E-value=11 Score=30.32 Aligned_cols=65 Identities=15% Similarity=0.234 Sum_probs=44.8
Q ss_pred CCCCChHHHHHHHHHHhhcCCC-cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeE
Q 025493 31 SDSLTDHERLIYDVIRSNKQDM-GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHL 99 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~-GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Y 99 (252)
.+++---+...|+-|..-.++- =|...-|-.++ ++.-..-..+|+.|.++|+|+.| .+|..+-+|
T Consensus 37 vnn~Vlfdqatydkl~kevp~~k~it~svl~dRl--kIngsLAr~alr~L~~kG~Ik~V--s~h~~q~IY 102 (110)
T KOG1767|consen 37 VNNAVLFDQATYDKLLKEVPKYKLITPSVLSDRL--KINGSLARAALRELSNKGVIKQV--SKHSKQVIY 102 (110)
T ss_pred hhhheeecHHHHHHHHHhcccceeecHHHhhhhh--hhchHHHHHHHHHHHhcchHHHH--hhcchheee
Confidence 3444443445555554326554 35555667788 89999999999999999999987 355566676
No 264
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=52.61 E-value=48 Score=26.67 Aligned_cols=52 Identities=6% Similarity=0.127 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 126 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 126 V~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
.|.+-..+++.|+..+..+..+|++.+. +|...+...++.|+-+|.|.....
T Consensus 6 lD~~D~~IL~~L~~d~r~~~~eia~~lg--------lS~~~v~~Ri~~L~~~GiI~~~~~ 57 (154)
T COG1522 6 LDDIDRRILRLLQEDARISNAELAERVG--------LSPSTVLRRIKRLEEEGVIKGYTA 57 (154)
T ss_pred ccHHHHHHHHHHHHhCCCCHHHHHHHHC--------CCHHHHHHHHHHHHHCCceeeEEE
Confidence 4567788999999998999999998765 899999999999999999997664
No 265
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=52.58 E-value=31 Score=33.37 Aligned_cols=37 Identities=11% Similarity=0.157 Sum_probs=34.1
Q ss_pred cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
.+.++....+|.+++ +++...++++|..|++.|+|.+
T Consensus 306 ~~g~~~t~~~La~~l--~~~~~~v~~iL~~L~~agLI~~ 342 (412)
T PRK04214 306 KHGKALDVDEIRRLE--PMGYDELGELLCELARIGLLRR 342 (412)
T ss_pred hcCCCCCHHHHHHHh--CCCHHHHHHHHHHHHhCCCeEe
Confidence 455799999999999 9999999999999999999974
No 266
>smart00753 PAM PCI/PINT associated module.
Probab=52.56 E-value=34 Score=25.09 Aligned_cols=50 Identities=14% Similarity=0.272 Sum_probs=36.4
Q ss_pred HHHHHHHH-HHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEE
Q 025493 125 FIKVVKSQ-CLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 125 fV~~l~~~-~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
+.+.++.. +..+.+..+..+.++|.+.+ .++.++++.+|-.|+.+|.|..
T Consensus 6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~--------~l~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00753 6 LQRKIRLTNLLQLSEPYSSISLSDLAKLL--------GLSVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHHHHHHHHHHHHhHHhceeeHHHHHHHh--------CcCHHHHHHHHHHHHHCCCeEE
Confidence 34444444 44555667788899988544 4678899999999999998864
No 267
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=52.56 E-value=34 Score=25.09 Aligned_cols=50 Identities=14% Similarity=0.272 Sum_probs=36.4
Q ss_pred HHHHHHHH-HHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEE
Q 025493 125 FIKVVKSQ-CLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 125 fV~~l~~~-~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
+.+.++.. +..+.+..+..+.++|.+.+ .++.++++.+|-.|+.+|.|..
T Consensus 6 l~~~~~~~~l~~l~~~y~~i~~~~i~~~~--------~l~~~~vE~~i~~~i~~~~l~~ 56 (88)
T smart00088 6 LQRKIRLTNLLQLSEPYSSISLSDLAKLL--------GLSVPEVEKLVSKAIRDGEISA 56 (88)
T ss_pred HHHHHHHHHHHHHhHHhceeeHHHHHHHh--------CcCHHHHHHHHHHHHHCCCeEE
Confidence 34444444 44555667788899988544 4678899999999999998864
No 268
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=52.45 E-value=28 Score=33.16 Aligned_cols=32 Identities=25% Similarity=0.312 Sum_probs=29.8
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
..++|.++. ++..+.|.+++..|+..|+|...
T Consensus 31 s~r~la~~~--~vsr~tv~~a~~~L~~~g~i~~~ 62 (431)
T PRK15481 31 PVRELASEL--GVNRNTVAAAYKRLVTAGLAQSQ 62 (431)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe
Confidence 478999999 99999999999999999999865
No 269
>smart00526 H15 Domain in histone families 1 and 5.
Probab=52.43 E-value=69 Score=22.66 Aligned_cols=54 Identities=17% Similarity=0.242 Sum_probs=40.2
Q ss_pred hHHHHHHHHHHhhcCCCcccHHHHHHHhhcC--C----ChHHHHHHHHHHHhcCCeeeee
Q 025493 36 DHERLIYDVIRSNKQDMGIWTRDMKRELKVN--L----PDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 36 ~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~--l----~~~~l~k~lK~Le~k~lIK~vk 89 (252)
....+|...|.+....+|.....|++-..-+ + +...|+++||.+..+|.+..+|
T Consensus 6 ~~~~mI~eAI~~l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~k 65 (66)
T smart00526 6 PYSEMITEAISALKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQVK 65 (66)
T ss_pred CHHHHHHHHHHHcCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeecC
Confidence 3456889999996666889888888743222 1 2356889999999999988765
No 270
>TIGR02018 his_ut_repres histidine utilization repressor, proteobacterial. This model represents a proteobacterial histidine utilization repressor. It is usually found clustered with the enzymes HutUHIG so that it can regulate its own expression as well. A number of species have several paralogs and may fine-tune the regulation according to levels of degradation intermediates such as urocanate. This family belongs to the larger GntR family of transcriptional regulators.
Probab=52.30 E-value=22 Score=30.99 Aligned_cols=40 Identities=13% Similarity=0.296 Sum_probs=34.1
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
.-++|..+. |....+|.++|..|++.|+|.++ ++|=.|..
T Consensus 27 sE~eLa~~~--~VSR~TVR~Al~~L~~eGli~r~-----~G~GtfV~ 66 (230)
T TIGR02018 27 SEHELVAQY--GCSRMTVNRALRELTDAGLLERR-----QGVGTFVA 66 (230)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe-----cCCEEEEc
Confidence 457899999 99999999999999999999987 35556653
No 271
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=52.22 E-value=58 Score=21.91 Aligned_cols=44 Identities=23% Similarity=0.429 Sum_probs=38.9
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
..||+-|..|..++.+ |...++|.... ++...++...++.+..|
T Consensus 3 ~~Lt~rE~~v~~l~~~-----G~s~~eia~~l--~is~~tV~~h~~~i~~K 46 (65)
T COG2771 3 ADLTPREREILRLVAQ-----GKSNKEIARIL--GISEETVKTHLRNIYRK 46 (65)
T ss_pred ccCCHHHHHHHHHHHC-----CCCHHHHHHHH--CCCHHHHHHHHHHHHHH
Confidence 4689999999999988 69999999999 99999999988888554
No 272
>KOG4603 consensus TBP-1 interacting protein [Signal transduction mechanisms]
Probab=52.19 E-value=83 Score=27.76 Aligned_cols=62 Identities=23% Similarity=0.285 Sum_probs=47.0
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhc-CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKV-NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~-~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
.+.|-+|++++.+ .|+-..+.|.-..+.- +|-.+.|.|+|-+|+..|-|+.- .+...|+|+.
T Consensus 6 ~~~e~ivl~~~~e--qNrP~ssq~v~~~lq~e~lgktavqk~Ld~La~~Gki~~K---~YGKqKIY~a 68 (201)
T KOG4603|consen 6 EDAEGIVLRYLQE--QNRPYSSQDVFGNLQREHLGKTAVQKTLDQLAQQGKIKEK---MYGKQKIYFA 68 (201)
T ss_pred cccHHHHHHHHHH--hcCCCchHHHHHHHHHHhccchHHHHHHHHHHHcCchhHH---hccceeeEee
Confidence 3456788888876 6777777776554432 68899999999999999999872 3557899975
No 273
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=52.09 E-value=22 Score=31.29 Aligned_cols=39 Identities=10% Similarity=0.346 Sum_probs=33.7
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
-++|..+. |....+|.++|..|++.|+|..++ ++-.|+.
T Consensus 32 E~eL~~~~--~VSR~TvR~Al~~L~~eGli~r~~-----G~GtfV~ 70 (240)
T PRK09764 32 ESALQTEF--GVSRVTVRQALRQLVEQQILESIQ-----GSGTYVK 70 (240)
T ss_pred HHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec-----CceeEEc
Confidence 48999999 999999999999999999999873 5555653
No 274
>PF03979 Sigma70_r1_1: Sigma-70 factor, region 1.1; InterPro: IPR007127 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 [, ]. This entry represents Region 1.1 which modulates DNA binding by region 2 and 4 when sigma is unbound by the core RNA polymerase [, ]. Region 1.1 is also involved in promoter binding.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2K6X_A.
Probab=51.97 E-value=28 Score=26.08 Aligned_cols=37 Identities=27% Similarity=0.311 Sum_probs=26.5
Q ss_pred hhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcC
Q 025493 137 IIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 137 i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDg 178 (252)
=+++|++|.++|.+++... .++.++|..|+.+|.--|
T Consensus 16 gK~~G~lT~~eI~~~L~~~-----~~~~e~id~i~~~L~~~g 52 (82)
T PF03979_consen 16 GKKKGYLTYDEINDALPED-----DLDPEQIDEIYDTLEDEG 52 (82)
T ss_dssp HHHHSS-BHHHHHHH-S-S--------HHHHHHHHHHHHTT-
T ss_pred HhhcCcCCHHHHHHHcCcc-----CCCHHHHHHHHHHHHHCC
Confidence 3468999999999999744 388999999999998777
No 275
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=51.90 E-value=38 Score=29.79 Aligned_cols=45 Identities=29% Similarity=0.404 Sum_probs=39.2
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
...||+-|+.|+.++.+ |...++|..++ +++.+++...+..+-.|
T Consensus 153 ~~~Lt~rE~~Vl~l~~~-----G~s~~eIA~~L--~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 153 SALLTHREKEILNKLRI-----GASNNEIARSL--FISENTVKTHLYNLFKK 197 (216)
T ss_pred cCCCCHHHHHHHHHHHc-----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 34699999999999988 89999999999 99999998888877544
No 276
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=51.61 E-value=37 Score=28.43 Aligned_cols=43 Identities=12% Similarity=0.125 Sum_probs=29.7
Q ss_pred HHHHHHHHhhhCCC--CCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 129 VKSQCLKQIIKLKV--ATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 129 l~~~~~~~i~~~~~--~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
.=+.|.+||..+.. +|+.+|++... +++++ |..+|-+|+|+-.
T Consensus 31 ~f~kV~~yLr~~p~~~ati~eV~e~tg--------Vs~~~----I~~~IreGRL~~~ 75 (137)
T TIGR03826 31 EFEKVYKFLRKHENRQATVSEIVEETG--------VSEKL----ILKFIREGRLQLK 75 (137)
T ss_pred HHHHHHHHHHHCCCCCCCHHHHHHHHC--------cCHHH----HHHHHHcCCeecc
Confidence 33567889998877 99999987542 34444 4556678888753
No 277
>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=51.04 E-value=73 Score=25.91 Aligned_cols=49 Identities=14% Similarity=0.194 Sum_probs=39.9
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 132 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 132 ~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
.++..|=..+.+|+.||++.+.+. -.++..-|..+|+.|+--|.|++.+
T Consensus 8 ~VM~vlW~~~~~t~~eI~~~l~~~----~~~~~tTv~T~L~rL~~KG~v~~~k 56 (130)
T TIGR02698 8 EVMRVVWTLGETTSRDIIRILAEK----KDWSDSTIKTLLGRLVDKGCLTTEK 56 (130)
T ss_pred HHHHHHHcCCCCCHHHHHHHHhhc----cCCcHHHHHHHHHHHHHCCceeeec
Confidence 455666567889999999999754 2477889999999999999998764
No 278
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=50.99 E-value=48 Score=27.87 Aligned_cols=47 Identities=15% Similarity=0.299 Sum_probs=39.3
Q ss_pred HHHHHHHhhh-CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEE
Q 025493 130 KSQCLKQIIK-LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 130 ~~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
...|+.|+.. +.+-|+.+|.+-+++ .++-..|+.+|+.|+-+|+|..
T Consensus 3 e~~Il~y~~~qNRPys~~di~~nL~~------~~~K~~v~k~Ld~L~~~g~i~~ 50 (169)
T PF07106_consen 3 EDAILEYMKEQNRPYSAQDIFDNLHN------KVGKTAVQKALDSLVEEGKIVE 50 (169)
T ss_pred HHHHHHHHHHcCCCCcHHHHHHHHHh------hccHHHHHHHHHHHHhCCCeee
Confidence 4678899875 457789999999986 4567899999999999999975
No 279
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=50.30 E-value=22 Score=26.37 Aligned_cols=35 Identities=11% Similarity=0.272 Sum_probs=25.9
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIK 77 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK 77 (252)
++..+++. -..+|+.++++.+.+ +++++.|+++++
T Consensus 19 l~~~i~~~-~~~~~ltQ~e~A~~l--gisq~~vS~l~~ 53 (80)
T PF13744_consen 19 LMAAIREL-REERGLTQAELAERL--GISQPRVSRLEN 53 (80)
T ss_dssp HHHHHHHH-HHCCT--HHHHHHHH--TS-HHHHHHHHT
T ss_pred HHHHHHHH-HHHcCCCHHHHHHHH--CCChhHHHHHHc
Confidence 44455555 667999999999999 999999999874
No 280
>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=50.30 E-value=38 Score=28.66 Aligned_cols=53 Identities=11% Similarity=-0.077 Sum_probs=40.2
Q ss_pred HHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 124 EFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 124 efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+|+..---.+++.|-.++..|-+||+.-+ .++..+|+.+|..|.-+|.|...+
T Consensus 10 ~~~g~~~v~Vl~aL~~~~~~tdEeLa~~L--------gi~~~~VRk~L~~L~e~~Lv~~~r 62 (158)
T TIGR00373 10 RAAEEEVGLVLFSLGIKGEFTDEEISLEL--------GIKLNEVRKALYALYDAGLADYKR 62 (158)
T ss_pred HHcChhHHHHHHHHhccCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCceeee
Confidence 33333334455566678889999999876 378999999999999999997544
No 281
>smart00049 DEP Domain found in Dishevelled, Egl-10, and Pleckstrin. Domain of unknown function present in signalling proteins that contain PH, rasGEF, rhoGEF, rhoGAP, RGS, PDZ domains. DEP domain in Drosophila dishevelled is essential to rescue planar polarity defects and induce JNK signalling (Cell 94, 109-118).
Probab=50.09 E-value=63 Score=23.22 Aligned_cols=56 Identities=13% Similarity=0.134 Sum_probs=41.3
Q ss_pred CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeec
Q 025493 142 VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKN 203 (252)
Q Consensus 142 ~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~ 203 (252)
.-|-.|+.+||.+.+. ..+.++...|.+.|+--|.|+.+.......|.+. ...||.
T Consensus 20 ~F~G~e~v~wL~~~~~---~~~r~eA~~l~~~ll~~g~i~~v~~~~~~~F~d~---~~~Yrf 75 (77)
T smart00049 20 CFTGSELVDWLMDNLE---IIDREEAVHLGQLLLDEGLIHHVNGPNKHTFKDS---KALYRF 75 (77)
T ss_pred eeEcHHHHHHHHHcCC---cCCHHHHHHHHHHHHHCCCEEEeCCCCcCccccC---CEEEEe
Confidence 4566788899998874 4678999999999999999999875333445332 355764
No 282
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=50.02 E-value=68 Score=29.56 Aligned_cols=60 Identities=15% Similarity=0.212 Sum_probs=45.6
Q ss_pred CCCCCChHHHHHHHHHH---hhcCCCcccHHHHHHH-------hhc-CCChHHHHHHHHHHHhcCCeeeeec
Q 025493 30 PSDSLTDHERLIYDVIR---SNKQDMGIWTRDMKRE-------LKV-NLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~---~~ag~~GIw~~dik~~-------~~~-~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
..++|+..+++++..|. . +++..+-.+++-.+ .+. -+..+++...|..||..|||....+
T Consensus 282 ~i~~l~~~~~~~l~ai~~~~~-~~~~~~~~~~~~~~y~~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~ 352 (365)
T TIGR02928 282 LIRGLPTHSKLVLLAIANLAA-NDEDPFRTGEVYEVYKEVCEDIGVDPLTQRRISDLLNELDMLGLVEAEER 352 (365)
T ss_pred HHHcCCHHHHHHHHHHHHHHh-cCCCCccHHHHHHHHHHHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEE
Confidence 45789999998888776 3 46667777766552 211 2778999999999999999998753
No 283
>PF06479 Ribonuc_2-5A: Ribonuclease 2-5A; InterPro: IPR010513 The proteins listed below share a common architecture with a protein kinase homology domain (see PDOC00100 from PROSITEDOC) followed by an ~135-residue globular kinase-extension nuclease (KEN) domain made of eight helices []: - Mammalian 2-5A-dependent RNase or RNase L (EC 3.1.26.-), an interferon- induced enzyme implicated in both the molecular mechanisms of interferon action and the fundamental control of RNA stability. 2-5A-dependent RNase is a unique enzyme in that it requires 2-5A, unusual oligoadenylates with 2',5'-phosphodiester linkages. RNase L is catalytically active only after binding to an unusual activator molecule containing a 5'-phosphorylated 2', 5'-linked oligoadenylate (2-5A), in the N-terminal half. RNase L consists of three domains, namely the N-terminal ankyrin repeat domain (see PDOC50088 from PROSITEDOC), the protein kinase homology domain, and the C-terminal KEN domain [, , ]. - Eukaryotic Ire1/Ern1, an ancient transmembrane sensor of endoplasmic reticulum (ER) stress with dual protein kinase and ribonuclease activities. In response to ER stress Ire1/Ern1 catalyzes the splicing of target mRNAs in a spliceosome-independent manner. Ire1/Ern1 is a type 1 transmembrane receptor consisting of an N-terminal ER luminal domain, a transmembrane segment and a cytoplasmic region. The cytoplasmic region encompasses a protein kinase domain followed by a C-terminal KEN domain [, ]. The dimerisation of the kinase domain activates the ribonuclease function of the KEN domain [].; GO: 0016891 endoribonuclease activity, producing 5'-phosphomonoesters, 0006397 mRNA processing; PDB: 3SDJ_D 3FBV_L 3LJ2_A 3SDM_A 3LJ0_A 2RIO_A 3LJ1_A 3P23_A.
Probab=50.02 E-value=7.5 Score=32.09 Aligned_cols=57 Identities=21% Similarity=0.427 Sum_probs=39.3
Q ss_pred CCCccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHH
Q 025493 107 SKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIV 171 (252)
Q Consensus 107 s~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL 171 (252)
+..+.||.|. ..+|.++++.|... ++..+-++.++.++|++..----++ .++++++|
T Consensus 32 ~~~v~~~~W~--~~ld~~l~~~l~~~-----R~Y~~~sv~DLLR~IRNk~~Hy~el-~~~~k~~l 88 (129)
T PF06479_consen 32 AEDVLGGDWD--KKLDPELLDDLGKY-----RKYDGDSVRDLLRAIRNKKHHYQEL-PEEVKEIL 88 (129)
T ss_dssp CCCCTTS-CG--GCSBHHHHHCCTTT-----SS--TT-HHHHHHHHHHHHHTCCCS--HHHHHHC
T ss_pred CCCCCCccHh--HHhCHHHHHHHHhc-----cCCCccCHHHHHHHHHcchHhHHHC-CHHHHHHh
Confidence 5567889997 67899999988753 5567889999999999886333344 66777765
No 284
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=49.93 E-value=57 Score=23.62 Aligned_cols=48 Identities=6% Similarity=0.152 Sum_probs=39.3
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
.-.++..|...+..|..+|.+.+ .++...|...|+.|+-.|.|++...
T Consensus 12 ~~~il~~l~~~~~~~~~~la~~~--------~~s~~~i~~~l~~L~~~g~v~~~~~ 59 (101)
T smart00347 12 QFLVLRILYEEGPLSVSELAKRL--------GVSPSTVTRVLDRLEKKGLIRRLPS 59 (101)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHH--------CCCchhHHHHHHHHHHCCCeEecCC
Confidence 44577777777889999998875 4667889999999999999998754
No 285
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=49.88 E-value=49 Score=29.78 Aligned_cols=51 Identities=10% Similarity=0.177 Sum_probs=43.5
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 127 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 127 ~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
+.-++.++++|.+++..|..|+++.+. +|..-|++-|+.|.-.|.|.++..
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~--------vS~~TirRdL~~Le~~g~i~r~~g 54 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLG--------ISPATARRDINKLDESGKLKKVRN 54 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHC--------cCHHHHHHHHHHHHHCCCEEEecC
Confidence 345677999999999999999999853 678889999999999999998763
No 286
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=49.87 E-value=59 Score=26.37 Aligned_cols=51 Identities=14% Similarity=0.179 Sum_probs=41.2
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 126 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 126 V~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
.+...+.++.++...+.++..+|++.+. ++...|...|+.|.-.|.|+..+
T Consensus 6 ~edyL~~I~~l~~~~~~~~~~ela~~l~--------vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 6 MEDYIEQIYLLIEEKGYARVSDIAEALS--------VHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred HHHHHHHHHHHHhcCCCcCHHHHHHHhC--------CChhHHHHHHHHHHHCCCEEEec
Confidence 3456667777788889999999998864 56788999999999999998654
No 287
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=49.70 E-value=1.3e+02 Score=24.84 Aligned_cols=107 Identities=17% Similarity=0.198 Sum_probs=61.8
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccC
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISG 112 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTG 112 (252)
-|+.+.+ ..+|+- |- .|+--.||.+++ .+...-|+|+|+...+-|-|.. ..+.....|+ .+|.
T Consensus 17 PLp~~~R--~rIvel-a~-~G~rp~~Isr~l--~Vs~gcVsKIl~Ry~eTGsi~P-g~iGGskprv-----~tp~----- 79 (125)
T PF00292_consen 17 PLPNELR--QRIVEL-AK-EGVRPCDISRQL--RVSHGCVSKILSRYRETGSIRP-GPIGGSKPRV-----ATPE----- 79 (125)
T ss_dssp SS-HHHH--HHHHHH-HH-TT--HHHHHHHH--T--HHHHHHHHHHHHHHS-SS-----S----SS-----S-HC-----
T ss_pred cCcHHHH--HHHHHH-hh-hcCCHHHHHHHH--ccchhHHHHHHHHHHHhcccCc-ccccCCCCCC-----CChH-----
Confidence 3555443 244555 53 599999999999 9999999999999999998865 3343222221 2332
Q ss_pred CccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcce--ecCHHHHHHHHH
Q 025493 113 GAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKV--DLTKQQIEEIVR 172 (252)
Q Consensus 113 G~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~--~Ls~~di~~IL~ 172 (252)
+-..+..|...+......||.+-+.+.||... .-|+..|-+||+
T Consensus 80 ----------------v~~~I~~~k~enP~ifawEiR~~L~~~gvc~~~~~PsvssInRilr 125 (125)
T PF00292_consen 80 ----------------VVEKIEQYKRENPTIFAWEIRDRLIADGVCDRSNVPSVSSINRILR 125 (125)
T ss_dssp ----------------HHHHHHHHHHH-TTS-HHHHHHHHHHTTSS-TTTS--HHHHHHHHH
T ss_pred ----------------HHHHHHHHHhcCCCcchHHHHHHHHHcCCCCCCCCCCHHHHHHhhC
Confidence 33445556667788889999999999998763 356666666653
No 288
>cd08767 Cdt1_c The C-terminal fold of replication licensing factor Cdt1 is essential for Cdt1 activity and directly interacts with MCM2-7 helicase. Cdt1 is a replication licensing factor in eukaryotes that recruits the Minichromosome Maintenance Complex (MCM2-7) to the Origin Recognition Complex (ORC). The Cdt1 protein is divided into three regions based on sequence comparison and biochemical analyses: the N-terminal region (Cdt1_n) binds DNA in a sequence-, strand-, and conformation-independent manner; the middle winged helix fold (Cdt1_m) binds geminin to inhibit both binding of the MCM complex to origins of replication and DNA; and the C-terminal region (Cdt1_c) is essential for Cdt1 activity and directly interacts with the MCM2-7 helicase. Precise duplication of chromosomal DNA is required for genomic stability during replication. Assembly of replication factors to start DNA replication in eukaryotes must occur only once per cell cycle. To form a pre-replicative complex on replicat
Probab=49.29 E-value=64 Score=26.29 Aligned_cols=48 Identities=21% Similarity=0.297 Sum_probs=38.5
Q ss_pred HHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHh
Q 025493 124 EFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVV 175 (252)
Q Consensus 124 efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLV 175 (252)
+..+.++..+.. .+++..|.+++...|..|. ...++.+|++.-|+.|.
T Consensus 45 ~la~~v~~if~s--~~k~~l~~e~l~~kl~~S~--~~~~s~~E~E~~l~LL~ 92 (126)
T cd08767 45 ELARILRNIFVS--EKKTVLPLEELVYKLQASY--PSILSRGEVEEHLRLLA 92 (126)
T ss_pred HHHHHHHHHHHh--cccccccHHHHHHHHHHhC--CCCCCHHHHHHHHHHHH
Confidence 455555555554 5778999999999999987 56788999999999998
No 289
>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=49.26 E-value=46 Score=25.91 Aligned_cols=47 Identities=9% Similarity=0.210 Sum_probs=35.6
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 132 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 132 ~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
.++.+|..++..|..+|.+.+. ++...+-.+|+.|+-+|.|++....
T Consensus 32 ~iL~~l~~~~~~t~~ela~~~~--------~~~~tvs~~l~~Le~~GlI~r~~~~ 78 (118)
T TIGR02337 32 RILRILAEQGSMEFTQLANQAC--------ILRPSLTGILARLERDGLVTRLKAS 78 (118)
T ss_pred HHHHHHHHcCCcCHHHHHHHhC--------CCchhHHHHHHHHHHCCCEEeccCC
Confidence 4556666777778888777643 4556788999999999999987643
No 290
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=49.02 E-value=88 Score=23.67 Aligned_cols=66 Identities=12% Similarity=0.186 Sum_probs=48.8
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCC------ChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNL------PDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV 102 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l------~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~ 102 (252)
...+.+|...|.+.....|.....|++-..-+. ....+.++|+.+..+|.+..++-.-..+ -|.|.
T Consensus 5 P~y~~MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~kG~g~~g--sfkl~ 76 (88)
T cd00073 5 PPYSEMVTEAIKALKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTGASG--SFKLS 76 (88)
T ss_pred CCHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeecCCCCcc--ceEeC
Confidence 456778999999988889999999988542222 2457889999999999999988543323 36654
No 291
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=48.98 E-value=1.4e+02 Score=23.88 Aligned_cols=70 Identities=14% Similarity=0.208 Sum_probs=43.6
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.++++.+.+ |++.++| ..-|+.|||.+...-.+ +. -+| +.+-|..|+. .
T Consensus 2 ~I~e~a~~~--gvs~~tl----R~Ye~~GLl~~~~r~~~-gy-----------------R~Y-----~~~~l~~l~~--I 50 (126)
T cd04783 2 TIGELAKAA--GVNVETI----RYYQRRGLLPEPPRPEG-GY-----------------RRY-----PEETVTRLRF--I 50 (126)
T ss_pred CHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCcCCC-CC-----------------eec-----CHHHHHHHHH--H
Confidence 467888899 9998876 78899999984221111 22 223 3444444432 2
Q ss_pred HHhhhCCCCCHHHHHHHHHHcC
Q 025493 135 KQIIKLKVATLEGISDSIKRSG 156 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~~ 156 (252)
..++. -..|+++|.+++....
T Consensus 51 ~~lr~-~G~sL~eI~~~l~~~~ 71 (126)
T cd04783 51 KRAQE-LGFTLDEIAELLELDD 71 (126)
T ss_pred HHHHH-cCCCHHHHHHHHhccc
Confidence 23344 4588999999997543
No 292
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=48.55 E-value=48 Score=26.77 Aligned_cols=44 Identities=27% Similarity=0.413 Sum_probs=38.4
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
..||+.|..|+.++.+ |.-.++|..+. ++..++|...++.|-+|
T Consensus 136 ~~Lt~~E~~il~~l~~-----g~~~~~Ia~~l--~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 136 DPLTKRERQVAEKLAQ-----GMAVKEIAAEL--GLSPKTVHVHRANLMEK 179 (196)
T ss_pred cCCCHHHHHHHHHHHC-----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 4699999999999877 57899999999 99999999988888654
No 293
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=48.54 E-value=1.2e+02 Score=23.23 Aligned_cols=69 Identities=7% Similarity=0.089 Sum_probs=44.0
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.+.++.+.+ |++..+ |+-.|++|||.+...-. +|-|+ ||.+=|+.|+.+
T Consensus 2 ~I~eva~~~--gvs~~t----lR~Ye~~GLl~p~~r~~-------------------~g~r~----Y~~~dv~~l~~I-- 50 (95)
T cd04780 2 RMSELSKRS--GVSVAT----IKYYLREGLLPEGRRLA-------------------PNQAE----YSEAHVERLRLI-- 50 (95)
T ss_pred CHHHHHHHH--CcCHHH----HHHHHHCCCCCCCcCCC-------------------CCCee----cCHHHHHHHHHH--
Confidence 467888888 888764 56789999987642221 22222 455555665544
Q ss_pred HHhhhCCCCCHHHHHHHHHH
Q 025493 135 KQIIKLKVATLEGISDSIKR 154 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~ 154 (252)
.++++.-..++++|.+.+..
T Consensus 51 ~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 51 RALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHcCCCHHHHHHHHHh
Confidence 33444346788888888876
No 294
>PRK03837 transcriptional regulator NanR; Provisional
Probab=48.18 E-value=36 Score=29.57 Aligned_cols=40 Identities=15% Similarity=0.314 Sum_probs=34.3
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
-.++|..+. |+..+.|..+|+.|+..|||... +++-.|+.
T Consensus 39 ~E~~Lae~~--gVSRt~VREAL~~L~~eGlv~~~-----~~~G~~V~ 78 (241)
T PRK03837 39 SERELMAFF--GVGRPAVREALQALKRKGLVQIS-----HGERARVS 78 (241)
T ss_pred CHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEe-----cCCceeEe
Confidence 679999999 99999999999999999999985 34555544
No 295
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=48.00 E-value=91 Score=21.60 Aligned_cols=66 Identities=15% Similarity=0.260 Sum_probs=39.6
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.++++.+.+ |++.++| +..|+++++...+ ...+++.| +.+=|+.|..+
T Consensus 2 ti~eva~~~--gvs~~tl----r~y~~~gll~~~~--~~~g~r~y----------------------~~~dv~~l~~i-- 49 (69)
T PF13411_consen 2 TIKEVAKLL--GVSPSTL----RYYEREGLLPPPR--DENGYRYY----------------------SEEDVERLREI-- 49 (69)
T ss_dssp EHHHHHHHT--TTTHHHH----HHHHHTTSSTTBE--STTSSEEE-----------------------HHHHHHHHHH--
T ss_pred cHHHHHHHH--CcCHHHH----HHHHHhcCccccc--ccCceeec----------------------cHHHHHHHHHH--
Confidence 467888899 9998776 5678899977766 23334444 33444444332
Q ss_pred HHhhhCCCCCHHHHHHHHH
Q 025493 135 KQIIKLKVATLEGISDSIK 153 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~ 153 (252)
..+.+ ...|+++|.+.++
T Consensus 50 ~~l~~-~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 50 KELRK-QGMSLEEIKKLLK 67 (69)
T ss_dssp HHHHH-TTTHHHHHHHHH-
T ss_pred HHHHH-CcCCHHHHHHHHc
Confidence 23334 4666777776665
No 296
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=47.90 E-value=31 Score=27.18 Aligned_cols=44 Identities=18% Similarity=0.246 Sum_probs=32.8
Q ss_pred CCChHHHHHHH----HHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHH
Q 025493 33 SLTDHERLIYD----VIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSL 79 (252)
Q Consensus 33 ~l~~~e~~vy~----~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~L 79 (252)
-||++|+.+.. ++.+ -=+.|+.+++|..++ |+..+.|+|.=+.|
T Consensus 32 lLTp~E~~~l~~R~~i~~~-Ll~~~~tQrEIa~~l--GiS~atIsR~sn~l 79 (94)
T TIGR01321 32 ILTRSEREDLGDRIRIVNE-LLNGNMSQREIASKL--GVSIATITRGSNNL 79 (94)
T ss_pred hCCHHHHHHHHHHHHHHHH-HHhCCCCHHHHHHHh--CCChhhhhHHHhhc
Confidence 47888876643 3332 226899999999999 99999888875554
No 297
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=47.80 E-value=20 Score=28.94 Aligned_cols=70 Identities=23% Similarity=0.387 Sum_probs=54.9
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccC
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPS 107 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs 107 (252)
-+|-..|.+||++.-+ - ..||-.++|..+. ++.+..+.-+++.|-.+||++. .-|+ ++=-=|+++--.|.
T Consensus 17 ~glk~~eI~IY~lLve-~-~~~mri~ei~rEl--~is~rtvr~~v~~l~rrGll~r-elvq-kgWvGYiya~~~P~ 86 (113)
T COG5625 17 IGLKKNEIRIYSLLVE-K-GRGMRIREIQREL--GISERTVRAAVAVLLRRGLLAR-ELVQ-KGWVGYIYATTPPP 86 (113)
T ss_pred cCCCcchhhhhhHHHH-h-cCCchHHHHHHHH--hHHHHHHHHHHHHHHHhhHHHH-HHHh-ccceeeEecCCCCc
Confidence 3566678999999988 4 4588999999999 9999999999999999999985 2233 35556776665554
No 298
>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=47.52 E-value=94 Score=26.81 Aligned_cols=47 Identities=9% Similarity=0.111 Sum_probs=39.3
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
...++.+|.+++.+|..+|++.+ .++..-+.+.|+.|+-.|.|++..
T Consensus 145 ~~~IL~~l~~~g~~s~~eia~~l--------~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 145 ELKVLEVLKAEGEKSVKNIAKKL--------GKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred HHHHHHHHHHcCCcCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEEc
Confidence 45678888888889999999876 356778999999999999999874
No 299
>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=47.50 E-value=61 Score=25.57 Aligned_cols=36 Identities=14% Similarity=0.309 Sum_probs=30.7
Q ss_pred CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 141 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 141 ~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+.+|.++|++.+. ++..-+.++++.|+-.|.|....
T Consensus 24 ~~~s~~eia~~~~--------i~~~~v~~il~~L~~~gli~~~~ 59 (132)
T TIGR00738 24 GPVSVKEIAERQG--------ISRSYLEKILRTLRRAGLVESVR 59 (132)
T ss_pred CcCcHHHHHHHHC--------cCHHHHHHHHHHHHHCCcEEecc
Confidence 4889999988754 67899999999999999998754
No 300
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=47.21 E-value=74 Score=24.09 Aligned_cols=52 Identities=12% Similarity=0.172 Sum_probs=39.4
Q ss_pred HHHHHHHHHHHHHhhhC---CCCCHHHHHHHHHH---cCCcceecCHHHHHHHHHHHhhcC
Q 025493 124 EFIKVVKSQCLKQIIKL---KVATLEGISDSIKR---SGAFKVDLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 124 efV~~l~~~~~~~i~~~---~~~T~~~I~~~i~~---~~i~~~~Ls~~di~~IL~tLVyDg 178 (252)
+-|..|-....+|-.+. ++.+.+|+.+.+++ .| ..++.++|+++++.+-.|+
T Consensus 7 ~~~~~~i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg---~k~t~~ev~~m~~~~D~d~ 64 (88)
T cd05029 7 QAIGLLVAIFHKYSGREGDKNTLSKKELKELIQKELTIG---SKLQDAEIAKLMEDLDRNK 64 (88)
T ss_pred HHHHHHHHHHHHHHccCCCCCEECHHHHHHHHHHHHhcC---CCCCHHHHHHHHHHhcCCC
Confidence 34666777777787754 49999999999975 24 4579999999999885443
No 301
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=47.08 E-value=70 Score=28.00 Aligned_cols=57 Identities=16% Similarity=0.221 Sum_probs=46.4
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCe
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGK 96 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~r 96 (252)
..||.-+..++.+|.= ++.|.+.+|..-- |... .++++.|+.+|||+++.--..++|
T Consensus 88 ~~LSraalEtLAiIAY---~QPiTR~eI~~iR--Gv~~---~~~i~~L~e~glI~~~g~~~~~Gr 144 (184)
T COG1386 88 RELSRAALETLAIIAY---KQPVTRSEIEEIR--GVAV---SQVISTLLERGLIREVGRRDTPGR 144 (184)
T ss_pred ccccHHHHHHHHHHHH---cCCccHHHHHHHh--CccH---HHHHHHHHHCCCeEecCCCCCCCC
Confidence 4699999999999966 6679999999877 5444 448999999999999976666665
No 302
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=47.00 E-value=47 Score=28.98 Aligned_cols=44 Identities=23% Similarity=0.440 Sum_probs=38.6
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
..||+.|..|+++|.+ |-..++|-.++ ++...+|...+..+-+|
T Consensus 147 ~~LT~RE~eVL~lla~-----G~snkeIA~~L--~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAE-----GLSNKEIAEEL--NLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHC-----CCCHHHHHHHH--CCCHhHHHHHHHHHHHH
Confidence 4799999999999999 99999999999 99999988777666544
No 303
>PF10711 DUF2513: Hypothetical protein (DUF2513); InterPro: IPR019650 The function of this family is not known.
Probab=46.77 E-value=56 Score=25.43 Aligned_cols=75 Identities=16% Similarity=0.143 Sum_probs=50.3
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccC
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSE 118 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d 118 (252)
|-|+-.||+ ...-..+. ....-. +....++.=+++.|...|||.....-...+.-.|...+|+++
T Consensus 8 R~iLl~iE~-~~~~~~~~-~~~~~~--~y~~~~i~YHl~lL~eagli~~~~~~~~~~~~~~~i~~LT~~----------- 72 (102)
T PF10711_consen 8 RDILLEIEE-NPDPPNPI-EEDEID--GYSKEEIAYHLKLLDEAGLIEGSVSGTMNGPYSFIIKRLTWS----------- 72 (102)
T ss_pred HHHHHHHHc-CCCcCccc-chhccc--CCCHHHHHHHHHHHHHCCCeeeccccccCCccchhhcccChh-----------
Confidence 456667777 65554443 111223 788889999999999999999976655445555666666666
Q ss_pred CcCCHHHHHHHHH
Q 025493 119 GSLDTEFIKVVKS 131 (252)
Q Consensus 119 ~e~D~efV~~l~~ 131 (252)
=.+|++.+|.
T Consensus 73 ---GHdFLd~IRd 82 (102)
T PF10711_consen 73 ---GHDFLDAIRD 82 (102)
T ss_pred ---HHHHHHHhcC
Confidence 2567776664
No 304
>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=46.28 E-value=1.1e+02 Score=24.57 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 141 KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 141 ~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+.+|.++|.+-+ .++..-+++|++.|+--|.|...+
T Consensus 24 ~~~s~~~ia~~~--------~ip~~~l~kil~~L~~~glv~s~~ 59 (135)
T TIGR02010 24 GPVTLADISERQ--------GISLSYLEQLFAKLRKAGLVKSVR 59 (135)
T ss_pred CcCcHHHHHHHH--------CcCHHHHHHHHHHHHHCCceEEEe
Confidence 468999998754 578999999999999999998765
No 305
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=45.84 E-value=83 Score=23.18 Aligned_cols=44 Identities=16% Similarity=0.185 Sum_probs=38.9
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHh
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVV 175 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLV 175 (252)
.+....+|+..+...|.+.|..-..+.| -..|+.+|+++.+.+.
T Consensus 18 ar~~~~k~l~~NPpine~mir~M~~QMG---~kpSekqi~Q~m~~mk 61 (64)
T PF03672_consen 18 ARKYMEKQLKENPPINEKMIRAMMMQMG---RKPSEKQIKQMMRSMK 61 (64)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHhC---CCccHHHHHHHHHHHH
Confidence 5677888999999999999999999999 6899999999988763
No 306
>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=45.80 E-value=98 Score=23.48 Aligned_cols=54 Identities=22% Similarity=0.339 Sum_probs=36.3
Q ss_pred HHHHHHhhh-CCCCCHHHHHHHHHHcCCcc---------------eecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 131 SQCLKQIIK-LKVATLEGISDSIKRSGAFK---------------VDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 131 ~~~~~~i~~-~~~~T~~~I~~~i~~~~i~~---------------~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+.+++.|.+ .+..|...|.+.++-+.-.+ ..++..+++++++.|+.+|.|....
T Consensus 7 ~~il~~V~~~~~~~~~~~ivdvlrGs~~~~i~~~~~~~l~~yG~gk~~~~~~~~~li~~Li~~g~L~~~~ 76 (106)
T PF09382_consen 7 KKILSCVQRLKQRFGLSQIVDVLRGSKSKKIREKGHDQLPTYGIGKDMSKDDWERLIRQLILEGYLSEDN 76 (106)
T ss_dssp HHHHHHHHHTTT-S-HHHHHHHHTT-S-CCCHHTTGGGSTTTTTTTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHHHHhccccHHHHHHHHHhccchhhhhcCCCcCcccCCcccCCHHHHHHHHHHHHHcCCceecC
Confidence 445555554 35788888888888654221 3579999999999999999996543
No 307
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=45.50 E-value=56 Score=29.21 Aligned_cols=85 Identities=16% Similarity=0.058 Sum_probs=59.6
Q ss_pred HHHHHHHhh---cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEec-ccccCCCccCCcc
Q 025493 40 LIYDVIRSN---KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAV-EFEPSKDISGGAW 115 (252)
Q Consensus 40 ~vy~~I~~~---ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~-~lePs~eiTGG~w 115 (252)
.|...|.++ .|..==--++|..+. |..-+.|.-+|+.|+.+|||-.= ++.-+|..- +..| ...---+|
T Consensus 18 ~i~~~I~~g~~~~G~~LP~EreLae~f--gVSR~~vREAl~~L~a~Glve~r-----~G~Gt~V~~~~~~~-~~~~~~~~ 89 (241)
T COG2186 18 QIGALIVSGELPPGDRLPSERELAERF--GVSRTVVREALKRLEAKGLVEIR-----QGSGTFVRPRSEWN-LDPLVLPL 89 (241)
T ss_pred HHHHHHHcCCCCCCCCCCCHHHHHHHH--CCCcHHHHHHHHHHHHCCCeeec-----CCCceEecCCccCc-cchhhhHH
Confidence 355666650 122222358999999 99999999999999999999873 366677752 2222 34445578
Q ss_pred ccCCcCCHHHHHHHHHH
Q 025493 116 YSEGSLDTEFIKVVKSQ 132 (252)
Q Consensus 116 y~d~e~D~efV~~l~~~ 132 (252)
..+..+|..++..|.+.
T Consensus 90 ~~~~~~~~~~~~~lle~ 106 (241)
T COG2186 90 RLLLEDDPDSIFDLLEA 106 (241)
T ss_pred HHHcccChhhHHHHHHH
Confidence 88888888888887765
No 308
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=45.40 E-value=22 Score=23.43 Aligned_cols=30 Identities=23% Similarity=0.401 Sum_probs=19.7
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhcCC
Q 025493 53 GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL 84 (252)
Q Consensus 53 GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l 84 (252)
|...++|.+.+ |++.++|.+.+|...+.|+
T Consensus 17 G~s~~~ia~~l--gvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 17 GWSIREIAKRL--GVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp T--HHHHHHHH--TS-HHHHHHHHT-------
T ss_pred CCCHHHHHHHH--CcCHHHHHHHHHHcccccc
Confidence 99999999999 9999999999999887774
No 309
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=45.35 E-value=33 Score=30.22 Aligned_cols=45 Identities=13% Similarity=0.199 Sum_probs=35.6
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
|.+==.-++|..+. |....+|.|+|..|++.|||.+. +++=.|..
T Consensus 32 G~~LPsE~eLa~~~--~VSR~TVR~Al~~L~~eGli~r~-----~G~GtfV~ 76 (241)
T PRK10079 32 GDYLPAEQQLAARY--EVNRHTLRRAIDQLVEKGWVQRR-----QGVGVLVL 76 (241)
T ss_pred CCcCCCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe-----cCCEEEEe
Confidence 33333357899999 99999999999999999999986 35556654
No 310
>COG4742 Predicted transcriptional regulator [Transcription]
Probab=45.32 E-value=37 Score=31.43 Aligned_cols=53 Identities=17% Similarity=0.265 Sum_probs=41.5
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccc
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEF 104 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~l 104 (252)
+-++-++.+ ..-...+|+..+ |.+...+...||.|+..+||-. ..++|.|.++
T Consensus 16 k~lLllL~e----gPkti~EI~~~l--~vs~~ai~pqiKkL~~~~LV~~-------~~~~Y~LS~~ 68 (260)
T COG4742 16 KDLLLLLKE----GPKTIEEIKNEL--NVSSSAILPQIKKLKDKGLVVQ-------EGDRYSLSSL 68 (260)
T ss_pred HHHHHHHHh----CCCCHHHHHHHh--CCCcHHHHHHHHHHhhCCCEEe-------cCCEEEecch
Confidence 334444444 234578999999 9999999999999999999987 3678988764
No 311
>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=45.14 E-value=99 Score=21.33 Aligned_cols=51 Identities=6% Similarity=0.118 Sum_probs=42.4
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 127 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 127 ~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
+-.+..++.+|...+..|+.+|.+.+. ++...+..=|+.|+--|.|+.++.
T Consensus 9 ~p~R~~Il~~L~~~~~~t~~ela~~l~--------~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 9 DPTRLRILRLLASNGPMTVSELAEELG--------ISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp SHHHHHHHHHHHHCSTBEHHHHHHHHT--------S-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred CHHHHHHHHHHhcCCCCCHHHHHHHHC--------CCHHHHHHHHHHHHHCCCeEEecc
Confidence 456778899998889999999999873 678888999999999999997753
No 312
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 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, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=44.83 E-value=67 Score=22.20 Aligned_cols=35 Identities=17% Similarity=0.314 Sum_probs=24.7
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
.++..|.+ .|+ ...-.++. ++.+..|++.|+.||+
T Consensus 5 ~~f~~v~~-~gs----~~~AA~~l--~is~~~vs~~i~~LE~ 39 (60)
T PF00126_consen 5 RYFLAVAE-TGS----ISAAAEEL--GISQSAVSRQIKQLEE 39 (60)
T ss_dssp HHHHHHHH-HSS----HHHHHHHC--TSSHHHHHHHHHHHHH
T ss_pred HHHHHHHH-hCC----HHHHHHHh--hccchHHHHHHHHHHH
Confidence 34455555 442 23345567 9999999999999997
No 313
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=44.67 E-value=1.2e+02 Score=24.15 Aligned_cols=69 Identities=12% Similarity=0.154 Sum_probs=40.7
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.+.++.+.+ |++..+ |.--|+.|||++.+--. +|--+|++ +=|..|+.+
T Consensus 2 ~IgevA~~~--gvs~~t----LRyYe~~GLl~p~~r~~------------------~gyR~Y~~-----~~l~~l~~I-- 50 (127)
T cd04784 2 KIGELAKKT--GCSVET----IRYYEKEGLLPAPARSA------------------NNYRLYDE-----EHLERLLFI-- 50 (127)
T ss_pred CHHHHHHHH--CcCHHH----HHHHHHCCCCCCCCcCC------------------CCCeecCH-----HHHHHHHHH--
Confidence 467788888 888755 56779999997532111 22233443 333333332
Q ss_pred HHhhhCCCCCHHHHHHHHHHc
Q 025493 135 KQIIKLKVATLEGISDSIKRS 155 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~ 155 (252)
..++.. ..|++||.+++...
T Consensus 51 ~~lr~~-G~sL~eI~~~l~~~ 70 (127)
T cd04784 51 RRCRSL-DMSLDEIRTLLQLQ 70 (127)
T ss_pred HHHHHc-CCCHHHHHHHHHhh
Confidence 223333 58899999988743
No 314
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=44.60 E-value=35 Score=29.80 Aligned_cols=32 Identities=6% Similarity=0.187 Sum_probs=30.3
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.-++|..+. |+..+.|..+|+.|+..|||...
T Consensus 33 sE~eLae~~--gVSRt~VReAL~~L~~eGlv~~~ 64 (239)
T PRK04984 33 AERELSELI--GVTRTTLREVLQRLARDGWLTIQ 64 (239)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEe
Confidence 578999999 99999999999999999999975
No 315
>COG1167 ARO8 Transcriptional regulators containing a DNA-binding HTH domain and an aminotransferase domain (MocR family) and their eukaryotic orthologs [Transcription / Amino acid transport and metabolism]
Probab=44.56 E-value=3.1e+02 Score=26.80 Aligned_cols=141 Identities=16% Similarity=0.190 Sum_probs=80.4
Q ss_pred HHHHHHHhhcCCCcc--------cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc-----ccCCeeeEEec----
Q 025493 40 LIYDVIRSNKQDMGI--------WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI-----HNKGKKHLMAV---- 102 (252)
Q Consensus 40 ~vy~~I~~~ag~~GI--------w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv-----~~~~rK~YmL~---- 102 (252)
.||+.|++ +=..|. .+|++...+ ++..+++.++.+.|+.+|+|-+..-- .......-...
T Consensus 8 ql~~~i~~-~I~~g~l~~g~rLPs~R~la~~l--~vs~~Tv~~ay~~L~~~G~i~~~~gs~~~~~~~~~~~~~~~~~~~~ 84 (459)
T COG1167 8 QLAEQLRE-AILSGRLKPGDRLPSIRQLAQDL--GVSRSTVSRAYEELEARGYIESRPGSAPPSGRPVRLELLKPSDPEL 84 (459)
T ss_pred HHHHHHHH-HHHcCCCCCCCcCCcHHHHHHHh--CCcHHHHHHHHHHHHhCcceeeccCCCcccccccccchhhhhhccc
Confidence 45666665 444444 478999999 99999999999999999999997621 00001111111
Q ss_pred -ccccCCCccCCccccCCcCCHHHHHHHHHHHHHHh------h---hCCCCCH-HHHHHHHH-HcCCcc----e--ec-C
Q 025493 103 -EFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQI------I---KLKVATL-EGISDSIK-RSGAFK----V--DL-T 163 (252)
Q Consensus 103 -~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i------~---~~~~~T~-~~I~~~i~-~~~i~~----~--~L-s 163 (252)
+-.|+.---++.|-...-|+.+-.........+.. . ..+++.+ +.|++|+. ..|+.. + .- +
T Consensus 85 ~~~~~~~i~f~~g~p~~~~fp~~~~~~~~~~~~~~~~~~~~~~y~~~~G~~~LR~~ia~~l~~~~g~~~~~~~IiiT~G~ 164 (459)
T COG1167 85 LEDDPSVIDFAGGLPDPSLFPLEALRRALARVLRNYGASLALQYGPTAGLPELREAIAAYLLARRGISCEPEQIVITSGA 164 (459)
T ss_pred ccCCCceecCCCCCCCcccCCHHHHHHHHHHHHhhcchhhhhcCCCCCCcHHHHHHHHHHHHHhcCCccCcCeEEEeCCH
Confidence 11133333333445556788776665555444322 1 1344444 48899998 667543 2 22 3
Q ss_pred HHHHHHHHHHHhhcCeeEEE
Q 025493 164 KQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 164 ~~di~~IL~tLVyDgkIE~v 183 (252)
.+-+.-+++.|.--|...-+
T Consensus 165 q~al~l~~~~l~~pGd~v~v 184 (459)
T COG1167 165 QQALDLLLRLLLDPGDTVLV 184 (459)
T ss_pred HHHHHHHHHHhCCCCCEEEE
Confidence 33444455555544544433
No 316
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=44.48 E-value=22 Score=24.42 Aligned_cols=25 Identities=16% Similarity=0.453 Sum_probs=19.1
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHH
Q 025493 51 DMGIWTRDMKRELKVNLPDNIVTKSIK 77 (252)
Q Consensus 51 ~~GIw~~dik~~~~~~l~~~~l~k~lK 77 (252)
.+||-.++|.+++ |++.+++++.++
T Consensus 8 ~~~it~~~La~~~--gis~~tl~~~~~ 32 (63)
T PF13443_consen 8 ERGITQKDLARKT--GISRSTLSRILN 32 (63)
T ss_dssp HTT--HHHHHHHH--T--HHHHHHHHT
T ss_pred HcCCCHHHHHHHH--CcCHHHHHHHHh
Confidence 4899999999999 999999999886
No 317
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=44.44 E-value=26 Score=32.19 Aligned_cols=53 Identities=19% Similarity=0.243 Sum_probs=43.4
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
.|..-|+++...++. .+=|.++|...-. ++..+++.+++-+||+||++-.++.
T Consensus 13 ~m~~~e~l~~laae~---hkiiTirdvae~~--ev~~n~lr~lasrLekkG~LeRi~r 65 (269)
T COG5340 13 SMRESELLSHLAAEG---HKIITIRDVAETL--EVAPNTLRELASRLEKKGWLERILR 65 (269)
T ss_pred hHHHHHHHHHHHHHh---CceEEeHHhhhhc--cCCHHHHHHHHhhhhhcchhhhhcC
Confidence 455667777766655 4567889988888 9999999999999999999999853
No 318
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=44.39 E-value=45 Score=29.95 Aligned_cols=37 Identities=11% Similarity=0.381 Sum_probs=33.5
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
++.++..+++.+++ +..+....|+|+.||..++|-.-
T Consensus 16 ~~~~~t~~ela~~l--~~S~qta~R~l~~le~~~~I~R~ 52 (214)
T COG1339 16 RGVKVTSSELAKRL--GVSSQTAARKLKELEDEGYITRT 52 (214)
T ss_pred cCccccHHHHHHHh--CcCcHHHHHHHHhhccCCcEEEE
Confidence 34679999999999 99999999999999999999763
No 319
>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=44.36 E-value=34 Score=23.78 Aligned_cols=40 Identities=15% Similarity=0.156 Sum_probs=30.0
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcCCC---hHHHHHHHHHH
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLP---DNIVTKSIKSL 79 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~---~~~l~k~lK~L 79 (252)
|--|.++|.+ +|+..++..+|-.++++ .+ ...|.|+++-|
T Consensus 8 eLgI~dii~~-~g~~~ls~~eia~~l~~-~~p~~~~~L~RimR~L 50 (51)
T PF08100_consen 8 ELGIPDIIHN-AGGGPLSLSEIAARLPT-SNPSAPPMLDRIMRLL 50 (51)
T ss_dssp HTTHHHHHHH-HTTS-BEHHHHHHTSTC-T-TTHHHHHHHHHHHH
T ss_pred HcCcHHHHHH-cCCCCCCHHHHHHHcCC-CCcchHHHHHHHHHHh
Confidence 4458899999 99999999999998841 33 34778888776
No 320
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=44.10 E-value=70 Score=26.32 Aligned_cols=47 Identities=19% Similarity=0.204 Sum_probs=35.1
Q ss_pred HHHHHHHHHHhhhC--CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcC
Q 025493 127 KVVKSQCLKQIIKL--KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 127 ~~l~~~~~~~i~~~--~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDg 178 (252)
+.|-+...+||+.. ..++.++=.+||++.| |+.+||++.|+..--+.
T Consensus 3 e~li~~A~~FL~~p~V~~sp~~~k~~FL~sKG-----Lt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 3 EDLIEQAVKFLQDPKVRNSPLEKKIAFLESKG-----LTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHHCTTTCCCS-HHHHHHHHHHCT-------HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHHhCCcccccCCHHHHHHHHHcCC-----CCHHHHHHHHHhcCCcc
Confidence 46777888999865 4566889999999998 88999999999876665
No 321
>PRK04158 transcriptional repressor CodY; Validated
Probab=44.08 E-value=34 Score=31.66 Aligned_cols=62 Identities=10% Similarity=0.300 Sum_probs=50.0
Q ss_pred CCCCCh-HHHHHHHHHHhhcCCCcccHH-HHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC
Q 025493 31 SDSLTD-HERLIYDVIRSNKQDMGIWTR-DMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG 95 (252)
Q Consensus 31 ~~~l~~-~e~~vy~~I~~~ag~~GIw~~-dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~ 95 (252)
++.||= |-..|..++++.-|++|+-.+ .|..+. |++.++|-.+|++||+-|+|.+ +|.--++
T Consensus 177 i~tLSySEleAv~hIf~eL~g~EG~lvASkiADrv--gITRSVIVNALRK~ESAGvIES-rSlGMKG 240 (256)
T PRK04158 177 INTLSYSELEAVEHIFEELDGNEGLLVASKIADRV--GITRSVIVNALRKLESAGVIES-RSLGMKG 240 (256)
T ss_pred HHhcCHhHHHHHHHHHHhcCCCcceEEeeeccccc--CCchhhhhhhhhhhhcccceee-ccCCCCc
Confidence 556665 334777888888999999865 577788 9999999999999999999999 6765543
No 322
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=43.99 E-value=70 Score=21.77 Aligned_cols=44 Identities=9% Similarity=0.240 Sum_probs=37.2
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
.|+.+|++++-+..= ..|.-..+|...- |++++++.|+.+..+.
T Consensus 2 kLs~~d~lll~L~~L---R~~~~~~~La~~F--gIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 2 KLSLEDQLLLTLMYL---RLNLTFQDLAYRF--GISQSTVSRIFHEWIP 45 (53)
T ss_pred CCCHHHHHHHHHHHH---HcCCcHhHHhhhe--eecHHHHHHHHHHHHH
Confidence 578888888888776 5678889999999 9999999999988754
No 323
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=43.66 E-value=32 Score=32.65 Aligned_cols=37 Identities=11% Similarity=0.238 Sum_probs=34.4
Q ss_pred cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
-=..|+-+++|..++ ||....++|-|+...++|+||=
T Consensus 22 YY~~gltQ~eIA~~L--giSR~~v~rlL~~Ar~~GiV~I 58 (321)
T COG2390 22 YYVEGLTQSEIAERL--GISRATVSRLLAKAREEGIVKI 58 (321)
T ss_pred HHhcCCCHHHHHHHh--CCCHHHHHHHHHHHHHCCeEEE
Confidence 456799999999999 9999999999999999999984
No 324
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=43.65 E-value=86 Score=24.89 Aligned_cols=45 Identities=27% Similarity=0.349 Sum_probs=35.7
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
...||+.|+.|+.++.+ |.-.++|..++ +++..+|...++.+-.|
T Consensus 147 ~~~lt~~e~~vl~l~~~-----g~~~~~Ia~~l--~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 147 PPLLTPRERQILKLITE-----GYTNRDIAEQL--SISIKTVETHRLNMMRK 191 (211)
T ss_pred ccCCCHHHHHHHHHHHC-----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 34699999999999866 45689999999 99988887777665443
No 325
>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=43.55 E-value=43 Score=24.71 Aligned_cols=39 Identities=13% Similarity=0.286 Sum_probs=30.3
Q ss_pred hhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 137 IIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 137 i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
.......+.++|++.+. ++.++++.+|-.|+.+|+|.-.
T Consensus 55 ~~~y~~i~~~~ia~~l~--------~~~~~vE~~l~~~I~~~~i~~~ 93 (105)
T PF01399_consen 55 SKPYSSISISEIAKALQ--------LSEEEVESILIDLISNGLIKAK 93 (105)
T ss_dssp HHC-SEEEHHHHHHHHT--------CCHHHHHHHHHHHHHTTSSEEE
T ss_pred HHHhcccchHHHHHHhc--------cchHHHHHHHHHHHHCCCEEEE
Confidence 34556778888887763 5669999999999999999743
No 326
>PF13833 EF-hand_8: EF-hand domain pair; PDB: 3KF9_A 1TTX_A 1WLZ_A 1ALV_A 1NX3_A 1ALW_A 1NX2_A 1NX1_A 1NX0_A 1DF0_A ....
Probab=43.37 E-value=40 Score=22.31 Aligned_cols=37 Identities=16% Similarity=0.258 Sum_probs=29.8
Q ss_pred CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcC
Q 025493 140 LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 140 ~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDg 178 (252)
.+..|.+++..++...|+.. ++.+++..|++.+=.|+
T Consensus 2 ~G~i~~~~~~~~l~~~g~~~--~s~~e~~~l~~~~D~~~ 38 (54)
T PF13833_consen 2 DGKITREEFRRALSKLGIKD--LSEEEVDRLFREFDTDG 38 (54)
T ss_dssp SSEEEHHHHHHHHHHTTSSS--SCHHHHHHHHHHHTTSS
T ss_pred cCEECHHHHHHHHHHhCCCC--CCHHHHHHHHHhcccCC
Confidence 35778999999997777543 99999999999876664
No 327
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=43.16 E-value=57 Score=24.33 Aligned_cols=62 Identities=11% Similarity=0.123 Sum_probs=41.5
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeeccc
Q 025493 130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVS 205 (252)
Q Consensus 130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~ 205 (252)
|=.++.+|...+.++..+|.+.+ .++...+.+-|+.|+-.|.|+..+.... +..+..|+++.
T Consensus 2 Rl~Il~~L~~~~~~~f~~L~~~l--------~lt~g~Ls~hL~~Le~~GyV~~~k~~~~------~~p~t~~~lT~ 63 (80)
T PF13601_consen 2 RLAILALLYANEEATFSELKEEL--------GLTDGNLSKHLKKLEEAGYVEVEKEFEG------RRPRTWYSLTD 63 (80)
T ss_dssp HHHHHHHHHHHSEEEHHHHHHHT--------T--HHHHHHHHHHHHHTTSEEEEEE-SS------S--EEEEEE-H
T ss_pred HHHHHHHHhhcCCCCHHHHHHHh--------CcCHHHHHHHHHHHHHCCCEEEEEeccC------CCCeEEEEECH
Confidence 44567777777778888887764 4778899999999999999997664321 12345676654
No 328
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=43.01 E-value=1e+02 Score=26.94 Aligned_cols=52 Identities=17% Similarity=0.216 Sum_probs=43.8
Q ss_pred HHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 37 HERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
+-..|+.++.+ -| -+.-.+|...+ ++-++.+.|+|-.|-..|+|.-.+....
T Consensus 19 ~~~~v~~~l~~-kg--e~tDeela~~l--~i~~~~vrriL~~L~e~~li~~~k~rd~ 70 (176)
T COG1675 19 EAVLVVDALLE-KG--ELTDEELAELL--GIKKNEVRRILYALYEDGLISYRKKRDE 70 (176)
T ss_pred hhhHHHHHHHh-cC--CcChHHHHHHh--CccHHHHHHHHHHHHhCCceEEEeeccc
Confidence 35667777777 55 58888999999 9999999999999999999998777654
No 329
>PF06648 DUF1160: Protein of unknown function (DUF1160); InterPro: IPR010594 This entry is represented by Autographa californica nuclear polyhedrosis virus (AcMNPV), Orf75; it is a family of uncharacterised viral proteins.
Probab=42.90 E-value=44 Score=27.58 Aligned_cols=65 Identities=15% Similarity=0.193 Sum_probs=52.2
Q ss_pred cccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 115 WYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 115 wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
|..|.+=|.-|-+.+.+++..||.+. .+.+.+..-+....- .+||..++.=+.+....|+.|..+
T Consensus 25 ylkel~~d~tf~~Kl~~Il~mFl~~e--id~e~~y~l~~~~d~--~~LT~~Qi~Yl~~~~~~n~~I~~I 89 (122)
T PF06648_consen 25 YLKELERDETFLDKLIKILKMFLNDE--IDVEDMYNLFGAVDG--LKLTRSQIDYLYNRVYNNRYIINI 89 (122)
T ss_pred HHHHhccCchHHHHHHHHHHHHHhCC--CCHHHHHHHHhcccH--hhcCHHHHHHHHHHHHccHHHHHH
Confidence 55666678889999999999999876 788999988886631 389999998888888888877643
No 330
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=42.86 E-value=88 Score=21.83 Aligned_cols=26 Identities=0% Similarity=0.045 Sum_probs=18.2
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCee
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIK 86 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK 86 (252)
.++++.+.+ ++++++|. ..|+++.+.
T Consensus 2 ~i~evA~~~--gvs~~tlR----~~~~~g~l~ 27 (67)
T cd04764 2 TIKEVSEII--GVKPHTLR----YYEKEFNLY 27 (67)
T ss_pred CHHHHHHHH--CcCHHHHH----HHHHhcCCC
Confidence 467788888 89988765 556665543
No 331
>PRK14135 recX recombination regulator RecX; Provisional
Probab=42.76 E-value=90 Score=27.94 Aligned_cols=59 Identities=17% Similarity=0.253 Sum_probs=46.2
Q ss_pred CCcCCHHHHHHHHHH---------HHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEE
Q 025493 118 EGSLDTEFIKVVKSQ---------CLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 118 d~e~D~efV~~l~~~---------~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
+.++|.+.++.|... .+.||.++ .-|-.+|.+.+.+.| ++.+.|+.+|+.|.-.|.|.-
T Consensus 39 g~~l~~~~~~~i~~~~~~~~a~~~Al~~L~~r-~~s~~el~~kL~~kg-----~~~~~Ie~vl~~l~~~~~ldD 106 (263)
T PRK14135 39 GKELDEEDLEEIQYADQVSKGKNLALYYLSYQ-MRTEKEVRDYLKKHE-----ISEEIISEVIDKLKEEKYIDD 106 (263)
T ss_pred CCcCCHHHHHHHHHHHHHHHHHHHHHHHhhhc-cccHHHHHHHHHHCC-----CCHHHHHHHHHHHHHcCCCCH
Confidence 578999988888643 45566555 445699999999887 458999999999999988753
No 332
>PRK10710 DNA-binding transcriptional regulator BaeR; Provisional
Probab=42.67 E-value=50 Score=27.52 Aligned_cols=48 Identities=13% Similarity=0.118 Sum_probs=38.7
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcC-----CC----hHHHHHHHHHHHhc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVN-----LP----DNIVTKSIKSLQNK 82 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~-----l~----~~~l~k~lK~Le~k 82 (252)
-.||+.|+.|+.++.+ ..++|+..++|-.+. . .. ...++++.++|+..
T Consensus 159 ~~Lt~~e~~il~~l~~-~~~~~~s~~~i~~~~--~~~~~~~~~~tv~~~i~~lr~kl~~~ 215 (240)
T PRK10710 159 LDLTPAEFRLLKTLSH-EPGKVFSREQLLNHL--YDDYRVVTDRTIDSHIKNLRRKLESL 215 (240)
T ss_pred eecCHHHHHHHHHHHh-CCCceEcHHHHHHHh--cCcCcCCCccCHHHHHHHHHHHhhcC
Confidence 3599999999999999 889999999999987 4 44 44667777778743
No 333
>PF13182 DUF4007: Protein of unknown function (DUF4007)
Probab=42.56 E-value=56 Score=30.24 Aligned_cols=90 Identities=16% Similarity=0.199 Sum_probs=61.5
Q ss_pred cchhHHHhhccCCCccccc-CCCCCCCCCCCChHHHHHHHHHH----hhcCCCcccHHHHHHHhh-c----CCChHHHHH
Q 025493 5 FTDLYLLGLAKGSGMSKRK-RPDSNAPSDSLTDHERLIYDVIR----SNKQDMGIWTRDMKRELK-V----NLPDNIVTK 74 (252)
Q Consensus 5 ~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~l~~~e~~vy~~I~----~~ag~~GIw~~dik~~~~-~----~l~~~~l~k 74 (252)
|.+|.|++.+.+++ .+++ +.. ..+|+ .+..+|.+++ ...|..-|-..+|-..-+ | +|+...|..
T Consensus 173 L~eLgLi~~~~~~~-~y~~~~~~----~~~l~-~~i~~YaL~~~~~~~~~~~~sis~~~L~~~~~sPGriF~L~~~~l~~ 246 (286)
T PF13182_consen 173 LGELGLIREVRGGG-RYRFNRGP----KPNLP-PEIFLYALLDFAERESPGRNSISFDELLNEPGSPGRIFKLDEESLAE 246 (286)
T ss_pred chhhCCeeEecCCC-eEEEcCCC----CCCCC-HHHHHHHHHHHHHHhCCCCcEEEHHHHhcCCCCcceEeccCHHHHHH
Confidence 67788888883333 3333 332 23566 5678888888 424888899999965321 1 799999999
Q ss_pred HHHHHHhc-CCeeeeeccccCCeeeEEec
Q 025493 75 SIKSLQNK-SLIKEVVNIHNKGKKHLMAV 102 (252)
Q Consensus 75 ~lK~Le~k-~lIK~vksv~~~~rK~YmL~ 102 (252)
.|..|++. +.|+-...- .-+.+|+.-
T Consensus 247 ~L~~l~~~~g~i~~~~Ta--Gl~qv~~~~ 273 (286)
T PF13182_consen 247 RLEQLEEIYGFISWSDTA--GLDQVYLKD 273 (286)
T ss_pred HHHHHHhhcCcEEEEEcC--CCeEEEecc
Confidence 99999999 888754322 247777664
No 334
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.21 E-value=1.6e+02 Score=22.64 Aligned_cols=70 Identities=14% Similarity=0.175 Sum_probs=42.6
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
+.+++.+.+ |++.++|. .-|+.|||.++++- .+.+. |++ +=|..|+.+
T Consensus 2 ~I~e~a~~~--gvs~~tLR----~ye~~Gll~p~r~~--~g~R~-----------------Y~~-----~dv~~l~~I-- 49 (96)
T cd04774 2 KVDEVAKRL--GLTKRTLK----YYEEIGLVSPERSE--GRYRL-----------------YSE-----EDLKRLERI-- 49 (96)
T ss_pred CHHHHHHHH--CcCHHHHH----HHHHCCCCCCCcCC--CCCEE-----------------ECH-----HHHHHHHHH--
Confidence 567888899 99988764 45788998754321 12323 333 223333332
Q ss_pred HHhhhCCCCCHHHHHHHHHHcC
Q 025493 135 KQIIKLKVATLEGISDSIKRSG 156 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~~ 156 (252)
..+.+....|+++|..++....
T Consensus 50 ~~L~~~~G~~l~ei~~~l~~~~ 71 (96)
T cd04774 50 LRLREVLGFSLQEVTHFLERPL 71 (96)
T ss_pred HHHHHHcCCCHHHHHHHHhccc
Confidence 2344424688999999997654
No 335
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=42.13 E-value=1.7e+02 Score=25.73 Aligned_cols=52 Identities=25% Similarity=0.437 Sum_probs=39.7
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC-eeeE
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG-KKHL 99 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~-rK~Y 99 (252)
||.++-- -++-+...+|...| +|..+.++-.+|.|+.-+|++.+ +.|| ||-|
T Consensus 31 iYgilyl--s~~Pmtl~Ei~E~l--g~Sks~vS~~lkkL~~~~lV~~~---~~~G~Rk~~ 83 (177)
T COG1510 31 IYGILYL--SRKPLTLDEIAEAL--GMSKSNVSMGLKKLQDWNLVKKV---FEKGDRKDY 83 (177)
T ss_pred Hhhhhee--cCCCccHHHHHHHH--CCCcchHHHHHHHHHhcchHHhh---hccCcchhh
Confidence 4444432 34567788999999 99999999999999999999886 3442 5555
No 336
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=42.10 E-value=64 Score=33.55 Aligned_cols=48 Identities=21% Similarity=0.466 Sum_probs=42.0
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcCCCh----HHHHHHHHHHHhcCCeeee
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPD----NIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~----~~l~k~lK~Le~k~lIK~v 88 (252)
+..|++++++ +..+++-.++|.+++ +++. ..+.++|+.|+..|.|...
T Consensus 4 ~~~il~~l~~-~~~~~~~~~~l~~~l--~~~~~~~~~~l~~~l~~l~~~g~l~~~ 55 (709)
T TIGR02063 4 RELILEFLKS-KKGKPISLKELAKAF--HLKGADEKKALRKRLRALEDDGLVKKN 55 (709)
T ss_pred HHHHHHHHHh-CCCCCCCHHHHHHHh--CCCChHHHHHHHHHHHHHHHCCCEEEc
Confidence 4469999999 999999999999999 8864 4699999999999999753
No 337
>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=42.02 E-value=44 Score=28.51 Aligned_cols=46 Identities=17% Similarity=0.330 Sum_probs=37.8
Q ss_pred HHHHHHHhhc-------CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 40 LIYDVIRSNK-------QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 40 ~vy~~I~~~a-------g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.||+.|++ . .+.=|-.++|..+. |+..+.|..+|+.|+..|||...
T Consensus 15 ~v~~~l~~-~I~~g~l~pG~~L~e~~La~~l--gVSRtpVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 15 LVQDEIER-AILSGELPPGAKLNESDIAARL--GVSRGPVREAFRALEEAGLVRNE 67 (212)
T ss_pred HHHHHHHH-HHHcCCCCCCCEecHHHHHHHh--CCChHHHHHHHHHHHHCCCEEEe
Confidence 57777776 3 23335678999999 99999999999999999999864
No 338
>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=41.98 E-value=28 Score=30.35 Aligned_cols=43 Identities=14% Similarity=0.236 Sum_probs=33.9
Q ss_pred hCCCCCHHHHHHHHHH-cCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 139 KLKVATLEGISDSIKR-SGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 139 ~~~~~T~~~I~~~i~~-~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
++.+=|+.|+-..+-+ .|| +...|..+|+.||-||+|...+-+
T Consensus 8 ~~~~y~lKELEK~~pK~~gI-----~~~~VKdvlq~LvDDglV~~EKiG 51 (188)
T PF03962_consen 8 SKDFYTLKELEKLAPKEKGI-----VSMSVKDVLQSLVDDGLVHVEKIG 51 (188)
T ss_pred cCCcccHHHHHHHcccccCC-----chhhHHHHHHHHhccccchhhhcc
Confidence 5567788888888776 564 567899999999999999765543
No 339
>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=41.83 E-value=63 Score=23.60 Aligned_cols=53 Identities=15% Similarity=0.228 Sum_probs=40.8
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM 100 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym 100 (252)
+-++|.+ . .-+.+.-|.++. .+--+.-.+++-.||..|+|-+... ++.|+|++
T Consensus 10 a~~~V~~-~--~~~S~S~lQR~~--~IGynrAariid~lE~~GiV~p~~g--~~~R~Vl~ 62 (63)
T smart00843 10 AVELVIE-T--QKASTSLLQRRL--RIGYNRAARLIDQLEEEGIVGPANG--SKPREVLV 62 (63)
T ss_pred HHHHHHH-h--CCCChHHHHHHH--hcchhHHHHHHHHHHHCcCCCCCCC--CCCCeecC
Confidence 3445555 4 345888899999 8999999999999999999998665 35677753
No 340
>PRK14134 recX recombination regulator RecX; Provisional
Probab=41.77 E-value=97 Score=28.66 Aligned_cols=59 Identities=17% Similarity=0.149 Sum_probs=46.9
Q ss_pred cCCcCCHHHHHHHHH---------HHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeE
Q 025493 117 SEGSLDTEFIKVVKS---------QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIM 181 (252)
Q Consensus 117 ~d~e~D~efV~~l~~---------~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE 181 (252)
.+.++|.+.++.|.. ..++||..+ .-|-.|+.+++.+.| ++++.|+++|+-|.-.|-|-
T Consensus 42 kG~eld~e~~~ei~~~~~~~~a~~~AL~~Ls~r-~rSe~Elr~KL~~k~-----~~~~~Ie~vI~~L~e~~yld 109 (283)
T PRK14134 42 KGKVIDVNSLNDIIKEDNYIKCKGYALKYIEKS-YKTEKQIKEKLYLKE-----YDEDAVNRVIRFLKEYNFID 109 (283)
T ss_pred CCCCcCHHHHHHHHHHHHHHHHHHHHHHHhccC-cchHHHHHHHHHhCC-----CCHHHHHHHHHHHHHCCCCC
Confidence 356999999988863 344555544 778999999999888 46899999999999988774
No 341
>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=41.68 E-value=61 Score=24.13 Aligned_cols=50 Identities=16% Similarity=0.201 Sum_probs=31.5
Q ss_pred HHHHHHHHhhhC-C---CCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 129 VKSQCLKQIIKL-K---VATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 129 l~~~~~~~i~~~-~---~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
+++.|+.||+.. + --=..|+..-+- +....+|..|++.||-+|+++=-.+
T Consensus 2 ~K~~Ile~L~~k~~~KskfYfkD~~k~~p-------d~k~R~vKKi~~~LV~Eg~l~yWSS 55 (67)
T PF08679_consen 2 AKQKILEFLEAKKKKKSKFYFKDFYKAFP-------DAKPREVKKIVNELVNEGKLEYWSS 55 (67)
T ss_dssp HHHHHHHHHSSCCCHSS-EEHHHHHHH-T-------TS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHHhccCCCCceeHHHHHHHCC-------CcCHHHHHHHHHHHHhhCeEEEEcC
Confidence 466777777621 1 112344444322 3458899999999999999986544
No 342
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=41.62 E-value=62 Score=28.89 Aligned_cols=44 Identities=20% Similarity=0.269 Sum_probs=39.4
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
..||+-|+.|+..+.+ |-..++|-..+ ++..++|+..|+.+-+|
T Consensus 178 ~~LT~rE~evl~~~a~-----G~t~~eIa~~l--~is~~TV~~h~~~~~~K 221 (240)
T PRK10188 178 MNFSKREKEILKWTAE-----GKTSAEIAMIL--SISENTVNFHQKNMQKK 221 (240)
T ss_pred CCCCHHHHHHHHHHHc-----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 4799999999999976 89999999999 99999999999887543
No 343
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=41.46 E-value=2e+02 Score=29.36 Aligned_cols=102 Identities=14% Similarity=0.222 Sum_probs=74.0
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDI 110 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~ei 110 (252)
...++++|. +.+.|.+.-.-..-|.+|+...+ +++...+.+.|+.|...|.+-.+. .-+|++
T Consensus 467 ~~~~~~~~~-~~~~i~~~~~~~~~~~~~~~~~~--~~~~~~~~~~l~~l~~~g~~~~~~------~~~~~~--------- 528 (581)
T TIGR00475 467 KSDFEKEED-IWQKIKGTFGTKGAWVREFAEEV--NGDEKVMLKRVRKAGHRGGETLIV------KDRLLK--------- 528 (581)
T ss_pred CCCCCHHHH-HHHHHHHHHhcCCCCHHHHHhhh--CCCHHHHHHHHHHHHhCCCEEEEe------CCeEHH---------
Confidence 346788888 77777764567889999999999 999999999999999988665552 234433
Q ss_pred cCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcC
Q 025493 111 SGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 111 TGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDg 178 (252)
+.+..++..++..|+.+..+-+. +|-.-...||+-|=..|
T Consensus 529 --------------------~~~~~~~~~~~~~~~~~~r~~~g--------~sRK~~i~lle~~D~~~ 568 (581)
T TIGR00475 529 --------------------KYINELKEEGGTFNVQQARDKLG--------LGRKLLIQLLEYFDRLG 568 (581)
T ss_pred --------------------HHHHHHHhcCCcCcHHHHHHHHC--------ccHHHHHHHHHHhhhCC
Confidence 56666777778888888877663 34455556666555544
No 344
>PRK15320 transcriptional activator SprB; Provisional
Probab=41.42 E-value=59 Score=29.54 Aligned_cols=48 Identities=13% Similarity=0.140 Sum_probs=40.4
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCee
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIK 86 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK 86 (252)
-.||+-|..|++++.+ |..+++|..+. ++...+|++-+..|-.|==++
T Consensus 163 ~~LSdREIEVL~LLAk-----G~SNKEIAekL--~LS~KTVSTYKnRLLeKLgAk 210 (251)
T PRK15320 163 PGVTQAKYALLILLSS-----GHPAIELAKKF--GLGTKTVSIYRKKVMYRLGMD 210 (251)
T ss_pred CCCCHHHHHHHHHHHc-----CCCHHHHHHHh--ccchhhHHHHHHHHHHHcCCC
Confidence 4689999999999998 99999999999 999999988888775543333
No 345
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=41.42 E-value=36 Score=31.01 Aligned_cols=51 Identities=16% Similarity=0.210 Sum_probs=39.1
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh---cCCeee
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN---KSLIKE 87 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~---k~lIK~ 87 (252)
.++.|+-.+..++..|.+ .|+-.-. .+++ +++|..|+|.||.||+ -.|..+
T Consensus 25 ~~~~m~l~~L~~f~av~e-~gs~s~A----A~~L--~isQpavS~~I~~LE~~lG~~LF~R 78 (317)
T PRK11482 25 TLRNIDLNLLTIFEAVYV-HKGIVNA----AKIL--NLTPSAISQSIQKLRVIFPDPLFIR 78 (317)
T ss_pred cccccchhHHHHHHHHHH-cCCHHHH----HHHh--CCChHHHHHHHHHHHHHhCCcceEe
Confidence 466788888888888888 7754333 3456 9999999999999998 455554
No 346
>PF01090 Ribosomal_S19e: Ribosomal protein S19e; InterPro: IPR001266 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3IZ6_S 3U5G_T 3U5C_T 3O30_M 3O2Z_M 3IZB_S 2XZN_T 2XZM_T 2V7F_A.
Probab=41.31 E-value=32 Score=29.03 Aligned_cols=46 Identities=11% Similarity=0.185 Sum_probs=29.7
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhc------------CCChHHHHHHHHHHHhcCCeeeee
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKV------------NLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~------------~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
|...|-- .| ++=...|++.-|- +=....+.++|++||+-|||...+
T Consensus 57 ilRklY~-~g--~~GV~~lr~~YGg~k~~G~~p~h~~~asg~iiR~~LqqLE~~glv~k~~ 114 (139)
T PF01090_consen 57 ILRKLYI-RG--PVGVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDP 114 (139)
T ss_dssp HHHHHHH-CT--SB-HHHHHHHH--EEEETSSCCEE--CHHHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHH-hc--CcchHHHHHHhCCCCCCCCCCCCCCCCCcHHHHHHHHHHHHCCCEEecC
Confidence 3344444 45 4555677765410 223459999999999999999975
No 347
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=41.31 E-value=42 Score=29.75 Aligned_cols=48 Identities=17% Similarity=0.225 Sum_probs=36.9
Q ss_pred HHHHHHHhh------cCCCcc-cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 40 LIYDVIRSN------KQDMGI-WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 40 ~vy~~I~~~------ag~~GI-w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
.||+.|++. .-+.=+ ..++|..+. |+..+.|..+|+.|+..|||...+
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~--gVSRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEML--DVTRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec
Confidence 466665541 122334 478999999 999999999999999999999763
No 348
>PRK00523 hypothetical protein; Provisional
Probab=41.29 E-value=1e+02 Score=23.29 Aligned_cols=43 Identities=26% Similarity=0.213 Sum_probs=38.3
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHH
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAV 174 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tL 174 (252)
.+....+|+..+...|.+.|..-..+.| -..|+.+|+++.+.+
T Consensus 26 ark~~~k~l~~NPpine~mir~M~~QMG---qKPSekki~Q~m~~m 68 (72)
T PRK00523 26 SKKMFKKQIRENPPITENMIRAMYMQMG---RKPSESQIKQVMRSV 68 (72)
T ss_pred HHHHHHHHHHHCcCCCHHHHHHHHHHhC---CCccHHHHHHHHHHH
Confidence 4667788899999999999999999999 688999999999876
No 349
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=41.10 E-value=24 Score=35.58 Aligned_cols=56 Identities=21% Similarity=0.220 Sum_probs=46.3
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
--||..|..|+--|-.-.=..|....||..+. +....++-++|-+||+||+|+...
T Consensus 421 P~LT~~e~kvl~kiP~~~ikrg~liedi~~~~--g~~eeev~~sl~kleskgfveeL~ 476 (593)
T COG1542 421 PYLTKYEIKVLIKIPRKYIKRGELIEDIQGHV--GGDEEEVIKSLGKLESKGFVEELP 476 (593)
T ss_pred cccchhHHHHHHhccccccchhhHHHHHHhhc--CccHHHHHHHHHHHhhcchHHHhc
Confidence 35788887766555432557799999999999 999999999999999999999874
No 350
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=41.05 E-value=17 Score=31.31 Aligned_cols=49 Identities=12% Similarity=0.016 Sum_probs=40.5
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
=++.++.+|..++.++..++++.+. .|..-|++=|+.|.-+|+++++..
T Consensus 8 R~~~Il~~l~~~~~~~~~~La~~~~--------vS~~TiRRDl~~L~~~g~~~r~~~ 56 (185)
T PRK04424 8 RQKALQELIEENPFITDEELAEKFG--------VSIQTIRLDRMELGIPELRERIKH 56 (185)
T ss_pred HHHHHHHHHHHCCCEEHHHHHHHHC--------cCHHHHHHHHHHHhcchHHHHHHH
Confidence 3567888999999999999887654 678889999999999999987653
No 351
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=41.00 E-value=1.7e+02 Score=22.62 Aligned_cols=68 Identities=10% Similarity=0.123 Sum_probs=42.4
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHH
Q 025493 54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQC 133 (252)
Q Consensus 54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~ 133 (252)
+.++++.+.+ |++.++|. .-|+.|||.+.+.- .+. -+|+ .+=|+.|+ .
T Consensus 2 ~~i~eva~~~--gvs~~tlR----~ye~~Gll~~~r~~--~g~-----------------R~Y~-----~~~l~~l~--~ 49 (102)
T cd04789 2 YTISELAEKA--GISRSTLL----YYEKLGLITGTRNA--NGY-----------------RLYP-----DSDLQRLL--L 49 (102)
T ss_pred CCHHHHHHHH--CcCHHHHH----HHHHCCCCCCCcCC--CCC-----------------eeCC-----HHHHHHHH--H
Confidence 3578889999 99987764 78999999863321 123 3343 33344444 2
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 025493 134 LKQIIKLKVATLEGISDSIKR 154 (252)
Q Consensus 134 ~~~i~~~~~~T~~~I~~~i~~ 154 (252)
..+++.. ..++++|.+++..
T Consensus 50 I~~l~~~-G~~l~ei~~~l~~ 69 (102)
T cd04789 50 IQQLQAG-GLSLKECLACLQG 69 (102)
T ss_pred HHHHHHC-CCCHHHHHHHHcC
Confidence 3334444 5778888887753
No 352
>TIGR00637 ModE_repress ModE molybdate transport repressor domain. ModE is a molybdate-activated repressor of the molybdate transport operon in E. coli. It consists of the domain represented by this model and two tandem copies of mop-like domain, where Mop proteins are a family of 68-residue molybdenum-pterin binding proteins of Clostridium pasteurianum. This model also represents the full length of a pair of archaeal proteins that lack Mop-like domains. PSI-BLAST analysis shows similarity to helix-turn-helix regulatory proteins.
Probab=40.93 E-value=53 Score=25.56 Aligned_cols=41 Identities=7% Similarity=0.099 Sum_probs=31.1
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
++..+..++..|.+ .|+---+ -+.+ |+.+..+++.|+.||+
T Consensus 2 ~~~~~l~~~~av~~-~gSis~A----A~~L--~iS~stvs~~I~~LE~ 42 (99)
T TIGR00637 2 ADPRRVALLKAIAR-MGSISQA----AKDA--GISYKSAWDYIRAMNN 42 (99)
T ss_pred CCHHHHHHHHHHHH-hCCHHHH----HHHH--CCCHHHHHHHHHHHHH
Confidence 45567778888888 6664333 3456 9999999999999997
No 353
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=40.59 E-value=3.3e+02 Score=26.71 Aligned_cols=54 Identities=19% Similarity=0.179 Sum_probs=33.4
Q ss_pred HHHHHHHhcCCeeeeeccccCCeeeEEecccccCCC---------ccCCccccCCcCCHHHHHHHHHHH
Q 025493 74 KSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKD---------ISGGAWYSEGSLDTEFIKVVKSQC 133 (252)
Q Consensus 74 k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~e---------iTGG~wy~d~e~D~efV~~l~~~~ 133 (252)
++=+.+|+-|+|.-=+.-- ++...+.|.++ ..+||.|-..=-|.+|++.+.+..
T Consensus 229 ~ad~~~e~~g~~~~c~~cg------~~~~~~~~~~~~c~~Cg~~~~~~GPlW~GpL~d~~f~e~~l~~~ 291 (380)
T COG1867 229 RADKLLENLGYIYHCSRCG------EIVGSFREVDEKCPHCGGKVHLAGPLWLGPLHDEEFIEEMLEIA 291 (380)
T ss_pred hHHHHHHhcCcEEEccccc------ceecccccccccCCcccccceeccCcccCcccCHHHHHHHHHHh
Confidence 3335566666554422111 44444555555 346888888888999999988844
No 354
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=40.49 E-value=47 Score=28.37 Aligned_cols=45 Identities=11% Similarity=0.249 Sum_probs=32.9
Q ss_pred HHHHHHHhhcCCCcccHHHHHHHhhcCC-------ChHH-------HHHHHHHHHhcCCeeeee
Q 025493 40 LIYDVIRSNKQDMGIWTRDMKRELKVNL-------PDNI-------VTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 40 ~vy~~I~~~ag~~GIw~~dik~~~~~~l-------~~~~-------l~k~lK~Le~k~lIK~vk 89 (252)
.|...|-. -| +|=...|++.. |. |.+. +.++|++||+-|||+..+
T Consensus 57 sIlR~vY~-~g--pvGV~~L~~~y--Gg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 57 SILRKVYI-DG--PVGVERLRTAY--GGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred HHHHHHHH-cC--CccHHHHHHHH--CCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 34555555 45 45557888888 66 5444 999999999999999754
No 355
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=40.48 E-value=73 Score=28.65 Aligned_cols=54 Identities=11% Similarity=0.151 Sum_probs=45.4
Q ss_pred CCCCChHHHHHHH-HHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHH-HHHhcCCeee
Q 025493 31 SDSLTDHERLIYD-VIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIK-SLQNKSLIKE 87 (252)
Q Consensus 31 ~~~l~~~e~~vy~-~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK-~Le~k~lIK~ 87 (252)
...++..|+..+. ++.. .++...-.+++...+ |.+...+.+.+. .|..++||.+
T Consensus 233 ~~~l~~~~~~~L~al~~~-~~~~~~~~~~ia~~l--g~~~~~~~~~~e~~Li~~~li~~ 288 (305)
T TIGR00635 233 ELGLDEIDRKLLSVLIEQ-FQGGPVGLKTLAAAL--GEDADTIEDVYEPYLLQIGFLQR 288 (305)
T ss_pred CCCCCHHHHHHHHHHHHH-hCCCcccHHHHHHHh--CCCcchHHHhhhHHHHHcCCccc
Confidence 4678888888777 6676 555568899999999 999999999999 6999999953
No 356
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=40.48 E-value=80 Score=25.50 Aligned_cols=48 Identities=8% Similarity=0.089 Sum_probs=34.9
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCC
Q 025493 132 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNG 187 (252)
Q Consensus 132 ~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g 187 (252)
.++..|...+..|..+|++.+ .++..-|-.+|+.|+-.|.|++....+
T Consensus 44 ~vL~~l~~~~~~t~~eLa~~l--------~i~~~tvsr~l~~Le~~GlI~R~~~~~ 91 (144)
T PRK11512 44 KVLCSIRCAACITPVELKKVL--------SVDLGALTRMLDRLVCKGWVERLPNPN 91 (144)
T ss_pred HHHHHHHHcCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHCCCEEeccCcc
Confidence 344455555666777776654 467788999999999999999987543
No 357
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=40.42 E-value=93 Score=27.35 Aligned_cols=36 Identities=11% Similarity=0.299 Sum_probs=32.3
Q ss_pred Ccc-cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 52 MGI-WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 52 ~GI-w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
.-+ .-++|..+. |+..+.|.-+|+.|+..|||...+
T Consensus 29 ~~LPsE~eLa~~~--gVSRtpVREAL~~L~~eGlV~~~~ 65 (251)
T PRK09990 29 QALPSERRLCEKL--GFSRSALREGLTVLRGRGIIETAQ 65 (251)
T ss_pred CcCcCHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEeC
Confidence 346 678999999 999999999999999999999863
No 358
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=40.28 E-value=1.9e+02 Score=23.02 Aligned_cols=67 Identities=13% Similarity=0.132 Sum_probs=42.8
Q ss_pred HHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHH
Q 025493 56 TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLK 135 (252)
Q Consensus 56 ~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~ 135 (252)
+.++.+.+ |++..+ |.--|+.|||.+.+. . |.++| |.+-|+.|+.+..
T Consensus 3 Igeva~~~--gvs~~t----lRyYe~~GLl~p~r~--~-gyR~Y----------------------~~~~l~~l~~I~~- 50 (118)
T cd04776 3 ISELAREF--DVTPRT----LRFYEDKGLLSPERR--G-QTRVY----------------------SRRDRARLKLILR- 50 (118)
T ss_pred HHHHHHHH--CcCHHH----HHHHHHCCCCCCcCC--C-Ccccc----------------------CHHHHHHHHHHHH-
Confidence 46778888 888765 467899999987432 1 33333 4444555544333
Q ss_pred HhhhCCCCCHHHHHHHHHHcC
Q 025493 136 QIIKLKVATLEGISDSIKRSG 156 (252)
Q Consensus 136 ~i~~~~~~T~~~I~~~i~~~~ 156 (252)
++.. ..|+++|.+++....
T Consensus 51 -lr~~-G~~L~~I~~~l~~~~ 69 (118)
T cd04776 51 -GKRL-GFSLEEIRELLDLYD 69 (118)
T ss_pred -HHHC-CCCHHHHHHHHHhhc
Confidence 4444 558999999998643
No 359
>PRK10955 DNA-binding transcriptional regulator CpxR; Provisional
Probab=40.08 E-value=18 Score=30.17 Aligned_cols=57 Identities=11% Similarity=0.094 Sum_probs=36.9
Q ss_pred CCChHHHHHHHHHHhhcCC--------CcccHHHHHHHhhcCCChHHHHHHHHHHHhc----CCeeeeecc
Q 025493 33 SLTDHERLIYDVIRSNKQD--------MGIWTRDMKRELKVNLPDNIVTKSIKSLQNK----SLIKEVVNI 91 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~--------~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k----~lIK~vksv 91 (252)
.||.-|..|+.++.++.|+ .-+|-.++.... +--...+.++.++|+.+ .+|+.|..+
T Consensus 156 ~Lt~~E~~~l~~l~~~~~~v~sr~~l~~~~~~~~~~~~~--~tv~~~i~~lr~Kl~~~~~~~~~i~tv~g~ 224 (232)
T PRK10955 156 ELTGTEFTLLYLLAQHLGQVVSREHLSQEVLGKRLTPFD--RAIDMHISNLRRKLPDRKDGHPWFKTLRGR 224 (232)
T ss_pred cCCHHHHHHHHHHHhCCCceEcHHHHHHHHhCCCCCCCC--cCHHHHHHHHHHhcccCCCCCCeEEEeccc
Confidence 6999999999999884544 355655543333 44456677777777643 356666544
No 360
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=39.70 E-value=82 Score=25.93 Aligned_cols=54 Identities=7% Similarity=0.234 Sum_probs=45.7
Q ss_pred HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEE
Q 025493 123 TEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 123 ~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
.+-++......++||..+ .-|..+|.+.+.+.| ++.+.|+++|+.|.-.|.|..
T Consensus 7 ~~~~~~a~~~al~~L~~r-~~s~~el~~kL~~kg-----~~~~~i~~vl~~l~~~~~ldD 60 (157)
T PRK00117 7 RRMYASARARALRLLARR-EHSRAELRRKLAAKG-----FSEEVIEAVLDRLKEEGLLDD 60 (157)
T ss_pred ccHHHHHHHHHHHHHccc-hhHHHHHHHHHHhcC-----CCHHHHHHHHHHHHHcCCCCH
Confidence 456778888899999888 667899999999988 468999999999999888753
No 361
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=39.61 E-value=55 Score=30.71 Aligned_cols=53 Identities=21% Similarity=0.305 Sum_probs=47.1
Q ss_pred CCChHHHHHHHHHHhhcCCCccc----HHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIW----TRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw----~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
.|+++..+||.+.+++.|-+-.| --|||+.- |+...+..|+|=.|-++|+|+.
T Consensus 222 ~l~~daq~Il~yL~~~gG~mpf~DKSsPEdIk~~F--giSKg~FKrAiGgL~K~g~I~q 278 (287)
T COG2996 222 MLDEDAQMILTYLESNGGFMPFNDKSSPEDIKATF--GISKGQFKRAIGGLMKAGKIKQ 278 (287)
T ss_pred hhhhhHHHHHHHHHHcCCccccCCCCCHHHHHHHh--CcCHHHHHHHHHHHHhCCeEEE
Confidence 47788899999999977766666 45899999 9999999999999999999987
No 362
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=39.56 E-value=60 Score=29.30 Aligned_cols=47 Identities=17% Similarity=0.237 Sum_probs=37.8
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHH----HHHHHHH
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVT----KSIKSLQ 80 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~----k~lK~Le 80 (252)
.+..|++.|+.|+.+-.- . .+|...++|-..+ |++...|. ++|++|-
T Consensus 215 al~~L~~rer~vl~l~y~-~-~~~~t~~eIA~~l--gvS~~~V~q~~~~Al~kLr 265 (270)
T TIGR02392 215 ALGSLDARSRRIIEARWL-D-DDKLTLQELAAEY--GVSAERIRQIEKNAMKKLK 265 (270)
T ss_pred HHHcCCHHHHHHHHHHhc-C-CCCcCHHHHHHHH--CCCHHHHHHHHHHHHHHHH
Confidence 456899999998887664 3 5699999999999 99999999 5555553
No 363
>TIGR02154 PhoB phosphate regulon transcriptional regulatory protein PhoB. PhoB is a DNA-binding response regulator protein acting with PhoR in a 2-component system responding to phosphate ion. PhoB acts as a positive regulator of gene expression for phosphate-related genes such as phoA, phoS, phoE and ugpAB as well as itself. It is often found proximal to genes for the high-affinity phosphate ABC transporter (pstSCAB; GenProp0190) and presumably regulates these as well.
Probab=39.49 E-value=37 Score=27.81 Aligned_cols=46 Identities=13% Similarity=0.135 Sum_probs=34.2
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHH-----HhhcCCChHHH----HHHHHHHHh
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKR-----ELKVNLPDNIV----TKSIKSLQN 81 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~-----~~~~~l~~~~l----~k~lK~Le~ 81 (252)
.||+-|..|+.++.+ .-++|+...+|.. +. ++..++| .++.++|..
T Consensus 154 ~Lt~~E~~il~~l~~-~~~~~~s~~~i~~~~~~~~~--~~~~~tv~~~i~~l~~Kl~~ 208 (226)
T TIGR02154 154 SLGPTEFRLLHFFMT-HPERVYSREQLLDRVWGRDV--YVEERTVDVHIRRLRKALNP 208 (226)
T ss_pred EcCHHHHHHHHHHHh-CCCceEcHHHHHHHhcCCCC--CCCCccHHHHHHHHHHhhcc
Confidence 599999999999999 8889988888843 44 5555554 555555653
No 364
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=39.37 E-value=1.4e+02 Score=26.03 Aligned_cols=48 Identities=15% Similarity=0.308 Sum_probs=42.6
Q ss_pred CCCChHHHHHHHHHHhhcC----CCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 32 DSLTDHERLIYDVIRSNKQ----DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag----~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
..||+-|+.|...=-+ .| .+.+-.+||.+++ |+..+.+...|+.=|+|
T Consensus 154 ~~LTdrQ~~vL~~A~~-~GYFd~PR~~~l~dLA~~l--GISkst~~ehLRrAe~K 205 (215)
T COG3413 154 NDLTDRQLEVLRLAYK-MGYFDYPRRVSLKDLAKEL--GISKSTLSEHLRRAERK 205 (215)
T ss_pred ccCCHHHHHHHHHHHH-cCCCCCCccCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 3699999999998888 88 6889999999999 99999999998887764
No 365
>PF13814 Replic_Relax: Replication-relaxation
Probab=39.33 E-value=74 Score=26.57 Aligned_cols=48 Identities=13% Similarity=0.103 Sum_probs=33.2
Q ss_pred ccHHHHHHHhhcCCChH---HHHHHHHHHHhcCCeeeeecc----ccCCeeeEEecc
Q 025493 54 IWTRDMKRELKVNLPDN---IVTKSIKSLQNKSLIKEVVNI----HNKGKKHLMAVE 103 (252)
Q Consensus 54 Iw~~dik~~~~~~l~~~---~l~k~lK~Le~k~lIK~vksv----~~~~rK~YmL~~ 103 (252)
+.+.+|..-. +.... .+.+.|+.|+..|+|+.++.- ......+|-|..
T Consensus 10 lt~~Qi~~l~--~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~ 64 (191)
T PF13814_consen 10 LTTDQIARLL--FPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTP 64 (191)
T ss_pred cCHHHHHHHH--cCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECH
Confidence 4455666666 44444 799999999999999998763 122456776643
No 366
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=39.29 E-value=72 Score=29.02 Aligned_cols=45 Identities=18% Similarity=0.258 Sum_probs=39.4
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
...||+.|+.|..++.+ |...++|-..+ +++.++|...++.+-.|
T Consensus 188 ~~~LT~RE~evl~l~a~-----G~s~~eIA~~L--~IS~~TVk~hl~~i~~K 232 (247)
T TIGR03020 188 AGLITAREAEILAWVRD-----GKTNEEIAAIL--GISSLTVKNHLQHIFKK 232 (247)
T ss_pred ccCCCHHHHHHHHHHHC-----CCCHHHHHHHH--CcCHHHHHHHHHHHHHH
Confidence 56899999999998755 89999999999 99999999999887543
No 367
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=39.21 E-value=78 Score=28.50 Aligned_cols=45 Identities=11% Similarity=0.224 Sum_probs=35.9
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
++.|+-.+..++..|.+ .|+- ..-.+++ ++.|..|+|.|++||..
T Consensus 19 ~~~~~l~~L~~f~avae-~gs~----s~AA~~L--~isQpavS~~I~~LE~~ 63 (314)
T PRK09508 19 LRMVDLNLLTVFDAVMQ-EQNI----TRAAHNL--GMSQPAVSNAVARLKVM 63 (314)
T ss_pred ccccChHHHHHHHHHHh-cCCH----HHHHHHh--CCCHHHHHHHHHHHHHh
Confidence 45688788888889988 7772 3335567 99999999999999973
No 368
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=39.09 E-value=29 Score=27.66 Aligned_cols=44 Identities=23% Similarity=0.445 Sum_probs=37.0
Q ss_pred HHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 39 RLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 39 ~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
-.|++.+-+ -+--||-. |...| |||.+.+.=+|+-||+.++|++
T Consensus 17 l~Vl~~v~e-eqPiGI~k--lS~~T--Gmp~HKVRYSLRVLEq~~iI~P 60 (101)
T COG3388 17 LSVLKVVLE-EQPIGIIK--LSDET--GMPEHKVRYSLRVLEQENIISP 60 (101)
T ss_pred HHHHHHHHH-hCCceeEe--echhc--CCchhhhhhhhhhhhhcCccCc
Confidence 356777777 78888764 67789 9999999999999999999975
No 369
>PF09279 EF-hand_like: Phosphoinositide-specific phospholipase C, efhand-like; InterPro: IPR015359 This domain is predominantly found in the enzyme phosphoinositol-specific phospholipase C. It adopts a structure consisting of a core of four alpha helices, in an EF like fold, and is required for functioning of the enzyme []. ; PDB: 3OHM_B 3QR0_A 2ZKM_X 2FJU_B 3QR1_D 1DJW_B 1DJI_B 1DJG_B 1QAS_B 2ISD_B ....
Probab=39.01 E-value=68 Score=23.36 Aligned_cols=48 Identities=17% Similarity=0.127 Sum_probs=34.4
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhc
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLD 177 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyD 177 (252)
|..+..+|-......|+++.++|+++.. -...++.+++++|++.-.-+
T Consensus 2 i~~if~~ys~~~~~mt~~~f~~FL~~eQ-~~~~~~~~~~~~li~~~~~~ 49 (83)
T PF09279_consen 2 IEEIFRKYSSDKEYMTAEEFRRFLREEQ-GEPRLTDEQAKELIEKFEPD 49 (83)
T ss_dssp HHHHHHHHCTTSSSEEHHHHHHHHHHTS-S-TTSSHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhCCCCcCCHHHHHHHHHHHh-ccccCcHHHHHHHHHHHccc
Confidence 4455556655578999999999998654 12245899999999985443
No 370
>TIGR03337 phnR transcriptional regulator protein. 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 Salmonella, Vibrio Aeromonas hydrophila, Hahella chejuensis and Psychromonas ingrahamii.
Probab=38.97 E-value=47 Score=28.68 Aligned_cols=33 Identities=18% Similarity=0.286 Sum_probs=30.2
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
.-++|..+. +++..++.++|..|+..|+|.+..
T Consensus 27 sE~eLa~~~--~Vsr~Tvr~Al~~L~~eGli~~~~ 59 (231)
T TIGR03337 27 SERDLGERF--NTTRVTIREALQQLEAEGLIYRED 59 (231)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCeEEEeC
Confidence 368899999 999999999999999999999864
No 371
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=38.97 E-value=76 Score=30.10 Aligned_cols=53 Identities=13% Similarity=0.295 Sum_probs=42.0
Q ss_pred CCCChHHHHHHH-----HHHhhcCCCcccHHHHHHH--hhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 32 DSLTDHERLIYD-----VIRSNKQDMGIWTRDMKRE--LKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 32 ~~l~~~e~~vy~-----~I~~~ag~~GIw~~dik~~--~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
+.|++-++.|+. +|+. +.=+-.++|.++ . ++...++.+-++.||+.|+|+..-
T Consensus 2 ~~l~~R~~~Il~~IV~~yi~~---~~pv~s~~l~~~~~l--~~S~aTIR~dm~~Le~~G~l~~~h 61 (339)
T PRK00082 2 SMLDERQREILRAIVEDYIAT---GEPVGSKTLSKRYGL--GVSSATIRNDMADLEELGLLEKPH 61 (339)
T ss_pred CccCHHHHHHHHHHHHHHHhc---CCCcCHHHHHHHhCC--CCChHHHHHHHHHHHhCCCcCCCc
Confidence 357776777776 5655 445668999977 7 899999999999999999998753
No 372
>PRK11367 hypothetical protein; Provisional
Probab=38.72 E-value=15 Score=36.62 Aligned_cols=26 Identities=31% Similarity=0.616 Sum_probs=18.4
Q ss_pred ccCCccccCCcCCHH---HHHHHHHHHHH
Q 025493 110 ISGGAWYSEGSLDTE---FIKVVKSQCLK 135 (252)
Q Consensus 110 iTGG~wy~d~e~D~e---fV~~l~~~~~~ 135 (252)
-|||+|||......+ +|+.+.+.+-+
T Consensus 17 wtGgsWYTGk~iE~~~~~~v~~~N~~l~~ 45 (476)
T PRK11367 17 WGGGTWYTGTQIQPGVEKFIKDFNDAKKK 45 (476)
T ss_pred hccccceechHHHHHHHHHHHHHHHHHHh
Confidence 489999999888877 45555544433
No 373
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=38.68 E-value=64 Score=32.30 Aligned_cols=66 Identities=18% Similarity=0.341 Sum_probs=49.3
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFE 105 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~le 105 (252)
.++.-+..+..++.+ |.=+..++|+..+ ++....++|.|..|.++|+++.+-+.+. -+-|+..+.+
T Consensus 399 ~~~~~~~~il~~~~e---n~~~T~~~L~~~l--~is~~~i~r~i~~Lv~~g~~~~~g~~~~--g~~~v~~~~~ 464 (467)
T COG2865 399 SLSERQEKILELIKE---NGKVTARELREIL--GISSETIRRRIANLVKRGLLKQLGSSGR--GTWYVKGEPE 464 (467)
T ss_pred ChhHHHHHHHHHHhh---ccccCHHHHHHHh--CcchhhHHHHHHHHhcccHHHHhCcCCC--CcEEecCCcc
Confidence 344444466666665 6779999999999 9999999999999999999999876432 3334444433
No 374
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=38.65 E-value=82 Score=28.42 Aligned_cols=45 Identities=16% Similarity=0.268 Sum_probs=36.1
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
.++.|+-.+-.++..|.+ .|+- ..=.+++ ++.|..|++.|+.||+
T Consensus 4 ~~~~mdl~~L~~f~av~e-~gs~----t~AA~~L--~iSQpavS~~I~~LE~ 48 (319)
T PRK10216 4 SLTTLDLNLLLCLQLLMQ-ERSV----TKAAKRM--NVTPSAVSKSLAKLRA 48 (319)
T ss_pred chhhcCHHHHHHHHHHHH-hCCH----HHHHHHh--CCCHHHHHHHHHHHHH
Confidence 356788888899999998 6642 2334567 9999999999999998
No 375
>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=38.49 E-value=50 Score=28.78 Aligned_cols=35 Identities=6% Similarity=0.136 Sum_probs=31.8
Q ss_pred cc-cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 53 GI-WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 53 GI-w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
=+ ..++|..+. |+..+.|.-+|+.||..|||...+
T Consensus 29 ~LpsE~~La~~l--gVSRtpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 29 ILPAERELSELI--GVTRTTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred cCcCHHHHHHHH--CcCHHHHHHHHHHHHHCCCEEEeC
Confidence 36 688999999 999999999999999999999764
No 376
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=38.29 E-value=1e+02 Score=22.42 Aligned_cols=37 Identities=5% Similarity=0.162 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHHHHhhh-------------CCCCCHHHHHHHHHHcCC
Q 025493 121 LDTEFIKVVKSQCLKQIIK-------------LKVATLEGISDSIKRSGA 157 (252)
Q Consensus 121 ~D~efV~~l~~~~~~~i~~-------------~~~~T~~~I~~~i~~~~i 157 (252)
.....++.|.+.+.+||++ +.-|++.||...+.+.||
T Consensus 24 ~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi 73 (77)
T PF07524_consen 24 ASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGI 73 (77)
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCC
Confidence 4567889999999999873 457888888888888886
No 377
>PRK01844 hypothetical protein; Provisional
Probab=37.93 E-value=1.2e+02 Score=22.81 Aligned_cols=43 Identities=9% Similarity=0.153 Sum_probs=38.5
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHH
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAV 174 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tL 174 (252)
.+....+|+.++...|.+.|..-..+.| -..|+.+|+++.+.+
T Consensus 25 ark~~~k~lk~NPpine~mir~Mm~QMG---qkPSekki~Q~m~~m 67 (72)
T PRK01844 25 ARKYMMNYLQKNPPINEQMLKMMMMQMG---QKPSQKKINQMMSAM 67 (72)
T ss_pred HHHHHHHHHHHCCCCCHHHHHHHHHHhC---CCccHHHHHHHHHHH
Confidence 4667788999999999999999999999 688999999999876
No 378
>COG1542 Uncharacterized conserved protein [Function unknown]
Probab=37.91 E-value=47 Score=33.56 Aligned_cols=147 Identities=20% Similarity=0.241 Sum_probs=91.8
Q ss_pred CCCCCCCChHHHHHHHHHHhhcCCCcccHH--------------HHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecccc
Q 025493 28 NAPSDSLTDHERLIYDVIRSNKQDMGIWTR--------------DMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHN 93 (252)
Q Consensus 28 ~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~--------------dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~ 93 (252)
....-.+.++|..++..|+. +|.+ .+..++ ++.+- ++-+|++||+.+|||+- |..
T Consensus 276 ~tppi~i~~dE~rlLk~Idk------L~kk~e~~~~Peik~iek~~~~e~--k~~Dl-vt~aL~~LEs~glik~e--v~k 344 (593)
T COG1542 276 KTPPIYILEDEIRLLKAIDK------LKKKHETNPAPEIKPIEKEIKWET--KIDDL-VTAALYTLESFGLIKRE--VVK 344 (593)
T ss_pred CCCCeeechhHHHHHHHHHH------HHhhhccCCCcccchHHHHhhHHh--cccch-HHHHHHhhhhccchhhh--hhh
Confidence 34455677888889999987 4433 344567 77777 89999999999999973 333
Q ss_pred CCeeeEEecc--------cccCCCccCC--ccccCCcCCH---HHHHHHHHH-----------------HHHHhhhCCCC
Q 025493 94 KGKKHLMAVE--------FEPSKDISGG--AWYSEGSLDT---EFIKVVKSQ-----------------CLKQIIKLKVA 143 (252)
Q Consensus 94 ~~rK~YmL~~--------lePs~eiTGG--~wy~d~e~D~---efV~~l~~~-----------------~~~~i~~~~~~ 143 (252)
.+.-+|.+.+ ++-|...+|= .=|+ .+||+ |..++-++. +-.-+.++.+.
T Consensus 345 ~g~l~yvlTe~Gekvle~l~k~vtA~GvKAIT~t-~ef~aPn~EW~eqa~~eglVs~gAiT~kGrl~akls~tikRkP~L 423 (593)
T COG1542 345 NGDLTYVLTEFGEKVLEDLEKSVTADGVKAITYT-EEFDAPNAEWYEQAKEEGLVSRGAITEKGRLYAKLSKTIKRKPYL 423 (593)
T ss_pred cCceEEEehhhhHHHHhcccCceeecceeEEEec-cccCCCCHHHHHHHHhcccccccCcCcchhHHHHHHHHHhcCccc
Confidence 3556888765 5666544443 2244 55554 233222221 22334466777
Q ss_pred CHHHHHHHHHHc------CC------cceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 144 TLEGISDSIKRS------GA------FKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 144 T~~~I~~~i~~~------~i------~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
|-.|+.-.++=- |. -.+.+..+++..-|..|.--|.|+.....
T Consensus 424 T~~e~kvl~kiP~~~ikrg~liedi~~~~g~~eeev~~sl~kleskgfveeL~n~ 478 (593)
T COG1542 424 TKYEIKVLIKIPRKYIKRGELIEDIQGHVGGDEEEVIKSLGKLESKGFVEELPNK 478 (593)
T ss_pred chhHHHHHHhccccccchhhHHHHHHhhcCccHHHHHHHHHHHhhcchHHHhccC
Confidence 777766554421 10 12456777787888888888888876543
No 379
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=37.89 E-value=72 Score=22.16 Aligned_cols=33 Identities=9% Similarity=0.233 Sum_probs=25.6
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHH
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSI 76 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~l 76 (252)
++....+ .|-+-|...+|...+ |++..+|.|=|
T Consensus 17 ~L~~l~~-~G~~~vSS~~La~~~--gi~~~qVRKDl 49 (50)
T PF06971_consen 17 YLEQLKE-EGVERVSSQELAEAL--GITPAQVRKDL 49 (50)
T ss_dssp HHHHHHH-TT-SEE-HHHHHHHH--TS-HHHHHHHH
T ss_pred HHHHHHH-cCCeeECHHHHHHHH--CCCHHHhcccC
Confidence 4566777 899999999999999 99999998743
No 380
>COG5309 Exo-beta-1,3-glucanase [Carbohydrate transport and metabolism]
Probab=37.89 E-value=44 Score=31.46 Aligned_cols=71 Identities=18% Similarity=0.217 Sum_probs=50.5
Q ss_pred ecccccCCCccC-----CccccCCcCCHHHHHHHHHHHHHHhh--------------hCCCCCHHHHHHHHHHcCCccee
Q 025493 101 AVEFEPSKDISG-----GAWYSEGSLDTEFIKVVKSQCLKQII--------------KLKVATLEGISDSIKRSGAFKVD 161 (252)
Q Consensus 101 L~~lePs~eiTG-----G~wy~d~e~D~efV~~l~~~~~~~i~--------------~~~~~T~~~I~~~i~~~~i~~~~ 161 (252)
|-++-|..+-.| |.||+|+--|.+== ++.++++-+.. +++-+|++++.++|.
T Consensus 89 le~v~pAa~~~g~kv~lGiw~tdd~~~~~~~-til~ay~~~~~~d~v~~v~VGnEal~r~~~tasql~~~I~-------- 159 (305)
T COG5309 89 LENVLPAAEASGFKVFLGIWPTDDIHDAVEK-TILSAYLPYNGWDDVTTVTVGNEALNRNDLTASQLIEYID-------- 159 (305)
T ss_pred hhhhHHHHHhcCceEEEEEeeccchhhhHHH-HHHHHHhccCCCCceEEEEechhhhhcCCCCHHHHHHHHH--------
Confidence 455677777777 99999875543221 44445444432 467899999999975
Q ss_pred cCHHHHHHHHHHHhhcCeeEEEe
Q 025493 162 LTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 162 Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+++..|..+-|||.|-.+.
T Consensus 160 ----~vrsav~~agy~gpV~T~d 178 (305)
T COG5309 160 ----DVRSAVKEAGYDGPVTTVD 178 (305)
T ss_pred ----HHHHHHHhcCCCCceeecc
Confidence 7888999999999987654
No 381
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=37.84 E-value=2.1e+02 Score=22.88 Aligned_cols=68 Identities=16% Similarity=0.188 Sum_probs=40.9
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.+.++.+.+ |++.++| +--|+.|||.+...-.+ |. -+|++ +=|+.|+.+
T Consensus 2 ~I~e~a~~~--gvs~~tl----RyYe~~GLl~~~~r~~~-g~-----------------R~Y~~-----~~~~~l~~I-- 50 (127)
T cd01108 2 NIGEAAKLT--GLSAKMI----RYYEEIGLIPPPSRSDN-GY-----------------RVYNQ-----RDIEELRFI-- 50 (127)
T ss_pred CHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCcCCC-Cc-----------------eecCH-----HHHHHHHHH--
Confidence 467788888 8887654 67899999975322122 22 23333 333444333
Q ss_pred HHhhhCCCCCHHHHHHHHHH
Q 025493 135 KQIIKLKVATLEGISDSIKR 154 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~ 154 (252)
.+++.. ..|+++|.+++..
T Consensus 51 ~~lr~~-G~sL~eI~~~l~~ 69 (127)
T cd01108 51 RRARDL-GFSLEEIRELLAL 69 (127)
T ss_pred HHHHHc-CCCHHHHHHHHHH
Confidence 334444 4589999998874
No 382
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=37.61 E-value=1.9e+02 Score=22.27 Aligned_cols=69 Identities=10% Similarity=0.129 Sum_probs=44.6
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHH
Q 025493 54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQC 133 (252)
Q Consensus 54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~ 133 (252)
.+++++.+.+ |++.++| .-.|++|||.+.++ ..+.+.| +.+=|+.|+.+.
T Consensus 2 ~~i~eva~~~--gvs~~tL----R~ye~~Gll~~~r~--~~g~R~Y----------------------~~~dl~~l~~I~ 51 (102)
T cd04775 2 YTIGQMSRKF--GVSRSTL----LYYESIGLIPSARS--EANYRLY----------------------SEADLSRLEKIV 51 (102)
T ss_pred CCHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCC--CCCCeee----------------------CHHHHHHHHHHH
Confidence 4678899999 9998776 78899999944221 1133333 344445554444
Q ss_pred HHHhhhCCCCCHHHHHHHHHHc
Q 025493 134 LKQIIKLKVATLEGISDSIKRS 155 (252)
Q Consensus 134 ~~~i~~~~~~T~~~I~~~i~~~ 155 (252)
. ++. ...|+++|.+++...
T Consensus 52 ~--l~~-~G~~l~ei~~~~~~~ 70 (102)
T cd04775 52 F--LQA-GGLPLEEIAGCLAQP 70 (102)
T ss_pred H--HHH-CCCCHHHHHHHHcCC
Confidence 3 334 468899999988653
No 383
>PRK10086 DNA-binding transcriptional regulator DsdC; Provisional
Probab=36.73 E-value=56 Score=29.44 Aligned_cols=45 Identities=18% Similarity=0.270 Sum_probs=35.7
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
..+|+-.+..++..|.+ .|+-.-. .+++ |++|..|++.|+.||+.
T Consensus 11 ~~~~~l~~L~~f~~va~-~gs~s~A----A~~L--~iSQpavS~~I~~LE~~ 55 (311)
T PRK10086 11 LNGWQLSKLHTFEVAAR-HQSFALA----ADEL--SLTPSAVSHRINQLEEE 55 (311)
T ss_pred hcCCcHHHHHHHHHHHH-cCCHHHH----HHHH--CCCHHHHHHHHHHHHHH
Confidence 45788888888888888 7764332 3456 99999999999999984
No 384
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=36.57 E-value=55 Score=28.96 Aligned_cols=33 Identities=18% Similarity=0.193 Sum_probs=30.2
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
--++|..+. |+..+.|..+|+.||..|||...+
T Consensus 34 sE~eLae~~--gVSRtpVREAL~~L~~eGlV~~~~ 66 (253)
T PRK11523 34 AERFIADEK--NVSRTVVREAIIMLEVEGYVEVRK 66 (253)
T ss_pred CHHHHHHHH--CCCHHHHHHHHHHHHHCCCEEEec
Confidence 368999999 999999999999999999999763
No 385
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=36.55 E-value=1.1e+02 Score=24.62 Aligned_cols=59 Identities=8% Similarity=0.183 Sum_probs=43.1
Q ss_pred HHHHHHHHHHhhcCCCcc-cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493 37 HERLIYDVIRSNKQDMGI-WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM 100 (252)
Q Consensus 37 ~e~~vy~~I~~~ag~~GI-w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym 100 (252)
+|.++=.+-.+ -++.-+ .--.|-.+. |+.-+.-.++|+.||++|.|+.|. +|...-+|.
T Consensus 43 dee~~~ki~KE-V~~~r~VTpy~la~r~--gI~~SvAr~vLR~LeeeGvv~lvs--knrR~~IY~ 102 (107)
T COG4901 43 DEELLDKIRKE-VPRERVVTPYVLASRY--GINGSVARIVLRHLEEEGVVQLVS--KNRRQAIYT 102 (107)
T ss_pred cHHHHHHHHHh-cccceeecHHHHHHHh--ccchHHHHHHHHHHHhCCceeeec--cCccceeee
Confidence 45455555666 676654 445678899 999999999999999999999873 333444554
No 386
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=36.39 E-value=55 Score=28.95 Aligned_cols=32 Identities=13% Similarity=0.259 Sum_probs=29.9
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
--++|..+. |+..+.|.-+|+.||..|||...
T Consensus 28 sE~eLae~~--gVSRtpVREAL~~Le~~GlV~~~ 59 (253)
T PRK10421 28 AERQLAMQL--GVSRNSLREALAKLVSEGVLLSR 59 (253)
T ss_pred CHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEe
Confidence 468999999 99999999999999999999975
No 387
>PRK00118 putative DNA-binding protein; Validated
Probab=36.36 E-value=1.1e+02 Score=24.49 Aligned_cols=43 Identities=19% Similarity=0.196 Sum_probs=35.2
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKS 78 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~ 78 (252)
+.+.|++.++.++.+-.. .|...++|...+ |++.+.|.+.|+.
T Consensus 14 ~~~~L~ekqRevl~L~y~----eg~S~~EIAe~l--GIS~~TV~r~L~R 56 (104)
T PRK00118 14 YGSLLTEKQRNYMELYYL----DDYSLGEIAEEF--NVSRQAVYDNIKR 56 (104)
T ss_pred HhccCCHHHHHHHHHHHH----cCCCHHHHHHHH--CcCHHHHHHHHHH
Confidence 345789999888866555 599999999999 9999999888764
No 388
>PRK10403 transcriptional regulator NarP; Provisional
Probab=36.34 E-value=92 Score=25.05 Aligned_cols=45 Identities=22% Similarity=0.349 Sum_probs=37.8
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
...||+.|..|..++.+ |...++|..++ ++..++|...++.+-+|
T Consensus 151 ~~~Lt~~e~~vl~~~~~-----g~s~~~ia~~l--~~s~~tv~~~~~~i~~k 195 (215)
T PRK10403 151 FSVLTERELDVLHELAQ-----GLSNKQIASVL--NISEQTVKVHIRNLLRK 195 (215)
T ss_pred cccCCHHHHHHHHHHHC-----CCCHHHHHHHc--CCCHHHHHHHHHHHHHH
Confidence 34699999999998876 58899999999 99999988888777544
No 389
>COG5051 RPL36A Ribosomal protein L36E [Translation, ribosomal structure and biogenesis]
Probab=36.23 E-value=50 Score=25.94 Aligned_cols=40 Identities=25% Similarity=0.285 Sum_probs=30.0
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHH
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTK 74 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k 74 (252)
+++|++.|+.+.++|++ ++|+-. ++-+|+++ +-+.+...|
T Consensus 47 iaGlsPyErr~i~Lirn-s~~krA-rKlakKRL--Gs~kRAkaK 86 (97)
T COG5051 47 IAGLSPYERRVIELIRN-SQDKRA-RKLAKKRL--GSLKRAKAK 86 (97)
T ss_pred HccCCHHHHHHHHHHHh-cccHHH-HHHHHHHh--hhHHHHHHH
Confidence 56899999999999999 888753 56677777 555544443
No 390
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=36.19 E-value=1.5e+02 Score=28.65 Aligned_cols=23 Identities=30% Similarity=0.332 Sum_probs=19.7
Q ss_pred ccCCccccCCcCCHHHHHHHHHH
Q 025493 110 ISGGAWYSEGSLDTEFIKVVKSQ 132 (252)
Q Consensus 110 iTGG~wy~d~e~D~efV~~l~~~ 132 (252)
..+||.|...=.|.+|++.+.+.
T Consensus 263 ~~~GPlW~G~l~d~~fl~~m~~~ 285 (374)
T TIGR00308 263 HLAGPLYAGPLHDKEFIEEVLRI 285 (374)
T ss_pred eeecCcccCccCCHHHHHHHHHh
Confidence 45899999999999999998764
No 391
>PF03501 S10_plectin: Plectin/S10 domain; InterPro: IPR005326 This presumed domain is found at the N terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding.; PDB: 2XZM_7 2XZN_7 3U5C_K 3U5G_K.
Probab=36.13 E-value=40 Score=26.71 Aligned_cols=26 Identities=31% Similarity=0.506 Sum_probs=22.6
Q ss_pred CCChHHHHHHHHHHHhcCCeeeeecc
Q 025493 66 NLPDNIVTKSIKSLQNKSLIKEVVNI 91 (252)
Q Consensus 66 ~l~~~~l~k~lK~Le~k~lIK~vksv 91 (252)
+.+-=.+-|++++|.+||++|+.=+=
T Consensus 34 ~vpNL~V~k~mqSL~SrgyVke~faW 59 (95)
T PF03501_consen 34 NVPNLHVIKAMQSLKSRGYVKEQFAW 59 (95)
T ss_dssp SSBHHHHHHHHHHHHHCTSEEEEECT
T ss_pred CCCcHHHHHHHhcccchhhhcCeecc
Confidence 67778999999999999999996544
No 392
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=36.12 E-value=1e+02 Score=22.63 Aligned_cols=41 Identities=12% Similarity=0.160 Sum_probs=26.3
Q ss_pred CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEeccccc
Q 025493 66 NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEP 106 (252)
Q Consensus 66 ~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~leP 106 (252)
.+.++.+...|+.|+..|+|..-+.=+..++=.|..+.|.-
T Consensus 36 pls~~r~~~~l~eL~~~gli~~~~~~~G~~~G~~~~~~l~~ 76 (85)
T PF09079_consen 36 PLSYRRFSDYLSELEMLGLIESERKGRGRGRGRTREISLNV 76 (85)
T ss_dssp ---HHHHHHHHHHHHHTTSEEEEEEE-TT-CTEEEEEEECS
T ss_pred CCCHHHHHHHHHHHHhCCCeEEEeecCCCCCCeEEEEEecC
Confidence 57889999999999999999886633332344455555543
No 393
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=35.99 E-value=80 Score=28.89 Aligned_cols=46 Identities=24% Similarity=0.181 Sum_probs=39.5
Q ss_pred HHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 38 ERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 38 e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.+-|...|.+ +++.-..+|+.+. |+.-.+|.=.+|.||.-|+|++=
T Consensus 176 ~k~I~~eiq~---~~~~t~~~ia~~l--~ls~aTV~~~lk~l~~~Gii~~~ 221 (240)
T COG3398 176 SKAIIYEIQE---NKCNTNLLIAYEL--NLSVATVAYHLKKLEELGIIPED 221 (240)
T ss_pred HHHHHHHHhc---CCcchHHHHHHHc--CccHHHHHHHHHHHHHcCCCccc
Confidence 3556666666 5678899999999 99999999999999999999984
No 394
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=35.78 E-value=2.3e+02 Score=22.64 Aligned_cols=68 Identities=13% Similarity=0.237 Sum_probs=41.5
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.+.++.+.+ |++..+ |.--|++|||.+...-.+ +.+ +|+ .+=|..|+. .
T Consensus 2 ~I~e~a~~~--gvs~~t----lRyYe~~GLl~p~~r~~~-gyR-----------------~Y~-----~~~l~~l~~--I 50 (127)
T TIGR02044 2 NIGQVAKLT--GLSSKM----IRYYEEKGLIPPPLRSEG-GYR-----------------TYT-----QQHLDELRL--I 50 (127)
T ss_pred CHHHHHHHH--CcCHHH----HHHHHHCCCCCCCCcCCC-CCe-----------------ecC-----HHHHHHHHH--H
Confidence 467788888 888765 468899999987532222 333 333 333444442 2
Q ss_pred HHhhhCCCCCHHHHHHHHHH
Q 025493 135 KQIIKLKVATLEGISDSIKR 154 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~ 154 (252)
..++.. ..|++||.+++..
T Consensus 51 ~~lr~~-G~sL~eI~~~l~~ 69 (127)
T TIGR02044 51 SRARQV-GFSLEECKELLNL 69 (127)
T ss_pred HHHHHC-CCCHHHHHHHHHh
Confidence 234444 4689999998873
No 395
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=35.43 E-value=65 Score=27.83 Aligned_cols=47 Identities=13% Similarity=0.130 Sum_probs=37.0
Q ss_pred HHHHHHHh------hcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 40 LIYDVIRS------NKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 40 ~vy~~I~~------~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.||+.|++ ...+.=+-.++|..+. |+..+.|.-+|+.|+..|||..+
T Consensus 11 ~vy~~i~~~I~~g~l~pG~~L~e~eLae~l--gVSRtpVREAL~~L~~eGlv~~~ 63 (224)
T PRK11534 11 DGYRWLKNDIIRGNFQPDEKLRMSLLTSRY--ALGVGPLREALSQLVAERLVTVV 63 (224)
T ss_pred HHHHHHHHHHHhCCCCCCCcCCHHHHHHHH--CCChHHHHHHHHHHHHCCCEEEe
Confidence 36666655 1123345678999999 99999999999999999999875
No 396
>PF07537 CamS: CamS sex pheromone cAM373 precursor; InterPro: IPR011426 This family includes CamS (Q8L313 from SWISSPROT), from which Staphylococcus aureus sex pheromone staph-cAM373 is processed. It also includes a number of uncharacterised bacterial proteins.; PDB: 3N2Q_A 3IB5_A 2QX2_A.
Probab=35.34 E-value=14 Score=35.06 Aligned_cols=76 Identities=21% Similarity=0.265 Sum_probs=42.9
Q ss_pred HhhccCCCcccccCCCCCCCCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeec
Q 025493 11 LGLAKGSGMSKRKRPDSNAPSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
|||+=++-..+.+..+-..+...++++|..-|. ..+..++|+.|-++.-+|.|+
T Consensus 114 IGLamNsv~yy~~e~~g~~~~~~Is~~e~~~~G-------------------------k~~A~~iv~rlR~~~~l~~vP- 167 (319)
T PF07537_consen 114 IGLAMNSVYYYQKEEDGPTYEVEISDEEMEAYG-------------------------KEMANKIVKRLRKKKGLKDVP- 167 (319)
T ss_dssp EEEEE-SEEEEESSTTS-EEEEES-HHHHHHHH-------------------------HHHHHHHHHHHHHCCCGSSS--
T ss_pred EEEEecceeeecccCCCceeeEecCHHHHHHHH-------------------------HHHHHHHHHHHHhccccCCCC-
Confidence 455555555555554444445567766644332 345678899997777445543
Q ss_pred cccCCeeeEEecccccCCCccCCccccC
Q 025493 91 IHNKGKKHLMAVEFEPSKDISGGAWYSE 118 (252)
Q Consensus 91 v~~~~rK~YmL~~lePs~eiTGG~wy~d 118 (252)
-+..||..+|..++.||.||..
T Consensus 168 ------I~ialy~q~~~~s~vpG~f~a~ 189 (319)
T PF07537_consen 168 ------IVIALYKQASKDSLVPGNFIAY 189 (319)
T ss_dssp ------EEEEEEE--BTT-SS--EEEEE
T ss_pred ------EEEEEEeeCCCCCCcCceEEEE
Confidence 3566888999999999999944
No 397
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=35.33 E-value=1.2e+02 Score=20.84 Aligned_cols=41 Identities=32% Similarity=0.457 Sum_probs=26.7
Q ss_pred CCCCChHHHH-HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 025493 31 SDSLTDHERL-IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKS 78 (252)
Q Consensus 31 ~~~l~~~e~~-vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~ 78 (252)
-..||-+|++ |.+.+++ |-..++|.++. |++.++|..++|.
T Consensus 4 R~~LTl~eK~~iI~~~e~-----g~s~~~ia~~f--gv~~sTv~~I~K~ 45 (53)
T PF04218_consen 4 RKSLTLEEKLEIIKRLEE-----GESKRDIAREF--GVSRSTVSTILKN 45 (53)
T ss_dssp SSS--HHHHHHHHHHHHC-----TT-HHHHHHHH--T--CCHHHHHHHC
T ss_pred CccCCHHHHHHHHHHHHc-----CCCHHHHHHHh--CCCHHHHHHHHHh
Confidence 3467776653 4555444 44899999999 9999999999985
No 398
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=35.21 E-value=2.1e+02 Score=22.17 Aligned_cols=71 Identities=15% Similarity=0.175 Sum_probs=44.2
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.++++.+.+ |++.++ |+--|++|||.+...-...|.+. ||.+=|+.|. ..
T Consensus 2 ~i~eva~~~--gis~~t----lR~ye~~GLi~p~~~~~~ngyR~----------------------Y~~~~i~~l~--~I 51 (108)
T cd01107 2 TIGEFAKLS--NLSIKA----LRYYDKIGLLKPAYVDPDTGYRY----------------------YSAEQLERLN--RI 51 (108)
T ss_pred CHHHHHHHH--CcCHHH----HHHHHHcCCCCCCcCCCCCCccc----------------------cCHHHHHHHH--HH
Confidence 467788888 888765 46789999997743221112222 3455555553 33
Q ss_pred HHhhhCCCCCHHHHHHHHHHcC
Q 025493 135 KQIIKLKVATLEGISDSIKRSG 156 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~~ 156 (252)
..+++. ..++++|.+.+....
T Consensus 52 ~~lr~~-G~sl~~i~~l~~~~~ 72 (108)
T cd01107 52 KYLRDL-GFPLEEIKEILDADN 72 (108)
T ss_pred HHHHHc-CCCHHHHHHHHhcCC
Confidence 344444 468899998887655
No 399
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=35.19 E-value=2.2e+02 Score=22.34 Aligned_cols=69 Identities=10% Similarity=0.144 Sum_probs=43.1
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.+.++.+.+ |++.++| .--|++|||.+...-. +|--+|++ +=|..|+.+
T Consensus 2 ~I~eva~~~--gvs~~tL----RyYe~~GLl~p~~r~~------------------~gyR~Y~~-----~~i~~l~~I-- 50 (123)
T cd04770 2 KIGELAKAA--GVSPDTI----RYYERIGLLPPPQRSE------------------NGYRLYGE-----ADLARLRFI-- 50 (123)
T ss_pred CHHHHHHHH--CcCHHHH----HHHHHCCCCCCCCCCC------------------CCCccCCH-----HHHHHHHHH--
Confidence 467888889 8988765 5789999998532111 22234544 334444332
Q ss_pred HHhhhCCCCCHHHHHHHHHHc
Q 025493 135 KQIIKLKVATLEGISDSIKRS 155 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~ 155 (252)
.+++.. ..|++||.+++...
T Consensus 51 ~~lr~~-G~sl~eI~~~l~~~ 70 (123)
T cd04770 51 RRAQAL-GFSLAEIRELLSLR 70 (123)
T ss_pred HHHHHC-CCCHHHHHHHHHhh
Confidence 233333 67899999998754
No 400
>COG5126 FRQ1 Ca2+-binding protein (EF-Hand superfamily) [Signal transduction mechanisms / Cytoskeleton / Cell division and chromosome partitioning / General function prediction only]
Probab=35.15 E-value=80 Score=27.14 Aligned_cols=111 Identities=14% Similarity=0.225 Sum_probs=71.3
Q ss_pred CCCCCCCChHH----HHHHHHHHhhcCCCcccHHHHHHHh---hcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEE
Q 025493 28 NAPSDSLTDHE----RLIYDVIRSNKQDMGIWTRDMKREL---KVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLM 100 (252)
Q Consensus 28 ~~~~~~l~~~e----~~vy~~I~~~ag~~GIw~~dik~~~---~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~Ym 100 (252)
......||.+| +..|++... -++.=|-+.+|.+-. |-|.+.+.+++.+..+=.
T Consensus 8 ~~~~~~~t~~qi~~lkeaF~l~D~-d~~G~I~~~el~~ilr~lg~~~s~~ei~~l~~~~d~------------------- 67 (160)
T COG5126 8 LLTFTQLTEEQIQELKEAFQLFDR-DSDGLIDRNELGKILRSLGFNPSEAEINKLFEEIDA------------------- 67 (160)
T ss_pred hhhcccCCHHHHHHHHHHHHHhCc-CCCCCCcHHHHHHHHHHcCCCCcHHHHHHHHHhccC-------------------
Confidence 34456778777 556777777 666666666665542 224555555554433211
Q ss_pred ecccccCCCccCCccccCCcCC-HHHHHHHHHHHHHHh--------------hhCCCCCHHHHHHHHHHcCCcceecCHH
Q 025493 101 AVEFEPSKDISGGAWYSEGSLD-TEFIKVVKSQCLKQI--------------IKLKVATLEGISDSIKRSGAFKVDLTKQ 165 (252)
Q Consensus 101 L~~lePs~eiTGG~wy~d~e~D-~efV~~l~~~~~~~i--------------~~~~~~T~~~I~~~i~~~~i~~~~Ls~~ 165 (252)
..+..| .+|+..|.......- .+-++++..++...++..| -.++++
T Consensus 68 ----------------~~~~idf~~Fl~~ms~~~~~~~~~Eel~~aF~~fD~d~dG~Is~~eL~~vl~~lg---e~~~de 128 (160)
T COG5126 68 ----------------GNETVDFPEFLTVMSVKLKRGDKEEELREAFKLFDKDHDGYISIGELRRVLKSLG---ERLSDE 128 (160)
T ss_pred ----------------CCCccCHHHHHHHHHHHhccCCcHHHHHHHHHHhCCCCCceecHHHHHHHHHhhc---ccCCHH
Confidence 112222 467777666653221 1358999999999999888 589999
Q ss_pred HHHHHHHHHhhc
Q 025493 166 QIEEIVRAVVLD 177 (252)
Q Consensus 166 di~~IL~tLVyD 177 (252)
+|+.+|+...-|
T Consensus 129 ev~~ll~~~d~d 140 (160)
T COG5126 129 EVEKLLKEYDED 140 (160)
T ss_pred HHHHHHHhcCCC
Confidence 999999999864
No 401
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=35.14 E-value=1e+02 Score=25.69 Aligned_cols=53 Identities=15% Similarity=0.205 Sum_probs=37.7
Q ss_pred CCChHHH--HHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 33 SLTDHER--LIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 33 ~l~~~e~--~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
..|++|+ +..++|+=.-.+.=+..+|+...| +++-+++.+.++.|+..|-|-.
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~T--GasR~Tvk~~lreLVa~G~l~~ 58 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRITIKQLVAKT--GASRNTVKRYLRELVARGDLYR 58 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHH--CCCHHHHHHHHHHHHHcCCeEe
Confidence 3566544 334444431123337889999999 9999999999999999887654
No 402
>cd00073 H15 linker histone 1 and histone 5 domains; the basic subunit of chromatin is the nucleosome, consisting of an octamer of core histones, two full turns of DNA, a linker histone (H1 or H5) and a variable length of linker DNA; H1/H5 are chromatin-associated proteins that bind to the exterior of nucleosomes and dramatically stabilize the highly condensed states of chromatin fibers; stabilization of higher order folding occurs through electrostatic neutralization of the linker DNA segments, through a highly positively charged carboxy- terminal domain known as the AKP helix (Ala, Lys, Pro); thought to be involved in specific protein-protein and protein-DNA interactions and play a role in suppressing core histone tail domain acetylation in the chromatin fiber
Probab=35.11 E-value=1.9e+02 Score=21.85 Aligned_cols=51 Identities=16% Similarity=0.219 Sum_probs=36.4
Q ss_pred hhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCC
Q 025493 137 IIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNG 187 (252)
Q Consensus 137 i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g 187 (252)
+.....+|...|..||....=....--..-+..-|..+|-.|.++++...|
T Consensus 18 l~er~GsS~~aI~kyI~~~y~~~~~~~~~~l~~aLkk~v~~G~l~~~kG~g 68 (88)
T cd00073 18 LKERKGSSLQAIKKYIEAKYKVDDENFNKLLKLALKKGVAKGKLVQVKGTG 68 (88)
T ss_pred cCCCCCcCHHHHHHHHHHHCCcchHHHHHHHHHHHHHHHHCCCeEeecCCC
Confidence 345678999999999998752111111335667799999999999987443
No 403
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=35.03 E-value=1.1e+02 Score=21.62 Aligned_cols=37 Identities=14% Similarity=0.331 Sum_probs=28.7
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIK 77 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK 77 (252)
++.|++-..++++ .|+-+.++-+++ +++...|++.++
T Consensus 4 ~~g~~i~~~~~~~----~~~t~~~lA~~~--gis~~tis~~~~ 40 (78)
T TIGR02607 4 HPGEILREEFLEP----LGLSIRALAKAL--GVSRSTLSRIVN 40 (78)
T ss_pred CHHHHHHHHHHHH----cCCCHHHHHHHh--CCCHHHHHHHHc
Confidence 4566655466666 688899999999 999999988653
No 404
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=34.99 E-value=1.6e+02 Score=24.58 Aligned_cols=51 Identities=16% Similarity=0.122 Sum_probs=45.6
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 126 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 126 V~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+|.+-..++..|++.+-.|..+|++-+ .+|..-+.+=++.|+-+|.|+...
T Consensus 12 lD~~D~~IL~~Lq~d~R~s~~eiA~~l--------glS~~tv~~Ri~rL~~~GvI~~~~ 62 (164)
T PRK11169 12 LDRIDRNILNELQKDGRISNVELSKRV--------GLSPTPCLERVRRLERQGFIQGYT 62 (164)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeEEEE
Confidence 688899999999999999999999855 588999999999999999998644
No 405
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=34.96 E-value=1.6e+02 Score=26.62 Aligned_cols=63 Identities=10% Similarity=0.219 Sum_probs=46.6
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC-CCCCcccccCCcceeecccC
Q 025493 130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN-GSGEFTNIPVGKVCYKNVSK 206 (252)
Q Consensus 130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~-g~~~f~~~~~g~~~YR~~~~ 206 (252)
++.++..+.+.+..|++||++-+ .+|..-+++=|+.|+-+|.|+..... |.| .....|+++.+
T Consensus 13 r~~il~lL~~~g~~sa~elA~~L--------gis~~avR~HL~~Le~~Glv~~~~~~~g~G------RP~~~y~Lt~~ 76 (218)
T COG2345 13 RERILELLKKSGPVSADELAEEL--------GISPMAVRRHLDDLEAEGLVEVERQQGGRG------RPAKLYRLTEK 76 (218)
T ss_pred HHHHHHHHhccCCccHHHHHHHh--------CCCHHHHHHHHHHHHhCcceeeeeccCCCC------CCceeeeeccc
Confidence 56778888888899999988744 47888999999999999999876432 222 12256777655
No 406
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=34.93 E-value=33 Score=25.16 Aligned_cols=50 Identities=18% Similarity=0.222 Sum_probs=36.4
Q ss_pred CCCChHHHHHHHHHHhhcCC-CcccHHHHHHHhhcCCChHHHHHHHHHHHhcC
Q 025493 32 DSLTDHERLIYDVIRSNKQD-MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKS 83 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~-~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~ 83 (252)
..|++.|+.|.+.|-+|-.. .-...++|..++ +..+..|.|-.|+|-=+|
T Consensus 12 ~~ls~~e~~Ia~yil~~~~~~~~~si~elA~~~--~vS~sti~Rf~kkLG~~g 62 (77)
T PF01418_consen 12 NSLSPTEKKIADYILENPDEIAFMSISELAEKA--GVSPSTIVRFCKKLGFSG 62 (77)
T ss_dssp GGS-HHHHHHHHHHHH-HHHHCT--HHHHHHHC--TS-HHHHHHHHHHCTTTC
T ss_pred hhCCHHHHHHHHHHHhCHHHHHHccHHHHHHHc--CCCHHHHHHHHHHhCCCC
Confidence 46899999999999873322 357889999999 999999999999874433
No 407
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=34.89 E-value=85 Score=28.33 Aligned_cols=48 Identities=8% Similarity=0.184 Sum_probs=41.2
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
++.++++|++++.++++|+.+.+. .|++-|++=|+.|.-.|++.++..
T Consensus 7 ~~~Il~~l~~~g~v~v~eLa~~~~--------VS~~TIRRDL~~Le~~g~l~R~hG 54 (253)
T COG1349 7 HQKILELLKEKGKVSVEELAELFG--------VSEMTIRRDLNELEEQGLLLRVHG 54 (253)
T ss_pred HHHHHHHHHHcCcEEHHHHHHHhC--------CCHHHHHHhHHHHHHCCcEEEEeC
Confidence 467888999999999999988664 678899999999999999999873
No 408
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=34.36 E-value=62 Score=28.54 Aligned_cols=40 Identities=15% Similarity=0.333 Sum_probs=34.4
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
.-++|..+. |+..+.|.-+|+.|+..|||...+ ++-.|+.
T Consensus 36 sE~eLa~~l--gVSRtpVREAL~~L~~eGlv~~~~-----~~G~~V~ 75 (254)
T PRK09464 36 PERELAKQF--DVSRPSLREAIQRLEAKGLLLRRQ-----GGGTFVQ 75 (254)
T ss_pred CHHHHHHHh--CCCHHHHHHHHHHHHHCCCEEEec-----CceeEEe
Confidence 678999999 999999999999999999999763 4555654
No 409
>TIGR03303 OM_YaeT outer membrane protein assembly complex, YaeT protein. Members of this protein family are the YaeT protein of the YaeT/YfiO complex for assembling proteins into the outer membrane of Gram-negative bacteria. This protein is similar in sequence and function to a non-essential paralog, YtfM, that is also in the Omp85 family. Members of this family typically have five tandem copies of the surface antigen variable number repeat (pfam07244), followed by an outer membrane beta-barrel domain (pfam01103), while the YtfM family typically has a single pfam07244 repeat.
Probab=34.15 E-value=2.3e+02 Score=28.58 Aligned_cols=102 Identities=12% Similarity=0.162 Sum_probs=66.9
Q ss_pred HHHHHHhhcCCCcccHHHHHHHh-hc----CCChHHHHHHHHHH----HhcCCeee-eecc-c-cCCeeeEEecccccCC
Q 025493 41 IYDVIRSNKQDMGIWTRDMKREL-KV----NLPDNIVTKSIKSL----QNKSLIKE-VVNI-H-NKGKKHLMAVEFEPSK 108 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~-~~----~l~~~~l~k~lK~L----e~k~lIK~-vksv-~-~~~rK~YmL~~lePs~ 108 (252)
+..-|+= .||+.++.++|+... +. -+.+..+....+.| .++|+..+ |... . .+..++-+.+.+.|-.
T Consensus 70 ~i~~i~~-~G~~~~~~~~l~~~~~~~~~g~~~~~~~~~~~~~~l~~~y~~~Gy~~a~V~~~~~~~~~~~~~v~~~v~eg~ 148 (741)
T TIGR03303 70 IINSIVF-SGNKEIKKDQLKKALVGIKKGEIFNRAKLEKDEKALKEFYRSRGKYNAKVEAKVTPLPRNRVDLEFNIKEGK 148 (741)
T ss_pred eEEEEEE-ECCccCCHHHHHHHHhhccCCCcCCHHHHHHHHHHHHHHHHHcCcceeEEEEEEEECCCCeEEEEEEEecCC
Confidence 3334555 799999999999887 32 36777887777777 77999853 4321 1 1334455555555433
Q ss_pred -------CccCCc--------------------cc-cCCcCCHHHHHHHHHHHHHHhhhCCCC
Q 025493 109 -------DISGGA--------------------WY-SEGSLDTEFIKVVKSQCLKQIIKLKVA 143 (252)
Q Consensus 109 -------eiTGG~--------------------wy-~d~e~D~efV~~l~~~~~~~i~~~~~~ 143 (252)
+++|.. |. .++.||.+.++..++.+..|+.+++|.
T Consensus 149 ~~~i~~i~~~Gn~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~i~~~y~~~Gy~ 211 (741)
T TIGR03303 149 KAKIKKINFVGNKAFSDSELRDVFALKESNFWSWFTGDDKYSKQKLEADLELLRSFYLNRGYL 211 (741)
T ss_pred EEEEEEEEEECCCcCCHHHHHHHHhcCcchhHHhccCCCeECHHHHhhhHHHHHHHHHhCCcE
Confidence 123321 22 246799999999999999999887764
No 410
>PF06207 DUF1002: Protein of unknown function (DUF1002); InterPro: IPR009343 This protein family has no known function. Its members are about 300 amino acids in length. It has so far been detected in Firmicute bacteria and some archaebacteria.
Probab=34.13 E-value=2.1e+02 Score=25.86 Aligned_cols=116 Identities=15% Similarity=0.178 Sum_probs=70.4
Q ss_pred cCCCcccHHHHHHHhhcCC-ChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHH
Q 025493 49 KQDMGIWTRDMKRELKVNL-PDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIK 127 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~~l-~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~ 127 (252)
+-.-||--.+|.-.++... -...|+=++|.+|..|-==.-..++.-+.-+....++.- ..+++.+=++
T Consensus 88 l~TAGv~da~I~Vasp~~VsG~sALtGVyKA~E~~G~~l~~~~k~~A~eEl~~t~~i~~-----------~~~~~~~k~~ 156 (225)
T PF06207_consen 88 LITAGVTDADIYVASPFPVSGESALTGVYKAYEATGEKLDEENKKVANEELVTTSEIAE-----------GDGIGDEKAN 156 (225)
T ss_pred HHHcCCCcceEEEeccccCcchHHHHHHHHHHHHcCCCCCHHHHHHHHHHHHHHHhhcc-----------ccCCCHHHHH
Confidence 3445666666666653222 244777777888765532222222222232333322211 4567777777
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHc-CCcceecCHHHHHHHHHHHh
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRS-GAFKVDLTKQQIEEIVRAVV 175 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~-~i~~~~Ls~~di~~IL~tLV 175 (252)
.+-..+-.-|.+...-|.+||.+-|.+. +--.+.||.+++++|++.|.
T Consensus 157 ~~i~~iK~~va~~~~~t~~eI~~IV~~~~~~~~i~ls~~q~~~i~~l~~ 205 (225)
T PF06207_consen 157 AAIAEIKEEVAKQKPKTDEEIRNIVNNVLNNYNINLSDEQIQQIVNLMK 205 (225)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 7777777777777777999999888754 11224599999999999875
No 411
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=33.95 E-value=79 Score=31.01 Aligned_cols=144 Identities=17% Similarity=0.233 Sum_probs=92.9
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeecc-----ccCCeeeE-Ee--ccc--
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNI-----HNKGKKHL-MA--VEF-- 104 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv-----~~~~rK~Y-mL--~~l-- 104 (252)
|-+| .|+++|++.+=.+-|.-|-|.+.+ +....+--|++|.-|++|++..++-| +.++|+-- -| .++
T Consensus 2 sKHe-qIL~Yie~L~vG~kISVR~Ia~~l--~VSeGTAYRAIKeAen~G~V~Ti~RvGTvRIekk~k~~Ie~LTf~Eiv~ 78 (432)
T COG4109 2 SKHE-QILNYIESLEVGKKISVRGIAKHL--KVSEGTAYRAIKEAENLGLVSTIPRVGTVRIEKKGKKNIERLTFAEIVN 78 (432)
T ss_pred CcHH-HHHHHHHhccccceeehHHhhhhC--CcccchHHHHHHHHHhcCceEecccceeEEEEeccchhhhhhhHHHHHH
Confidence 3344 688999998889999999999999 99999999999999999999877654 22222210 00 000
Q ss_pred ccCCCccCCccccCCcCCHHHHHHHH-HHHHHHhh--------------------------hCCCCCHHHHHHHHHHcCC
Q 025493 105 EPSKDISGGAWYSEGSLDTEFIKVVK-SQCLKQII--------------------------KLKVATLEGISDSIKRSGA 157 (252)
Q Consensus 105 ePs~eiTGG~wy~d~e~D~efV~~l~-~~~~~~i~--------------------------~~~~~T~~~I~~~i~~~~i 157 (252)
--+.++-||-==-+-+|..=.|..+. +.+.+|+. .-|+.+-++|.++-++.++
T Consensus 79 iidgqVLgG~~Gl~k~~sKFvIGAMt~~~i~rY~~~g~LlIVGnR~~iq~lAL~~~~AVLvTGGF~~s~evi~lAne~~l 158 (432)
T COG4109 79 IIDGQVLGGRAGLEKELSKFVIGAMTLDAILRYLDPGGLLIVGNREDIQLLALENGNAVLVTGGFDVSDEVIKLANEKGL 158 (432)
T ss_pred hhccceeccccchhhhhhhhhhhhhhHHHHHhhcCCCceEEEecHHHHHHHHHhcCCeEEEeCCCCccHHHHHhhcccCC
Confidence 12334556632122234333344443 45677775 1378889999999888885
Q ss_pred c--ceecCHHHHHHHHHHHhhcCeeE
Q 025493 158 F--KVDLTKQQIEEIVRAVVLDNQIM 181 (252)
Q Consensus 158 ~--~~~Ls~~di~~IL~tLVyDgkIE 181 (252)
. +.....=-|..+++.-.+|.+|.
T Consensus 159 PvlstsYDTFTVAtmIN~Al~n~lIK 184 (432)
T COG4109 159 PVLSTSYDTFTVATMINKALSNQLIK 184 (432)
T ss_pred ceEEecccceeHHHHHHHHHHHhhhh
Confidence 4 22333334556666666666654
No 412
>PRK11642 exoribonuclease R; Provisional
Probab=33.90 E-value=1.1e+02 Score=32.59 Aligned_cols=51 Identities=10% Similarity=0.303 Sum_probs=41.6
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCCh----HHHHHHHHHHHhcCCeee
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPD----NIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~----~~l~k~lK~Le~k~lIK~ 87 (252)
..++..| .|++++.+ .+ +++-.++|-+++ +++. ..+.++|+.|+..|.|..
T Consensus 16 ~~~~~~~-~Il~~l~~-~~-~~~~~~~L~~~l--~l~~~~~~~~l~~~L~~L~~~g~l~~ 70 (813)
T PRK11642 16 NPIPSRE-FILEHLTK-RE-KPASREELAVEL--NIEGEEQLEALRRRLRAMERDGQLVF 70 (813)
T ss_pred CCCCCHH-HHHHHHHh-cC-CCCCHHHHHHHh--CCCChHHHHHHHHHHHHHHHCCCEEE
Confidence 3464444 58889887 66 999999999999 8874 459999999999999974
No 413
>COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain [Signal transduction mechanisms]
Probab=33.50 E-value=1.3e+02 Score=28.65 Aligned_cols=62 Identities=13% Similarity=0.142 Sum_probs=48.4
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcc--cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCC
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGI--WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKG 95 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GI--w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~ 95 (252)
....|+.++..|+..|+. .-..== -...|.+.+ .|+...+...||.|-..+||.. +.+...+
T Consensus 7 ~~~~l~~~D~rlLraiE~-~mR~~e~VP~~~i~~~a--r~~~~~~~~~L~~L~~l~lv~r-~~~~y~G 70 (304)
T COG0478 7 AYPKLSKEDFRLLRAIEG-GMRSHEWVPLELIKKRA--RMDEEELLYRLKRLDKLKLVSR-RTISYEG 70 (304)
T ss_pred hhhhcCHHHHHHHHHHHh-cccccccccHHHHHHHc--CCCHHHHHHHHHHHHhcCceec-cCCccee
Confidence 456799999999999999 222222 245688899 9999999999999999999998 5544433
No 414
>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=33.42 E-value=88 Score=27.55 Aligned_cols=58 Identities=19% Similarity=0.348 Sum_probs=38.2
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCccccc
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIP 195 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~ 195 (252)
+.+...+||..+..+.+++++... .|+.+|+-.-|+.|.-+|.|.-|..+ -|-|..++
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f--------~l~t~~~i~ri~~L~~~g~ltGv~Dd-rGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEF--------GLRTQDVINRIQELEAEGRLTGVIDD-RGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH---------S-HHHHHHHHHHHHHHSSS-EEE-T-T--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHHHc--------CCCHHHHHHHHHHHHHCCCceeeEcC-CCCeEEec
Confidence 444555788888888888888654 58899999999999999999988744 35665553
No 415
>TIGR02356 adenyl_thiF thiazole biosynthesis adenylyltransferase ThiF, E. coli subfamily. Members of the HesA/MoeB/ThiF family of proteins (pfam00899) include a number of members encoded in the midst of thiamine biosynthetic operons. This mix of known and putative ThiF proteins shows a deep split in phylogenetic trees, with the Escherichia. coli ThiF and the E. coli MoeB proteins seemingly more closely related than E. coli ThiF and Campylobacter (for example) ThiF. This model represents the more widely distributed clade of ThiF proteins such found in E. coli.
Probab=33.38 E-value=1.7e+02 Score=25.29 Aligned_cols=72 Identities=7% Similarity=-0.003 Sum_probs=42.9
Q ss_pred CccCCccccCCcCCHHHHHHHHHHHHHHhh------hCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCee
Q 025493 109 DISGGAWYSEGSLDTEFIKVVKSQCLKQII------KLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQI 180 (252)
Q Consensus 109 eiTGG~wy~d~e~D~efV~~l~~~~~~~i~------~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkI 180 (252)
.+.--.+|++++....=++.+.+.+...-. ....++.+.+.+++++..+.=.....-+.+..++.+...-.+
T Consensus 60 NL~Rq~l~~~~diG~~Ka~~~~~~l~~~np~v~i~~~~~~i~~~~~~~~~~~~D~Vi~~~d~~~~r~~l~~~~~~~~i 137 (202)
T TIGR02356 60 NLQRQILFTEEDVGRPKVEVAAQRLRELNSDIQVTALKERVTAENLELLINNVDLVLDCTDNFATRYLINDACVALGT 137 (202)
T ss_pred chhhhhccChhhCCChHHHHHHHHHHHhCCCCEEEEehhcCCHHHHHHHHhCCCEEEECCCCHHHHHHHHHHHHHcCC
Confidence 354456788877777777777777665321 123456667777887665432233344566667766665544
No 416
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=33.37 E-value=99 Score=25.22 Aligned_cols=46 Identities=17% Similarity=0.257 Sum_probs=35.1
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHH----HHHHHHHHh
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIV----TKSIKSLQN 81 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l----~k~lK~Le~ 81 (252)
.+..|++.++.|+.+-.- .|...++|...+ |++.+.| .|+++.|-+
T Consensus 115 ~l~~L~~~~r~vl~L~~~----~g~s~~EIA~~l--gis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 115 ALAQLSPEHRAVLVRSYY----RGWSTAQIAADL--GIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred HHHhCCHHHHHHHHHHHH----cCCCHHHHHHHH--CcCHHHHHHHHHHHHHHHHH
Confidence 356778888888777654 488999999999 9999887 666666643
No 417
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=32.93 E-value=2.2e+02 Score=27.51 Aligned_cols=24 Identities=17% Similarity=0.266 Sum_probs=20.8
Q ss_pred ccCCccccCCcCCHHHHHHHHHHH
Q 025493 110 ISGGAWYSEGSLDTEFIKVVKSQC 133 (252)
Q Consensus 110 iTGG~wy~d~e~D~efV~~l~~~~ 133 (252)
..+||.|...=.|.||++.+.+..
T Consensus 272 ~~~GPlW~G~l~d~~fl~~~~~~~ 295 (382)
T PRK04338 272 GTAGPLWLGPLHDKEFVEEMLEEA 295 (382)
T ss_pred eeccccccCccCCHHHHHHHHHHh
Confidence 568999999999999999997755
No 418
>COG3132 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.62 E-value=22 Score=31.48 Aligned_cols=94 Identities=13% Similarity=0.202 Sum_probs=55.9
Q ss_pred CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCH
Q 025493 66 NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATL 145 (252)
Q Consensus 66 ~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~ 145 (252)
||.+.+|...|+.|++|+||..|.. +|- +-|+- --+.+=|.|=+|...=|..| -.+--.+.-|+
T Consensus 49 nLse~eVq~~l~~L~~r~lvr~~sg----sRv--~kyeh-----rfcnsefgdlkl~~~evali-----~lLlLRGaQTp 112 (215)
T COG3132 49 NLSESEVQEQLDNLEKRHLVRTVSG----SRV--TKYEH-----RFCNSEFGDLKLSAAEVALI-----TLLLLRGAQTP 112 (215)
T ss_pred cCCHHHHHHHHHHHHHhhhHHHhhc----chH--HHHHH-----HHhhccccceeechHHHHHH-----HHHHHcCCCCh
Confidence 9999999999999999999998752 121 11111 11222233444444333332 22333567777
Q ss_pred HHHHHHHHHcCCcceecCHHHHHHHHHHHhhcC
Q 025493 146 EGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 146 ~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDg 178 (252)
.|+..--++.--+ =+.++++.-|+.|.--+
T Consensus 113 gELrtRanRm~~F---sdv~e~e~~Le~La~R~ 142 (215)
T COG3132 113 GELRTRANRMYEF---SDVAEVEHTLERLANRE 142 (215)
T ss_pred hHHHHHHHhhhcc---chHHHHHHHHHHHhcCC
Confidence 7776654443211 24678888899998765
No 419
>TIGR02719 repress_PhaQ poly-beta-hydroxybutyrate-responsive repressor. Members of this family are transcriptional regulatory proteins found in the vicinity of poly-beta-hydroxybutyrate (PHB) operons in several species of Bacillus. This protein appears to have repressor activity modulated by PHB itself. This protein belongs to the larger PadR family (see pfam03551).
Probab=32.57 E-value=3e+02 Score=23.01 Aligned_cols=67 Identities=12% Similarity=-0.009 Sum_probs=46.0
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCCCCCcccccCCcceeecccC
Q 025493 132 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNGSGEFTNIPVGKVCYKNVSK 206 (252)
Q Consensus 132 ~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g~~~f~~~~~g~~~YR~~~~ 206 (252)
.|+..|.. +...-=+|.+.|+..|+ ..++...+-.+|+.|+-+|.|+....... ..+.++.|+++..
T Consensus 28 ~IL~~L~~-~p~hGYeI~q~l~~~g~--~~v~~GtLYp~L~RLE~~GlI~~~~~~~~-----~gp~RK~Y~LTe~ 94 (138)
T TIGR02719 28 FLLLCLKD-WNLHGYKLIQMLMDFGF--SSVDQGNVYRTLRKLEKDNLISSQWDTSA-----EGPAKRIYSLTDA 94 (138)
T ss_pred HHHHHHcc-CCCCHHHHHHHHHHcCC--CCCCcChHHHHHHHHHHCCCEEEEeeecC-----CCCCcEEEEECHH
Confidence 34444444 45677889999988763 45788999999999999999987432211 1234678887643
No 420
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=32.44 E-value=91 Score=23.74 Aligned_cols=46 Identities=15% Similarity=0.251 Sum_probs=35.9
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
.+..|++.|+.|..+.-- .|...++|...+ |++...|.+.++....
T Consensus 107 ~l~~L~~~~~~ii~~~~~----~g~s~~eIA~~l--~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 107 ALEKLPEREREVLVLRYL----EGLSYKEIAEIL--GISVGTVKRRLKRARK 152 (158)
T ss_pred HHHhCCHHHHHHHhhHHh----cCCCHHHHHHHH--CCCHHHHHHHHHHHHH
Confidence 455788888888655433 478999999999 9999999988887643
No 421
>COG0150 PurM Phosphoribosylaminoimidazole (AIR) synthetase [Nucleotide transport and metabolism]
Probab=32.28 E-value=50 Score=31.80 Aligned_cols=90 Identities=16% Similarity=0.202 Sum_probs=51.3
Q ss_pred HHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHH--
Q 025493 58 DMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLK-- 135 (252)
Q Consensus 58 dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~-- 135 (252)
.|...+ .-|.+.-.|-+-.|.+...||.+ . .||||-|. +.|.+..=+
T Consensus 216 ~l~e~L--L~PTrIYvk~vL~l~~~~~vkg~---A----------------HITGGG~~----------eNl~Rv~p~~l 264 (345)
T COG0150 216 TLGEEL--LEPTRIYVKPVLALIKEGDVKGM---A----------------HITGGGFV----------ENLPRVLPEGL 264 (345)
T ss_pred CHHHHh--cCCceeehHHHHHHHhcCCcceE---E----------------EecCCChh----------hhChhhcCccc
Confidence 677777 66777777744444444455554 2 37888766 223322211
Q ss_pred -HhhhCCCCCHHHHHHHHHHcC-Cc--------------ceecCHHHHHHHHHHHhhcC
Q 025493 136 -QIIKLKVATLEGISDSIKRSG-AF--------------KVDLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 136 -~i~~~~~~T~~~I~~~i~~~~-i~--------------~~~Ls~~di~~IL~tLVyDg 178 (252)
+.-.....++.+|-+||.+.| +. -+-+.++|.+++++.|---|
T Consensus 265 ~a~id~~~~~~p~iF~~i~~~G~v~~~EM~rtFNmGvG~v~iv~~e~~~~~~~~l~~~g 323 (345)
T COG0150 265 GAVIDKPSWPPPPIFKWLQKAGNVEREEMYRTFNMGVGMVLIVPEEDAEKALALLKEQG 323 (345)
T ss_pred eEEEcCCCCCCcHHHHHHHHhcCCCHHHHHHHhcCccceEEEEcHHHHHHHHHHHHhcC
Confidence 111222333455555555554 22 26789999999999998665
No 422
>PF13518 HTH_28: Helix-turn-helix domain
Probab=32.24 E-value=94 Score=20.16 Aligned_cols=30 Identities=23% Similarity=0.406 Sum_probs=27.4
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhcCC
Q 025493 53 GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL 84 (252)
Q Consensus 53 GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l 84 (252)
|...+++..+. +++..+|.+-++..+..|+
T Consensus 12 g~s~~~~a~~~--gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 12 GESVREIAREF--GISRSTVYRWIKRYREGGI 41 (52)
T ss_pred CCCHHHHHHHH--CCCHhHHHHHHHHHHhcCH
Confidence 55899999999 9999999999999999883
No 423
>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=32.22 E-value=1.7e+02 Score=22.25 Aligned_cols=36 Identities=11% Similarity=0.223 Sum_probs=27.5
Q ss_pred CCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 140 LKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 140 ~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
...+|..||++.+ .++.+-|.++|+.|+-+|.|++.
T Consensus 45 ~~~is~~eLa~~~--------g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 45 QDRVTATVIAELT--------GLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred CCccCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCeeee
Confidence 3456666666654 36678899999999999999864
No 424
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=32.16 E-value=5.6e+02 Score=26.09 Aligned_cols=100 Identities=12% Similarity=0.119 Sum_probs=67.3
Q ss_pred CCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHH
Q 025493 50 QDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVV 129 (252)
Q Consensus 50 g~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l 129 (252)
-..|+-..+|+.++ ..........|..|.. |+.. +- .+-|.+..| .++.+-- +
T Consensus 424 ~~~g~~~~~l~~~~--~~~~~~~~~~l~~~~~---~~~~------~~-~~~~~~~~~-------------~~~~~~~--~ 476 (581)
T TIGR00475 424 DVKGVDKERLERMA--SLNEELLKTAIEKLIG---TYKI------GG-WLHIPDHKS-------------DFEKEED--I 476 (581)
T ss_pred hccCCCHHHHHhhc--cCChHHHHHHHHHHHH---heEe------CC-EEECCCCCC-------------CCCHHHH--H
Confidence 34899999999998 5667788888888877 3332 11 122222222 2334432 5
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 130 KSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 130 ~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
.+.+...++ ...|++.|+.+-+ .+.+.+++++++.|+-.|.+.++..
T Consensus 477 ~~~i~~~~~-~~~~~~~~~~~~~--------~~~~~~~~~~l~~l~~~g~~~~~~~ 523 (581)
T TIGR00475 477 WQKIKGTFG-TKGAWVREFAEEV--------NGDEKVMLKRVRKAGHRGGETLIVK 523 (581)
T ss_pred HHHHHHHHh-cCCCCHHHHHhhh--------CCCHHHHHHHHHHHHhCCCEEEEeC
Confidence 556666555 5688888888733 3568889999999999999888764
No 425
>PRK11302 DNA-binding transcriptional regulator HexR; Provisional
Probab=32.15 E-value=62 Score=28.88 Aligned_cols=52 Identities=21% Similarity=0.308 Sum_probs=43.8
Q ss_pred CCCCChHHHHHHHHHHhhcCC-CcccHHHHHHHhhcCCChHHHHHHHHHHHhcCC
Q 025493 31 SDSLTDHERLIYDVIRSNKQD-MGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL 84 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~-~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l 84 (252)
...||+-|+.|.++|.+|-.. .-+..++|-.++ +..+.+|.|-.|+|==+|+
T Consensus 11 ~~~Lt~~e~~Ia~yil~n~~~v~~~si~~lA~~~--~vS~aTv~Rf~kklG~~gf 63 (284)
T PRK11302 11 LEHLSKSERKVAEVILASPQTAIHSSIATLAKMA--NVSEPTVNRFCRSLDTKGF 63 (284)
T ss_pred HhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHh--CCCHHHHHHHHHHcCCCCH
Confidence 457999999999999994333 246889999999 9999999999999966665
No 426
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=32.13 E-value=1.5e+02 Score=26.29 Aligned_cols=110 Identities=15% Similarity=0.192 Sum_probs=0.0
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHH---------HHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKS---------IKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~---------lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
+.+||.+|..++....+ .|+...|..=+..-. .+--..+.|. ..-|.+-++|+-.+++..
T Consensus 1 ~~~~~~~e~~l~~~~~~-~~d~~a~~~L~~~y~--~~v~~~~~~~~~~~~~~~~~eDl~Qe~~i~l~~~~~~-------- 69 (251)
T PRK07670 1 MQSLTYEEQKLWDRWKE-ERDPDAADELIRRYM--PLVHYHVQRISVGLPKSVSKDDLKSLGMLGLYDALEK-------- 69 (251)
T ss_pred CcchhHHHHHHHHHHHH-cCCHHHHHHHHHHHH--HHHHHHHHHHHhhCCCCCCHHHHHHHHHHHHHHHHHH--------
Q ss_pred cccccCCCccCCccccC---CcCCHHHHHHHHHHHHHHhhhCC--------------------------CCCHHHHHHHH
Q 025493 102 VEFEPSKDISGGAWYSE---GSLDTEFIKVVKSQCLKQIIKLK--------------------------VATLEGISDSI 152 (252)
Q Consensus 102 ~~lePs~eiTGG~wy~d---~e~D~efV~~l~~~~~~~i~~~~--------------------------~~T~~~I~~~i 152 (252)
|.. ..|-+=+.-.++..|.+|++++. .||.++|+..+
T Consensus 70 --------------f~~~~~~~f~tyl~~~irn~~~d~lR~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~eia~~l 135 (251)
T PRK07670 70 --------------FDPSRDLKFDTYASFRIRGAIIDGLRKEDWLPRSMREKTKKVEAAIEKLEQRYMRNVTPKEVAAEL 135 (251)
T ss_pred --------------cCcccCCCHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHh
Q ss_pred HHcCCcceecCHHHHHHHHHH
Q 025493 153 KRSGAFKVDLTKQQIEEIVRA 173 (252)
Q Consensus 153 ~~~~i~~~~Ls~~di~~IL~t 173 (252)
. ++.++|+.++..
T Consensus 136 ~--------~~~~~v~~~~~~ 148 (251)
T PRK07670 136 G--------MTEEEVEATMNE 148 (251)
T ss_pred C--------cCHHHHHHHHHH
No 427
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=32.06 E-value=1.2e+02 Score=24.57 Aligned_cols=47 Identities=21% Similarity=0.227 Sum_probs=39.1
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCC
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL 84 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l 84 (252)
...||..|+.|+.++.+ |.-.++|..+. ++..++|...++.|-.|=-
T Consensus 141 ~~~lt~~E~~vl~~l~~-----g~~~~~I~~~l--~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 141 LDSLSKQEISVMRYILD-----GKDNNDIAEKM--FISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cccCCHHHHHHHHHHHc-----CCCHHHHHHHh--CCCHHHHHHHHHHHHHHcC
Confidence 34699999999999987 45789999999 9999999988888866543
No 428
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=31.99 E-value=97 Score=24.92 Aligned_cols=43 Identities=9% Similarity=-0.038 Sum_probs=31.7
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHH----HHHHHHH
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIV----TKSIKSL 79 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l----~k~lK~L 79 (252)
+..|++.++.|+.+-.- .|...++|...+ |++.++| .|+++.|
T Consensus 104 l~~Lp~~~r~v~~l~~~----~g~s~~EIA~~l--gis~~tV~~~l~Rar~~L 150 (160)
T PRK09642 104 LRELPENYRDVVLAHYL----EEKSYQEIALQE--KIEVKTVEMKLYRARKWI 150 (160)
T ss_pred HHhCCHHHHHHHHHHHH----hCCCHHHHHHHH--CCCHHHHHHHHHHHHHHH
Confidence 45667766666655443 689999999999 9999988 5555555
No 429
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=31.92 E-value=1.3e+02 Score=27.36 Aligned_cols=49 Identities=6% Similarity=0.058 Sum_probs=41.8
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
.=+..++++|++++.+|+.|+++.+ ..|..-|++=|+.|.-.|.+.++.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l--------~VS~~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALY--------GVSTVTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHH--------CCCHHHHHHHHHHHHhCCCeEEEe
Confidence 3456788999999999999999987 356788999999999999999876
No 430
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=31.74 E-value=1.3e+02 Score=24.32 Aligned_cols=44 Identities=20% Similarity=0.338 Sum_probs=38.2
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
-.|+.-|..|..++.+ |...++|..++ ++..++|...++.+-+|
T Consensus 148 ~~lt~re~~vl~~l~~-----g~s~~eIa~~l--~~s~~tv~~~~~~~~~k 191 (210)
T PRK09935 148 TVLSNREVTILRYLVS-----GLSNKEIADQL--LLSNKTVSAHKSNIYGK 191 (210)
T ss_pred ccCCHHHHHHHHHHHc-----CCCHHHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 3589999999998877 59999999999 99999999998888554
No 431
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=31.70 E-value=1.4e+02 Score=24.37 Aligned_cols=53 Identities=21% Similarity=0.273 Sum_probs=42.4
Q ss_pred CCChHHHHHHHHHHhhcCCC------------cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 33 SLTDHERLIYDVIRSNKQDM------------GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~------------GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
..+..+++...+..- +... -+-+.+|-.-+ |+....++|.++.|+..|+|..-
T Consensus 140 ~~~~~~r~~~~l~~l-~~~~~~~~~~~~~~~~~~~~~~ia~~~--g~~~~~vsr~l~~l~~~g~i~~~ 204 (214)
T COG0664 140 RKDVEERLARFLLNL-GRRLGIATEDGILIPLPLTHKDLAEYL--GLSRETVSRILKELRKDGLISVR 204 (214)
T ss_pred hccHHHHHHHHHHHH-hhccCCCCCCCcEEeccCCHHHHHHHh--CCchhhHHHHHHHHHhCCcEeeC
Confidence 445567776666665 5543 47788999999 99999999999999999999874
No 432
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=31.64 E-value=77 Score=28.18 Aligned_cols=43 Identities=23% Similarity=0.348 Sum_probs=33.3
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
.|+-.+..++..|.+ .|+- ..-..++ |+.|..|++.||+||+.
T Consensus 4 ~~~l~~L~~f~~v~~-~gs~----s~AA~~L--~isQ~avS~~i~~LE~~ 46 (302)
T PRK09791 4 QVKIHQIRAFVEVAR-QGSI----RGASRML--NMSQPALTKSIQELEEG 46 (302)
T ss_pred cccHHHHHHHHHHHH-cCCH----HHHHHHh--CCChHHHHHHHHHHHHH
Confidence 467777788888888 7743 3334567 99999999999999983
No 433
>COG3763 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.27 E-value=1.8e+02 Score=21.88 Aligned_cols=44 Identities=18% Similarity=0.268 Sum_probs=38.7
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHh
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVV 175 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLV 175 (252)
-+++..+++..+...|.+.|..-..+.| ...|+..|+++.+...
T Consensus 25 ark~~~k~lk~NPpine~~iR~M~~qmG---qKpSe~kI~Qvm~~i~ 68 (71)
T COG3763 25 ARKQMKKQLKDNPPINEEMIRMMMAQMG---QKPSEKKINQVMRSII 68 (71)
T ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhC---CCchHHHHHHHHHHHH
Confidence 4677889999999999999999999999 6889999999987654
No 434
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=31.09 E-value=2.6e+02 Score=21.81 Aligned_cols=69 Identities=12% Similarity=0.158 Sum_probs=43.0
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.++++.+.+ |++.++| ..-|..|||.+...-.+ +.+.| +.+=|+.|+.+
T Consensus 2 ~i~eva~~~--gvs~~tl----R~ye~~Gll~p~~~~~~-g~R~Y----------------------~~~dl~~l~~I-- 50 (108)
T cd04773 2 TIGELAHLL--GVPPSTL----RHWEKEGLLSPDREPET-GYRVY----------------------DPSDVRDARLI-- 50 (108)
T ss_pred CHHHHHHHH--CcCHHHH----HHHHHCCCCCCCcCCCC-Cceee----------------------CHHHHHHHHHH--
Confidence 567888889 8988766 45688999987543222 33333 33334444433
Q ss_pred HHhhhCCCCCHHHHHHHHHHc
Q 025493 135 KQIIKLKVATLEGISDSIKRS 155 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~ 155 (252)
..+... ..++++|.+++...
T Consensus 51 ~~lr~~-G~~l~~I~~~l~~~ 70 (108)
T cd04773 51 HLLRRG-GYLLEQIATVVEQL 70 (108)
T ss_pred HHHHHC-CCCHHHHHHHHHHh
Confidence 344444 45888899888754
No 435
>TIGR02531 yecD_yerC TrpR-related protein YerC/YecD. This model represents a protein subfamily found mostly in the Firmicutes (Bacillus and allies). This family is similar in sequence to the trp operon repressor TrpR described by TIGR01321, and represents a distinct clade within the broader family described by pfam01371. At least one species, Xylella fastidiosa, in the Proteobacteria, has a member of both this family and TIGR01321. Several genomes with a member of this family do not synthesize tryptophan, and members of this family should not be considered trp operon repressors without new evidence.
Probab=30.96 E-value=91 Score=24.03 Aligned_cols=37 Identities=14% Similarity=0.252 Sum_probs=28.4
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIK 77 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK 77 (252)
.|++- ..|..++.+ |++.++|...+ +++..+|.|+.|
T Consensus 36 ~Ls~R-~~I~~ll~~-----G~S~~eIA~~L--gISrsTIyRi~R 72 (88)
T TIGR02531 36 SLAQR-LQVAKMLKQ-----GKTYSDIEAET--GASTATISRVKR 72 (88)
T ss_pred hhhHH-HHHHHHHHC-----CCCHHHHHHHH--CcCHHHHHHHHH
Confidence 35555 455555544 88999999999 999999999665
No 436
>PRK00215 LexA repressor; Validated
Probab=30.90 E-value=2.3e+02 Score=24.17 Aligned_cols=37 Identities=16% Similarity=0.141 Sum_probs=30.3
Q ss_pred CCCCCHHHHHHHHHHcCCcceec-CHHHHHHHHHHHhhcCeeEEEe
Q 025493 140 LKVATLEGISDSIKRSGAFKVDL-TKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 140 ~~~~T~~~I~~~i~~~~i~~~~L-s~~di~~IL~tLVyDgkIE~v~ 184 (252)
...+|..||++.+. + +..-+..+|++|+-.|.|++..
T Consensus 21 ~~~~s~~ela~~~~--------~~~~~tv~~~l~~L~~~g~i~~~~ 58 (205)
T PRK00215 21 GYPPSRREIADALG--------LRSPSAVHEHLKALERKGFIRRDP 58 (205)
T ss_pred CCCCCHHHHHHHhC--------CCChHHHHHHHHHHHHCCCEEeCC
Confidence 34688999988764 5 5678999999999999998764
No 437
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=30.89 E-value=78 Score=28.21 Aligned_cols=43 Identities=14% Similarity=0.150 Sum_probs=32.5
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
.|+-.+..++..|.+ .|+-.-. ..++ +++|..|++.|+.||+.
T Consensus 3 ~m~l~~L~~F~~v~e-~gs~s~A----A~~L--~isqpavS~~I~~LE~~ 45 (296)
T PRK11062 3 HINYNHLYYFWMVCK-EGSVVGA----AEAL--FLTPQTITGQIKALEER 45 (296)
T ss_pred ccCHHHHHHHHHHHh-cCCHHHH----HHHh--CCChHHHHHHHHHHHHH
Confidence 466677778888888 6654322 3456 99999999999999984
No 438
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=30.88 E-value=2.8e+02 Score=22.62 Aligned_cols=29 Identities=17% Similarity=0.124 Sum_probs=22.9
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.++.++.+.+ |++.++|. ..|++|||...
T Consensus 2 ysI~eVA~~~--GVs~~TLR----~wE~~GLl~p~ 30 (120)
T cd04767 2 YPIGVVAELL--NIHPETLR----IWERHGLIKPA 30 (120)
T ss_pred CCHHHHHHHH--CcCHHHHH----HHHHCCCCCCc
Confidence 3577888889 89888664 78999999764
No 439
>PF03801 Ndc80_HEC: HEC/Ndc80p family; InterPro: IPR005550 Members of this family are components of the mitotic spindle. It has been shown that Ndc80 from yeast is part of a complex called the Ndc80p complex []. This complex is thought to bind to the microtubules of the spindle.; PDB: 3IZ0_E 2VE7_B 2IGP_A.
Probab=30.63 E-value=2e+02 Score=24.20 Aligned_cols=60 Identities=10% Similarity=0.087 Sum_probs=37.1
Q ss_pred CHHHHHHHHHHHHHHhhhCCC------------CCHHH---HHHHHHHcCCcceecC---HHHHHHHHHHHhhcC-eeE
Q 025493 122 DTEFIKVVKSQCLKQIIKLKV------------ATLEG---ISDSIKRSGAFKVDLT---KQQIEEIVRAVVLDN-QIM 181 (252)
Q Consensus 122 D~efV~~l~~~~~~~i~~~~~------------~T~~~---I~~~i~~~~i~~~~Ls---~~di~~IL~tLVyDg-kIE 181 (252)
|.++.....+.+..||..+++ ||..| |.+||-+.=-.+..+. +|||-.+++.|-|=. .|-
T Consensus 34 Dk~~q~~~~~~I~~fL~~~~~~~~~is~k~l~~Pt~kdf~~I~~fL~~~idp~~~~~~k~eeev~~~lK~L~YP~~~is 112 (157)
T PF03801_consen 34 DKSYQQECIRKIYEFLSEHGFESHPISPKTLKSPTQKDFVEIFNFLFRQIDPNFKFGKKFEEEVPFLLKALGYPFATIS 112 (157)
T ss_dssp -HHHHHHHHHHHHHHHHHTT--SS---TTTTSS--HHHHHHHHHHHHHTTSTT---SSTHHHHHHHHHHHTT-SS----
T ss_pred CHHHHHHHHHHHHHHHHHcCCCCccccccccCCCCHHHHHHHHHHHHHHhCCCCCcCcCHHHHHHHHHHHhCCCccccC
Confidence 999999999999999987665 55544 5566666522233333 668888899888887 443
No 440
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=30.54 E-value=58 Score=28.39 Aligned_cols=28 Identities=18% Similarity=0.343 Sum_probs=21.4
Q ss_pred ChHHHHHHHHHHHhcCCeeeeeccccCCee
Q 025493 68 PDNIVTKSIKSLQNKSLIKEVVNIHNKGKK 97 (252)
Q Consensus 68 ~~~~l~k~lK~Le~k~lIK~vksv~~~~rK 97 (252)
.-..+.++|++||+-|||...+. +.+|+
T Consensus 118 Sg~iiR~~LQqLE~~glVek~~~--~~GR~ 145 (169)
T PTZ00095 118 SGKILRWICQQLEKLGLVEQGPK--KKGRR 145 (169)
T ss_pred chHHHHHHHHHHHHCCCEEecCC--CCCCE
Confidence 45789999999999999997532 24553
No 441
>PF08097 Toxin_26: Conotoxin T-superfamily; InterPro: IPR012631 This family consists of the T-superfamily of conotoxins. Eight different T-superfamily peptides from five Conus species were identified. These peptides share a consensus signal sequence, and a conserved arrangement of cysteine residues. T-superfamily peptides were found expressed in venom ducts of all major feeding types of Conus, suggesting that the T-superfamily is a large and diverse group of peptides, widely distributed in the 500 different Conus species [].; GO: 0005576 extracellular region
Probab=30.52 E-value=21 Score=17.37 Aligned_cols=9 Identities=44% Similarity=1.231 Sum_probs=6.8
Q ss_pred CCCCccccC
Q 025493 224 GVCPQINFC 232 (252)
Q Consensus 224 g~CPv~~~C 232 (252)
+.|||+.-|
T Consensus 1 fccpviryc 9 (11)
T PF08097_consen 1 FCCPVIRYC 9 (11)
T ss_pred CCcchhhee
Confidence 359998776
No 442
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=30.35 E-value=2.5e+02 Score=21.40 Aligned_cols=70 Identities=14% Similarity=0.183 Sum_probs=42.4
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.+.++.+.+ |++..+| +.-|+.|||.+...-. .+. -+|++ +=|..|+.+
T Consensus 2 ~i~eva~~~--gvs~~tl----R~ye~~Gll~p~~~~~-~gy-----------------R~Y~~-----~~~~~l~~I-- 50 (97)
T cd04782 2 TTGEFAKLC--GISKQTL----FHYDKIGLFKPEIVKE-NGY-----------------RYYTL-----EQFEQLDII-- 50 (97)
T ss_pred CHHHHHHHH--CcCHHHH----HHHHHCCCCCCCccCC-CCC-----------------ccCCH-----HHHHHHHHH--
Confidence 456788888 8887654 6679999997753111 122 23433 333444332
Q ss_pred HHhhhCCCCCHHHHHHHHHHcC
Q 025493 135 KQIIKLKVATLEGISDSIKRSG 156 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~~ 156 (252)
.+++.. ..++++|.+++....
T Consensus 51 ~~lr~~-G~~l~eI~~~l~~~~ 71 (97)
T cd04782 51 LLLKEL-GISLKEIKDYLDNRN 71 (97)
T ss_pred HHHHHc-CCCHHHHHHHHhcCC
Confidence 234444 578899999987643
No 443
>TIGR02036 dsdC D-serine deaminase transcriptional activator. This family, part of the LysR family of transcriptional regulators, activates transcription of the gene for D-serine deaminase, dsdA. Trusted members of this family so far are found adjacent to dsdA and only in Gammaproteobacteria, including E. coli, Vibrio cholerae, and Colwellia psychrerythraea.
Probab=30.27 E-value=90 Score=27.98 Aligned_cols=51 Identities=18% Similarity=0.263 Sum_probs=37.9
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc---CCeee
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK---SLIKE 87 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k---~lIK~ 87 (252)
.+.+++-.+..++-.|.+ .|+= ..=-.++ +++|..|++.|+.||+. .|...
T Consensus 4 ~~~~~~l~~L~~F~~va~-~gs~----s~AA~~L--~isQpavS~~I~~LE~~lg~~Lf~R 57 (302)
T TIGR02036 4 RLNSFQLSKMHTFEVAAR-HQSF----SLAAEEL--SLTPSAISHRINQLEEELGIQLFVR 57 (302)
T ss_pred cccCcCHHHHHHHHHHHH-hCCH----HHHHHHH--CCCHHHHHHHHHHHHHHhCCceEEE
Confidence 456788888888888888 6652 2224467 99999999999999983 44444
No 444
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=30.23 E-value=57 Score=21.60 Aligned_cols=26 Identities=8% Similarity=0.365 Sum_probs=20.4
Q ss_pred CCcccHHHHHHHhhcCCChHHHHHHHHH
Q 025493 51 DMGIWTRDMKRELKVNLPDNIVTKSIKS 78 (252)
Q Consensus 51 ~~GIw~~dik~~~~~~l~~~~l~k~lK~ 78 (252)
..|+.++++...+ |++.+.|++.++.
T Consensus 7 ~~gls~~~la~~~--gis~~~i~~~~~g 32 (55)
T PF01381_consen 7 EKGLSQKELAEKL--GISRSTISRIENG 32 (55)
T ss_dssp HTTS-HHHHHHHH--TS-HHHHHHHHTT
T ss_pred HcCCCHHHHHHHh--CCCcchhHHHhcC
Confidence 3789999999999 9999999887754
No 445
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=30.18 E-value=3.2e+02 Score=22.64 Aligned_cols=69 Identities=14% Similarity=0.157 Sum_probs=43.0
Q ss_pred ccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHH
Q 025493 54 IWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQC 133 (252)
Q Consensus 54 Iw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~ 133 (252)
..+.++.+.+ |++..+ |.--|+.|||++...-.+ +.+.| |.+-|+.|+.
T Consensus 8 ~~IgevAk~~--Gvs~~T----LRyYE~~GLl~p~~r~~~-gyR~Y----------------------~~~~l~rl~~-- 56 (144)
T PRK13752 8 LTIGVFAKAA--GVNVET----IRFYQRKGLLPEPDKPYG-SIRRY----------------------GEADVTRVRF-- 56 (144)
T ss_pred ccHHHHHHHH--CcCHHH----HHHHHHCCCCCCCccCCC-CCeec----------------------CHHHHHHHHH--
Confidence 6678888889 888765 567899999986432222 33333 3333343332
Q ss_pred HHHhhhCCCCCHHHHHHHHHH
Q 025493 134 LKQIIKLKVATLEGISDSIKR 154 (252)
Q Consensus 134 ~~~i~~~~~~T~~~I~~~i~~ 154 (252)
...++..+ .++++|.+++..
T Consensus 57 I~~lr~~G-~sL~eI~~ll~~ 76 (144)
T PRK13752 57 VKSAQRLG-FSLDEIAELLRL 76 (144)
T ss_pred HHHHHHcC-CCHHHHHHHHhc
Confidence 23344454 589999999864
No 446
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=30.08 E-value=1e+02 Score=26.98 Aligned_cols=44 Identities=14% Similarity=0.216 Sum_probs=36.1
Q ss_pred CCCCCChHHHHHHHHHHhhcCC-CcccHHHHHHHhhcCCChHHHHHHH
Q 025493 30 PSDSLTDHERLIYDVIRSNKQD-MGIWTRDMKRELKVNLPDNIVTKSI 76 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~-~GIw~~dik~~~~~~l~~~~l~k~l 76 (252)
.+..|++.++.|+.+..- .++ +|...++|...+ |++.+.|.+.+
T Consensus 172 ~l~~Lp~~~R~i~~l~y~-~~~~e~~S~~EIA~~l--gis~~tV~~~~ 216 (233)
T PRK05803 172 KIDILDEREKEVIEMRYG-LGNGKEKTQREIAKAL--GISRSYVSRIE 216 (233)
T ss_pred HHHhCCHHHHHHHHHHhC-CCCCCCcCHHHHHHHH--CcCHHHHHHHH
Confidence 456889999999988774 443 899999999999 99998886664
No 447
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=29.82 E-value=1.1e+02 Score=22.19 Aligned_cols=25 Identities=16% Similarity=0.271 Sum_probs=21.7
Q ss_pred CCChHHHHHHHHHHHhcCCeeeeec
Q 025493 66 NLPDNIVTKSIKSLQNKSLIKEVVN 90 (252)
Q Consensus 66 ~l~~~~l~k~lK~Le~k~lIK~vks 90 (252)
-+..+.+..+|..||..|+|..-++
T Consensus 43 ~l~~~~~~~~l~~L~~~gli~~~~~ 67 (87)
T cd08768 43 PLTQRRISDLLSELEMLGLLETEVS 67 (87)
T ss_pred CCcHHHHHHHHHHHHHcCCeEEEEe
Confidence 5788999999999999999987544
No 448
>COG5174 TFA2 Transcription initiation factor IIE, beta subunit [Transcription]
Probab=29.79 E-value=1.8e+02 Score=26.95 Aligned_cols=98 Identities=14% Similarity=0.288 Sum_probs=64.7
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCC-
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEG- 119 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~- 119 (252)
++.+++...+.+||..++|+.-- |+ +.--+..||+.+-|=-...=+-..-++ .||.++
T Consensus 149 llk~lrsq~t~~Gls~k~L~Dgw----pn--v~~~veeLek~~eIliLrt~kDg~p~~---------------vW~n~~n 207 (285)
T COG5174 149 LLKVLRSQGTEEGLSMKKLMDGW----PN--VVPFVEELEKSNEILILRTDKDGSPVV---------------VWNNTQN 207 (285)
T ss_pred HHHHHHhhcccccccHHHhhcCC----Cc--ccHHHHHHhhcCcEEEEeecCCCCceE---------------EEeCCCC
Confidence 44567776889999999999843 32 334577888877665544222222222 499877
Q ss_pred ---cCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHH
Q 025493 120 ---SLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQI 167 (252)
Q Consensus 120 ---e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di 167 (252)
-.|.||+....+ -..|+..|+.+-++..|+-.....+.-+
T Consensus 208 ~~c~vD~ef~~~W~~--------V~ip~~~dL~reL~~~GLKptsvdp~t~ 250 (285)
T COG5174 208 LECPVDPEFKSLWNQ--------VRIPTYHDLIRELNTAGLKPTSVDPNTK 250 (285)
T ss_pred cCCCCCHHHHHHHHh--------CCCchHHHHHHHHHhcCCCccccCcchh
Confidence 468899876544 3478889999999999976554444433
No 449
>COG3743 Uncharacterized conserved protein [Function unknown]
Probab=29.69 E-value=38 Score=28.37 Aligned_cols=48 Identities=21% Similarity=0.164 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEE
Q 025493 125 FIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 125 fV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v 183 (252)
.|.-|--.+.+-|..++.-|..||.. +|..||..|=+.|-|+|+|++-
T Consensus 71 ~I~GIGPk~e~~Ln~~GI~tfaQIAA-----------wt~~di~~id~~l~f~GRi~RD 118 (133)
T COG3743 71 RISGIGPKLEKVLNELGIFTFAQIAA-----------WTRADIAWIDDYLNFDGRIERD 118 (133)
T ss_pred hhcccCHHHHHHHHHcCCccHHHHHh-----------cCHHHHHHHHhhcCCcchhHHH
Confidence 33333344445555555555555554 5889999999999999999863
No 450
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=29.68 E-value=80 Score=27.24 Aligned_cols=47 Identities=9% Similarity=0.162 Sum_probs=37.0
Q ss_pred HHHHHHHhh--cC----CCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeee
Q 025493 40 LIYDVIRSN--KQ----DMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEV 88 (252)
Q Consensus 40 ~vy~~I~~~--ag----~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~v 88 (252)
.||+.|.+. .| +.-|-..+|..+. |+.-+.|..+|+.|+..|||...
T Consensus 15 ~v~~~l~~~I~~g~l~pG~~L~e~~La~~l--gVSRtpVREAL~~L~~eGLV~~~ 67 (221)
T PRK11414 15 QVENDLKHQLSIGALKPGARLITKNLAEQL--GMSITPVREALLRLVSVNALSVA 67 (221)
T ss_pred HHHHHHHHHHHhCCCCCCCccCHHHHHHHH--CCCchhHHHHHHHHHHCCCEEec
Confidence 366666551 12 3556778999999 99999999999999999999864
No 451
>cd00052 EH Eps15 homology domain; found in proteins implicated in endocytosis, vesicle transport, and signal transduction. The alignment contains a pair of EF-hand motifs, typically one of them is canonical and binds to Ca2+, while the other may not bind to Ca2+. A hydrophobic binding pocket is formed by residues from both EF-hand motifs. The EH domain binds to proteins containing NPF (class I), [WF]W or SWG (class II), or H[TS]F (class III) sequence motifs.
Probab=29.63 E-value=1.2e+02 Score=20.33 Aligned_cols=34 Identities=12% Similarity=0.079 Sum_probs=26.8
Q ss_pred hCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhc
Q 025493 139 KLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLD 177 (252)
Q Consensus 139 ~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyD 177 (252)
..+..|.+|+..++++.|+ +.++++++++.+-.+
T Consensus 12 ~~G~i~~~el~~~l~~~g~-----~~~~~~~i~~~~d~~ 45 (67)
T cd00052 12 GDGLISGDEARPFLGKSGL-----PRSVLAQIWDLADTD 45 (67)
T ss_pred CCCcCcHHHHHHHHHHcCC-----CHHHHHHHHHHhcCC
Confidence 3478999999999998763 788899998876543
No 452
>PRK10082 cell density-dependent motility repressor; Provisional
Probab=29.47 E-value=1.4e+02 Score=26.69 Aligned_cols=44 Identities=7% Similarity=0.140 Sum_probs=33.7
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
..+|+-.+..++..|.+ .|+= ..=.+++ ++.|..|++.||.||+
T Consensus 8 ~~~m~~~~l~~F~av~e-~gS~----t~AA~~L--~iSQpavS~~I~~LE~ 51 (303)
T PRK10082 8 LHNIETKWLYDFLTLEK-CRNF----SQAAVSR--NVSQPAFSRRIRALEQ 51 (303)
T ss_pred ccccchHHHHHHHHHHh-cCCH----HHHHHHh--CCChHHHHHHHHHHHH
Confidence 45677778788888887 6652 2234567 9999999999999997
No 453
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=29.26 E-value=79 Score=29.66 Aligned_cols=37 Identities=14% Similarity=0.207 Sum_probs=33.7
Q ss_pred cCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeee
Q 025493 49 KQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKE 87 (252)
Q Consensus 49 ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~ 87 (252)
==.+|.-|.+|-+++ |+....|+|.|+.=.+.|+|+=
T Consensus 25 YY~~g~tQ~eIA~~l--giSR~~VsRlL~~Ar~~GiV~I 61 (318)
T PRK15418 25 YYHDGLTQSEIGERL--GLTRLKVSRLLEKGRQSGIIRV 61 (318)
T ss_pred HHhcCCCHHHHHHHh--CCCHHHHHHHHHHHHHcCcEEE
Confidence 345799999999999 9999999999999999999973
No 454
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=29.01 E-value=1.3e+02 Score=26.41 Aligned_cols=45 Identities=20% Similarity=0.351 Sum_probs=38.3
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
...||+.|+.|+..+. .|-..++|-..+ +++.+++...|+....|
T Consensus 169 ~~~Lt~re~evl~~~a-----~G~t~~eIa~~l--~is~~Tv~~~l~~~~~k 213 (232)
T TIGR03541 169 AGVLSEREREVLAWTA-----LGRRQADIAAIL--GISERTVENHLRSARRK 213 (232)
T ss_pred hccCCHHHHHHHHHHH-----CCCCHHHHHHHH--CcCHHHHHHHHHHHHHH
Confidence 4579999999999974 478899999999 99999999888887543
No 455
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=28.94 E-value=1.3e+02 Score=26.68 Aligned_cols=40 Identities=8% Similarity=0.134 Sum_probs=28.2
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHh
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQN 81 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~ 81 (252)
+-.+..++-.|.+ .|+ ...=..++ +++|..|++.||+||+
T Consensus 2 ~l~~L~~f~~v~~-~gS----~s~AA~~L--~itQpavS~~i~~LE~ 41 (305)
T PRK11151 2 NIRDLEYLVALAE-HRH----FRRAADSC--HVSQPTLSGQIRKLED 41 (305)
T ss_pred CHHHHHHHHHHHH-hCC----HHHHHHHh--CCCchHHHHHHHHHHH
Confidence 3445556666666 552 33334567 9999999999999997
No 456
>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=28.76 E-value=90 Score=26.57 Aligned_cols=62 Identities=18% Similarity=0.170 Sum_probs=45.6
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCe-eeEE
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGK-KHLM 100 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~r-K~Ym 100 (252)
...||.-...++.+|.= ++.|.+.+|-.-- |.. -..+|++|.++|||+.+..-..++| .+|-
T Consensus 77 ~~~LS~aalEtLAiIAY---~QPiTr~eIe~IR--Gv~---s~~~i~~L~e~glI~~~gr~~~~Grp~ly~ 139 (159)
T PF04079_consen 77 PPKLSQAALETLAIIAY---KQPITRAEIEEIR--GVN---SDSVIKTLLERGLIEEVGRKDTPGRPILYG 139 (159)
T ss_dssp CHHHHHHHHHHHHHHHH---H-SEEHHHHHHHH--TS-----HCHHHHHHHTTSEEEEEE-TTTT--EEEE
T ss_pred cCCCCHHHHHHHHHHHh---cCCcCHHHHHHHc--CCC---hHHHHHHHHHCCCEEecCcCCCCCCCeEee
Confidence 45788888888888865 6799999999888 444 4567899999999999987766674 3443
No 457
>PF13099 DUF3944: Domain of unknown function (DUF3944)
Probab=28.62 E-value=81 Score=20.57 Aligned_cols=18 Identities=11% Similarity=0.433 Sum_probs=15.6
Q ss_pred ecCHHHHHHHHHHHhhcC
Q 025493 161 DLTKQQIEEIVRAVVLDN 178 (252)
Q Consensus 161 ~Ls~~di~~IL~tLVyDg 178 (252)
++|.+|++.+++.|++|.
T Consensus 12 ~cs~edL~~L~~~Lt~dk 29 (35)
T PF13099_consen 12 ECSNEDLKDLVDILTHDK 29 (35)
T ss_pred HCCHHHHHHHHHHHhcCC
Confidence 356999999999999993
No 458
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=28.61 E-value=65 Score=28.26 Aligned_cols=50 Identities=12% Similarity=0.130 Sum_probs=36.2
Q ss_pred CCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc---CCeee
Q 025493 31 SDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK---SLIKE 87 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k---~lIK~ 87 (252)
...|+-.+..++..|.+ .|+- ..=..++ ++.|..|++.||.||+. .|+.+
T Consensus 4 ~~~~~l~~l~~f~~v~~-~gs~----t~AA~~L--~itq~avS~~i~~LE~~lg~~Lf~R 56 (294)
T PRK09986 4 LYRIDLKLLRYFLAVAE-ELHF----GRAAARL--NISQPPLSIHIKELEDQLGTPLFIR 56 (294)
T ss_pred hhhhhHHHHHHHHHHHH-hcCH----HHHHHHh--CCCCCHHHHHHHHHHHHhCCeeEee
Confidence 35577778888888888 6642 2223466 99999999999999983 45544
No 459
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=28.44 E-value=2.3e+02 Score=28.52 Aligned_cols=104 Identities=10% Similarity=0.125 Sum_probs=65.3
Q ss_pred HHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHH
Q 025493 72 VTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDS 151 (252)
Q Consensus 72 l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~ 151 (252)
+.|+.+.++..||-+..=. .....-.+++.--.+.++.+...==...+- -.+..+..|+.|+...++.|..++.+-
T Consensus 350 i~rm~~~~~~~gl~~p~f~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~il~~~~en~~~T~~~L~~~ 425 (467)
T COG2865 350 IRRMFDLMEENGLPKPEFE-EDNDYVTVILHGKGENEDETEEKVTRQEET---SLSERQEKILELIKENGKVTARELREI 425 (467)
T ss_pred HHHHHHHHHHcCCCCceee-ccCCeEEEEEeccchHHHhhcccccccccc---ChhHHHHHHHHHHhhccccCHHHHHHH
Confidence 4455556666666555322 223455555544444433333211111111 134455689999999999999999876
Q ss_pred HHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeCC
Q 025493 152 IKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSNG 187 (252)
Q Consensus 152 i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~g 187 (252)
+. +|.+.+...|.-|+-.|++++.-+++
T Consensus 426 l~--------is~~~i~r~i~~Lv~~g~~~~~g~~~ 453 (467)
T COG2865 426 LG--------ISSETIRRRIANLVKRGLLKQLGSSG 453 (467)
T ss_pred hC--------cchhhHHHHHHHHhcccHHHHhCcCC
Confidence 65 77899999999999999998875443
No 460
>PRK15479 transcriptional regulatory protein TctD; Provisional
Probab=28.32 E-value=1.9e+02 Score=23.46 Aligned_cols=56 Identities=14% Similarity=0.231 Sum_probs=38.2
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcC-----CChH----HHHHHHHHHHhcC-Ceeeeecc
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVN-----LPDN----IVTKSIKSLQNKS-LIKEVVNI 91 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~-----l~~~----~l~k~lK~Le~k~-lIK~vksv 91 (252)
.||+-|..|+.++-. .-+......+|...+ . +..+ .++++.++|...+ .|+.|..+
T Consensus 148 ~Lt~~E~~il~~l~~-~~~~~~~~~~i~~~l--~~~~~~~~~~tv~~~i~~ir~kl~~~~~~i~t~~~~ 213 (221)
T PRK15479 148 ALTPREQALLTVLMY-RRTRPVSRQQLFEQV--FSLNDEVSPESIELYIHRLRKKLQGSDVRITTLRGL 213 (221)
T ss_pred ecCHHHHHHHHHHHh-CCCCcCcHHHHHHHh--cCCCCCCCcccHHHHHHHHHHhcCCCCCcEEEeccc
Confidence 599999999998888 666778888888776 3 4444 4555556665443 45555443
No 461
>PRK13413 mpi multiple promoter invertase; Provisional
Probab=28.23 E-value=1.5e+02 Score=25.37 Aligned_cols=38 Identities=21% Similarity=0.385 Sum_probs=29.8
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHH
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKS 78 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~ 78 (252)
+.+.+..|+.+.. +|...++|.+.+ |++.+++.|.+|.
T Consensus 158 ~~~~~~~i~~~~~-----~g~s~~~iak~l--gis~~Tv~r~~k~ 195 (200)
T PRK13413 158 LTGKEEKIKKLLD-----KGTSKSEIARKL--GVSRTTLARFLKT 195 (200)
T ss_pred cchhHHHHHHHHH-----CCCCHHHHHHHH--CCCHHHHHHHHHh
Confidence 3445556666543 478999999999 9999999999984
No 462
>PF11784 DUF3320: Protein of unknown function (DUF3320); InterPro: IPR021754 This family is conserved in Proteobacteria and Chlorobi families. Many members are annotated as being putative DNA helicase-related proteins.
Probab=28.23 E-value=1.7e+02 Score=20.17 Aligned_cols=43 Identities=9% Similarity=0.083 Sum_probs=36.8
Q ss_pred CCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHc-CCcce
Q 025493 118 EGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRS-GAFKV 160 (252)
Q Consensus 118 d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~-~i~~~ 160 (252)
|..|+.+--..|.+.+..-|..-+.+..+.+.+-|.+. |++++
T Consensus 2 ~~f~~~~~~~~L~~~i~~Iv~~EgPI~~~~L~~Ri~~a~G~~R~ 45 (52)
T PF11784_consen 2 DDFYHPEYRPQLARMIRQIVEVEGPIHEDELARRIARAWGLSRA 45 (52)
T ss_pred cchhhhhHHHHHHHHHHHHHHHcCCccHHHHHHHHHHHcCcccc
Confidence 56788888999999999999999999999999988866 65543
No 463
>PF08870 DUF1832: Domain of unknown function (DUF1832); InterPro: IPR014969 This entry describes the DndE protein encoded by an operon associated with a sulphur-containing modification to DNA []. The operon is sporadically distributed in bacteria, much like some restriction enzyme operons. DndE is a putative carboxylase homologous to NCAIR synthetases.
Probab=28.19 E-value=2.8e+02 Score=22.26 Aligned_cols=61 Identities=16% Similarity=0.304 Sum_probs=36.6
Q ss_pred HHHHHHhhcCCCh-HHHHHHH--HHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHH
Q 025493 57 RDMKRELKVNLPD-NIVTKSI--KSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQC 133 (252)
Q Consensus 57 ~dik~~~~~~l~~-~~l~k~l--K~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~ 133 (252)
+.|+++| |+.+ +++-|+= .+|+.-...-.....- .=..|++.-+|+ |+++.-|...|++.|
T Consensus 13 ~~Lk~~t--gi~~~Nil~R~A~~~SL~~~~~~~~~~~~~------------d~g~e~~~~t~~--Ge~~~~~~~ll~q~~ 76 (113)
T PF08870_consen 13 KKLKRRT--GITPWNILCRIAFCRSLEEPSIPSDEDIKD------------DSGLELNWKTFT--GEYDDIYEALLKQRY 76 (113)
T ss_pred HHHHHhc--CCCcccHHHHHHHHHHHccCCCCCCCccCC------------CCCeEEeeeeec--CchHHHHHHHHHHHh
Confidence 3467788 9999 8888863 4555443332111110 112334444444 899999999998888
No 464
>COG4190 Predicted transcriptional regulator [Transcription]
Probab=28.13 E-value=2e+02 Score=24.39 Aligned_cols=57 Identities=12% Similarity=0.110 Sum_probs=45.3
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccC
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNK 94 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~ 94 (252)
-|++.-+.++.+|.+ .+--...++...+ +=.-..|.+-|..|+.-|+|---+.++.+
T Consensus 61 vLsp~nleLl~~Ia~---~~P~Si~ElAe~v--gRdv~nvhr~Ls~l~~~GlI~fe~~gq~k 117 (144)
T COG4190 61 VLSPRNLELLELIAQ---EEPASINELAELV--GRDVKNVHRTLSTLADLGLIFFEEDGQRK 117 (144)
T ss_pred HhChhHHHHHHHHHh---cCcccHHHHHHHh--CcchHHHHHHHHHHHhcCeEEEecCCccc
Confidence 456666666666655 5566778999999 99999999999999999999988876553
No 465
>PF10931 DUF2735: Protein of unknown function (DUF2735); InterPro: IPR021232 Some members in this family of proteins are annotated as glutamine synthetase translation inhibitor however this function can not be confirmed.
Probab=28.09 E-value=18 Score=25.40 Aligned_cols=14 Identities=29% Similarity=0.710 Sum_probs=10.7
Q ss_pred cCCCccCCccccCC
Q 025493 106 PSKDISGGAWYSEG 119 (252)
Q Consensus 106 Ps~eiTGG~wy~d~ 119 (252)
.-..+++|.||+|.
T Consensus 31 ~~~~~~~~sWYHee 44 (51)
T PF10931_consen 31 VCPAADSGSWYHEE 44 (51)
T ss_pred cCceecCccchHHH
Confidence 34568999999874
No 466
>PRK01177 hypothetical protein; Provisional
Probab=27.98 E-value=36 Score=28.74 Aligned_cols=26 Identities=19% Similarity=0.368 Sum_probs=21.3
Q ss_pred cCCCCCCCccccCCCCCccCcccccc
Q 025493 220 SVPCGVCPQINFCTPDGVISPKTCVY 245 (252)
Q Consensus 220 ~vPCg~CPv~~~C~~gG~IsP~tC~Y 245 (252)
...|..||..+.|+|.|...+..|..
T Consensus 94 ~~~C~~c~~~~~c~P~G~~~g~k~~I 119 (140)
T PRK01177 94 FVTCPDIEKCNLVRPEGLFEGDKVKI 119 (140)
T ss_pred CCCCCCccccccCccccccCCCeEEE
Confidence 33488999999999999888777754
No 467
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=27.94 E-value=94 Score=27.90 Aligned_cols=48 Identities=10% Similarity=0.253 Sum_probs=35.1
Q ss_pred CCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc---CCeee
Q 025493 33 SLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK---SLIKE 87 (252)
Q Consensus 33 ~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k---~lIK~ 87 (252)
.|+-.+..++-.+.+ .|+-. .-..++ ++.|..|++.||.||+. .|+..
T Consensus 3 ~~~l~~L~~f~av~~-~gS~s----~AAe~L--~isqsavS~~Ik~LE~~lg~~Lf~R 53 (309)
T PRK11013 3 AVSLRHIEIFHAVMT-AGSLT----EAARLL--HTSQPTVSRELARFEKVIGLKLFER 53 (309)
T ss_pred CccHHHHHHHHHHHH-hCcHH----HHHHHH--CCCcHHHHHHHHHHHHHhCceeeee
Confidence 466677778888888 66532 234456 99999999999999984 55554
No 468
>COG3611 DnaB Replication initiation/membrane attachment protein [DNA replication, recombination, and repair]
Probab=27.85 E-value=2e+02 Score=28.53 Aligned_cols=90 Identities=16% Similarity=0.311 Sum_probs=55.1
Q ss_pred HHHHHHHhhcC-CCcccHHHHHHH--hhc-CCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCcc
Q 025493 40 LIYDVIRSNKQ-DMGIWTRDMKRE--LKV-NLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAW 115 (252)
Q Consensus 40 ~vy~~I~~~ag-~~GIw~~dik~~--~~~-~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~w 115 (252)
-+|+..-.-+- ..-.|+.-+-.. +|. ++....+.+.++.||+-||+|...+ . .... ++|++-|. +.=--|
T Consensus 38 sLY~~li~e~~~~~~~~S~~l~h~~l~gm~~i~l~~~~e~~~kLealgLlkty~~-~--~~s~-~~~el~~P--L~~~eF 111 (417)
T COG3611 38 SLYQWLISEVNIQNRLWSEILNHLNLLGMLNINLKTIIEAIDKLEALGLLKTYVK-Q--DESQ-YVYELIPP--LSPEEF 111 (417)
T ss_pred HHHHHHHHHHhhccchhHHHHHHHHHhcccccCHHHHHHHHHHHhhhhhHHHhhc-c--CCcE-EEEEeeCC--CCHHHh
Confidence 34443332144 456676666553 211 4556789999999999999999876 2 2333 33444333 223357
Q ss_pred ccCCcCCHHHHHHHHHHHHH
Q 025493 116 YSEGSLDTEFIKVVKSQCLK 135 (252)
Q Consensus 116 y~d~e~D~efV~~l~~~~~~ 135 (252)
|.|+-|...+++.+-..=+.
T Consensus 112 f~~~~l~~~L~~kiG~~~y~ 131 (417)
T COG3611 112 FQDPMLNELLYSKIGKVRYQ 131 (417)
T ss_pred ccCHHHHHHHHHHHhHHHHH
Confidence 78888888888777655443
No 469
>PRK10094 DNA-binding transcriptional activator AllS; Provisional
Probab=27.76 E-value=1.5e+02 Score=26.74 Aligned_cols=42 Identities=10% Similarity=0.099 Sum_probs=30.6
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
|+-++..++..|.+ .|+ -..-.+++ |+.|..|++.||.||+.
T Consensus 2 ~~~~~L~~f~~v~e-~gs----~s~AA~~L--~iSQpavS~~I~~LE~~ 43 (308)
T PRK10094 2 FDPETLRTFIAVAE-TGS----FSKAAERL--CKTTATISYRIKLLEEN 43 (308)
T ss_pred CCHHHHHHHHHHHH-hCC----HHHHHHHh--cCCHHHHHHHHHHHHHH
Confidence 34456667777777 554 23445677 99999999999999973
No 470
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=27.74 E-value=1.4e+02 Score=24.92 Aligned_cols=49 Identities=20% Similarity=0.299 Sum_probs=36.9
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHH----HHHHHHHHhcCC
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIV----TKSIKSLQNKSL 84 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l----~k~lK~Le~k~l 84 (252)
.+..|++.++.|+.+..- .|...++|...+ |++.+.| .|+.+.|...+|
T Consensus 128 ~l~~L~~~~r~i~~l~~~----~g~s~~EIAe~l--gis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 128 LINDLEKLDREIFIRRYL----LGEKIEEIAKKL--GLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred HHHhCCHHHHHHHHHHHH----ccCCHHHHHHHH--CCCHHHHHHHHHHHHHHHHHccc
Confidence 466889999999877544 378999999999 8887765 556666666555
No 471
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=27.53 E-value=1.4e+02 Score=26.82 Aligned_cols=48 Identities=10% Similarity=0.117 Sum_probs=40.8
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
=++.++.+|++++.+++.|+++.+. +|..-|++=|+.|.-.|+|.++.
T Consensus 6 R~~~Il~~L~~~~~v~v~eLa~~l~--------VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 6 RQAAILEYLQKQGKTSVEELAQYFD--------TTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred HHHHHHHHHHHcCCEEHHHHHHHHC--------CCHHHHHHHHHHHHHCCCEEEEE
Confidence 3567889999999999999998763 67788888899999999999876
No 472
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=27.42 E-value=1.6e+02 Score=24.57 Aligned_cols=40 Identities=20% Similarity=0.248 Sum_probs=30.6
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHH
Q 025493 131 SQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRA 173 (252)
Q Consensus 131 ~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~t 173 (252)
..+...++.+...|.+|+.+.+++.|+. +|..-|-+.|+-
T Consensus 5 ~~i~~Li~~~~i~tqeeL~~~L~~~G~~---vsqaTIsRdL~e 44 (146)
T TIGR01529 5 ERIKEIITEEKISTQEELVALLKAEGIE---VTQATVSRDLRE 44 (146)
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHHhCCC---cCHHHHHHHHHH
Confidence 3456677889999999999999999953 667777664443
No 473
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=27.41 E-value=1.5e+02 Score=18.53 Aligned_cols=28 Identities=21% Similarity=0.298 Sum_probs=16.4
Q ss_pred CCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHH
Q 025493 121 LDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKR 154 (252)
Q Consensus 121 ~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~ 154 (252)
+|.|-|+-++++. ....|.+||.+|+..
T Consensus 1 LD~EW~~Li~eA~------~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 1 LDEEWVELIKEAK------ESGLSKEEIREFLEF 28 (30)
T ss_dssp --HHHHHHHHHHH------HTT--HHHHHHHHHH
T ss_pred CCHHHHHHHHHHH------HcCCCHHHHHHHHHh
Confidence 4667777666653 357788888888764
No 474
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=27.36 E-value=84 Score=29.10 Aligned_cols=41 Identities=20% Similarity=0.398 Sum_probs=35.3
Q ss_pred cccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEe
Q 025493 53 GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMA 101 (252)
Q Consensus 53 GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL 101 (252)
-+-++||.++. +++...|+-.+|.|.+.|||.+ .+|--|-+
T Consensus 25 ~v~q~eIA~~l--giT~QaVsehiK~Lv~eG~i~~------~gR~~Y~i 65 (260)
T COG1497 25 RVKQKEIAKKL--GITLQAVSEHIKELVKEGLIEK------EGRGEYEI 65 (260)
T ss_pred CCCHHHHHHHc--CCCHHHHHHHHHHHHhccceee------cCCeeEEE
Confidence 36799999999 9999999999999999999998 25555644
No 475
>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=27.33 E-value=2.3e+02 Score=20.07 Aligned_cols=48 Identities=13% Similarity=0.176 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeE
Q 025493 126 IKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIM 181 (252)
Q Consensus 126 V~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE 181 (252)
-..+-+.+..+|-+++..|+.+|.+..+ |+..+|+..|-+|+--|.+.
T Consensus 11 fG~~~~~V~~~Ll~~G~ltl~~i~~~t~--------l~~~~Vk~~L~~LiQh~~v~ 58 (62)
T PF08221_consen 11 FGEIVAKVGEVLLSRGRLTLREIVRRTG--------LSPKQVKKALVVLIQHNLVQ 58 (62)
T ss_dssp HHHHHHHHHHHHHHC-SEEHHHHHHHHT----------HHHHHHHHHHHHHTTSEE
T ss_pred cChHHHHHHHHHHHcCCcCHHHHHHHhC--------CCHHHHHHHHHHHHHcCCee
Confidence 3456777888888999999999987544 88999999999998776553
No 476
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=27.12 E-value=2.6e+02 Score=20.66 Aligned_cols=49 Identities=12% Similarity=0.203 Sum_probs=33.2
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 129 VKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 129 l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
..+.|...|.++...|=+|+.+.+.+.||. .|..-|-+-|+.| .|.+++
T Consensus 6 R~~~I~~li~~~~i~sQ~eL~~~L~~~Gi~---vTQaTiSRDLkeL----~~vKv~ 54 (70)
T PF01316_consen 6 RQELIKELISEHEISSQEELVELLEEEGIE---VTQATISRDLKEL----GAVKVP 54 (70)
T ss_dssp HHHHHHHHHHHS---SHHHHHHHHHHTT-T-----HHHHHHHHHHH----T-EEEE
T ss_pred HHHHHHHHHHHCCcCCHHHHHHHHHHcCCC---cchhHHHHHHHHc----CcEEee
Confidence 456788889999999999999999999964 6677777777766 345565
No 477
>KOG1276 consensus Protoporphyrinogen oxidase [Coenzyme transport and metabolism]
Probab=27.10 E-value=1.2e+02 Score=30.45 Aligned_cols=68 Identities=15% Similarity=0.185 Sum_probs=54.2
Q ss_pred ccCCccccCCcCC----HHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCe
Q 025493 110 ISGGAWYSEGSLD----TEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQ 179 (252)
Q Consensus 110 iTGG~wy~d~e~D----~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgk 179 (252)
.+||.||+++..+ .|+|+...+...+.|.-.+-|+..-++ +.+.-|.+-.++-.|+.+-++..+-|..
T Consensus 388 m~gg~~~~n~~~~~~S~ee~~~~v~~alq~~Lgi~~~P~~~~v~--l~~~ciPqy~vGh~~~le~a~~~l~~~~ 459 (491)
T KOG1276|consen 388 MMGGGGSTNTSLAVPSPEELVNAVTSALQKMLGISNKPVSVNVH--LWKNCIPQYTVGHDDVLEAAKSMLTDSP 459 (491)
T ss_pred EecccccccCcCCCCCHHHHHHHHHHHHHHHhCCCCCcccccce--ehhhcccceecchHHHHHHHHHHHHhCC
Confidence 4599999988876 578888888888888766666655555 8888999999999999888888877754
No 478
>PF06897 DUF1269: Protein of unknown function (DUF1269); InterPro: IPR009200 There are currently no experimental data for members of this group or their homologues. However, these proteins are predicted to contain two or more transmembrane segments.
Probab=27.06 E-value=1.7e+02 Score=23.14 Aligned_cols=59 Identities=22% Similarity=0.386 Sum_probs=44.0
Q ss_pred ccCCcCCHHHHHHHHHHHHHH----hhhCCCCCHHHHHHHHHHcC--CcceecCHHHHHHHHHHH
Q 025493 116 YSEGSLDTEFIKVVKSQCLKQ----IIKLKVATLEGISDSIKRSG--AFKVDLTKQQIEEIVRAV 174 (252)
Q Consensus 116 y~d~e~D~efV~~l~~~~~~~----i~~~~~~T~~~I~~~i~~~~--i~~~~Ls~~di~~IL~tL 174 (252)
++|-.+|.+|++.+.+.+..= +---...+.+.+.+.+++.+ +.+..|+.++-++|-++|
T Consensus 35 l~d~gI~d~~~~ev~~~L~~GssAl~~lv~~~~~d~v~~~l~~~gg~v~~t~ls~~~e~~L~~al 99 (102)
T PF06897_consen 35 LSDYGIDDEFIKEVGEALKPGSSALFLLVDEATEDKVDAALRKFGGKVLRTSLSEEDEDELQEAL 99 (102)
T ss_pred HhhCCCCHHHHHHHHhhcCCCceEEEEEeccCCHHHHHHHHHhcCCEEEeccCCHHHHHHHHHHH
Confidence 568889999988888765310 00124678999999999987 556779999988887776
No 479
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=27.04 E-value=76 Score=28.37 Aligned_cols=52 Identities=15% Similarity=0.213 Sum_probs=43.4
Q ss_pred CCCCChHHHHHHHHHHhhcCCC-cccHHHHHHHhhcCCChHHHHHHHHHHHhcCC
Q 025493 31 SDSLTDHERLIYDVIRSNKQDM-GIWTRDMKRELKVNLPDNIVTKSIKSLQNKSL 84 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~~-GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~l 84 (252)
...||+-|+.|.++|-+|-..- .+..++|-+++ +..+.+|.|-.|+|==+|+
T Consensus 7 ~~~Lt~~e~~ia~yil~n~~~v~~~si~elA~~~--~vS~aTv~Rf~kklG~~Gf 59 (278)
T PRK11557 7 YPGLAQSDRKLADYLLLQPDTARHLSSQQLANEA--GVSQSSVVKFAQKLGYKGF 59 (278)
T ss_pred hhhCCHHHHHHHHHHHhCHHHHHhcCHHHHHHHh--CCCHHHHHHHHHHcCCCCH
Confidence 4579999999999999943333 47899999999 9999999999999865554
No 480
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=27.02 E-value=2e+02 Score=25.00 Aligned_cols=47 Identities=13% Similarity=0.009 Sum_probs=36.6
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 132 QCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 132 ~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
.++..|..++.+|..+|++++. ++..-+-.+|+.|+-+|.|++.+..
T Consensus 49 ~iL~~L~~~~~itq~eLa~~l~--------l~~sTvtr~l~rLE~kGlI~R~~~~ 95 (185)
T PRK13777 49 HILWIAYHLKGASISEIAKFGV--------MHVSTAFNFSKKLEERGYLTFSKKE 95 (185)
T ss_pred HHHHHHHhCCCcCHHHHHHHHC--------CCHhhHHHHHHHHHHCCCEEecCCC
Confidence 4667777778889999988643 2345588899999999999988643
No 481
>PLN00034 mitogen-activated protein kinase kinase; Provisional
Probab=26.93 E-value=2.1e+02 Score=26.05 Aligned_cols=75 Identities=16% Similarity=0.227 Sum_probs=45.3
Q ss_pred HHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHH
Q 025493 75 SIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKR 154 (252)
Q Consensus 75 ~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~ 154 (252)
+|+.|...++++-.-.... +..+|++++.-+ ||.......++..++..+..++. .-++|+++
T Consensus 125 ~l~~l~h~~iv~~~~~~~~-~~~~~lv~e~~~-----~~~L~~~~~~~~~~~~~i~~qi~------------~aL~~LH~ 186 (353)
T PLN00034 125 ILRDVNHPNVVKCHDMFDH-NGEIQVLLEFMD-----GGSLEGTHIADEQFLADVARQIL------------SGIAYLHR 186 (353)
T ss_pred HHHhCCCCCcceeeeEecc-CCeEEEEEecCC-----CCcccccccCCHHHHHHHHHHHH------------HHHHHHHH
Confidence 4556666677765544443 567899987644 55554444455555444433332 24567778
Q ss_pred cCCcceecCHHHH
Q 025493 155 SGAFKVDLTKQQI 167 (252)
Q Consensus 155 ~~i~~~~Ls~~di 167 (252)
.||..-+|..+.|
T Consensus 187 ~~ivHrDlkp~NI 199 (353)
T PLN00034 187 RHIVHRDIKPSNL 199 (353)
T ss_pred CCEeecCCCHHHE
Confidence 8888888887765
No 482
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=26.93 E-value=1.4e+02 Score=24.70 Aligned_cols=44 Identities=23% Similarity=0.372 Sum_probs=32.9
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHH----HHHHHH
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVT----KSIKSL 79 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~----k~lK~L 79 (252)
.+..|++.++.|+.+-.- .|...++|...+ |++...|. |+++.|
T Consensus 132 ~l~~L~~~~r~vl~l~~~----~~~s~~eIA~~l--gis~~~V~~~l~ra~~~L 179 (186)
T PRK13919 132 ALKALSPEERRVIEVLYY----QGYTHREAAQLL--GLPLGTLKTRARRALSRL 179 (186)
T ss_pred HHHhCCHHHHHHHHHHHH----cCCCHHHHHHHH--CcCHHHHHHHHHHHHHHH
Confidence 455677777777766443 589999999999 99998887 455555
No 483
>TIGR03787 marine_sort_RR proteobacterial dedicated sortase system response regulator. This model describes a family of DNA-binding response regulator proteins, associated with an adjacent histidine kinase (TIGR03785) to form a two-component system. This system co-occurs with, and often is adjacent to, a proteobacterial variant form of the protein sorting transpeptidase called sortase (TIGR03784), and a single target protein for the sortase. We give this protein the gene symbol pdsR, for Proteobacterial Dedicated Sortase system Response regulator.
Probab=26.90 E-value=1.6e+02 Score=24.29 Aligned_cols=59 Identities=15% Similarity=0.138 Sum_probs=36.6
Q ss_pred CCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHH----HHHHHHHHHhc----CCeeeeecc
Q 025493 32 DSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNI----VTKSIKSLQNK----SLIKEVVNI 91 (252)
Q Consensus 32 ~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~----l~k~lK~Le~k----~lIK~vksv 91 (252)
-.||.-|..|+.++-+ ..+.=+...+|......++..++ ++++-++|+.. .+|+.|..+
T Consensus 155 ~~Lt~~E~~il~~l~~-~~g~v~s~~~i~~~~~~~~~~~tv~~~v~rlr~Kl~~~~~~~~~i~tv~g~ 221 (227)
T TIGR03787 155 IDLTVTEFWMVHALAK-HPGHVKSRQQLMDAAKIVVDDSTITSHIKRIRKKFQAVDDNFDCIQTVYGM 221 (227)
T ss_pred ecCCHHHHHHHHHHHh-CCCccccHHHHHHHhhhcCCccCHHHHHHHHHHHhccCCCCCCeEEEecce
Confidence 3599999999999988 54444577778333211555554 45555566532 356666554
No 484
>PF09494 Slx4: Slx4 endonuclease; InterPro: IPR018574 The Slx4 protein is a heteromeric structure-specific endonuclease found in fungi. Slx4 with Slx1 acts as a nuclease on branched DNA substrates, particularly simple-Y, 5'-flap, or replication fork structures by cleaving the strand bearing the 5' non-homologous arm at the branch junction and thus generating ligatable nicked products from 5'-flap or replication fork substrates [].
Probab=26.73 E-value=2.1e+02 Score=20.35 Aligned_cols=35 Identities=17% Similarity=0.167 Sum_probs=27.3
Q ss_pred hCCCCCHHHHHHHHHHcCCcce-ecCHHHHHHHHHH
Q 025493 139 KLKVATLEGISDSIKRSGAFKV-DLTKQQIEEIVRA 173 (252)
Q Consensus 139 ~~~~~T~~~I~~~i~~~~i~~~-~Ls~~di~~IL~t 173 (252)
...+..++|++.+++.+|+.-. .++..++++-++.
T Consensus 21 ~YePI~L~el~~~L~~~g~~~~~~~~~~~l~~~lD~ 56 (64)
T PF09494_consen 21 MYEPINLEELHAWLKASGIGFDRKVDPSKLKEWLDS 56 (64)
T ss_pred cCCCccHHHHHHHHHHcCCCccceeCHHHHHHHHHH
Confidence 3468999999999998886433 6788888877764
No 485
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=26.71 E-value=3.5e+02 Score=21.98 Aligned_cols=69 Identities=13% Similarity=0.169 Sum_probs=40.6
Q ss_pred cHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeeeccccCCeeeEEecccccCCCccCCccccCCcCCHHHHHHHHHHHH
Q 025493 55 WTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVVNIHNKGKKHLMAVEFEPSKDISGGAWYSEGSLDTEFIKVVKSQCL 134 (252)
Q Consensus 55 w~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vksv~~~~rK~YmL~~lePs~eiTGG~wy~d~e~D~efV~~l~~~~~ 134 (252)
.+.++.+.+ |++..+ |.--|+.|||.+...-. +|--.|+ .+-|+.|..+.
T Consensus 2 ~Ige~a~~~--gvs~~t----LRyYE~~GLl~p~~r~~------------------~gyR~Y~-----~~~v~~l~~I~- 51 (131)
T cd04786 2 KIGELAKRS--GMAASR----IRFYEAEGLLSSVERSA------------------NGYRDYP-----PETVWVLEIIS- 51 (131)
T ss_pred CHHHHHHHH--CcCHHH----HHHHHHCCCCCCCCcCC------------------CCCeecC-----HHHHHHHHHHH-
Confidence 467788888 888765 46779999997632211 1222343 33333333222
Q ss_pred HHhhhCCCCCHHHHHHHHHHc
Q 025493 135 KQIIKLKVATLEGISDSIKRS 155 (252)
Q Consensus 135 ~~i~~~~~~T~~~I~~~i~~~ 155 (252)
.++..|+ |+++|.+++...
T Consensus 52 -~lr~~Gf-sL~eI~~ll~~~ 70 (131)
T cd04786 52 -SAQQAGF-SLDEIRQLLPAD 70 (131)
T ss_pred -HHHHcCC-CHHHHHHHHhcc
Confidence 2445544 899999998743
No 486
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=26.48 E-value=1.3e+02 Score=24.12 Aligned_cols=42 Identities=24% Similarity=0.401 Sum_probs=31.9
Q ss_pred CCCCCChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHH
Q 025493 30 PSDSLTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIK 77 (252)
Q Consensus 30 ~~~~l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK 77 (252)
.+..|++.++.|+.+..- .|...++|...+ |++.+.|...|.
T Consensus 106 ~l~~L~~~~r~v~~l~~~----~~~s~~EIA~~l--gis~~tV~~~l~ 147 (163)
T PRK07037 106 ALSELPARTRYAFEMYRL----HGETQKDIAREL--GVSPTLVNFMIR 147 (163)
T ss_pred HHHhCCHHHHHHHHHHHH----cCCCHHHHHHHH--CCCHHHHHHHHH
Confidence 345677777777766554 488899999999 999988776544
No 487
>smart00526 H15 Domain in histone families 1 and 5.
Probab=26.45 E-value=2.3e+02 Score=19.87 Aligned_cols=48 Identities=15% Similarity=0.212 Sum_probs=32.6
Q ss_pred hhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 137 IIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 137 i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
+...+.+|...|..||...--....--...+..-|+.+|-.|.+++++
T Consensus 18 l~er~GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~l~q~k 65 (66)
T smart00526 18 LKERKGSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGKLVQVK 65 (66)
T ss_pred cCCCCCCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCceeecC
Confidence 456778999999999998631000000234566689999999998753
No 488
>PRK02302 hypothetical protein; Provisional
Probab=26.40 E-value=83 Score=24.62 Aligned_cols=23 Identities=17% Similarity=0.313 Sum_probs=20.3
Q ss_pred CChHHHHHHHHHHHhcCCeeeee
Q 025493 67 LPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 67 l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
+++..+..+++.|.+.+++|.|.
T Consensus 43 vn~~~~e~~~~kl~~l~fVk~Ve 65 (89)
T PRK02302 43 VNKEDVEQKLEELSKLKFVKKVR 65 (89)
T ss_pred ECHHHHHHHHHHHhcCCCeeEEc
Confidence 47889999999999999999983
No 489
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=26.40 E-value=2e+02 Score=22.95 Aligned_cols=46 Identities=11% Similarity=0.141 Sum_probs=31.9
Q ss_pred HHHHhhhC-CCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEeeC
Q 025493 133 CLKQIIKL-KVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKSN 186 (252)
Q Consensus 133 ~~~~i~~~-~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~~ 186 (252)
++..|... +..|..+|.+.+ .++..-|-.+++.|+-+|.|++.+..
T Consensus 36 vL~~l~~~~~~~t~~eLa~~l--------~~~~~tvt~~v~~Le~~GlV~r~~~~ 82 (144)
T PRK03573 36 TLHNIHQLPPEQSQIQLAKAI--------GIEQPSLVRTLDQLEEKGLISRQTCA 82 (144)
T ss_pred HHHHHHHcCCCCCHHHHHHHh--------CCChhhHHHHHHHHHHCCCEeeecCC
Confidence 44444433 345666666554 35667888999999999999998753
No 490
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=26.34 E-value=11 Score=24.69 Aligned_cols=14 Identities=36% Similarity=1.049 Sum_probs=11.0
Q ss_pred ccCCccccCCcCCH
Q 025493 110 ISGGAWYSEGSLDT 123 (252)
Q Consensus 110 iTGG~wy~d~e~D~ 123 (252)
--||.||..+||+.
T Consensus 24 ~C~G~W~d~~el~~ 37 (41)
T PF13453_consen 24 SCGGIWFDAGELEK 37 (41)
T ss_pred CCCeEEccHHHHHH
Confidence 35999998888853
No 491
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=26.28 E-value=1.4e+02 Score=26.33 Aligned_cols=53 Identities=25% Similarity=0.326 Sum_probs=33.9
Q ss_pred CCCChHHHH---------HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 32 DSLTDHERL---------IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 32 ~~l~~~e~~---------vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
+.||+.=++ |.+.+.+..+...|..+||..+| ++....| +.+|+..++|+..+
T Consensus 120 rPLSdlG~~sY~sYW~~~i~~~L~~~~~~~~isi~~is~~T--gi~~~DI---i~tL~~l~~l~~~~ 181 (188)
T PF01853_consen 120 RPLSDLGRLSYRSYWRRVILEYLLEFKGKKSISIKDISQET--GIRPEDI---ISTLQQLGMLKYYK 181 (188)
T ss_dssp SS--HHHHHHHHHHHHHHHHHHHHHTSSE--EEHHHHHHHH---BTHHHH---HHHHHHTT-EEEET
T ss_pred CccCHHHHHHHHHHHHHHHHHHHHhcCCCCeEEHHHHHHHH--CCCHHHH---HHHHHHCCCEEEEC
Confidence 457765444 45667773444589999999999 9988776 56777778888764
No 492
>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=26.24 E-value=1.3e+02 Score=21.83 Aligned_cols=48 Identities=13% Similarity=0.261 Sum_probs=30.7
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecC--HHHHHHHHHHHhhcCeeEEE
Q 025493 128 VVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLT--KQQIEEIVRAVVLDNQIMEV 183 (252)
Q Consensus 128 ~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls--~~di~~IL~tLVyDgkIE~v 183 (252)
.+.+.|+.||...+..|+-.|...+ .|+ ..||-++|-.|.-.|+|-+.
T Consensus 4 ~~ee~Il~~L~~~g~~~a~~ia~~~--------~L~~~kk~VN~~LY~L~k~g~v~k~ 53 (66)
T PF02295_consen 4 DLEEKILDFLKELGGSTATAIAKAL--------GLSVPKKEVNRVLYRLEKQGKVCKE 53 (66)
T ss_dssp HHHHHHHHHHHHHTSSEEEHHHHHH--------HHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred hHHHHHHHHHHhcCCccHHHHHHHh--------CcchhHHHHHHHHHHHHHCCCEeeC
Confidence 4455566666555433333333322 233 68999999999999999764
No 493
>PRK05473 hypothetical protein; Provisional
Probab=26.14 E-value=92 Score=24.26 Aligned_cols=68 Identities=6% Similarity=0.063 Sum_probs=52.2
Q ss_pred ccCCcCCHHHHHHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 116 YSEGSLDTEFIKVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 116 y~d~e~D~efV~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
|.-++-+..-|..+...++.-|..+||--..||..||-+-. ..=-=+-.+.+.+++.+..|..||++.
T Consensus 10 F~~~~~~~~~v~eiL~~Vy~AL~EKGYNPinQiVGYllSGD-PaYItsh~nAR~lIrkiERDEilEeLv 77 (86)
T PRK05473 10 FDFDDEKKKDVREILTTVYDALEEKGYNPINQIVGYLLSGD-PAYIPRHNDARNLIRKLERDEILEELV 77 (86)
T ss_pred eeCCcccHHHHHHHHHHHHHHHHHcCCChHHHHHhhhccCC-CCccCCcccHHHHHHHHhHHHHHHHHH
Confidence 33344456678889999999999999999999999998554 222235678899999999998888653
No 494
>PHA00738 putative HTH transcription regulator
Probab=26.01 E-value=3.3e+02 Score=22.08 Aligned_cols=51 Identities=16% Similarity=0.148 Sum_probs=43.0
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEee
Q 025493 127 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVKS 185 (252)
Q Consensus 127 ~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~~ 185 (252)
|..|..|+.+|...+..++.+|.+.+ .+|..-|-+=|.+|.--|.|+..+.
T Consensus 11 dptRr~IL~lL~~~e~~~V~eLae~l--------~lSQptVS~HLKvLreAGLV~srK~ 61 (108)
T PHA00738 11 KILRRKILELIAENYILSASLISHTL--------LLSYTTVLRHLKILNEQGYIELYKE 61 (108)
T ss_pred CHHHHHHHHHHHHcCCccHHHHHHhh--------CCCHHHHHHHHHHHHHCCceEEEEE
Confidence 46788999999887778898988866 4788889999999999999987664
No 495
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=25.94 E-value=1.5e+02 Score=25.87 Aligned_cols=47 Identities=17% Similarity=0.217 Sum_probs=36.8
Q ss_pred CCCCChHHHHHHHHHHhhcCC-CcccHHHHHHHhhcCCChHHHHHH----HHHHH
Q 025493 31 SDSLTDHERLIYDVIRSNKQD-MGIWTRDMKRELKVNLPDNIVTKS----IKSLQ 80 (252)
Q Consensus 31 ~~~l~~~e~~vy~~I~~~ag~-~GIw~~dik~~~~~~l~~~~l~k~----lK~Le 80 (252)
+..|++.++.|+.+..- .+. +|...++|...+ |++...|.+. +++|.
T Consensus 172 i~~L~~~~r~il~l~y~-~~~~e~~S~~EIAe~l--gis~~tV~~~~~rAl~~Lr 223 (227)
T TIGR02846 172 LSVLDGREREVIEMRYG-LGDGRRKTQREIAKIL--GISRSYVSRIEKRALMKLY 223 (227)
T ss_pred HHhCCHHHHHHHHHHHc-CCCCCCcCHHHHHHHH--CCCHHHHHHHHHHHHHHHH
Confidence 57888888888888764 454 799999999999 9998877554 55554
No 496
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=25.83 E-value=1.8e+02 Score=25.84 Aligned_cols=51 Identities=8% Similarity=0.116 Sum_probs=38.3
Q ss_pred HHHHHHH--HHHHhhhCCCCCHHHHHHHHHHcCCcceecCHHHHHHHHHHHhhcCeeEEEe
Q 025493 126 IKVVKSQ--CLKQIIKLKVATLEGISDSIKRSGAFKVDLTKQQIEEIVRAVVLDNQIMEVK 184 (252)
Q Consensus 126 V~~l~~~--~~~~i~~~~~~T~~~I~~~i~~~~i~~~~Ls~~di~~IL~tLVyDgkIE~v~ 184 (252)
|..+.+. ++.++...+..|+.||++.+ .|...-+..||++|+--|.|++..
T Consensus 10 v~sl~r~l~IL~~l~~~~~l~l~eia~~l--------gl~kstv~Rll~tL~~~G~l~~~~ 62 (257)
T PRK15090 10 VSSVLKVFGILQALGEEREIGITELSQRV--------MMSKSTVYRFLQTMKTLGYVAQEG 62 (257)
T ss_pred cHHHHHHHHHHHHhhcCCCCCHHHHHHHH--------CcCHHHHHHHHHHHHHCCCEEEcC
Confidence 4444433 55666666678999998764 477888999999999999999853
No 497
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=25.67 E-value=1e+02 Score=27.98 Aligned_cols=42 Identities=7% Similarity=0.173 Sum_probs=31.6
Q ss_pred CChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 34 LTDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 34 l~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
|+-.+..++..|.+ .|+- ..--+++ ++.|..|++.||+||+.
T Consensus 2 m~l~~L~~f~av~~-~gs~----s~AA~~L--~iSqpaVS~~Ik~LE~~ 43 (317)
T PRK15421 2 IEVKHLKTLQALRN-CGSL----AAAAATL--HQTQSALSHQFSDLEQR 43 (317)
T ss_pred ccHHHHHHHHHHHH-cCCH----HHHHHHh--CCCHHHHHHHHHHHHHH
Confidence 45566677778888 7743 3334567 99999999999999974
No 498
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=25.65 E-value=1.5e+02 Score=22.65 Aligned_cols=44 Identities=11% Similarity=0.292 Sum_probs=36.8
Q ss_pred HHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhcCCeeeee
Q 025493 41 IYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNKSLIKEVV 89 (252)
Q Consensus 41 vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k~lIK~vk 89 (252)
|=++|+. -|. +..++|..+. ++|...|.-.|..|+.+|-|..|.
T Consensus 7 lRd~l~~-~gr--~s~~~Ls~~~--~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 7 VRDLLAL-RGR--MEAAQISQTL--NTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHHH-cCc--ccHHHHHHHH--CcCHHHHHHHHHHHHHCCCeEeec
Confidence 4456666 444 4568999999 999999999999999999999985
No 499
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=25.62 E-value=1e+02 Score=27.11 Aligned_cols=41 Identities=7% Similarity=0.180 Sum_probs=29.0
Q ss_pred ChHHHHHHHHHHhhcCCCcccHHHHHHHhhcCCChHHHHHHHHHHHhc
Q 025493 35 TDHERLIYDVIRSNKQDMGIWTRDMKRELKVNLPDNIVTKSIKSLQNK 82 (252)
Q Consensus 35 ~~~e~~vy~~I~~~ag~~GIw~~dik~~~~~~l~~~~l~k~lK~Le~k 82 (252)
+-.+..++..|.+ .|+- ..-.+++ ++.|..|++.||+||+.
T Consensus 2 ~l~~L~~f~~v~~-~gs~----s~AA~~L--~isqsavS~~i~~LE~~ 42 (296)
T PRK11242 2 LLRHIRYFLAVAE-HGNF----TRAAEAL--HVSQPTLSQQIRQLEES 42 (296)
T ss_pred ChHHHHHHHHHHH-hCCH----HHHHHHc--CCCchHHHHHHHHHHHH
Confidence 4455566667767 5532 2334567 99999999999999983
No 500
>PF07508 Recombinase: Recombinase; InterPro: IPR011109 This domain is usually found associated with IPR006119 from INTERPRO in putative integrases/recombinases of mobile genetic elements of diverse bacteria and phages.
Probab=25.61 E-value=2.8e+02 Score=20.47 Aligned_cols=53 Identities=15% Similarity=0.169 Sum_probs=42.0
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHcCCcc---eecCHHHHHHHHHHHhhcCeeEE
Q 025493 127 KVVKSQCLKQIIKLKVATLEGISDSIKRSGAFK---VDLTKQQIEEIVRAVVLDNQIME 182 (252)
Q Consensus 127 ~~l~~~~~~~i~~~~~~T~~~I~~~i~~~~i~~---~~Ls~~di~~IL~tLVyDgkIE~ 182 (252)
+.++.+.-.|+ ...++.+|++++++.|+.. ...+...|..||.-=.|=|...-
T Consensus 5 ~vVr~if~~~~---~g~s~~~I~~~ln~~gi~~~~~~~W~~~~v~~iL~np~y~G~~~~ 60 (102)
T PF07508_consen 5 EVVREIFELYL---EGYSLRQIARELNEKGIPTPRGKKWSKSTVRRILRNPAYAGYRVY 60 (102)
T ss_pred HHHHHHHHHHH---cCCCHHHHHHHHHhcCCccccCCcccHHHHHHHHhhhhccceEEe
Confidence 45555555565 6789999999999999853 45689999999999999887653
Done!