Query 038379
Match_columns 93
No_of_seqs 109 out of 193
Neff 2.3
Searched_HMMs 46136
Date Fri Mar 29 10:24:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038379.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038379hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1767 40S ribosomal protein 100.0 3.3E-30 7.3E-35 183.0 1.6 68 1-92 40-107 (110)
2 PRK09334 30S ribosomal protein 99.9 3.1E-27 6.7E-32 160.3 3.7 66 1-90 21-86 (86)
3 PF03297 Ribosomal_S25: S25 ri 99.9 3E-27 6.4E-32 164.0 2.8 67 1-91 39-105 (105)
4 COG4901 Ribosomal protein S25 99.7 7.9E-18 1.7E-22 119.4 3.1 68 1-92 39-106 (107)
5 PF00392 GntR: Bacterial regul 94.2 0.026 5.5E-07 34.1 1.3 33 48-80 27-59 (64)
6 smart00345 HTH_GNTR helix_turn 93.5 0.055 1.2E-06 30.3 1.8 30 50-79 25-54 (60)
7 PF13412 HTH_24: Winged helix- 93.3 0.034 7.4E-07 31.7 0.7 30 43-76 19-48 (48)
8 PRK04984 fatty acid metabolism 92.8 0.079 1.7E-06 38.0 2.0 65 1-79 1-65 (239)
9 PF01978 TrmB: Sugar-specific 92.7 0.15 3.2E-06 30.9 2.9 40 43-88 24-63 (68)
10 PF12802 MarR_2: MarR family; 92.5 0.078 1.7E-06 30.7 1.5 33 43-79 23-55 (62)
11 smart00419 HTH_CRP helix_turn_ 91.6 0.16 3.5E-06 27.8 1.9 33 45-77 8-40 (48)
12 PRK03837 transcriptional regul 91.2 0.18 3.9E-06 36.0 2.4 34 47-80 39-72 (241)
13 PF13463 HTH_27: Winged helix 90.9 0.33 7.1E-06 28.4 2.9 34 43-80 20-53 (68)
14 TIGR02404 trehalos_R_Bsub treh 90.7 0.16 3.4E-06 36.6 1.8 34 47-80 26-59 (233)
15 smart00418 HTH_ARSR helix_turn 90.5 0.32 6.9E-06 26.7 2.5 37 51-88 16-52 (66)
16 TIGR02325 C_P_lyase_phnF phosp 90.5 0.17 3.8E-06 36.0 1.7 34 47-80 34-67 (238)
17 PRK14165 winged helix-turn-hel 90.2 0.27 5.9E-06 37.6 2.7 41 43-87 23-63 (217)
18 cd07377 WHTH_GntR Winged helix 89.4 0.34 7.5E-06 27.5 2.1 28 51-78 31-58 (66)
19 PRK11402 DNA-binding transcrip 89.3 0.26 5.7E-06 35.7 2.0 60 7-80 9-68 (241)
20 PRK09764 DNA-binding transcrip 89.2 0.27 5.9E-06 35.8 2.0 34 47-80 31-64 (240)
21 PF01047 MarR: MarR family; I 89.2 0.26 5.6E-06 28.5 1.5 33 43-79 19-51 (59)
22 TIGR02018 his_ut_repres histid 88.9 0.27 5.8E-06 35.4 1.8 34 47-80 27-60 (230)
23 COG2188 PhnF Transcriptional r 88.8 0.5 1.1E-05 34.9 3.2 64 6-83 6-69 (236)
24 PF13730 HTH_36: Helix-turn-he 88.5 0.32 7E-06 28.0 1.6 27 49-75 29-55 (55)
25 cd00090 HTH_ARSR Arsenical Res 88.4 1 2.2E-05 25.1 3.6 37 51-88 26-62 (78)
26 PRK10225 DNA-binding transcrip 88.2 0.37 8.1E-06 35.1 2.1 34 47-80 35-68 (257)
27 COG1846 MarR Transcriptional r 88.1 0.38 8.3E-06 29.5 1.8 30 50-79 41-70 (126)
28 PRK14999 histidine utilization 88.0 0.33 7.2E-06 35.3 1.7 33 47-79 38-70 (241)
29 PF08220 HTH_DeoR: DeoR-like h 87.9 0.58 1.3E-05 28.3 2.5 33 43-79 16-48 (57)
30 TIGR03338 phnR_burk phosphonat 87.7 0.34 7.4E-06 34.0 1.6 32 48-79 37-68 (212)
31 PF08222 HTH_CodY: CodY helix- 87.6 0.66 1.4E-05 30.7 2.8 46 42-92 5-50 (61)
32 PRK10079 phosphonate metabolis 87.3 0.39 8.5E-06 34.9 1.8 58 7-79 12-69 (241)
33 smart00529 HTH_DTXR Helix-turn 86.8 0.56 1.2E-05 29.2 2.0 29 51-79 5-33 (96)
34 TIGR02812 fadR_gamma fatty aci 86.7 0.45 9.7E-06 34.2 1.8 33 47-79 32-64 (235)
35 PF01325 Fe_dep_repress: Iron 86.1 0.41 9E-06 29.6 1.2 32 43-78 24-55 (60)
36 PRK10421 DNA-binding transcrip 85.4 0.56 1.2E-05 34.3 1.8 33 47-79 28-60 (253)
37 PF09012 FeoC: FeoC like trans 85.1 0.77 1.7E-05 28.3 2.1 36 43-82 16-51 (69)
38 cd00092 HTH_CRP helix_turn_hel 84.9 0.58 1.3E-05 27.1 1.4 29 51-79 31-59 (67)
39 PRK09464 pdhR transcriptional 84.7 0.62 1.4E-05 33.8 1.7 34 47-80 36-69 (254)
40 PRK11512 DNA-binding transcrip 84.6 0.84 1.8E-05 30.9 2.3 33 43-79 56-88 (144)
41 PRK11534 DNA-binding transcrip 84.6 0.63 1.4E-05 33.2 1.7 32 50-81 35-66 (224)
42 PF05158 RNA_pol_Rpc34: RNA po 84.6 1.1 2.5E-05 35.8 3.3 38 51-88 106-145 (327)
43 PRK09990 DNA-binding transcrip 84.5 0.65 1.4E-05 33.7 1.8 34 47-80 33-66 (251)
44 PRK11523 DNA-binding transcrip 84.5 0.65 1.4E-05 33.9 1.7 33 48-80 35-67 (253)
45 TIGR02337 HpaR homoprotocatech 84.4 0.87 1.9E-05 29.8 2.2 33 43-79 44-76 (118)
46 PF14502 HTH_41: Helix-turn-he 84.3 0.75 1.6E-05 28.9 1.7 37 39-80 5-41 (48)
47 TIGR03337 phnR transcriptional 84.2 0.65 1.4E-05 32.9 1.6 33 48-80 28-60 (231)
48 PF13545 HTH_Crp_2: Crp-like h 83.8 0.79 1.7E-05 27.4 1.7 28 49-76 32-59 (76)
49 PRK13509 transcriptional repre 81.9 1.1 2.4E-05 33.7 2.2 33 43-79 21-53 (251)
50 PRK10434 srlR DNA-bindng trans 81.9 1.3 2.7E-05 33.5 2.5 33 43-79 21-53 (256)
51 smart00420 HTH_DEOR helix_turn 81.5 1.2 2.6E-05 24.2 1.7 33 43-79 16-48 (53)
52 COG3355 Predicted transcriptio 81.5 0.85 1.8E-05 33.0 1.4 29 51-79 48-76 (126)
53 PRK11414 colanic acid/biofilm 81.4 0.74 1.6E-05 32.9 1.0 30 50-79 39-68 (221)
54 TIGR01889 Staph_reg_Sar staphy 81.4 0.95 2.1E-05 29.8 1.5 33 43-79 45-77 (109)
55 TIGR01610 phage_O_Nterm phage 81.2 0.89 1.9E-05 29.8 1.3 32 43-78 49-80 (95)
56 smart00347 HTH_MARR helix_turn 80.2 0.93 2E-05 27.2 1.0 32 43-78 26-57 (101)
57 TIGR02787 codY_Gpos GTP-sensin 79.9 0.93 2E-05 36.4 1.2 29 51-79 204-232 (251)
58 PRK09333 30S ribosomal protein 79.6 1.8 3.8E-05 32.3 2.5 25 54-78 90-114 (150)
59 PRK10906 DNA-binding transcrip 79.5 1.9 4.1E-05 32.7 2.7 32 43-78 21-52 (252)
60 COG2186 FadR Transcriptional r 79.4 1.1 2.3E-05 33.6 1.3 31 47-77 36-66 (241)
61 smart00550 Zalpha Z-DNA-bindin 78.9 1.3 2.8E-05 27.6 1.4 34 43-80 24-57 (68)
62 PRK10870 transcriptional repre 77.8 1.7 3.6E-05 31.2 1.9 33 43-79 73-105 (176)
63 PF02082 Rrf2: Transcriptional 77.8 2 4.3E-05 27.1 2.0 37 43-83 27-63 (83)
64 PF01090 Ribosomal_S19e: Ribos 77.7 2.4 5.3E-05 31.2 2.7 26 54-79 89-114 (139)
65 COG1339 Transcriptional regula 76.5 2.1 4.6E-05 33.9 2.3 49 32-86 12-60 (214)
66 PF01726 LexA_DNA_bind: LexA D 76.4 1.3 2.8E-05 28.0 0.9 36 43-80 25-61 (65)
67 COG1321 TroR Mn-dependent tran 76.4 2.1 4.6E-05 30.9 2.1 29 51-79 30-58 (154)
68 TIGR02944 suf_reg_Xantho FeS a 75.9 2.2 4.7E-05 28.5 1.9 32 43-78 27-58 (130)
69 PRK11014 transcriptional repre 75.7 2.5 5.3E-05 29.0 2.2 33 50-82 30-62 (141)
70 PTZ00095 40S ribosomal protein 75.3 3.7 8E-05 31.3 3.2 25 54-78 114-138 (169)
71 COG1349 GlpR Transcriptional r 75.1 2.6 5.7E-05 31.9 2.4 33 43-79 21-53 (253)
72 COG2512 Predicted membrane-ass 74.6 3.6 7.8E-05 32.3 3.1 41 43-87 212-252 (258)
73 PRK04158 transcriptional repre 74.1 2.5 5.4E-05 33.9 2.2 31 43-77 203-233 (256)
74 PF12840 HTH_20: Helix-turn-he 73.4 2.3 5E-05 25.3 1.4 33 43-79 26-58 (61)
75 smart00344 HTH_ASNC helix_turn 73.2 2.9 6.2E-05 26.6 1.9 28 51-78 23-50 (108)
76 PRK03573 transcriptional regul 73.2 2 4.4E-05 28.8 1.3 33 43-79 48-80 (144)
77 PF07106 TBPIP: Tat binding pr 73.1 6.2 0.00014 27.8 3.8 34 56-90 29-62 (169)
78 PRK09802 DNA-binding transcrip 70.8 3.9 8.4E-05 31.3 2.5 34 43-80 33-66 (269)
79 smart00346 HTH_ICLR helix_turn 70.5 2.7 5.9E-05 25.7 1.3 32 43-78 22-53 (91)
80 COG4465 CodY Pleiotropic trans 70.2 3.8 8.3E-05 33.3 2.4 32 43-78 206-237 (261)
81 PF14947 HTH_45: Winged helix- 70.1 2.9 6.4E-05 26.4 1.4 27 51-77 25-51 (77)
82 TIGR00738 rrf2_super rrf2 fami 70.1 3.7 7.9E-05 27.0 1.9 32 43-78 27-58 (132)
83 TIGR01884 cas_HTH CRISPR locus 69.9 5.6 0.00012 28.7 3.0 30 51-80 163-192 (203)
84 COG1522 Lrp Transcriptional re 69.3 5 0.00011 26.7 2.5 30 51-80 28-57 (154)
85 TIGR02702 SufR_cyano iron-sulf 69.0 5.3 0.00011 28.8 2.7 32 43-78 17-48 (203)
86 COG3177 Fic family protein [Fu 67.9 4 8.7E-05 32.4 2.1 42 42-87 305-346 (348)
87 PRK03902 manganese transport t 67.9 4.4 9.5E-05 27.6 2.0 28 51-78 28-55 (142)
88 PF04703 FaeA: FaeA-like prote 67.8 6.4 0.00014 25.1 2.6 30 51-80 21-50 (62)
89 PRK11050 manganese transport r 67.5 3.4 7.3E-05 29.0 1.4 31 43-77 53-83 (152)
90 PRK15481 transcriptional regul 67.4 4.3 9.3E-05 31.6 2.1 28 51-78 35-62 (431)
91 PF09339 HTH_IclR: IclR helix- 65.8 4.4 9.5E-05 23.5 1.5 31 43-77 20-50 (52)
92 PF00325 Crp: Bacterial regula 65.1 4.9 0.00011 23.0 1.5 25 51-75 8-32 (32)
93 TIGR02010 IscR iron-sulfur clu 64.0 6 0.00013 27.0 2.1 36 40-80 25-60 (135)
94 PF08784 RPA_C: Replication pr 63.5 5.4 0.00012 25.8 1.7 41 22-75 55-95 (102)
95 PRK11169 leucine-responsive tr 62.9 7.8 0.00017 27.2 2.6 28 51-78 34-61 (164)
96 PRK13777 transcriptional regul 61.4 5.5 0.00012 29.6 1.6 33 43-79 61-93 (185)
97 PF10007 DUF2250: Uncharacteri 61.2 7.8 0.00017 26.5 2.2 30 51-80 27-56 (92)
98 PF05732 RepL: Firmicute plasm 61.1 12 0.00026 27.3 3.3 35 40-78 74-108 (165)
99 PF03551 PadR: Transcriptional 60.4 31 0.00066 21.0 4.6 35 54-88 26-64 (75)
100 PF09397 Ftsk_gamma: Ftsk gamm 60.0 7.5 0.00016 25.1 1.9 36 43-82 22-57 (65)
101 COG2238 RPS19A Ribosomal prote 60.0 8.6 0.00019 29.1 2.5 25 55-79 91-115 (147)
102 PRK04424 fatty acid biosynthes 59.0 2.6 5.6E-05 30.7 -0.4 33 43-79 23-55 (185)
103 COG1386 scpB Chromosome segreg 58.8 7.8 0.00017 29.1 2.1 28 52-79 110-137 (184)
104 PF01638 HxlR: HxlR-like helix 58.7 17 0.00036 23.2 3.4 29 51-79 24-53 (90)
105 smart00843 Ftsk_gamma This dom 58.5 7.6 0.00016 25.1 1.7 35 43-81 21-55 (63)
106 PF01475 FUR: Ferric uptake re 58.5 31 0.00067 22.5 4.7 35 56-90 39-73 (120)
107 PF01022 HTH_5: Bacterial regu 58.4 8.1 0.00018 22.1 1.7 30 43-76 17-46 (47)
108 PF04157 EAP30: EAP30/Vps36 fa 56.6 7.2 0.00016 28.9 1.6 29 43-75 192-220 (223)
109 TIGR03697 NtcA_cyano global ni 56.0 7.1 0.00015 26.2 1.3 29 49-77 147-175 (193)
110 PF13601 HTH_34: Winged helix 54.9 11 0.00024 24.1 2.1 28 51-78 20-47 (80)
111 PRK09954 putative kinase; Prov 54.5 6.8 0.00015 29.9 1.2 30 43-76 19-48 (362)
112 cd04761 HTH_MerR-SF Helix-Turn 54.2 11 0.00023 20.7 1.7 28 62-89 13-40 (49)
113 cd07153 Fur_like Ferric uptake 54.2 29 0.00063 22.2 3.9 33 56-88 32-64 (116)
114 COG1725 Predicted transcriptio 54.0 7.5 0.00016 28.0 1.3 59 6-78 10-68 (125)
115 COG1802 GntR Transcriptional r 53.8 6.9 0.00015 28.2 1.1 34 48-81 42-75 (230)
116 COG1959 Predicted transcriptio 52.4 9.8 0.00021 27.0 1.7 36 43-82 27-62 (150)
117 PF03428 RP-C: Replication pro 52.1 11 0.00024 28.1 2.0 37 40-78 67-104 (177)
118 PHA02943 hypothetical protein; 51.7 16 0.00034 28.2 2.7 30 51-80 30-59 (165)
119 PRK11920 rirA iron-responsive 51.4 8.6 0.00019 27.3 1.2 34 43-80 26-59 (153)
120 PRK11179 DNA-binding transcrip 50.3 17 0.00036 25.2 2.5 28 51-78 29-56 (153)
121 PF07848 PaaX: PaaX-like prote 49.0 44 0.00095 21.4 4.1 37 51-88 29-65 (70)
122 PRK11753 DNA-binding transcrip 49.0 10 0.00022 26.0 1.2 27 51-77 174-200 (211)
123 TIGR00122 birA_repr_reg BirA b 48.9 14 0.00031 22.2 1.7 26 51-76 19-44 (69)
124 COG3888 Predicted transcriptio 48.9 12 0.00027 31.3 1.9 27 51-77 26-52 (321)
125 TIGR02698 CopY_TcrY copper tra 48.3 39 0.00084 23.4 4.1 40 51-91 28-67 (130)
126 PF13814 Replic_Relax: Replica 47.0 32 0.0007 23.6 3.5 28 61-88 28-61 (191)
127 PRK13918 CRP/FNR family transc 46.1 12 0.00026 25.5 1.2 26 51-76 155-180 (202)
128 TIGR00498 lexA SOS regulatory 45.7 16 0.00035 25.8 1.9 29 51-79 31-60 (199)
129 PRK11161 fumarate/nitrate redu 44.0 15 0.00033 25.8 1.5 29 50-78 189-217 (235)
130 PF04492 Phage_rep_O: Bacterio 43.7 21 0.00045 24.4 2.1 33 39-76 53-85 (100)
131 PF14394 DUF4423: Domain of un 43.6 16 0.00034 26.6 1.6 34 47-80 41-76 (171)
132 PRK10411 DNA-binding transcrip 43.4 20 0.00043 27.0 2.2 32 43-78 20-51 (240)
133 PF04079 DUF387: Putative tran 43.3 10 0.00022 27.6 0.6 36 53-88 101-139 (159)
134 PF03965 Penicillinase_R: Peni 42.8 71 0.0015 21.0 4.5 39 52-91 28-66 (115)
135 PRK10857 DNA-binding transcrip 42.6 20 0.00044 25.9 2.0 32 43-78 27-58 (164)
136 smart00422 HTH_MERR helix_turn 40.8 18 0.0004 21.1 1.3 35 51-89 6-41 (70)
137 PF00376 MerR: MerR family reg 39.4 30 0.00065 19.7 2.0 27 61-87 11-38 (38)
138 PRK00215 LexA repressor; Valid 39.0 32 0.00068 24.5 2.5 31 51-81 29-60 (205)
139 cd04371 DEP DEP domain, named 38.7 47 0.001 20.0 3.0 24 57-80 45-68 (81)
140 PRK06474 hypothetical protein; 38.5 38 0.00082 24.6 2.9 39 51-89 32-75 (178)
141 KOG1502 Flavonol reductase/cin 37.4 80 0.0017 26.0 4.9 69 10-83 99-192 (327)
142 PRK06266 transcription initiat 36.1 25 0.00054 25.9 1.7 31 47-77 38-68 (178)
143 COG1167 ARO8 Transcriptional r 35.9 29 0.00062 28.3 2.1 59 7-79 4-62 (459)
144 COG5340 Predicted transcriptio 35.7 20 0.00043 29.5 1.2 40 31-79 25-64 (269)
145 PRK05638 threonine synthase; V 35.1 43 0.00093 27.1 3.0 39 51-90 390-430 (442)
146 PF00610 DEP: Domain found in 35.0 43 0.00092 20.1 2.3 28 56-83 35-62 (74)
147 PRK09391 fixK transcriptional 34.6 31 0.00068 24.8 2.0 28 50-77 184-211 (230)
148 PRK10402 DNA-binding transcrip 34.3 34 0.00074 24.4 2.1 28 50-77 174-201 (226)
149 PRK12423 LexA repressor; Provi 34.2 32 0.0007 25.0 2.0 33 44-78 26-59 (202)
150 PF08279 HTH_11: HTH domain; 33.7 38 0.00082 19.2 1.9 27 43-73 17-43 (55)
151 COG2345 Predicted transcriptio 33.5 31 0.00067 26.9 1.9 28 51-78 31-58 (218)
152 TIGR00281 segregation and cond 32.7 27 0.00059 26.2 1.4 36 53-88 106-144 (186)
153 COG0789 SoxR Predicted transcr 32.6 23 0.0005 22.9 0.9 29 61-89 12-41 (124)
154 PRK09462 fur ferric uptake reg 31.7 96 0.0021 21.3 3.9 32 57-88 50-81 (148)
155 cd04448 DEP_PIKfyve DEP (Dishe 31.6 53 0.0012 21.4 2.5 23 60-82 48-70 (81)
156 KOG3411 40S ribosomal protein 31.2 48 0.001 25.1 2.5 22 56-77 94-115 (143)
157 PF01976 DUF116: Protein of un 30.8 20 0.00044 26.1 0.5 18 59-76 95-112 (158)
158 PRK15431 ferrous iron transpor 30.8 47 0.001 22.5 2.2 29 51-79 22-50 (78)
159 PF03492 Methyltransf_7: SAM d 30.7 77 0.0017 25.2 3.7 44 34-77 173-218 (334)
160 PRK05472 redox-sensing transcr 30.6 49 0.0011 23.9 2.4 31 39-74 31-61 (213)
161 PRK11886 bifunctional biotin-- 29.9 45 0.00097 25.6 2.2 28 51-78 24-52 (319)
162 cd04449 DEP_DEPDC5-like DEP (D 29.4 59 0.0013 20.9 2.4 24 58-81 48-71 (83)
163 cd04766 HTH_HspR Helix-Turn-He 29.4 41 0.00089 21.4 1.7 35 51-89 7-41 (91)
164 cd04769 HTH_MerR2 Helix-Turn-H 29.4 36 0.00079 22.7 1.5 28 62-89 13-40 (116)
165 cd04762 HTH_MerR-trunc Helix-T 29.4 46 0.001 17.3 1.6 28 62-89 13-40 (49)
166 PF09824 ArsR: ArsR transcript 29.2 24 0.00052 26.9 0.6 46 3-76 13-58 (160)
167 TIGR03433 padR_acidobact trans 29.1 59 0.0013 21.2 2.4 27 52-78 32-58 (100)
168 PHA00738 putative HTH transcri 28.9 93 0.002 22.3 3.5 37 51-89 32-68 (108)
169 cd00073 H15 linker histone 1 a 28.8 89 0.0019 20.2 3.2 24 59-82 45-68 (88)
170 PF12689 Acid_PPase: Acid Phos 28.2 79 0.0017 23.3 3.2 58 11-88 45-106 (169)
171 cd04450 DEP_RGS7-like DEP (Dis 27.4 79 0.0017 20.4 2.8 27 57-83 45-71 (88)
172 COG3432 Predicted transcriptio 27.3 1.1E+02 0.0024 21.2 3.6 25 54-78 40-64 (95)
173 TIGR03418 chol_sulf_TF putativ 27.1 36 0.00078 24.3 1.2 34 51-84 21-54 (291)
174 cd01279 HTH_HspR-like Helix-Tu 27.0 46 0.001 21.8 1.6 35 51-89 7-41 (98)
175 PF05238 CENP-N: Kinetochore p 26.6 67 0.0015 26.3 2.8 31 47-77 349-379 (400)
176 smart00526 H15 Domain in histo 26.6 79 0.0017 19.0 2.5 20 59-78 45-64 (66)
177 smart00049 DEP Domain found in 26.4 1E+02 0.0022 18.6 3.0 24 57-80 37-60 (77)
178 PRK09834 DNA-binding transcrip 26.4 57 0.0012 24.3 2.2 29 51-79 32-60 (263)
179 COG2390 DeoR Transcriptional r 25.8 37 0.00081 27.5 1.2 34 43-80 28-61 (321)
180 cd01282 HTH_MerR-like_sg3 Heli 25.6 39 0.00085 22.5 1.1 28 62-89 13-40 (112)
181 TIGR00331 hrcA heat shock gene 25.4 50 0.0011 26.4 1.8 32 43-78 23-56 (337)
182 cd04781 HTH_MerR-like_sg6 Heli 25.2 45 0.00097 22.4 1.3 28 62-89 13-40 (120)
183 PF00538 Linker_histone: linke 24.7 1E+02 0.0022 19.2 2.8 22 59-80 45-66 (77)
184 PF13338 DUF4095: Domain of un 24.4 65 0.0014 20.2 1.9 19 61-79 2-20 (124)
185 PRK08061 rpsN 30S ribosomal pr 24.4 93 0.002 20.1 2.6 34 43-80 25-58 (61)
186 PF13411 MerR_1: MerR HTH fami 24.0 60 0.0013 18.9 1.6 28 62-89 13-40 (69)
187 PF04182 B-block_TFIIIC: B-blo 23.7 87 0.0019 19.6 2.4 30 51-80 24-53 (75)
188 PF14242 DUF4342: Domain of un 23.5 2.3E+02 0.0051 18.9 4.7 37 49-85 5-42 (84)
189 PF10557 Cullin_Nedd8: Cullin 23.5 1.2E+02 0.0026 18.7 3.0 26 54-79 39-64 (68)
190 cd04789 HTH_Cfa Helix-Turn-Hel 23.4 48 0.001 21.8 1.2 35 51-89 7-41 (102)
191 cd04787 HTH_HMRTR_unk Helix-Tu 23.4 48 0.0011 22.6 1.3 28 62-89 13-41 (133)
192 cd04775 HTH_Cfa-like Helix-Tur 22.8 59 0.0013 21.3 1.5 35 51-89 7-41 (102)
193 cd00592 HTH_MerR-like Helix-Tu 22.5 43 0.00094 21.1 0.8 28 62-89 13-40 (100)
194 cd01107 HTH_BmrR Helix-Turn-He 22.4 44 0.00095 22.1 0.9 28 62-89 13-42 (108)
195 cd04777 HTH_MerR-like_sg1 Heli 22.3 46 0.00099 21.7 0.9 26 62-88 13-38 (107)
196 PLN02522 ATP citrate (pro-S)-l 22.1 80 0.0017 28.0 2.6 21 59-79 307-327 (608)
197 TIGR02044 CueR Cu(I)-responsiv 22.1 51 0.0011 22.3 1.2 29 61-89 12-41 (127)
198 PRK10141 DNA-binding transcrip 21.4 1.6E+02 0.0034 20.5 3.5 38 51-89 36-73 (117)
199 TIGR01950 SoxR redox-sensitive 21.3 69 0.0015 22.6 1.7 28 62-89 14-41 (142)
200 COG4109 Predicted transcriptio 21.2 81 0.0018 27.5 2.4 36 51-86 25-60 (432)
201 COG4860 Uncharacterized protei 21.2 46 0.001 25.7 0.9 46 3-76 20-65 (170)
202 PF14217 DUF4327: Domain of un 21.2 24 0.00053 23.5 -0.5 21 63-88 8-28 (68)
203 PRK12704 phosphodiesterase; Pr 21.2 97 0.0021 26.5 2.9 43 36-78 240-282 (520)
204 cd01105 HTH_GlnR-like Helix-Tu 21.1 66 0.0014 20.6 1.5 34 51-88 7-41 (88)
205 PRK04172 pheS phenylalanyl-tRN 21.0 83 0.0018 26.1 2.4 33 43-79 22-54 (489)
206 COG0640 ArsR Predicted transcr 20.9 1.7E+02 0.0038 16.4 3.1 27 51-77 45-71 (110)
207 PF00126 HTH_1: Bacterial regu 20.5 84 0.0018 18.5 1.7 35 51-85 19-53 (60)
208 TIGR03319 YmdA_YtgF conserved 20.4 91 0.002 26.6 2.5 42 36-77 234-275 (514)
209 cd04780 HTH_MerR-like_sg5 Heli 20.1 65 0.0014 21.1 1.3 28 62-89 13-41 (95)
No 1
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=3.3e-30 Score=182.98 Aligned_cols=68 Identities=40% Similarity=0.571 Sum_probs=66.7
Q ss_pred CeeechhhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 1 MVLFDQGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 1 ~VlfDk~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
||||||+||||+++|+|. | |+| |||+ ++||++|||||||+||+||.++|+|++|++
T Consensus 40 ~Vlfdqatydkl~kevp~---------------~----k~i-t~sv----l~dRlkIngsLAr~alr~L~~kG~Ik~Vs~ 95 (110)
T KOG1767|consen 40 AVLFDQATYDKLLKEVPK---------------Y----KLI-TPSV----LSDRLKINGSLARAALRELSNKGVIKQVSK 95 (110)
T ss_pred heeecHHHHHHHHHhccc---------------c----eee-cHHH----hhhhhhhchHHHHHHHHHHHhcchHHHHhh
Confidence 799999999999999999 9 999 9999 999999999999999999999999999999
Q ss_pred ccceEEEEeecC
Q 038379 81 YASQQIYTRVIN 92 (93)
Q Consensus 81 ~~~Q~IYTR~~~ 92 (93)
|++|+||||+++
T Consensus 96 h~~q~IYTrat~ 107 (110)
T KOG1767|consen 96 HSKQVIYTRATA 107 (110)
T ss_pred cchheeeccccc
Confidence 999999999986
No 2
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=99.93 E-value=3.1e-27 Score=160.25 Aligned_cols=66 Identities=18% Similarity=0.304 Sum_probs=63.9
Q ss_pred CeeechhhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 1 MVLFDQGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 1 ~VlfDk~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+|+||++||||+.+|||+ + |+| ||++ +++|++|+|||||+||+||+++|+|++|++
T Consensus 21 ~v~~dk~t~dkl~kEV~~---------------~----K~I-Tps~----lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~ 76 (86)
T PRK09334 21 IITLDEELLKRVAKEVKK---------------E----KIV-TPYT----LASKYGIKISVAKKVLRELEKRGVLVLYSK 76 (86)
T ss_pred eeecCHHHHHHHHHHhcc---------------C----cEE-cHHH----HHHHhcchHHHHHHHHHHHHHCCCEEEEec
Confidence 589999999999999999 9 999 9999 999999999999999999999999999999
Q ss_pred ccceEEEEee
Q 038379 81 YASQQIYTRV 90 (93)
Q Consensus 81 ~~~Q~IYTR~ 90 (93)
|++|.|||.+
T Consensus 77 ~~~q~IYt~~ 86 (86)
T PRK09334 77 NRRTPIYVPA 86 (86)
T ss_pred CCCeEEeccC
Confidence 9999999953
No 3
>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=99.93 E-value=3e-27 Score=164.01 Aligned_cols=67 Identities=39% Similarity=0.587 Sum_probs=64.7
Q ss_pred CeeechhhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 1 MVLFDQGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 1 ~VlfDk~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+|+||++||||+.+|||+ + |+| ||++ ++||++|+|||||++|+||+++|+|++|++
T Consensus 39 ~v~~d~~~~~kl~kEV~~---------------~----K~I-Tp~~----lserlkI~~SlAr~~Lr~L~~kG~Ik~V~k 94 (105)
T PF03297_consen 39 AVLFDKETYDKLLKEVPK---------------M----KLI-TPSV----LSERLKINGSLARKALRELESKGLIKPVSK 94 (105)
T ss_dssp CSCCTCHHHHHHHHHCTT---------------S----SCE-CHHH----HHHHHCCSCHHHHHHHHHHHHCCSSEEEEC
T ss_pred ceEecHHHHHHHHHHhcc---------------C----cEe-eHHH----HHHhHhhHHHHHHHHHHHHHHCCCEEEEec
Confidence 589999999999999999 8 999 9999 999999999999999999999999999999
Q ss_pred ccceEEEEeec
Q 038379 81 YASQQIYTRVI 91 (93)
Q Consensus 81 ~~~Q~IYTR~~ 91 (93)
||+|.||||++
T Consensus 95 ~~~~~IYtr~~ 105 (105)
T PF03297_consen 95 HHRQRIYTRAT 105 (105)
T ss_dssp CTTCEEEEES-
T ss_pred cCCeEEEecCC
Confidence 99999999975
No 4
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=99.70 E-value=7.9e-18 Score=119.39 Aligned_cols=68 Identities=25% Similarity=0.329 Sum_probs=64.9
Q ss_pred CeeechhhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 1 MVLFDQGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 1 ~VlfDk~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+|.+|+++||++.+|||. + ++| ||+. +.+|++|+||+||.+||+|+++|.|.++++
T Consensus 39 av~vdee~~~ki~KEV~~---------------~----r~V-Tpy~----la~r~gI~~SvAr~vLR~LeeeGvv~lvsk 94 (107)
T COG4901 39 AVTVDEELLDKIRKEVPR---------------E----RVV-TPYV----LASRYGINGSVARIVLRHLEEEGVVQLVSK 94 (107)
T ss_pred hhhccHHHHHHHHHhccc---------------c----eee-cHHH----HHHHhccchHHHHHHHHHHHhCCceeeecc
Confidence 478999999999999999 8 898 9999 999999999999999999999999999999
Q ss_pred ccceEEEEeecC
Q 038379 81 YASQQIYTRVIN 92 (93)
Q Consensus 81 ~~~Q~IYTR~~~ 92 (93)
|+.|-||+|+-.
T Consensus 95 nrR~~IY~~a~a 106 (107)
T COG4901 95 NRRQAIYTRAKA 106 (107)
T ss_pred CccceeeecccC
Confidence 999999999753
No 5
>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=94.24 E-value=0.026 Score=34.06 Aligned_cols=33 Identities=21% Similarity=0.196 Sum_probs=28.3
Q ss_pred cccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 48 EAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 48 ~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
|+.++++++++=+-+|+|++.|++.|+|.....
T Consensus 27 ~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 27 ERELAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 344999999999999999999999999987643
No 6
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=93.51 E-value=0.055 Score=30.35 Aligned_cols=30 Identities=17% Similarity=0.227 Sum_probs=27.1
Q ss_pred cccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 50 GFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 50 ~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
.+++++.++-+-++++++.|+++|+|..+.
T Consensus 25 ~la~~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 25 ELAAQLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 389999999999999999999999997653
No 7
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=93.29 E-value=0.034 Score=31.69 Aligned_cols=30 Identities=30% Similarity=0.321 Sum_probs=26.1
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIR 76 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik 76 (93)
|.+- +++++.++.+-+++.|++|+++|+|+
T Consensus 19 t~~e----la~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 19 TQKE----LAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp -HHH----HHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CHHH----HHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 6666 99999999999999999999999985
No 8
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=92.76 E-value=0.079 Score=38.02 Aligned_cols=65 Identities=14% Similarity=0.105 Sum_probs=44.4
Q ss_pred CeeechhhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 1 MVLFDQGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 1 ~VlfDk~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
||+=++..++.+...+.+.+. ...++-|-||= +|..+++++.||=+-.|.||+.|++.|+|...-
T Consensus 1 ~~~~~~~~~~~~~~~l~~~I~---------~g~l~pG~~LP-----sE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 1 MVIKAQSPAGFAEEYIIESIW---------NNRFPPGSILP-----AERELSELIGVTRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred CcccccCHHHHHHHHHHHHHH---------cCCCCCCCcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 455566666666666666221 11122222553 456699999999999999999999999998643
No 9
>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=92.69 E-value=0.15 Score=30.86 Aligned_cols=40 Identities=25% Similarity=0.295 Sum_probs=34.3
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEE
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYT 88 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYT 88 (93)
|..- +++.+.|+-|-++++|+.|+++|+|+..... ..+|.
T Consensus 24 t~~e----Ia~~l~i~~~~v~~~L~~L~~~GlV~~~~~~--~~~Y~ 63 (68)
T PF01978_consen 24 TAEE----IAEELGISRSTVYRALKSLEEKGLVEREEGR--PKVYR 63 (68)
T ss_dssp EHHH----HHHHHTSSHHHHHHHHHHHHHTTSEEEEEEC--CEEEE
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHHHCCCEEEEcCc--eEEEE
Confidence 6666 9999999999999999999999999988643 45665
No 10
>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=92.54 E-value=0.078 Score=30.68 Aligned_cols=33 Identities=27% Similarity=0.267 Sum_probs=29.4
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|++- +++.+.++-|-+++.++.|+++|+|....
T Consensus 23 t~~~----la~~l~~~~~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 23 TQSE----LAERLGISKSTVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp EHHH----HHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence 7777 99999999999999999999999998864
No 11
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=91.57 E-value=0.16 Score=27.76 Aligned_cols=33 Identities=21% Similarity=0.223 Sum_probs=28.2
Q ss_pred cCCcccccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 45 TGNEAGFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 45 s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
......+++.+.++-+-++++|+.|+++|+|..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 333455899999999999999999999999975
No 12
>PRK03837 transcriptional regulator NanR; Provisional
Probab=91.20 E-value=0.18 Score=36.02 Aligned_cols=34 Identities=12% Similarity=0.266 Sum_probs=30.5
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+|..+++++.||=+-.|.||+.|+++|+|...-.
T Consensus 39 ~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~ 72 (241)
T PRK03837 39 SERELMAFFGVGRPAVREALQALKRKGLVQISHG 72 (241)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4667999999999999999999999999988643
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=90.87 E-value=0.33 Score=28.40 Aligned_cols=34 Identities=29% Similarity=0.289 Sum_probs=28.3
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
|++- +++.+.++-+-++++|+.|+++|+|.....
T Consensus 20 t~~~----l~~~~~~~~~~vs~~i~~L~~~glv~~~~~ 53 (68)
T PF13463_consen 20 TQSD----LAERLGISKSTVSRIIKKLEEKGLVEKERD 53 (68)
T ss_dssp EHHH----HHHHTT--HHHHHHHHHHHHHTTSEEEEEE
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHHHCCCEEecCC
Confidence 6666 999999999999999999999999987743
No 14
>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=90.74 E-value=0.16 Score=36.57 Aligned_cols=34 Identities=21% Similarity=0.161 Sum_probs=30.2
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
.|.-++++++||=.-.|+||++|+++|+|.....
T Consensus 26 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G 59 (233)
T TIGR02404 26 SEHELMDQYGASRETVRKALNLLTEAGYIQKIQG 59 (233)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4566999999999999999999999999987643
No 15
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=90.52 E-value=0.32 Score=26.68 Aligned_cols=37 Identities=19% Similarity=0.231 Sum_probs=29.9
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEE
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYT 88 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYT 88 (93)
+++.+.++-+-++++|+.|+++|+|...... ....|+
T Consensus 16 i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~-~~~~~~ 52 (66)
T smart00418 16 LAEILGLSQSTVSHHLKKLREAGLVESRREG-KRVYYS 52 (66)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCeeeeecC-CEEEEE
Confidence 8888999999999999999999999866543 334454
No 16
>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=90.46 E-value=0.17 Score=36.02 Aligned_cols=34 Identities=26% Similarity=0.296 Sum_probs=30.2
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
.|.-+++++.+|=.-.|+||++|+++|+|.....
T Consensus 34 sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G 67 (238)
T TIGR02325 34 AEMQLAERFGVNRHTVRRAIAALVERGLLRAEQG 67 (238)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4566999999999999999999999999987643
No 17
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=90.23 E-value=0.27 Score=37.65 Aligned_cols=41 Identities=27% Similarity=0.227 Sum_probs=35.1
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEE
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIY 87 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IY 87 (93)
|++. +++.+.++-+-+++.|+.|+++|+|.....-..|.|+
T Consensus 23 S~~e----LA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~ 63 (217)
T PRK14165 23 SSSE----FANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLIT 63 (217)
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEE
Confidence 7777 9999999999999999999999999887655555554
No 18
>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=89.38 E-value=0.34 Score=27.53 Aligned_cols=28 Identities=18% Similarity=0.246 Sum_probs=26.1
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
+++.+.|+-+-++++|+.|+++|+|...
T Consensus 31 la~~~~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 31 LAEELGVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 8899999999999999999999998754
No 19
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=89.30 E-value=0.26 Score=35.70 Aligned_cols=60 Identities=23% Similarity=0.208 Sum_probs=41.9
Q ss_pred hhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 7 GTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 7 ~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
..|.++..++.+ +--...-+.|. ||= .|.-+++.+.+|=.-+|+||.+|+++|+|.....
T Consensus 9 p~y~qI~~~i~~-----~I~~G~~~~g~----kLP-----sE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G 68 (241)
T PRK11402 9 LLYATVRQRLLD-----DIAQGVYQAGQ----QIP-----TENELCTQYNVSRITIRKAISDLVADGVLIRWQG 68 (241)
T ss_pred cHHHHHHHHHHH-----HHHcCCCCCCC----cCc-----CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 346666666655 11111224455 665 4555999999999999999999999999987643
No 20
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=89.25 E-value=0.27 Score=35.84 Aligned_cols=34 Identities=18% Similarity=0.282 Sum_probs=30.0
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
.|.-+++++.||-.-.|+||++|+++|+|...-.
T Consensus 31 sE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G 64 (240)
T PRK09764 31 TESALQTEFGVSRVTVRQALRQLVEQQILESIQG 64 (240)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4556999999999999999999999999987643
No 21
>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=89.15 E-value=0.26 Score=28.52 Aligned_cols=33 Identities=30% Similarity=0.280 Sum_probs=28.9
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|.+- +++.++++-|-+.+.++.|+++|+|..-.
T Consensus 19 ~~~~----la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 19 TQSE----LAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp EHHH----HHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHH----HHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 6666 99999999999999999999999998764
No 22
>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=88.91 E-value=0.27 Score=35.42 Aligned_cols=34 Identities=18% Similarity=0.200 Sum_probs=29.8
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
.|.-+++++++|=.-.|+||.+|+++|+|...-.
T Consensus 27 sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G 60 (230)
T TIGR02018 27 SEHELVAQYGCSRMTVNRALRELTDAGLLERRQG 60 (230)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4556999999999999999999999999977543
No 23
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=88.83 E-value=0.5 Score=34.95 Aligned_cols=64 Identities=20% Similarity=0.200 Sum_probs=44.8
Q ss_pred hhhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeeccc
Q 038379 6 QGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYAS 83 (93)
Q Consensus 6 k~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~ 83 (93)
...|.++..++.+ +-....-+.|. ||= .|.-+++++.+|=.=.|+||++|+++|+|........
T Consensus 6 ~plY~qI~~~i~~-----~I~~G~~~~G~----~LP-----sE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~Gt 69 (236)
T COG2188 6 MPLYQQIAEDIRQ-----RIESGELPPGD----KLP-----SERELAEQFGVSRMTVRKALDELVEEGLIVRRQGKGT 69 (236)
T ss_pred CccHHHHHHHHHH-----HHHhCCCCCCC----CCC-----CHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecCee
Confidence 3456677766666 11112233444 553 3455999999999999999999999999998765543
No 24
>PF13730 HTH_36: Helix-turn-helix domain
Probab=88.53 E-value=0.32 Score=28.03 Aligned_cols=27 Identities=30% Similarity=0.342 Sum_probs=24.5
Q ss_pred ccccceeeeeHHHHHHHHHHHHHcCCe
Q 038379 49 AGFNCLVHISGSLASRAIKDLVARGSI 75 (93)
Q Consensus 49 ~~~~~rlkI~gSLAr~alkdL~~kG~I 75 (93)
.-+++.++++-+=.+++|++|+++|+|
T Consensus 29 ~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 29 ETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 348999999999999999999999987
No 25
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=88.40 E-value=1 Score=25.07 Aligned_cols=37 Identities=22% Similarity=0.222 Sum_probs=30.0
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEE
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYT 88 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYT 88 (93)
+++.+.|+-+-++++++.|+++|+|...... ....|.
T Consensus 26 i~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~ 62 (78)
T cd00090 26 LAERLGLSQSTVSRHLKKLEEAGLVESRREG-RRVYYS 62 (78)
T ss_pred HHHHHCcCHhHHHHHHHHHHHCCCeEEEEec-cEEEEE
Confidence 7888999999999999999999999886543 334443
No 26
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=88.19 E-value=0.37 Score=35.14 Aligned_cols=34 Identities=12% Similarity=0.225 Sum_probs=30.1
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+|..+++++.||-+-.|.||+.|++.|+|...-.
T Consensus 35 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 68 (257)
T PRK10225 35 PEREIAEMLDVTRTVVREALIMLEIKGLVEVRRG 68 (257)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3556999999999999999999999999987654
No 27
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=88.15 E-value=0.38 Score=29.48 Aligned_cols=30 Identities=20% Similarity=0.273 Sum_probs=27.7
Q ss_pred cccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 50 GFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 50 ~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
.+++++.++.|-..+.++.|+++|+|+..-
T Consensus 41 ~la~~l~i~~~~vt~~l~~Le~~glv~r~~ 70 (126)
T COG1846 41 ELAERLGLDRSTVTRLLKRLEDKGLIERLR 70 (126)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence 388999999999999999999999998873
No 28
>PRK14999 histidine utilization repressor; Provisional
Probab=87.95 E-value=0.33 Score=35.29 Aligned_cols=33 Identities=21% Similarity=0.271 Sum_probs=29.7
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
.|..+++++.+|=+-.|+||.+|+++|+|...-
T Consensus 38 sE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 38 SEAELVAQYGFSRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 466699999999999999999999999997654
No 29
>PF08220 HTH_DeoR: DeoR-like helix-turn-helix domain; InterPro: IPR001034 The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after the Escherichia coli protein DeoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively. DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerisation domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping [, ].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=87.88 E-value=0.58 Score=28.26 Aligned_cols=33 Identities=15% Similarity=0.160 Sum_probs=29.7
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|..- +++.+.||-+=+|+=|.+|+++|+|+.+.
T Consensus 16 s~~e----la~~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 16 SVKE----LAEEFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred EHHH----HHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 6666 99999999999999999999999988763
No 30
>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=87.65 E-value=0.34 Score=34.04 Aligned_cols=32 Identities=19% Similarity=0.228 Sum_probs=28.4
Q ss_pred cccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 48 EAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 48 ~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|..+++++.||-+-.|.||+.|++.|+|...-
T Consensus 37 e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~ 68 (212)
T TIGR03338 37 ESDIAARLGVSRGPVREAFRALEEAGLVRNEK 68 (212)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEec
Confidence 34499999999999999999999999997643
No 31
>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=87.57 E-value=0.66 Score=30.70 Aligned_cols=46 Identities=24% Similarity=0.335 Sum_probs=31.1
Q ss_pred EeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEeecC
Q 038379 42 FTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYTRVIN 92 (93)
Q Consensus 42 ~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR~~~ 92 (93)
+|.|- ++|++.|+-|+--.|||.|++-|+|..=| ..---.|-+..|
T Consensus 5 lvas~----iAd~~GiTRSvIVNALRKleSaGvIesrS-lGmKGT~ikvlN 50 (61)
T PF08222_consen 5 LVASK----IADRVGITRSVIVNALRKLESAGVIESRS-LGMKGTYIKVLN 50 (61)
T ss_dssp E-HHH----HHHHHT--HHHHHHHHHHHHHTTSEEEEE-TTSS-EEEEE--
T ss_pred ehHHH----HHHHhCccHHHHHHHHHHHHhcCceeecc-cCCCceeeeeec
Confidence 36777 99999999999999999999999997322 112246666654
No 32
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=87.27 E-value=0.39 Score=34.91 Aligned_cols=58 Identities=22% Similarity=0.251 Sum_probs=43.0
Q ss_pred hhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 7 GTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 7 ~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
..|..+...+.+-+ . + .-+.|. ||= .|.-+++.+.||=.-+|+||++|+++|+|....
T Consensus 12 p~Y~qi~~~L~~~I---~--~-~~~~G~----~LP-----sE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~ 69 (241)
T PRK10079 12 TRYQEIAAKLEQEL---R--Q-HYRCGD----YLP-----AEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQ 69 (241)
T ss_pred CHHHHHHHHHHHHH---h--c-ccCCCC----cCC-----CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 35777777777721 1 2 334555 654 455699999999999999999999999998654
No 33
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=86.79 E-value=0.56 Score=29.25 Aligned_cols=29 Identities=14% Similarity=0.198 Sum_probs=26.6
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+++.++|+-|-.+++++.|+++|+|....
T Consensus 5 la~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 5 IAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 78899999999999999999999998754
No 34
>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=86.66 E-value=0.45 Score=34.19 Aligned_cols=33 Identities=12% Similarity=0.243 Sum_probs=29.5
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+|..+++++.||=+-.|.||+.|++.|+|...-
T Consensus 32 sE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 32 AERELSELIGVTRTTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence 455699999999999999999999999998654
No 35
>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=86.12 E-value=0.41 Score=29.59 Aligned_cols=32 Identities=13% Similarity=0.201 Sum_probs=28.4
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
+++- ++++++|+-|=+..+++.|.++|+|..-
T Consensus 24 ~~~~----iA~~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 24 RTKD----IAERLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp BHHH----HHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred cHHH----HHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence 7777 9999999999999999999999999753
No 36
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=85.43 E-value=0.56 Score=34.27 Aligned_cols=33 Identities=18% Similarity=0.202 Sum_probs=29.3
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+|.-+++++.||=+-.|.||+.|++.|+|...-
T Consensus 28 sE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~ 60 (253)
T PRK10421 28 AERQLAMQLGVSRNSLREALAKLVSEGVLLSRR 60 (253)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 355599999999999999999999999998653
No 37
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=85.09 E-value=0.77 Score=28.26 Aligned_cols=36 Identities=17% Similarity=0.237 Sum_probs=29.5
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeecc
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYA 82 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~ 82 (93)
|..- ++..++++-+..+..|..|+.+|.|+.+...+
T Consensus 16 S~~e----La~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 16 SLAE----LAREFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp EHHH----HHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 5555 89999999999999999999999999987654
No 38
>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=84.85 E-value=0.58 Score=27.05 Aligned_cols=29 Identities=21% Similarity=0.272 Sum_probs=27.2
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+++.+.++-+-++++|+.|+++|+|....
T Consensus 31 la~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 31 IADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 99999999999999999999999998754
No 39
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=84.71 E-value=0.62 Score=33.82 Aligned_cols=34 Identities=21% Similarity=0.171 Sum_probs=30.2
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+|..+++++.||=+-.|.||+.|++.|+|...-.
T Consensus 36 sE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~ 69 (254)
T PRK09464 36 PERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG 69 (254)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4566999999999999999999999999987643
No 40
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=84.64 E-value=0.84 Score=30.90 Aligned_cols=33 Identities=15% Similarity=0.306 Sum_probs=30.5
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|++- +++++.++-|-..++++.|+++|+|....
T Consensus 56 t~~e----La~~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 56 TPVE----LKKVLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred CHHH----HHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 6666 99999999999999999999999999874
No 41
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=84.63 E-value=0.63 Score=33.17 Aligned_cols=32 Identities=13% Similarity=0.113 Sum_probs=28.7
Q ss_pred cccceeeeeHHHHHHHHHHHHHcCCeeeeeec
Q 038379 50 GFNCLVHISGSLASRAIKDLVARGSIRMISAY 81 (93)
Q Consensus 50 ~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~ 81 (93)
.+++++.||-+-.|.||+.|++.|+|..+...
T Consensus 35 eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~ 66 (224)
T PRK11534 35 LLTSRYALGVGPLREALSQLVAERLVTVVNQK 66 (224)
T ss_pred HHHHHHCCChHHHHHHHHHHHHCCCEEEeCCC
Confidence 49999999999999999999999999876443
No 42
>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=84.58 E-value=1.1 Score=35.80 Aligned_cols=38 Identities=11% Similarity=0.274 Sum_probs=27.6
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee--eeccceEEEE
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI--SAYASQQIYT 88 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V--s~~~~Q~IYT 88 (93)
+-.+.++.-+...++||.|++|++||.| .++.+..||-
T Consensus 106 i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Ym 145 (327)
T PF05158_consen 106 IKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYM 145 (327)
T ss_dssp HHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEE
T ss_pred HHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEE
Confidence 3456677788999999999999999999 4666888885
No 43
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=84.53 E-value=0.65 Score=33.68 Aligned_cols=34 Identities=21% Similarity=0.167 Sum_probs=30.2
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+|..+++++.||=+-.|.||+.|+..|+|...-.
T Consensus 33 sE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 33 SERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 4566999999999999999999999999987643
No 44
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=84.50 E-value=0.65 Score=33.93 Aligned_cols=33 Identities=18% Similarity=0.121 Sum_probs=29.2
Q ss_pred cccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 48 EAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 48 ~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
|..+++++.||=+-.|.||+.|++.|+|.....
T Consensus 35 E~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~ 67 (253)
T PRK11523 35 ERFIADEKNVSRTVVREAIIMLEVEGYVEVRKG 67 (253)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 445999999999999999999999999986543
No 45
>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=84.35 E-value=0.87 Score=29.75 Aligned_cols=33 Identities=12% Similarity=0.056 Sum_probs=29.8
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|++. +++.+.++-+-..+.++.|+++|+|....
T Consensus 44 t~~e----la~~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 44 EFTQ----LANQACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred CHHH----HHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence 6666 99999999999999999999999999873
No 46
>PF14502 HTH_41: Helix-turn-helix domain
Probab=84.29 E-value=0.75 Score=28.87 Aligned_cols=37 Identities=22% Similarity=0.262 Sum_probs=32.3
Q ss_pred eEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 39 KLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 39 Kli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
++= |.+- +++++.++-.....||+.|++.|-|+..++
T Consensus 5 Ri~-tI~e----~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~r 41 (48)
T PF14502_consen 5 RIP-TISE----YSEKFGVSRGTIQNALKFLEENGAIKLESR 41 (48)
T ss_pred ccC-CHHH----HHHHhCcchhHHHHHHHHHHHCCcEEeeec
Confidence 554 6666 899999999999999999999999998764
No 47
>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=84.23 E-value=0.65 Score=32.94 Aligned_cols=33 Identities=18% Similarity=0.136 Sum_probs=29.5
Q ss_pred cccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 48 EAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 48 ~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
|+.+++++.|+=...|+||+.|+++|+|.....
T Consensus 28 E~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g 60 (231)
T TIGR03337 28 ERDLGERFNTTRVTIREALQQLEAEGLIYREDR 60 (231)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeCC
Confidence 556999999999999999999999999987653
No 48
>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=83.83 E-value=0.79 Score=27.40 Aligned_cols=28 Identities=25% Similarity=0.318 Sum_probs=26.1
Q ss_pred ccccceeeeeHHHHHHHHHHHHHcCCee
Q 038379 49 AGFNCLVHISGSLASRAIKDLVARGSIR 76 (93)
Q Consensus 49 ~~~~~rlkI~gSLAr~alkdL~~kG~Ik 76 (93)
.-+++.+.++-.-..+.|++|.++|+|.
T Consensus 32 ~~iA~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 32 EEIADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp HHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 3399999999999999999999999997
No 49
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=81.93 E-value=1.1 Score=33.68 Aligned_cols=33 Identities=24% Similarity=0.241 Sum_probs=30.1
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|..- +++++.++-+=+||=|++|+++|+|+.+-
T Consensus 21 ~~~e----la~~l~vS~~TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 21 TVEK----VIERLGISPATARRDINKLDESGKLKKVR 53 (251)
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence 7777 99999999999999999999999998753
No 50
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=81.90 E-value=1.3 Score=33.49 Aligned_cols=33 Identities=9% Similarity=0.114 Sum_probs=30.2
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+..- +++.+.++.+=+||=|++|+++|+|+.+-
T Consensus 21 ~v~e----La~~l~VS~~TIRRDL~~Le~~g~l~r~~ 53 (256)
T PRK10434 21 SVEE----LAQYFDTTGTTIRKDLVILEHAGTVIRTY 53 (256)
T ss_pred EHHH----HHHHHCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 7777 99999999999999999999999998763
No 51
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=81.54 E-value=1.2 Score=24.22 Aligned_cols=33 Identities=15% Similarity=0.243 Sum_probs=28.7
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|... +++.+.++=+-+++.|+.|+++|+|....
T Consensus 16 s~~~----l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 16 SVEE----LAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred CHHH----HHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 5556 88999999999999999999999997653
No 52
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=81.49 E-value=0.85 Score=33.02 Aligned_cols=29 Identities=17% Similarity=0.273 Sum_probs=27.4
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+++.++++=|-|.+||+-|.+.|+|...-
T Consensus 48 lae~lnr~rStv~rsl~~L~~~GlV~Rek 76 (126)
T COG3355 48 LAEILNRSRSTVYRSLQNLLEAGLVEREK 76 (126)
T ss_pred HHHHHCccHHHHHHHHHHHHHcCCeeeee
Confidence 99999999999999999999999998763
No 53
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=81.39 E-value=0.74 Score=32.85 Aligned_cols=30 Identities=13% Similarity=0.138 Sum_probs=27.6
Q ss_pred cccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 50 GFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 50 ~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
.+++++.||=+-.|.||+.|++.|+|....
T Consensus 39 ~La~~lgVSRtpVREAL~~L~~eGLV~~~~ 68 (221)
T PRK11414 39 NLAEQLGMSITPVREALLRLVSVNALSVAP 68 (221)
T ss_pred HHHHHHCCCchhHHHHHHHHHHCCCEEecC
Confidence 499999999999999999999999998653
No 54
>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=81.36 E-value=0.95 Score=29.76 Aligned_cols=33 Identities=21% Similarity=0.136 Sum_probs=30.3
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|++. +++.+.++-|-..++|+.|+++|+|....
T Consensus 45 t~~e----L~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 45 TLKE----IIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred cHHH----HHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 6666 99999999999999999999999999874
No 55
>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=81.17 E-value=0.89 Score=29.83 Aligned_cols=32 Identities=34% Similarity=0.225 Sum_probs=28.9
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
|.+- +++.+.++=+-.+++|++|+++|+|+.-
T Consensus 49 s~~e----La~~~g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 49 TATV----IAELTGLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence 6666 9999999999999999999999999853
No 56
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=80.21 E-value=0.93 Score=27.23 Aligned_cols=32 Identities=22% Similarity=0.324 Sum_probs=28.0
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
|++- +++.+.++-+-.+++|++|+++|+|...
T Consensus 26 ~~~~----la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 26 SVSE----LAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred CHHH----HHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 5555 7888999999999999999999999876
No 57
>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=79.92 E-value=0.93 Score=36.43 Aligned_cols=29 Identities=28% Similarity=0.274 Sum_probs=27.0
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+++++.|+-|..++|++.|++.|+|+.-+
T Consensus 204 LAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 204 IADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 99999999999999999999999997644
No 58
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=79.61 E-value=1.8 Score=32.29 Aligned_cols=25 Identities=24% Similarity=0.381 Sum_probs=21.7
Q ss_pred eeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 54 LVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 54 rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
..+=+||++|.+|+.||+-|+|+..
T Consensus 90 ~~~~sg~iiR~~LqqLE~~glVek~ 114 (150)
T PRK09333 90 FVKGSGSIIRKILQQLEKAGLVEKT 114 (150)
T ss_pred cccCccHHHHHHHHHHHHCCCeeeC
Confidence 4456899999999999999999864
No 59
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=79.50 E-value=1.9 Score=32.67 Aligned_cols=32 Identities=16% Similarity=0.160 Sum_probs=29.9
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
|..- +++++.|+-+=+||-|++|+++|+|+.+
T Consensus 21 ~~~e----la~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 21 STEE----LVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred eHHH----HHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 7777 9999999999999999999999999886
No 60
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=79.41 E-value=1.1 Score=33.60 Aligned_cols=31 Identities=23% Similarity=0.345 Sum_probs=28.4
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
.|.-+++++.||=+.-|.||+.|+++|+|..
T Consensus 36 ~EreLae~fgVSR~~vREAl~~L~a~Glve~ 66 (241)
T COG2186 36 SERELAERFGVSRTVVREALKRLEAKGLVEI 66 (241)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHCCCeee
Confidence 4666999999999999999999999999965
No 61
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=78.86 E-value=1.3 Score=27.60 Aligned_cols=34 Identities=12% Similarity=0.135 Sum_probs=30.2
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
|... +++.+.|+-+-+++.|..|+++|+|.....
T Consensus 24 ta~e----La~~lgl~~~~v~r~L~~L~~~G~V~~~~~ 57 (68)
T smart00550 24 TALQ----LAKNLGLPKKEVNRVLYSLEKKGKVCKQGG 57 (68)
T ss_pred CHHH----HHHHHCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 6666 999999999999999999999999977543
No 62
>PRK10870 transcriptional repressor MprA; Provisional
Probab=77.79 E-value=1.7 Score=31.21 Aligned_cols=33 Identities=24% Similarity=0.335 Sum_probs=30.0
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|++- +++.+.++.+-+.+.++.|+++|+|....
T Consensus 73 t~~e----La~~l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 73 QPSE----LSCALGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred CHHH----HHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 5555 89999999999999999999999999884
No 63
>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=77.77 E-value=2 Score=27.06 Aligned_cols=37 Identities=19% Similarity=0.159 Sum_probs=31.0
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeeccc
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYAS 83 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~ 83 (93)
|... +++++.++=+..++.++.|++.|+|+.......
T Consensus 27 s~~e----iA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~G 63 (83)
T PF02082_consen 27 SSKE----IAERLGISPSYLRKILQKLKKAGLIESSRGRGG 63 (83)
T ss_dssp EHHH----HHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTS
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCC
Confidence 7777 999999999999999999999999987654433
No 64
>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=77.65 E-value=2.4 Score=31.17 Aligned_cols=26 Identities=23% Similarity=0.378 Sum_probs=21.1
Q ss_pred eeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 54 LVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 54 rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
..+=+||++|.+|+.||+-|+|....
T Consensus 89 ~~~asg~iiR~~LqqLE~~glv~k~~ 114 (139)
T PF01090_consen 89 FVKASGSIIRKILQQLEKAGLVEKDP 114 (139)
T ss_dssp E--CHHHHHHHHHHHHHHTTSEEEET
T ss_pred CCCCCcHHHHHHHHHHHHCCCEEecC
Confidence 34567899999999999999998764
No 65
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=76.54 E-value=2.1 Score=33.92 Aligned_cols=49 Identities=29% Similarity=0.284 Sum_probs=38.7
Q ss_pred ccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEE
Q 038379 32 EGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYASQQI 86 (93)
Q Consensus 32 ~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~I 86 (93)
+|+.-++|+ |++- ++.++.+|+--|.|.|++|+..|.|..-.....|.|
T Consensus 12 ~~a~~~~~~--t~~e----la~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i 60 (214)
T COG1339 12 RGAVRGVKV--TSSE----LAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLI 60 (214)
T ss_pred hhhhcCccc--cHHH----HHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEE
Confidence 455444443 7777 999999999999999999999999987765566655
No 66
>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=76.39 E-value=1.3 Score=28.01 Aligned_cols=36 Identities=22% Similarity=0.195 Sum_probs=27.1
Q ss_pred eccCCcccccceeeee-HHHHHHHHHHHHHcCCeeeeee
Q 038379 43 TSTGNEAGFNCLVHIS-GSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~-gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
.||. ..+.+.+.++ -|-+..-|+.|+++|.|+....
T Consensus 25 ~Pt~--rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 25 PPTV--REIAEALGLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp ---H--HHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred CCCH--HHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence 5665 3377888886 8889999999999999987643
No 67
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=76.35 E-value=2.1 Score=30.90 Aligned_cols=29 Identities=14% Similarity=0.137 Sum_probs=27.1
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
++++++|+-|-+..+++.|.++|+|..+-
T Consensus 30 iA~~L~Vsp~sVt~ml~rL~~~GlV~~~~ 58 (154)
T COG1321 30 IAERLKVSPPSVTEMLKRLERLGLVEYEP 58 (154)
T ss_pred HHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence 89999999999999999999999998753
No 68
>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=75.90 E-value=2.2 Score=28.50 Aligned_cols=32 Identities=13% Similarity=0.178 Sum_probs=28.7
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
|..- +++++.|+-+.+++.|+.|++.|+|...
T Consensus 27 s~~e----ia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 27 SAAE----IAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred cHHH----HHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 5555 8999999999999999999999999764
No 69
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=75.72 E-value=2.5 Score=28.98 Aligned_cols=33 Identities=12% Similarity=0.154 Sum_probs=29.4
Q ss_pred cccceeeeeHHHHHHHHHHHHHcCCeeeeeecc
Q 038379 50 GFNCLVHISGSLASRAIKDLVARGSIRMISAYA 82 (93)
Q Consensus 50 ~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~ 82 (93)
-+++++.|+-+-.|++++.|.+.|+|+......
T Consensus 30 ~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~ 62 (141)
T PRK11014 30 EVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKN 62 (141)
T ss_pred HHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCC
Confidence 399999999999999999999999998775443
No 70
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=75.29 E-value=3.7 Score=31.33 Aligned_cols=25 Identities=20% Similarity=0.177 Sum_probs=21.8
Q ss_pred eeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 54 LVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 54 rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
..+=+||++|.+|+.||+-|++...
T Consensus 114 ~~~aSg~iiR~~LQqLE~~glVek~ 138 (169)
T PTZ00095 114 TVRASGKILRWICQQLEKLGLVEQG 138 (169)
T ss_pred ccCCchHHHHHHHHHHHHCCCEEec
Confidence 3456899999999999999999865
No 71
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=75.13 E-value=2.6 Score=31.88 Aligned_cols=33 Identities=15% Similarity=0.228 Sum_probs=30.5
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+..- ++++++||..=.||=|++|+++|+++.+-
T Consensus 21 ~v~e----La~~~~VS~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 21 SVEE----LAELFGVSEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred EHHH----HHHHhCCCHHHHHHhHHHHHHCCcEEEEe
Confidence 7777 99999999999999999999999999863
No 72
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=74.55 E-value=3.6 Score=32.26 Aligned_cols=41 Identities=20% Similarity=0.199 Sum_probs=33.4
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEE
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIY 87 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IY 87 (93)
|.+- +...+..+=+=.+|+|++||++|+|+..-.-..+.|-
T Consensus 212 ~Q~e----L~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V~ 252 (258)
T COG2512 212 TQAE----LRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIVE 252 (258)
T ss_pred eHHH----HHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEEE
Confidence 5555 7777888889999999999999999998766665543
No 73
>PRK04158 transcriptional repressor CodY; Validated
Probab=74.07 E-value=2.5 Score=33.87 Aligned_cols=31 Identities=23% Similarity=0.275 Sum_probs=28.7
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
+.|- ++||+.|+-|+--.|||.|++-|+|.-
T Consensus 203 vASk----iADrvgITRSVIVNALRK~ESAGvIES 233 (256)
T PRK04158 203 VASK----IADRVGITRSVIVNALRKLESAGVIES 233 (256)
T ss_pred Eeee----cccccCCchhhhhhhhhhhhcccceee
Confidence 5777 899999999999999999999999964
No 74
>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=73.38 E-value=2.3 Score=25.28 Aligned_cols=33 Identities=27% Similarity=0.203 Sum_probs=28.8
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|.+- +++.+.++-|-+++-|+.|++.|+|+..-
T Consensus 26 t~~e----la~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 26 TVSE----LAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp EHHH----HHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred CHHH----HHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 6667 89999999999999999999999998753
No 75
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=73.19 E-value=2.9 Score=26.63 Aligned_cols=28 Identities=25% Similarity=0.231 Sum_probs=26.2
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
+++.+.++-+-+++.++.|+++|.|+.+
T Consensus 23 la~~l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 23 LAKKVGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCeece
Confidence 8999999999999999999999999843
No 76
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=73.15 E-value=2 Score=28.75 Aligned_cols=33 Identities=15% Similarity=0.197 Sum_probs=29.8
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|++- +++++.++-|-..+.++.|+++|+|....
T Consensus 48 t~~e----La~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 48 SQIQ----LAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred CHHH----HHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 5555 99999999999999999999999999884
No 77
>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=73.12 E-value=6.2 Score=27.83 Aligned_cols=34 Identities=26% Similarity=0.435 Sum_probs=29.5
Q ss_pred eeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEee
Q 038379 56 HISGSLASRAIKDLVARGSIRMISAYASQQIYTRV 90 (93)
Q Consensus 56 kI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR~ 90 (93)
+|+-+.+.++|..|+++|.|..= .+..|.||--.
T Consensus 29 ~~~K~~v~k~Ld~L~~~g~i~~K-~~GKqkiY~~~ 62 (169)
T PF07106_consen 29 KVGKTAVQKALDSLVEEGKIVEK-EYGKQKIYFAN 62 (169)
T ss_pred hccHHHHHHHHHHHHhCCCeeee-eecceEEEeeC
Confidence 48889999999999999999774 48999999754
No 78
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=70.84 E-value=3.9 Score=31.26 Aligned_cols=34 Identities=12% Similarity=0.047 Sum_probs=30.6
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
|..- +++.+.|+.+=+||=|+.|+++|+++.+-.
T Consensus 33 tv~e----La~~l~VS~~TIRRDL~~Le~~G~l~r~~G 66 (269)
T PRK09802 33 QVND----LSALYGVSTVTIRNDLAFLEKQGIAVRAYG 66 (269)
T ss_pred eHHH----HHHHHCCCHHHHHHHHHHHHhCCCeEEEeC
Confidence 6666 999999999999999999999999997643
No 79
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=70.52 E-value=2.7 Score=25.66 Aligned_cols=32 Identities=22% Similarity=0.157 Sum_probs=28.8
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
|.+- +++.+.++-|-+++.|+.|++.|+|...
T Consensus 22 t~~~----ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 22 TLAE----LAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred CHHH----HHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 5666 8999999999999999999999999874
No 80
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=70.20 E-value=3.8 Score=33.34 Aligned_cols=32 Identities=22% Similarity=0.241 Sum_probs=29.2
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
+.|. ++||+.|+-|+--.|||.|++.|.|.-=
T Consensus 206 vASk----iADrvGITRSVIVNALRKlESAGvIeSR 237 (261)
T COG4465 206 VASK----IADRVGITRSVIVNALRKLESAGVIESR 237 (261)
T ss_pred eehh----hhhhhCchHHHHHHHHHHhhhcCceeec
Confidence 5788 9999999999999999999999999643
No 81
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=70.14 E-value=2.9 Score=26.39 Aligned_cols=27 Identities=19% Similarity=0.258 Sum_probs=22.4
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
++...++|-+.+++.|++|+++|+|+.
T Consensus 25 i~~~~~L~~~~~~~yL~~L~~~gLI~~ 51 (77)
T PF14947_consen 25 IMYKANLNYSTLKKYLKELEEKGLIKK 51 (77)
T ss_dssp HHTTST--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHhCcCHHHHHHHHHHHHHCcCeeC
Confidence 677888999999999999999999943
No 82
>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=70.08 E-value=3.7 Score=27.03 Aligned_cols=32 Identities=16% Similarity=0.176 Sum_probs=29.0
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
|... +++.++|+-+..++.++.|++.|+|...
T Consensus 27 s~~e----ia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 27 SVKE----IAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred cHHH----HHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 6666 9999999999999999999999999754
No 83
>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=69.87 E-value=5.6 Score=28.71 Aligned_cols=30 Identities=20% Similarity=0.173 Sum_probs=28.1
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+++.+.++-|-+++.|+.|+++|+|+....
T Consensus 163 ia~~l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 163 IAKKLGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 899999999999999999999999998864
No 84
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=69.29 E-value=5 Score=26.70 Aligned_cols=30 Identities=33% Similarity=0.294 Sum_probs=27.8
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+++++.++-+=.++-++.|+++|+|+-...
T Consensus 28 ia~~lglS~~~v~~Ri~~L~~~GiI~~~~~ 57 (154)
T COG1522 28 LAERVGLSPSTVLRRIKRLEEEGVIKGYTA 57 (154)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCceeeEEE
Confidence 899999999999999999999999998754
No 85
>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=69.01 E-value=5.3 Score=28.83 Aligned_cols=32 Identities=28% Similarity=0.318 Sum_probs=28.9
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
|.+- +++++.|+-+-+++.|+.|+++|+|...
T Consensus 17 t~~e----LA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 17 TAAA----LAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 5555 8999999999999999999999999876
No 86
>COG3177 Fic family protein [Function unknown]
Probab=67.94 E-value=4 Score=32.37 Aligned_cols=42 Identities=19% Similarity=0.446 Sum_probs=35.5
Q ss_pred EeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEE
Q 038379 42 FTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIY 87 (93)
Q Consensus 42 ~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IY 87 (93)
+|..- .....+|+-+=|++.|++|+++|.+..+....+...|
T Consensus 305 ~t~~~----~~~~~~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~~~~ 346 (348)
T COG3177 305 LTAAE----IEAILGVSKATATRDLKELLELGILEEVKGRGRSKLY 346 (348)
T ss_pred ccHHH----HHHHhCccHHHHHHHHHHHHhCCCeeecCCCCCceec
Confidence 46666 7788899999999999999999999999877665554
No 87
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=67.85 E-value=4.4 Score=27.59 Aligned_cols=28 Identities=7% Similarity=0.043 Sum_probs=25.9
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
+++.++|+-+=++++|+.|+++|+|...
T Consensus 28 la~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 28 IAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred HHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 8999999999999999999999999743
No 88
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=67.82 E-value=6.4 Score=25.08 Aligned_cols=30 Identities=13% Similarity=0.066 Sum_probs=26.4
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+++.+.|+-+-||.-|..|+..|.|+.+-.
T Consensus 21 iA~~~gls~~~aR~yL~~Le~eG~V~~~~~ 50 (62)
T PF04703_consen 21 IADALGLSIYQARYYLEKLEKEGKVERSPV 50 (62)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHCTSEEEES-
T ss_pred HHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 899999999999999999999999998643
No 89
>PRK11050 manganese transport regulator MntR; Provisional
Probab=67.47 E-value=3.4 Score=29.05 Aligned_cols=31 Identities=16% Similarity=0.295 Sum_probs=28.4
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
|++- +++.++|+-|-.+++|+.|+++|+|..
T Consensus 53 t~~e----LA~~l~is~stVsr~l~~Le~~GlI~r 83 (152)
T PRK11050 53 RQVD----IAARLGVSQPTVAKMLKRLARDGLVEM 83 (152)
T ss_pred CHHH----HHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 6666 999999999999999999999999865
No 90
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=67.37 E-value=4.3 Score=31.58 Aligned_cols=28 Identities=18% Similarity=0.198 Sum_probs=26.4
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
+++.++||-+-.++|++.|+++|+|...
T Consensus 35 la~~~~vsr~tv~~a~~~L~~~g~i~~~ 62 (431)
T PRK15481 35 LASELGVNRNTVAAAYKRLVTAGLAQSQ 62 (431)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 9999999999999999999999999754
No 91
>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=65.80 E-value=4.4 Score=23.50 Aligned_cols=31 Identities=19% Similarity=0.258 Sum_probs=26.9
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
|.+- +++++.++-|=+.+.++.|++.|+++.
T Consensus 20 t~~e----ia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 20 TLSE----IARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp EHHH----HHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CHHH----HHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 5566 899999999999999999999999874
No 92
>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=65.06 E-value=4.9 Score=22.99 Aligned_cols=25 Identities=24% Similarity=0.325 Sum_probs=19.1
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCe
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSI 75 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~I 75 (93)
+++.+..+---.+|++++|+++|+|
T Consensus 8 iA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 8 IADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp HHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 4455556666789999999999997
No 93
>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=63.98 E-value=6 Score=26.96 Aligned_cols=36 Identities=17% Similarity=0.098 Sum_probs=31.4
Q ss_pred EEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 40 LCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 40 li~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
.+ |... ++++++|+.+..++.++.|.+.|+|.-...
T Consensus 25 ~~-s~~~----ia~~~~ip~~~l~kil~~L~~~glv~s~~G 60 (135)
T TIGR02010 25 PV-TLAD----ISERQGISLSYLEQLFAKLRKAGLVKSVRG 60 (135)
T ss_pred cC-cHHH----HHHHHCcCHHHHHHHHHHHHHCCceEEEeC
Confidence 44 7777 999999999999999999999999986533
No 94
>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=63.46 E-value=5.4 Score=25.79 Aligned_cols=41 Identities=20% Similarity=0.267 Sum_probs=27.8
Q ss_pred hhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCe
Q 038379 22 LVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSI 75 (93)
Q Consensus 22 ~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~I 75 (93)
++|+ ..-+.+|. .... +..++.++-.=.|.||++|.+.|.|
T Consensus 55 ~i~~-~~~~~~Gv--------~v~~----I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 55 FIKQ-QPNSEEGV--------HVDE----IAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHC-----TTTE--------EHHH----HHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHh-cCCCCCcc--------cHHH----HHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 4444 45566665 3333 6777899999999999999999987
No 95
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=62.92 E-value=7.8 Score=27.22 Aligned_cols=28 Identities=18% Similarity=0.172 Sum_probs=26.3
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
++++++++.|-.++=|+.|++.|.|+-.
T Consensus 34 iA~~lglS~~tv~~Ri~rL~~~GvI~~~ 61 (164)
T PRK11169 34 LSKRVGLSPTPCLERVRRLERQGFIQGY 61 (164)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence 9999999999999999999999999853
No 96
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=61.43 E-value=5.5 Score=29.65 Aligned_cols=33 Identities=18% Similarity=0.087 Sum_probs=29.3
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|++- +++.+.+..|-+.+.|+.|+++|+|....
T Consensus 61 tq~e----La~~l~l~~sTvtr~l~rLE~kGlI~R~~ 93 (185)
T PRK13777 61 SISE----IAKFGVMHVSTAFNFSKKLEERGYLTFSK 93 (185)
T ss_pred CHHH----HHHHHCCCHhhHHHHHHHHHHCCCEEecC
Confidence 6666 88999999888999999999999999873
No 97
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=61.23 E-value=7.8 Score=26.52 Aligned_cols=30 Identities=13% Similarity=0.152 Sum_probs=26.7
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
++-++++.-.-++.++++|++.|+|..+..
T Consensus 27 ia~~l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 27 IARRLKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 566789999999999999999999998864
No 98
>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=61.07 E-value=12 Score=27.33 Aligned_cols=35 Identities=31% Similarity=0.322 Sum_probs=30.8
Q ss_pred EEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 40 LCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 40 li~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
++.|... +++.+.++=+--+++|++|+++|+|..+
T Consensus 74 v~~t~~~----ia~~l~iS~~Tv~r~ik~L~e~~iI~k~ 108 (165)
T PF05732_consen 74 VVATQKE----IAEKLGISKPTVSRAIKELEEKNIIKKI 108 (165)
T ss_pred EEeeHHH----HHHHhCCCHHHHHHHHHHHHhCCcEEEc
Confidence 4447666 9999999999999999999999999876
No 99
>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=60.35 E-value=31 Score=21.03 Aligned_cols=35 Identities=23% Similarity=0.176 Sum_probs=26.9
Q ss_pred eeeeeHHHHHHHHHHHHHcCCeeeeeec----cceEEEE
Q 038379 54 LVHISGSLASRAIKDLVARGSIRMISAY----ASQQIYT 88 (93)
Q Consensus 54 rlkI~gSLAr~alkdL~~kG~Ik~Vs~~----~~Q~IYT 88 (93)
...|+-+---.+|+.|+++|+|.....- ....+|+
T Consensus 26 ~~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~ 64 (75)
T PF03551_consen 26 FWKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYR 64 (75)
T ss_dssp TEETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEE
T ss_pred CcccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEE
Confidence 3567777788999999999999988654 3455664
No 100
>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=60.01 E-value=7.5 Score=25.09 Aligned_cols=36 Identities=17% Similarity=0.131 Sum_probs=26.8
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeecc
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYA 82 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~ 82 (93)
+.|. +--+|+|.=.=|.+.+..|++.|+|-+-....
T Consensus 22 S~S~----lQR~~rIGynrAariid~LE~~GiVs~~~~~~ 57 (65)
T PF09397_consen 22 SISL----LQRKFRIGYNRAARIIDQLEEEGIVSPANGSK 57 (65)
T ss_dssp CHHH----HHHHHT--HHHHHHHHHHHHHCTSBE---TTS
T ss_pred cHHH----HHHHhCCCHHHHHHHHHHHHHCCCCCCCCCCC
Confidence 5666 78899999999999999999999998875543
No 101
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=59.99 E-value=8.6 Score=29.08 Aligned_cols=25 Identities=20% Similarity=0.300 Sum_probs=21.8
Q ss_pred eeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 55 VHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 55 lkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
.+=+||+.|.+|++|++-|++...-
T Consensus 91 ~~gsgsI~RkilqqLE~~G~V~k~~ 115 (147)
T COG2238 91 RKGSGSIIRKVLQQLEKAGLVEKTP 115 (147)
T ss_pred hcCCchHHHHHHHHHHHCCceeecC
Confidence 4568999999999999999997654
No 102
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=58.95 E-value=2.6 Score=30.67 Aligned_cols=33 Identities=12% Similarity=-0.108 Sum_probs=29.8
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+... +++.+.+|.+=+||=|.+|+++|+++.+-
T Consensus 23 ~~~~----La~~~~vS~~TiRRDl~~L~~~g~~~r~~ 55 (185)
T PRK04424 23 TDEE----LAEKFGVSIQTIRLDRMELGIPELRERIK 55 (185)
T ss_pred EHHH----HHHHHCcCHHHHHHHHHHHhcchHHHHHH
Confidence 6666 99999999999999999999999998763
No 103
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=58.82 E-value=7.8 Score=29.13 Aligned_cols=28 Identities=32% Similarity=0.484 Sum_probs=24.4
Q ss_pred cceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 52 NCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 52 ~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
++--.|+|+=+.++|+.|.++|+|+.+-
T Consensus 110 ~eI~~iRGv~~~~~i~~L~e~glI~~~g 137 (184)
T COG1386 110 SEIEEIRGVAVSQVISTLLERGLIREVG 137 (184)
T ss_pred HHHHHHhCccHHHHHHHHHHCCCeEecC
Confidence 3455789999999999999999999985
No 104
>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=58.73 E-value=17 Score=23.19 Aligned_cols=29 Identities=21% Similarity=0.234 Sum_probs=22.3
Q ss_pred cccee-eeeHHHHHHHHHHHHHcCCeeeee
Q 038379 51 FNCLV-HISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 51 ~~~rl-kI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+..++ .|+-..-.+.|++|++.|+|....
T Consensus 24 l~~~l~~is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 24 LQRRLPGISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHHHSTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHhcchhHHHHHHHHHHHHHHcchhhccc
Confidence 34455 677788889999999999998864
No 105
>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=58.47 E-value=7.6 Score=25.13 Aligned_cols=35 Identities=17% Similarity=0.173 Sum_probs=29.7
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeec
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAY 81 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~ 81 (93)
+.|. +--+++|.=.=|.+.+..|++.|+|-+....
T Consensus 21 S~S~----lQR~~~IGynrAariid~lE~~GiV~p~~g~ 55 (63)
T smart00843 21 STSL----LQRRLRIGYNRAARLIDQLEEEGIVGPANGS 55 (63)
T ss_pred ChHH----HHHHHhcchhHHHHHHHHHHHCcCCCCCCCC
Confidence 5555 7889999999999999999999999886443
No 106
>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=58.46 E-value=31 Score=22.55 Aligned_cols=35 Identities=26% Similarity=0.195 Sum_probs=26.5
Q ss_pred eeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEee
Q 038379 56 HISGSLASRAIKDLVARGSIRMISAYASQQIYTRV 90 (93)
Q Consensus 56 kI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR~ 90 (93)
.|+-|-.=|+|+.|++.|+|..+....+...|...
T Consensus 39 ~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~ 73 (120)
T PF01475_consen 39 RISLATVYRTLDLLEEAGLIRKIEFGDGESRYELS 73 (120)
T ss_dssp T--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEES
T ss_pred CcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeec
Confidence 35555567999999999999999777677777654
No 107
>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=58.44 E-value=8.1 Score=22.07 Aligned_cols=30 Identities=23% Similarity=0.240 Sum_probs=26.0
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIR 76 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik 76 (93)
|++- +++.++++=|-.++=|+.|.+.|+|+
T Consensus 17 ~~~e----l~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 17 TVSE----LAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp EHHH----HHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred chhh----HHHhccccchHHHHHHHHHHHCcCee
Confidence 4555 89999999999999999999999986
No 108
>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=56.62 E-value=7.2 Score=28.87 Aligned_cols=29 Identities=21% Similarity=0.204 Sum_probs=24.7
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCe
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSI 75 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~I 75 (93)
|..- +++.++++-.+|+.+|.+++++|++
T Consensus 192 t~~~----l~~~~~ws~~~a~~~L~~~~~~G~l 220 (223)
T PF04157_consen 192 TASE----LAEKLGWSVERAKEALEELEREGLL 220 (223)
T ss_dssp EHHH----HHHHHTB-HHHHHHHHHHHHHTTSE
T ss_pred CHHH----HHHHhCCCHHHHHHHHHHHHhCCCE
Confidence 5555 7888999999999999999999987
No 109
>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=55.97 E-value=7.1 Score=26.25 Aligned_cols=29 Identities=14% Similarity=0.150 Sum_probs=26.6
Q ss_pred ccccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 49 AGFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 49 ~~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
.-+++.+.++-.-.+|+|++|.++|+|+.
T Consensus 147 ~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 147 QAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred HHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 34999999999999999999999999965
No 110
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=54.95 E-value=11 Score=24.14 Aligned_cols=28 Identities=14% Similarity=0.207 Sum_probs=24.0
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
+.+.+.++-|-.++-|+.|++.|+|+.-
T Consensus 20 L~~~l~lt~g~Ls~hL~~Le~~GyV~~~ 47 (80)
T PF13601_consen 20 LKEELGLTDGNLSKHLKKLEEAGYVEVE 47 (80)
T ss_dssp HHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHhCcCHHHHHHHHHHHHHCCCEEEE
Confidence 7888999999999999999999999865
No 111
>PRK09954 putative kinase; Provisional
Probab=54.52 E-value=6.8 Score=29.95 Aligned_cols=30 Identities=27% Similarity=0.404 Sum_probs=27.5
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIR 76 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik 76 (93)
|.+- +++.+.|+-+=+++.|+.|+++|.|+
T Consensus 19 s~~~----la~~l~~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 19 QQNE----IADILQISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred CHHH----HHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence 6666 89999999999999999999999995
No 112
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=54.25 E-value=11 Score=20.67 Aligned_cols=28 Identities=7% Similarity=0.166 Sum_probs=20.4
Q ss_pred HHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
..+.|+..+++|+|.+......+..|+.
T Consensus 13 ~~~tlr~~~~~g~l~~~~~~~~~~~y~~ 40 (49)
T cd04761 13 SPSTLRYYERIGLLSPARTEGGYRLYSD 40 (49)
T ss_pred CHHHHHHHHHCCCCCCCcCCCCCEEeCH
Confidence 4567889999999985444447777864
No 113
>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=54.15 E-value=29 Score=22.23 Aligned_cols=33 Identities=24% Similarity=0.228 Sum_probs=24.4
Q ss_pred eeeHHHHHHHHHHHHHcCCeeeeeeccceEEEE
Q 038379 56 HISGSLASRAIKDLVARGSIRMISAYASQQIYT 88 (93)
Q Consensus 56 kI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYT 88 (93)
+|+-+=.-|.|+.|++.|+|+.+..-.+..-|.
T Consensus 32 ~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~ 64 (116)
T cd07153 32 SISLATVYRTLELLEEAGLVREIELGDGKARYE 64 (116)
T ss_pred CCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEE
Confidence 466666779999999999999986444334453
No 114
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=53.97 E-value=7.5 Score=27.98 Aligned_cols=59 Identities=17% Similarity=0.251 Sum_probs=40.0
Q ss_pred hhhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 6 QGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 6 k~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
++.|+.+...+..-. --..-..|. || ||++| ++..+.||---.+||.++|+..|.|.-.
T Consensus 10 ~PIY~QI~~qIk~~I-----~~g~l~pGd----kL---PSvRe--lA~~~~VNpnTv~raY~eLE~eG~i~t~ 68 (125)
T COG1725 10 KPIYEQIANQIKEQI-----ASGELKPGD----KL---PSVRE--LAKDLGVNPNTVQRAYQELEREGIVETK 68 (125)
T ss_pred CCHHHHHHHHHHHHH-----HhCCcCCCC----CC---CcHHH--HHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 445666666555500 011234566 65 55544 8889999999999999999999999654
No 115
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=53.79 E-value=6.9 Score=28.16 Aligned_cols=34 Identities=18% Similarity=0.213 Sum_probs=29.9
Q ss_pred cccccceeeeeHHHHHHHHHHHHHcCCeeeeeec
Q 038379 48 EAGFNCLVHISGSLASRAIKDLVARGSIRMISAY 81 (93)
Q Consensus 48 ~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~ 81 (93)
|..+++++.||=+-.|.||..|++.|+|......
T Consensus 42 e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~r 75 (230)
T COG1802 42 EEELAEELGVSRTPVREALRRLEAEGLVEIEPNR 75 (230)
T ss_pred HHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCC
Confidence 5559999999999999999999999999887433
No 116
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=52.43 E-value=9.8 Score=27.01 Aligned_cols=36 Identities=17% Similarity=0.177 Sum_probs=31.8
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeeecc
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISAYA 82 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~ 82 (93)
|... ++++.+|+-+..++.+..|...|+|+-+....
T Consensus 27 s~~~----IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~ 62 (150)
T COG1959 27 SSAE----IAERQGISPSYLEKILSKLRKAGLVKSVRGKG 62 (150)
T ss_pred cHHH----HHHHhCcCHHHHHHHHHHHHHcCCEEeecCCC
Confidence 6666 99999999999999999999999999876543
No 117
>PF03428 RP-C: Replication protein C N-terminal domain; InterPro: IPR005090 Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids []. They may be involved in plasmid replication and stabilisation functions.
Probab=52.11 E-value=11 Score=28.11 Aligned_cols=37 Identities=19% Similarity=0.104 Sum_probs=31.0
Q ss_pred EEEeccCCccccccee-eeeHHHHHHHHHHHHHcCCeeee
Q 038379 40 LCFTSTGNEAGFNCLV-HISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 40 li~T~s~~~~~~~~rl-kI~gSLAr~alkdL~~kG~Ik~V 78 (93)
.|.-||. +-+++++ .++.+--|+.|+.|++.|+|.+=
T Consensus 67 piVfpSN--~~La~r~~G~s~~tlrR~l~~LveaGLI~rr 104 (177)
T PF03428_consen 67 PIVFPSN--AQLAERLNGMSERTLRRHLARLVEAGLIVRR 104 (177)
T ss_pred ceeecCH--HHHHHHHcCCCHHHHHHHHHHHHHCCCeeec
Confidence 4445655 4589999 99999999999999999999885
No 118
>PHA02943 hypothetical protein; Provisional
Probab=51.66 E-value=16 Score=28.17 Aligned_cols=30 Identities=20% Similarity=0.267 Sum_probs=28.4
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+++++.+|-|-|+-+|+-|+..|.|+.|..
T Consensus 30 IAkaLGlS~~qa~~~LyvLErEG~VkrV~~ 59 (165)
T PHA02943 30 IANKLGVSHSMARNALYQLAKEGMVLKVEI 59 (165)
T ss_pred HHHHHCCCHHHHHHHHHHHHHcCceEEEee
Confidence 899999999999999999999999999863
No 119
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=51.37 E-value=8.6 Score=27.26 Aligned_cols=34 Identities=12% Similarity=0.155 Sum_probs=30.8
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
|... ++++.+|+-+..++.++.|...|+|+-...
T Consensus 26 s~~e----IA~~~~is~~~L~kIl~~L~~aGlv~S~rG 59 (153)
T PRK11920 26 RIPE----IARAYGVSELFLFKILQPLVEAGLVETVRG 59 (153)
T ss_pred cHHH----HHHHHCcCHHHHHHHHHHHHHCCCEEeecC
Confidence 6677 999999999999999999999999987654
No 120
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=50.32 E-value=17 Score=25.20 Aligned_cols=28 Identities=11% Similarity=0.059 Sum_probs=26.2
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
+++.++++-+-.++-++.|++.|.|+-.
T Consensus 29 iA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 29 LAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 8999999999999999999999999843
No 121
>PF07848 PaaX: PaaX-like protein; InterPro: IPR012906 This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid []. The gene product has been shown to bind to the promoter sites and repress their transcription []. ; PDB: 3KFW_X 3L09_B.
Probab=49.04 E-value=44 Score=21.42 Aligned_cols=37 Identities=22% Similarity=0.254 Sum_probs=26.4
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEE
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYT 88 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYT 88 (93)
+-+.+-|+-+-+|.||--|.++|++..-- -.....|.
T Consensus 29 ll~~~Gv~e~avR~alsRl~~~G~L~~~r-~Gr~~~Y~ 65 (70)
T PF07848_consen 29 LLAAFGVSESAVRTALSRLVRRGWLESER-RGRRSYYR 65 (70)
T ss_dssp HHCCTT--HHHHHHHHHHHHHTTSEEEEC-CCTEEEEE
T ss_pred HHHHcCCChHHHHHHHHHHHHcCceeeee-cCccceEe
Confidence 44567799999999999999999998753 33344553
No 122
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=48.96 E-value=10 Score=25.98 Aligned_cols=27 Identities=26% Similarity=0.326 Sum_probs=25.3
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
+++.+.++=.-.+|++++|.++|+|+.
T Consensus 174 lA~~lG~tr~tvsR~l~~l~~~gii~~ 200 (211)
T PRK11753 174 IGRIVGCSREMVGRVLKMLEDQGLISA 200 (211)
T ss_pred HHHHhCCCHHHHHHHHHHHHHCCCEEe
Confidence 899999999999999999999999974
No 123
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=48.90 E-value=14 Score=22.20 Aligned_cols=26 Identities=15% Similarity=0.146 Sum_probs=24.2
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIR 76 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik 76 (93)
+++++.++-+-.++.|+.|++.|+.-
T Consensus 19 La~~l~vS~~tv~~~l~~L~~~g~~i 44 (69)
T TIGR00122 19 LGEALGMSRTAVNKHIQTLREWGVDV 44 (69)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 88999999999999999999999954
No 124
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=48.85 E-value=12 Score=31.26 Aligned_cols=27 Identities=26% Similarity=0.380 Sum_probs=24.9
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
+.+....+-|-++.||.+|+++|.|+.
T Consensus 26 Ieel~GlSKStvSEaLs~LE~~giv~R 52 (321)
T COG3888 26 IEELMGLSKSTVSEALSELEKQGIVKR 52 (321)
T ss_pred HHHHhCcchhHHHHHHHHHHhcCeeee
Confidence 788888999999999999999999975
No 125
>TIGR02698 CopY_TcrY copper transport repressor, CopY/TcrY family. This family includes metal-fist type transcriptional repressors of copper transport systems such as copYZAB of Enterococcus hirae and tcrYAZB (transferble copper resistance) of an Enterocuccus faecium plasmid. High levels of copper can displace zinc and prevent binding by the repressor, activating efflux by copper resistance transporters. The most closely related proteins excluded by this model are antibiotic resistance regulators including the methicillin resistance regulatory protein MecI.
Probab=48.31 E-value=39 Score=23.37 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=28.9
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEeec
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYTRVI 91 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR~~ 91 (93)
+.++..++=+-.+..|+.|++||+|... +..+..+|+-.+
T Consensus 28 l~~~~~~~~tTv~T~L~rL~~KG~v~~~-k~gr~~~Y~p~v 67 (130)
T TIGR02698 28 LAEKKDWSDSTIKTLLGRLVDKGCLTTE-KEGRKFIYTALV 67 (130)
T ss_pred HhhccCCcHHHHHHHHHHHHHCCceeee-cCCCcEEEEecC
Confidence 3344456677888999999999999765 334556887654
No 126
>PF13814 Replic_Relax: Replication-relaxation
Probab=47.00 E-value=32 Score=23.61 Aligned_cols=28 Identities=21% Similarity=0.274 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHcCCeeeeeec------cceEEEE
Q 038379 61 LASRAIKDLVARGSIRMISAY------ASQQIYT 88 (93)
Q Consensus 61 LAr~alkdL~~kG~Ik~Vs~~------~~Q~IYT 88 (93)
=+++.|+.|.+.|+|...... ..+.||.
T Consensus 28 ~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~ 61 (191)
T PF13814_consen 28 TARRRLKRLRELGLVDRFRRRVGARGGSQPYVYY 61 (191)
T ss_pred HHHHHHHHHhhCCcEEeecccccccCCCcceEEE
Confidence 689999999999999988653 5667876
No 127
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=46.11 E-value=12 Score=25.54 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=25.2
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIR 76 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik 76 (93)
+++.+.++-.-.+|+|++|+++|+|+
T Consensus 155 iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 155 LAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred HHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 99999999999999999999999997
No 128
>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=45.69 E-value=16 Score=25.83 Aligned_cols=29 Identities=24% Similarity=0.202 Sum_probs=26.5
Q ss_pred ccceeeee-HHHHHHHHHHHHHcCCeeeee
Q 038379 51 FNCLVHIS-GSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 51 ~~~rlkI~-gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+++.+.++ -|-.++.|+.|+++|+|....
T Consensus 31 la~~~~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 31 IARAVGLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred HHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence 89999998 889999999999999998764
No 129
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=44.04 E-value=15 Score=25.82 Aligned_cols=29 Identities=10% Similarity=0.153 Sum_probs=26.3
Q ss_pred cccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 50 GFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 50 ~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
-+++.+.++=.-.+|++++|.++|+|+.-
T Consensus 189 ~iA~~lG~sr~tvsR~l~~l~~~g~I~~~ 217 (235)
T PRK11161 189 DIGNYLGLTVETISRLLGRFQKSGMLAVK 217 (235)
T ss_pred HHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 39999999999999999999999999853
No 130
>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=43.71 E-value=21 Score=24.44 Aligned_cols=33 Identities=21% Similarity=0.344 Sum_probs=29.4
Q ss_pred eEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCee
Q 038379 39 KLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIR 76 (93)
Q Consensus 39 Kli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik 76 (93)
-.| |.+- +.+.-.++-+=.++|+++|+++|+|.
T Consensus 53 d~I-s~sq----~~e~tg~~~~~V~~al~~Li~~~vI~ 85 (100)
T PF04492_consen 53 DRI-SNSQ----IAEMTGLSRDHVSKALNELIRRGVII 85 (100)
T ss_pred cee-eHHH----HHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 366 8888 89999999999999999999999994
No 131
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=43.64 E-value=16 Score=26.62 Aligned_cols=34 Identities=15% Similarity=0.058 Sum_probs=29.7
Q ss_pred Cccccccee--eeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 47 NEAGFNCLV--HISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 47 ~~~~~~~rl--kI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+.+.++.++ .|+..=++.+|+-|++-|+|+.-..
T Consensus 41 d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 41 DPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred CHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence 445589999 9999999999999999999998744
No 132
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=43.39 E-value=20 Score=26.97 Aligned_cols=32 Identities=19% Similarity=0.271 Sum_probs=28.7
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
|..- +++.+.++-+=+||-|++|+++|.|+..
T Consensus 20 ~~~e----La~~l~VS~~TiRRdL~~L~~~~~l~r~ 51 (240)
T PRK10411 20 TTEA----LAEQLNVSKETIRRDLNELQTQGKILRN 51 (240)
T ss_pred cHHH----HHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 6666 9999999999999999999999999763
No 133
>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=43.26 E-value=10 Score=27.63 Aligned_cols=36 Identities=25% Similarity=0.356 Sum_probs=24.1
Q ss_pred ceeeeeHHHHHHHHHHHHHcCCeeeeee---ccceEEEE
Q 038379 53 CLVHISGSLASRAIKDLVARGSIRMISA---YASQQIYT 88 (93)
Q Consensus 53 ~rlkI~gSLAr~alkdL~~kG~Ik~Vs~---~~~Q~IYT 88 (93)
+--.|+|.=+...|+.|.++|+|+..-. ..+-.+|.
T Consensus 101 eIe~IRGv~s~~~i~~L~e~glI~~~gr~~~~Grp~ly~ 139 (159)
T PF04079_consen 101 EIEEIRGVNSDSVIKTLLERGLIEEVGRKDTPGRPILYG 139 (159)
T ss_dssp HHHHHHTS--HCHHHHHHHTTSEEEEEE-TTTT--EEEE
T ss_pred HHHHHcCCChHHHHHHHHHCCCEEecCcCCCCCCCeEee
Confidence 3446788889999999999999999853 23344553
No 134
>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=42.83 E-value=71 Score=21.02 Aligned_cols=39 Identities=15% Similarity=0.145 Sum_probs=27.8
Q ss_pred cceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEeec
Q 038379 52 NCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYTRVI 91 (93)
Q Consensus 52 ~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR~~ 91 (93)
.+...++=|-.+..|+.|++||+|..-. .....+|+-.+
T Consensus 28 ~~~~~~~~sTv~t~L~rL~~Kg~l~~~~-~gr~~~Y~p~i 66 (115)
T PF03965_consen 28 PEERSWAYSTVQTLLNRLVEKGFLTREK-IGRAYVYSPLI 66 (115)
T ss_dssp CTTSS--HHHHHHHHHHHHHTTSEEEEE-ETTCEEEEESS
T ss_pred HhccccchhHHHHHHHHHHhCCceeEee-cCCceEEEeCC
Confidence 3334455677788999999999999864 46778898654
No 135
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=42.61 E-value=20 Score=25.89 Aligned_cols=32 Identities=16% Similarity=0.081 Sum_probs=29.5
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
|... ++++++|+....++.|+.|.+.|++.-.
T Consensus 27 s~~e----IA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 27 PLAD----ISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred cHHH----HHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 6666 9999999999999999999999999865
No 136
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=40.84 E-value=18 Score=21.06 Aligned_cols=35 Identities=14% Similarity=0.180 Sum_probs=24.0
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee-eeccceEEEEe
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI-SAYASQQIYTR 89 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V-s~~~~Q~IYTR 89 (93)
+++++.|+ .+.|+..+++|+|.+. .....+..|+.
T Consensus 6 va~~~gvs----~~tlr~~~~~gli~~~~~~~~g~r~y~~ 41 (70)
T smart00422 6 VAKLAGVS----VRTLRYYERIGLLPPPIRTEGGYRLYSD 41 (70)
T ss_pred HHHHHCcC----HHHHHHHHHCCCCCCCccCCCCCEecCH
Confidence 44444443 5678889999999986 44556677763
No 137
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 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 is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=39.39 E-value=30 Score=19.70 Aligned_cols=27 Identities=11% Similarity=0.178 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHcCCe-eeeeeccceEEE
Q 038379 61 LASRAIKDLVARGSI-RMISAYASQQIY 87 (93)
Q Consensus 61 LAr~alkdL~~kG~I-k~Vs~~~~Q~IY 87 (93)
+..+.|+..+++|+| .+.-..+....|
T Consensus 11 vs~~tlR~ye~~Gll~~~~r~~~g~R~Y 38 (38)
T PF00376_consen 11 VSPRTLRYYEREGLLPPPERTEGGYRRY 38 (38)
T ss_dssp S-HHHHHHHHHTTSS-SSEETTTS-EEE
T ss_pred CCHHHHHHHHHCCCCCCCccCCCCeecC
Confidence 346789999999999 554444444443
No 138
>PRK00215 LexA repressor; Validated
Probab=39.01 E-value=32 Score=24.48 Aligned_cols=31 Identities=23% Similarity=0.180 Sum_probs=27.5
Q ss_pred ccceeee-eHHHHHHHHHHHHHcCCeeeeeec
Q 038379 51 FNCLVHI-SGSLASRAIKDLVARGSIRMISAY 81 (93)
Q Consensus 51 ~~~rlkI-~gSLAr~alkdL~~kG~Ik~Vs~~ 81 (93)
+++.+.+ +-|-+.+.|+.|+++|+|......
T Consensus 29 la~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 29 IADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 8899999 889999999999999999887544
No 139
>cd04371 DEP DEP domain, named after Dishevelled, Egl-10, and Pleckstrin, where this domain was first discovered. The function of this domain is still not clear, but it is believed to be important for the membrane association of the signaling proteins in which it is present. New studies show that the DEP domain of Sst2, a yeast RGS protein is necessary and sufficient for receptor interaction.
Probab=38.71 E-value=47 Score=19.98 Aligned_cols=24 Identities=25% Similarity=0.252 Sum_probs=22.3
Q ss_pred eeHHHHHHHHHHHHHcCCeeeeee
Q 038379 57 ISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 57 I~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
.+.+-|.+..++|.+.|+|..|..
T Consensus 45 ~~r~ea~~~~~~ll~~g~i~~v~~ 68 (81)
T cd04371 45 ITREEAVELGQALLKHGLIHHVSD 68 (81)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeCC
Confidence 788899999999999999999985
No 140
>PRK06474 hypothetical protein; Provisional
Probab=38.49 E-value=38 Score=24.61 Aligned_cols=39 Identities=13% Similarity=0.316 Sum_probs=30.0
Q ss_pred cccee-eeeHHHHHHHHHHHHHcCCeeeeeec----cceEEEEe
Q 038379 51 FNCLV-HISGSLASRAIKDLVARGSIRMISAY----ASQQIYTR 89 (93)
Q Consensus 51 ~~~rl-kI~gSLAr~alkdL~~kG~Ik~Vs~~----~~Q~IYTR 89 (93)
+.+.+ .|+.+-..+-|+.|++.|+|+.+... .....|..
T Consensus 32 l~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~ 75 (178)
T PRK06474 32 LVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAI 75 (178)
T ss_pred HHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEe
Confidence 56666 68889999999999999999998643 23455653
No 141
>KOG1502 consensus Flavonol reductase/cinnamoyl-CoA reductase [Defense mechanisms]
Probab=37.36 E-value=80 Score=26.05 Aligned_cols=69 Identities=13% Similarity=0.243 Sum_probs=49.4
Q ss_pred hhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcc-----------cccceee--------------eeHHHHHH
Q 038379 10 DKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEA-----------GFNCLVH--------------ISGSLASR 64 (93)
Q Consensus 10 dK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~-----------~~~~rlk--------------I~gSLAr~ 64 (93)
+-+-|++.-++....+|.+.. +++ |+|||+|.--- .+.|.-. ++=-||.+
T Consensus 99 ~li~pav~Gt~nVL~ac~~~~---sVk--rvV~TSS~aAv~~~~~~~~~~~vvdE~~wsd~~~~~~~~~~Y~~sK~lAEk 173 (327)
T KOG1502|consen 99 ELIDPAVKGTKNVLEACKKTK---SVK--RVVYTSSTAAVRYNGPNIGENSVVDEESWSDLDFCRCKKLWYALSKTLAEK 173 (327)
T ss_pred hhhhHHHHHHHHHHHHHhccC---Ccc--eEEEeccHHHhccCCcCCCCCcccccccCCcHHHHHhhHHHHHHHHHHHHH
Confidence 356788888999999999987 222 78899986111 1112211 67789999
Q ss_pred HHHHHHHcCCeeeeeeccc
Q 038379 65 AIKDLVARGSIRMISAYAS 83 (93)
Q Consensus 65 alkdL~~kG~Ik~Vs~~~~ 83 (93)
|-.++.+++-+.+|+-+..
T Consensus 174 aAw~fa~e~~~~lv~inP~ 192 (327)
T KOG1502|consen 174 AAWEFAKENGLDLVTINPG 192 (327)
T ss_pred HHHHHHHhCCccEEEecCC
Confidence 9999999998888876544
No 142
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=36.07 E-value=25 Score=25.93 Aligned_cols=31 Identities=6% Similarity=-0.030 Sum_probs=27.7
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
.+..+++.++|+.--.|+.|..|.+.|++.-
T Consensus 38 tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~ 68 (178)
T PRK06266 38 TDEEIAEQTGIKLNTVRKILYKLYDARLADY 68 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 4455999999999999999999999999974
No 143
>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=35.92 E-value=29 Score=28.28 Aligned_cols=59 Identities=27% Similarity=0.252 Sum_probs=42.7
Q ss_pred hhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 7 GTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 7 ~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
..|.++...+.+ .....+-+.|. ||= +.-. ++..+.++-|-..+|.++|+++|+|.-..
T Consensus 4 ~~y~ql~~~i~~-----~I~~g~l~~g~----rLP-s~R~----la~~l~vs~~Tv~~ay~~L~~~G~i~~~~ 62 (459)
T COG1167 4 PLYQQLAEQLRE-----AILSGRLKPGD----RLP-SIRQ----LAQDLGVSRSTVSRAYEELEARGYIESRP 62 (459)
T ss_pred cHHHHHHHHHHH-----HHHcCCCCCCC----cCC-cHHH----HHHHhCCcHHHHHHHHHHHHhCcceeecc
Confidence 356666666666 22334445556 665 4445 89999999999999999999999997653
No 144
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=35.72 E-value=20 Score=29.45 Aligned_cols=40 Identities=18% Similarity=0.194 Sum_probs=34.3
Q ss_pred cccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 31 QEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 31 ~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
.+|. |+| |.-- +.|...+.-+.+|.++-.|++||.+..|-
T Consensus 25 ae~h----kii-Tird----vae~~ev~~n~lr~lasrLekkG~LeRi~ 64 (269)
T COG5340 25 AEGH----KII-TIRD----VAETLEVAPNTLRELASRLEKKGWLERIL 64 (269)
T ss_pred HHhC----ceE-EeHH----hhhhccCCHHHHHHHHhhhhhcchhhhhc
Confidence 3566 887 8877 88889999999999999999999998773
No 145
>PRK05638 threonine synthase; Validated
Probab=35.10 E-value=43 Score=27.15 Aligned_cols=39 Identities=15% Similarity=0.149 Sum_probs=28.2
Q ss_pred ccceee--eeHHHHHHHHHHHHHcCCeeeeeeccceEEEEee
Q 038379 51 FNCLVH--ISGSLASRAIKDLVARGSIRMISAYASQQIYTRV 90 (93)
Q Consensus 51 ~~~rlk--I~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR~ 90 (93)
+.+.+. ++-+-.++.|+.|++.|+|..-..... .+|-+.
T Consensus 390 l~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~-~~~Y~L 430 (442)
T PRK05638 390 IWKALGKPLKYQAVYQHIKELEELGLIEEAYRKGR-RVYYKL 430 (442)
T ss_pred HHHHHcccCCcchHHHHHHHHHHCCCEEEeecCCC-cEEEEE
Confidence 556676 888899999999999999976433334 444433
No 146
>PF00610 DEP: Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP); InterPro: IPR000591 This entry represents the DEP (Dishevelled, Egl-10 and Pleckstrin) domain, a globular domain of about 80 residues that is found in over 50 proteins involved in G-protein signalling pathways. It was named after the three proteins it was initially found in: Dishevelled (Dsh and Dvl), which play a key role in the transduction of the Wg/Wnt signal from the cell surface to the nucleus; it is a segment polarity protein required to establish coherent arrays of polarized cells and segments in embryos, and plays a role in wingless signalling. Egl-10, which regulates G-protein signalling in the central nervous system. Pleckstrin, the major substrate of protein kinase C in platelets; Pleckstrin contains two PH domains flanking the DEP domain. Mammalian regulators of G-protein signalling also contain these domains, and regulate signal transduction by increasing the GTPase activity of G-protein alpha subunits, thereby driving them into their inactive GDP-bound form. It has been proposed that the DEP domain could play a selective role in targeting DEP domain-containing proteins to specific subcellular membranous sites, perhaps even to specific G protein-coupled signaling pathways [, ]. Nuclear magnetic resonance spectroscopy has revealed that the DEP domain comprises a three-helix bundle, a beta-hairpin 'arm' composed of two beta-strands and two short beta-strands in the C-terminal region [].; GO: 0035556 intracellular signal transduction; PDB: 1UHW_A 1V3F_A 2YSR_A 2CSO_A 1W4M_A 2PBI_C 1O7F_A 2BYV_E 1FSH_A 3ML6_D ....
Probab=34.95 E-value=43 Score=20.12 Aligned_cols=28 Identities=18% Similarity=0.133 Sum_probs=23.5
Q ss_pred eeeHHHHHHHHHHHHHcCCeeeeeeccc
Q 038379 56 HISGSLASRAIKDLVARGSIRMISAYAS 83 (93)
Q Consensus 56 kI~gSLAr~alkdL~~kG~Ik~Vs~~~~ 83 (93)
..+-+-|...-++|.+.|+|..|...+.
T Consensus 35 ~~~r~eA~~l~q~Ll~~g~i~~v~~~~~ 62 (74)
T PF00610_consen 35 VRDREEAVQLGQELLDHGFIEHVSDKSK 62 (74)
T ss_dssp TSSHHHHHHHHHHHHHCTSEEESSSSSH
T ss_pred ccCHHHHHHHHHHHHHCCCEEECCCCCC
Confidence 4566788899999999999999987663
No 147
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=34.55 E-value=31 Score=24.78 Aligned_cols=28 Identities=25% Similarity=0.324 Sum_probs=25.0
Q ss_pred cccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 50 GFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 50 ~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
-+++.+.++=.-.+|+|++|+++|+|..
T Consensus 184 ~IA~~lGisretlsR~L~~L~~~GlI~~ 211 (230)
T PRK09391 184 DIADYLGLTIETVSRALSQLQDRGLIGL 211 (230)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence 3889999999989999999999999953
No 148
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=34.30 E-value=34 Score=24.37 Aligned_cols=28 Identities=7% Similarity=0.058 Sum_probs=25.2
Q ss_pred cccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 50 GFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 50 ~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
.+++.+.++=.-.+|+|++|+++|+|..
T Consensus 174 ~lA~~lG~sretvsR~L~~L~~~G~I~~ 201 (226)
T PRK10402 174 QAAEYLGVSYRHLLYVLAQFIQDGYLKK 201 (226)
T ss_pred HHHHHHCCcHHHHHHHHHHHHHCCCEEe
Confidence 3888999998889999999999999976
No 149
>PRK12423 LexA repressor; Provisional
Probab=34.21 E-value=32 Score=24.98 Aligned_cols=33 Identities=21% Similarity=0.270 Sum_probs=27.2
Q ss_pred ccCCcccccceeee-eHHHHHHHHHHHHHcCCeeee
Q 038379 44 STGNEAGFNCLVHI-SGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 44 ~s~~~~~~~~rlkI-~gSLAr~alkdL~~kG~Ik~V 78 (93)
||. +.+++.+.+ +=|-.+++|+.|+++|+|..-
T Consensus 26 Ps~--~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~ 59 (202)
T PRK12423 26 PSL--AEIAQAFGFASRSVARKHVQALAEAGLIEVV 59 (202)
T ss_pred CCH--HHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence 555 448899995 777889999999999999864
No 150
>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=33.67 E-value=38 Score=19.21 Aligned_cols=27 Identities=26% Similarity=0.277 Sum_probs=24.4
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcC
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARG 73 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG 73 (93)
|..- +++.+.||=.-.++-|++|.+.|
T Consensus 17 t~~e----La~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 17 TAKE----LAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp EHHH----HHHHCTS-HHHHHHHHHHHHHTT
T ss_pred CHHH----HHHHhCCCHHHHHHHHHHHHHCC
Confidence 7777 99999999999999999999999
No 151
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=33.51 E-value=31 Score=26.90 Aligned_cols=28 Identities=25% Similarity=0.262 Sum_probs=26.1
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
++++|.|+.--||+=|++|+++|++.--
T Consensus 31 lA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 31 LAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 8899999999999999999999998755
No 152
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=32.66 E-value=27 Score=26.22 Aligned_cols=36 Identities=22% Similarity=0.345 Sum_probs=26.5
Q ss_pred ceeeeeHHHHHHHHHHHHHcCCeeeeee---ccceEEEE
Q 038379 53 CLVHISGSLASRAIKDLVARGSIRMISA---YASQQIYT 88 (93)
Q Consensus 53 ~rlkI~gSLAr~alkdL~~kG~Ik~Vs~---~~~Q~IYT 88 (93)
+--.|+|.=+...|+.|.++|+|+..-. ..+-.+|.
T Consensus 106 eIe~IRGv~s~~~l~~L~ergLI~~~Gr~~~~Grp~ly~ 144 (186)
T TIGR00281 106 RINEIRGVKSYQIVDDLVEKGLVVELGRKDTPGRSFIYE 144 (186)
T ss_pred HHHHHcCCCHHHHHHHHHHCCCeEecCcCCCCCCCeeeh
Confidence 4456788888999999999999998721 33445564
No 153
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=32.59 E-value=23 Score=22.88 Aligned_cols=29 Identities=14% Similarity=0.188 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHcCCeeeeeec-cceEEEEe
Q 038379 61 LASRAIKDLVARGSIRMISAY-ASQQIYTR 89 (93)
Q Consensus 61 LAr~alkdL~~kG~Ik~Vs~~-~~Q~IYTR 89 (93)
+..+.|+.-+++|+|.+.... +...+|+.
T Consensus 12 vs~~tLRyYE~~GLl~p~~~~~~gyR~Ys~ 41 (124)
T COG0789 12 VSVRTLRFYERKGLLSPERRDEGGYRYYTP 41 (124)
T ss_pred CCHHHHHHHHHcCCCCCcccCCCCceecCH
Confidence 446789999999999998555 58888874
No 154
>PRK09462 fur ferric uptake regulator; Provisional
Probab=31.66 E-value=96 Score=21.28 Aligned_cols=32 Identities=9% Similarity=0.168 Sum_probs=23.0
Q ss_pred eeHHHHHHHHHHHHHcCCeeeeeeccceEEEE
Q 038379 57 ISGSLASRAIKDLVARGSIRMISAYASQQIYT 88 (93)
Q Consensus 57 I~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYT 88 (93)
|+-+=.=|.|+.|++.|+|+.+.-......|-
T Consensus 50 i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~ 81 (148)
T PRK09462 50 IGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE 81 (148)
T ss_pred CCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEE
Confidence 33344459999999999999986544555564
No 155
>cd04448 DEP_PIKfyve DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in fungal RhoGEF (GDP/GTP exchange factor) PIKfyve-like proteins. PIKfyve contains N-terminal Fyve finger and DEP domains, a central chaperonin-like domain and a C-terminal PIPK (phosphatidylinositol phosphate kinase) domain. PIKfyve-like proteins are important phosphatidylinositol (3)-monophosphate (PtdIns(3)P)-5-kinases, producing PtdIns(3,5)P2, which plays a major role in multivesicular body (MVB) sorting and control of retrograde traffic from the vacuole back to the endosome and/or Golgi. PIKfyve itself has been shown to be play a role in regulating early-endosome-to-trans-Golgi network (TGN) retrograde trafficking.
Probab=31.61 E-value=53 Score=21.36 Aligned_cols=23 Identities=22% Similarity=0.102 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHcCCeeeeeecc
Q 038379 60 SLASRAIKDLVARGSIRMISAYA 82 (93)
Q Consensus 60 SLAr~alkdL~~kG~Ik~Vs~~~ 82 (93)
.=|-..-+.|.++|+|..|..++
T Consensus 48 ~eAv~~gq~Ll~~g~i~hV~~~~ 70 (81)
T cd04448 48 VQAIAIGQALLDAGWIECVSDDD 70 (81)
T ss_pred HHHHHHHHHHHHCCCEEecCCCC
Confidence 45777788999999999998665
No 156
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=31.19 E-value=48 Score=25.06 Aligned_cols=22 Identities=23% Similarity=0.418 Sum_probs=18.7
Q ss_pred eeeHHHHHHHHHHHHHcCCeee
Q 038379 56 HISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 56 kI~gSLAr~alkdL~~kG~Ik~ 77 (93)
.-+|+.+|++|+.|+.-|++..
T Consensus 94 ~as~~i~rkvlQ~Le~~~~ve~ 115 (143)
T KOG3411|consen 94 DASGGIARKVLQALEKMGIVEK 115 (143)
T ss_pred ccccHHHHHHHHHHHhCCceee
Confidence 4578999999999999988753
No 157
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=30.84 E-value=20 Score=26.09 Aligned_cols=18 Identities=33% Similarity=0.534 Sum_probs=15.4
Q ss_pred HHHHHHHHHHHHHcCCee
Q 038379 59 GSLASRAIKDLVARGSIR 76 (93)
Q Consensus 59 gSLAr~alkdL~~kG~Ik 76 (93)
||+|++.+++..-++.|-
T Consensus 95 gt~ar~~ik~~~p~~iig 112 (158)
T PF01976_consen 95 GTLARKIIKEYRPKAIIG 112 (158)
T ss_pred hHHHHHHHHHhCCCEEEE
Confidence 899999999998886653
No 158
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=30.84 E-value=47 Score=22.47 Aligned_cols=29 Identities=10% Similarity=0.176 Sum_probs=27.2
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
++..|+.+-++.+.-|..|+++|-|..|.
T Consensus 22 Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 22 ISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 78889999999999999999999999996
No 159
>PF03492 Methyltransf_7: SAM dependent carboxyl methyltransferase; InterPro: IPR005299 This family of plant methyltransferases contains enzymes that act on a variety of substrates including salicylic acid, jasmonic acid and 7-Methylxanthine. Caffeine is synthesized through sequential three-step methylation of xanthine derivatives at positions 7-N, 3-N, and 1-N. The protein 7-methylxanthine methyltransferase (designated as CaMXMT) catalyses the second step to produce theobromine [].; GO: 0008168 methyltransferase activity; PDB: 2EFJ_A 1M6E_X 2EG5_C 3B5I_B.
Probab=30.65 E-value=77 Score=25.18 Aligned_cols=44 Identities=20% Similarity=0.148 Sum_probs=26.0
Q ss_pred ceeeeeEEEeccCCcc--cccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 34 TKMFVKLCFTSTGNEA--GFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 34 ~~~~vKli~T~s~~~~--~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
.+.|+++++|-.+... ..+.-...---+...+++||+++|+|..
T Consensus 173 Lv~GG~mvl~~~gr~~~~~~~~~~~~~~~~l~~~l~dMv~eGlI~~ 218 (334)
T PF03492_consen 173 LVPGGRMVLTFLGRDEEDPSSTGSCMLWDLLADALRDMVAEGLISE 218 (334)
T ss_dssp EEEEEEEEEEEEE-STSSTTSTTCCCHHHHHHHHHHHHHHTTSS-H
T ss_pred eccCcEEEEEEeeccccccccCCcchHHHHHHHHHHHHHHcCCcCH
Confidence 4566677766544221 1111112334578999999999999964
No 160
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=30.58 E-value=49 Score=23.93 Aligned_cols=31 Identities=6% Similarity=0.079 Sum_probs=27.3
Q ss_pred eEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCC
Q 038379 39 KLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGS 74 (93)
Q Consensus 39 Kli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~ 74 (93)
.-+ ++.. +++.+.|+.+..||=|..|...|.
T Consensus 31 ~~v-s~~~----L~~~~~v~~~tirrDl~~l~~~G~ 61 (213)
T PRK05472 31 ERV-SSKE----LAEALGVDSAQIRKDLSYFGEFGK 61 (213)
T ss_pred cEE-eHHH----HHHHhCcCHHHHHHHHHHHHhcCC
Confidence 455 7777 999999999999999999999884
No 161
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=29.94 E-value=45 Score=25.58 Aligned_cols=28 Identities=21% Similarity=0.156 Sum_probs=25.5
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCC-eeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGS-IRMI 78 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~-Ik~V 78 (93)
+++++.|+-+-.+++|+.|++.|+ |.-+
T Consensus 24 LA~~lgvsr~tV~~~l~~L~~~G~~i~~~ 52 (319)
T PRK11886 24 LGEELGISRAAIWKHIQTLEEWGLDIFSV 52 (319)
T ss_pred HHHHHCCCHHHHHHHHHHHHHCCCceEEe
Confidence 899999999999999999999999 6444
No 162
>cd04449 DEP_DEPDC5-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in DEPDC5-like proteins. DEPDC5, in human also known as KIAA0645, is a DEP domain containing protein of unknown function.
Probab=29.44 E-value=59 Score=20.91 Aligned_cols=24 Identities=21% Similarity=0.217 Sum_probs=19.5
Q ss_pred eHHHHHHHHHHHHHcCCeeeeeec
Q 038379 58 SGSLASRAIKDLVARGSIRMISAY 81 (93)
Q Consensus 58 ~gSLAr~alkdL~~kG~Ik~Vs~~ 81 (93)
+-.=|....+.|.+.|+|..|+..
T Consensus 48 ~r~eAv~lgq~Ll~~g~I~hv~~~ 71 (83)
T cd04449 48 TREEAVELGQELMNEGLIEHVSGR 71 (83)
T ss_pred CHHHHHHHHHHHHHCCCEEecCCC
Confidence 334577888999999999999864
No 163
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. 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 specific coactivator molecules.
Probab=29.42 E-value=41 Score=21.42 Aligned_cols=35 Identities=9% Similarity=0.076 Sum_probs=23.8
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
+++.+.|+ .+.|+..++.|+|.+....+....|+.
T Consensus 7 ~A~~~gvs----~~tLr~ye~~Gli~p~r~~~g~R~y~~ 41 (91)
T cd04766 7 AAELSGMH----PQTLRLYERLGLLSPSRTDGGTRRYSE 41 (91)
T ss_pred HHHHHCcC----HHHHHHHHHCCCcCCCcCCCCCeeECH
Confidence 44444443 567899999999998644455667763
No 164
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.40 E-value=36 Score=22.66 Aligned_cols=28 Identities=14% Similarity=0.227 Sum_probs=22.1
Q ss_pred HHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
..+.|+.-++.|+|.++.......+|+.
T Consensus 13 s~~tLryYe~~GLi~p~~~~~~yR~Y~~ 40 (116)
T cd04769 13 TIKAIRLYEEKGLLPSPKRSGNYRVYDA 40 (116)
T ss_pred CHHHHHHHHHCCCCCCCCCCCCceeeCH
Confidence 4578999999999999765556678864
No 165
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=29.35 E-value=46 Score=17.34 Aligned_cols=28 Identities=11% Similarity=0.351 Sum_probs=19.2
Q ss_pred HHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
.++.|+.++++|.+...........|+.
T Consensus 13 s~~tl~~~~~~g~~~~~~~~~~~~~~~~ 40 (49)
T cd04762 13 SPSTLRRWVKEGKLKAIRTPGGHRRFPE 40 (49)
T ss_pred CHHHHHHHHHcCCCCceeCCCCceecCH
Confidence 4567788888999876544446666653
No 166
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=29.19 E-value=24 Score=26.94 Aligned_cols=46 Identities=17% Similarity=0.173 Sum_probs=38.3
Q ss_pred eechhhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCee
Q 038379 3 LFDQGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIR 76 (93)
Q Consensus 3 lfDk~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik 76 (93)
.||.++|.|+|.++-+ .-+ |-.- +.+.+.-.+ ++||+-|..-|+|.
T Consensus 13 ~f~s~~~kkV~~~Ls~--------------------~W~-T~~E----l~e~~G~d~---~~~L~~LkK~gLiE 58 (160)
T PF09824_consen 13 TFNSEVYKKVYDELSK--------------------GWM-TEEE----LEEKYGKDV---RESLLILKKGGLIE 58 (160)
T ss_pred HhCCHHHHHHHHHHHh--------------------ccC-CHHH----HHHHHCcCH---HHHHHHHHHcCchh
Confidence 6899999999999998 466 7666 788876665 89999999999985
No 167
>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=29.05 E-value=59 Score=21.17 Aligned_cols=27 Identities=19% Similarity=0.178 Sum_probs=21.9
Q ss_pred cceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 52 NCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 52 ~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
...+.|+-+-.-.+|+.|+++|+|...
T Consensus 32 ~~~~~i~~gtlY~~L~rLe~~GlI~~~ 58 (100)
T TIGR03433 32 EDVLQVEEGSLYPALHRLERRGWIAAE 58 (100)
T ss_pred CCccccCCCcHHHHHHHHHHCCCeEEE
Confidence 345677777788999999999999973
No 168
>PHA00738 putative HTH transcription regulator
Probab=28.86 E-value=93 Score=22.26 Aligned_cols=37 Identities=19% Similarity=0.283 Sum_probs=30.2
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
+++.+.++-+-.++=|+-|.+.|+|.. ....+++|-+
T Consensus 32 Lae~l~lSQptVS~HLKvLreAGLV~s--rK~Gr~vyY~ 68 (108)
T PHA00738 32 ISHTLLLSYTTVLRHLKILNEQGYIEL--YKEGRTLYAK 68 (108)
T ss_pred HHHhhCCCHHHHHHHHHHHHHCCceEE--EEECCEEEEE
Confidence 789999999999999999999999975 3344555544
No 169
>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=28.78 E-value=89 Score=20.18 Aligned_cols=24 Identities=25% Similarity=0.321 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHcCCeeeeeecc
Q 038379 59 GSLASRAIKDLVARGSIRMISAYA 82 (93)
Q Consensus 59 gSLAr~alkdL~~kG~Ik~Vs~~~ 82 (93)
-++.+++|+.++++|.+..+....
T Consensus 45 ~~~l~~aLkk~v~~G~l~~~kG~g 68 (88)
T cd00073 45 NKLLKLALKKGVAKGKLVQVKGTG 68 (88)
T ss_pred HHHHHHHHHHHHHCCCeEeecCCC
Confidence 578889999999999999987543
No 170
>PF12689 Acid_PPase: Acid Phosphatase; InterPro: IPR010036 This entry represents two closely related clades of sequences from eukaryotes and archaea. The mouse enzyme has been characterised as a phosphatase and has been positively identified as a member of the haloacid dehalogenase (HAD) superfamily by site-directed mutagenesis of the active site residues [, ].; GO: 0016791 phosphatase activity; PDB: 1U7P_A 1U7O_A 2WM8_A.
Probab=28.21 E-value=79 Score=23.25 Aligned_cols=58 Identities=22% Similarity=0.305 Sum_probs=28.7
Q ss_pred hhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHc---CCeeee-eeccceEE
Q 038379 11 KHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVAR---GSIRMI-SAYASQQI 86 (93)
Q Consensus 11 K~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~k---G~Ik~V-s~~~~Q~I 86 (93)
+++|++|.-|--.+. .|. ++.+-|.++ ....|+++|+.|.=. |..+.. .-....+|
T Consensus 45 ~lypdv~~iL~~L~~------~gv----~lavASRt~----------~P~~A~~~L~~l~i~~~~~~~~~~~~~F~~~eI 104 (169)
T PF12689_consen 45 SLYPDVPEILQELKE------RGV----KLAVASRTD----------EPDWARELLKLLEIDDADGDGVPLIEYFDYLEI 104 (169)
T ss_dssp ---TTHHHHHHHHHH------CT------EEEEE--S-----------HHHHHHHHHHTT-C----------CCECEEEE
T ss_pred EeCcCHHHHHHHHHH------CCC----EEEEEECCC----------ChHHHHHHHHhcCCCccccccccchhhcchhhe
Confidence 577888886665554 455 888444332 238999999998655 222222 33445667
Q ss_pred EE
Q 038379 87 YT 88 (93)
Q Consensus 87 YT 88 (93)
|.
T Consensus 105 ~~ 106 (169)
T PF12689_consen 105 YP 106 (169)
T ss_dssp SS
T ss_pred ec
Confidence 75
No 171
>cd04450 DEP_RGS7-like DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in RGS (regulator of G-protein signaling) proteins of the subfamily R7. This subgroup contains RGS7, RGS6, RGS9 and RGS11. They share a common domain architecture, containing, beside the RGS domain, a DEP domain and a GGL (G-protein gamma subunit-like ) domain. RGS proteins are GTPase-activating (GAP) proteins of heterotrimeric G proteins by increasing the rate of GTP hydrolysis of the alpha subunit. The fungal homologs, like yeast Sst2, share a related common domain architecture, containing RGS and DEP domains. Sst2 has been identified as the principal regulator of mating pheromone signaling and recently the DEP domain of Sst2 has been shown to be necessary and sufficient to mediate receptor interaction.
Probab=27.44 E-value=79 Score=20.42 Aligned_cols=27 Identities=26% Similarity=0.121 Sum_probs=22.6
Q ss_pred eeHHHHHHHHHHHHHcCCeeeeeeccc
Q 038379 57 ISGSLASRAIKDLVARGSIRMISAYAS 83 (93)
Q Consensus 57 I~gSLAr~alkdL~~kG~Ik~Vs~~~~ 83 (93)
++..=|...-..|...|+|.+|..+++
T Consensus 45 ~~~~EA~~~~~~ll~~gli~~V~~~~~ 71 (88)
T cd04450 45 VDPSEALEIAALFVKYGLITPVSDHRS 71 (88)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCCcc
Confidence 566778888899999999999987653
No 172
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=27.34 E-value=1.1e+02 Score=21.23 Aligned_cols=25 Identities=24% Similarity=0.171 Sum_probs=20.5
Q ss_pred eeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 54 LVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 54 rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
..++|=..|+.-|++|+++|+|..-
T Consensus 40 ~aNlny~~~~~yi~~L~~~Gli~~~ 64 (95)
T COG3432 40 GANLNYKRAQKYIEMLVEKGLIIKQ 64 (95)
T ss_pred ecCcCHHHHHHHHHHHHhCCCEEec
Confidence 4457888999999999999966554
No 173
>TIGR03418 chol_sulf_TF putative choline sulfate-utilization transcription factor. Members of this protein family are transcription factors of the LysR family. Their genes typically are divergently transcribed from choline-sulfatase genes. That enzyme makes choline, a precursor to the osmoprotectant glycine-betaine, available by hydrolysis of choline sulfate.
Probab=27.13 E-value=36 Score=24.29 Aligned_cols=34 Identities=9% Similarity=-0.049 Sum_probs=25.6
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccce
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQ 84 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q 84 (93)
-+++++|+-|-.++.|++||++==.+......+.
T Consensus 21 AA~~L~itqpavS~~Ik~LE~~lg~~LF~R~~r~ 54 (291)
T TIGR03418 21 AARELGSTQPAVSQQVKRLEEELGTPLFERGHRG 54 (291)
T ss_pred HHHHhCCCHHHHHHHHHHHHHHhCcHHhhcCCCc
Confidence 4689999999999999999986545554444333
No 174
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. 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 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=27.05 E-value=46 Score=21.79 Aligned_cols=35 Identities=11% Similarity=0.133 Sum_probs=25.0
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
+++++.|+ ...|+..++.|+|.+.-..+.+..|+.
T Consensus 7 va~~~gVs----~~tLR~ye~~Gli~p~r~~~g~R~Ys~ 41 (98)
T cd01279 7 AAELLGIH----PQTLRVYDRLGLVSPARTNGGGRRYSN 41 (98)
T ss_pred HHHHHCcC----HHHHHHHHHCCCCCCCcCCCCCeeECH
Confidence 55555554 456788899999998644567788874
No 175
>PF05238 CENP-N: Kinetochore protein CHL4 like; InterPro: IPR007902 This family includes CHL4 that is involved in chromosome segregation []. It is required for chromosome stability but is non-essential for growth. Chl4 is a component of the central kinetochore, which mediates the attachment of the centromere to the mitotic spindle by forming essential interactions between the microtubule-associated outer kinetochore proteins and the centromere-associated inner kinetochore proteins. It is required for the establishment of bipolar spindle-microtubule attachments and proper chromosome segregation. Sgo1, Chl4, and Iml3 are all important for retaining centromeric cohesion until the onset of anaphase II [].
Probab=26.64 E-value=67 Score=26.28 Aligned_cols=31 Identities=19% Similarity=0.229 Sum_probs=27.6
Q ss_pred CcccccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 47 NEAGFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 47 ~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
.+.-+.++++.+|+=-=.+|++|+++|+|..
T Consensus 349 ~~~~~~i~lkfsG~dVfaGLr~La~~GiiD~ 379 (400)
T PF05238_consen 349 DEEPPRIKLKFSGPDVFAGLRELAEAGIIDP 379 (400)
T ss_pred CCCCceEEEEEECchHHHHHHHHHHcCCcCc
Confidence 4556899999999999999999999999865
No 176
>smart00526 H15 Domain in histone families 1 and 5.
Probab=26.62 E-value=79 Score=19.04 Aligned_cols=20 Identities=40% Similarity=0.501 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHcCCeeee
Q 038379 59 GSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 59 gSLAr~alkdL~~kG~Ik~V 78 (93)
-++-+.+|+.++++|.+..+
T Consensus 45 ~~~l~~~Lk~~v~~G~l~q~ 64 (66)
T smart00526 45 RSLLKLALKKLVASGKLVQV 64 (66)
T ss_pred HHHHHHHHHHHHhcCceeec
Confidence 47889999999999998765
No 177
>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=26.42 E-value=1e+02 Score=18.61 Aligned_cols=24 Identities=21% Similarity=0.181 Sum_probs=21.4
Q ss_pred eeHHHHHHHHHHHHHcCCeeeeee
Q 038379 57 ISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 57 I~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
.+-+-|.+..+.|.+.|+|.+|..
T Consensus 37 ~~r~eA~~l~~~ll~~g~i~~v~~ 60 (77)
T smart00049 37 IDREEAVHLGQLLLDEGLIHHVNG 60 (77)
T ss_pred CCHHHHHHHHHHHHHCCCEEEeCC
Confidence 467889999999999999999984
No 178
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=26.42 E-value=57 Score=24.30 Aligned_cols=29 Identities=17% Similarity=0.272 Sum_probs=27.0
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+++++.++-|=+.|.|+.|++.|++....
T Consensus 32 ia~~lgl~kstv~RlL~tL~~~g~v~~~~ 60 (263)
T PRK09834 32 LAELTGLHRTTVRRLLETLQEEGYVRRSA 60 (263)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence 89999999999999999999999998754
No 179
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=25.82 E-value=37 Score=27.45 Aligned_cols=34 Identities=18% Similarity=0.192 Sum_probs=29.8
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
|.+- +++++.|+=..++|.|+...++|+++-=..
T Consensus 28 tQ~e----IA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~ 61 (321)
T COG2390 28 TQSE----IAERLGISRATVSRLLAKAREEGIVKISIN 61 (321)
T ss_pred CHHH----HHHHhCCCHHHHHHHHHHHHHCCeEEEEeC
Confidence 6666 999999999999999999999999985433
No 180
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). 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=25.57 E-value=39 Score=22.50 Aligned_cols=28 Identities=11% Similarity=0.138 Sum_probs=22.2
Q ss_pred HHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
..++|+.-++.|+|.+.-..+....|+.
T Consensus 13 s~~tlR~Ye~~GLl~p~r~~~g~R~Y~~ 40 (112)
T cd01282 13 SVRSLRYYEEQGLLVPERSANGYRDYDE 40 (112)
T ss_pred CHHHHHHHHHCCCCCCCcCCCCCeecCH
Confidence 3578999999999998655567778864
No 181
>TIGR00331 hrcA heat shock gene repressor HrcA. In Bacillus subtilis, hrcA is the first gene of the dnaK operon and so is itself a heat shock gene.
Probab=25.42 E-value=50 Score=26.41 Aligned_cols=32 Identities=19% Similarity=0.098 Sum_probs=28.3
Q ss_pred eccCCcccccce--eeeeHHHHHHHHHHHHHcCCeeee
Q 038379 43 TSTGNEAGFNCL--VHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 43 T~s~~~~~~~~r--lkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
++.. ++++ +.+|.+=+|+-+.+|++.|++...
T Consensus 23 ~s~~----l~~~~~~~vS~aTiR~d~~~Le~~G~l~~~ 56 (337)
T TIGR00331 23 GSKT----LLEKYNLGLSSATIRNDMADLEDLGFIEKP 56 (337)
T ss_pred CHHH----HHhhcCCCCChHHHHHHHHHHHHCCCccCC
Confidence 5555 8889 999999999999999999999875
No 182
>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=25.22 E-value=45 Score=22.36 Aligned_cols=28 Identities=14% Similarity=0.242 Sum_probs=22.7
Q ss_pred HHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
...+|+.-+++|++.+.-.......|+.
T Consensus 13 s~~tlRyYe~~GLl~p~~~~~gyR~Y~~ 40 (120)
T cd04781 13 PASTLRYYEEKGLIASIGRRGLRRQYDP 40 (120)
T ss_pred CHHHHHHHHHCCCCCCCcCCCCceecCH
Confidence 3578999999999999865567788874
No 183
>PF00538 Linker_histone: linker histone H1 and H5 family; InterPro: IPR005818 Histone proteins have central roles in both chromatin organisation (as structural units of the nucleosome) and gene regulation (as dynamic components that have a direct impact on DNA transcription and replication). Eukaryotic DNA wraps around a histone octamer to form a nucleosome, the first order of compaction of eukaryotic chromatin. The core histone octamer is composed of a central H3-H4 tetramer and two flanking H2A-H2B dimers. Each of the core histone contains a common structural motif, called the histone fold, which facilitates the interactions between the individual core histones. In addition to the core histones, there is a "linker histone" called H1 (or H5 in avian species). The linker histones present in all multicellular eukaryotes are the most divergent group of histones, with numerous cell type- and stage-specific variant. Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known [, ]. The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA. The linker histones, which do not contain the histone fold motif, are critical to the higher-order compaction of chromatin, because they bind to internucleosomal DNA and facilitate interactions between individual nucleosomes. In addition, H1 variants have been shown to be involved in the regulation of developmental genes. A common feature of this protein family is a tripartite structure in which a globular (H15) domain of about 80 amino acids is flanked by two less structured N- and C-terminal tails. The H15 domain is also characterised by high sequence homology among the family of linker histones. The highly conserved H15 domain is essential for the binding of H1 or H5 to the nucleosome. It consists of a three helix bundle (I-III), with a beta-hairpin at the C terminus. There is also a short three-residue stretch between helices I and II that is in the beta-strand conformation. Together with the C-terminal beta-hairpin, this strand forms the third strand of an antiparallel beta-sheet [, , , ]. Proteins known to contain a H15 domain are: - Eukaryotic histone H1. The histones H1 constitute a family with many variants, differing in their affinity for chromatin. Several variants are simultaneously present in a single cell. For example, the nucleated erythrocytes of birds contain both H1 and H5, the latter being an extreme variant of H1. - Eukaryotic MHYST family of histone acetyltransferase. Histone acetyltransferases transfer an acetyl group from acetyl-CoA to the epsylon- amino group of lysine within the basic NH2-termini of histones, which bind the acidic phosphates of DNA []. This entry represents the H15 domain.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 2LSO_A 2RQP_A 1UHM_A 1UST_A 1GHC_A 1HST_A 1YQA_A 1USS_A.
Probab=24.72 E-value=1e+02 Score=19.24 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHcCCeeeeee
Q 038379 59 GSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 59 gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
.++-++||+.++++|.+..+..
T Consensus 45 ~~~l~~aLk~~v~~G~l~~~kg 66 (77)
T PF00538_consen 45 KSRLKRALKRGVEKGKLVQVKG 66 (77)
T ss_dssp HHHHHHHHHHHHHCTSEEECSC
T ss_pred HHHHHHHHHHHHHCCcEEeecc
Confidence 4678999999999999998863
No 184
>PF13338 DUF4095: Domain of unknown function (DUF4095)
Probab=24.41 E-value=65 Score=20.23 Aligned_cols=19 Identities=32% Similarity=0.625 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHcCCeeeee
Q 038379 61 LASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 61 LAr~alkdL~~kG~Ik~Vs 79 (93)
+.+++|+.++++|.+..+.
T Consensus 2 ~sr~~l~~~~~~G~l~rl~ 20 (124)
T PF13338_consen 2 ISRRALRRLVRRGELIRLR 20 (124)
T ss_pred cCHHHHHHHHHCCCEEEee
Confidence 3578999999999998875
No 185
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=24.37 E-value=93 Score=20.09 Aligned_cols=34 Identities=15% Similarity=0.207 Sum_probs=28.0
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
-.+++..|+.-+++ |.|..++++..+|+|--|.+
T Consensus 25 ~~tGR~rgvir~fg----l~R~~FRe~A~~G~ipGv~K 58 (61)
T PRK08061 25 ERCGRPHSVYRKFG----LCRICFRELAYKGQIPGVKK 58 (61)
T ss_pred ecCCCCcceeccCC----ccHHHHHHHHHcCcCCCeee
Confidence 45677778888886 89999999999999966654
No 186
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=24.00 E-value=60 Score=18.91 Aligned_cols=28 Identities=7% Similarity=0.116 Sum_probs=21.2
Q ss_pred HHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
....|+..+++|++.+.-....+..|+-
T Consensus 13 s~~tlr~y~~~gll~~~~~~~g~r~y~~ 40 (69)
T PF13411_consen 13 SPSTLRYYEREGLLPPPRDENGYRYYSE 40 (69)
T ss_dssp THHHHHHHHHTTSSTTBESTTSSEEE-H
T ss_pred CHHHHHHHHHhcCcccccccCceeeccH
Confidence 4677999999999888775666678873
No 187
>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=23.66 E-value=87 Score=19.58 Aligned_cols=30 Identities=23% Similarity=0.174 Sum_probs=26.2
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISA 80 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~ 80 (93)
+...+++...-.-..++.|+++|+|...+.
T Consensus 24 L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 24 LSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred HHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 777888888888999999999999988765
No 188
>PF14242 DUF4342: Domain of unknown function (DUF4342)
Probab=23.55 E-value=2.3e+02 Score=18.88 Aligned_cols=37 Identities=16% Similarity=0.302 Sum_probs=29.8
Q ss_pred ccccceeeeeHHHHHHHHHHHHHcCCeeee-eeccceE
Q 038379 49 AGFNCLVHISGSLASRAIKDLVARGSIRMI-SAYASQQ 85 (93)
Q Consensus 49 ~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V-s~~~~Q~ 85 (93)
..+.|.+.++|+=--..+|||..+|-.+.+ .+...+.
T Consensus 5 ~~~~e~~~~~g~~~~~~iK~li~kGNv~Ri~Ikk~~~t 42 (84)
T PF14242_consen 5 KSWTEEFQVKGEELVDKIKELIKKGNVTRIIIKKDDKT 42 (84)
T ss_pred ccccceeeecHHHHHHHHHHHHHhcCeEEEEEEcCCeE
Confidence 347789999999999999999999999887 3444443
No 189
>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=23.50 E-value=1.2e+02 Score=18.66 Aligned_cols=26 Identities=19% Similarity=0.061 Sum_probs=19.5
Q ss_pred eeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 54 LVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 54 rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
.+..+-+.-+++|..|.++|.|+.-.
T Consensus 39 ~f~~~~~~ik~~Ie~LIekeyi~Rd~ 64 (68)
T PF10557_consen 39 RFPPSVSDIKKRIESLIEKEYIERDE 64 (68)
T ss_dssp TS---HHHHHHHHHHHHHTTSEEEES
T ss_pred CcCCCHHHHHHHHHHHHHhhhhhcCC
Confidence 44556689999999999999998753
No 190
>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=23.43 E-value=48 Score=21.81 Aligned_cols=35 Identities=14% Similarity=0.068 Sum_probs=24.9
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
+++++.|+ .++|+.-++.|+|.+........+|+.
T Consensus 7 va~~~gvs----~~tlR~ye~~Gll~~~r~~~g~R~Y~~ 41 (102)
T cd04789 7 LAEKAGIS----RSTLLYYEKLGLITGTRNANGYRLYPD 41 (102)
T ss_pred HHHHHCcC----HHHHHHHHHCCCCCCCcCCCCCeeCCH
Confidence 45555544 467889999999998654566778863
No 191
>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=23.42 E-value=48 Score=22.64 Aligned_cols=28 Identities=11% Similarity=0.209 Sum_probs=21.3
Q ss_pred HHHHHHHHHHcCCeeeeeec-cceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAY-ASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~-~~Q~IYTR 89 (93)
..++||.-++.|+|.+.... +....|+.
T Consensus 13 s~~TLRyYE~~GLl~p~r~~~~gyR~Y~~ 41 (133)
T cd04787 13 TPDTVRFYTRIGLLRPTRDPVNGYRLYSE 41 (133)
T ss_pred CHHHHHHHHHCCCCCCCcCCCCCeeeCCH
Confidence 35689999999999997443 56677763
No 192
>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=22.82 E-value=59 Score=21.30 Aligned_cols=35 Identities=14% Similarity=0.157 Sum_probs=24.1
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
+++++.|+ .++|+..+++|+|.+.-..+....|+.
T Consensus 7 va~~~gvs----~~tLR~ye~~Gll~~~r~~~g~R~Y~~ 41 (102)
T cd04775 7 MSRKFGVS----RSTLLYYESIGLIPSARSEANYRLYSE 41 (102)
T ss_pred HHHHHCcC----HHHHHHHHHCCCCCCCCCCCCCeeeCH
Confidence 55555544 567899999999955544456677863
No 193
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.48 E-value=43 Score=21.15 Aligned_cols=28 Identities=11% Similarity=0.249 Sum_probs=20.7
Q ss_pred HHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
....|+..+++|+|.+....+...+|+.
T Consensus 13 ~~~tlr~~~~~Gll~~~~~~~g~r~y~~ 40 (100)
T cd00592 13 SVRTLRYYEEKGLLPPERSENGYRLYSE 40 (100)
T ss_pred CHHHHHHHHHCCCcCCCcCCCCCcccCH
Confidence 4567889999999986554456677874
No 194
>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=22.45 E-value=44 Score=22.07 Aligned_cols=28 Identities=11% Similarity=0.150 Sum_probs=21.3
Q ss_pred HHHHHHHHHHcCCeeeeee--ccceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISA--YASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~--~~~Q~IYTR 89 (93)
...+|+.-+++|+|.+... .+....|+.
T Consensus 13 s~~tlR~ye~~GLi~p~~~~~~ngyR~Y~~ 42 (108)
T cd01107 13 SIKALRYYDKIGLLKPAYVDPDTGYRYYSA 42 (108)
T ss_pred CHHHHHHHHHcCCCCCCcCCCCCCccccCH
Confidence 4578999999999998642 356677864
No 195
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), 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=22.29 E-value=46 Score=21.74 Aligned_cols=26 Identities=8% Similarity=0.152 Sum_probs=19.7
Q ss_pred HHHHHHHHHHcCCeeeeeeccceEEEE
Q 038379 62 ASRAIKDLVARGSIRMISAYASQQIYT 88 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~~~Q~IYT 88 (93)
..++|+.-++.|+|.+.. .+....|+
T Consensus 13 s~~tlRyYe~~GLl~p~~-~~g~r~Y~ 38 (107)
T cd04777 13 TIDTVRHYIDLGLLIPEK-KGGQYFFD 38 (107)
T ss_pred CHHHHHHHHHCCCcCCcc-CCCccccC
Confidence 356899999999999853 34556675
No 196
>PLN02522 ATP citrate (pro-S)-lyase
Probab=22.11 E-value=80 Score=28.01 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHcCCeeeee
Q 038379 59 GSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 59 gSLAr~alkdL~~kG~Ik~Vs 79 (93)
+.++++++++|+++|.|.++.
T Consensus 307 ~~~~~~~~~~~~~~~~~~~~~ 327 (608)
T PLN02522 307 EAAIKETFEKLVEEGKIIPVK 327 (608)
T ss_pred HHHHHHHHHHHHhCCceeecC
Confidence 568899999999999999864
No 197
>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=22.09 E-value=51 Score=22.27 Aligned_cols=29 Identities=24% Similarity=0.287 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHcCCeeeee-eccceEEEEe
Q 038379 61 LASRAIKDLVARGSIRMIS-AYASQQIYTR 89 (93)
Q Consensus 61 LAr~alkdL~~kG~Ik~Vs-~~~~Q~IYTR 89 (93)
+..++||.-+++|+|.+.. ..+....|+.
T Consensus 12 vs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~ 41 (127)
T TIGR02044 12 LSSKMIRYYEEKGLIPPPLRSEGGYRTYTQ 41 (127)
T ss_pred cCHHHHHHHHHCCCCCCCCcCCCCCeecCH
Confidence 3467899999999999863 3467778874
No 198
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=21.43 E-value=1.6e+02 Score=20.52 Aligned_cols=38 Identities=16% Similarity=0.029 Sum_probs=30.5
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
+++.+.++=|-.++=|+.|.+-|+|..-.. .....|..
T Consensus 36 la~~l~lsqstvS~HL~~L~~AGLV~~~r~-Gr~~~Y~l 73 (117)
T PRK10141 36 LCTALDQSQPKISRHLALLRESGLLLDRKQ-GKWVHYRL 73 (117)
T ss_pred HHHHHCcCHHHHHHHHHHHHHCCceEEEEE-cCEEEEEE
Confidence 788999999999999999999999987543 34445543
No 199
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=21.33 E-value=69 Score=22.64 Aligned_cols=28 Identities=29% Similarity=0.343 Sum_probs=22.3
Q ss_pred HHHHHHHHHHcCCeeeeeeccceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAYASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~~~Q~IYTR 89 (93)
...+||.-+++|+|.+.-....+..|+.
T Consensus 14 s~~tLRyYE~~GLl~~~r~~~g~R~Y~~ 41 (142)
T TIGR01950 14 AVSALHFYESKGLITSIRNSGNQRRYKR 41 (142)
T ss_pred CHHHHHHHHHCCCCCCccCCCCCEEECH
Confidence 3578999999999998655566788874
No 200
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=21.22 E-value=81 Score=27.51 Aligned_cols=36 Identities=25% Similarity=0.274 Sum_probs=30.6
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceEE
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQI 86 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~I 86 (93)
++..++++-.-|-|||||-+.+|+..-+-....-+|
T Consensus 25 Ia~~l~VSeGTAYRAIKeAen~G~V~Ti~RvGTvRI 60 (432)
T COG4109 25 IAKHLKVSEGTAYRAIKEAENLGLVSTIPRVGTVRI 60 (432)
T ss_pred hhhhCCcccchHHHHHHHHHhcCceEecccceeEEE
Confidence 899999999999999999999999987765554444
No 201
>COG4860 Uncharacterized protein conserved in archaea [Function unknown]
Probab=21.22 E-value=46 Score=25.73 Aligned_cols=46 Identities=22% Similarity=0.151 Sum_probs=36.5
Q ss_pred eechhhhhhhhhhhhhhhhhhhhcCccccccceeeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCee
Q 038379 3 LFDQGTYDKHFPTLRECLFLVRSCGKVSQEGTKMFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIR 76 (93)
Q Consensus 3 lfDk~TydK~~kev~~~~~~~~~~~~~~~~g~~~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik 76 (93)
.||.+||.|++..+.+ +.+ |-.. +-+.. |+=.||||.-|-.-|+|.
T Consensus 20 ~~~set~rKl~~aLst--------------------gW~-T~~e----iee~i---G~eg~RaL~iLkkagmlE 65 (170)
T COG4860 20 AADSETKRKLLLALST--------------------GWI-TLPE----IEEKI---GKEGRRALLILKKAGMLE 65 (170)
T ss_pred HcccHHHHHHHHHHhh--------------------cce-eHHH----HHHHh---chhhHHHHHHHHhhcchh
Confidence 4789999999999988 566 8777 55554 677788999999888874
No 202
>PF14217 DUF4327: Domain of unknown function (DUF4327)
Probab=21.18 E-value=24 Score=23.47 Aligned_cols=21 Identities=33% Similarity=0.547 Sum_probs=14.9
Q ss_pred HHHHHHHHHcCCeeeeeeccceEEEE
Q 038379 63 SRAIKDLVARGSIRMISAYASQQIYT 88 (93)
Q Consensus 63 r~alkdL~~kG~Ik~Vs~~~~Q~IYT 88 (93)
++=-+.|+++|.|+ ++|.|||
T Consensus 8 q~ear~LV~~g~v~-----r~qpI~~ 28 (68)
T PF14217_consen 8 QDEARSLVESGVVS-----RQQPIYT 28 (68)
T ss_pred HHHHHHHHHcCCCC-----ccCcHHH
Confidence 34458899999995 4566665
No 203
>PRK12704 phosphodiesterase; Provisional
Probab=21.16 E-value=97 Score=26.48 Aligned_cols=43 Identities=23% Similarity=0.205 Sum_probs=30.9
Q ss_pred eeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeeee
Q 038379 36 MFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMI 78 (93)
Q Consensus 36 ~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~V 78 (93)
-||-|||..+.+---+|+---++--.|+.+|..|...|.|+|.
T Consensus 240 tgvd~iiddtp~~v~ls~~~~~rre~a~~~l~~l~~dg~i~P~ 282 (520)
T PRK12704 240 TGVDLIIDDTPEAVILSGFDPIRREIARLALEKLVQDGRIHPA 282 (520)
T ss_pred hCCeEEEcCCCCeEEEecCChhhHHHHHHHHHHHHhcCCcCCC
Confidence 3668887766633334444445556999999999999999885
No 204
>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=21.07 E-value=66 Score=20.60 Aligned_cols=34 Identities=24% Similarity=0.374 Sum_probs=24.1
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeecc-ceEEEE
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYA-SQQIYT 88 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~-~Q~IYT 88 (93)
+++.+.|+ .+.|+..+++|+|.+..... ....|+
T Consensus 7 vA~~~gvs----~~tLR~ye~~Gll~p~r~~~~g~R~Ys 41 (88)
T cd01105 7 VSKLTGVS----PRQLRYWEEKGLIKSIRSDGGGQRKYS 41 (88)
T ss_pred HHHHHCcC----HHHHHHHHHCCCCCCCccCCCCceecC
Confidence 55555444 56788999999999765443 677886
No 205
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=21.01 E-value=83 Score=26.13 Aligned_cols=33 Identities=15% Similarity=0.126 Sum_probs=29.5
Q ss_pred eccCCcccccceeeeeHHHHHHHHHHHHHcCCeeeee
Q 038379 43 TSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRMIS 79 (93)
Q Consensus 43 T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs 79 (93)
|++. +++++.++-|-..++++.|+++|+|....
T Consensus 22 s~~e----LA~~l~l~~~tVt~~i~~Le~kGlV~~~~ 54 (489)
T PRK04172 22 TLEE----LAEKLGLPPEAVMRAAEWLEEKGLVKVEE 54 (489)
T ss_pred CHHH----HHHHhCcCHHHHHHHHHHHHhCCCEEEEe
Confidence 6666 89999999999999999999999998754
No 206
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=20.94 E-value=1.7e+02 Score=16.39 Aligned_cols=27 Identities=22% Similarity=0.251 Sum_probs=24.1
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
+++.+.++-+-.+.-|+.|.+.|+|..
T Consensus 45 l~~~~~~~~~~v~~hL~~L~~~glv~~ 71 (110)
T COG0640 45 LAEALGLSQSTVSHHLKVLREAGLVEL 71 (110)
T ss_pred HHHHHCCChhHHHHHHHHHHHCCCeEE
Confidence 666668899999999999999999998
No 207
>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=20.45 E-value=84 Score=18.46 Aligned_cols=35 Identities=23% Similarity=0.126 Sum_probs=25.2
Q ss_pred ccceeeeeHHHHHHHHHHHHHcCCeeeeeeccceE
Q 038379 51 FNCLVHISGSLASRAIKDLVARGSIRMISAYASQQ 85 (93)
Q Consensus 51 ~~~rlkI~gSLAr~alkdL~~kG~Ik~Vs~~~~Q~ 85 (93)
-++.++|+-|-.++.|++|++.==.+.+.......
T Consensus 19 AA~~l~is~~~vs~~i~~LE~~lg~~Lf~r~~~~~ 53 (60)
T PF00126_consen 19 AAEELGISQSAVSRQIKQLEEELGVPLFERSGRGL 53 (60)
T ss_dssp HHHHCTSSHHHHHHHHHHHHHHHTS-SEEECSSSE
T ss_pred HHHHhhccchHHHHHHHHHHHHhCCeEEEECCCCe
Confidence 56889999999999999999864444444444433
No 208
>TIGR03319 YmdA_YtgF conserved hypothetical protein YmdA/YtgF.
Probab=20.42 E-value=91 Score=26.62 Aligned_cols=42 Identities=19% Similarity=0.211 Sum_probs=33.1
Q ss_pred eeeeEEEeccCCcccccceeeeeHHHHHHHHHHHHHcCCeee
Q 038379 36 MFVKLCFTSTGNEAGFNCLVHISGSLASRAIKDLVARGSIRM 77 (93)
Q Consensus 36 ~~vKli~T~s~~~~~~~~rlkI~gSLAr~alkdL~~kG~Ik~ 77 (93)
-||-|||-.+.+.--+||-=-|+--+||.+|..|...|-|-|
T Consensus 234 tgvd~iiddtp~~v~ls~fdp~rreia~~~l~~li~dgrihp 275 (514)
T TIGR03319 234 TGVDLIIDDTPEAVILSGFDPVRREIARMALEKLIQDGRIHP 275 (514)
T ss_pred hCceEEEcCCCCeEEecCCchHHHHHHHHHHHHHHHcCCCCH
Confidence 467888877765555666666777999999999999998865
No 209
>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=20.05 E-value=65 Score=21.15 Aligned_cols=28 Identities=18% Similarity=0.191 Sum_probs=20.3
Q ss_pred HHHHHHHHHHcCCeeeeeec-cceEEEEe
Q 038379 62 ASRAIKDLVARGSIRMISAY-ASQQIYTR 89 (93)
Q Consensus 62 Ar~alkdL~~kG~Ik~Vs~~-~~Q~IYTR 89 (93)
..+.|+..+++|+|.+.... .....|+.
T Consensus 13 s~~tlR~Ye~~GLl~p~~r~~~g~r~Y~~ 41 (95)
T cd04780 13 SVATIKYYLREGLLPEGRRLAPNQAEYSE 41 (95)
T ss_pred CHHHHHHHHHCCCCCCCcCCCCCCeecCH
Confidence 45689999999999986433 34567763
Done!