Query psy1871
Match_columns 139
No_of_seqs 133 out of 219
Neff 3.9
Searched_HMMs 46136
Date Fri Aug 16 18:27:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1871.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1871hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1767|consensus 100.0 1.5E-49 3.2E-54 295.2 6.7 109 20-136 2-110 (110)
2 PF03297 Ribosomal_S25: S25 ri 100.0 7E-48 1.5E-52 284.6 7.4 105 20-132 1-105 (105)
3 COG4901 Ribosomal protein S25 100.0 1.3E-35 2.8E-40 220.0 6.3 106 20-133 1-106 (107)
4 PRK09334 30S ribosomal protein 100.0 7.6E-35 1.6E-39 209.2 8.7 81 51-131 6-86 (86)
5 PF13412 HTH_24: Winged helix- 97.0 0.00074 1.6E-08 41.8 3.1 42 76-117 7-48 (48)
6 PF00392 GntR: Bacterial regul 97.0 0.0023 5E-08 41.8 5.2 49 72-120 4-58 (64)
7 PF08220 HTH_DeoR: DeoR-like h 96.8 0.0026 5.6E-08 41.5 4.3 45 75-119 3-47 (57)
8 smart00345 HTH_GNTR helix_turn 96.7 0.0071 1.5E-07 37.2 5.8 37 83-119 17-53 (60)
9 cd07377 WHTH_GntR Winged helix 96.6 0.0081 1.8E-07 37.7 5.7 49 71-119 4-58 (66)
10 PF01978 TrmB: Sugar-specific 96.6 0.0076 1.6E-07 39.6 5.7 46 83-130 19-64 (68)
11 PF14502 HTH_41: Helix-turn-he 96.5 0.0058 1.3E-07 40.2 4.5 41 83-123 3-43 (48)
12 smart00418 HTH_ARSR helix_turn 96.5 0.011 2.4E-07 35.9 5.4 45 85-130 9-53 (66)
13 PF04703 FaeA: FaeA-like prote 96.2 0.011 2.5E-07 40.1 4.6 43 86-128 15-57 (62)
14 PF02082 Rrf2: Transcriptional 96.0 0.034 7.3E-07 38.1 6.3 51 80-130 19-69 (83)
15 cd00090 HTH_ARSR Arsenical Res 95.9 0.032 6.9E-07 34.6 5.6 44 87-131 21-64 (78)
16 PF12802 MarR_2: MarR family; 95.8 0.026 5.6E-07 35.7 4.9 34 87-120 22-55 (62)
17 PF13463 HTH_27: Winged helix 95.7 0.042 9E-07 35.2 5.6 47 83-129 15-63 (68)
18 PF08222 HTH_CodY: CodY helix- 95.7 0.027 5.9E-07 38.8 4.8 34 86-119 4-37 (61)
19 PRK13509 transcriptional repre 95.7 0.019 4E-07 47.0 4.8 49 71-119 4-52 (251)
20 smart00419 HTH_CRP helix_turn_ 95.6 0.024 5.2E-07 33.8 4.0 32 87-118 9-40 (48)
21 TIGR02325 C_P_lyase_phnF phosp 95.6 0.035 7.5E-07 43.5 5.9 39 82-120 28-66 (238)
22 PF09012 FeoC: FeoC like trans 95.6 0.012 2.6E-07 39.4 2.7 47 77-123 5-51 (69)
23 PRK09764 DNA-binding transcrip 95.6 0.036 7.8E-07 44.2 6.0 39 82-120 25-63 (240)
24 TIGR02404 trehalos_R_Bsub treh 95.6 0.036 7.8E-07 43.7 5.9 39 82-120 20-58 (233)
25 PRK10906 DNA-binding transcrip 95.5 0.022 4.8E-07 46.8 4.7 48 72-119 5-52 (252)
26 TIGR02018 his_ut_repres histid 95.5 0.038 8.2E-07 43.6 5.9 39 82-120 21-59 (230)
27 PRK11534 DNA-binding transcrip 95.5 0.032 6.8E-07 43.7 5.3 52 69-121 8-65 (224)
28 smart00420 HTH_DEOR helix_turn 95.5 0.063 1.4E-06 32.1 5.5 45 72-120 4-48 (53)
29 PF01325 Fe_dep_repress: Iron 95.4 0.028 6.1E-07 37.3 4.0 37 83-119 19-55 (60)
30 PRK03837 transcriptional regul 95.3 0.035 7.6E-07 43.6 5.1 50 71-120 16-71 (241)
31 PRK10225 DNA-binding transcrip 95.3 0.048 1E-06 43.7 5.9 50 71-120 12-67 (257)
32 PRK14165 winged helix-turn-hel 95.3 0.042 9E-07 45.2 5.6 50 80-129 15-64 (217)
33 cd00092 HTH_CRP helix_turn_hel 95.3 0.047 1E-06 34.7 4.7 36 85-120 24-59 (67)
34 TIGR02787 codY_Gpos GTP-sensin 95.3 0.048 1E-06 46.4 6.0 59 62-120 173-232 (251)
35 PRK10434 srlR DNA-bindng trans 95.3 0.024 5.3E-07 46.4 4.1 48 72-119 5-52 (256)
36 PHA02943 hypothetical protein; 95.2 0.066 1.4E-06 43.1 6.1 55 75-130 14-68 (165)
37 PF09339 HTH_IclR: IclR helix- 95.1 0.05 1.1E-06 34.3 4.3 32 87-118 19-50 (52)
38 COG1349 GlpR Transcriptional r 95.0 0.034 7.5E-07 45.7 4.2 47 73-119 6-52 (253)
39 PF12840 HTH_20: Helix-turn-he 95.0 0.045 9.8E-07 35.4 3.9 50 72-121 10-59 (61)
40 PF01047 MarR: MarR family; I 94.9 0.051 1.1E-06 34.2 4.0 34 87-120 18-51 (59)
41 PRK11402 DNA-binding transcrip 94.8 0.064 1.4E-06 42.6 5.3 38 82-119 29-66 (241)
42 COG1522 Lrp Transcriptional re 94.8 0.076 1.6E-06 39.0 5.2 48 69-120 9-56 (154)
43 COG3355 Predicted transcriptio 94.8 0.14 3E-06 39.5 6.8 61 68-132 27-92 (126)
44 TIGR03338 phnR_burk phosphonat 94.7 0.08 1.7E-06 40.9 5.5 49 70-119 13-67 (212)
45 smart00550 Zalpha Z-DNA-bindin 94.7 0.06 1.3E-06 36.2 4.2 34 87-120 23-56 (68)
46 PRK10421 DNA-binding transcrip 94.7 0.089 1.9E-06 42.1 5.9 50 71-120 5-60 (253)
47 COG2188 PhnF Transcriptional r 94.7 0.062 1.3E-06 43.3 5.0 40 82-121 27-66 (236)
48 PRK14999 histidine utilization 94.7 0.079 1.7E-06 42.2 5.4 38 82-119 32-69 (241)
49 PRK04984 fatty acid metabolism 94.5 0.073 1.6E-06 42.0 4.9 49 71-119 10-64 (239)
50 TIGR02702 SufR_cyano iron-sulf 94.5 0.078 1.7E-06 41.8 5.0 47 87-133 16-66 (203)
51 PRK09990 DNA-binding transcrip 94.5 0.12 2.5E-06 41.2 6.0 52 70-121 9-66 (251)
52 PF13730 HTH_36: Helix-turn-he 94.5 0.057 1.2E-06 33.8 3.4 30 87-116 26-55 (55)
53 PF09397 Ftsk_gamma: Ftsk gamm 94.4 0.041 9E-07 37.8 2.9 59 70-128 4-62 (65)
54 TIGR02337 HpaR homoprotocatech 94.4 0.067 1.5E-06 38.3 4.1 54 77-130 33-88 (118)
55 PRK09802 DNA-binding transcrip 94.4 0.06 1.3E-06 44.6 4.3 49 72-120 17-65 (269)
56 PRK11014 transcriptional repre 94.4 0.11 2.4E-06 38.7 5.4 45 81-125 20-64 (141)
57 TIGR03337 phnR transcriptional 94.3 0.12 2.7E-06 40.2 5.7 39 82-120 21-59 (231)
58 TIGR02812 fadR_gamma fatty aci 94.3 0.092 2E-06 41.4 5.0 50 71-120 9-64 (235)
59 smart00843 Ftsk_gamma This dom 94.1 0.061 1.3E-06 36.9 3.1 54 70-123 3-56 (63)
60 PRK11523 DNA-binding transcrip 94.1 0.097 2.1E-06 41.9 4.8 51 70-120 10-66 (253)
61 PF01726 LexA_DNA_bind: LexA D 93.8 0.11 2.4E-06 35.2 3.9 34 88-121 27-61 (65)
62 PRK10079 phosphonate metabolis 93.8 0.12 2.6E-06 41.2 4.8 48 73-120 21-69 (241)
63 PRK09464 pdhR transcriptional 93.7 0.14 2.9E-06 40.9 5.0 51 70-120 12-68 (254)
64 PRK11512 DNA-binding transcrip 93.7 0.12 2.5E-06 38.3 4.2 37 84-120 52-88 (144)
65 smart00346 HTH_ICLR helix_turn 93.6 0.16 3.5E-06 34.1 4.5 34 86-119 20-53 (91)
66 TIGR01884 cas_HTH CRISPR locus 93.4 0.17 3.6E-06 39.9 4.9 52 76-129 147-198 (203)
67 TIGR02010 IscR iron-sulfur clu 93.4 0.2 4.4E-06 37.1 5.1 41 83-123 22-62 (135)
68 PRK10411 DNA-binding transcrip 93.2 0.18 3.9E-06 41.2 4.9 53 74-129 6-58 (240)
69 PRK11414 colanic acid/biofilm 93.1 0.14 3.1E-06 40.1 4.1 49 71-120 14-68 (221)
70 smart00347 HTH_MARR helix_turn 93.0 0.21 4.5E-06 33.2 4.2 35 86-120 24-58 (101)
71 PRK03573 transcriptional regul 93.0 0.19 4.1E-06 36.9 4.4 42 86-127 46-89 (144)
72 TIGR00738 rrf2_super rrf2 fami 92.9 0.18 3.8E-06 36.5 4.1 38 82-119 21-58 (132)
73 TIGR01610 phage_O_Nterm phage 92.8 0.23 4.9E-06 35.3 4.4 37 83-119 44-80 (95)
74 PRK10870 transcriptional repre 92.8 0.17 3.6E-06 39.4 4.1 36 85-120 70-105 (176)
75 TIGR02944 suf_reg_Xantho FeS a 92.8 0.16 3.4E-06 37.1 3.7 35 85-119 24-58 (130)
76 PRK04424 fatty acid biosynthes 92.7 0.077 1.7E-06 41.9 2.1 48 72-119 7-54 (185)
77 PF04157 EAP30: EAP30/Vps36 fa 92.7 0.22 4.8E-06 40.0 4.8 46 72-117 174-221 (223)
78 smart00344 HTH_ASNC helix_turn 92.5 0.33 7.1E-06 33.9 4.9 45 70-118 5-49 (108)
79 PF13545 HTH_Crp_2: Crp-like h 92.4 0.39 8.5E-06 31.3 4.9 32 86-117 28-59 (76)
80 TIGR01889 Staph_reg_Sar staphy 92.1 0.24 5.3E-06 35.4 3.9 36 85-120 42-77 (109)
81 smart00529 HTH_DTXR Helix-turn 92.0 0.26 5.7E-06 33.6 3.9 32 89-120 2-33 (96)
82 PF09756 DDRGK: DDRGK domain; 91.8 0.27 5.9E-06 39.9 4.3 59 73-131 100-158 (188)
83 PRK03902 manganese transport t 91.7 0.4 8.6E-06 35.6 4.8 36 84-119 20-55 (142)
84 COG2512 Predicted membrane-ass 91.5 0.79 1.7E-05 38.6 6.9 81 51-131 175-255 (258)
85 COG1846 MarR Transcriptional r 91.5 0.44 9.4E-06 32.3 4.5 41 90-130 40-82 (126)
86 COG4465 CodY Pleiotropic trans 91.5 0.34 7.4E-06 41.3 4.7 54 67-120 184-238 (261)
87 COG1802 GntR Transcriptional r 91.2 0.31 6.6E-06 38.5 4.0 56 65-120 13-73 (230)
88 PF08279 HTH_11: HTH domain; 91.2 1 2.2E-05 28.1 5.6 28 87-114 16-43 (55)
89 cd07153 Fur_like Ferric uptake 90.7 0.74 1.6E-05 32.5 5.2 45 85-129 15-64 (116)
90 PF01022 HTH_5: Bacterial regu 90.6 0.58 1.3E-05 29.0 4.0 33 85-117 14-46 (47)
91 COG1321 TroR Mn-dependent tran 90.5 0.52 1.1E-05 36.7 4.6 50 71-120 9-58 (154)
92 cd04761 HTH_MerR-SF Helix-Turn 90.5 0.38 8.3E-06 28.9 3.1 39 88-130 2-40 (49)
93 COG1725 Predicted transcriptio 90.5 0.7 1.5E-05 35.4 5.2 48 82-132 31-78 (125)
94 PRK11050 manganese transport r 90.4 0.57 1.2E-05 35.7 4.7 34 85-118 50-83 (152)
95 TIGR00122 birA_repr_reg BirA b 90.4 1.5 3.2E-05 28.8 6.1 34 87-120 14-47 (69)
96 COG1959 Predicted transcriptio 90.3 0.53 1.2E-05 36.2 4.5 46 85-130 24-69 (150)
97 PRK11920 rirA iron-responsive 90.2 0.59 1.3E-05 35.9 4.6 41 85-125 23-63 (153)
98 PRK04158 transcriptional repre 90.1 0.26 5.7E-06 41.9 2.8 60 59-118 173-233 (256)
99 PRK09954 putative kinase; Prov 90.1 0.32 7E-06 40.7 3.3 42 76-117 7-48 (362)
100 PF01475 FUR: Ferric uptake re 90.0 1.6 3.5E-05 31.3 6.5 54 77-132 16-74 (120)
101 PF00325 Crp: Bacterial regula 89.9 0.64 1.4E-05 28.0 3.7 30 87-116 3-32 (32)
102 PF14947 HTH_45: Winged helix- 89.8 1.1 2.4E-05 30.6 5.3 41 76-117 10-50 (77)
103 PF10007 DUF2250: Uncharacteri 89.7 0.5 1.1E-05 34.4 3.7 38 84-121 19-56 (92)
104 PRK11169 leucine-responsive tr 89.5 0.79 1.7E-05 35.1 4.9 43 76-118 18-60 (164)
105 PRK06266 transcription initiat 89.5 0.45 9.7E-06 37.8 3.5 49 70-118 20-68 (178)
106 PF08784 RPA_C: Replication pr 89.4 0.58 1.3E-05 33.0 3.8 46 71-116 50-95 (102)
107 TIGR00498 lexA SOS regulatory 89.4 0.51 1.1E-05 36.6 3.8 53 70-122 8-62 (199)
108 PF00376 MerR: MerR family reg 89.3 0.64 1.4E-05 28.4 3.4 37 88-128 1-38 (38)
109 smart00422 HTH_MERR helix_turn 89.1 0.43 9.4E-06 30.6 2.7 40 87-130 1-41 (70)
110 PRK15481 transcriptional regul 89.0 0.68 1.5E-05 39.5 4.6 49 71-119 8-62 (431)
111 PF05158 RNA_pol_Rpc34: RNA po 88.7 0.86 1.9E-05 39.4 5.0 67 63-131 79-147 (327)
112 cd01105 HTH_GlnR-like Helix-Tu 88.3 0.51 1.1E-05 32.9 2.8 41 86-130 1-42 (88)
113 PRK13777 transcriptional regul 88.1 0.85 1.8E-05 36.5 4.3 37 84-120 57-93 (185)
114 PRK10857 DNA-binding transcrip 87.9 1 2.2E-05 35.2 4.6 47 83-131 22-68 (164)
115 TIGR02698 CopY_TcrY copper tra 87.9 0.81 1.7E-05 34.3 3.8 46 87-133 19-68 (130)
116 PRK11179 DNA-binding transcrip 87.8 1.3 2.7E-05 33.5 4.9 46 69-118 10-55 (153)
117 cd01279 HTH_HspR-like Helix-Tu 87.7 0.62 1.3E-05 33.2 3.0 42 86-131 1-42 (98)
118 cd04766 HTH_HspR Helix-Turn-He 87.6 0.69 1.5E-05 32.2 3.1 41 86-130 1-41 (91)
119 PRK11753 DNA-binding transcrip 87.3 1.4 3.1E-05 33.2 4.9 41 86-128 168-208 (211)
120 PRK15090 DNA-binding transcrip 87.0 1.5 3.3E-05 35.4 5.2 36 86-121 28-63 (257)
121 PRK09834 DNA-binding transcrip 86.3 1.5 3.3E-05 35.6 4.9 37 87-123 27-63 (263)
122 PF12728 HTH_17: Helix-turn-he 86.2 1.2 2.7E-05 27.4 3.4 40 86-130 1-40 (51)
123 COG2186 FadR Transcriptional r 85.9 1.5 3.2E-05 35.7 4.6 58 71-131 13-76 (241)
124 TIGR01764 excise DNA binding d 85.5 1.6 3.5E-05 25.6 3.6 40 86-130 1-40 (49)
125 PRK11886 bifunctional biotin-- 85.3 1.8 4E-05 36.2 5.0 40 77-116 9-48 (319)
126 PRK12423 LexA repressor; Provi 85.2 1.4 3E-05 34.8 4.1 49 71-119 9-59 (202)
127 cd04789 HTH_Cfa Helix-Turn-Hel 85.1 0.86 1.9E-05 32.6 2.6 40 87-130 2-41 (102)
128 cd04775 HTH_Cfa-like Helix-Tur 84.9 1 2.2E-05 32.2 2.9 41 87-131 2-42 (102)
129 COG0789 SoxR Predicted transcr 84.4 0.99 2.1E-05 32.1 2.7 40 88-131 2-42 (124)
130 PF03965 Penicillinase_R: Peni 84.4 4.1 9E-05 29.3 6.0 46 87-133 18-67 (115)
131 cd04762 HTH_MerR-trunc Helix-T 84.3 1.2 2.7E-05 25.8 2.7 40 87-130 1-40 (49)
132 PF13601 HTH_34: Winged helix 84.1 2.2 4.7E-05 29.5 4.2 34 86-119 14-47 (80)
133 COG0735 Fur Fe2+/Zn2+ uptake r 83.8 3 6.5E-05 31.8 5.3 46 71-130 40-85 (145)
134 PF05732 RepL: Firmicute plasm 83.8 2.2 4.8E-05 33.5 4.6 45 83-131 72-116 (165)
135 cd04767 HTH_HspR-like_MBC Heli 83.7 1.2 2.6E-05 33.7 3.0 41 86-131 1-41 (120)
136 cd04770 HTH_HMRTR Helix-Turn-H 83.4 0.89 1.9E-05 33.0 2.1 40 87-130 1-41 (123)
137 cd04768 HTH_BmrR-like Helix-Tu 83.3 1.2 2.7E-05 31.4 2.7 41 87-131 1-42 (96)
138 COG1733 Predicted transcriptio 83.3 2 4.4E-05 32.1 4.1 35 73-121 38-72 (120)
139 PF13411 MerR_1: MerR HTH fami 83.2 1.6 3.5E-05 28.0 3.1 39 88-130 2-40 (69)
140 PRK13918 CRP/FNR family transc 83.1 2.5 5.4E-05 31.8 4.5 32 86-117 149-180 (202)
141 PRK15002 redox-sensitivie tran 82.6 1.5 3.2E-05 34.2 3.2 42 85-130 10-51 (154)
142 PRK10681 DNA-binding transcrip 82.3 1.6 3.4E-05 35.7 3.4 44 71-114 6-49 (252)
143 PRK00215 LexA repressor; Valid 82.1 2.4 5.1E-05 33.0 4.2 39 87-125 24-63 (205)
144 PRK05472 redox-sensing transcr 82.0 1.4 3E-05 34.9 2.9 50 66-115 10-61 (213)
145 PRK11569 transcriptional repre 81.9 2.5 5.4E-05 34.7 4.4 35 86-120 43-77 (274)
146 TIGR00373 conserved hypothetic 81.7 3.7 8E-05 31.9 5.1 42 76-117 18-59 (158)
147 PF13814 Replic_Relax: Replica 81.7 2.7 5.9E-05 31.8 4.3 51 82-132 5-64 (191)
148 PRK09333 30S ribosomal protein 81.3 2.2 4.8E-05 33.8 3.7 34 87-120 68-115 (150)
149 cd04769 HTH_MerR2 Helix-Turn-H 80.8 1.9 4E-05 31.3 3.0 40 88-131 2-41 (116)
150 TIGR02431 pcaR_pcaU beta-ketoa 80.3 2.6 5.5E-05 33.8 3.9 33 86-118 24-56 (248)
151 TIGR02054 MerD mercuric resist 80.2 1.6 3.5E-05 32.7 2.6 43 85-131 2-45 (120)
152 cd04781 HTH_MerR-like_sg6 Heli 80.1 1.8 3.9E-05 31.6 2.7 40 88-131 2-41 (120)
153 PRK10163 DNA-binding transcrip 80.1 3.3 7.2E-05 34.0 4.6 34 86-119 40-73 (271)
154 PF02002 TFIIE_alpha: TFIIE al 80.1 1.5 3.1E-05 31.2 2.2 36 84-119 25-60 (105)
155 COG1414 IclR Transcriptional r 80.0 3.2 7E-05 33.9 4.5 36 87-122 20-55 (246)
156 cd00592 HTH_MerR-like Helix-Tu 80.0 1.6 3.6E-05 30.2 2.4 40 87-130 1-40 (100)
157 PRK06474 hypothetical protein; 79.6 6.2 0.00013 31.0 5.8 46 87-132 27-77 (178)
158 PF05331 DUF742: Protein of un 79.2 2.3 4.9E-05 32.1 3.1 33 86-118 55-87 (114)
159 cd01107 HTH_BmrR Helix-Turn-He 79.1 1.8 3.9E-05 31.1 2.4 40 88-131 2-43 (108)
160 cd01282 HTH_MerR-like_sg3 Heli 78.9 2 4.4E-05 31.1 2.7 40 88-131 2-41 (112)
161 cd04774 HTH_YfmP Helix-Turn-He 78.7 2.5 5.5E-05 30.0 3.1 39 88-130 2-40 (96)
162 PRK05638 threonine synthase; V 78.5 4.1 9E-05 35.8 4.9 43 87-129 385-429 (442)
163 PF01090 Ribosomal_S19e: Ribos 78.3 2.5 5.3E-05 33.1 3.1 25 98-122 92-116 (139)
164 PRK11161 fumarate/nitrate redu 78.2 3.5 7.5E-05 32.0 3.9 32 87-118 185-216 (235)
165 PF12793 SgrR_N: Sugar transpo 77.8 7.6 0.00016 28.8 5.5 49 72-120 4-53 (115)
166 PF01399 PCI: PCI domain; Int 77.6 17 0.00037 24.2 6.8 47 83-129 57-103 (105)
167 KOG2760|consensus 77.5 4.4 9.5E-05 37.0 4.8 50 69-118 364-413 (432)
168 COG3177 Fic family protein [Fu 77.5 3.7 8E-05 35.4 4.3 57 72-128 289-346 (348)
169 PRK13752 putative transcriptio 77.4 2.6 5.7E-05 32.2 3.0 45 83-131 4-49 (144)
170 TIGR03697 NtcA_cyano global ni 77.4 3.8 8.3E-05 30.4 3.8 32 87-118 144-175 (193)
171 PRK09462 fur ferric uptake reg 76.9 7 0.00015 29.3 5.2 44 86-129 33-81 (148)
172 cd04787 HTH_HMRTR_unk Helix-Tu 76.7 2.6 5.7E-05 31.3 2.8 40 88-131 2-42 (133)
173 TIGR01950 SoxR redox-sensitive 76.6 3.1 6.7E-05 31.8 3.2 41 87-131 2-42 (142)
174 COG2390 DeoR Transcriptional r 76.5 4.2 9.1E-05 35.3 4.4 37 87-123 27-63 (321)
175 cd04763 HTH_MlrA-like Helix-Tu 76.5 2.3 5E-05 27.7 2.2 39 88-130 2-41 (68)
176 cd04783 HTH_MerR1 Helix-Turn-H 76.5 2.5 5.5E-05 31.0 2.6 39 88-130 2-41 (126)
177 COG1339 Transcriptional regula 76.3 4.2 9E-05 34.1 4.1 49 80-129 14-62 (214)
178 cd04782 HTH_BltR Helix-Turn-He 75.7 2.4 5.2E-05 30.0 2.2 40 87-130 1-41 (97)
179 cd01110 HTH_SoxR Helix-Turn-He 75.7 3.2 7E-05 31.4 3.1 41 87-131 2-42 (139)
180 cd04765 HTH_MlrA-like_sg2 Heli 75.3 3.2 7E-05 29.7 2.8 40 87-130 1-41 (99)
181 cd04777 HTH_MerR-like_sg1 Heli 75.3 2.8 6.2E-05 29.8 2.5 38 88-130 2-39 (107)
182 PF05158 RNA_pol_Rpc34: RNA po 75.1 13 0.00029 32.2 7.0 63 69-133 10-73 (327)
183 cd04776 HTH_GnyR Helix-Turn-He 75.1 2.8 6.2E-05 30.8 2.6 38 88-130 2-39 (118)
184 PRK13749 transcriptional regul 74.8 2.4 5.2E-05 32.0 2.2 43 85-131 2-45 (121)
185 PF13384 HTH_23: Homeodomain-l 74.8 2.6 5.7E-05 25.6 2.0 29 87-115 18-46 (50)
186 TIGR02044 CueR Cu(I)-responsiv 74.7 2.9 6.3E-05 30.8 2.6 40 88-131 2-42 (127)
187 cd04772 HTH_TioE_rpt1 First He 74.5 3.3 7.2E-05 29.5 2.7 39 88-130 2-41 (99)
188 COG2865 Predicted transcriptio 74.4 3.5 7.6E-05 37.8 3.5 58 76-133 406-463 (467)
189 PRK09391 fixK transcriptional 74.3 6.9 0.00015 30.8 4.7 31 87-117 180-210 (230)
190 PF09286 Pro-kuma_activ: Pro-k 74.3 16 0.00035 26.9 6.5 61 70-130 25-91 (143)
191 cd04773 HTH_TioE_rpt2 Second H 74.0 3.7 8.1E-05 29.6 2.9 41 87-131 1-42 (108)
192 COG3398 Uncharacterized protei 73.9 7.1 0.00015 33.3 4.9 49 80-132 112-160 (240)
193 PF14394 DUF4423: Domain of un 73.9 6.7 0.00014 30.8 4.5 41 81-121 33-76 (171)
194 COG2345 Predicted transcriptio 73.7 4.5 9.8E-05 33.6 3.7 50 84-133 23-76 (218)
195 PF12651 RHH_3: Ribbon-helix-h 73.2 10 0.00022 23.7 4.4 37 65-113 5-42 (44)
196 cd04784 HTH_CadR-PbrR Helix-Tu 72.5 3.7 8E-05 30.1 2.6 40 88-131 2-42 (127)
197 TIGR02043 ZntR Zn(II)-responsi 72.4 3.8 8.2E-05 30.5 2.7 40 87-130 2-42 (131)
198 PF03444 HrcA_DNA-bdg: Winged 71.9 4.6 0.0001 28.9 2.9 36 84-119 21-56 (78)
199 PF03428 RP-C: Replication pro 71.9 8 0.00017 31.0 4.6 34 87-120 71-105 (177)
200 PRK09514 zntR zinc-responsive 71.8 4.4 9.4E-05 30.7 3.0 41 87-131 2-43 (140)
201 PRK04172 pheS phenylalanyl-tRN 71.8 11 0.00023 34.0 5.8 44 77-120 11-54 (489)
202 cd04790 HTH_Cfa-like_unk Helix 71.0 3.2 6.9E-05 32.5 2.1 41 87-131 2-43 (172)
203 cd04788 HTH_NolA-AlbR Helix-Tu 70.8 5.4 0.00012 28.1 3.1 40 88-131 2-42 (96)
204 PTZ00095 40S ribosomal protein 70.8 5.2 0.00011 32.4 3.3 23 98-120 117-139 (169)
205 cd04779 HTH_MerR-like_sg4 Heli 70.0 5.4 0.00012 30.3 3.1 40 88-131 2-41 (134)
206 cd01104 HTH_MlrA-CarA Helix-Tu 69.3 5 0.00011 25.6 2.4 40 88-131 2-42 (68)
207 PRK04214 rbn ribonuclease BN/u 69.3 10 0.00023 33.2 5.1 46 73-118 297-342 (412)
208 COG3432 Predicted transcriptio 69.1 6.7 0.00015 28.9 3.3 47 86-133 31-77 (95)
209 PF13518 HTH_28: Helix-turn-he 69.1 5.7 0.00012 23.9 2.6 33 88-120 14-46 (52)
210 smart00088 PINT motif in prote 68.8 23 0.00051 23.6 5.8 48 84-131 22-69 (88)
211 smart00753 PAM PCI/PINT associ 68.8 23 0.00051 23.6 5.8 48 84-131 22-69 (88)
212 PRK10402 DNA-binding transcrip 68.3 8.4 0.00018 30.1 4.0 32 87-118 170-201 (226)
213 COG2238 RPS19A Ribosomal prote 68.1 5.1 0.00011 31.9 2.7 23 98-120 93-115 (147)
214 cd04785 HTH_CadR-PbrR-like Hel 68.1 4.5 9.7E-05 29.8 2.3 40 87-130 1-41 (126)
215 cd01108 HTH_CueR Helix-Turn-He 68.0 5.6 0.00012 29.3 2.8 40 88-131 2-42 (127)
216 cd01106 HTH_TipAL-Mta Helix-Tu 67.8 6.7 0.00014 27.7 3.0 41 87-131 1-42 (103)
217 cd01111 HTH_MerD Helix-Turn-He 67.3 5.8 0.00013 28.8 2.7 40 88-131 2-42 (107)
218 PRK09392 ftrB transcriptional 66.9 12 0.00025 29.1 4.5 28 88-115 175-202 (236)
219 TIGR00331 hrcA heat shock gene 66.7 6 0.00013 34.1 3.1 37 83-119 18-56 (337)
220 COG1675 TFA1 Transcription ini 66.7 11 0.00025 30.4 4.5 50 74-123 20-70 (176)
221 COG3888 Predicted transcriptio 66.5 7.2 0.00016 34.3 3.5 45 74-118 6-52 (321)
222 PRK10263 DNA translocase FtsK; 66.4 7.5 0.00016 40.0 4.1 61 70-130 1291-1351(1355)
223 cd04780 HTH_MerR-like_sg5 Heli 66.3 6.5 0.00014 28.0 2.7 39 88-130 2-41 (95)
224 PF07848 PaaX: PaaX-like prote 65.3 19 0.00041 24.7 4.8 39 90-129 27-65 (70)
225 PRK15431 ferrous iron transpor 64.8 14 0.00029 26.5 4.1 37 84-120 14-50 (78)
226 PF15436 PGBA_N: Plasminogen-b 64.5 23 0.00051 29.6 6.0 54 70-123 101-158 (218)
227 COG1378 Predicted transcriptio 64.4 11 0.00024 31.3 4.2 45 84-130 28-72 (247)
228 smart00351 PAX Paired Box doma 64.2 9.3 0.0002 28.3 3.3 34 87-120 34-67 (125)
229 PRK11639 zinc uptake transcrip 63.8 22 0.00049 27.5 5.5 39 86-124 41-84 (169)
230 cd04778 HTH_MerR-like_sg2 Heli 62.8 6.2 0.00014 32.3 2.4 41 87-131 2-42 (219)
231 PHA03103 double-strand RNA-bin 62.5 24 0.00051 28.8 5.6 58 72-129 13-70 (183)
232 PHA00738 putative HTH transcri 62.3 16 0.00036 27.6 4.3 43 86-130 26-68 (108)
233 TIGR02051 MerR Hg(II)-responsi 62.3 9.9 0.00021 28.0 3.2 39 88-130 1-40 (124)
234 PF01638 HxlR: HxlR-like helix 61.2 23 0.00051 24.3 4.7 32 89-120 21-53 (90)
235 cd01109 HTH_YyaN Helix-Turn-He 61.0 6.7 0.00014 28.1 2.0 40 88-131 2-42 (113)
236 PF01402 RHH_1: Ribbon-helix-h 61.0 23 0.00049 20.6 4.0 35 66-112 3-38 (39)
237 KOG3054|consensus 60.5 22 0.00047 31.1 5.3 58 73-130 201-258 (299)
238 PF09507 CDC27: DNA polymerase 60.2 9.2 0.0002 32.4 3.0 29 85-113 1-29 (430)
239 cd04764 HTH_MlrA-like_sg1 Heli 60.0 10 0.00023 24.4 2.6 41 87-131 1-41 (67)
240 COG4565 CitB Response regulato 59.7 19 0.00041 30.4 4.7 51 69-119 155-206 (224)
241 PRK00135 scpB segregation and 59.5 17 0.00037 29.2 4.3 42 85-129 103-147 (188)
242 TIGR02716 C20_methyl_CrtF C-20 59.5 13 0.00029 30.5 3.7 42 72-118 14-55 (306)
243 PF08461 HTH_12: Ribonuclease 59.2 12 0.00025 25.2 2.8 36 85-120 12-52 (66)
244 cd00131 PAX Paired Box domain 59.0 12 0.00025 28.0 3.1 51 68-120 17-67 (128)
245 PF04182 B-block_TFIIIC: B-blo 58.9 22 0.00047 24.0 4.2 45 77-121 7-53 (75)
246 PRK10227 DNA-binding transcrip 58.9 8.6 0.00019 29.0 2.4 40 88-131 2-42 (135)
247 PF09106 SelB-wing_2: Elongati 58.6 29 0.00062 22.3 4.6 47 72-118 3-52 (59)
248 PRK00082 hrcA heat-inducible t 58.5 10 0.00022 32.7 3.1 39 81-119 20-60 (339)
249 PF09743 DUF2042: Uncharacteri 58.4 21 0.00045 30.3 4.8 66 63-131 103-173 (272)
250 TIGR02047 CadR-PbrR Cd(II)/Pb( 58.1 8.3 0.00018 28.6 2.1 39 88-130 2-41 (127)
251 TIGR01529 argR_whole arginine 57.4 32 0.0007 26.4 5.4 21 108-129 40-60 (146)
252 PF04492 Phage_rep_O: Bacterio 57.3 25 0.00055 25.7 4.5 34 83-116 51-84 (100)
253 COG1386 scpB Chromosome segreg 56.9 20 0.00042 29.0 4.2 43 86-131 106-151 (184)
254 PRK15043 transcriptional regul 56.8 12 0.00025 31.6 3.0 43 85-131 2-45 (243)
255 smart00531 TFIIE Transcription 56.5 11 0.00024 28.6 2.6 34 85-118 14-47 (147)
256 PF05584 Sulfolobus_pRN: Sulfo 56.2 26 0.00057 24.7 4.3 44 86-129 18-64 (72)
257 PF03551 PadR: Transcriptional 56.1 33 0.00071 22.6 4.6 35 96-130 27-65 (75)
258 COG5340 Predicted transcriptio 55.3 11 0.00024 32.5 2.7 41 83-123 27-67 (269)
259 TIGR02147 Fsuc_second hypothet 55.1 18 0.00039 30.7 3.9 53 68-120 110-173 (271)
260 PRK15418 transcriptional regul 55.1 23 0.00051 30.2 4.7 38 86-123 29-66 (318)
261 PF06163 DUF977: Bacterial pro 54.9 24 0.00052 27.5 4.2 54 73-129 13-66 (127)
262 PRK10141 DNA-binding transcrip 53.3 50 0.0011 24.7 5.7 44 87-131 31-74 (117)
263 PF13551 HTH_29: Winged helix- 53.1 10 0.00023 25.7 1.8 33 88-120 14-46 (112)
264 PF01316 Arg_repressor: Argini 52.9 37 0.00079 23.4 4.5 33 83-131 33-65 (70)
265 PRK10265 chaperone-modulator p 52.8 22 0.00047 25.6 3.5 41 86-130 7-47 (101)
266 PF04079 DUF387: Putative tran 52.8 29 0.00062 27.2 4.5 41 87-130 97-140 (159)
267 PF09202 Rio2_N: Rio2, N-termi 52.4 48 0.0011 23.4 5.2 46 73-118 11-56 (82)
268 cd04371 DEP DEP domain, named 52.1 28 0.00061 22.8 3.8 42 66-121 27-68 (81)
269 PF00126 HTH_1: Bacterial regu 51.9 23 0.0005 22.5 3.2 42 88-129 15-56 (60)
270 PF13404 HTH_AsnC-type: AsnC-t 51.3 23 0.0005 21.8 3.0 39 69-111 4-42 (42)
271 PF06969 HemN_C: HemN C-termin 51.3 33 0.00071 21.9 3.9 32 87-118 21-53 (66)
272 COG0640 ArsR Predicted transcr 51.2 58 0.0013 20.4 5.1 35 86-120 39-73 (110)
273 PF07106 TBPIP: Tat binding pr 51.0 55 0.0012 25.0 5.7 47 87-134 17-65 (169)
274 TIGR00281 segregation and cond 50.3 28 0.00061 28.1 4.2 42 87-131 102-146 (186)
275 TIGR00635 ruvB Holliday juncti 49.6 25 0.00053 28.5 3.8 40 77-117 247-287 (305)
276 TIGR03433 padR_acidobact trans 49.0 34 0.00075 24.1 4.0 36 96-131 35-74 (100)
277 cd04786 HTH_MerR-like_sg7 Heli 48.6 17 0.00038 27.2 2.6 39 88-130 2-41 (131)
278 KOG3341|consensus 48.3 22 0.00047 30.5 3.3 34 85-118 189-222 (249)
279 PF04433 SWIRM: SWIRM domain; 48.3 27 0.00059 23.9 3.3 34 84-117 51-85 (86)
280 TIGR03879 near_KaiC_dom probab 48.2 10 0.00022 26.7 1.1 31 87-117 33-63 (73)
281 PF14579 HHH_6: Helix-hairpin- 46.1 9.2 0.0002 26.6 0.7 54 69-125 35-88 (90)
282 PF06224 HTH_42: Winged helix 45.4 42 0.00091 27.6 4.6 61 70-130 164-226 (327)
283 PLN00158 histone H2B; Provisio 44.6 46 0.001 25.5 4.3 42 68-109 56-105 (116)
284 PF12298 Bot1p: Eukaryotic mit 44.6 27 0.00059 27.9 3.2 46 67-113 15-60 (172)
285 TIGR01714 phage_rep_org_N phag 43.7 47 0.001 25.2 4.3 41 88-131 53-93 (119)
286 TIGR02277 PaaX_trns_reg phenyl 43.6 40 0.00086 28.4 4.2 38 90-128 24-61 (280)
287 COG1497 Predicted transcriptio 43.2 45 0.00097 28.8 4.5 56 72-129 10-66 (260)
288 PF05043 Mga: Mga helix-turn-h 42.6 24 0.00051 23.8 2.3 40 73-112 17-56 (87)
289 smart00421 HTH_LUXR helix_turn 42.4 36 0.00078 19.8 2.8 26 87-112 19-44 (58)
290 PRK13824 replication initiatio 42.3 46 0.001 29.8 4.6 43 88-131 84-127 (404)
291 PF06413 Neugrin: Neugrin; In 41.9 38 0.00081 28.2 3.8 35 72-108 17-51 (225)
292 PLN02853 Probable phenylalanyl 41.8 65 0.0014 30.0 5.6 47 75-121 6-53 (492)
293 COG1167 ARO8 Transcriptional r 41.8 35 0.00075 30.3 3.8 50 72-121 8-63 (459)
294 PF13591 MerR_2: MerR HTH fami 41.5 48 0.001 22.9 3.7 32 87-122 1-32 (84)
295 COG4109 Predicted transcriptio 41.4 36 0.00078 31.2 3.8 47 84-130 17-63 (432)
296 KOG3233|consensus 41.4 11 0.00023 33.1 0.5 47 83-129 97-145 (297)
297 PF09107 SelB-wing_3: Elongati 41.4 74 0.0016 20.5 4.4 37 84-120 8-44 (50)
298 PF09114 MotA_activ: Transcrip 41.1 42 0.00091 25.1 3.5 49 78-129 22-72 (96)
299 PF06224 HTH_42: Winged helix 40.7 65 0.0014 26.5 5.0 61 72-132 85-154 (327)
300 PF09681 Phage_rep_org_N: N-te 40.5 49 0.0011 24.9 3.9 42 87-131 54-95 (121)
301 cd04448 DEP_PIKfyve DEP (Dishe 40.1 30 0.00066 24.1 2.6 24 100-123 47-70 (81)
302 PRK04280 arginine repressor; P 40.0 80 0.0017 24.4 5.1 22 108-130 42-63 (148)
303 cd04449 DEP_DEPDC5-like DEP (D 39.4 31 0.00066 23.9 2.5 49 62-123 24-72 (83)
304 PF01710 HTH_Tnp_IS630: Transp 39.1 26 0.00056 25.6 2.2 41 70-116 58-98 (119)
305 TIGR02844 spore_III_D sporulat 39.1 21 0.00045 25.3 1.6 33 75-108 9-41 (80)
306 PF11972 HTH_13: HTH DNA bindi 38.8 38 0.00083 22.7 2.8 30 83-112 10-39 (54)
307 PF04545 Sigma70_r4: Sigma-70, 38.2 47 0.001 20.2 3.0 25 87-111 21-45 (50)
308 COG1654 BirA Biotin operon rep 38.1 81 0.0018 22.3 4.5 43 82-124 15-57 (79)
309 cd06170 LuxR_C_like C-terminal 37.9 46 0.001 19.6 2.9 26 87-112 16-41 (57)
310 PTZ00326 phenylalanyl-tRNA syn 37.6 88 0.0019 29.1 5.8 39 85-123 20-58 (494)
311 PF10557 Cullin_Nedd8: Cullin 37.2 1.2E+02 0.0026 20.0 5.0 29 93-121 37-65 (68)
312 PF08438 MMR_HSR1_C: GTPase of 37.1 19 0.00041 27.0 1.2 47 70-126 10-56 (109)
313 PF09824 ArsR: ArsR transcript 37.1 35 0.00077 27.5 2.8 47 67-117 12-58 (160)
314 PRK15466 carboxysome structura 36.8 39 0.00084 27.4 3.0 53 66-118 103-156 (166)
315 cd06171 Sigma70_r4 Sigma70, re 36.4 55 0.0012 18.4 2.9 26 87-112 27-52 (55)
316 PF13011 LZ_Tnp_IS481: leucine 36.0 54 0.0012 23.7 3.4 38 87-124 26-63 (85)
317 PF00610 DEP: Domain found in 35.9 47 0.001 21.6 2.9 31 95-125 33-63 (74)
318 PF02796 HTH_7: Helix-turn-hel 35.6 22 0.00047 21.8 1.1 22 87-108 22-43 (45)
319 PF06971 Put_DNA-bind_N: Putat 34.1 37 0.0008 22.1 2.1 34 73-106 13-48 (50)
320 cd04450 DEP_RGS7-like DEP (Dis 33.9 76 0.0016 22.1 3.8 27 98-124 45-71 (88)
321 PF05595 DUF771: Domain of unk 33.4 50 0.0011 23.3 2.8 44 65-108 2-46 (91)
322 TIGR03453 partition_RepA plasm 33.3 43 0.00093 28.8 2.9 42 85-130 32-74 (387)
323 PRK03341 arginine repressor; P 33.2 1.2E+02 0.0025 24.2 5.2 54 73-130 16-75 (168)
324 KOG4068|consensus 32.5 65 0.0014 26.3 3.6 34 98-131 66-100 (174)
325 smart00049 DEP Domain found in 32.5 74 0.0016 20.8 3.4 44 64-121 17-60 (77)
326 PF04760 IF2_N: Translation in 32.4 58 0.0013 20.4 2.8 29 85-116 2-31 (54)
327 PF03374 ANT: Phage antirepres 32.4 93 0.002 21.8 4.1 41 72-118 13-53 (111)
328 PF02319 E2F_TDP: E2F/DP famil 32.4 1.6E+02 0.0034 19.8 5.3 47 77-124 16-67 (71)
329 PF13613 HTH_Tnp_4: Helix-turn 32.4 55 0.0012 20.6 2.6 26 87-112 20-45 (53)
330 KOG4062|consensus 32.3 1E+02 0.0022 25.4 4.7 66 57-123 73-142 (178)
331 PRK10046 dpiA two-component re 32.2 93 0.002 23.9 4.4 51 70-120 160-211 (225)
332 PF13542 HTH_Tnp_ISL3: Helix-t 32.2 89 0.0019 18.8 3.5 39 70-110 13-51 (52)
333 PHA01747 putative ATP-dependen 30.7 53 0.0011 30.2 3.2 42 70-113 328-371 (425)
334 cd00073 H15 linker histone 1 a 30.3 1.5E+02 0.0033 20.5 4.8 32 100-131 45-76 (88)
335 cd00569 HTH_Hin_like Helix-tur 30.3 73 0.0016 15.7 2.6 18 88-105 23-40 (42)
336 PF02022 Integrase_Zn: Integra 29.0 69 0.0015 19.9 2.6 22 88-109 11-32 (40)
337 smart00342 HTH_ARAC helix_turn 28.8 73 0.0016 19.7 2.8 25 87-111 2-26 (84)
338 COG0664 Crp cAMP-binding prote 28.5 89 0.0019 22.7 3.6 35 85-119 170-204 (214)
339 PRK00080 ruvB Holliday junctio 28.2 83 0.0018 26.2 3.8 49 71-120 262-311 (328)
340 KOG3411|consensus 27.7 60 0.0013 25.8 2.6 22 99-120 96-117 (143)
341 PRK13626 transcriptional regul 27.7 1.3E+02 0.0029 27.0 5.2 47 73-119 9-56 (552)
342 PRK13182 racA polar chromosome 26.7 76 0.0017 25.3 3.1 39 88-131 2-41 (175)
343 PLN03083 E3 UFM1-protein ligas 26.5 98 0.0021 30.6 4.3 66 63-131 107-176 (803)
344 PF02831 gpW: gpW; InterPro: 26.3 1.4E+02 0.0031 20.6 4.0 32 101-132 8-39 (68)
345 PF09743 DUF2042: Uncharacteri 26.0 1.5E+02 0.0033 25.1 5.0 67 62-131 163-234 (272)
346 PRK10512 selenocysteinyl-tRNA- 26.0 1.3E+02 0.0029 28.1 5.0 60 62-121 538-601 (614)
347 COG3398 Uncharacterized protei 25.9 1.7E+02 0.0037 25.1 5.2 59 72-131 174-232 (240)
348 PF00538 Linker_histone: linke 25.7 93 0.002 20.9 3.0 23 101-123 46-68 (77)
349 PF00292 PAX: 'Paired box' dom 25.3 74 0.0016 24.5 2.7 35 86-120 33-67 (125)
350 PF14330 DUF4387: Domain of un 25.0 85 0.0018 23.4 2.9 31 67-101 22-53 (99)
351 PF06218 NPR2: Nitrogen permea 24.7 1.2E+02 0.0025 27.7 4.3 59 72-132 206-264 (428)
352 PRK05066 arginine repressor; P 24.3 2.4E+02 0.0052 22.1 5.5 21 108-129 48-68 (156)
353 PF05119 Terminase_4: Phage te 24.3 1.2E+02 0.0025 20.7 3.4 46 71-116 2-49 (100)
354 PRK10512 selenocysteinyl-tRNA- 23.3 1.5E+02 0.0034 27.7 4.9 47 74-121 495-541 (614)
355 PHA01623 hypothetical protein 23.1 2.3E+02 0.0049 18.6 4.4 39 62-112 13-52 (56)
356 PRK09751 putative ATP-dependen 23.1 90 0.0019 32.8 3.6 47 72-118 975-1021(1490)
357 cd04441 DEP_2_DEP6 DEP (Dishev 23.1 84 0.0018 22.4 2.5 24 100-123 51-74 (85)
358 PF01381 HTH_3: Helix-turn-hel 22.7 70 0.0015 19.3 1.8 40 61-100 13-52 (55)
359 PRK04217 hypothetical protein; 22.4 98 0.0021 23.1 2.8 23 87-109 59-81 (110)
360 cd04442 DEP_1_DEP6 DEP (Dishev 22.2 94 0.002 22.0 2.6 25 99-123 46-70 (82)
361 PF00196 GerE: Bacterial regul 22.0 1.1E+02 0.0024 19.0 2.7 26 88-113 20-45 (58)
362 PF09940 DUF2172: Domain of un 21.7 1.1E+02 0.0023 27.9 3.4 30 88-117 357-386 (386)
363 TIGR03826 YvyF flagellar opero 21.6 84 0.0018 24.4 2.4 46 70-119 28-75 (137)
364 PF13812 PPR_3: Pentatricopept 21.6 1.1E+02 0.0024 16.1 2.3 16 100-115 17-32 (34)
365 COG1763 MobB Molybdopterin-gua 21.4 1.1E+02 0.0025 24.0 3.2 27 100-126 16-42 (161)
366 PF12627 PolyA_pol_RNAbd: Prob 21.4 1.1E+02 0.0024 19.2 2.6 52 68-119 3-56 (64)
367 PF03397 Rhabdo_matrix: Rhabdo 21.3 46 0.00099 26.9 0.9 20 88-107 34-53 (168)
368 PRK14997 LysR family transcrip 21.1 1.7E+02 0.0036 23.2 4.1 43 88-130 18-60 (301)
369 TIGR00475 selB selenocysteine- 21.0 1.8E+02 0.0039 27.0 4.8 48 73-121 476-523 (581)
370 PRK13239 alkylmercury lyase; P 20.9 1.1E+02 0.0024 25.2 3.2 41 71-111 21-61 (206)
371 PF04967 HTH_10: HTH DNA bindi 20.8 1.3E+02 0.0029 19.6 2.9 27 86-112 23-49 (53)
372 TIGR02937 sigma70-ECF RNA poly 20.8 1.2E+02 0.0027 20.4 2.9 26 87-112 127-152 (158)
373 PRK10341 DNA-binding transcrip 20.6 1.9E+02 0.0041 23.3 4.4 43 88-130 23-65 (312)
374 PRK08061 rpsN 30S ribosomal pr 20.4 77 0.0017 21.6 1.8 28 91-122 32-59 (61)
375 PHA01748 hypothetical protein 20.4 2.6E+02 0.0056 18.4 4.3 36 66-113 6-42 (60)
376 PF05402 PqqD: Coenzyme PQQ sy 20.3 1.7E+02 0.0036 18.5 3.3 28 90-117 37-68 (68)
No 1
>KOG1767|consensus
Probab=100.00 E-value=1.5e-49 Score=295.19 Aligned_cols=109 Identities=67% Similarity=0.986 Sum_probs=102.5
Q ss_pred CCCCCCCCCCCCCCcchhhhhhccCCCCccccccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccc
Q psy1871 20 HPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVR 99 (139)
Q Consensus 20 mppK~~~~~~~~~~~~~~~k~~~a~sggk~kKKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~ 99 (139)
||++++..+ +++++++.+||+++||||||||+|||+||+|+||++|||||++|||+|+|||||+|+|||+||
T Consensus 2 ~~~k~q~sK--------~~k~~~~~~ggk~~KKKWskGk~kdkvnn~Vlfdqatydkl~kevp~~k~it~svl~dRlkIn 73 (110)
T KOG1767|consen 2 MPKKQQLSK--------EKKAPAASSGGKAKKKKWSKGKVKDKVNNAVLFDQATYDKLLKEVPKYKLITPSVLSDRLKIN 73 (110)
T ss_pred CccccccCc--------hhccccccCCCcccccccccchHHHHhhhheeecHHHHHHHHHhcccceeecHHHhhhhhhhc
Confidence 666655544 578889999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHcCCeeEEeecCceEEEeccCCCCC
Q psy1871 100 GSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKGDD 136 (139)
Q Consensus 100 ~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k~~~ 136 (139)
|||||++||||.++|+|++|++||+|.||||+++.++
T Consensus 74 gsLAr~alr~L~~kG~Ik~Vs~h~~q~IYTrat~~~~ 110 (110)
T KOG1767|consen 74 GSLARAALRELSNKGVIKQVSKHSKQVIYTRATASED 110 (110)
T ss_pred hHHHHHHHHHHHhcchHHHHhhcchheeeccccccCC
Confidence 9999999999999999999999999999999998765
No 2
>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=100.00 E-value=7e-48 Score=284.60 Aligned_cols=105 Identities=73% Similarity=1.035 Sum_probs=79.6
Q ss_pred CCCCCCCCCCCCCCcchhhhhhccCCCCccccccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccc
Q psy1871 20 HPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVR 99 (139)
Q Consensus 20 mppK~~~~~~~~~~~~~~~k~~~a~sggk~kKKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~ 99 (139)
||||+++.+ +++++++++||++++||||||+++||+||+|+||++|||+|++|||+|++||||+|||||+|+
T Consensus 1 M~pK~~~~k--------~~k~~~~~~~~k~~KKKwsKgk~kek~~~~v~~d~~~~~kl~kEV~~~K~ITp~~lserlkI~ 72 (105)
T PF03297_consen 1 MPPKKQKSK--------KQKAKKAKSGGKAKKKKWSKGKVKEKLNNAVLFDKETYDKLLKEVPKMKLITPSVLSERLKIN 72 (105)
T ss_dssp -----------------------TT------SSS--SS-SCHHHCCCSCCTCHHHHHHHHHCTTSSCECHHHHHHHHCCS
T ss_pred CCCCcccch--------hhHHHHHhccCccccccccccchHHHHhcceEecHHHHHHHHHHhccCcEeeHHHHHHhHhhH
Confidence 999975554 467778999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871 100 GSLARKALEELLQKGLIKQVVKHHAQVIYTRTT 132 (139)
Q Consensus 100 ~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~ 132 (139)
+||||++||||+++|+|++|++||+|.||||+|
T Consensus 73 ~SlAr~~Lr~L~~kG~Ik~V~k~~~~~IYtr~~ 105 (105)
T PF03297_consen 73 GSLARKALRELESKGLIKPVSKHHRQRIYTRAT 105 (105)
T ss_dssp CHHHHHHHHHHHHCCSSEEEECCTTCEEEEES-
T ss_pred HHHHHHHHHHHHHCCCEEEEeccCCeEEEecCC
Confidence 999999999999999999999999999999986
No 3
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-35 Score=220.04 Aligned_cols=106 Identities=35% Similarity=0.565 Sum_probs=99.7
Q ss_pred CCCCCCCCCCCCCCcchhhhhhccCCCCccccccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccc
Q psy1871 20 HPPKKDTKGGSSKQPQKTQKKKEGGSGGKAKKKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVR 99 (139)
Q Consensus 20 mppK~~~~~~~~~~~~~~~k~~~a~sggk~kKKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~ 99 (139)
|||+.|-.+ +.|+.++.+|+++.+|||++++.+|...++|+||+++||++++|||++++||||+|++||+|+
T Consensus 1 m~pk~qlsK--------~~Ka~~~~a~~~k~kKK~~~k~~k~~~~~av~vdee~~~ki~KEV~~~r~VTpy~la~r~gI~ 72 (107)
T COG4901 1 MAPKSQLSK--------EKKAEKAKAGTAKDKKKWSKKKKKEEARRAVTVDEELLDKIRKEVPRERVVTPYVLASRYGIN 72 (107)
T ss_pred CcchhHHHH--------HHHHHHHHhhhhhhhhccccccccchhhhhhhccHHHHHHHHHhcccceeecHHHHHHHhccc
Confidence 788866654 577788899999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871 100 GSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK 133 (139)
Q Consensus 100 ~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k 133 (139)
+||||.+||+|+++|+|++|++||||.||+|+..
T Consensus 73 ~SvAr~vLR~LeeeGvv~lvsknrR~~IY~~a~a 106 (107)
T COG4901 73 GSVARIVLRHLEEEGVVQLVSKNRRQAIYTRAKA 106 (107)
T ss_pred hHHHHHHHHHHHhCCceeeeccCccceeeecccC
Confidence 9999999999999999999999999999999764
No 4
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=100.00 E-value=7.6e-35 Score=209.23 Aligned_cols=81 Identities=25% Similarity=0.374 Sum_probs=76.7
Q ss_pred cccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 51 KKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 51 KKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+|+=.++..++.+||+|+||++|||||++|||+|++||||+|||||+|++||||++||||+++|+|++|++||+|.|||+
T Consensus 6 ~k~~~~~~~~~~~~n~v~~dk~t~dkl~kEV~~~K~ITps~lserlkI~~SlAr~~Lr~L~~kG~Ik~V~~~~~q~IYt~ 85 (86)
T PRK09334 6 KKKEGSKTEKEIKSTIITLDEELLKRVAKEVKKEKIVTPYTLASKYGIKISVAKKVLRELEKRGVLVLYSKNRRTPIYVP 85 (86)
T ss_pred cccccccchhhhhhceeecCHHHHHHHHHHhccCcEEcHHHHHHHhcchHHHHHHHHHHHHHCCCEEEEecCCCeEEecc
Confidence 34556777899999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred c
Q psy1871 131 T 131 (139)
Q Consensus 131 a 131 (139)
+
T Consensus 86 ~ 86 (86)
T PRK09334 86 A 86 (86)
T ss_pred C
Confidence 4
No 5
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=97.03 E-value=0.00074 Score=41.78 Aligned_cols=42 Identities=31% Similarity=0.425 Sum_probs=32.7
Q ss_pred HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
+|+..+-...-+|...||++++++.+-+.+.|++|+++|+|+
T Consensus 7 ~Il~~l~~~~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 7 KILNYLRENPRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHCTTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 344444334448999999999999999999999999999985
No 6
>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=96.97 E-value=0.0023 Score=41.84 Aligned_cols=49 Identities=27% Similarity=0.373 Sum_probs=36.7
Q ss_pred HHHHHHHhhCCC-----Ceee-chHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 72 ASYDKLLKEVPA-----YKLI-TPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 72 ~tydKl~KEVpk-----~KlI-TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
..|+.|..+|-. -..+ |-..||++|+|+-+.+|++|+.|++.|+|....
T Consensus 4 ~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~ 58 (64)
T PF00392_consen 4 QIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRP 58 (64)
T ss_dssp HHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEEC
Confidence 345555554433 2455 999999999999999999999999999997654
No 7
>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=96.78 E-value=0.0026 Score=41.53 Aligned_cols=45 Identities=22% Similarity=0.356 Sum_probs=38.4
Q ss_pred HHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 75 DKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 75 dKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
++|+.-+.....+|...||+.|+|+-+-+|+=|.+|+++|+|..+
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 345555555678999999999999999999999999999997654
No 8
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=96.72 E-value=0.0071 Score=37.25 Aligned_cols=37 Identities=27% Similarity=0.369 Sum_probs=32.2
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
+..+-|...||++|+|+-+-.+++|+.|++.|+|..+
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~ 53 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRR 53 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 3344489999999999999999999999999998654
No 9
>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=96.64 E-value=0.0081 Score=37.68 Aligned_cols=49 Identities=27% Similarity=0.361 Sum_probs=38.6
Q ss_pred HHHHHHHHhhCC------CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 71 KASYDKLLKEVP------AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 71 k~tydKl~KEVp------k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
+++++.|...+. .-.+.|...||+.++|+-+-++++|..|++.|+|...
T Consensus 4 ~~~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~ 58 (66)
T cd07377 4 EQIADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAEGLVERR 58 (66)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 456666666632 2344569999999999999999999999999998654
No 10
>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=96.63 E-value=0.0076 Score=39.62 Aligned_cols=46 Identities=24% Similarity=0.322 Sum_probs=38.5
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
...=.|...||+.++|.-+-+..+|+.|+++|+|...... ..+|..
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~--~~~Y~a 64 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGR--PKVYRA 64 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEEC--CEEEEE
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCc--eEEEEE
Confidence 3344799999999999999999999999999999888743 456653
No 11
>PF14502 HTH_41: Helix-turn-helix domain
Probab=96.51 E-value=0.0058 Score=40.20 Aligned_cols=41 Identities=29% Similarity=0.284 Sum_probs=37.4
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
.-++=|.+.+|++|++....-..||+.|++.|.|.+.++.|
T Consensus 3 GdRi~tI~e~~~~~~vs~GtiQ~Alk~Le~~gaI~Le~rGh 43 (48)
T PF14502_consen 3 GDRIPTISEYSEKFGVSRGTIQNALKFLEENGAIKLESRGH 43 (48)
T ss_pred CcccCCHHHHHHHhCcchhHHHHHHHHHHHCCcEEeeecCc
Confidence 34677999999999999999999999999999999998766
No 12
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.45 E-value=0.011 Score=35.94 Aligned_cols=45 Identities=20% Similarity=0.263 Sum_probs=37.2
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
.-+|...|++.++++-+-++++|+.|.++|+|.....++ ...|.-
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~-~~~~~~ 53 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGK-RVYYSL 53 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCC-EEEEEE
Confidence 346999999999999999999999999999998765544 445543
No 13
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=96.17 E-value=0.011 Score=40.12 Aligned_cols=43 Identities=19% Similarity=0.251 Sum_probs=33.4
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY 128 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY 128 (139)
-+|...||+.++|+.+-||..|..|++.|.|+.+-..+....|
T Consensus 15 p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~ 57 (62)
T PF04703_consen 15 PLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTY 57 (62)
T ss_dssp -EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-E
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCccee
Confidence 3788999999999999999999999999999986543333334
No 14
>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=95.96 E-value=0.034 Score=38.11 Aligned_cols=51 Identities=27% Similarity=0.347 Sum_probs=38.0
Q ss_pred hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 80 EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 80 EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
..+....+|...||++++++-+..+++|+.|.+.|+|.-....+....-.|
T Consensus 19 ~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~ 69 (83)
T PF02082_consen 19 RHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLAR 69 (83)
T ss_dssp CTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS
T ss_pred hCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecC
Confidence 344555599999999999999999999999999999876654434333333
No 15
>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=95.94 E-value=0.032 Score=34.63 Aligned_cols=44 Identities=30% Similarity=0.412 Sum_probs=37.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
+|...|++.++|..+-++++|+.|++.|+|...... +...|.-.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~~~ 64 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG-RRVYYSLT 64 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec-cEEEEEeC
Confidence 899999999999999999999999999999887554 44555544
No 16
>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=95.83 E-value=0.026 Score=35.66 Aligned_cols=34 Identities=29% Similarity=0.450 Sum_probs=31.3
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+|++.|++.+++.-+-.-++++.|+++|+|....
T Consensus 22 ~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~~ 55 (62)
T PF12802_consen 22 LTQSELAERLGISKSTVSRIVKRLEKKGLVERER 55 (62)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence 6999999999999999999999999999998864
No 17
>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=95.71 E-value=0.042 Score=35.20 Aligned_cols=47 Identities=23% Similarity=0.328 Sum_probs=35.0
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEe
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYT 129 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYt 129 (139)
...-+|+..|++.+++.-+-+.++|+.|+++|+|.... .++|..+|.
T Consensus 15 ~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~~~~d~R~~~~~ 63 (68)
T PF13463_consen 15 SDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKERDPHDKRSKRYR 63 (68)
T ss_dssp -TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEEESSCTTSEEEE
T ss_pred cCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecCCCCcCCeeEEE
Confidence 34567899999999999999999999999999997774 335544443
No 18
>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=95.69 E-value=0.027 Score=38.77 Aligned_cols=34 Identities=24% Similarity=0.378 Sum_probs=29.0
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
++|.|.|||+++|+-|+--.+||-|++-|+|..-
T Consensus 4 ~lvas~iAd~~GiTRSvIVNALRKleSaGvIesr 37 (61)
T PF08222_consen 4 RLVASKIADRVGITRSVIVNALRKLESAGVIESR 37 (61)
T ss_dssp EE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEE
T ss_pred eehHHHHHHHhCccHHHHHHHHHHHHhcCceeec
Confidence 6899999999999999999999999999999843
No 19
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=95.69 E-value=0.019 Score=47.01 Aligned_cols=49 Identities=27% Similarity=0.361 Sum_probs=44.2
Q ss_pred HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
.+-.++|++.+-....+|...|+++|+|+.+-+|+=|++|+++|+|..+
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 3556778888888999999999999999999999999999999999764
No 20
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=95.64 E-value=0.024 Score=33.85 Aligned_cols=32 Identities=25% Similarity=0.414 Sum_probs=30.2
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
+|...||+.++++-+-+.++|+.|++.|+|..
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~ 40 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISR 40 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 68899999999999999999999999999964
No 21
>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=95.61 E-value=0.035 Score=43.55 Aligned_cols=39 Identities=23% Similarity=0.371 Sum_probs=35.7
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
|+.+|=|=..|+++|+|+-...|+||.+|+.+|+|...-
T Consensus 28 ~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 66 (238)
T TIGR02325 28 AGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQ 66 (238)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 567888999999999999999999999999999987653
No 22
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=95.60 E-value=0.012 Score=39.35 Aligned_cols=47 Identities=15% Similarity=0.245 Sum_probs=36.7
Q ss_pred HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
|..-+-....+|...||.+|++.-+..+..|..|+.+|.|..+..+.
T Consensus 5 i~~~l~~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 5 IRDYLRERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HHHHHHHS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 33334455788999999999999999999999999999999987554
No 23
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=95.59 E-value=0.036 Score=44.25 Aligned_cols=39 Identities=23% Similarity=0.387 Sum_probs=35.2
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
|+.++=|=..|+++|+|+-...|+||.+|+.+|+|..+-
T Consensus 25 ~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~ 63 (240)
T PRK09764 25 PGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQ 63 (240)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 456787999999999999999999999999999997654
No 24
>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=95.59 E-value=0.036 Score=43.75 Aligned_cols=39 Identities=21% Similarity=0.244 Sum_probs=35.4
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
|..+|=|=..|+++|+|+-...|+||++|+++|+|..+.
T Consensus 20 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 58 (233)
T TIGR02404 20 EGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKIQ 58 (233)
T ss_pred CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 467888999999999999999999999999999987654
No 25
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=95.55 E-value=0.022 Score=46.75 Aligned_cols=48 Identities=17% Similarity=0.250 Sum_probs=42.9
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
+-.++|+..+.....+|...|+++|+|+-+-+|+=|.+|+++|+|..+
T Consensus 5 ~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 5 QRHDAIIELVKQQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 456777788878889999999999999999999999999999998764
No 26
>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=95.54 E-value=0.038 Score=43.64 Aligned_cols=39 Identities=18% Similarity=0.295 Sum_probs=35.0
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
|+.+|=|-..||++|+|+-...|+||.+|+++|+|..+-
T Consensus 21 ~g~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~ 59 (230)
T TIGR02018 21 PGHRIPSEHELVAQYGCSRMTVNRALRELTDAGLLERRQ 59 (230)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 567888999999999999999999999999999986543
No 27
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=95.52 E-value=0.032 Score=43.71 Aligned_cols=52 Identities=23% Similarity=0.266 Sum_probs=42.8
Q ss_pred eCHHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 69 FDKASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 69 ~Dk~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
+-+..|+.|...|-+ .++ +...||++|+|+-+--|-||+.|+..|+|..+-+
T Consensus 8 ~~~~vy~~i~~~I~~g~l~pG~~L-~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~ 65 (224)
T PRK11534 8 TALDGYRWLKNDIIRGNFQPDEKL-RMSLLTSRYALGVGPLREALSQLVAERLVTVVNQ 65 (224)
T ss_pred hhHHHHHHHHHHHHhCCCCCCCcC-CHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCC
Confidence 345678888887654 444 7789999999999999999999999999987543
No 28
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.50 E-value=0.063 Score=32.13 Aligned_cols=45 Identities=22% Similarity=0.317 Sum_probs=37.1
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
..++-|..+ ..+|...|++.|++.-+-+++.|..|++.|+|....
T Consensus 4 ~il~~l~~~----~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 4 QILELLAQQ----GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHc----CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 455555543 347999999999999999999999999999997654
No 29
>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=95.39 E-value=0.028 Score=37.29 Aligned_cols=37 Identities=24% Similarity=0.307 Sum_probs=32.5
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
.-..|++..||++|+|+-+-+-..|+.|+++|+|...
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~ 55 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYE 55 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEec
Confidence 4567899999999999999999999999999998653
No 30
>PRK03837 transcriptional regulator NanR; Provisional
Probab=95.35 E-value=0.035 Score=43.59 Aligned_cols=50 Identities=20% Similarity=0.239 Sum_probs=41.1
Q ss_pred HHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 71 KASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 71 k~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+..|+.|...|-. .++-+-..||++|+|+-+..|.||+.|+.+|+|...-
T Consensus 16 ~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~ 71 (241)
T PRK03837 16 EEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISH 71 (241)
T ss_pred HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4567777766544 3444899999999999999999999999999998754
No 31
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=95.34 E-value=0.048 Score=43.66 Aligned_cols=50 Identities=22% Similarity=0.187 Sum_probs=41.4
Q ss_pred HHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 71 KASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 71 k~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
...|+.|...|-. .++-|-..||++|+|+-+-.|.||+.|+..|+|...-
T Consensus 12 ~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 12 QEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4567777776643 4555788999999999999999999999999998654
No 32
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=95.33 E-value=0.042 Score=45.22 Aligned_cols=50 Identities=20% Similarity=0.238 Sum_probs=42.2
Q ss_pred hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 80 EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 80 EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
.+.+.--||.+.||++++++-+-+.+.|+.|+++|+|......+.+.|+.
T Consensus 15 ~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~L 64 (217)
T PRK14165 15 AVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLITI 64 (217)
T ss_pred ccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEEE
Confidence 34444568999999999999999999999999999999876666676665
No 33
>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=95.29 E-value=0.047 Score=34.67 Aligned_cols=36 Identities=22% Similarity=0.305 Sum_probs=33.0
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
--+|...||+.++++-+-+.++|+.|+++|+|....
T Consensus 24 ~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 24 LPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 447999999999999999999999999999998754
No 34
>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=95.28 E-value=0.048 Score=46.36 Aligned_cols=59 Identities=19% Similarity=0.326 Sum_probs=50.4
Q ss_pred hhccceeeCHHHHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 62 KLNNQVLFDKASYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 62 Klnn~Vl~Dk~tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
.++..-+-.-+..++|+.+.... -.++-+.||++++|+-|..|.+||.|++.|+|..-.
T Consensus 173 Ai~tLSySEleAv~~IL~~L~~~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 173 AINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred HHHhccHhHHHHHHHHHHHhccccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 34444455678899999999994 889999999999999999999999999999997543
No 35
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=95.28 E-value=0.024 Score=46.45 Aligned_cols=48 Identities=15% Similarity=0.169 Sum_probs=43.0
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
+=.++|+..+....-||...||+.|+|+.+-.|+=|++|+++|+|..+
T Consensus 5 eR~~~Il~~L~~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 5 QRQAAILEYLQKQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHHHHHHcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 345678888888888999999999999999999999999999998775
No 36
>PHA02943 hypothetical protein; Provisional
Probab=95.17 E-value=0.066 Score=43.09 Aligned_cols=55 Identities=29% Similarity=0.303 Sum_probs=45.6
Q ss_pred HHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 75 DKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 75 dKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+.|+.-+ +.-.-|.+.||++|+++-|-|+-+|.-||++|.|+.|..+.....+.+
T Consensus 14 ~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l~ 68 (165)
T PHA02943 14 IKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCLD 68 (165)
T ss_pred HHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEEC
Confidence 3444444 667779999999999999999999999999999999987776655554
No 37
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=95.09 E-value=0.05 Score=34.35 Aligned_cols=32 Identities=22% Similarity=0.416 Sum_probs=29.4
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
+|.+.||+++++.-|-+.++|+.|++.|+|..
T Consensus 19 ~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~ 50 (52)
T PF09339_consen 19 LTLSEIARALGLPKSTVHRLLQTLVEEGYVER 50 (52)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHCcCeec
Confidence 69999999999999999999999999999864
No 38
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=95.00 E-value=0.034 Score=45.66 Aligned_cols=47 Identities=23% Similarity=0.315 Sum_probs=43.3
Q ss_pred HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
=.++|+..+-....|+...||++|+|+-...|+=|++|+++|++..+
T Consensus 6 R~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 6 RHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 45788888999999999999999999999999999999999998765
No 39
>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=94.96 E-value=0.045 Score=35.43 Aligned_cols=50 Identities=22% Similarity=0.251 Sum_probs=40.6
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
++--+|+..+....=.|.+.|+++++|.-+.+..=|+.|++-|+|..+-.
T Consensus 10 p~R~~Il~~L~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~~ 59 (61)
T PF12840_consen 10 PTRLRILRLLASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVERE 59 (61)
T ss_dssp HHHHHHHHHHHHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEE
T ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecc
Confidence 55556666664555679999999999999999999999999999988754
No 40
>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=94.94 E-value=0.051 Score=34.24 Aligned_cols=34 Identities=32% Similarity=0.462 Sum_probs=31.1
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+|++.||+.+++.-|-.-++++.|+++|+|..-.
T Consensus 18 ~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 18 ITQSELAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 8999999999999999999999999999998753
No 41
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=94.85 E-value=0.064 Score=42.65 Aligned_cols=38 Identities=18% Similarity=0.302 Sum_probs=34.9
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
|+.+|=|=..||++|+|+-...|+||.+|+++|+|...
T Consensus 29 ~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~ 66 (241)
T PRK11402 29 AGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRW 66 (241)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 35689999999999999999999999999999998764
No 42
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=94.80 E-value=0.076 Score=38.95 Aligned_cols=48 Identities=21% Similarity=0.333 Sum_probs=43.1
Q ss_pred eCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 69 FDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+|...++-|+.+.+ ++-..||++++++.+-.+.-++.|++.|+|+-+.
T Consensus 9 ~D~~IL~~L~~d~r----~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 9 IDRRILRLLQEDAR----ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred HHHHHHHHHHHhCC----CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEE
Confidence 56777888888887 8999999999999999999999999999998763
No 43
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.80 E-value=0.14 Score=39.45 Aligned_cols=61 Identities=25% Similarity=0.347 Sum_probs=49.2
Q ss_pred eeCHHHHHHHHh-hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe----ecCceEEEeccC
Q psy1871 68 LFDKASYDKLLK-EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV----KHHAQVIYTRTT 132 (139)
Q Consensus 68 l~Dk~tydKl~K-EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs----kh~~q~IYtra~ 132 (139)
-.|-+.|..|+. +-| .|.-.|||++++.-|.+.++|+-|.+.|+|...- +++.-.||-+..
T Consensus 27 ~~Dv~v~~~LL~~~~~----~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~i~ 92 (126)
T COG3355 27 ELDVEVYKALLEENGP----LTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKPID 92 (126)
T ss_pred HHHHHHHHHHHhhcCC----cCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEecCC
Confidence 357788999994 544 4999999999999999999999999999998863 345556775543
No 44
>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=94.74 E-value=0.08 Score=40.91 Aligned_cols=49 Identities=27% Similarity=0.415 Sum_probs=39.8
Q ss_pred CHHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 70 DKASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 70 Dk~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
....|+.|...| |+.++ +-..||++|+|+-+--|.||+.|+..|+|...
T Consensus 13 ~~~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~ 67 (212)
T TIGR03338 13 TTLVQDEIERAILSGELPPGAKL-NESDIAARLGVSRGPVREAFRALEEAGLVRNE 67 (212)
T ss_pred HHHHHHHHHHHHHcCCCCCCCEe-cHHHHHHHhCCChHHHHHHHHHHHHCCCEEEe
Confidence 345666666665 34566 88999999999999999999999999998754
No 45
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=94.74 E-value=0.06 Score=36.21 Aligned_cols=34 Identities=18% Similarity=0.138 Sum_probs=31.7
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+|...||+.++|.-+-++++|..|+++|+|....
T Consensus 23 ~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~ 56 (68)
T smart00550 23 STALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQG 56 (68)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 8999999999999999999999999999986643
No 46
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=94.73 E-value=0.089 Score=42.12 Aligned_cols=50 Identities=20% Similarity=0.256 Sum_probs=41.3
Q ss_pred HHHHHHHHhhCC------CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 71 KASYDKLLKEVP------AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 71 k~tydKl~KEVp------k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+..|+.|...|- ..+|-|-..||++|+|+-+-.|.||+.|+..|+|...-
T Consensus 5 ~~v~~~L~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~ 60 (253)
T PRK10421 5 DEVADRVRALIEEKNLEAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRR 60 (253)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 466777777763 34555789999999999999999999999999997543
No 47
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=94.72 E-value=0.062 Score=43.33 Aligned_cols=40 Identities=35% Similarity=0.471 Sum_probs=36.1
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
|+.++=|=..||++|+|+=...|+||++|+++|+|....+
T Consensus 27 ~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G 66 (236)
T COG2188 27 PGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQG 66 (236)
T ss_pred CCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEec
Confidence 4578889999999999999999999999999999987654
No 48
>PRK14999 histidine utilization repressor; Provisional
Probab=94.65 E-value=0.079 Score=42.20 Aligned_cols=38 Identities=16% Similarity=0.284 Sum_probs=34.3
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
|+.+|=|=..||++|+|+-...|+||.+|+.+|+|...
T Consensus 32 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~ 69 (241)
T PRK14999 32 PHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRL 69 (241)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 45678799999999999999999999999999998553
No 49
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=94.53 E-value=0.073 Score=41.96 Aligned_cols=49 Identities=18% Similarity=0.272 Sum_probs=39.5
Q ss_pred HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
+..|+.|...| |+.+|-|-..||++|+|+-+..|.||+.|+..|+|...
T Consensus 10 ~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~ 64 (239)
T PRK04984 10 GFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQ 64 (239)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 34566665555 34456689999999999999999999999999999754
No 50
>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=94.50 E-value=0.078 Score=41.75 Aligned_cols=47 Identities=23% Similarity=0.343 Sum_probs=38.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe----ecCceEEEeccCC
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV----KHHAQVIYTRTTK 133 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs----kh~~q~IYtra~k 133 (139)
+|...||++++|+-+-.++.|+.|+++|+|.... .+++..+|.-..+
T Consensus 16 ~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~LT~~ 66 (203)
T TIGR02702 16 ATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQLSRQ 66 (203)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEEECcc
Confidence 8999999999999999999999999999998762 3455666654333
No 51
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=94.49 E-value=0.12 Score=41.18 Aligned_cols=52 Identities=17% Similarity=0.233 Sum_probs=43.2
Q ss_pred CHHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 70 DKASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 70 Dk~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
....|+.|...| |+.+|=|-..||++|+|+=+-.|-||+.|+..|+|...-+
T Consensus 9 ~~~v~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 9 ADVVAERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 356788888777 4455658899999999999999999999999999986543
No 52
>PF13730 HTH_36: Helix-turn-helix domain
Probab=94.47 E-value=0.057 Score=33.82 Aligned_cols=30 Identities=30% Similarity=0.460 Sum_probs=28.0
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLI 116 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlI 116 (139)
-+-..||++++++-+-.+++|++|++.|+|
T Consensus 26 pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 26 PSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 367899999999999999999999999987
No 53
>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=94.44 E-value=0.041 Score=37.78 Aligned_cols=59 Identities=10% Similarity=0.240 Sum_probs=44.4
Q ss_pred CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871 70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY 128 (139)
Q Consensus 70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY 128 (139)
+.++|++...=|-...-++.|-|--+|+|...-|-+++.+||+.|+|-+-..+..-.|+
T Consensus 4 ~D~ly~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~~~~~R~Vl 62 (65)
T PF09397_consen 4 EDPLYEEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPANGSKPREVL 62 (65)
T ss_dssp TSTTHHHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---TTSEEEB-
T ss_pred ccHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCCCCCCCeec
Confidence 35678887777777888999999999999999999999999999999988655433343
No 54
>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=94.41 E-value=0.067 Score=38.25 Aligned_cols=54 Identities=11% Similarity=0.165 Sum_probs=40.9
Q ss_pred HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEec
Q psy1871 77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYTR 130 (139)
Q Consensus 77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYtr 130 (139)
++-.+-...-+|++.||+++++.-+..-++|+.|+++|+|.... .++|...|.-
T Consensus 33 iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v~L 88 (118)
T TIGR02337 33 ILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYISL 88 (118)
T ss_pred HHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEEEE
Confidence 33333334458999999999999999999999999999999863 3445544443
No 55
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=94.40 E-value=0.06 Score=44.63 Aligned_cols=49 Identities=12% Similarity=0.148 Sum_probs=43.3
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+=.++|+..+.....||...||+.|+|+.+-+|+=|.+|+++|++..+.
T Consensus 17 eR~~~Il~~L~~~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~ 65 (269)
T PRK09802 17 ERREQIIQRLRQQGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAY 65 (269)
T ss_pred HHHHHHHHHHHHcCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 4567777788777779999999999999999999999999999998654
No 56
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=94.38 E-value=0.11 Score=38.73 Aligned_cols=45 Identities=20% Similarity=0.264 Sum_probs=37.7
Q ss_pred CCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871 81 VPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQ 125 (139)
Q Consensus 81 Vpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q 125 (139)
.+.-..++...||++++|+-.-.|++|+.|...|+|..+.+.+..
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~~GG 64 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGKNGG 64 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCCCCC
Confidence 333357899999999999999999999999999999877654433
No 57
>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=94.32 E-value=0.12 Score=40.23 Aligned_cols=39 Identities=31% Similarity=0.377 Sum_probs=35.7
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
|+.++=|...|+++|+|+-...|+||++|+.+|+|....
T Consensus 21 ~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~ 59 (231)
T TIGR03337 21 PGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYRED 59 (231)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeC
Confidence 567888999999999999999999999999999997654
No 58
>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=94.30 E-value=0.092 Score=41.38 Aligned_cols=50 Identities=16% Similarity=0.163 Sum_probs=40.9
Q ss_pred HHHHHHHHhhCC------CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 71 KASYDKLLKEVP------AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 71 k~tydKl~KEVp------k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+..|+.|...|- +.++-|-..||++|+|+-+-.|-||+.|+..|+|...-
T Consensus 9 ~~v~~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 9 GFAEEYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence 456666666654 34555899999999999999999999999999998654
No 59
>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=94.10 E-value=0.061 Score=36.90 Aligned_cols=54 Identities=17% Similarity=0.313 Sum_probs=48.2
Q ss_pred CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
++++|+....=|....-+++|.|=-+|+|...-|-+++.+||+.|+|-+...+.
T Consensus 3 ~D~ly~~a~~~V~~~~~~S~S~lQR~~~IGynrAariid~lE~~GiV~p~~g~~ 56 (63)
T smart00843 3 EDELYDEAVELVIETQKASTSLLQRRLRIGYNRAARLIDQLEEEGIVGPANGSK 56 (63)
T ss_pred ccHHHHHHHHHHHHhCCCChHHHHHHHhcchhHHHHHHHHHHHCcCCCCCCCCC
Confidence 467889888888888999999999999999999999999999999998865443
No 60
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=94.09 E-value=0.097 Score=41.89 Aligned_cols=51 Identities=16% Similarity=0.181 Sum_probs=41.5
Q ss_pred CHHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 70 DKASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 70 Dk~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
-...|+.|...|-+ .+|-|-..||++|+|+-+-.|.||+.|+..|+|...-
T Consensus 10 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~ 66 (253)
T PRK11523 10 YQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRK 66 (253)
T ss_pred HHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 35567777766544 4666789999999999999999999999999997544
No 61
>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=93.83 E-value=0.11 Score=35.18 Aligned_cols=34 Identities=26% Similarity=0.360 Sum_probs=30.2
Q ss_pred chHHHHhhhccc-hHHHHHHHHHHHHcCCeeEEee
Q psy1871 88 TPSVVSERLKVR-GSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 88 TPsvlseRlkI~-~SLARkaLreL~~kGlIk~Vsk 121 (139)
|..+|++.|+++ -|-+..-|+.|+++|+|.....
T Consensus 27 t~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~ 61 (65)
T PF01726_consen 27 TVREIAEALGLKSTSTVQRHLKALERKGYIRRDPG 61 (65)
T ss_dssp -HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCC
T ss_pred CHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCC
Confidence 778999999998 9999999999999999987654
No 62
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=93.81 E-value=0.12 Score=41.19 Aligned_cols=48 Identities=19% Similarity=0.263 Sum_probs=38.3
Q ss_pred HHHHHHhhC-CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 73 SYDKLLKEV-PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 73 tydKl~KEV-pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+.++|..+. |+.+|=|=..||++|+|+-...|+||.+|+.+|+|...-
T Consensus 21 L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~ 69 (241)
T PRK10079 21 LEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQ 69 (241)
T ss_pred HHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 344443333 356888889999999999999999999999999997543
No 63
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=93.74 E-value=0.14 Score=40.89 Aligned_cols=51 Identities=20% Similarity=0.188 Sum_probs=42.4
Q ss_pred CHHHHHHHHhhCCC------CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 70 DKASYDKLLKEVPA------YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 70 Dk~tydKl~KEVpk------~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
.+..|+.|...|-. .+|-|-..||++|+|+-+..|-||+.|+..|+|...-
T Consensus 12 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~ 68 (254)
T PRK09464 12 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQ 68 (254)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 35677777777644 4555889999999999999999999999999998654
No 64
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=93.67 E-value=0.12 Score=38.33 Aligned_cols=37 Identities=24% Similarity=0.328 Sum_probs=34.1
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
..-+|++.||+++++.-|-.=++|..|+++|+|....
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 3459999999999999999999999999999999873
No 65
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=93.58 E-value=0.16 Score=34.12 Aligned_cols=34 Identities=29% Similarity=0.347 Sum_probs=32.0
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
-+|++.||+.++|+-+-+++.|+.|++.|+|...
T Consensus 20 ~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~ 53 (91)
T smart00346 20 GLTLAELAERLGLSKSTAHRLLNTLQELGYVEQD 53 (91)
T ss_pred CcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeec
Confidence 4899999999999999999999999999999764
No 66
>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=93.37 E-value=0.17 Score=39.87 Aligned_cols=52 Identities=25% Similarity=0.260 Sum_probs=40.1
Q ss_pred HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
+++.-+-...-+|...||+++++.-|.+++.|+.|++.|+|..... +...|.
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~--r~~~~~ 198 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR--KGKRYS 198 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC--CccEEE
Confidence 3444443334589999999999999999999999999999998763 444444
No 67
>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=93.36 E-value=0.2 Score=37.14 Aligned_cols=41 Identities=24% Similarity=0.232 Sum_probs=35.4
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
.-..+|...||++++|.....+++|+.|.+.|+|.-+...+
T Consensus 22 ~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~~G~~ 62 (135)
T TIGR02010 22 ETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSVRGPG 62 (135)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEeCCC
Confidence 34578999999999999999999999999999997654433
No 68
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=93.16 E-value=0.18 Score=41.15 Aligned_cols=53 Identities=23% Similarity=0.357 Sum_probs=43.7
Q ss_pred HHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 74 YDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 74 ydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
.++|+..+.+...+|...|++.|+|+-+-+|+-|.+|+++|+|+. .|...+|.
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r---~~Gga~~~ 58 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILR---NHGRAKYI 58 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEE---ecCeEEEe
Confidence 456777777788999999999999999999999999999999875 34444554
No 69
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=93.14 E-value=0.14 Score=40.07 Aligned_cols=49 Identities=16% Similarity=0.177 Sum_probs=40.5
Q ss_pred HHHHHHHHhhCC------CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 71 KASYDKLLKEVP------AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 71 k~tydKl~KEVp------k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+..|+.|...|- +.++ +...||++|+|+-+-.|-||+.|+..|+|....
T Consensus 14 e~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~ 68 (221)
T PRK11414 14 LQVENDLKHQLSIGALKPGARL-ITKNLAEQLGMSITPVREALLRLVSVNALSVAP 68 (221)
T ss_pred HHHHHHHHHHHHhCCCCCCCcc-CHHHHHHHHCCCchhHHHHHHHHHHCCCEEecC
Confidence 557777777764 4566 568999999999999999999999999997543
No 70
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=92.98 E-value=0.21 Score=33.19 Aligned_cols=35 Identities=31% Similarity=0.469 Sum_probs=32.4
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
-+|+..|++.++++-+-..++|+.|++.|+|....
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~~ 58 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRLP 58 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEecC
Confidence 48999999999999999999999999999998763
No 71
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=92.97 E-value=0.19 Score=36.94 Aligned_cols=42 Identities=14% Similarity=0.199 Sum_probs=36.0
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEE
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVI 127 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~I 127 (139)
-+|++.||+++++.-|-.-+++..|+++|+|..+. .++|...
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~~ 89 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAKR 89 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCeee
Confidence 46899999999999999999999999999999984 4455443
No 72
>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=92.94 E-value=0.18 Score=36.47 Aligned_cols=38 Identities=26% Similarity=0.382 Sum_probs=34.1
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
++-..+|...||++++|+.+..+++|+.|.+.|+|...
T Consensus 21 ~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 21 PDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 44458899999999999999999999999999998654
No 73
>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=92.80 E-value=0.23 Score=35.27 Aligned_cols=37 Identities=16% Similarity=0.244 Sum_probs=33.7
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
...-+|++.||+.+++.=+-..++|.+|+++|+|...
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~ 80 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQ 80 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeee
Confidence 3567899999999999999999999999999999754
No 74
>PRK10870 transcriptional repressor MprA; Provisional
Probab=92.77 E-value=0.17 Score=39.44 Aligned_cols=36 Identities=28% Similarity=0.310 Sum_probs=33.6
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
.-+|++.||+++++..+-.-++|..|+++|+|....
T Consensus 70 ~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 70 HSIQPSELSCALGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 458999999999999999999999999999999973
No 75
>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=92.76 E-value=0.16 Score=37.10 Aligned_cols=35 Identities=14% Similarity=0.271 Sum_probs=32.4
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
..+|...||++++|+-+..+++|+.|++.|+|..+
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 46899999999999999999999999999999664
No 76
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=92.73 E-value=0.077 Score=41.88 Aligned_cols=48 Identities=19% Similarity=0.127 Sum_probs=42.2
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
+=.+.|+..+.....+|...||++|+|+.+-+|+=|++|++.|++..+
T Consensus 7 ~R~~~Il~~l~~~~~~~~~~La~~~~vS~~TiRRDl~~L~~~g~~~r~ 54 (185)
T PRK04424 7 ERQKALQELIEENPFITDEELAEKFGVSIQTIRLDRMELGIPELRERI 54 (185)
T ss_pred HHHHHHHHHHHHCCCEEHHHHHHHHCcCHHHHHHHHHHHhcchHHHHH
Confidence 345667777777889999999999999999999999999999998664
No 77
>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=92.69 E-value=0.22 Score=40.04 Aligned_cols=46 Identities=28% Similarity=0.295 Sum_probs=40.1
Q ss_pred HHHHHHHhhC--CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 72 ASYDKLLKEV--PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 72 ~tydKl~KEV--pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
....+|+.=+ .....+|+..|++.++++..+|+.+|.+|+..|++-
T Consensus 174 ~~~~~il~~~~~~~~g~vt~~~l~~~~~ws~~~a~~~L~~~~~~G~l~ 221 (223)
T PF04157_consen 174 KDQSRILELAEEENGGGVTASELAEKLGWSVERAKEALEELEREGLLW 221 (223)
T ss_dssp HHHHHHHHHH--TTTSEEEHHHHHHHHTB-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHHHhhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCEe
Confidence 4556777777 778999999999999999999999999999999974
No 78
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=92.52 E-value=0.33 Score=33.89 Aligned_cols=45 Identities=20% Similarity=0.361 Sum_probs=37.2
Q ss_pred CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
|...+.-|..+ .-+|.+.||++++++-+-+++.|+.|+++|+|..
T Consensus 5 D~~il~~L~~~----~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~ 49 (108)
T smart00344 5 DRKILEELQKD----ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKG 49 (108)
T ss_pred HHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeec
Confidence 45555555554 2478999999999999999999999999999983
No 79
>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=92.41 E-value=0.39 Score=31.34 Aligned_cols=32 Identities=22% Similarity=0.379 Sum_probs=30.5
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
-+|...||+-++++-.-.-++|++|+++|+|.
T Consensus 28 ~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~ 59 (76)
T PF13545_consen 28 PLTQEEIADMLGVSRETVSRILKRLKDEGIIE 59 (76)
T ss_dssp ESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEE
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEE
Confidence 47899999999999999999999999999997
No 80
>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=92.08 E-value=0.24 Score=35.38 Aligned_cols=36 Identities=17% Similarity=0.238 Sum_probs=33.5
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
.-+|++.||+.+++.-|-.-++++.|+++|+|..+.
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 458999999999999999999999999999999874
No 81
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=92.03 E-value=0.26 Score=33.57 Aligned_cols=32 Identities=28% Similarity=0.399 Sum_probs=29.2
Q ss_pred hHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 89 PSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 89 PsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+..||++++|+-|-..++|+.|+++|+|....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 57899999999999999999999999987754
No 82
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=91.84 E-value=0.27 Score=39.88 Aligned_cols=59 Identities=14% Similarity=0.273 Sum_probs=45.3
Q ss_pred HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
++..+..-|...|+|....||..|+++..-+-.-|++|+..|.|.-|.-.++..||+-.
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs~ 158 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYISE 158 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE---
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEecH
Confidence 67778888888899999999999999999999999999999999999999999999843
No 83
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=91.69 E-value=0.4 Score=35.63 Aligned_cols=36 Identities=19% Similarity=0.118 Sum_probs=32.4
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
...+|.+.||+.|+|+-+-+..+|+.|+++|+|...
T Consensus 20 ~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~ 55 (142)
T PRK03902 20 KGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYE 55 (142)
T ss_pred CCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEe
Confidence 456799999999999999999999999999999754
No 84
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=91.54 E-value=0.79 Score=38.61 Aligned_cols=81 Identities=19% Similarity=0.172 Sum_probs=63.5
Q ss_pred cccccchhhhhhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 51 KKKWSKGKVRDKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 51 KKKWSKgKvkdKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
.-.|+.+=-.+-..+-.-|+++-.+=|.=..-+-=-||.++|...+++.=+-.-++|++||++|+|+..-+++++.|-.+
T Consensus 175 ~~~~~~~~~~~~~~~~~~L~~~e~~il~~i~~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V~l~ 254 (258)
T COG2512 175 EPLLSRGDELRVLVNEYDLNEDEKEILDLIRERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIVELR 254 (258)
T ss_pred hhccccccccccccccCCCCHHHHHHHHHHHHhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEEEEe
Confidence 44588876666666666666655554444444555789999999999999999999999999999999999998887665
Q ss_pred c
Q psy1871 131 T 131 (139)
Q Consensus 131 a 131 (139)
.
T Consensus 255 ~ 255 (258)
T COG2512 255 D 255 (258)
T ss_pred c
Confidence 3
No 85
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=91.52 E-value=0.44 Score=32.33 Aligned_cols=41 Identities=27% Similarity=0.385 Sum_probs=33.7
Q ss_pred HHHHhhhccchHHHHHHHHHHHHcCCeeEEe--ecCceEEEec
Q psy1871 90 SVVSERLKVRGSLARKALEELLQKGLIKQVV--KHHAQVIYTR 130 (139)
Q Consensus 90 svlseRlkI~~SLARkaLreL~~kGlIk~Vs--kh~~q~IYtr 130 (139)
+.|+++++|..|-.-++|+.|+++|+|...- .++|..++.-
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~l 82 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRL 82 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeecCCccccceeeEEE
Confidence 8999999999999999999999999999873 2344444443
No 86
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=91.49 E-value=0.34 Score=41.26 Aligned_cols=54 Identities=19% Similarity=0.317 Sum_probs=45.7
Q ss_pred eeeCHHHHHHHHhhCCC-CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 67 VLFDKASYDKLLKEVPA-YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 67 Vl~Dk~tydKl~KEVpk-~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
-.-.-+.++-|..|.-. .=+++.|.||||.+|+-|+-=.|||.||+-|+|.-=|
T Consensus 184 SYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESAGvIeSRS 238 (261)
T COG4465 184 SYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 238 (261)
T ss_pred cHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhcCceeecc
Confidence 33456677888888876 5789999999999999999999999999999997543
No 87
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=91.24 E-value=0.31 Score=38.50 Aligned_cols=56 Identities=20% Similarity=0.281 Sum_probs=46.2
Q ss_pred cceeeCHHHHHHHHhhCCCCe-----eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 65 NQVLFDKASYDKLLKEVPAYK-----LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 65 n~Vl~Dk~tydKl~KEVpk~K-----lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
.........|+.|...|-.-. -|+...||++|+|+-.--|.||..|+..|+|...-
T Consensus 13 ~~~~~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p 73 (230)
T COG1802 13 KPDTLADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEP 73 (230)
T ss_pred CcccHHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecC
Confidence 344556677888888776654 37999999999999999999999999999998763
No 88
>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=91.16 E-value=1 Score=28.07 Aligned_cols=28 Identities=32% Similarity=0.430 Sum_probs=26.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcC
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKG 114 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kG 114 (139)
||...||+.|+|+-...++-|.+|.+.|
T Consensus 16 it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 16 ITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 9999999999999999999999999999
No 89
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=90.72 E-value=0.74 Score=32.48 Aligned_cols=45 Identities=22% Similarity=0.337 Sum_probs=37.1
Q ss_pred eeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 85 KLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 85 KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
.-+|...|.+++ +|+.+-.-+.|+.|++.|+|..+.-..+...|-
T Consensus 15 ~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~~~~~~~~y~ 64 (116)
T cd07153 15 GHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIELGDGKARYE 64 (116)
T ss_pred CCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEEeCCCceEEE
Confidence 457999999998 688888999999999999999987555445564
No 90
>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=90.61 E-value=0.58 Score=28.96 Aligned_cols=33 Identities=27% Similarity=0.363 Sum_probs=29.4
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
.=.|+..|++.+++.-|....=|+.|++.|+|.
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~ 46 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVE 46 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHHCcCee
Confidence 336899999999999999999999999999985
No 91
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=90.53 E-value=0.52 Score=36.66 Aligned_cols=50 Identities=18% Similarity=0.236 Sum_probs=39.6
Q ss_pred HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
++.+.-|+.-+-+--.++...||++|+|.-+-+...|+.|++.|+|..+-
T Consensus 9 edYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~ 58 (154)
T COG1321 9 EDYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP 58 (154)
T ss_pred HHHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence 33444444333356788999999999999999999999999999987654
No 92
>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=90.48 E-value=0.38 Score=28.91 Aligned_cols=39 Identities=18% Similarity=0.170 Sum_probs=30.6
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
|+..+|+.++|+-+ .|+..+++|+|.+....+++..|+.
T Consensus 2 ~~~e~a~~~gv~~~----tlr~~~~~g~l~~~~~~~~~~~y~~ 40 (49)
T cd04761 2 TIGELAKLTGVSPS----TLRYYERIGLLSPARTEGGYRLYSD 40 (49)
T ss_pred cHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCEEeCH
Confidence 77899999988766 5788899999986544457778875
No 93
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=90.48 E-value=0.7 Score=35.43 Aligned_cols=48 Identities=19% Similarity=0.346 Sum_probs=41.4
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT 132 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~ 132 (139)
|..+|=|.-.+|..++||--..++|.++|++.|+|.. .++...|+...
T Consensus 31 pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t---~rg~G~fV~~~ 78 (125)
T COG1725 31 PGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVET---KRGKGTFVTED 78 (125)
T ss_pred CCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE---ecCeeEEEcCC
Confidence 6689999999999999999999999999999999754 56667777644
No 94
>PRK11050 manganese transport regulator MntR; Provisional
Probab=90.43 E-value=0.57 Score=35.73 Aligned_cols=34 Identities=24% Similarity=0.300 Sum_probs=31.2
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
.-+|+..||++|+|+-|-..++|+.|++.|+|..
T Consensus 50 ~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r 83 (152)
T PRK11050 50 GEARQVDIAARLGVSQPTVAKMLKRLARDGLVEM 83 (152)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEE
Confidence 3479999999999999999999999999999864
No 95
>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=90.39 E-value=1.5 Score=28.78 Aligned_cols=34 Identities=18% Similarity=0.199 Sum_probs=30.5
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+|...||++++|+-+..++.|+.|++.|+.....
T Consensus 14 ~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~ 47 (69)
T TIGR00122 14 FSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV 47 (69)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 5789999999999999999999999999965444
No 96
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=90.34 E-value=0.53 Score=36.16 Aligned_cols=46 Identities=24% Similarity=0.305 Sum_probs=39.5
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
..+|...||++.+|+-+.-+++|..|.+.|+|+-+-....-..-.|
T Consensus 24 ~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~Lar 69 (150)
T COG1959 24 GPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLAR 69 (150)
T ss_pred CcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCCC
Confidence 4889999999999999999999999999999999876665544443
No 97
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=90.19 E-value=0.59 Score=35.87 Aligned_cols=41 Identities=22% Similarity=0.271 Sum_probs=36.0
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQ 125 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q 125 (139)
..+|...||++++|+-+--+++|+.|.+.|+|.-+-..+.-
T Consensus 23 ~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~rG~~GG 63 (153)
T PRK11920 23 KLSRIPEIARAYGVSELFLFKILQPLVEAGLVETVRGRNGG 63 (153)
T ss_pred CcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeecCCCCC
Confidence 46799999999999999999999999999999887654443
No 98
>PRK04158 transcriptional repressor CodY; Validated
Probab=90.10 E-value=0.26 Score=41.94 Aligned_cols=60 Identities=20% Similarity=0.348 Sum_probs=52.7
Q ss_pred hhhhhccceeeCHHHHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 59 VRDKLNNQVLFDKASYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 59 vkdKlnn~Vl~Dk~tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
+++-++..-+-.-+..+-|..|.-.. =+++.|-||||.+|+-|+-=.|||-||+-|+|.-
T Consensus 173 V~~Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrvgITRSVIVNALRK~ESAGvIES 233 (256)
T PRK04158 173 VQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIES 233 (256)
T ss_pred HHHHHHhcCHhHHHHHHHHHHhcCCCcceEEeeecccccCCchhhhhhhhhhhhcccceee
Confidence 56666666666778889999999885 7889999999999999999999999999999965
No 99
>PRK09954 putative kinase; Provisional
Probab=90.10 E-value=0.32 Score=40.72 Aligned_cols=42 Identities=24% Similarity=0.373 Sum_probs=36.4
Q ss_pred HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
+|++.+.+...||.+.||++|+|+-+-+++.|+.|+++|+|.
T Consensus 7 ~il~~l~~~~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~ 48 (362)
T PRK09954 7 EILAILRRNPLIQQNEIADILQISRSRVAAHIMDLMRKGRIK 48 (362)
T ss_pred HHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcC
Confidence 455555555689999999999999999999999999999985
No 100
>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=89.97 E-value=1.6 Score=31.26 Aligned_cols=54 Identities=26% Similarity=0.415 Sum_probs=41.1
Q ss_pred HHhhCCCCeeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871 77 LLKEVPAYKLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT 132 (139)
Q Consensus 77 l~KEVpk~KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~ 132 (139)
++.+-+. -+|+..|-++| +|+.|-.-+.|+.|++.|+|..+...++...|-.+.
T Consensus 16 ~l~~~~~--~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~~~~~~Y~~~~ 74 (120)
T PF01475_consen 16 LLKESPE--HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFGDGESRYELST 74 (120)
T ss_dssp HHHHHSS--SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEETTSEEEEEESS
T ss_pred HHHcCCC--CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcCCCcceEeecC
Confidence 3444444 67888888887 466667799999999999999998887888887665
No 101
>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=89.92 E-value=0.64 Score=27.99 Aligned_cols=30 Identities=23% Similarity=0.400 Sum_probs=25.9
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLI 116 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlI 116 (139)
+|-..||+-++.+....-++|..|+++|+|
T Consensus 3 mtr~diA~~lG~t~ETVSR~l~~l~~~glI 32 (32)
T PF00325_consen 3 MTRQDIADYLGLTRETVSRILKKLERQGLI 32 (32)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHHHTTSE
T ss_pred cCHHHHHHHhCCcHHHHHHHHHHHHHcCCC
Confidence 577899999999999999999999999997
No 102
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=89.78 E-value=1.1 Score=30.57 Aligned_cols=41 Identities=29% Similarity=0.296 Sum_probs=29.6
Q ss_pred HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
.|++.+. ..-.+++.|+...+++.+.+.+.|++|+++|+|.
T Consensus 10 ~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~ 50 (77)
T PF14947_consen 10 DILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIK 50 (77)
T ss_dssp HHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCee
Confidence 3444433 3445689999999999999999999999999993
No 103
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=89.68 E-value=0.5 Score=34.43 Aligned_cols=38 Identities=29% Similarity=0.309 Sum_probs=33.5
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
+-.=+|-.+|-++++...-.+.+|++|++.|||..|..
T Consensus 19 ~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g 56 (92)
T PF10007_consen 19 AGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEG 56 (92)
T ss_pred HCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecC
Confidence 33346889999999999999999999999999999874
No 104
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=89.54 E-value=0.79 Score=35.06 Aligned_cols=43 Identities=19% Similarity=0.291 Sum_probs=35.5
Q ss_pred HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
+|+.....--=+|.+.||++++++-+-.++=|+.|++.|+|.-
T Consensus 18 ~IL~~Lq~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 18 NILNELQKDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred HHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 4444444444567899999999999999999999999999974
No 105
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=89.45 E-value=0.45 Score=37.85 Aligned_cols=49 Identities=18% Similarity=0.149 Sum_probs=42.8
Q ss_pred CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
+.++..+|+.-++....+|-..||+.|+|+..-.|++|..|.+.|||..
T Consensus 20 ~~~~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~ 68 (178)
T PRK06266 20 GDEEGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADY 68 (178)
T ss_pred CCccHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEE
Confidence 4566677777777777899999999999999999999999999999874
No 106
>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=89.44 E-value=0.58 Score=32.96 Aligned_cols=46 Identities=17% Similarity=0.210 Sum_probs=32.8
Q ss_pred HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871 71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLI 116 (139)
Q Consensus 71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlI 116 (139)
+..|+=|...-..-.=|....|+++|+++..=-|.+|++|.+.|.|
T Consensus 50 ~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 50 DKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp HHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred HHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 3344433331333345889999999999999999999999999986
No 107
>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=89.41 E-value=0.51 Score=36.59 Aligned_cols=53 Identities=17% Similarity=0.186 Sum_probs=39.5
Q ss_pred CHHHHHHHHhhCCCC-eeechHHHHhhhccc-hHHHHHHHHHHHHcCCeeEEeec
Q psy1871 70 DKASYDKLLKEVPAY-KLITPSVVSERLKVR-GSLARKALEELLQKGLIKQVVKH 122 (139)
Q Consensus 70 Dk~tydKl~KEVpk~-KlITPsvlseRlkI~-~SLARkaLreL~~kGlIk~Vskh 122 (139)
+.+.++-|....-.. .-.|...||+++++. -|.....|+.|+++|+|......
T Consensus 8 q~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~~ 62 (199)
T TIGR00498 8 QQEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPGK 62 (199)
T ss_pred HHHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCCC
Confidence 455666666433221 125677999999999 89999999999999999886543
No 108
>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=89.33 E-value=0.64 Score=28.39 Aligned_cols=37 Identities=22% Similarity=0.168 Sum_probs=25.6
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCe-eEEeecCceEEE
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLI-KQVVKHHAQVIY 128 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlI-k~Vskh~~q~IY 128 (139)
|...+|+.++|+.+ .||..+++||| .+.-..+....|
T Consensus 1 ti~e~A~~~gvs~~----tlR~ye~~Gll~~~~r~~~g~R~Y 38 (38)
T PF00376_consen 1 TIGEVAKLLGVSPR----TLRYYEREGLLPPPERTEGGYRRY 38 (38)
T ss_dssp EHHHHHHHHTS-HH----HHHHHHHTTSS-SSEETTTS-EEE
T ss_pred CHHHHHHHHCCCHH----HHHHHHHCCCCCCCccCCCCeecC
Confidence 56789999988754 69999999999 555444444444
No 109
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=89.07 E-value=0.43 Score=30.65 Aligned_cols=40 Identities=18% Similarity=0.119 Sum_probs=30.9
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEE-eecCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQV-VKHHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~V-skh~~q~IYtr 130 (139)
.|+..+|+.++|+-+ .||.++++|+|.+. ...++...|+.
T Consensus 1 ~s~~eva~~~gvs~~----tlr~~~~~gli~~~~~~~~g~r~y~~ 41 (70)
T smart00422 1 YTIGEVAKLAGVSVR----TLRYYERIGLLPPPIRTEGGYRLYSD 41 (70)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCEecCH
Confidence 378999999998765 47788899999986 44556677874
No 110
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=88.97 E-value=0.68 Score=39.51 Aligned_cols=49 Identities=18% Similarity=0.284 Sum_probs=39.0
Q ss_pred HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
+..++.|..+| |..++=+.-.||+.|+|+-+..++|+++|+++|+|...
T Consensus 8 ~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~ 62 (431)
T PRK15481 8 NEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQ 62 (431)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 34555555555 34566678899999999999999999999999999643
No 111
>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=88.73 E-value=0.86 Score=39.41 Aligned_cols=67 Identities=24% Similarity=0.245 Sum_probs=42.5
Q ss_pred hccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE--eecCceEEEecc
Q psy1871 63 LNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV--VKHHAQVIYTRT 131 (139)
Q Consensus 63 lnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V--skh~~q~IYtra 131 (139)
+++.---+.-.|+-|. |- .-+=|.-..|-.+.++.-+.-.++|+.|+++++|+.| .+|+...||.-.
T Consensus 79 ~~~l~~~e~lvy~~I~-~a-g~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml~ 147 (327)
T PF05158_consen 79 LKGLSDEERLVYQLIE-EA-GNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYMLY 147 (327)
T ss_dssp --SSSCCHHHHHHHHH-HH-TTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEES
T ss_pred hcCCCHHHHHHHHHHH-Hh-CCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEEc
Confidence 3333333343444443 22 2345667889999999999999999999999999999 466678899754
No 112
>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=88.26 E-value=0.51 Score=32.92 Aligned_cols=41 Identities=29% Similarity=0.246 Sum_probs=32.8
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC-ceEEEec
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH-AQVIYTR 130 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~-~q~IYtr 130 (139)
+.|+..+|+.++|+.+. ||..+++|+|.+..... +...|+.
T Consensus 1 ~~ti~evA~~~gvs~~t----LR~ye~~Gll~p~r~~~~g~R~Ys~ 42 (88)
T cd01105 1 VIGIGEVSKLTGVSPRQ----LRYWEEKGLIKSIRSDGGGQRKYSL 42 (88)
T ss_pred CcCHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCceecCH
Confidence 36899999999988765 78889999999865443 7788874
No 113
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=88.14 E-value=0.85 Score=36.53 Aligned_cols=37 Identities=16% Similarity=0.011 Sum_probs=33.3
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
..-+|++.||+.+.+..|-.-++|..|+++|+|....
T Consensus 57 ~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~~ 93 (185)
T PRK13777 57 LKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFSK 93 (185)
T ss_pred CCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEecC
Confidence 3458999999999999998999999999999999873
No 114
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=87.91 E-value=1 Score=35.16 Aligned_cols=47 Identities=19% Similarity=0.160 Sum_probs=37.7
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
.-..+|...||++++|.....+++|+.|.+.|+|.-+...+. =|.-+
T Consensus 22 ~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~G--Gy~La 68 (164)
T PRK10857 22 EAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPGG--GYLLG 68 (164)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCCC--Ceecc
Confidence 345789999999999999999999999999999986433333 35543
No 115
>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=87.90 E-value=0.81 Score=34.30 Aligned_cols=46 Identities=22% Similarity=0.228 Sum_probs=35.9
Q ss_pred echHHHHhh----hccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871 87 ITPSVVSER----LKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK 133 (139)
Q Consensus 87 ITPsvlseR----lkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k 133 (139)
+|+..|.+. +++.-+..+..|+.|+++|+|... +.++..+|++...
T Consensus 19 ~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~-k~gr~~~Y~p~vs 68 (130)
T TIGR02698 19 TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE-KEGRKFIYTALVS 68 (130)
T ss_pred CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee-cCCCcEEEEecCC
Confidence 488885555 478999999999999999999765 4456778987543
No 116
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=87.75 E-value=1.3 Score=33.49 Aligned_cols=46 Identities=15% Similarity=0.285 Sum_probs=39.0
Q ss_pred eCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 69 FDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
+|...++-|+.+ -=++.+.||++++++-+-.++=++.|++.|+|.-
T Consensus 10 ~D~~Il~~Lq~d----~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~ 55 (153)
T PRK11179 10 LDRGILEALMEN----ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITG 55 (153)
T ss_pred HHHHHHHHHHHc----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeee
Confidence 466677777777 3357799999999999999999999999999974
No 117
>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=87.71 E-value=0.62 Score=33.20 Aligned_cols=42 Identities=21% Similarity=0.221 Sum_probs=33.1
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
+.|.+.+|+.++|+.+. ||..++.|+|.+.-..++...|+..
T Consensus 1 ~~~i~eva~~~gVs~~t----LR~ye~~Gli~p~r~~~g~R~Ys~~ 42 (98)
T cd01279 1 LYPISVAAELLGIHPQT----LRVYDRLGLVSPARTNGGGRRYSNN 42 (98)
T ss_pred CcCHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCeeECHH
Confidence 35889999999988765 6788999999885445677888753
No 118
>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=87.59 E-value=0.69 Score=32.15 Aligned_cols=41 Identities=17% Similarity=0.135 Sum_probs=32.6
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+.|...+|+.++|+.+. ||..++.|+|.+.-..+....|+.
T Consensus 1 ~~~i~e~A~~~gvs~~t----Lr~ye~~Gli~p~r~~~g~R~y~~ 41 (91)
T cd04766 1 VYVISVAAELSGMHPQT----LRLYERLGLLSPSRTDGGTRRYSE 41 (91)
T ss_pred CcCHHHHHHHHCcCHHH----HHHHHHCCCcCCCcCCCCCeeECH
Confidence 35889999999998765 788899999998654456677875
No 119
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=87.28 E-value=1.4 Score=33.25 Aligned_cols=41 Identities=22% Similarity=0.341 Sum_probs=33.8
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY 128 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY 128 (139)
-+|...||+.++++-.-.-++|++|+++|+|.. .++...||
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~--~~~~i~i~ 208 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISA--HGKTIVVY 208 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEe--cCCEEEEe
Confidence 478899999999999999999999999999863 23344444
No 120
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=87.01 E-value=1.5 Score=35.39 Aligned_cols=36 Identities=19% Similarity=0.187 Sum_probs=32.7
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
-+|.+.||++++++-|-+.++|+.|++.|++.....
T Consensus 28 ~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~ 63 (257)
T PRK15090 28 EIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGE 63 (257)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 479999999999999999999999999999877543
No 121
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=86.33 E-value=1.5 Score=35.62 Aligned_cols=37 Identities=19% Similarity=0.349 Sum_probs=33.2
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
+|.+.||++++++-|-+.++|+.|++.|+|......+
T Consensus 27 ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~ 63 (263)
T PRK09834 27 ATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDD 63 (263)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCC
Confidence 7899999999999999999999999999998764333
No 122
>PF12728 HTH_17: Helix-turn-helix domain
Probab=86.24 E-value=1.2 Score=27.41 Aligned_cols=40 Identities=15% Similarity=0.128 Sum_probs=30.6
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
++|+..+|+-|+|+-+- ++.+..+|.|..+. ..+...|.+
T Consensus 1 ~lt~~e~a~~l~is~~t----v~~~~~~g~i~~~~-~g~~~~~~~ 40 (51)
T PF12728_consen 1 YLTVKEAAELLGISRST----VYRWIRQGKIPPFK-IGRKWRIPK 40 (51)
T ss_pred CCCHHHHHHHHCcCHHH----HHHHHHcCCCCeEE-eCCEEEEeH
Confidence 57999999999986555 66777899998884 556555554
No 123
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=85.86 E-value=1.5 Score=35.72 Aligned_cols=58 Identities=22% Similarity=0.377 Sum_probs=44.5
Q ss_pred HHHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 71 KASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 71 k~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
...+++|...| |.-+|=|-..|||+|+|+=+.-|-+|+.|+.+|+|.. .++-.+|++.
T Consensus 13 ~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~---r~G~Gt~V~~ 76 (241)
T COG2186 13 DEVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEI---RQGSGTFVRP 76 (241)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeee---cCCCceEecC
Confidence 44555565554 4567878899999999999999999999999999743 3445567654
No 124
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=85.51 E-value=1.6 Score=25.58 Aligned_cols=40 Identities=18% Similarity=0.203 Sum_probs=29.4
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
++|+..+|+.|+|+ +.-|+.|.+.|.|..+.. .+...|.+
T Consensus 1 ~lt~~e~a~~lgis----~~ti~~~~~~g~i~~~~~-g~~~~~~~ 40 (49)
T TIGR01764 1 YLTVEEAAEYLGVS----KDTVYRLIHEGELPAYRV-GRHYRIPR 40 (49)
T ss_pred CCCHHHHHHHHCCC----HHHHHHHHHcCCCCeEEe-CCeEEEeH
Confidence 47899999999875 456777888999887654 34555654
No 125
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=85.27 E-value=1.8 Score=36.15 Aligned_cols=40 Identities=20% Similarity=0.198 Sum_probs=33.6
Q ss_pred HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871 77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLI 116 (139)
Q Consensus 77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlI 116 (139)
|+..+..-..++...||++|+|+-+-.++.|+.|++.|+.
T Consensus 9 il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~ 48 (319)
T PRK11886 9 LLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLD 48 (319)
T ss_pred HHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCc
Confidence 3333444577889999999999999999999999999993
No 126
>PRK12423 LexA repressor; Provisional
Probab=85.19 E-value=1.4 Score=34.85 Aligned_cols=49 Identities=20% Similarity=0.252 Sum_probs=37.6
Q ss_pred HHHHHHHHhhCCCCee-echHHHHhhhcc-chHHHHHHHHHHHHcCCeeEE
Q psy1871 71 KASYDKLLKEVPAYKL-ITPSVVSERLKV-RGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 71 k~tydKl~KEVpk~Kl-ITPsvlseRlkI-~~SLARkaLreL~~kGlIk~V 119 (139)
.+.++.|...+-...+ =|...||+.|++ +-+..+..|+.|+++|+|...
T Consensus 9 ~~il~~l~~~i~~~g~~Ps~~eia~~~g~~s~~~v~~~l~~L~~~G~l~~~ 59 (202)
T PRK12423 9 AAILAFIRERIAQAGQPPSLAEIAQAFGFASRSVARKHVQALAEAGLIEVV 59 (202)
T ss_pred HHHHHHHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEec
Confidence 4566777665433333 388999999995 788889999999999999764
No 127
>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=85.06 E-value=0.86 Score=32.60 Aligned_cols=40 Identities=23% Similarity=0.205 Sum_probs=32.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+|...||++++|+.+. ||.-++.|+|.+.-......+|+.
T Consensus 2 ~~i~eva~~~gvs~~t----lR~ye~~Gll~~~r~~~g~R~Y~~ 41 (102)
T cd04789 2 YTISELAEKAGISRST----LLYYEKLGLITGTRNANGYRLYPD 41 (102)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCeeCCH
Confidence 5889999999998765 779999999998654567788874
No 128
>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=84.88 E-value=1 Score=32.20 Aligned_cols=41 Identities=22% Similarity=0.212 Sum_probs=32.0
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
.|...||++++|+.+ .||..++.|+|.+.-..++...|+..
T Consensus 2 ~~i~eva~~~gvs~~----tLR~ye~~Gll~~~r~~~g~R~Y~~~ 42 (102)
T cd04775 2 YTIGQMSRKFGVSRS----TLLYYESIGLIPSARSEANYRLYSEA 42 (102)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCCeeeCHH
Confidence 588999999998865 57999999999554444567788753
No 129
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=84.45 E-value=0.99 Score=32.11 Aligned_cols=40 Identities=23% Similarity=0.182 Sum_probs=33.3
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec-CceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH-HAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh-~~q~IYtra 131 (139)
|...||++++|+. +.||.-++.|||.+.... ++.++|+..
T Consensus 2 ~I~eva~~~gvs~----~tLRyYE~~GLl~p~~~~~~gyR~Ys~~ 42 (124)
T COG0789 2 TIGEVAKLTGVSV----RTLRFYERKGLLSPERRDEGGYRYYTPE 42 (124)
T ss_pred cHHHHHHHhCCCH----HHHHHHHHcCCCCCcccCCCCceecCHH
Confidence 6788999997765 579999999999998665 588999864
No 130
>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=84.43 E-value=4.1 Score=29.25 Aligned_cols=46 Identities=20% Similarity=0.226 Sum_probs=35.8
Q ss_pred echHHHHhhhc----cchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871 87 ITPSVVSERLK----VRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK 133 (139)
Q Consensus 87 ITPsvlseRlk----I~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k 133 (139)
+|...|.+.|. +.-|..+..|+.|++||+|..-. .++..+|.+...
T Consensus 18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~-~gr~~~Y~p~is 67 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREK-IGRAYVYSPLIS 67 (115)
T ss_dssp EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEE-ETTCEEEEESSS
T ss_pred CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEee-cCCceEEEeCCc
Confidence 67777777765 56889999999999999998864 467889987653
No 131
>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=84.27 E-value=1.2 Score=25.81 Aligned_cols=40 Identities=20% Similarity=0.285 Sum_probs=28.7
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+|...+|+.|+|+-+ -|+.+.++|.+.......+...|..
T Consensus 1 ~s~~e~a~~lgvs~~----tl~~~~~~g~~~~~~~~~~~~~~~~ 40 (49)
T cd04762 1 LTTKEAAELLGVSPS----TLRRWVKEGKLKAIRTPGGHRRFPE 40 (49)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHcCCCCceeCCCCceecCH
Confidence 367889999988654 4677788899876554456667764
No 132
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=84.08 E-value=2.2 Score=29.55 Aligned_cols=34 Identities=24% Similarity=0.205 Sum_probs=29.5
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
=+|.+.|.+.++++-|-..+-|+.|++.|+|..-
T Consensus 14 ~~~f~~L~~~l~lt~g~Ls~hL~~Le~~GyV~~~ 47 (80)
T PF13601_consen 14 EATFSELKEELGLTDGNLSKHLKKLEEAGYVEVE 47 (80)
T ss_dssp EEEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEE
Confidence 4789999999999999999999999999999864
No 133
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=83.83 E-value=3 Score=31.76 Aligned_cols=46 Identities=24% Similarity=0.352 Sum_probs=33.8
Q ss_pred HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+++|+.|.++.|+..+-|+ -++|+.|++.|+|..+.-..+...|--
T Consensus 40 eei~~~l~~~~p~islaTV--------------Yr~L~~l~e~Glv~~~~~~~~~~~y~~ 85 (145)
T COG0735 40 EELYEELREEGPGISLATV--------------YRTLKLLEEAGLVHRLEFEGGKTRYEL 85 (145)
T ss_pred HHHHHHHHHhCCCCCHhHH--------------HHHHHHHHHCCCEEEEEeCCCEEEEec
Confidence 5667777777776555444 578999999999999987666666643
No 134
>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=83.80 E-value=2.2 Score=33.53 Aligned_cols=45 Identities=22% Similarity=0.347 Sum_probs=36.8
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
+.=+.|-..||+.++++-+--.++|++|+++|+|..+ ++.+|-=+
T Consensus 72 N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~----~~G~Y~iN 116 (165)
T PF05732_consen 72 NAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKI----RNGAYMIN 116 (165)
T ss_pred CeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEc----cCCeEEEC
Confidence 3456788999999999999999999999999999876 23356544
No 135
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=83.75 E-value=1.2 Score=33.72 Aligned_cols=41 Identities=29% Similarity=0.408 Sum_probs=33.7
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
+.|...||++++|+.+ .||..+++|+|.+.. .++++.|+..
T Consensus 1 lysI~eVA~~~GVs~~----TLR~wE~~GLl~p~r-~~G~R~Ys~~ 41 (120)
T cd04767 1 LYPIGVVAELLNIHPE----TLRIWERHGLIKPAR-RNGQRLYSNN 41 (120)
T ss_pred CCCHHHHHHHHCcCHH----HHHHHHHCCCCCCcC-CCCcEEECHH
Confidence 3588999999998877 477999999999864 5788999853
No 136
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=83.42 E-value=0.89 Score=32.97 Aligned_cols=40 Identities=10% Similarity=0.167 Sum_probs=31.7
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtr 130 (139)
.|...||++++|+.+ .||.-++.|||.+..+ .++.+.|+.
T Consensus 1 ~~I~eva~~~gvs~~----tLRyYe~~GLl~p~~r~~~gyR~Y~~ 41 (123)
T cd04770 1 MKIGELAKAAGVSPD----TIRYYERIGLLPPPQRSENGYRLYGE 41 (123)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCCCccCCH
Confidence 377899999998765 6899999999997644 456678875
No 137
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=83.34 E-value=1.2 Score=31.41 Aligned_cols=41 Identities=17% Similarity=0.120 Sum_probs=33.0
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
.|.+.||+.++|+.+ .||.-++.|+|.++.. .++...|+..
T Consensus 1 ~ti~eva~~~gvs~~----tLRyye~~Gll~p~~~~~~gyR~Y~~~ 42 (96)
T cd04768 1 LTIGEFAKLAGVSIR----TLRHYDDIGLFKPAKIAENGYRYYSYA 42 (96)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCeeeCCHH
Confidence 378899999998876 5899999999999754 5567888753
No 138
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=83.30 E-value=2 Score=32.07 Aligned_cols=35 Identities=34% Similarity=0.688 Sum_probs=31.0
Q ss_pred HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
=|..|.+.+|. ||+-+|++|| ++|++.|+|....-
T Consensus 38 RF~eL~r~i~~---Is~k~Ls~~L-----------k~Le~~Glv~R~~~ 72 (120)
T COG1733 38 RFNELRRSIGG---ISPKMLSRRL-----------KELEEDGLVERVVY 72 (120)
T ss_pred cHHHHHHHccc---cCHHHHHHHH-----------HHHHHCCCEEeeec
Confidence 58889999998 9999999986 89999999988754
No 139
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=83.22 E-value=1.6 Score=28.04 Aligned_cols=39 Identities=23% Similarity=0.234 Sum_probs=31.0
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
|...||+.++|+-+ .||..+++|+|.+.-..++...|+.
T Consensus 2 ti~eva~~~gvs~~----tlr~y~~~gll~~~~~~~g~r~y~~ 40 (69)
T PF13411_consen 2 TIKEVAKLLGVSPS----TLRYYEREGLLPPPRDENGYRYYSE 40 (69)
T ss_dssp EHHHHHHHTTTTHH----HHHHHHHTTSSTTBESTTSSEEE-H
T ss_pred cHHHHHHHHCcCHH----HHHHHHHhcCcccccccCceeeccH
Confidence 77899999998655 5899999999888775666688874
No 140
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=83.12 E-value=2.5 Score=31.80 Aligned_cols=32 Identities=19% Similarity=0.250 Sum_probs=30.3
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
-+|-..||+-++++-.-.-++|++|+++|+|.
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 36999999999999999999999999999997
No 141
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=82.64 E-value=1.5 Score=34.19 Aligned_cols=42 Identities=38% Similarity=0.423 Sum_probs=35.7
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
.++|...||.+++|+.+ .||.-++.|||.++-..++...|+.
T Consensus 10 ~~~~IgevAk~~gvs~~----TlRyYE~~GLi~~~r~~~g~R~Y~~ 51 (154)
T PRK15002 10 ALLTPGEVAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKR 51 (154)
T ss_pred ccccHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEECH
Confidence 67899999999999875 5899999999999655566788875
No 142
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=82.33 E-value=1.6 Score=35.70 Aligned_cols=44 Identities=14% Similarity=0.077 Sum_probs=37.9
Q ss_pred HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcC
Q psy1871 71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKG 114 (139)
Q Consensus 71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kG 114 (139)
.+=.++|+.-+.....||...||+.|+|+....|+=|++|+..|
T Consensus 6 ~eR~~~I~~~l~~~~~v~v~eLa~~~~VS~~TIRRDL~~Le~~~ 49 (252)
T PRK10681 6 DERIGQLLQALKRSDKLHLKDAAALLGVSEMTIRRDLNAHSAPV 49 (252)
T ss_pred HHHHHHHHHHHHHcCCCcHHHHHHHhCCCHHHHHHHHHHhhcCe
Confidence 34456777788888899999999999999999999999999644
No 143
>PRK00215 LexA repressor; Validated
Probab=82.05 E-value=2.4 Score=33.03 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=33.5
Q ss_pred echHHHHhhhcc-chHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871 87 ITPSVVSERLKV-RGSLARKALEELLQKGLIKQVVKHHAQ 125 (139)
Q Consensus 87 ITPsvlseRlkI-~~SLARkaLreL~~kGlIk~Vskh~~q 125 (139)
+|...||+.+++ .-|-+-+.|+.|+++|+|.......|.
T Consensus 24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~ 63 (205)
T PRK00215 24 PSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRSRA 63 (205)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCCcce
Confidence 588899999999 889999999999999999887544443
No 144
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=81.98 E-value=1.4 Score=34.86 Aligned_cols=50 Identities=22% Similarity=0.219 Sum_probs=42.9
Q ss_pred ceeeCHHHHHHHHhhCCCCe--eechHHHHhhhccchHHHHHHHHHHHHcCC
Q psy1871 66 QVLFDKASYDKLLKEVPAYK--LITPSVVSERLKVRGSLARKALEELLQKGL 115 (139)
Q Consensus 66 ~Vl~Dk~tydKl~KEVpk~K--lITPsvlseRlkI~~SLARkaLreL~~kGl 115 (139)
.++---+.|.+|++.+.... .||...||+.++|+.+..|+=|..|+..|.
T Consensus 10 ~~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~ 61 (213)
T PRK05472 10 ATIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFGK 61 (213)
T ss_pred HHHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCC
Confidence 33334567888888888887 999999999999999999999999999985
No 145
>PRK11569 transcriptional repressor IclR; Provisional
Probab=81.87 E-value=2.5 Score=34.67 Aligned_cols=35 Identities=17% Similarity=0.325 Sum_probs=32.0
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
-+|.+.||+++++.-|-+-++|..|++.|++....
T Consensus 43 ~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~ 77 (274)
T PRK11569 43 SVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG 77 (274)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 37999999999999999999999999999997643
No 146
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=81.73 E-value=3.7 Score=31.89 Aligned_cols=42 Identities=26% Similarity=0.215 Sum_probs=36.2
Q ss_pred HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
.+..-++....+|.-.||+.|+|+..--|++|..|.+.|||.
T Consensus 18 ~Vl~aL~~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 18 LVLFSLGIKGEFTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred HHHHHHhccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 344455555679999999999999999999999999999995
No 147
>PF13814 Replic_Relax: Replication-relaxation
Probab=81.68 E-value=2.7 Score=31.76 Aligned_cols=51 Identities=20% Similarity=0.301 Sum_probs=42.6
Q ss_pred CCCeeechHHHHhhhccchH---HHHHHHHHHHHcCCeeEEee------cCceEEEeccC
Q psy1871 82 PAYKLITPSVVSERLKVRGS---LARKALEELLQKGLIKQVVK------HHAQVIYTRTT 132 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~S---LARkaLreL~~kGlIk~Vsk------h~~q~IYtra~ 132 (139)
-.++++|...|+.-+..... -+++.|+.|.+.|+|..+.. .+...||.=..
T Consensus 5 ~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~Lt~ 64 (191)
T PF13814_consen 5 ARHRFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYLTP 64 (191)
T ss_pred HHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEECH
Confidence 35789999999999999997 79999999999999998865 35677887543
No 148
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=81.28 E-value=2.2 Score=33.81 Aligned_cols=34 Identities=24% Similarity=0.364 Sum_probs=28.6
Q ss_pred echHHHHhhhcc--------------chHHHHHHHHHHHHcCCeeEEe
Q psy1871 87 ITPSVVSERLKV--------------RGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 87 ITPsvlseRlkI--------------~~SLARkaLreL~~kGlIk~Vs 120 (139)
|....|+..|+. ++|+.|.+|+.||+-|+|....
T Consensus 68 vGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 68 VGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred ccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 566777777777 5899999999999999998754
No 149
>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=80.80 E-value=1.9 Score=31.33 Aligned_cols=40 Identities=15% Similarity=0.155 Sum_probs=32.5
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
|...+|++++|+.+ .||.-++.|||.++..+....+|+..
T Consensus 2 ~ige~a~~~gvs~~----tLryYe~~GLi~p~~~~~~yR~Y~~~ 41 (116)
T cd04769 2 YIGELAQQTGVTIK----AIRLYEEKGLLPSPKRSGNYRVYDAQ 41 (116)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCceeeCHH
Confidence 66789999988765 68999999999998666677888753
No 150
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=80.27 E-value=2.6 Score=33.80 Aligned_cols=33 Identities=24% Similarity=0.294 Sum_probs=30.9
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
=+|.++||+++++.-|-+-++|..|++.|++..
T Consensus 24 ~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 24 RLTLTDVAEATGLTRAAARRFLLTLVELGYVTS 56 (248)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 368999999999999999999999999999875
No 151
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=80.23 E-value=1.6 Score=32.71 Aligned_cols=43 Identities=21% Similarity=0.273 Sum_probs=35.2
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
...|...||++++|+.+ .||.-++.|||.+..+ .++..+|+..
T Consensus 2 ~~~tI~elA~~~gvs~~----tlR~Ye~~GLL~p~~r~~~gyR~Y~~~ 45 (120)
T TIGR02054 2 NAYTISRLAEDAGVSVH----VVRDYLLRGLLHPVRRTTSGYGIFDDA 45 (120)
T ss_pred CCCcHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeeCCHH
Confidence 45788999999999875 5899999999999844 4678888753
No 152
>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=80.12 E-value=1.8 Score=31.59 Aligned_cols=40 Identities=20% Similarity=0.228 Sum_probs=33.6
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
|...||++++|+.+ .||.-++.|+|.++-.+++...|+..
T Consensus 2 ~IgevA~~~gvs~~----tlRyYe~~GLl~p~~~~~gyR~Y~~~ 41 (120)
T cd04781 2 DIAEVARQSGLPAS----TLRYYEEKGLIASIGRRGLRRQYDPQ 41 (120)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCceecCHH
Confidence 67889999998765 58999999999998666788899853
No 153
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=80.10 E-value=3.3 Score=33.95 Aligned_cols=34 Identities=21% Similarity=0.068 Sum_probs=31.6
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
-+|.+.||+++++.-|-+-++|..|++.|++..-
T Consensus 40 ~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~ 73 (271)
T PRK10163 40 SSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD 73 (271)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 4899999999999999999999999999998664
No 154
>PF02002 TFIIE_alpha: TFIIE alpha subunit; InterPro: IPR024550 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation, together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits, TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF []. This entry represents a helix-turn-helix (HTH) domain found in eukaryotic TFIIE-alpha []. It is also found in proteins from archaebacteria that are presumed to be TFIIE-alpha subunits [], the transcriptional regulator SarR, and also DNA-directed RNA polymerase III subunit Rpc3.; PDB: 1VD4_A 1Q1H_A.
Probab=80.09 E-value=1.5 Score=31.15 Aligned_cols=36 Identities=22% Similarity=0.296 Sum_probs=27.9
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
...+|-..|++.++++..-.|++|..|.+.|+|...
T Consensus 25 ~~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 25 KGELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp H--B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred cCCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 357899999999999999999999999999999665
No 155
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=80.01 E-value=3.2 Score=33.89 Aligned_cols=36 Identities=22% Similarity=0.369 Sum_probs=32.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh 122 (139)
+|.+.||+++++.-|-+.+.|..|++.|++..-..+
T Consensus 20 l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~ 55 (246)
T COG1414 20 LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPED 55 (246)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 789999999999999999999999999998775433
No 156
>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=79.96 E-value=1.6 Score=30.22 Aligned_cols=40 Identities=23% Similarity=0.218 Sum_probs=30.8
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
.|+..+|+.++|+-+. |+..++.|+|.+.....+..+|+.
T Consensus 1 ~~~~eva~~~gi~~~t----lr~~~~~Gll~~~~~~~g~r~y~~ 40 (100)
T cd00592 1 YTIGEVAKLLGVSVRT----LRYYEEKGLLPPERSENGYRLYSE 40 (100)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHCCCcCCCcCCCCCcccCH
Confidence 3788999999988654 678899999986544456778875
No 157
>PRK06474 hypothetical protein; Provisional
Probab=79.64 E-value=6.2 Score=31.03 Aligned_cols=46 Identities=17% Similarity=0.320 Sum_probs=37.4
Q ss_pred echHHHHhhh-ccchHHHHHHHHHHHHcCCeeEEeec----CceEEEeccC
Q psy1871 87 ITPSVVSERL-KVRGSLARKALEELLQKGLIKQVVKH----HAQVIYTRTT 132 (139)
Q Consensus 87 ITPsvlseRl-kI~~SLARkaLreL~~kGlIk~Vskh----~~q~IYtra~ 132 (139)
.|+..|++++ +|..+..-+-|+.|++-|+|..+... .+..+|.-+.
T Consensus 27 ~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~~~ 77 (178)
T PRK06474 27 LTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAINE 77 (178)
T ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEecc
Confidence 7999999999 78888899999999999999998642 3445665443
No 158
>PF05331 DUF742: Protein of unknown function (DUF742); InterPro: IPR007995 This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=79.19 E-value=2.3 Score=32.09 Aligned_cols=33 Identities=18% Similarity=0.352 Sum_probs=31.0
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
.++.++||.++++-.+++|..+-+|.+.|+|.-
T Consensus 55 ~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v 87 (114)
T PF05331_consen 55 PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRV 87 (114)
T ss_pred CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEE
Confidence 679999999999999999999999999999854
No 159
>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=79.08 E-value=1.8 Score=31.08 Aligned_cols=40 Identities=18% Similarity=0.106 Sum_probs=32.0
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee--cCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK--HHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk--h~~q~IYtra 131 (139)
|...||++++|+.+ .||.-+++|+|.+.-. .+....|+..
T Consensus 2 ~i~eva~~~gis~~----tlR~ye~~GLi~p~~~~~~ngyR~Y~~~ 43 (108)
T cd01107 2 TIGEFAKLSNLSIK----ALRYYDKIGLLKPAYVDPDTGYRYYSAE 43 (108)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHcCCCCCCcCCCCCCccccCHH
Confidence 67899999998876 5899999999988643 2577888753
No 160
>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=78.86 E-value=2 Score=31.09 Aligned_cols=40 Identities=15% Similarity=0.116 Sum_probs=32.6
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
|...||++++|+.+ .||.-++.|||.+.-..++...|+..
T Consensus 2 ~i~eva~~~gvs~~----tlR~Ye~~GLl~p~r~~~g~R~Y~~~ 41 (112)
T cd01282 2 RIGELAARTGVSVR----SLRYYEEQGLLVPERSANGYRDYDEA 41 (112)
T ss_pred CHHHHHHHHCCCHH----HHHHHHHCCCCCCCcCCCCCeecCHH
Confidence 67889999998765 58999999999986555677888753
No 161
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=78.66 E-value=2.5 Score=30.05 Aligned_cols=39 Identities=18% Similarity=0.236 Sum_probs=31.4
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
|+..+|++++|+.+ .||.-++.|+|.++-..++..+|+.
T Consensus 2 ~I~e~a~~~gvs~~----tLR~ye~~Gll~p~r~~~g~R~Y~~ 40 (96)
T cd04774 2 KVDEVAKRLGLTKR----TLKYYEEIGLVSPERSEGRYRLYSE 40 (96)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCEEECH
Confidence 67899999988765 4788899999997665667778874
No 162
>PRK05638 threonine synthase; Validated
Probab=78.47 E-value=4.1 Score=35.85 Aligned_cols=43 Identities=19% Similarity=0.275 Sum_probs=35.1
Q ss_pred echHHHHhhhc--cchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 87 ITPSVVSERLK--VRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 87 ITPsvlseRlk--I~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
.+.+.|+++|+ ++-+...+.|+.|++.|||....+..+...|.
T Consensus 385 ~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~ 429 (442)
T PRK05638 385 MYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYK 429 (442)
T ss_pred ccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEE
Confidence 68999999998 88889999999999999997654444544454
No 163
>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=78.31 E-value=2.5 Score=33.14 Aligned_cols=25 Identities=36% Similarity=0.547 Sum_probs=21.1
Q ss_pred cchHHHHHHHHHHHHcCCeeEEeec
Q psy1871 98 VRGSLARKALEELLQKGLIKQVVKH 122 (139)
Q Consensus 98 I~~SLARkaLreL~~kGlIk~Vskh 122 (139)
=++|+.|.+|++||+-|+|....++
T Consensus 92 asg~iiR~~LqqLE~~glv~k~~~~ 116 (139)
T PF01090_consen 92 ASGSIIRKILQQLEKAGLVEKDPKG 116 (139)
T ss_dssp CHHHHHHHHHHHHHHTTSEEEETTT
T ss_pred CCcHHHHHHHHHHHHCCCEEecCCC
Confidence 3578999999999999999887533
No 164
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=78.18 E-value=3.5 Score=31.96 Aligned_cols=32 Identities=13% Similarity=0.217 Sum_probs=29.8
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
||-..||+-++++-.-.-++|++|.++|+|..
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~ 216 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAV 216 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 68899999999999988889999999999985
No 165
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=77.77 E-value=7.6 Score=28.84 Aligned_cols=49 Identities=20% Similarity=0.223 Sum_probs=42.8
Q ss_pred HHHHHHHhhCCCCe-eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 72 ASYDKLLKEVPAYK-LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 72 ~tydKl~KEVpk~K-lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+.|.+|..-.+... -||...||+.|..+-==||.+|+.|.+.|.|.-..
T Consensus 4 ~~y~~L~~~~~~~~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~p 53 (115)
T PF12793_consen 4 EQYQRLWQHYGGQPVEVTLDELAELLFCSRRNARTLLKKMQEEGWITWQP 53 (115)
T ss_pred HHHHHHHHHcCCCCcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeeeC
Confidence 46888888887654 48999999999999999999999999999998763
No 166
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=77.62 E-value=17 Score=24.24 Aligned_cols=47 Identities=23% Similarity=0.356 Sum_probs=41.4
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
.|.-|+.+.+|+.+++...-+...|.+|-..|.|.-..-|..+.|+.
T Consensus 57 ~y~~i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~ 103 (105)
T PF01399_consen 57 PYSSISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVF 103 (105)
T ss_dssp C-SEEEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE
T ss_pred HhcccchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEe
Confidence 68999999999999999999999999999999999877666666654
No 167
>KOG2760|consensus
Probab=77.49 E-value=4.4 Score=37.03 Aligned_cols=50 Identities=22% Similarity=0.304 Sum_probs=47.1
Q ss_pred eCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 69 FDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
-|++.+-.++-+|++....|.+.+|.+++|...||+--|-..|..|+|..
T Consensus 364 ~~~e~l~~~l~~V~~~etl~a~e~A~~l~is~~lakErLl~AE~~G~lcR 413 (432)
T KOG2760|consen 364 SDEEKLVDALEDVSKSETLTASELAKKLGISLGLAKERLLNAEDEGLLCR 413 (432)
T ss_pred chHHHHHHHHHhccCcchhhHHHHHHHhCchHHHHHHHHHHHHhcCCeee
Confidence 47889999999999999999999999999999999999999999999865
No 168
>COG3177 Fic family protein [Function unknown]
Probab=77.47 E-value=3.7 Score=35.35 Aligned_cols=57 Identities=21% Similarity=0.281 Sum_probs=46.6
Q ss_pred HHHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871 72 ASYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY 128 (139)
Q Consensus 72 ~tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY 128 (139)
..++++...+-.. ..+|...++--++|+-+-|++-|.+|.+.|++..+..+.+...|
T Consensus 289 ~~~~~l~~~~~~~~~~~t~~~~~~~~~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~~~~ 346 (348)
T COG3177 289 ERIGQLNVLLFGQEGYLTAAEIEAILGVSKATATRDLKELLELGILEEVKGRGRSKLY 346 (348)
T ss_pred hhHHHHHHHHhccCCCccHHHHHHHhCccHHHHHHHHHHHHhCCCeeecCCCCCceec
Confidence 3344344555544 89999999999999999999999999999999999877776655
No 169
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=77.40 E-value=2.6 Score=32.23 Aligned_cols=45 Identities=18% Similarity=0.146 Sum_probs=35.6
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
+....|...||.+++|+.+ .||.-++.|||.+..+ .++.++|+..
T Consensus 4 ~~~~~~IgevAk~~Gvs~~----TLRyYE~~GLl~p~~r~~~gyR~Y~~~ 49 (144)
T PRK13752 4 NLENLTIGVFAKAAGVNVE----TIRFYQRKGLLPEPDKPYGSIRRYGEA 49 (144)
T ss_pred CCCcccHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeecCHH
Confidence 3445899999999998765 6999999999987543 4567899854
No 170
>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=77.39 E-value=3.8 Score=30.39 Aligned_cols=32 Identities=19% Similarity=0.271 Sum_probs=30.4
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
+|...||+-++++-...=++|++|+++|+|..
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 69999999999999999999999999999865
No 171
>PRK09462 fur ferric uptake regulator; Provisional
Probab=76.90 E-value=7 Score=29.26 Aligned_cols=44 Identities=9% Similarity=0.227 Sum_probs=30.8
Q ss_pred eechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 86 LITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 86 lITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
-+|+..|-+++ +|+.+-.-+.|+.|++.|+|..+.-......|-
T Consensus 33 h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~ 81 (148)
T PRK09462 33 HVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE 81 (148)
T ss_pred CCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEE
Confidence 35666666655 245566679999999999999986544555664
No 172
>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=76.69 E-value=2.6 Score=31.33 Aligned_cols=40 Identities=10% Similarity=0.172 Sum_probs=32.1
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec-CceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH-HAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh-~~q~IYtra 131 (139)
|...+|++++|+.+ .||.-++.|||.+.... ++.+.|+..
T Consensus 2 ~IgE~A~~~gvs~~----TLRyYE~~GLl~p~r~~~~gyR~Y~~~ 42 (133)
T cd04787 2 KVKELANAAGVTPD----TVRFYTRIGLLRPTRDPVNGYRLYSEK 42 (133)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCeeeCCHH
Confidence 67889999998865 68999999999996543 677888753
No 173
>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=76.60 E-value=3.1 Score=31.76 Aligned_cols=41 Identities=32% Similarity=0.315 Sum_probs=33.1
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
.|...||++++|+.+ .||.-++.|||.+.-..++...|+..
T Consensus 2 ~~IgevA~~~Gvs~~----tLRyYE~~GLl~~~r~~~g~R~Y~~~ 42 (142)
T TIGR01950 2 LTVGELAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKRD 42 (142)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEECHH
Confidence 477899999998865 58999999999986555667889753
No 174
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=76.54 E-value=4.2 Score=35.31 Aligned_cols=37 Identities=22% Similarity=0.398 Sum_probs=33.3
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
+|.+.||+||+|+=....+.|....++|+|+.-..++
T Consensus 27 ltQ~eIA~~LgiSR~~v~rlL~~Ar~~GiV~I~i~~~ 63 (321)
T COG2390 27 LTQSEIAERLGISRATVSRLLAKAREEGIVKISINSP 63 (321)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHCCeEEEEeCCC
Confidence 5899999999999999999999999999998755544
No 175
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=76.53 E-value=2.3 Score=27.66 Aligned_cols=39 Identities=15% Similarity=0.213 Sum_probs=28.8
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHc-CCeeEEeecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQK-GLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~k-GlIk~Vskh~~q~IYtr 130 (139)
|.+.+|++++|+-+. ||..+.+ |++.+.....+...|+.
T Consensus 2 ~i~e~A~~~gVs~~t----lr~ye~~~gl~~~~r~~~g~R~yt~ 41 (68)
T cd04763 2 TIGEVALLTGIKPHV----LRAWEREFGLLKPQRSDGGHRLFND 41 (68)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHhcCCCCCCcCCCCCcccCH
Confidence 778999999998765 5677876 98876543445567874
No 176
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=76.53 E-value=2.5 Score=30.98 Aligned_cols=39 Identities=13% Similarity=0.136 Sum_probs=30.9
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEE-eecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQV-VKHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~V-skh~~q~IYtr 130 (139)
|...+|++++|+.+ .||..++.|||.+. -..++.+.|+.
T Consensus 2 ~I~e~a~~~gvs~~----tlR~Ye~~GLl~~~~r~~~gyR~Y~~ 41 (126)
T cd04783 2 TIGELAKAAGVNVE----TIRYYQRRGLLPEPPRPEGGYRRYPE 41 (126)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCH
Confidence 67899999998876 57999999999954 33456778874
No 177
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=76.26 E-value=4.2 Score=34.10 Aligned_cols=49 Identities=29% Similarity=0.403 Sum_probs=40.4
Q ss_pred hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 80 EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 80 EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
++-+ =.+|-+.+|+++.++.--|-+.|.+|+..|+|..-...+.|.|=.
T Consensus 14 a~~~-~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~i 62 (214)
T COG1339 14 AVRG-VKVTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLITI 62 (214)
T ss_pred hhcC-ccccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEEe
Confidence 3445 457999999999999999999999999999998766556676643
No 178
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=75.72 E-value=2.4 Score=29.98 Aligned_cols=40 Identities=18% Similarity=0.153 Sum_probs=31.2
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtr 130 (139)
.|...||+.++|+.+ .||.-++.|+|.+... .+....|+.
T Consensus 1 ~~i~eva~~~gvs~~----tlR~ye~~Gll~p~~~~~~gyR~Y~~ 41 (97)
T cd04782 1 FTTGEFAKLCGISKQ----TLFHYDKIGLFKPEIVKENGYRYYTL 41 (97)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCccCCH
Confidence 367899999988765 5899999999998643 355678874
No 179
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=75.71 E-value=3.2 Score=31.39 Aligned_cols=41 Identities=34% Similarity=0.285 Sum_probs=33.5
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
+|...||++++|+.+ .||.-+++|||.+.-..++...|+..
T Consensus 2 ~~I~EvA~~~Gvs~~----tLRyYE~~GLl~p~r~~~g~R~Y~~~ 42 (139)
T cd01110 2 LSVGEVAKRSGVAVS----ALHFYEQKGLIASWRNAGNQRRYPRD 42 (139)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCeEECHH
Confidence 477899999998876 58999999999987556677889753
No 180
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=75.34 E-value=3.2 Score=29.73 Aligned_cols=40 Identities=18% Similarity=0.153 Sum_probs=31.5
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHc-CCeeEEeecCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQK-GLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~k-GlIk~Vskh~~q~IYtr 130 (139)
.|+..+|+.++|+-+. ||..+.+ |+|.+....++...|+.
T Consensus 1 yti~EvA~~~gVs~~t----LR~ye~~~gli~p~r~~~g~R~Yt~ 41 (99)
T cd04765 1 FSIGEVAEILGLPPHV----LRYWETEFPQLKPVKRAGGRRYYRP 41 (99)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHHcCCCCCcCCCCCCeeeCH
Confidence 3788999999998775 6788887 88877655667888874
No 181
>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=75.27 E-value=2.8 Score=29.81 Aligned_cols=38 Identities=8% Similarity=0.161 Sum_probs=29.9
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
|...||++++|+.+ .||.-++.|||.+.. .++...|+.
T Consensus 2 ~Ige~a~~~gvs~~----tlRyYe~~GLl~p~~-~~g~r~Y~~ 39 (107)
T cd04777 2 KIGKFAKKNNITID----TVRHYIDLGLLIPEK-KGGQYFFDE 39 (107)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCcCCcc-CCCccccCH
Confidence 67889999998765 799999999999854 345567764
No 182
>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=75.10 E-value=13 Score=32.18 Aligned_cols=63 Identities=19% Similarity=0.228 Sum_probs=46.5
Q ss_pred eCHHHHHHHHhhCCCCeeechHHHHhh-hccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871 69 FDKASYDKLLKEVPAYKLITPSVVSER-LKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK 133 (139)
Q Consensus 69 ~Dk~tydKl~KEVpk~KlITPsvlseR-lkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k 133 (139)
+.+.+|+.+..- |.-+.+|...|.+. .++....--.+|++|.++|+|+++. .....+|--.+.
T Consensus 10 ~~~~l~~~~~~~-~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~-~~~~l~~~~~~~ 73 (327)
T PF05158_consen 10 LEKKLLELCREN-PSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLK-KGGGLSYKAVSE 73 (327)
T ss_dssp HHHHHHHHHHH----SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE--SSSEEEEE--S
T ss_pred HHHHHHHHHHHh-cCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEE-cCCEEEEEEeCH
Confidence 456788888887 88999999999999 6888999999999999999999998 444467765443
No 183
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=75.09 E-value=2.8 Score=30.78 Aligned_cols=38 Identities=24% Similarity=0.338 Sum_probs=31.2
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
|...||+.++|+.+ .||.-++.|||.+. +..+..+|+.
T Consensus 2 ~Igeva~~~gvs~~----tlRyYe~~GLl~p~-r~~gyR~Y~~ 39 (118)
T cd04776 2 TISELAREFDVTPR----TLRFYEDKGLLSPE-RRGQTRVYSR 39 (118)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCc-CCCCccccCH
Confidence 67889999988765 58999999999995 4447888875
No 184
>PRK13749 transcriptional regulator MerD; Provisional
Probab=74.82 E-value=2.4 Score=31.98 Aligned_cols=43 Identities=16% Similarity=0.189 Sum_probs=34.7
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
...|...||.+.+|+.. .||.-++.|||.++.+ .++..+|+..
T Consensus 2 ~~~tIgelA~~~gvS~~----tiR~YE~~GLl~p~~r~~~gyR~Y~~~ 45 (121)
T PRK13749 2 SAYTVSRLALDAGVSVH----IVRDYLLRGLLRPVACTTGGYGLFDDA 45 (121)
T ss_pred CCCcHHHHHHHHCCCHH----HHHHHHHCCCCCCCCcCCCCCccCCHH
Confidence 34688999999998874 6899999999999844 4677888753
No 185
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=74.76 E-value=2.6 Score=25.62 Aligned_cols=29 Identities=21% Similarity=0.280 Sum_probs=18.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCC
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGL 115 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGl 115 (139)
.|...||+.|+|+-+-.++.++...+.|+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-------
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence 58899999999999999999999998885
No 186
>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=74.71 E-value=2.9 Score=30.77 Aligned_cols=40 Identities=18% Similarity=0.214 Sum_probs=31.8
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
|...||++++|+.+ .||.-++.|||.+..+ .++...|+..
T Consensus 2 ~I~e~a~~~gvs~~----tlRyYe~~GLl~p~~r~~~gyR~Y~~~ 42 (127)
T TIGR02044 2 NIGQVAKLTGLSSK----MIRYYEEKGLIPPPLRSEGGYRTYTQQ 42 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHH
Confidence 56889999888764 6899999999998643 5678888753
No 187
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=74.49 E-value=3.3 Score=29.47 Aligned_cols=39 Identities=15% Similarity=0.181 Sum_probs=31.2
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEe-ecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVV-KHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs-kh~~q~IYtr 130 (139)
|++.||+.++|+.+. ||..++.|+|.++. ..+....|+.
T Consensus 2 ~i~e~A~~~gvs~~t----lR~Ye~~Gll~~~~r~~~g~R~Y~~ 41 (99)
T cd04772 2 RTVDLARAIGLSPQT----VRNYESLGLIPPAERTANGYRIYTD 41 (99)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHcCCCCCCCcCCCCCeecCH
Confidence 788999999988764 78999999999863 3456778875
No 188
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=74.42 E-value=3.5 Score=37.79 Aligned_cols=58 Identities=21% Similarity=0.342 Sum_probs=48.8
Q ss_pred HHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871 76 KLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK 133 (139)
Q Consensus 76 Kl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k 133 (139)
++..=++.-.-+|+..|.+.|+|+-..|++.|.+|.+.|+++.+-.+.+...|++.-.
T Consensus 406 ~il~~~~en~~~T~~~L~~~l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v~~~~ 463 (467)
T COG2865 406 KILELIKENGKVTARELREILGISSETIRRRIANLVKRGLLKQLGSSGRGTWYVKGEP 463 (467)
T ss_pred HHHHHHhhccccCHHHHHHHhCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEecCCc
Confidence 4444444456899999999999999999999999999999999988888888886543
No 189
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=74.33 E-value=6.9 Score=30.83 Aligned_cols=31 Identities=23% Similarity=0.371 Sum_probs=28.8
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
+|-..||+.++++-.-.-++|++|+++|+|.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~ 210 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIG 210 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEE
Confidence 6889999999999998889999999999985
No 190
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=74.28 E-value=16 Score=26.92 Aligned_cols=61 Identities=21% Similarity=0.240 Sum_probs=39.3
Q ss_pred CHHHHHHHHhhC-----CCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 70 DKASYDKLLKEV-----PAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 70 Dk~tydKl~KEV-----pk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+.+.++....|| |+| +++|+..+.++|.-.-.-...+..-|.+.|+-.......+..|-..
T Consensus 25 n~~~L~~~l~~vsdP~s~~Ygk~Lt~~e~~~~~~p~~~~v~~V~~wL~~~G~~~~~~~~~~~~i~~~ 91 (143)
T PF09286_consen 25 NLDALEQYLAEVSDPGSPNYGKYLTPEEFAALFAPSPEDVAAVKSWLKSHGLTVVEVSANGDWITVS 91 (143)
T ss_dssp THHHHHHHHHHHHTTTSTTTT----HHHHHHHHS--HHHHHHHHHHHHHCT-EEEEEETTTTEEEEE
T ss_pred CHHHHHHHHHhCcCCCCcccccCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCceeEEeCCCCEEEEE
Confidence 456677777776 444 9999999999999999999999999999997544323344445443
No 191
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=73.97 E-value=3.7 Score=29.59 Aligned_cols=41 Identities=20% Similarity=0.238 Sum_probs=32.2
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec-CceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH-HAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh-~~q~IYtra 131 (139)
.|+..+|+.++|+.+ .||..++.|+|.++-.. ++...|+..
T Consensus 1 ~~i~eva~~~gvs~~----tlR~ye~~Gll~p~~~~~~g~R~Y~~~ 42 (108)
T cd04773 1 MTIGELAHLLGVPPS----TLRHWEKEGLLSPDREPETGYRVYDPS 42 (108)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCceeeCHH
Confidence 377899999988765 58889999999987543 567788753
No 192
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=73.91 E-value=7.1 Score=33.26 Aligned_cols=49 Identities=24% Similarity=0.194 Sum_probs=40.4
Q ss_pred hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871 80 EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT 132 (139)
Q Consensus 80 EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~ 132 (139)
+-|.+.+ +++++-+.|+-|.||=-||+|++.++|.-+.-|.+.. |.+++
T Consensus 112 ~nPG~~l---sEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g~~~-yfpa~ 160 (240)
T COG3398 112 PNPGFSL---SELRANLYINRSTLRYHLRILESNPLIEAGRVGGALR-YFPAD 160 (240)
T ss_pred cCCCccH---HHHHHhcCCChHHHHHHHHHHHhCcchhhhccCCceE-EccCC
Confidence 4566554 9999999999999999999999999999998777664 44443
No 193
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=73.90 E-value=6.7 Score=30.82 Aligned_cols=41 Identities=32% Similarity=0.458 Sum_probs=34.9
Q ss_pred CCCCeee-chHHHHhhh--ccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 81 VPAYKLI-TPSVVSERL--KVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 81 Vpk~KlI-TPsvlseRl--kI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
+|-+..- +|..||.|+ +|+..=++.+|.-|++-|+|+.-..
T Consensus 33 ~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 33 LPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred hhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence 3344444 999999999 9999999999999999999988643
No 194
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=73.70 E-value=4.5 Score=33.64 Aligned_cols=50 Identities=20% Similarity=0.325 Sum_probs=39.3
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe----ecCceEEEeccCC
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV----KHHAQVIYTRTTK 133 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs----kh~~q~IYtra~k 133 (139)
.-=+|...||++|+|+.--+|+=|..|+++|++.-.. ..|-+.+|-...+
T Consensus 23 ~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~~~~~g~GRP~~~y~Lt~~ 76 (218)
T COG2345 23 SGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVERQQGGRGRPAKLYRLTEK 76 (218)
T ss_pred cCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeeeeccCCCCCCceeeeeccc
Confidence 3446889999999999999999999999999987652 2445566665444
No 195
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=73.20 E-value=10 Score=23.73 Aligned_cols=37 Identities=41% Similarity=0.502 Sum_probs=30.8
Q ss_pred cceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchH-HHHHHHHHHHHc
Q psy1871 65 NQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGS-LARKALEELLQK 113 (139)
Q Consensus 65 n~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~S-LARkaLreL~~k 113 (139)
-.+.+|++++++|. .+|+..+|..| |-+.||++|.++
T Consensus 5 ~t~~l~~el~~~L~------------~ls~~t~i~~S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 5 FTFSLDKELYEKLK------------ELSEETGIPKSKLLREALEDYLEK 42 (44)
T ss_pred EEEecCHHHHHHHH------------HHHHHHCCCHHHHHHHHHHHHHHh
Confidence 35788999999995 79999999877 788899888764
No 196
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=72.51 E-value=3.7 Score=30.09 Aligned_cols=40 Identities=8% Similarity=0.160 Sum_probs=32.0
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
|...||.+++|+.+ .||.-++.|||.+..+ .++...|+..
T Consensus 2 ~IgevA~~~gvs~~----tLRyYe~~GLl~p~~r~~~gyR~Y~~~ 42 (127)
T cd04784 2 KIGELAKKTGCSVE----TIRYYEKEGLLPAPARSANNYRLYDEE 42 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHH
Confidence 67889999998765 6999999999987543 4677888753
No 197
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc 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-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=72.39 E-value=3.8 Score=30.53 Aligned_cols=40 Identities=20% Similarity=0.233 Sum_probs=32.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtr 130 (139)
.|...||++++|+.+ .||.-++.|+|.+..+ .++...|+.
T Consensus 2 ~~I~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~ 42 (131)
T TIGR02043 2 FQIGELAKLCGVTSD----TLRFYEKNGLIKPAGRTDSGYRLYTD 42 (131)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCH
Confidence 578999999998865 6899999999998644 456778874
No 198
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=71.92 E-value=4.6 Score=28.87 Aligned_cols=36 Identities=17% Similarity=0.271 Sum_probs=31.7
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
-.-|...+|++.++++-...|..+.+|++-|||.-+
T Consensus 21 ~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 21 GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 356788899999999999999999999999998543
No 199
>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=71.91 E-value=8 Score=30.99 Aligned_cols=34 Identities=26% Similarity=0.366 Sum_probs=30.1
Q ss_pred echHHHHhhh-ccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 87 ITPSVVSERL-KVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 87 ITPsvlseRl-kI~~SLARkaLreL~~kGlIk~Vs 120 (139)
.+-..||+++ ++..+--|+.|++|.+-|||..=.
T Consensus 71 pSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrD 105 (177)
T PF03428_consen 71 PSNAQLAERLNGMSERTLRRHLARLVEAGLIVRRD 105 (177)
T ss_pred cCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeecc
Confidence 3446899999 999999999999999999998854
No 200
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=71.81 E-value=4.4 Score=30.65 Aligned_cols=41 Identities=17% Similarity=0.223 Sum_probs=32.9
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
.|...||++++|+.+ .||.-++.|+|.+..+ .++.+.|+..
T Consensus 2 ~~I~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~~ 43 (140)
T PRK09514 2 YRIGELAKLAEVTPD----TLRFYEKQGLMDPEVRTEGGYRLYTEQ 43 (140)
T ss_pred CcHHHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCCeeeCHH
Confidence 578999999988764 6899999999998643 4567888753
No 201
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=71.76 E-value=11 Score=34.00 Aligned_cols=44 Identities=30% Similarity=0.290 Sum_probs=36.0
Q ss_pred HHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 77 LLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
+++-+....-+|+..||+++++.-+-.-+++..|+++|+|....
T Consensus 11 vL~~L~~~~~~s~~eLA~~l~l~~~tVt~~i~~Le~kGlV~~~~ 54 (489)
T PRK04172 11 VLKALKELKEATLEELAEKLGLPPEAVMRAAEWLEEKGLVKVEE 54 (489)
T ss_pred HHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHHHHHhCCCEEEEe
Confidence 33333333457999999999999999999999999999998754
No 202
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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 domain
Probab=71.03 E-value=3.2 Score=32.50 Aligned_cols=41 Identities=15% Similarity=0.217 Sum_probs=32.8
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
+|.+.||++++|+. ..||..++.|||.+..+ .+..+.|+..
T Consensus 2 ~~I~evA~~~gvs~----~tLRyYe~~GLl~p~~r~~~gyR~Y~~~ 43 (172)
T cd04790 2 LTISQLARQFGLSR----STLLYYERIGLLSPSARSESNYRLYGER 43 (172)
T ss_pred CCHHHHHHHHCcCH----HHHHHHHHCCCCCCCccCCCCCccCCHH
Confidence 68899999999875 45899999999998643 4567788753
No 203
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=70.84 E-value=5.4 Score=28.11 Aligned_cols=40 Identities=15% Similarity=0.216 Sum_probs=31.9
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEe-ecCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVV-KHHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs-kh~~q~IYtra 131 (139)
|...||++++|+.+ .||.-++.|+|.+.. ..++...|+..
T Consensus 2 ~i~eva~~~gvs~~----tlR~ye~~Gll~p~~r~~~gyR~Y~~~ 42 (96)
T cd04788 2 KIGELARRTGLSVR----TLHHYDHIGLLSPSQRTEGGHRLYDRA 42 (96)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCceeeCHH
Confidence 67889999998765 589999999999864 35677888753
No 204
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=70.77 E-value=5.2 Score=32.36 Aligned_cols=23 Identities=26% Similarity=0.344 Sum_probs=20.5
Q ss_pred cchHHHHHHHHHHHHcCCeeEEe
Q psy1871 98 VRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 98 I~~SLARkaLreL~~kGlIk~Vs 120 (139)
=++|++|.+|++||+-|+|....
T Consensus 117 aSg~iiR~~LQqLE~~glVek~~ 139 (169)
T PTZ00095 117 ASGKILRWICQQLEKLGLVEQGP 139 (169)
T ss_pred CchHHHHHHHHHHHHCCCEEecC
Confidence 57899999999999999998753
No 205
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). 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=69.98 E-value=5.4 Score=30.35 Aligned_cols=40 Identities=13% Similarity=0.112 Sum_probs=32.2
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
|++.+|+.++|+.+ .||.-++.|+|.+.-..+....|+..
T Consensus 2 ~I~e~a~~~gvs~~----TLR~Ye~~GLl~p~r~~~g~R~Y~~~ 41 (134)
T cd04779 2 RIGQLAHLAGVSKR----TIDYYTNLGLLTPERSDSNYRYYDET 41 (134)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCeeECHH
Confidence 77899999998765 68899999999976555677788753
No 206
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=69.35 E-value=5 Score=25.62 Aligned_cols=40 Identities=18% Similarity=0.178 Sum_probs=28.7
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHc-CCeeEEeecCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQK-GLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~k-GlIk~Vskh~~q~IYtra 131 (139)
|+..||++++|+-+.-|. .+++ |++.+....++...|+..
T Consensus 2 s~~eva~~~gvs~~tlr~----w~~~~g~~~~~r~~~~~r~yt~~ 42 (68)
T cd01104 2 TIGAVARLTGVSPDTLRA----WERRYGLPAPQRTDGGHRLYSEA 42 (68)
T ss_pred CHHHHHHHHCcCHHHHHH----HHHhCCCCCCCcCCCCCeecCHH
Confidence 788999999998887665 4443 887765544566788753
No 207
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=69.31 E-value=10 Score=33.18 Aligned_cols=46 Identities=15% Similarity=0.079 Sum_probs=37.0
Q ss_pred HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
++..+.+....-+-+|+..|++++++...+.+.+|.+|++-|+|..
T Consensus 297 iL~~l~~~~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~ 342 (412)
T PRK04214 297 LLGRLDQARKHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRR 342 (412)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEe
Confidence 3444543333445779999999999999999999999999999974
No 208
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=69.13 E-value=6.7 Score=28.94 Aligned_cols=47 Identities=26% Similarity=0.224 Sum_probs=32.5
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCC
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTK 133 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k 133 (139)
-+.|.-|.=.-|++..+|++.|++|+++|+|.... +++..+|.-..+
T Consensus 31 ~~~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~-~~~~~~y~lT~K 77 (95)
T COG3432 31 GIGITRIIYGANLNYKRAQKYIEMLVEKGLIIKQD-NGRRKVYELTEK 77 (95)
T ss_pred CCCceeeeeecCcCHHHHHHHHHHHHhCCCEEecc-CCccceEEEChh
Confidence 34445555566889999999999999999666554 444445554334
No 209
>PF13518 HTH_28: Helix-turn-helix domain
Probab=69.09 E-value=5.7 Score=23.92 Aligned_cols=33 Identities=6% Similarity=0.073 Sum_probs=29.0
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
|...+|.+|+|+-+..+..++...+.|+--+..
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G~~~l~~ 46 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGGIEGLKP 46 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcCHHHhcc
Confidence 889999999999999999999999999644443
No 210
>smart00088 PINT motif in proteasome subunits, Int-6, Nip-1 and TRIP-15. Also called the PCI (Proteasome, COP9, Initiation factor 3) domain. Unknown function.
Probab=68.78 E-value=23 Score=23.58 Aligned_cols=48 Identities=15% Similarity=0.192 Sum_probs=40.2
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
|+-||-..|++.+++...-+...|.++...|.|.--.-|..+.|+...
T Consensus 22 y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~ 69 (88)
T smart00088 22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE 69 (88)
T ss_pred hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECC
Confidence 788999999999999999999999999999999775555555555543
No 211
>smart00753 PAM PCI/PINT associated module.
Probab=68.78 E-value=23 Score=23.58 Aligned_cols=48 Identities=15% Similarity=0.192 Sum_probs=40.2
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
|+-||-..|++.+++...-+...|.++...|.|.--.-|..+.|+...
T Consensus 22 y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~~~ 69 (88)
T smart00753 22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEFEE 69 (88)
T ss_pred hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEECC
Confidence 788999999999999999999999999999999775555555555543
No 212
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=68.31 E-value=8.4 Score=30.10 Aligned_cols=32 Identities=22% Similarity=0.228 Sum_probs=29.5
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
.|-..||+.++++-.---++|++|+++|+|..
T Consensus 170 ~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~ 201 (226)
T PRK10402 170 EKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKK 201 (226)
T ss_pred chHHHHHHHHCCcHHHHHHHHHHHHHCCCEEe
Confidence 48899999999999888889999999999976
No 213
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=68.12 E-value=5.1 Score=31.90 Aligned_cols=23 Identities=35% Similarity=0.575 Sum_probs=20.4
Q ss_pred cchHHHHHHHHHHHHcCCeeEEe
Q psy1871 98 VRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 98 I~~SLARkaLreL~~kGlIk~Vs 120 (139)
=.+|+.|++|++||+-|+|..+-
T Consensus 93 gsgsI~RkilqqLE~~G~V~k~~ 115 (147)
T COG2238 93 GSGSIIRKVLQQLEKAGLVEKTP 115 (147)
T ss_pred CCchHHHHHHHHHHHCCceeecC
Confidence 46899999999999999987765
No 214
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=68.06 E-value=4.5 Score=29.81 Aligned_cols=40 Identities=13% Similarity=0.184 Sum_probs=31.5
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtr 130 (139)
.|...||++++|+.+ .||.-++.|+|.+..+ .++...|+.
T Consensus 1 ~~I~e~a~~~gvs~~----tlR~Ye~~Gll~~~~r~~~g~R~Y~~ 41 (126)
T cd04785 1 LSIGELARRTGVNVE----TIRYYESIGLLPEPARTAGGYRLYGA 41 (126)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCccccCH
Confidence 367899999998765 5899999999987643 456778875
No 215
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=67.99 E-value=5.6 Score=29.32 Aligned_cols=40 Identities=10% Similarity=0.129 Sum_probs=31.6
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEe-ecCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVV-KHHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs-kh~~q~IYtra 131 (139)
|...||++++|+.+ .||.-++.|||.+.. ..++.+.|+..
T Consensus 2 ~I~e~a~~~gvs~~----tlRyYe~~GLl~~~~r~~~g~R~Y~~~ 42 (127)
T cd01108 2 NIGEAAKLTGLSAK----MIRYYEEIGLIPPPSRSDNGYRVYNQR 42 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHH
Confidence 67899999988765 689999999998654 35677888753
No 216
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=67.77 E-value=6.7 Score=27.71 Aligned_cols=41 Identities=22% Similarity=0.206 Sum_probs=30.8
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
.|+..+|+.++|+-+ .||..++.|+|.+... .++...|+..
T Consensus 1 ~ti~eva~~~gvs~~----tlR~ye~~Gll~~~~~~~~g~R~y~~~ 42 (103)
T cd01106 1 YTVGEVAKLTGVSVR----TLHYYDEIGLLKPSRRTENGYRLYTEE 42 (103)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCceeeCHH
Confidence 378899999988765 5788999999987533 3456778753
No 217
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which 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 N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=67.30 E-value=5.8 Score=28.78 Aligned_cols=40 Identities=15% Similarity=0.232 Sum_probs=32.1
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
|...||+.++|+.. .||..++.|+|.++.+ .++...|+..
T Consensus 2 ~Ige~A~~~gvs~~----tlR~ye~~GLl~p~~r~~~g~R~Y~~~ 42 (107)
T cd01111 2 SISQLALDAGVSVH----IVRDYLLRGLLHPVARTEGGYGLFDDC 42 (107)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCHH
Confidence 67889999998865 5899999999998743 4577888753
No 218
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=66.88 E-value=12 Score=29.08 Aligned_cols=28 Identities=18% Similarity=0.256 Sum_probs=25.5
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCC
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGL 115 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGl 115 (139)
|...||+.++++-.-.-++|++|+++|+
T Consensus 175 t~~~iA~~lG~tretvsR~l~~L~~~gl 202 (236)
T PRK09392 175 EKRVLASYLGMTPENLSRAFAALASHGV 202 (236)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHhCCe
Confidence 3467999999999999999999999995
No 219
>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=66.74 E-value=6 Score=34.13 Aligned_cols=37 Identities=16% Similarity=0.293 Sum_probs=33.2
Q ss_pred CCeeechHHHHhh--hccchHHHHHHHHHHHHcCCeeEE
Q psy1871 83 AYKLITPSVVSER--LKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 83 k~KlITPsvlseR--lkI~~SLARkaLreL~~kGlIk~V 119 (139)
+..-|+...|+++ ++++.+.+|+-|.+|++.|+|..+
T Consensus 18 ~~~pv~s~~l~~~~~~~vS~aTiR~d~~~Le~~G~l~~~ 56 (337)
T TIGR00331 18 TGQPVGSKTLLEKYNLGLSSATIRNDMADLEDLGFIEKP 56 (337)
T ss_pred cCCCcCHHHHHhhcCCCCChHHHHHHHHHHHHCCCccCC
Confidence 4577899999999 888899999999999999999774
No 220
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=66.68 E-value=11 Score=30.39 Aligned_cols=50 Identities=18% Similarity=0.204 Sum_probs=41.1
Q ss_pred HHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE-eecC
Q psy1871 74 YDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV-VKHH 123 (139)
Q Consensus 74 ydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V-skh~ 123 (139)
.=.+.+.++.--.+|=-.||++++|....-|++|.-|-+.|+|... .++.
T Consensus 20 ~~~v~~~l~~kge~tDeela~~l~i~~~~vrriL~~L~e~~li~~~k~rd~ 70 (176)
T COG1675 20 AVLVVDALLEKGELTDEELAELLGIKKNEVRRILYALYEDGLISYRKKRDE 70 (176)
T ss_pred hhHHHHHHHhcCCcChHHHHHHhCccHHHHHHHHHHHHhCCceEEEeeccc
Confidence 4556666666448899999999999999999999999999999854 4443
No 221
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=66.47 E-value=7.2 Score=34.30 Aligned_cols=45 Identities=27% Similarity=0.417 Sum_probs=40.4
Q ss_pred HHHHHhhCCCCee--echHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 74 YDKLLKEVPAYKL--ITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 74 ydKl~KEVpk~Kl--ITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
-|||..|..+..= |..+.|.+=+++.=|.+--+|.+||++|.|+.
T Consensus 6 reklir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~R 52 (321)
T COG3888 6 REKLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKR 52 (321)
T ss_pred HHHHHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeee
Confidence 4677888877766 89999999999999999999999999999986
No 222
>PRK10263 DNA translocase FtsK; Provisional
Probab=66.39 E-value=7.5 Score=40.05 Aligned_cols=61 Identities=11% Similarity=0.195 Sum_probs=52.2
Q ss_pred CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
++++|+....=|-...-.+.|-|=.||+|...-|.+++..||++|+|-+...+..-.|+.+
T Consensus 1291 ~D~l~~~a~~~v~~~~~~S~S~lQR~~~iGynRAariid~lE~~Giv~p~~gsk~ReVl~~ 1351 (1355)
T PRK10263 1291 LDPLFDQAVQFVTEKRKASISGVQRQFRIGYNRAARIIEQMEAQGIVSEQGHNGNREVLAP 1351 (1355)
T ss_pred ccHHHHHHHHHHHhcCccCHHHHHHHhhcChHHHHHHHHHHHHCCcCCCCCCCCCCeEcCC
Confidence 4688999988888889999999999999999999999999999999988755554455554
No 223
>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=66.33 E-value=6.5 Score=27.96 Aligned_cols=39 Identities=23% Similarity=0.279 Sum_probs=29.9
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec-CceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH-HAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh-~~q~IYtr 130 (139)
|...||+.++|+.+ .||..+++|+|.+..++ .....|+.
T Consensus 2 ~I~eva~~~gvs~~----tlR~Ye~~GLl~p~~r~~~g~r~Y~~ 41 (95)
T cd04780 2 RMSELSKRSGVSVA----TIKYYLREGLLPEGRRLAPNQAEYSE 41 (95)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCCeecCH
Confidence 56789999988765 68999999999996543 33467764
No 224
>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=65.31 E-value=19 Score=24.67 Aligned_cols=39 Identities=21% Similarity=0.307 Sum_probs=29.9
Q ss_pred HHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 90 SVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 90 svlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
-.+.+.|+|+-+-+|.+|--|.++|++...-.. +...|.
T Consensus 27 i~ll~~~Gv~e~avR~alsRl~~~G~L~~~r~G-r~~~Y~ 65 (70)
T PF07848_consen 27 IRLLAAFGVSESAVRTALSRLVRRGWLESERRG-RRSYYR 65 (70)
T ss_dssp HHHHCCTT--HHHHHHHHHHHHHTTSEEEECCC-TEEEEE
T ss_pred HHHHHHcCCChHHHHHHHHHHHHcCceeeeecC-ccceEe
Confidence 456789999999999999999999999876544 455664
No 225
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=64.83 E-value=14 Score=26.52 Aligned_cols=37 Identities=14% Similarity=0.191 Sum_probs=33.7
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
..-.+...||..|+...++-+..|..|+.+|-|..|.
T Consensus 14 ~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 14 RGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred cCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 4456778999999999999999999999999999985
No 226
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=64.45 E-value=23 Score=29.58 Aligned_cols=54 Identities=24% Similarity=0.490 Sum_probs=42.8
Q ss_pred CHHHHHHHHhhCCCCeeechHHHHhhhccch-HHHHHHHHHHHHc---CCeeEEeecC
Q psy1871 70 DKASYDKLLKEVPAYKLITPSVVSERLKVRG-SLARKALEELLQK---GLIKQVVKHH 123 (139)
Q Consensus 70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~-SLARkaLreL~~k---GlIk~Vskh~ 123 (139)
|+++|++|....|+..+|.|-.++--|.-++ .=-|.-||.++.. |+|-.|..++
T Consensus 101 n~e~Y~~i~~~~~~i~fihpDl~aa~L~~~g~~P~~~dfrkfc~~~svGli~iv~~n~ 158 (218)
T PF15436_consen 101 NQETYEKIKSSYPNINFIHPDLFAAFLSENGHDPTREDFRKFCNQYSVGLIFIVLKNK 158 (218)
T ss_pred CHHHHHHHHHhCCCceEecHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCEEEEEEcCc
Confidence 9999999999999999999999999884333 3347778888874 7766665544
No 227
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=64.43 E-value=11 Score=31.27 Aligned_cols=45 Identities=22% Similarity=0.213 Sum_probs=37.5
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+.--|+..||+..+|--+=.-.+|+-|+.+|++... .++-..|..
T Consensus 28 ~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~--~g~P~~y~a 72 (247)
T COG1378 28 LGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVI--EGRPKKYRA 72 (247)
T ss_pred hCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEee--CCCCceEEe
Confidence 445699999999999999999999999999999876 445556653
No 228
>smart00351 PAX Paired Box domain.
Probab=64.20 E-value=9.3 Score=28.26 Aligned_cols=34 Identities=24% Similarity=0.318 Sum_probs=31.1
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
.|...||++|+|+-+.+.+.++...+.|.+.+..
T Consensus 34 ~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~ 67 (125)
T smart00351 34 VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGA 67 (125)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcC
Confidence 3789999999999999999999999999988853
No 229
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=63.83 E-value=22 Score=27.54 Aligned_cols=39 Identities=21% Similarity=0.359 Sum_probs=27.8
Q ss_pred eechHHHHhhhc-----cchHHHHHHHHHHHHcCCeeEEeecCc
Q psy1871 86 LITPSVVSERLK-----VRGSLARKALEELLQKGLIKQVVKHHA 124 (139)
Q Consensus 86 lITPsvlseRlk-----I~~SLARkaLreL~~kGlIk~Vskh~~ 124 (139)
-+|+..|-++|+ |+.+-.-+.|+.|++.|+|..+....+
T Consensus 41 hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~~~~ 84 (169)
T PRK11639 41 AISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNS 84 (169)
T ss_pred CCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEecCCc
Confidence 456666666553 455556689999999999999864443
No 230
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). 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=62.78 E-value=6.2 Score=32.27 Aligned_cols=41 Identities=10% Similarity=0.139 Sum_probs=33.3
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
.|...||++.+|+.+ .||.++++|||.+....++..+|+..
T Consensus 2 y~i~elA~~~Gvs~~----tIR~Ye~~GLL~p~r~~~~~r~Y~~~ 42 (219)
T cd04778 2 YRIDDLARAAGTTVR----NVRAYQDRGLLPPPRRRGRVAIYNDS 42 (219)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCcccCHH
Confidence 367889999998876 58999999999987665667788853
No 231
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=62.55 E-value=24 Score=28.80 Aligned_cols=58 Identities=21% Similarity=0.179 Sum_probs=47.7
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
++..++..+++--..+|.-.||-+|+|+=|-+-+.|=.|.+.|.+..+..+.--+-++
T Consensus 13 ~lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~~~~pp~w~~~ 70 (183)
T PHA03103 13 ELVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMSDSNPPKWFKT 70 (183)
T ss_pred HHHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecCCCCCCCcccc
Confidence 3556777777877899999999999999999999999999999998776555444443
No 232
>PHA00738 putative HTH transcription regulator
Probab=62.26 E-value=16 Score=27.58 Aligned_cols=43 Identities=19% Similarity=0.382 Sum_probs=34.4
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
-.+...|++.|.+.-+..-+=|+-|++-|||..- ...+.+|.+
T Consensus 26 ~~~V~eLae~l~lSQptVS~HLKvLreAGLV~sr--K~Gr~vyY~ 68 (108)
T PHA00738 26 ILSASLISHTLLLSYTTVLRHLKILNEQGYIELY--KEGRTLYAK 68 (108)
T ss_pred CccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEE--EECCEEEEE
Confidence 3788999999999999999999999999999653 333444443
No 233
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. 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-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=62.25 E-value=9.9 Score=27.96 Aligned_cols=39 Identities=15% Similarity=0.151 Sum_probs=30.6
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtr 130 (139)
|...+|++++|+.+ .||.-++.|+|.+..+ .++.+.|+.
T Consensus 1 ~I~e~a~~~gvs~~----tlR~Ye~~GLl~~~~r~~~g~R~Y~~ 40 (124)
T TIGR02051 1 TIGELAKAAGVNVE----TIRYYERKGLLPEPDRPEGGYRRYPE 40 (124)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCEeECH
Confidence 56789999998876 5789999999986533 467788875
No 234
>PF01638 HxlR: HxlR-like helix-turn-helix; InterPro: IPR002577 The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde []. The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH []. The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. ; PDB: 2F2E_B 3DF8_A 1Z7U_B 1YYV_A 4A5M_D 4A5N_B 2FSW_A 2HZT_D.
Probab=61.23 E-value=23 Score=24.34 Aligned_cols=32 Identities=28% Similarity=0.400 Sum_probs=20.9
Q ss_pred hHHHHhhh-ccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 89 PSVVSERL-KVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 89 PsvlseRl-kI~~SLARkaLreL~~kGlIk~Vs 120 (139)
.+.|.+++ +|+-.+--.-|++|++.|+|....
T Consensus 21 f~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 21 FSELQRRLPGISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHhcchhHHHHHHHHHHHHHHcchhhccc
Confidence 34444455 455555555579999999998864
No 235
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; 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 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=61.04 E-value=6.7 Score=28.15 Aligned_cols=40 Identities=20% Similarity=0.257 Sum_probs=30.6
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
|...+|+.++|+.+ .||..++.|+|.+..+ .++...|+..
T Consensus 2 ~i~e~a~~~gvs~~----tlr~ye~~gll~~~~r~~~gyR~Y~~~ 42 (113)
T cd01109 2 TIKEVAEKTGLSAD----TLRYYEKEGLLPPVKRDENGIRDFTEE 42 (113)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCccCCHH
Confidence 67899999988765 5899999999976533 3466788753
No 236
>PF01402 RHH_1: Ribbon-helix-helix protein, copG family; InterPro: IPR002145 CopG, also known as RepA, is responsible for the regulation of plasmid copy number. It binds to the repAB promoter and controls synthesis of the plasmid replication initiator protein RepB. Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' motif, nevertheless CopG displays a fully defined HTH-motif structure that is involved not in DNA-binding, but in the maintenance of the intrinsic dimeric functional structure and cooperativity [, ].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2BJ3_B 2BJ8_A 2BJ1_A 2BJ9_A 2BJ7_B 1EA4_L 2CPG_C 1B01_B 2BA3_A 2K9I_B ....
Probab=61.02 E-value=23 Score=20.57 Aligned_cols=35 Identities=26% Similarity=0.404 Sum_probs=26.8
Q ss_pred ceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchH-HHHHHHHHHHH
Q psy1871 66 QVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGS-LARKALEELLQ 112 (139)
Q Consensus 66 ~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~S-LARkaLreL~~ 112 (139)
.|-+|++++++|. .+|++.+++.| +-|.+|+++.+
T Consensus 3 ti~l~~~~~~~l~------------~~a~~~g~s~s~~ir~ai~~~l~ 38 (39)
T PF01402_consen 3 TIRLPDELYERLD------------ELAKELGRSRSELIREAIREYLE 38 (39)
T ss_dssp EEEEEHHHHHHHH------------HHHHHHTSSHHHHHHHHHHHHHH
T ss_pred EEEeCHHHHHHHH------------HHHHHHCcCHHHHHHHHHHHHHh
Confidence 4678999999985 57888888765 66777777654
No 237
>KOG3054|consensus
Probab=60.55 E-value=22 Score=31.06 Aligned_cols=58 Identities=17% Similarity=0.346 Sum_probs=49.8
Q ss_pred HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
++.-+..-|.+.|+|---.||.-|+++--.+=.=|++|...|+|.=|.-.+.-.||+-
T Consensus 201 ll~eFv~YIk~nKvV~ledLas~f~Lrtqd~inriq~~l~eg~ltGVmDDRGKfIYIS 258 (299)
T KOG3054|consen 201 LLSEFVEYIKKNKVVPLEDLASEFGLRTQDSINRIQELLAEGLLTGVMDDRGKFIYIS 258 (299)
T ss_pred HHHHHHHHHHhcCeeeHHHHHHHhCccHHHHHHHHHHHHHhhhheeeecCCCceEEec
Confidence 3344444456679999999999999999998889999999999999999999999984
No 238
>PF09507 CDC27: DNA polymerase subunit Cdc27; InterPro: IPR019038 This protein forms the C subunit of DNA polymerase delta. It carries the essential residues for binding to the Pol1 subunit of polymerase alpha, from residues 293-332, which are characterised by the motif D--G--VT, referred to as the DPIM motif. The first 160 residues of the protein form the minimal domain for binding to the B subunit, Cdc1, of polymerase delta, the final 10 C-terminal residues, 362-372, being the DNA sliding clamp, PCNA, binding motif. ; GO: 0006260 DNA replication, 0005634 nucleus; PDB: 1U76_B 3E0J_B.
Probab=60.23 E-value=9.2 Score=32.42 Aligned_cols=29 Identities=28% Similarity=0.326 Sum_probs=23.6
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHc
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQK 113 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~k 113 (139)
|+||=--||..|+|.+..|+++|.++.++
T Consensus 1 k~VTYk~LSr~l~ihvn~AK~~L~ef~~~ 29 (430)
T PF09507_consen 1 KVVTYKWLSRELGIHVNQAKQMLYEFHEK 29 (430)
T ss_dssp --EEHHHHHHHHT--HHHHHHHHHHHHHH
T ss_pred CeeeHHHHHHHhCCCHHHHHHHHHHHHHh
Confidence 58999999999999999999999999874
No 239
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=59.98 E-value=10 Score=24.37 Aligned_cols=41 Identities=20% Similarity=0.069 Sum_probs=28.5
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
.|+..||+.++|+-+. ||..+++|.+......++...|+..
T Consensus 1 ~~i~evA~~~gvs~~t----lR~~~~~g~l~~~~~~~g~R~y~~~ 41 (67)
T cd04764 1 YTIKEVSEIIGVKPHT----LRYYEKEFNLYIPRTENGRRYYTDE 41 (67)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHhcCCCCCCCCCCceeeCHH
Confidence 3678999999998774 6788887665433334456778753
No 240
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=59.66 E-value=19 Score=30.43 Aligned_cols=51 Identities=20% Similarity=0.334 Sum_probs=44.6
Q ss_pred eCHHHHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 69 FDKASYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 69 ~Dk~tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
+|.-|+++|...+.-. --.|.-++|+.++|+=.-||+=|.-|++.|.|..=
T Consensus 155 i~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 155 LDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAE 206 (224)
T ss_pred cCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEE
Confidence 7999999998877622 45699999999999999999999999999999763
No 241
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=59.52 E-value=17 Score=29.22 Aligned_cols=42 Identities=36% Similarity=0.458 Sum_probs=32.5
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec---CceEEEe
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH---HAQVIYT 129 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh---~~q~IYt 129 (139)
.=||-+.|++..+++. -.+|++|.++|+|..+-+. .+-.+|.
T Consensus 103 qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e~gr~~~~Grp~ly~ 147 (188)
T PRK00135 103 QPITRIEIDEIRGVNS---DGALQTLLAKGLIKEVGRKEVPGRPILYG 147 (188)
T ss_pred CCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEEcCcCCCCCCCeeee
Confidence 4578999999999995 7999999999999876322 2445664
No 242
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=59.45 E-value=13 Score=30.50 Aligned_cols=42 Identities=12% Similarity=0.024 Sum_probs=35.3
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
.++|.|.. - -.|+..||++++++-...++.||.|..-|++..
T Consensus 14 glfd~L~~-g----p~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~ 55 (306)
T TIGR02716 14 DLFSHMAE-G----PKDLATLAADTGSVPPRLEMLLETLRQMRVINL 55 (306)
T ss_pred CcHHHHhc-C----CCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEe
Confidence 34566643 2 359999999999999999999999999999975
No 243
>PF08461 HTH_12: Ribonuclease R winged-helix domain; InterPro: IPR013668 This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea.
Probab=59.17 E-value=12 Score=25.21 Aligned_cols=36 Identities=31% Similarity=0.502 Sum_probs=27.2
Q ss_pred eeechHHHHhhhccch-----HHHHHHHHHHHHcCCeeEEe
Q psy1871 85 KLITPSVVSERLKVRG-----SLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 85 KlITPsvlseRlkI~~-----SLARkaLreL~~kGlIk~Vs 120 (139)
.-++...|++.|..++ .--|+-|++|++.|+++.+.
T Consensus 12 ~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~g 52 (66)
T PF08461_consen 12 KPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKVG 52 (66)
T ss_pred CCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccccC
Confidence 3567788888886553 55689999999999877544
No 244
>cd00131 PAX Paired Box domain
Probab=59.00 E-value=12 Score=28.01 Aligned_cols=51 Identities=18% Similarity=0.260 Sum_probs=38.9
Q ss_pred eeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 68 LFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 68 l~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
-+..++-.+|..=+- .=.++..||.+|+|+-+...+.++...+.|.+.+..
T Consensus 17 ~lS~d~R~rIv~~~~--~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~ 67 (128)
T cd00131 17 PLPDSIRQRIVELAQ--SGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGA 67 (128)
T ss_pred cCCHHHHHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCC
Confidence 344455555553321 235899999999999999999999999999988753
No 245
>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=58.92 E-value=22 Score=24.05 Aligned_cols=45 Identities=31% Similarity=0.318 Sum_probs=37.3
Q ss_pred HHhhCCC--CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 77 LLKEVPA--YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 77 l~KEVpk--~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
++.+|.+ +.=||.+.|+..+++...-.-..++-|++.|||....-
T Consensus 7 ~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 7 LLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred HHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 4555554 35589999999999999999999999999999987644
No 246
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=58.91 E-value=8.6 Score=29.04 Aligned_cols=40 Identities=20% Similarity=0.249 Sum_probs=31.7
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
|...||++++|+.+ .||.-++.|||.+..+ .+...+|+..
T Consensus 2 ~Ige~a~~~gvs~~----tlRyYE~~GLl~p~~r~~~gyR~Y~~~ 42 (135)
T PRK10227 2 NISDVAKITGLTSK----AIRFYEEKGLVTPPMRSENGYRTYTQQ 42 (135)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCcccCCHH
Confidence 56789999988764 6999999999998754 4667788753
No 247
>PF09106 SelB-wing_2: Elongation factor SelB, winged helix ; InterPro: IPR015190 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 2". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2V9V_A 1LVA_A 2PLY_A 2UWM_A.
Probab=58.63 E-value=29 Score=22.32 Aligned_cols=47 Identities=21% Similarity=0.268 Sum_probs=37.5
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhh---ccchHHHHHHHHHHHHcCCeeE
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERL---KVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRl---kI~~SLARkaLreL~~kGlIk~ 118 (139)
+.++...++-|--.=+....|-.|+ ++..-+...+|+.|+++|.|+.
T Consensus 3 ~~L~~yH~~~Plr~G~~keeLrsrl~~~~l~~k~~~~ll~~l~~~g~l~~ 52 (59)
T PF09106_consen 3 EILAEYHRENPLRPGMPKEELRSRLFKPRLPPKLFNALLEALVAEGRLKV 52 (59)
T ss_dssp HHHHHHHHH-TTSS-EEHHHHHHHCST-TS-HCCHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHHCcCccCcCHHHHHHHHhhccCCHHHHHHHHHHHHHCCCeee
Confidence 3566677777877778889999999 8899999999999999999865
No 248
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=58.51 E-value=10 Score=32.75 Aligned_cols=39 Identities=21% Similarity=0.365 Sum_probs=33.4
Q ss_pred CCCCeeechHHHHhh--hccchHHHHHHHHHHHHcCCeeEE
Q psy1871 81 VPAYKLITPSVVSER--LKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 81 Vpk~KlITPsvlseR--lkI~~SLARkaLreL~~kGlIk~V 119 (139)
+-...-|+-..|+++ |+++-+..|+-|.+|++.|+|...
T Consensus 20 i~~~~pv~s~~l~~~~~l~~S~aTIR~dm~~Le~~G~l~~~ 60 (339)
T PRK00082 20 IATGEPVGSKTLSKRYGLGVSSATIRNDMADLEELGLLEKP 60 (339)
T ss_pred HhcCCCcCHHHHHHHhCCCCChHHHHHHHHHHHhCCCcCCC
Confidence 335577889999977 999999999999999999998753
No 249
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=58.37 E-value=21 Score=30.28 Aligned_cols=66 Identities=17% Similarity=0.262 Sum_probs=51.8
Q ss_pred hccceeeCHHHHHHHHhhCCCC----eeechHHHHhhhccchHHHH-HHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 63 LNNQVLFDKASYDKLLKEVPAY----KLITPSVVSERLKVRGSLAR-KALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 63 lnn~Vl~Dk~tydKl~KEVpk~----KlITPsvlseRlkI~~SLAR-kaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
+.+--+++..-+|.|..|+-.. -.||.+.+|.+|++.+.+.. .++.. .--++|.-+.... .|||.+
T Consensus 103 l~~gelit~~Yld~l~~Eine~Lqe~G~vsi~eLa~~~~Lp~efl~~~li~~-~lg~~I~g~~d~~--~lyT~a 173 (272)
T PF09743_consen 103 LVQGELITDSYLDSLAEEINEKLQESGQVSISELAKQYDLPSEFLKEELISK-RLGKIIKGRLDGD--VLYTEA 173 (272)
T ss_pred EECCEEccHHHHHHHHHHHHHHHHHcCeEeHHHHHHhcCCcHHHHHHHHhhh-hcCcceeEEEeCC--EEecHH
Confidence 5566799999999999998874 89999999999999999988 44443 4455666655444 899864
No 250
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal 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-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=58.09 E-value=8.3 Score=28.55 Aligned_cols=39 Identities=13% Similarity=0.182 Sum_probs=30.7
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEe-ecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVV-KHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs-kh~~q~IYtr 130 (139)
|...||++++|+.+ .||.-++.|||.+.. ..++..+|+.
T Consensus 2 ~I~e~a~~~gvs~~----tlR~Ye~~GLl~~~~r~~~gyR~Y~~ 41 (127)
T TIGR02047 2 KIGELAQKTGVSVE----TIRFYEKQGLLPPPARTDNNYRVYTV 41 (127)
T ss_pred cHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCCcCCH
Confidence 67889999988765 699999999998653 3456778874
No 251
>TIGR01529 argR_whole arginine repressor. This model includes most members of the arginine-responsive transcriptional regulator family ArgR. This hexameric protein binds DNA at its amino end to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbor-joining tree, some of these paralogous sequences show long branches and differ significantly in an otherwise well-conserved C-terminal region motif GT[VIL][AC]GDDT. These paralogs are excluded from the seed and score in the gray zone of this model, between trusted and noise cutoffs.
Probab=57.41 E-value=32 Score=26.36 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=16.2
Q ss_pred HHHHHcCCeeEEeecCceEEEe
Q psy1871 108 EELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 108 reL~~kGlIk~Vskh~~q~IYt 129 (139)
|+|.+-|+++... .+.+..|.
T Consensus 40 RdL~elglvk~~~-~~g~~~Y~ 60 (146)
T TIGR01529 40 RDLRELGAVKVRD-EDGSYVYS 60 (146)
T ss_pred HHHHHcCCEEEEC-CCCcEEEe
Confidence 4889999998666 56667785
No 252
>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=57.27 E-value=25 Score=25.67 Aligned_cols=34 Identities=29% Similarity=0.426 Sum_probs=32.1
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLI 116 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlI 116 (139)
++-.||-+.+++.-++.-+-..++|.+|.+.|+|
T Consensus 51 k~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI 84 (100)
T PF04492_consen 51 KMDRISNSQIAEMTGLSRDHVSKALNELIRRGVI 84 (100)
T ss_pred ccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCE
Confidence 4578999999999999999999999999999999
No 253
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=56.85 E-value=20 Score=28.95 Aligned_cols=43 Identities=30% Similarity=0.402 Sum_probs=31.4
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee---cCceEEEecc
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK---HHAQVIYTRT 131 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk---h~~q~IYtra 131 (139)
=||-+.|.+-.+++.+ ++|+.|.++|+|+.+-+ -.|-.+|.-.
T Consensus 106 PiTR~eI~~iRGv~~~---~~i~~L~e~glI~~~g~~~~~Grp~ly~tT 151 (184)
T COG1386 106 PVTRSEIEEIRGVAVS---QVISTLLERGLIREVGRRDTPGRPYLYGTT 151 (184)
T ss_pred CccHHHHHHHhCccHH---HHHHHHHHCCCeEecCCCCCCCCceeeecc
Confidence 3788888877666665 49999999999999863 3345566543
No 254
>PRK15043 transcriptional regulator MirA; Provisional
Probab=56.77 E-value=12 Score=31.62 Aligned_cols=43 Identities=16% Similarity=0.181 Sum_probs=35.1
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHH-cCCeeEEeecCceEEEecc
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQ-KGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~-kGlIk~Vskh~~q~IYtra 131 (139)
.+.|...||++++|+.. .||.-++ .|+|.+.-..++.+.|+..
T Consensus 2 ~~ytIgeVA~~~GVs~~----TLR~wErr~GLL~P~Rt~~G~R~Ys~~ 45 (243)
T PRK15043 2 ALYTIGEVALLCDINPV----TLRAWQRRYGLLKPQRTDGGHRLFNDA 45 (243)
T ss_pred CCCCHHHHHHHHCcCHH----HHHHHHHhcCCCCCccCCCCCEEECHH
Confidence 46789999999999876 5888986 6999997656778899854
No 255
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=56.46 E-value=11 Score=28.64 Aligned_cols=34 Identities=29% Similarity=0.286 Sum_probs=30.7
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
..+|--.||+.++|+..--|++|..|.+.+++..
T Consensus 14 ~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~ 47 (147)
T smart00531 14 GCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKI 47 (147)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchh
Confidence 4689999999999999999999999999887643
No 256
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=56.17 E-value=26 Score=24.72 Aligned_cols=44 Identities=16% Similarity=0.158 Sum_probs=37.1
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEE---eecCceEEEe
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQV---VKHHAQVIYT 129 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~V---skh~~q~IYt 129 (139)
.+|--.|.++.+|+=+..-..|..|.++|+|..= .......+|-
T Consensus 18 c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~~~gkk~R~Yc 64 (72)
T PF05584_consen 18 CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRKFGGKKYREYC 64 (72)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEEecCeEEEEEE
Confidence 7899999999999999999999999999999763 3344556664
No 257
>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=56.14 E-value=33 Score=22.62 Aligned_cols=35 Identities=23% Similarity=0.276 Sum_probs=26.8
Q ss_pred hccchHHHHHHHHHHHHcCCeeEEeec----CceEEEec
Q psy1871 96 LKVRGSLARKALEELLQKGLIKQVVKH----HAQVIYTR 130 (139)
Q Consensus 96 lkI~~SLARkaLreL~~kGlIk~Vskh----~~q~IYtr 130 (139)
+.|+-+---.+|+.|+++|+|...... +...+|.=
T Consensus 27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~i 65 (75)
T PF03551_consen 27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYRI 65 (75)
T ss_dssp EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEEE
T ss_pred cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEEE
Confidence 456677788999999999999987543 45566763
No 258
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=55.32 E-value=11 Score=32.48 Aligned_cols=41 Identities=27% Similarity=0.375 Sum_probs=37.5
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
..++||.-.++|-+.+.-+..|.++-.|+++|.|..|-++.
T Consensus 27 ~hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeRi~rG~ 67 (269)
T COG5340 27 GHKIITIRDVAETLEVAPNTLRELASRLEKKGWLERILRGR 67 (269)
T ss_pred hCceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhhhcCcc
Confidence 35999999999999999999999999999999999987654
No 259
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=55.13 E-value=18 Score=30.65 Aligned_cols=53 Identities=15% Similarity=0.288 Sum_probs=40.1
Q ss_pred eeCHHHHH--------HHHhhCCCCeee-chHHHHhhhc--cchHHHHHHHHHHHHcCCeeEEe
Q psy1871 68 LFDKASYD--------KLLKEVPAYKLI-TPSVVSERLK--VRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 68 l~Dk~tyd--------Kl~KEVpk~KlI-TPsvlseRlk--I~~SLARkaLreL~~kGlIk~Vs 120 (139)
.+|.+.|+ -|+.=+|-+..= +|..||++++ |+..=++.+|+-|++-|+|+...
T Consensus 110 ~L~~~~~~y~~~W~~~virel~~~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~ 173 (271)
T TIGR02147 110 VLAADQFEYYRHWYNSVIRELLGVMPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNE 173 (271)
T ss_pred eccHHHHHHHHHHHHHHHHHHhhcCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECC
Confidence 46777776 222333444455 7899999999 88888899999999999998753
No 260
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=55.13 E-value=23 Score=30.19 Aligned_cols=38 Identities=26% Similarity=0.316 Sum_probs=34.2
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
=.|.+.||++|+|+=+..-++|.+-.+.|+++.-.+|.
T Consensus 29 g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~ 66 (318)
T PRK15418 29 GLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSR 66 (318)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCC
Confidence 35999999999999999999999999999998876654
No 261
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=54.86 E-value=24 Score=27.46 Aligned_cols=54 Identities=15% Similarity=0.211 Sum_probs=42.4
Q ss_pred HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
+..+|..=|-..-=+|...++..++++-..+++.|++|++.|.|-. |.+-.||.
T Consensus 13 Lk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~G~l~~---~G~~GvF~ 66 (127)
T PF06163_consen 13 LKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVARGDLYR---HGRSGVFP 66 (127)
T ss_pred HHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCCeEe---CCCccccc
Confidence 4445555555567789999999999999999999999999999744 45445665
No 262
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=53.34 E-value=50 Score=24.68 Aligned_cols=44 Identities=16% Similarity=0.141 Sum_probs=36.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
.|+..|++.+++.-|..-+=|+.|.+-|||...-.+ +...|.-+
T Consensus 31 ~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~G-r~~~Y~l~ 74 (117)
T PRK10141 31 LCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQG-KWVHYRLS 74 (117)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEc-CEEEEEEC
Confidence 788999999999999999999999999999876544 44556543
No 263
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.07 E-value=10 Score=25.75 Aligned_cols=33 Identities=15% Similarity=0.175 Sum_probs=29.9
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
|+..+|+.++|+-+...+.++...+.|+-.++.
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~ 46 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLP 46 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHh
Confidence 899999999999999999999999999655555
No 264
>PF01316 Arg_repressor: Arginine repressor, DNA binding domain; InterPro: IPR020900 The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes, an example of the latter being Giardia lamblia (Giardia intestinalis) []. The three-enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 10% of total cell protein []. Most prokaryotic arginine deiminase pathways are under the control of a repressor gene, termed ArgR []. This is a negative regulator, and will only release the arginine deiminase operon for expression in the presence of arginine []. The crystal structure of apo-ArgR from Bacillus stearothermophilus has been determined to 2.5A by means of X-ray crystallography []. The protein exists as a hexamer of identical subunits, and is shown to have six DNA-binding domains, clustered around a central oligomeric core when bound to arginine. It predominantly interacts with A.T residues in ARG boxes. This hexameric protein binds DNA at its N terminus to repress arginine biosyntheis or activate arginine catabolism. Some species have several ArgR paralogs. In a neighbour-joining tree, some of these paralogous sequences show long branches and differ significantly from the well-conserved C-terminal region. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0006525 arginine metabolic process; PDB: 1AOY_A 3V4G_A 3LAJ_D 3FHZ_A 3LAP_B 3ERE_D 2P5L_C 1F9N_D 2P5K_A 1B4A_A ....
Probab=52.89 E-value=37 Score=23.43 Aligned_cols=33 Identities=18% Similarity=0.308 Sum_probs=20.5
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
++. ||.++|| |+|.+=|+++. .......+|.-.
T Consensus 33 Gi~-vTQaTiS--------------RDLkeL~~vKv-~~~~g~~~Y~l~ 65 (70)
T PF01316_consen 33 GIE-VTQATIS--------------RDLKELGAVKV-PDGNGKYRYVLP 65 (70)
T ss_dssp T-T---HHHHH--------------HHHHHHT-EEE-ECTTSSEEEE-T
T ss_pred CCC-cchhHHH--------------HHHHHcCcEEe-eCCCCCEEEEec
Confidence 555 6666666 88899999984 456677889843
No 265
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=52.81 E-value=22 Score=25.62 Aligned_cols=41 Identities=15% Similarity=0.161 Sum_probs=32.9
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
-+|-..+++..+|.-++ |.+|.+-|+|.+...+..++.|..
T Consensus 7 ~lt~~Elc~~~gi~~~~----l~eLve~GlIep~~~~~~~~~F~~ 47 (101)
T PRK10265 7 TFTITEFCLHTGVSEEE----LNEIVGLGVIEPREIQETTWVFDD 47 (101)
T ss_pred EeeHHHHHHHHCcCHHH----HHHHHHCCCeecCCCCcccceECH
Confidence 37888999999777654 899999999999776667777764
No 266
>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=52.77 E-value=29 Score=27.19 Aligned_cols=41 Identities=27% Similarity=0.433 Sum_probs=26.9
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee---cCceEEEec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK---HHAQVIYTR 130 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk---h~~q~IYtr 130 (139)
||-+.|-+--++ =+..+|+.|.++|+|+.+-+ ..|-.+|.-
T Consensus 97 iTr~eIe~IRGv---~s~~~i~~L~e~glI~~~gr~~~~Grp~ly~t 140 (159)
T PF04079_consen 97 ITRAEIEEIRGV---NSDSVIKTLLERGLIEEVGRKDTPGRPILYGT 140 (159)
T ss_dssp EEHHHHHHHHTS-----HCHHHHHHHTTSEEEEEE-TTTT--EEEEE
T ss_pred cCHHHHHHHcCC---ChHHHHHHHHHCCCEEecCcCCCCCCCeEeeh
Confidence 555666554444 48899999999999999864 345666754
No 267
>PF09202 Rio2_N: Rio2, N-terminal; InterPro: IPR015285 This N-terminal domain is found in RIO2 kinases, and is structurally homologous to the winged helix (wHTH) domain. It adopts a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1TQP_A 1ZAR_A 1TQI_A 1ZAO_A 1TQM_A.
Probab=52.38 E-value=48 Score=23.36 Aligned_cols=46 Identities=9% Similarity=0.124 Sum_probs=38.5
Q ss_pred HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
++.-|...-.++.+|-...|...-+++.+-+...|..|...|+|..
T Consensus 11 vL~aiE~gmk~hE~VP~~~I~~~s~l~~~~~~~~L~~L~~~kLv~~ 56 (82)
T PF09202_consen 11 VLRAIEMGMKNHEWVPLELIEKISGLSEGEVEKRLKRLVKLKLVSR 56 (82)
T ss_dssp HHHHHHTTTTT-SSEEHHHHHHHHT--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHcccCCccCCHHHHHHHhCcCHHHHHHHHHHHHhcCCccc
Confidence 4556777788999999999999999999999999999999999876
No 268
>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=52.05 E-value=28 Score=22.80 Aligned_cols=42 Identities=26% Similarity=0.305 Sum_probs=33.5
Q ss_pred ceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 66 QVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 66 ~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
.++.-.+..+=|....+. ...+-|..+.++|.+.|+|..|..
T Consensus 27 ~~F~G~e~v~WL~~~~~~--------------~~r~ea~~~~~~ll~~g~i~~v~~ 68 (81)
T cd04371 27 NCFTGSELVDWLLDNLEA--------------ITREEAVELGQALLKHGLIHHVSD 68 (81)
T ss_pred ceeEcHHHHHHHHHhCCC--------------CCHHHHHHHHHHHHHCCCEEEeCC
Confidence 455577777777765543 778899999999999999999986
No 269
>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=51.87 E-value=23 Score=22.54 Aligned_cols=42 Identities=14% Similarity=0.130 Sum_probs=32.7
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
+.+..|+.++|+-|-..+.|++||+.==+.++.++++...-|
T Consensus 15 s~~~AA~~l~is~~~vs~~i~~LE~~lg~~Lf~r~~~~~~lT 56 (60)
T PF00126_consen 15 SISAAAEELGISQSAVSRQIKQLEEELGVPLFERSGRGLRLT 56 (60)
T ss_dssp SHHHHHHHCTSSHHHHHHHHHHHHHHHTS-SEEECSSSEEE-
T ss_pred CHHHHHHHhhccchHHHHHHHHHHHHhCCeEEEECCCCeeEC
Confidence 457789999999999999999999976666777766665555
No 270
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=51.29 E-value=23 Score=21.84 Aligned_cols=39 Identities=18% Similarity=0.235 Sum_probs=28.1
Q ss_pred eCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHH
Q psy1871 69 FDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELL 111 (139)
Q Consensus 69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~ 111 (139)
+|...++-|..+ ++ .+...||++++++.+-..+=++.|+
T Consensus 4 ~D~~Il~~Lq~d-~r---~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 4 LDRKILRLLQED-GR---RSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHHHH--TT---S-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHc-CC---ccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 466677777777 32 4779999999999999888888775
No 271
>PF06969 HemN_C: HemN C-terminal domain; InterPro: IPR010723 Proteins containing this domain are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX [], one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain suggest it may be a substrate binding domain.; GO: 0004109 coproporphyrinogen oxidase activity, 0006779 porphyrin-containing compound biosynthetic process, 0055114 oxidation-reduction process, 0005737 cytoplasm; PDB: 1OLT_A.
Probab=51.28 E-value=33 Score=21.88 Aligned_cols=32 Identities=31% Similarity=0.404 Sum_probs=24.6
Q ss_pred echHHHHhhhccchHHH-HHHHHHHHHcCCeeE
Q psy1871 87 ITPSVVSERLKVRGSLA-RKALEELLQKGLIKQ 118 (139)
Q Consensus 87 ITPsvlseRlkI~~SLA-RkaLreL~~kGlIk~ 118 (139)
|....+.++++....-. ...|+.|.+.|+|..
T Consensus 21 i~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~ 53 (66)
T PF06969_consen 21 IDLSEFEQRFGIDFAEEFQKELEELQEDGLLEI 53 (66)
T ss_dssp EEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEE
Confidence 56788999999885444 888999999999865
No 272
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=51.20 E-value=58 Score=20.42 Aligned_cols=35 Identities=23% Similarity=0.239 Sum_probs=31.3
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
-.++..+++.++++.+....-|..|.+.|+|....
T Consensus 39 ~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~~ 73 (110)
T COG0640 39 ELTVGELAEALGLSQSTVSHHLKVLREAGLVELRR 73 (110)
T ss_pred CccHHHHHHHHCCChhHHHHHHHHHHHCCCeEEEe
Confidence 45689999999999999999999999999999843
No 273
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=50.98 E-value=55 Score=25.01 Aligned_cols=47 Identities=26% Similarity=0.316 Sum_probs=36.7
Q ss_pred echHHHHhhh--ccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccCCC
Q psy1871 87 ITPSVVSERL--KVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTTKG 134 (139)
Q Consensus 87 ITPsvlseRl--kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~k~ 134 (139)
.+...|++=| +|.=+.+-++|..|.++|.|..=. -+.|.||..+...
T Consensus 17 ys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~-~GKqkiY~~~Q~~ 65 (169)
T PF07106_consen 17 YSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKE-YGKQKIYFANQDE 65 (169)
T ss_pred CcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeee-ecceEEEeeCccc
Confidence 3556677777 577799999999999999996533 4678999987653
No 274
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=50.34 E-value=28 Score=28.06 Aligned_cols=42 Identities=26% Similarity=0.451 Sum_probs=28.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEee---cCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK---HHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk---h~~q~IYtra 131 (139)
||-+.|.+--+++ +..+|+.|.++|+|+.+-+ ..|-.+|.-.
T Consensus 102 ITr~eIe~IRGv~---s~~~l~~L~ergLI~~~Gr~~~~Grp~ly~TT 146 (186)
T TIGR00281 102 ITRARINEIRGVK---SYQIVDDLVEKGLVVELGRKDTPGRSFIYETT 146 (186)
T ss_pred cCHHHHHHHcCCC---HHHHHHHHHHCCCeEecCcCCCCCCCeeehhh
Confidence 4555555544444 6899999999999998832 3456677643
No 275
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=49.57 E-value=25 Score=28.48 Aligned_cols=40 Identities=18% Similarity=0.243 Sum_probs=33.5
Q ss_pred HHhhCCCCeeechHHHHhhhccchHHHHHHHH-HHHHcCCee
Q psy1871 77 LLKEVPAYKLITPSVVSERLKVRGSLARKALE-ELLQKGLIK 117 (139)
Q Consensus 77 l~KEVpk~KlITPsvlseRlkI~~SLARkaLr-eL~~kGlIk 117 (139)
+.+.+..- -++...+|++|++..+-++.+++ .|.++|+|.
T Consensus 247 l~~~~~~~-~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~ 287 (305)
T TIGR00635 247 LIEQFQGG-PVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQ 287 (305)
T ss_pred HHHHhCCC-cccHHHHHHHhCCCcchHHHhhhHHHHHcCCcc
Confidence 54555444 36889999999999999999999 699999995
No 276
>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=48.99 E-value=34 Score=24.08 Aligned_cols=36 Identities=25% Similarity=0.290 Sum_probs=26.5
Q ss_pred hccchHHHHHHHHHHHHcCCeeEE---e-ecCceEEEecc
Q psy1871 96 LKVRGSLARKALEELLQKGLIKQV---V-KHHAQVIYTRT 131 (139)
Q Consensus 96 lkI~~SLARkaLreL~~kGlIk~V---s-kh~~q~IYtra 131 (139)
+.|+-+---.+|+.|+++|+|... + .+++..+|.=.
T Consensus 35 ~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~iT 74 (100)
T TIGR03433 35 LQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYRLT 74 (100)
T ss_pred cccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEEEC
Confidence 467778888999999999999984 2 23445666543
No 277
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=48.57 E-value=17 Score=27.23 Aligned_cols=39 Identities=15% Similarity=0.177 Sum_probs=30.4
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtr 130 (139)
+...||++++|+.+ .||.-++.|||.+..+ .++...|+.
T Consensus 2 ~Ige~a~~~gvs~~----tLRyYE~~GLl~p~~r~~~gyR~Y~~ 41 (131)
T cd04786 2 KIGELAKRSGMAAS----RIRFYEAEGLLSSVERSANGYRDYPP 41 (131)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCH
Confidence 56789999988875 5999999999988533 456678874
No 278
>KOG3341|consensus
Probab=48.30 E-value=22 Score=30.46 Aligned_cols=34 Identities=32% Similarity=0.321 Sum_probs=30.9
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
-++|.|.+-+.|+..-+-|+.+|.+|.++||.=.
T Consensus 189 gyvt~s~l~~~l~We~~Ra~qaLe~lv~egL~Wi 222 (249)
T KOG3341|consen 189 GYVTISLLKANLGWERSRAIQALEHLVKEGLAWI 222 (249)
T ss_pred CceeHHHHHHhccchHHHHHHHHHHHHhccceee
Confidence 3599999999999999999999999999999643
No 279
>PF04433 SWIRM: SWIRM domain; InterPro: IPR007526 The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; GO: 0005515 protein binding; PDB: 2Z3Y_A 2UXN_A 2Y48_A 2HKO_A 2XAF_A 2X0L_A 2XAJ_A 2UXX_A 2V1D_A 2L3D_A ....
Probab=48.26 E-value=27 Score=23.87 Aligned_cols=34 Identities=24% Similarity=0.271 Sum_probs=28.1
Q ss_pred CeeechHHHHhhhc-cchHHHHHHHHHHHHcCCee
Q psy1871 84 YKLITPSVVSERLK-VRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 84 ~KlITPsvlseRlk-I~~SLARkaLreL~~kGlIk 117 (139)
...+|....-+-++ +..+++.++..-|+..|+|.
T Consensus 51 ~~~lt~~~~~~~i~~~d~~~~~ri~~FL~~~G~IN 85 (86)
T PF04433_consen 51 NKYLTKTDARKLIKGIDVNKIRRIYDFLERWGLIN 85 (86)
T ss_dssp TS---HHHHHHHTTSSSHHHHHHHHHHHHHTTSSS
T ss_pred CCcccHHHHHHHccccCHHHHHHHHHHHHHcCccC
Confidence 46689999988888 99999999999999999984
No 280
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=48.17 E-value=10 Score=26.69 Aligned_cols=31 Identities=23% Similarity=0.190 Sum_probs=28.1
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
.|...||++++|+-+-.+..+..+.+.|.+.
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~ 63 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKGETKAGGLV 63 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhcCcccchHH
Confidence 4779999999999999999999999988764
No 281
>PF14579 HHH_6: Helix-hairpin-helix motif; PDB: 2HPM_A 2HPI_A 3E0D_A 3F2C_A 3F2B_A 3F2D_A 2HQA_A 2HNH_A.
Probab=46.13 E-value=9.2 Score=26.59 Aligned_cols=54 Identities=19% Similarity=0.282 Sum_probs=42.3
Q ss_pred eCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871 69 FDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQ 125 (139)
Q Consensus 69 ~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q 125 (139)
+..++.++|..|-.+-.+-+...+.+|+. .+-+..|+.|..-|.......|+|+
T Consensus 35 lg~~~a~~I~~~R~~g~f~s~~df~~R~~---~i~~~~le~Li~aGafd~~~~~~R~ 88 (90)
T PF14579_consen 35 LGEEVAEKIVEERENGPFKSLEDFIQRLP---KINKRQLEALIKAGAFDSFGKSRRQ 88 (90)
T ss_dssp S-HHHHHHHHHHHHCSS-SSHHHHHHHS----TS-HHHHHHHHHTTTTTTCSSCHHH
T ss_pred CCHHHHHHHHHhHhcCCCCCHHHHHHHHh---cCCHHHHHHHHHCCCccccChhhhh
Confidence 46889999999998888999999999995 5557889999999988777665553
No 282
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=45.43 E-value=42 Score=27.62 Aligned_cols=61 Identities=20% Similarity=0.255 Sum_probs=46.1
Q ss_pred CHHHHHHHH-hhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCce-EEEec
Q psy1871 70 DKASYDKLL-KEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQ-VIYTR 130 (139)
Q Consensus 70 Dk~tydKl~-KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q-~IYtr 130 (139)
+.+.+..|. .=+-.+=..|+..++.-++++.+.+|++|.+|.+.|-|..|.-.... ..|.-
T Consensus 164 ~~ea~~~Lv~Ryl~~~GPat~~d~a~w~gl~~~~~r~~l~~l~~~~~L~~v~~~~G~~~~~~~ 226 (327)
T PF06224_consen 164 REEALAELVRRYLRAYGPATLADFAWWSGLPKTQARRALAQLVEEGELVEVEVEGGKEPLYDL 226 (327)
T ss_pred HHHHHHHHHHHHHHHcCCccHHHHHHHhccCHHHHHHHHHhhccCCcEEEEEEcCcceeEEec
Confidence 344444444 44455789999999999999999999999999999999998765323 35553
No 283
>PLN00158 histone H2B; Provisional
Probab=44.60 E-value=46 Score=25.54 Aligned_cols=42 Identities=26% Similarity=0.391 Sum_probs=33.5
Q ss_pred eeCHHHHHHHHhhC------CCCeeechHHH--HhhhccchHHHHHHHHH
Q psy1871 68 LFDKASYDKLLKEV------PAYKLITPSVV--SERLKVRGSLARKALEE 109 (139)
Q Consensus 68 l~Dk~tydKl~KEV------pk~KlITPsvl--seRlkI~~SLARkaLre 109 (139)
.|..++|++|..|- .+-.-||+-.| |=||=+.|.||+-|+.|
T Consensus 56 SfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvLpgELaKhAvsE 105 (116)
T PLN00158 56 SFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSE 105 (116)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhccHHHHHHHHHH
Confidence 48899999999984 34467888776 56888899999988876
No 284
>PF12298 Bot1p: Eukaryotic mitochondrial regulator protein ; InterPro: IPR021036 This entry represents Ribosomal protein S35, which localises to the mitochondria in live cells and co-fractionates with purified mitochondrial ribosomes. This group of proteins have a novel function in the control of cell respiration by acting on the mitochondrial protein synthesis machinery and a role in mitochondrial integrity. Observations also indicate that in Schizosaccharomyces pombe (Fission yeast), alterations of mitochondrial function are linked to changes in cell cycle and cell morphology control mechanisms [].
Probab=44.59 E-value=27 Score=27.94 Aligned_cols=46 Identities=7% Similarity=0.034 Sum_probs=37.3
Q ss_pred eeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHc
Q psy1871 67 VLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQK 113 (139)
Q Consensus 67 Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~k 113 (139)
-.+++++=+.|+.++-.-.. |+-.||.+|+|+.+-..+|||--+-+
T Consensus 15 ~~lse~~r~~Iy~~~~~~~~-sv~~vS~~ygi~~~RV~AIvrLkeiE 60 (172)
T PF12298_consen 15 PVLSEELREQIYEDVMQDGK-SVREVSQKYGIKIQRVEAIVRLKEIE 60 (172)
T ss_pred CcCCHHHHHHHHHHHHhCCC-CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 35678888888888876655 99999999999999999998755443
No 285
>TIGR01714 phage_rep_org_N phage replisome organizer, putative, N-terminal region. This model represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region covered by this model is N-terminal to the low-complexity region.
Probab=43.66 E-value=47 Score=25.18 Aligned_cols=41 Identities=17% Similarity=0.199 Sum_probs=35.5
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
|+-+||..++-....-|.||.-|+.-|+|..... ..||..+
T Consensus 53 ~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~d~---g~i~i~~ 93 (119)
T TIGR01714 53 NAEMLATMFNRNVGDIRITLQTLESLGLIEKKNN---GDIFLEN 93 (119)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC---CcEEehh
Confidence 8999999999999999999999999999998752 2466654
No 286
>TIGR02277 PaaX_trns_reg phenylacetic acid degradation operon negative regulatory protein PaaX. This transcriptional regulator is always found in association with operons believed to be involved in the degradation of phenylacetic acid. The gene product has been shown to bind to the promoter sites and repress their transcription.
Probab=43.60 E-value=40 Score=28.41 Aligned_cols=38 Identities=21% Similarity=0.321 Sum_probs=31.2
Q ss_pred HHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEE
Q psy1871 90 SVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIY 128 (139)
Q Consensus 90 svlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IY 128 (139)
..+.+.++|+-+..|.+|.-|+++|+|...... +...|
T Consensus 24 i~l~~~~gi~~~~vr~al~RL~~~G~l~~~~~g-rr~~Y 61 (280)
T TIGR02277 24 IEFLAGLGINERLVRTAVSRLVAQGWLQSERKG-RRSFY 61 (280)
T ss_pred HHHHHhcCCCcchHHHHHHHHHHCCCEEeeecC-CCCEE
Confidence 467899999999999999999999999886433 33455
No 287
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=43.18 E-value=45 Score=28.82 Aligned_cols=56 Identities=16% Similarity=0.293 Sum_probs=42.4
Q ss_pred HHHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 72 ASYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 72 ~tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
.|--.|+-|+--+ .-+-|..||+.|+|+.-----=|++|.+.|+|.. ++|.-..-|
T Consensus 10 ~t~fqIL~ei~~~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~--~gR~~Y~iT 66 (260)
T COG1497 10 LTRFQILSEIAVRQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEK--EGRGEYEIT 66 (260)
T ss_pred chHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceee--cCCeeEEEe
Confidence 3455666676554 6788999999999999888888999999999976 444344444
No 288
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=42.56 E-value=24 Score=23.78 Aligned_cols=40 Identities=18% Similarity=0.167 Sum_probs=29.5
Q ss_pred HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHH
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQ 112 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~ 112 (139)
..=.|.+.+-..+.+|...+|+.+.|+-|-.++.|++|..
T Consensus 17 ~~~~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~~ 56 (87)
T PF05043_consen 17 LNYQLLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLNK 56 (87)
T ss_dssp HHHHHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 3334555555678899999999999999999999988765
No 289
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=42.37 E-value=36 Score=19.81 Aligned_cols=26 Identities=19% Similarity=0.427 Sum_probs=22.7
Q ss_pred echHHHHhhhccchHHHHHHHHHHHH
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQ 112 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~ 112 (139)
.|...||+.|+|+-+..+..++.+..
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 48899999999999999998887654
No 290
>PRK13824 replication initiation protein RepC; Provisional
Probab=42.30 E-value=46 Score=29.80 Aligned_cols=43 Identities=26% Similarity=0.385 Sum_probs=32.9
Q ss_pred chHHHHhh-hccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 88 TPSVVSER-LKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseR-lkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
+-..||+| +++..+--|+.|+.|++-|||..=..-++.. |.|.
T Consensus 84 SN~~La~r~~Gms~~tlrRhla~LveaGLI~rrDSpNGKR-yarr 127 (404)
T PRK13824 84 SNAQLSLRAHGMAGATLRRHLAALVEAGLIIRRDSPNGKR-YARK 127 (404)
T ss_pred hHHHHHHHHcCCCHHHHHHHHHHHHHCCCeEeecCCCCcc-ccee
Confidence 33579999 5999999999999999999998764333333 5543
No 291
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=41.91 E-value=38 Score=28.20 Aligned_cols=35 Identities=29% Similarity=0.269 Sum_probs=28.2
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHH
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALE 108 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLr 108 (139)
+.+-.|.++.|. ..|+..|||.|+|.-...|+||+
T Consensus 17 ~~ir~L~~~~p~--~~t~~~Lae~F~vspe~irrILk 51 (225)
T PF06413_consen 17 EQIRYLHKEDPE--EWTVERLAESFKVSPEAIRRILK 51 (225)
T ss_pred HHHHHHHHhCcc--ccCHHHHHhhCCCCHHHHHHHHh
Confidence 445566777776 35889999999999999999986
No 292
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=41.82 E-value=65 Score=29.99 Aligned_cols=47 Identities=6% Similarity=0.020 Sum_probs=37.8
Q ss_pred HHHHhhCCCCe-eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 75 DKLLKEVPAYK-LITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 75 dKl~KEVpk~K-lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
.+|+.-..... .+++..+|+.+++.-.-.-.++..|+++|+|..-..
T Consensus 6 ~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~ 53 (492)
T PLN02853 6 EALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDI 53 (492)
T ss_pred HHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEE
Confidence 45555555544 479999999999999999999999999998876543
No 293
>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=41.79 E-value=35 Score=30.27 Aligned_cols=50 Identities=24% Similarity=0.306 Sum_probs=40.7
Q ss_pred HHHHHHHhhC------CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 72 ASYDKLLKEV------PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 72 ~tydKl~KEV------pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
.+++.|..+| |..++=+.-.+|+.|+|+.+.--++.++|+.+|+|.-..+
T Consensus 8 ql~~~i~~~I~~g~l~~g~rLPs~R~la~~l~vs~~Tv~~ay~~L~~~G~i~~~~g 63 (459)
T COG1167 8 QLAEQLREAILSGRLKPGDRLPSIRQLAQDLGVSRSTVSRAYEELEARGYIESRPG 63 (459)
T ss_pred HHHHHHHHHHHcCCCCCCCcCCcHHHHHHHhCCcHHHHHHHHHHHHhCcceeeccC
Confidence 4455555555 3468888899999999999999999999999999976543
No 294
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=41.46 E-value=48 Score=22.94 Aligned_cols=32 Identities=25% Similarity=0.365 Sum_probs=26.1
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeec
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKH 122 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh 122 (139)
||-..+++.++|.-+. |.+|.+.|+|.+....
T Consensus 1 is~~e~~~~~~i~~~~----l~~lve~Gli~p~~~~ 32 (84)
T PF13591_consen 1 ISLEEFCEACGIEPEF----LRELVEEGLIEPEGEE 32 (84)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHCCCeeecCCC
Confidence 5778888888877654 8999999999997655
No 295
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=41.44 E-value=36 Score=31.21 Aligned_cols=47 Identities=23% Similarity=0.253 Sum_probs=40.5
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
=+=|+.--+|..|+++-..|-+|++|.+..|++.-+-+....+|=.+
T Consensus 17 G~kISVR~Ia~~l~VSeGTAYRAIKeAen~G~V~Ti~RvGTvRIekk 63 (432)
T COG4109 17 GKKISVRGIAKHLKVSEGTAYRAIKEAENLGLVSTIPRVGTVRIEKK 63 (432)
T ss_pred cceeehHHhhhhCCcccchHHHHHHHHHhcCceEecccceeEEEEec
Confidence 36688999999999999999999999999999988877776666544
No 296
>KOG3233|consensus
Probab=41.38 E-value=11 Score=33.10 Aligned_cols=47 Identities=26% Similarity=0.333 Sum_probs=39.1
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE--eecCceEEEe
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV--VKHHAQVIYT 129 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V--skh~~q~IYt 129 (139)
.-+=|+--+|=.|-++...+-.++|+-||++.|||-| .++.+-.||.
T Consensus 97 g~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKkLIKsVKsv~n~~~KvYm 145 (297)
T KOG3233|consen 97 GNEGIWSKEIKRKSNLPQTVVNKILKSLESKKLIKSVKSVKNSRKKVYM 145 (297)
T ss_pred CCCceeeehhhhccCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCceEEE
Confidence 3345566678889999999999999999999999998 4677767875
No 297
>PF09107 SelB-wing_3: Elongation factor SelB, winged helix ; InterPro: IPR015191 This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing []. Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3". The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity []. ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2PJP_A 2UWM_A 1WSU_B 1LVA_A 2PLY_A.
Probab=41.36 E-value=74 Score=20.53 Aligned_cols=37 Identities=24% Similarity=0.196 Sum_probs=33.2
Q ss_pred CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 84 YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 84 ~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
...||++.+=|.++++=-.|-.+|+.|...|+.+.+-
T Consensus 8 ~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~g 44 (50)
T PF09107_consen 8 NGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVG 44 (50)
T ss_dssp TSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred CCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeC
Confidence 4578999999999999999999999999999998875
No 298
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=41.06 E-value=42 Score=25.07 Aligned_cols=49 Identities=29% Similarity=0.401 Sum_probs=33.1
Q ss_pred HhhCCCCeeechHHHHhhh--ccchHHHHHHHHHHHHcCCeeEEeecCceEEEe
Q psy1871 78 LKEVPAYKLITPSVVSERL--KVRGSLARKALEELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 78 ~KEVpk~KlITPsvlseRl--kI~~SLARkaLreL~~kGlIk~Vskh~~q~IYt 129 (139)
+=-|-+-.|||++.|+|-+ ..+-+.--.-+--|..+|+|.. ++...|-|
T Consensus 22 lI~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKkglIEK---SGDGlv~T 72 (96)
T PF09114_consen 22 LIQVAKKNFITASEVREALATEMNKASVNSNIGVLIKKGLIEK---SGDGLVIT 72 (96)
T ss_dssp HHHHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHHHTTSEEE---ETTEEEE-
T ss_pred HHHHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHHHcCcccc---cCCceEEe
Confidence 3345566899999999988 6777777777889999999764 44444443
No 299
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=40.68 E-value=65 Score=26.52 Aligned_cols=61 Identities=21% Similarity=0.135 Sum_probs=47.9
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccc--------hHHHHHHHHHHHHcCCeeEEeec-CceEEEeccC
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVR--------GSLARKALEELLQKGLIKQVVKH-HAQVIYTRTT 132 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~--------~SLARkaLreL~~kGlIk~Vskh-~~q~IYtra~ 132 (139)
+..+.++..+-.-.-+|...|.+.+... .+....+|+.|...|.|...-.. ..+..|....
T Consensus 85 ~~~~~v~~~L~~~gplt~~eL~~~l~~~~~~~~~~~~~~~~~~l~~l~~~G~l~~~~~~~g~~~~y~l~~ 154 (327)
T PF06224_consen 85 RLAEAVLDALRADGPLTRAELREALAEAGWWGWGGPSSPWKHLLEYLWYRGLLCVGPRPRGRWRTYDLTE 154 (327)
T ss_pred HHHHHHHHHHHhcCCCCHHHHHHHhhhccccCCCCCCchHHHHHHHHHhCCeEEEeccCCCceEEEechH
Confidence 3355566666566788999999998776 45889999999999999888755 6678888654
No 300
>PF09681 Phage_rep_org_N: N-terminal phage replisome organiser (Phage_rep_org_N); InterPro: IPR010056 This entry is represented by the N-terminal domain of Bacteriophage A500, Gp45. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. The proteins in this entry contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The low-complexity region is adjacent to this N-terminal domain.
Probab=40.51 E-value=49 Score=24.89 Aligned_cols=42 Identities=24% Similarity=0.231 Sum_probs=35.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
.|+-+||..++.....-+.||.-|.+-|+|.... ...||..+
T Consensus 54 y~~e~LA~~~~~~~~~V~~AL~~f~k~glIe~~e---d~~i~i~~ 95 (121)
T PF09681_consen 54 YTAEMLALEFDRPVDTVRLALAVFQKLGLIEIDE---DGVIYIPN 95 (121)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec---CCeEEeec
Confidence 4888999999999999999999999999998743 34677654
No 301
>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=40.12 E-value=30 Score=24.11 Aligned_cols=24 Identities=25% Similarity=0.188 Sum_probs=20.3
Q ss_pred hHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 100 GSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 100 ~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
-.=|-.+-+.|.+.|+|..|..+|
T Consensus 47 R~eAv~~gq~Ll~~g~i~hV~~~~ 70 (81)
T cd04448 47 RVQAIAIGQALLDAGWIECVSDDD 70 (81)
T ss_pred HHHHHHHHHHHHHCCCEEecCCCC
Confidence 346778889999999999998776
No 302
>PRK04280 arginine repressor; Provisional
Probab=40.02 E-value=80 Score=24.44 Aligned_cols=22 Identities=14% Similarity=0.185 Sum_probs=15.2
Q ss_pred HHHHHcCCeeEEeecCceEEEec
Q psy1871 108 EELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 108 reL~~kGlIk~Vskh~~q~IYtr 130 (139)
|+|.+=|++|. ...+.+..|.-
T Consensus 42 RDikeL~lvKv-~~~~G~~~Y~l 63 (148)
T PRK04280 42 RDIKELHLVKV-PLPDGRYKYSL 63 (148)
T ss_pred HHHHHcCCEEe-ecCCCcEEEee
Confidence 78888899884 33445677763
No 303
>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=39.41 E-value=31 Score=23.93 Aligned_cols=49 Identities=20% Similarity=0.285 Sum_probs=33.5
Q ss_pred hhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 62 KLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 62 Klnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
+.-..+++-.+..|=|...++. + .+-.=|-.+.+.|.+.|+|..|+.+|
T Consensus 24 ~~~~~cF~G~e~VdWL~~~~~~--~-----------~~r~eAv~lgq~Ll~~g~I~hv~~~~ 72 (83)
T cd04449 24 GLPSNCFIGSEAVSWLINNFED--V-----------DTREEAVELGQELMNEGLIEHVSGRH 72 (83)
T ss_pred ccCCcceEhHHHHHHHHHhCCC--C-----------CCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 3445556677777777665442 1 22345888899999999999998644
No 304
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=39.09 E-value=26 Score=25.56 Aligned_cols=41 Identities=29% Similarity=0.343 Sum_probs=27.7
Q ss_pred CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCe
Q psy1871 70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLI 116 (139)
Q Consensus 70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlI 116 (139)
|.+.+..+..+ +.=+|..++|++|+|..|..-.+|+ .-|+.
T Consensus 58 d~~~L~~~v~~---~pd~tl~Ela~~l~Vs~~ti~~~Lk---rlg~t 98 (119)
T PF01710_consen 58 DRDELKALVEE---NPDATLRELAERLGVSPSTIWRALK---RLGIT 98 (119)
T ss_pred cHHHHHHHHHH---CCCcCHHHHHHHcCCCHHHHHHHHH---HcCch
Confidence 66666666655 4556889999999997776555544 44554
No 305
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=39.05 E-value=21 Score=25.32 Aligned_cols=33 Identities=15% Similarity=0.030 Sum_probs=25.9
Q ss_pred HHHHhhCCCCeeechHHHHhhhccchHHHHHHHH
Q psy1871 75 DKLLKEVPAYKLITPSVVSERLKVRGSLARKALE 108 (139)
Q Consensus 75 dKl~KEVpk~KlITPsvlseRlkI~~SLARkaLr 108 (139)
..|..-+-. .-+|...||+.++|+.+..+++|.
T Consensus 9 ~~I~e~l~~-~~~ti~dvA~~~gvS~~TVsr~L~ 41 (80)
T TIGR02844 9 LEIGKYIVE-TKATVRETAKVFGVSKSTVHKDVT 41 (80)
T ss_pred HHHHHHHHH-CCCCHHHHHHHhCCCHHHHHHHhc
Confidence 344444555 677999999999999999999774
No 306
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=38.81 E-value=38 Score=22.70 Aligned_cols=30 Identities=23% Similarity=0.324 Sum_probs=26.7
Q ss_pred CCeeechHHHHhhhccchHHHHHHHHHHHH
Q psy1871 83 AYKLITPSVVSERLKVRGSLARKALEELLQ 112 (139)
Q Consensus 83 k~KlITPsvlseRlkI~~SLARkaLreL~~ 112 (139)
...+||...+++.++|+-.-|.+.+++|..
T Consensus 10 ~~P~Vsa~mva~~L~vT~~~A~~li~eLg~ 39 (54)
T PF11972_consen 10 SRPLVSAPMVAKELGVTPQAAQRLIAELGL 39 (54)
T ss_pred hCccccHHHHHHHhCCCHHHHHHHHHHhhc
Confidence 457999999999999999999999988765
No 307
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=38.24 E-value=47 Score=20.18 Aligned_cols=25 Identities=32% Similarity=0.462 Sum_probs=20.4
Q ss_pred echHHHHhhhccchHHHHHHHHHHH
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELL 111 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~ 111 (139)
.|-..||+.|+++-+-.++.++...
T Consensus 21 ~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 21 LTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp -SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred CCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 4779999999999999888776554
No 308
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=38.05 E-value=81 Score=22.27 Aligned_cols=43 Identities=14% Similarity=0.245 Sum_probs=36.6
Q ss_pred CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCc
Q psy1871 82 PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHA 124 (139)
Q Consensus 82 pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~ 124 (139)
-+..+++--.|++.|+|+-.---+.++.|.+.|+=...++++.
T Consensus 15 ~~~~~~SGe~La~~LgiSRtaVwK~Iq~Lr~~G~~I~s~~~kG 57 (79)
T COG1654 15 LTGNFVSGEKLAEELGISRTAVWKHIQQLREEGVDIESVRGKG 57 (79)
T ss_pred cCCCcccHHHHHHHHCccHHHHHHHHHHHHHhCCceEecCCCc
Confidence 3456788899999999999999999999999999777776654
No 309
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=37.90 E-value=46 Score=19.56 Aligned_cols=26 Identities=12% Similarity=0.264 Sum_probs=22.5
Q ss_pred echHHHHhhhccchHHHHHHHHHHHH
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQ 112 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~ 112 (139)
.|...+|+.++++-+..+..++.+..
T Consensus 16 ~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 16 KTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 48899999999999999988887654
No 310
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=37.62 E-value=88 Score=29.08 Aligned_cols=39 Identities=15% Similarity=0.250 Sum_probs=33.4
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
..+++..+|+.+++.-.-...++..|+++|+|..-..-.
T Consensus 20 ~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~~~ 58 (494)
T PTZ00326 20 EIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMKKS 58 (494)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEE
Confidence 448999999999999999999999999999887654433
No 311
>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=37.16 E-value=1.2e+02 Score=20.04 Aligned_cols=29 Identities=24% Similarity=0.285 Sum_probs=21.8
Q ss_pred HhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 93 SERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 93 seRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
..+|.+..+.-++.|+.|.++|.|..-..
T Consensus 37 ~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~ 65 (68)
T PF10557_consen 37 KKRFPPSVSDIKKRIESLIEKEYIERDED 65 (68)
T ss_dssp TTTS---HHHHHHHHHHHHHTTSEEEESS
T ss_pred cCCcCCCHHHHHHHHHHHHHhhhhhcCCC
Confidence 33778889999999999999999987543
No 312
>PF08438 MMR_HSR1_C: GTPase of unknown function C-terminal; InterPro: IPR013646 This domain is found at the C terminus of IPR002917 from INTERPRO in archaeal and eukaryotic GTP-binding proteins. ; PDB: 1WXQ_A.
Probab=37.06 E-value=19 Score=26.97 Aligned_cols=47 Identities=21% Similarity=0.280 Sum_probs=27.0
Q ss_pred CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceE
Q psy1871 70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQV 126 (139)
Q Consensus 70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~ 126 (139)
..+..+||..+.|...+|-.|..+| -+||.+.+.|+|.-+.....-.
T Consensus 10 a~~ni~kl~~~~~~~~vVp~SA~aE----------l~Lr~a~k~g~I~Y~pGd~~F~ 56 (109)
T PF08438_consen 10 ADENIEKLKEKYPDEPVVPTSAAAE----------LALRKAAKAGLIDYIPGDSDFE 56 (109)
T ss_dssp -HHHHHHHHHHHTT-EEEEE-HHHH----------HHHHS-SSS----S--------
T ss_pred cHhHHHHHHHhCCCCceeeccHHHH----------HHHHHHHHCCCEEeCCCCCceE
Confidence 6788999999999999998887665 5799999999998766554433
No 313
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=37.06 E-value=35 Score=27.51 Aligned_cols=47 Identities=26% Similarity=0.364 Sum_probs=40.4
Q ss_pred eeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 67 VLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 67 Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
..|+-++|.+++.++.+ ..+|-.+|.|+++-.+ +.+|.-|..-|||.
T Consensus 12 ~~f~s~~~kkV~~~Ls~-~W~T~~El~e~~G~d~---~~~L~~LkK~gLiE 58 (160)
T PF09824_consen 12 QTFNSEVYKKVYDELSK-GWMTEEELEEKYGKDV---RESLLILKKGGLIE 58 (160)
T ss_pred HHhCCHHHHHHHHHHHh-ccCCHHHHHHHHCcCH---HHHHHHHHHcCchh
Confidence 46888999999877765 5789999999999888 88999999999985
No 314
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=36.75 E-value=39 Score=27.43 Aligned_cols=53 Identities=25% Similarity=0.284 Sum_probs=41.5
Q ss_pred ceeeCHHHHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 66 QVLFDKASYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 66 ~Vl~Dk~tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
.+..+.+.-|-|+-++-.. .=.|.-.|+.+|.....-||.+|++|.+.|-+..
T Consensus 103 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 156 (166)
T PRK15466 103 APVIVAESADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRK 156 (166)
T ss_pred CCCCChhhHHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhccchhh
Confidence 4445555566666665553 4568999999999999999999999999998865
No 315
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=36.38 E-value=55 Score=18.45 Aligned_cols=26 Identities=23% Similarity=0.327 Sum_probs=21.9
Q ss_pred echHHHHhhhccchHHHHHHHHHHHH
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQ 112 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~ 112 (139)
.|+..||+.++++.+..++.++....
T Consensus 27 ~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 27 LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 58899999999999998888876543
No 316
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=36.03 E-value=54 Score=23.70 Aligned_cols=38 Identities=13% Similarity=0.001 Sum_probs=33.0
Q ss_pred echHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCc
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHA 124 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~ 124 (139)
.+++.+|+.|+|+-..|.+-+.-..+.|.-=+...+++
T Consensus 26 ~~~a~aA~~~gVS~~Ta~kW~~Ryra~G~~GL~DRSSR 63 (85)
T PF13011_consen 26 WPVAHAAAEFGVSRRTAYKWLARYRAEGEAGLQDRSSR 63 (85)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHHcCcccccccCCC
Confidence 36799999999999999999999999988777766654
No 317
>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=35.91 E-value=47 Score=21.59 Aligned_cols=31 Identities=26% Similarity=0.272 Sum_probs=26.0
Q ss_pred hhccchHHHHHHHHHHHHcCCeeEEeecCce
Q psy1871 95 RLKVRGSLARKALEELLQKGLIKQVVKHHAQ 125 (139)
Q Consensus 95 RlkI~~SLARkaLreL~~kGlIk~Vskh~~q 125 (139)
.+..+-+-|..+.++|.+.|+|..|..++.+
T Consensus 33 ~~~~~r~eA~~l~q~Ll~~g~i~~v~~~~~~ 63 (74)
T PF00610_consen 33 GFVRDREEAVQLGQELLDHGFIEHVSDKSKQ 63 (74)
T ss_dssp TSTSSHHHHHHHHHHHHHCTSEEESSSSSHS
T ss_pred ccccCHHHHHHHHHHHHHCCCEEECCCCCCC
Confidence 4456778899999999999999999887743
No 318
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=35.62 E-value=22 Score=21.78 Aligned_cols=22 Identities=14% Similarity=0.232 Sum_probs=16.9
Q ss_pred echHHHHhhhccchHHHHHHHH
Q psy1871 87 ITPSVVSERLKVRGSLARKALE 108 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLr 108 (139)
+|...||+.|+|.-+.-.++|+
T Consensus 22 ~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 22 MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp --HHHHHHHTTS-HHHHHHHHC
T ss_pred CCHHHHHHHHCcCHHHHHHHHh
Confidence 7899999999999998888775
No 319
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=34.07 E-value=37 Score=22.08 Aligned_cols=34 Identities=18% Similarity=0.305 Sum_probs=23.5
Q ss_pred HHHHHHhhCCC--CeeechHHHHhhhccchHHHHHH
Q psy1871 73 SYDKLLKEVPA--YKLITPSVVSERLKVRGSLARKA 106 (139)
Q Consensus 73 tydKl~KEVpk--~KlITPsvlseRlkI~~SLARka 106 (139)
.|-+++++... ...|+-..||+.++|+.+.-|+=
T Consensus 13 ~Y~r~L~~l~~~G~~~vSS~~La~~~gi~~~qVRKD 48 (50)
T PF06971_consen 13 LYLRYLEQLKEEGVERVSSQELAEALGITPAQVRKD 48 (50)
T ss_dssp HHHHHHHHHHHTT-SEE-HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHcCCeeECHHHHHHHHCCCHHHhccc
Confidence 34455555543 58899999999999999988863
No 320
>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=33.90 E-value=76 Score=22.07 Aligned_cols=27 Identities=30% Similarity=0.320 Sum_probs=22.4
Q ss_pred cchHHHHHHHHHHHHcCCeeEEeecCc
Q psy1871 98 VRGSLARKALEELLQKGLIKQVVKHHA 124 (139)
Q Consensus 98 I~~SLARkaLreL~~kGlIk~Vskh~~ 124 (139)
++..=|..+-.+|.+.|+|.+|..++.
T Consensus 45 ~~~~EA~~~~~~ll~~gli~~V~~~~~ 71 (88)
T cd04450 45 VDPSEALEIAALFVKYGLITPVSDHRS 71 (88)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCCcc
Confidence 455668888999999999999987664
No 321
>PF05595 DUF771: Domain of unknown function (DUF771) ; InterPro: IPR008489 This entry is represented by Bacteriophage bIL285, Orf7. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of uncharacterised ORFs found in Bacteriophage and Lactococcus lactis.
Probab=33.36 E-value=50 Score=23.35 Aligned_cols=44 Identities=20% Similarity=0.198 Sum_probs=36.7
Q ss_pred cceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHH-HHHHH
Q psy1871 65 NQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLA-RKALE 108 (139)
Q Consensus 65 n~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLA-RkaLr 108 (139)
..|+++++-|+.|.+....-...|-..|.++++.+-.-. ..+|.
T Consensus 2 d~vii~k~ey~el~~~~~~~~~W~~~dl~k~~~~s~~wi~~~il~ 46 (91)
T PF05595_consen 2 DKVIIDKEEYEELKKKDLEGKWWDMKDLRKRTGKSREWIKENILY 46 (91)
T ss_pred CeEEeeHHHHHHHHHHhhccceeeHHHHHHHHCCCHHHHHHHccc
Confidence 368999999999999999999999999999998655544 35554
No 322
>TIGR03453 partition_RepA plasmid partitioning protein RepA. Members of this family are the RepA (or ParA) protein involved in replicon partitioning. All known examples occur in bacterial species with two or more replicons, on a plasmid or the smaller chromosome. Note that an apparent exception may be seen as a pseudomolecule from assembly of an incompletely sequenced genome. Members of this family belong to a larger family that also includes the enzyme cobyrinic acid a,c-diamide synthase, but assignment of that name to members of this family would be in error.
Probab=33.28 E-value=43 Score=28.78 Aligned_cols=42 Identities=24% Similarity=0.218 Sum_probs=31.2
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEec
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTR 130 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtr 130 (139)
...|...+|++++|+-+. ||..+.+|++-.+.+ .++.+.|+.
T Consensus 32 ~~~~i~eva~~~gv~~~t----lr~~e~~~~~~~~~r~~~g~r~yt~ 74 (387)
T TIGR03453 32 RKFTSGEVAKLLGVSDSY----LRQLSLEGKGPEPETLSNGRRSYTL 74 (387)
T ss_pred ccCCHHHHHHHHCcCHHH----HHHHHHcCCCCCCCcCCCCceeeCH
Confidence 567999999999998776 566899998765533 345566763
No 323
>PRK03341 arginine repressor; Provisional
Probab=33.23 E-value=1.2e+02 Score=24.17 Aligned_cols=54 Identities=11% Similarity=0.195 Sum_probs=35.0
Q ss_pred HHHHHHhhCCCCeeechHHHHhhh-----ccchHHHHHHHHHHHHcCCeeEEeecCceE-EEec
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERL-----KVRGSLARKALEELLQKGLIKQVVKHHAQV-IYTR 130 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRl-----kI~~SLARkaLreL~~kGlIk~Vskh~~q~-IYtr 130 (139)
-.+.|..-+.+..+.|...|++.| .++-+--+ |+|.+-|++| |.....+. +|+-
T Consensus 16 R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~vTQaTiS---RDl~eL~~~K-v~~~~G~~~~Y~l 75 (168)
T PRK03341 16 RQARIVAILSRQSVRSQAELAALLADEGIEVTQATLS---RDLDELGAVK-LRGADGGLGVYVV 75 (168)
T ss_pred HHHHHHHHHHHCCCccHHHHHHHHHHcCCcccHHHHH---HHHHHhcCEe-eecCCCCEEEEEe
Confidence 345555666677899999999999 55444444 5566668887 33344444 8863
No 324
>KOG4068|consensus
Probab=32.47 E-value=65 Score=26.35 Aligned_cols=34 Identities=32% Similarity=0.422 Sum_probs=26.9
Q ss_pred cchHHHHHHHHHHHHcCCeeEEeecC-ceEEEecc
Q psy1871 98 VRGSLARKALEELLQKGLIKQVVKHH-AQVIYTRT 131 (139)
Q Consensus 98 I~~SLARkaLreL~~kGlIk~Vskh~-~q~IYtra 131 (139)
+..++-+.+|.+|+.+|++.+..+.+ +-.||=|.
T Consensus 66 Ls~~~i~~Il~~l~k~g~~e~~Dk~rt~f~I~Wrs 100 (174)
T KOG4068|consen 66 LSQEFIDEILEELEKKGLAEPTDKRRTRFFIYWRS 100 (174)
T ss_pred CCHHHHHHHHHHHHHccCCcccccCceEEEEEEcC
Confidence 45677899999999999999998754 44577664
No 325
>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=32.47 E-value=74 Score=20.81 Aligned_cols=44 Identities=20% Similarity=0.183 Sum_probs=32.1
Q ss_pred ccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 64 NNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 64 nn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
-+.++.=.+..+=|..... -.+-+-|..+.+.|.+.|+|..|..
T Consensus 17 ~~~~F~G~e~v~wL~~~~~--------------~~~r~eA~~l~~~ll~~g~i~~v~~ 60 (77)
T smart00049 17 YPNCFTGSELVDWLMDNLE--------------IIDREEAVHLGQLLLDEGLIHHVNG 60 (77)
T ss_pred CcceeEcHHHHHHHHHcCC--------------cCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 3445555666666665553 1456889999999999999999984
No 326
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=32.44 E-value=58 Score=20.39 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=21.9
Q ss_pred eeechHHHHhhhccchHHHHHHHHHH-HHcCCe
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEEL-LQKGLI 116 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL-~~kGlI 116 (139)
.-||.+.||+.|++.. ..+|+.| .+.|+-
T Consensus 2 ~~i~V~elAk~l~v~~---~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 2 EKIRVSELAKELGVPS---KEIIKKLFKELGIM 31 (54)
T ss_dssp -EE-TTHHHHHHSSSH---HHHHHHH-HHHTS-
T ss_pred CceEHHHHHHHHCcCH---HHHHHHHHHhCCcC
Confidence 4578999999999984 5788999 448986
No 327
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=32.39 E-value=93 Score=21.80 Aligned_cols=41 Identities=22% Similarity=0.262 Sum_probs=31.8
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
+.||.+...- .++|...+|.-|+|. .+...+.|.+.|+|-.
T Consensus 13 ~~~d~~~~~~---~~~ti~~~AK~L~i~---~~~l~~~Lr~~g~l~~ 53 (111)
T PF03374_consen 13 EFYDAFVDSD---GLYTIREAAKLLGIG---RNKLFQWLREKGWLYR 53 (111)
T ss_pred HHHHHHHcCC---CCccHHHHHHHhCCC---HHHHHHHHHhCCceEE
Confidence 4456655443 688999999999887 7788888888999865
No 328
>PF02319 E2F_TDP: E2F/DP family winged-helix DNA-binding domain; InterPro: IPR003316 The mammalian transcription factor E2F plays an important role in regulating the expression of genes that are required for passage through the cell cycle. Multiple E2F family members have been identified that bind to DNA as heterodimers, interacting with proteins known as DP - the dimerisation partners [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005667 transcription factor complex; PDB: 1CF7_B.
Probab=32.36 E-value=1.6e+02 Score=19.78 Aligned_cols=47 Identities=23% Similarity=0.346 Sum_probs=34.7
Q ss_pred HHhhCCCCeeechHHHHhhh---ccchH--HHHHHHHHHHHcCCeeEEeecCc
Q psy1871 77 LLKEVPAYKLITPSVVSERL---KVRGS--LARKALEELLQKGLIKQVVKHHA 124 (139)
Q Consensus 77 l~KEVpk~KlITPsvlseRl---kI~~S--LARkaLreL~~kGlIk~Vskh~~ 124 (139)
+....|. ..|+...+|+.| ++.-. =---++.=|++=|+|....++.-
T Consensus 16 ~~~~~~~-~~i~l~~ia~~l~~~~~k~~~RRlYDI~NVLealgli~K~~k~~~ 67 (71)
T PF02319_consen 16 LFESSPD-KSISLNEIADKLISENVKTQRRRLYDIINVLEALGLIEKQSKNSY 67 (71)
T ss_dssp HHHHCCC-TEEEHHHHHHHCHHHCCHHHCHHHHHHHHHHHHCTSEEEEETTEE
T ss_pred HHHHCCC-CcccHHHHHHHHcccccccccchhhHHHHHHHHhCceeecCCCce
Confidence 5556677 899999999999 77322 22346788999999988766543
No 329
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=32.36 E-value=55 Score=20.60 Aligned_cols=26 Identities=15% Similarity=0.221 Sum_probs=22.6
Q ss_pred echHHHHhhhccchHHHHHHHHHHHH
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQ 112 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~ 112 (139)
.|-..||.+|+|+-|-+-+++++.+.
T Consensus 20 ~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 20 LTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred CcHhHHhhheeecHHHHHHHHHHHHH
Confidence 46688999999999999999988764
No 330
>KOG4062|consensus
Probab=32.34 E-value=1e+02 Score=25.37 Aligned_cols=66 Identities=18% Similarity=0.170 Sum_probs=52.8
Q ss_pred hhhhhhhc-cceeeCHHHHHHHHh---hCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 57 GKVRDKLN-NQVLFDKASYDKLLK---EVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 57 gKvkdKln-n~Vl~Dk~tydKl~K---EVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
-+..++++ +.++++.+-+-++.+ +||.=+++|=+.||.|.+ +=|-||++=+.+....+--+|-.||
T Consensus 73 le~~~~~p~~~~~~~t~F~~kVw~al~~i~~Gev~tY~~iA~~iG-~PsaaRaVg~A~~~n~la~lvPcHR 142 (178)
T KOG4062|consen 73 LEAIEEFPVHPVMRGTDFQRKVWDALCEIPYGEVSTYGQIARRIG-NPSAARAVGSAMAHNNLAILVPCHR 142 (178)
T ss_pred hhhcccCCccceeccchHHHHHHHHHhccCCCceeeHHHHHHHhC-CcHHHHHHHHHHccCCCcEEeccee
Confidence 34567777 688888888877665 566669999999999988 6789999999999888887776665
No 331
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=32.16 E-value=93 Score=23.93 Aligned_cols=51 Identities=22% Similarity=0.199 Sum_probs=37.7
Q ss_pred CHHHHHHHHhhCCCC-eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 70 DKASYDKLLKEVPAY-KLITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 70 Dk~tydKl~KEVpk~-KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
|.-|...++.-+-.. .=.|-..||++|+|+-..++.=+..|++.|++..--
T Consensus 160 ~~Lt~r~Vl~~~~~g~~g~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~ 211 (225)
T PRK10046 160 DPLTLNAVRKLFKEPGVQHTAETVAQALTISRTTARRYLEYCASRHLIIAEI 211 (225)
T ss_pred CHHHHHHHHHHHHcCCCCcCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEe
Confidence 444444444333321 125889999999999999999999999999998754
No 332
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=32.16 E-value=89 Score=18.83 Aligned_cols=39 Identities=21% Similarity=0.134 Sum_probs=30.0
Q ss_pred CHHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHH
Q psy1871 70 DKASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEEL 110 (139)
Q Consensus 70 Dk~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL 110 (139)
...+-..|+.+.-.. .|-..||+.++|.-+..++++.+.
T Consensus 13 T~~~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 13 TKRLEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 344555666666665 788999999999999999998764
No 333
>PHA01747 putative ATP-dependent protease
Probab=30.69 E-value=53 Score=30.20 Aligned_cols=42 Identities=19% Similarity=0.143 Sum_probs=37.2
Q ss_pred CHHHHHHHHhhCCCC--eeechHHHHhhhccchHHHHHHHHHHHHc
Q psy1871 70 DKASYDKLLKEVPAY--KLITPSVVSERLKVRGSLARKALEELLQK 113 (139)
Q Consensus 70 Dk~tydKl~KEVpk~--KlITPsvlseRlkI~~SLARkaLreL~~k 113 (139)
|.+.+|||. +|.. +-||...++.-+.+..+++|..++.+.++
T Consensus 328 ~sA~LDRIh--i~g~~~pkIs~d~~~sG~vL~~tilr~~i~~~q~~ 371 (425)
T PHA01747 328 TKAILDRIA--IIIVNEKKITYDDIISGRVLYPTILRGLISLVQSK 371 (425)
T ss_pred chHHhhhhh--hcccccCcCCHHHhcccceeHHHHHHHHHHHHHHH
Confidence 788899999 6664 66899999999999999999999999875
No 334
>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=30.34 E-value=1.5e+02 Score=20.55 Aligned_cols=32 Identities=25% Similarity=0.234 Sum_probs=24.8
Q ss_pred hHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 100 GSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 100 ~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
-++-+.+|+.+.++|.|..+..+....-|--+
T Consensus 45 ~~~l~~aLkk~v~~G~l~~~kG~g~~gsfkl~ 76 (88)
T cd00073 45 NKLLKLALKKGVAKGKLVQVKGTGASGSFKLS 76 (88)
T ss_pred HHHHHHHHHHHHHCCCeEeecCCCCccceEeC
Confidence 46778899999999999999976555555543
No 335
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=30.28 E-value=73 Score=15.74 Aligned_cols=18 Identities=22% Similarity=0.259 Sum_probs=14.4
Q ss_pred chHHHHhhhccchHHHHH
Q psy1871 88 TPSVVSERLKVRGSLARK 105 (139)
Q Consensus 88 TPsvlseRlkI~~SLARk 105 (139)
|...+++.++|.-+...+
T Consensus 23 s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 23 SVAEIARRLGVSRSTLYR 40 (42)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 889999999988766544
No 336
>PF02022 Integrase_Zn: Integrase Zinc binding domain The structure of the N-terminal zinc binding domain.; InterPro: IPR003308 Retroviral integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains: an N-terminal zinc binding domain, a central catalytic core and a C-terminal DNA-binding domain [, ]. Often found as part of the POL polyprotein.; GO: 0008270 zinc ion binding; PDB: 1E0E_A 3F9K_F 1E27_C 1K6Y_B 1WJD_A 1WJB_A 1WJF_A 1WJE_B 3HPG_B 3HPH_C ....
Probab=29.03 E-value=69 Score=19.94 Aligned_cols=22 Identities=5% Similarity=0.270 Sum_probs=16.8
Q ss_pred chHHHHhhhccchHHHHHHHHH
Q psy1871 88 TPSVVSERLKVRGSLARKALEE 109 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLre 109 (139)
.+-.|+++|+|.-.+||.|++.
T Consensus 11 n~~~L~~~f~ip~~vAk~IV~~ 32 (40)
T PF02022_consen 11 NAKALRHKFGIPRLVAKQIVNQ 32 (40)
T ss_dssp -HHHHHHHHT--HHHHHHHHHH
T ss_pred CHHHHHHHHccCHHHHHHHHHH
Confidence 3567999999999999999875
No 337
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=28.82 E-value=73 Score=19.72 Aligned_cols=25 Identities=12% Similarity=0.121 Sum_probs=18.8
Q ss_pred echHHHHhhhccchHHHHHHHHHHH
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELL 111 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~ 111 (139)
+|...||++++++.+.-.+++++..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 4678888888888887777776654
No 338
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=28.46 E-value=89 Score=22.66 Aligned_cols=35 Identities=26% Similarity=0.284 Sum_probs=31.7
Q ss_pred eeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 85 KLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 85 KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
--+|...+++-++++..-.-++|.+|...|+|..-
T Consensus 170 ~~~~~~~ia~~~g~~~~~vsr~l~~l~~~g~i~~~ 204 (214)
T COG0664 170 LPLTHKDLAEYLGLSRETVSRILKELRKDGLISVR 204 (214)
T ss_pred ccCCHHHHHHHhCCchhhHHHHHHHHHhCCcEeeC
Confidence 46899999999999999999999999999998653
No 339
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=28.25 E-value=83 Score=26.20 Aligned_cols=49 Identities=12% Similarity=0.198 Sum_probs=38.4
Q ss_pred HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHH-HHHHcCCeeEEe
Q psy1871 71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALE-ELLQKGLIKQVV 120 (139)
Q Consensus 71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLr-eL~~kGlIk~Vs 120 (139)
...+.-+.+.++.- -++..++|+.++...+-+...++ .|...|+|....
T Consensus 262 ~~~l~~~~~~~~~~-~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~ 311 (328)
T PRK00080 262 RKYLRTIIEKFGGG-PVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTP 311 (328)
T ss_pred HHHHHHHHHHcCCC-ceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCC
Confidence 34444455555544 48999999999999999999999 999999996433
No 340
>KOG3411|consensus
Probab=27.68 E-value=60 Score=25.78 Aligned_cols=22 Identities=32% Similarity=0.582 Sum_probs=18.7
Q ss_pred chHHHHHHHHHHHHcCCeeEEe
Q psy1871 99 RGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 99 ~~SLARkaLreL~~kGlIk~Vs 120 (139)
.++++|++|+.|+.-|+|..=-
T Consensus 96 s~~i~rkvlQ~Le~~~~ve~hp 117 (143)
T KOG3411|consen 96 SGGIARKVLQALEKMGIVEKHP 117 (143)
T ss_pred ccHHHHHHHHHHHhCCceeeCC
Confidence 5799999999999999976543
No 341
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=27.68 E-value=1.3e+02 Score=27.03 Aligned_cols=47 Identities=17% Similarity=0.173 Sum_probs=38.8
Q ss_pred HHHHHHhhC-CCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 73 SYDKLLKEV-PAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 73 tydKl~KEV-pk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
-|.+|..-. ..---||-..||+.|..+-==||.+|+.|+++|.|.=-
T Consensus 9 ~~~~L~~~~~~~~~~~~l~~la~~l~cs~R~~~~~l~~~~~~gwl~w~ 56 (552)
T PRK13626 9 QFIRLWQCCEGKSQETTLNELAELLNCSRRHMRTLLNTMQQRGWLTWQ 56 (552)
T ss_pred HHHHHHHhcCCCcceeeHHHHHHHhcCChhHHHHHHHHHHHCCCeeee
Confidence 366666554 33347899999999999999999999999999999865
No 342
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=26.67 E-value=76 Score=25.33 Aligned_cols=39 Identities=15% Similarity=0.220 Sum_probs=29.3
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEee-cCceEEEecc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVK-HHAQVIYTRT 131 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk-h~~q~IYtra 131 (139)
|++.+|++++|+.+.. |--+++|.|. +.+ .++..+|+..
T Consensus 2 ti~evA~~lGVS~~TL----Rrw~k~g~L~-~~R~~~G~R~y~~~ 41 (175)
T PRK13182 2 KTPFVAKKLGVSPKTV----QRWVKQLNLP-CEKNEYGHYIFTEE 41 (175)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHcCCCC-CCcCCCCCEEECHH
Confidence 7899999999998764 5566688885 554 3577888753
No 343
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=26.45 E-value=98 Score=30.62 Aligned_cols=66 Identities=20% Similarity=0.329 Sum_probs=50.7
Q ss_pred hccceeeCHHHHHHHHhhCCC----CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 63 LNNQVLFDKASYDKLLKEVPA----YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 63 lnn~Vl~Dk~tydKl~KEVpk----~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
+-+--||+..-+|.|..||-. .-.|+.+.||.+|.+..-+.+.+|++... ++|+=.. .+..+||.+
T Consensus 107 l~~GeLit~~Yld~iaeEIne~LqE~G~isI~eLa~~~~Lpsefl~~~l~~rlG-~iI~g~~--~g~~lyT~a 176 (803)
T PLN03083 107 LVQGEIISQSYWDSIAEEINERLQECSQIALAELARQLQVGSELVTSMLEPRLG-TIVKARL--EGGQLYTPA 176 (803)
T ss_pred EecCEecchHHHHHHHHHHHHHHHHcCcChHHHHHHhcCChHHHHHHHHHHHhc-cceEEEe--cCCEEecHH
Confidence 344568899999999988854 57899999999999999999999987644 3444433 345679864
No 344
>PF02831 gpW: gpW; InterPro: IPR004174 GpW is a 68 residue protein known to be present in phage particles. Extracts of phage-infected cells lacking GpW contain DNA-filled heads, and active tails, but no infectious virions. GpW is required for the addition of GpFII to the head, which is, in turn, required for the attachment of tails. Since GpFII and tails are known to be attached at the connector, GpW is also likely to assemble at this site. The addition of GpW to filled heads increases the DNase resistance of the packaged DNA, suggesting that GpW either forms a plug at the connector to prevent ejection of the DNA, or binds directly to the DNA. The large number of positively charged residues in GpW (its calculated pI is 10.8) is consistent with a role in DNA interaction [].; GO: 0019067 viral assembly, maturation, egress, and release; PDB: 2L6Q_A 2L6R_A 1HYW_A.
Probab=26.26 E-value=1.4e+02 Score=20.62 Aligned_cols=32 Identities=28% Similarity=0.323 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871 101 SLARKALEELLQKGLIKQVVKHHAQVIYTRTT 132 (139)
Q Consensus 101 SLARkaLreL~~kGlIk~Vskh~~q~IYtra~ 132 (139)
.-|+.|+.+|..=.-.+-|..+.+.+=|+.+.
T Consensus 8 ~~a~~A~h~L~tG~~vvsv~~dgrsV~Yt~a~ 39 (68)
T PF02831_consen 8 AEARAAYHDLLTGQRVVSVQGDGRSVTYTQAN 39 (68)
T ss_dssp HHHHHHHHHHHCS-SEEEEEETTEEEEEEGGG
T ss_pred HHHHHHHHHHHhCCceeEeecCCeEEEEecCC
Confidence 46899999999987778899999998999864
No 345
>PF09743 DUF2042: Uncharacterized conserved protein (DUF2042); InterPro: IPR018611 The ubiquitin fold modifier 1 (Ufm1) is the most recently discovered ubiquitin-like modifier whose conjugation (ufmylation) system is conserved in multicellular organisms. Ufm1 is known to covalently attach with cellular protein(s) via a specific E1-activating enzyme (Uba5), an E2-conjugating enzyme (Ufc1), and a E3-ligating enzyme []. This entry represents E3 UFM1-protein ligase 1.
Probab=26.03 E-value=1.5e+02 Score=25.14 Aligned_cols=67 Identities=19% Similarity=0.286 Sum_probs=52.8
Q ss_pred hhccceeeCHHHHHHHHhhCCC-----CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 62 KLNNQVLFDKASYDKLLKEVPA-----YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 62 Klnn~Vl~Dk~tydKl~KEVpk-----~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
.++..+++.++-.++...-|-. .+-+..+.|..++++...+.-.+|.+|.+.|-|.=...+ .+|++.
T Consensus 163 ~~d~~~lyT~ayv~r~ka~iRG~l~a~T~Pt~l~~l~~~~~~~~~l~~~il~~Li~~~~l~G~i~G---~~yvP~ 234 (272)
T PF09743_consen 163 RLDGDVLYTEAYVARQKARIRGALSAITRPTPLSSLLKRYGFEEKLFQSILEELIKSGELPGSIVG---ASYVPD 234 (272)
T ss_pred EEeCCEEecHHHHHHHHHHHHHHHhcCccceEHHHHHHHhCCcHHHHHHHHHHHHhcCcceEEEEC---CEEech
Confidence 4455588888888777666554 367778999999999999999999999999988776655 677764
No 346
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=26.03 E-value=1.3e+02 Score=28.12 Aligned_cols=60 Identities=13% Similarity=0.140 Sum_probs=51.0
Q ss_pred hhccceeeCHHHHHHHHhhCCC----CeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 62 KLNNQVLFDKASYDKLLKEVPA----YKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 62 Klnn~Vl~Dk~tydKl~KEVpk----~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
++++..+|+.+.|+++...+-. ..-||.+.+=|.++++-=.|-..|+.|.+.|+.+.+-.
T Consensus 538 ~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~g~sRK~~i~lLE~~D~~~~T~r~g~ 601 (614)
T PRK10512 538 AIVKDRYYRNDRIVQFANMIRELDQECGSTCAADFRDRLGVGRKLAIQILEYFDRIGFTRRRGN 601 (614)
T ss_pred EecCCEEECHHHHHHHHHHHHHHHhhCCcEeHHHHHHHhCccHHHHHHHHHHhccCCCEEEECC
Confidence 5778889999999855554443 57899999999999999999999999999999988763
No 347
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=25.93 E-value=1.7e+02 Score=25.07 Aligned_cols=59 Identities=17% Similarity=0.227 Sum_probs=49.7
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEecc
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRT 131 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra 131 (139)
+|-..|.-|+.+-+.-|.-.||.++++++..-+=.+..|++-|+|..=- ..+-.||.=+
T Consensus 174 ~~~k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~~~~-~Gr~iiy~in 232 (240)
T COG3398 174 ETSKAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEELGIIPEDR-EGRSIIYSIN 232 (240)
T ss_pred hhHHHHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcCCCcccc-cCceEEEEeC
Confidence 4567889999999999999999999999999999999999999997743 3445566543
No 348
>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=25.69 E-value=93 Score=20.90 Aligned_cols=23 Identities=30% Similarity=0.329 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHcCCeeEEeecC
Q psy1871 101 SLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 101 SLARkaLreL~~kGlIk~Vskh~ 123 (139)
++-+++|+.+.++|.+..|..+.
T Consensus 46 ~~l~~aLk~~v~~G~l~~~kg~G 68 (77)
T PF00538_consen 46 SRLKRALKRGVEKGKLVQVKGKG 68 (77)
T ss_dssp HHHHHHHHHHHHCTSEEECSCST
T ss_pred HHHHHHHHHHHHCCcEEeecccC
Confidence 56789999999999999987443
No 349
>PF00292 PAX: 'Paired box' domain; InterPro: IPR001523 The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see IPR001356 from INTERPRO) [, ]. Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 6PAX_A 1K78_E 1MDM_A 2K27_A 1PDN_C.
Probab=25.32 E-value=74 Score=24.46 Aligned_cols=35 Identities=23% Similarity=0.290 Sum_probs=25.8
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHHcCCeeEEe
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQKGLIKQVV 120 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vs 120 (139)
=+.|..||.+|.|.-+-..++|....+-|.|.+-.
T Consensus 33 G~rp~~Isr~l~Vs~gcVsKIl~Ry~eTGsi~Pg~ 67 (125)
T PF00292_consen 33 GVRPCDISRQLRVSHGCVSKILSRYRETGSIRPGP 67 (125)
T ss_dssp T--HHHHHHHHT--HHHHHHHHHHHHHHS-SS---
T ss_pred cCCHHHHHHHHccchhHHHHHHHHHHHhcccCccc
Confidence 35799999999999999999999999999998854
No 350
>PF14330 DUF4387: Domain of unknown function (DUF4387)
Probab=25.04 E-value=85 Score=23.36 Aligned_cols=31 Identities=19% Similarity=0.547 Sum_probs=25.2
Q ss_pred eee-CHHHHHHHHhhCCCCeeechHHHHhhhccchH
Q psy1871 67 VLF-DKASYDKLLKEVPAYKLITPSVVSERLKVRGS 101 (139)
Q Consensus 67 Vl~-Dk~tydKl~KEVpk~KlITPsvlseRlkI~~S 101 (139)
++| |++.|+++.. ..++|+..+|+-|+|.-+
T Consensus 22 I~F~~~e~Y~~vk~----s~~l~~~~ia~Ly~i~~~ 53 (99)
T PF14330_consen 22 IIFKDKEAYERVKA----SGVLTPELIARLYGIDPE 53 (99)
T ss_pred EEECCHHHHHHHHH----cCccCHHHHHHHHCCCHH
Confidence 344 8999999864 568999999999998754
No 351
>PF06218 NPR2: Nitrogen permease regulator 2; InterPro: IPR009348 This family of regulators are involved in post-translational control of nitrogen permease.
Probab=24.65 E-value=1.2e+02 Score=27.70 Aligned_cols=59 Identities=17% Similarity=0.224 Sum_probs=50.1
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEeccC
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTRTT 132 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtra~ 132 (139)
-|+.||.--|-... +...||.--.+..+|.|.+||+|.==|.|.++.-=.-..||+...
T Consensus 206 lT~qkIlP~IdGvn--~V~rIa~ladvd~~Lv~~ci~hL~yYg~v~lidiFqfsNiY~~t~ 264 (428)
T PF06218_consen 206 LTMQKILPYIDGVN--HVRRIAQLADVDYELVKECIQHLLYYGCVILIDIFQFSNIYAPTP 264 (428)
T ss_pred HHHHHhhhhccCcc--HHHHHHHHHcCCHHHHHHHHHHHHhhCeeEEeeehhccceeecch
Confidence 47788888777755 568899999999999999999999999999998766677888654
No 352
>PRK05066 arginine repressor; Provisional
Probab=24.35 E-value=2.4e+02 Score=22.07 Aligned_cols=21 Identities=14% Similarity=0.352 Sum_probs=14.0
Q ss_pred HHHHHcCCeeEEeecCceEEEe
Q psy1871 108 EELLQKGLIKQVVKHHAQVIYT 129 (139)
Q Consensus 108 reL~~kGlIk~Vskh~~q~IYt 129 (139)
|+|.+=|++| |-....+.+|.
T Consensus 48 RDikeL~lvK-v~~~~G~~~Y~ 68 (156)
T PRK05066 48 RMLTKFGAVR-TRNAKMEMVYC 68 (156)
T ss_pred HHHHHcCCEE-eeCCCCCEEEE
Confidence 7888888888 33344456776
No 353
>PF05119 Terminase_4: Phage terminase, small subunit; InterPro: IPR006448 This entry is represented by Streptococcus phage 7201, Orf21. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This group of sequences describe the distinct family of phage (and integrated prophage) putative terminase small subunit sequnces. Members tend to be encoded by the gene adjacent to the phage terminase large subunit gene.
Probab=24.34 E-value=1.2e+02 Score=20.67 Aligned_cols=46 Identities=24% Similarity=0.320 Sum_probs=39.6
Q ss_pred HHHHHHHHhhCCCCeeechHHH--HhhhccchHHHHHHHHHHHHcCCe
Q psy1871 71 KASYDKLLKEVPAYKLITPSVV--SERLKVRGSLARKALEELLQKGLI 116 (139)
Q Consensus 71 k~tydKl~KEVpk~KlITPsvl--seRlkI~~SLARkaLreL~~kGlI 116 (139)
++.|++|..+.....++++..+ -++|=...+.-+.+-++|.+.|++
T Consensus 2 k~~w~~i~~~L~~~~~l~~~D~~~l~~yc~~~~~~~~~~~~l~~~G~~ 49 (100)
T PF05119_consen 2 KKEWKRIVPELKELGILSNLDVPLLERYCEAYSRYREAEKELKKEGFV 49 (100)
T ss_pred hHHHHHHHHHHHHcCCCcHhHHHHHHHHHHHHHHHHHHHHHHHHcCce
Confidence 4678889999888888888764 578888899999999999999998
No 354
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=23.28 E-value=1.5e+02 Score=27.70 Aligned_cols=47 Identities=17% Similarity=0.134 Sum_probs=34.7
Q ss_pred HHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 74 YDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 74 ydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
.++|..-.+ ..--+...|++.+++.-...+.+|+.|.+.|.+..|+.
T Consensus 495 ~~~l~~~~~-~~p~~~~~~~~~l~~~~~~~~~~l~~l~~~g~lv~l~~ 541 (614)
T PRK10512 495 WQKAEPLFG-DEPWWVRDLAKETGTDEQAMRLTLRQAAQQGIITAIVK 541 (614)
T ss_pred HHHHHHHHh-cCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 455554333 22233355888899999999999999999999988874
No 355
>PHA01623 hypothetical protein
Probab=23.13 E-value=2.3e+02 Score=18.57 Aligned_cols=39 Identities=23% Similarity=0.241 Sum_probs=27.5
Q ss_pred hhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchH-HHHHHHHHHHH
Q psy1871 62 KLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGS-LARKALEELLQ 112 (139)
Q Consensus 62 Klnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~S-LARkaLreL~~ 112 (139)
+..=.|-+|++++++|. ..|++.+++-| +-|.||+++..
T Consensus 13 ~~r~sVrldeel~~~Ld------------~y~~~~g~~rSe~IreAI~~yL~ 52 (56)
T PHA01623 13 KAVFGIYMDKDLKTRLK------------VYCAKNNLQLTQAIEEAIKEYLQ 52 (56)
T ss_pred ceeEEEEeCHHHHHHHH------------HHHHHcCCCHHHHHHHHHHHHHH
Confidence 34456889999999996 45666666543 56778887765
No 356
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=23.13 E-value=90 Score=32.78 Aligned_cols=47 Identities=19% Similarity=0.336 Sum_probs=36.8
Q ss_pred HHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeE
Q psy1871 72 ASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQ 118 (139)
Q Consensus 72 ~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~ 118 (139)
++-+=+..=.-.+==+|...++++|++-.+++..+|+.|+..|.+..
T Consensus 975 ~~~~l~~r~~~~~gp~~~~~~a~~~gl~~~~~~~~l~~l~~~g~~~~ 1021 (1490)
T PRK09751 975 PLRDLFLRYLRAHALVTAEQLAHEFSLGIAIVEEQLQQLREQGLVMN 1021 (1490)
T ss_pred HHHHHHHHHHhccCCCcHHHHHHHhCCCHHHHHHHHHHHHhCCCEEe
Confidence 33333333334445589999999999999999999999999999866
No 357
>cd04441 DEP_2_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 2 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=23.10 E-value=84 Score=22.45 Aligned_cols=24 Identities=29% Similarity=0.448 Sum_probs=19.9
Q ss_pred hHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 100 GSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 100 ~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
-.-|....+.|.+.|+|.-|...|
T Consensus 51 R~eAv~lgq~Ll~~gii~HV~~~h 74 (85)
T cd04441 51 RREAVQLCRRLLEHGIIQHVSNKH 74 (85)
T ss_pred HHHHHHHHHHHHHCCCEEecCCCC
Confidence 356888899999999999998544
No 358
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=22.73 E-value=70 Score=19.27 Aligned_cols=40 Identities=13% Similarity=0.141 Sum_probs=25.8
Q ss_pred hhhccceeeCHHHHHHHHhhCCCCeeechHHHHhhhccch
Q psy1871 61 DKLNNQVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRG 100 (139)
Q Consensus 61 dKlnn~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~ 100 (139)
..+...+=++..++.++........+=+...||+-|++..
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~ 52 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSP 52 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEH
T ss_pred HHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCH
Confidence 3444444477888888887766666666677777777654
No 359
>PRK04217 hypothetical protein; Provisional
Probab=22.35 E-value=98 Score=23.08 Aligned_cols=23 Identities=22% Similarity=0.299 Sum_probs=18.8
Q ss_pred echHHHHhhhccchHHHHHHHHH
Q psy1871 87 ITPSVVSERLKVRGSLARKALEE 109 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLre 109 (139)
+|...||++|+|+-+..+..|+.
T Consensus 59 lS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 59 LTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 38899999999998877766654
No 360
>cd04442 DEP_1_DEP6 DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in DEP6-like proteins. DEP6 proteins contain two DEP and a PDZ domain. Their function is unknown.
Probab=22.25 E-value=94 Score=21.97 Aligned_cols=25 Identities=28% Similarity=0.461 Sum_probs=20.6
Q ss_pred chHHHHHHHHHHHHcCCeeEEeecC
Q psy1871 99 RGSLARKALEELLQKGLIKQVVKHH 123 (139)
Q Consensus 99 ~~SLARkaLreL~~kGlIk~Vskh~ 123 (139)
+-.=|-.+-+.|.+.|+|..|...|
T Consensus 46 sR~eAv~lgq~Ll~~gvi~HV~~~h 70 (82)
T cd04442 46 DRETAIKIMQKLLDHSIIHHVCDEH 70 (82)
T ss_pred CHHHHHHHHHHHHHCCCEEeccCCc
Confidence 4456888899999999999997654
No 361
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=22.05 E-value=1.1e+02 Score=19.03 Aligned_cols=26 Identities=12% Similarity=0.281 Sum_probs=21.4
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHc
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQK 113 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~k 113 (139)
|+..||+.++|+.+--+.-++.+..+
T Consensus 20 ~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 20 SNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp -HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred CcchhHHhcCcchhhHHHHHHHHHHH
Confidence 67899999999999988888877654
No 362
>PF09940 DUF2172: Domain of unknown function (DUF2172); InterPro: IPR012353 The proteins in this entry are encoded by genes located in polysaccharide biosynthesis gene clusters, and are therefore believed to be involved in polysaccharide biosynthesis. The ste gene cluster (for Streptomyces eps) is involved in exopolysaccharide EPS 139A biosynthesis in Streptomyces sp. 139 []. Members of this group exhibit distant sequence similarity to aminopeptidases (IPR007484 from INTERPRO, MEROPS peptidase family M28).; PDB: 3K9T_A.
Probab=21.71 E-value=1.1e+02 Score=27.90 Aligned_cols=30 Identities=27% Similarity=0.326 Sum_probs=24.5
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCee
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIK 117 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk 117 (139)
+.-.||||.++....-..+++.|.+.|||+
T Consensus 357 slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 357 SLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp EHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 446799999999999999999999999986
No 363
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=21.61 E-value=84 Score=24.36 Aligned_cols=46 Identities=20% Similarity=0.260 Sum_probs=30.8
Q ss_pred CHHHHHHHHhhCCCCee--echHHHHhhhccchHHHHHHHHHHHHcCCeeEE
Q psy1871 70 DKASYDKLLKEVPAYKL--ITPSVVSERLKVRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 70 Dk~tydKl~KEVpk~Kl--ITPsvlseRlkI~~SLARkaLreL~~kGlIk~V 119 (139)
+++.|+++..=+-...- -|.+.|||.++|...+-.+ +..+|=|...
T Consensus 28 ~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~----~IreGRL~~~ 75 (137)
T TIGR03826 28 EEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILK----FIREGRLQLK 75 (137)
T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHH----HHHcCCeecc
Confidence 35667776655544433 6889999999999877444 4455665543
No 364
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=21.56 E-value=1.1e+02 Score=16.12 Aligned_cols=16 Identities=19% Similarity=0.393 Sum_probs=13.1
Q ss_pred hHHHHHHHHHHHHcCC
Q psy1871 100 GSLARKALEELLQKGL 115 (139)
Q Consensus 100 ~SLARkaLreL~~kGl 115 (139)
...|..+++++.+.|+
T Consensus 17 ~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 17 PDAALQLFDEMKEQGV 32 (34)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 4568899999999985
No 365
>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]
Probab=21.45 E-value=1.1e+02 Score=23.98 Aligned_cols=27 Identities=26% Similarity=0.315 Sum_probs=22.3
Q ss_pred hHHHHHHHHHHHHcCCeeEEeecCceE
Q psy1871 100 GSLARKALEELLQKGLIKQVVKHHAQV 126 (139)
Q Consensus 100 ~SLARkaLreL~~kGlIk~Vskh~~q~ 126 (139)
-+|..+++++|.++|+-.-+.+|+...
T Consensus 16 TTLie~lv~~L~~~G~rVa~iKH~hh~ 42 (161)
T COG1763 16 TTLIEKLVRKLKARGYRVATVKHAHHD 42 (161)
T ss_pred hhHHHHHHHHHHhCCcEEEEEEecCCC
Confidence 368899999999999988887776554
No 366
>PF12627 PolyA_pol_RNAbd: Probable RNA and SrmB- binding site of polymerase A; PDB: 1OU5_B 3H38_A 3H3A_B 3H39_B 3H37_A 3AQN_A 3AQK_A 3AQM_B 3AQL_B 1MIY_A ....
Probab=21.42 E-value=1.1e+02 Score=19.24 Aligned_cols=52 Identities=13% Similarity=0.240 Sum_probs=39.9
Q ss_pred eeCHHHHHHHHhhCCCCeeechHHHHhhhc--cchHHHHHHHHHHHHcCCeeEE
Q psy1871 68 LFDKASYDKLLKEVPAYKLITPSVVSERLK--VRGSLARKALEELLQKGLIKQV 119 (139)
Q Consensus 68 l~Dk~tydKl~KEVpk~KlITPsvlseRlk--I~~SLARkaLreL~~kGlIk~V 119 (139)
-+|++|.+-|.+-++...-|++.-|.+-+. +.++-+..+++.|.+-|++..+
T Consensus 3 ~ie~~t~~ai~~~~~~L~~is~ERi~~El~kil~~~~~~~~~~~l~~~gll~~i 56 (64)
T PF12627_consen 3 KIEPETEEAIKENAELLSKISKERIREELEKILSSPNPSRAFKLLDELGLLEYI 56 (64)
T ss_dssp EE-HHHHHHHHHHGGGGGGS-HHHHHHHHHHHHTSTTHHHHHHHHHHTTCHHHH
T ss_pred ccCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHcCCCHHHHHHHHHHcCCHHHH
Confidence 479999999999999888888887777664 3566778899999998887543
No 367
>PF03397 Rhabdo_matrix: Rhabdovirus matrix protein; InterPro: IPR005060 The matrix (M) proteins of Rabies virus (RV) plays a key role in both assembly and budding of progeny virions. A PPPY motif (PY motif or late-budding domain) is conserved in the M proteins. These PY motifs are important for virus budding and for mediating interactions with specific cellular proteins containing WW domains.
Probab=21.33 E-value=46 Score=26.94 Aligned_cols=20 Identities=25% Similarity=0.343 Sum_probs=19.0
Q ss_pred chHHHHhhhccchHHHHHHH
Q psy1871 88 TPSVVSERLKVRGSLARKAL 107 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaL 107 (139)
+|+++-|++...++||++||
T Consensus 34 ~P~~l~eKi~~aM~LA~AIl 53 (168)
T PF03397_consen 34 RPTNLTEKIYYAMKLAAAIL 53 (168)
T ss_pred CCCchhhHHHHHHHHHHHHH
Confidence 69999999999999999997
No 368
>PRK14997 LysR family transcriptional regulator; Provisional
Probab=21.06 E-value=1.7e+02 Score=23.18 Aligned_cols=43 Identities=12% Similarity=0.067 Sum_probs=37.4
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+-+.-|++|+|+=|--=+.|++||++==..+..++++...-|.
T Consensus 18 s~s~AA~~L~isQpavS~~I~~LE~~lG~~LF~R~~r~~~lT~ 60 (301)
T PRK14997 18 GFAAAGRALDEPKSKLSRRIAQLEERLGVRLIQRTTRQFNVTE 60 (301)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHhCCEeeeeccCcceEcH
Confidence 5577899999999999999999999988889988888877664
No 369
>TIGR00475 selB selenocysteine-specific elongation factor SelB. In prokaryotes, the incorporation of selenocysteine as the 21st amino acid, encoded by TGA, requires several elements: SelC is the tRNA itself, SelD acts as a donor of reduced selenium, SelA modifies a serine residue on SelC into selenocysteine, and SelB is a selenocysteine-specific translation elongation factor. 3-prime or 5-prime non-coding elements of mRNA have been found as probable structures for directing selenocysteine incorporation. This model describes the elongation factor SelB, a close homolog rf EF-Tu. It may function by replacing EF-Tu. A C-terminal domain not found in EF-Tu is in all SelB sequences in the seed alignment except that from Methanococcus jannaschii. This model does not find an equivalent protein for eukaryotes.
Probab=20.99 E-value=1.8e+02 Score=26.98 Aligned_cols=48 Identities=15% Similarity=0.055 Sum_probs=38.5
Q ss_pred HHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHHHcCCeeEEee
Q psy1871 73 SYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELLQKGLIKQVVK 121 (139)
Q Consensus 73 tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~~kGlIk~Vsk 121 (139)
..++|..... +..-+...+++.+++.-...+.+|+.|...|.+..+..
T Consensus 476 ~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~ 523 (581)
T TIGR00475 476 IWQKIKGTFG-TKGAWVREFAEEVNGDEKVMLKRVRKAGHRGGETLIVK 523 (581)
T ss_pred HHHHHHHHHh-cCCCCHHHHHhhhCCCHHHHHHHHHHHHhCCCEEEEeC
Confidence 3555555443 55567788899999999999999999999999888875
No 370
>PRK13239 alkylmercury lyase; Provisional
Probab=20.95 E-value=1.1e+02 Score=25.24 Aligned_cols=41 Identities=12% Similarity=0.075 Sum_probs=35.7
Q ss_pred HHHHHHHHhhCCCCeeechHHHHhhhccchHHHHHHHHHHH
Q psy1871 71 KASYDKLLKEVPAYKLITPSVVSERLKVRGSLARKALEELL 111 (139)
Q Consensus 71 k~tydKl~KEVpk~KlITPsvlseRlkI~~SLARkaLreL~ 111 (139)
...+--|+.++-+=+=+|++.|++++++...-++++|++|.
T Consensus 21 ~~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 21 ATLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred hHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 34666778888888899999999999999999999999974
No 371
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=20.82 E-value=1.3e+02 Score=19.62 Aligned_cols=27 Identities=22% Similarity=0.192 Sum_probs=21.3
Q ss_pred eechHHHHhhhccchHHHHHHHHHHHH
Q psy1871 86 LITPSVVSERLKVRGSLARKALEELLQ 112 (139)
Q Consensus 86 lITPsvlseRlkI~~SLARkaLreL~~ 112 (139)
=+|-..||+.|+|.-|-.-.-||.-++
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 478899999999999887766665544
No 372
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=20.78 E-value=1.2e+02 Score=20.41 Aligned_cols=26 Identities=12% Similarity=0.194 Sum_probs=22.1
Q ss_pred echHHHHhhhccchHHHHHHHHHHHH
Q psy1871 87 ITPSVVSERLKVRGSLARKALEELLQ 112 (139)
Q Consensus 87 ITPsvlseRlkI~~SLARkaLreL~~ 112 (139)
.|...||+.|+++-+-.++.+.....
T Consensus 127 ~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 127 LSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 48899999999999999888877654
No 373
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=20.63 E-value=1.9e+02 Score=23.29 Aligned_cols=43 Identities=12% Similarity=0.152 Sum_probs=37.4
Q ss_pred chHHHHhhhccchHHHHHHHHHHHHcCCeeEEeecCceEEEec
Q psy1871 88 TPSVVSERLKVRGSLARKALEELLQKGLIKQVVKHHAQVIYTR 130 (139)
Q Consensus 88 TPsvlseRlkI~~SLARkaLreL~~kGlIk~Vskh~~q~IYtr 130 (139)
+-+..|++|+|+=|-.-+.|+.||+.==..+..++++...-|.
T Consensus 23 s~s~AA~~L~iSQpavS~~I~~LE~~lg~~LF~R~~r~~~lT~ 65 (312)
T PRK10341 23 SIGSAAKELGLTQPAVSKIINDIEDYFGVELIVRKNTGVTLTP 65 (312)
T ss_pred CHHHHHHHhCCChHHHHHHHHHHHHHhCCeEEEEcCCCceECh
Confidence 4577899999999999999999999988899988888766664
No 374
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=20.41 E-value=77 Score=21.62 Aligned_cols=28 Identities=36% Similarity=0.405 Sum_probs=21.9
Q ss_pred HHHhhhccchHHHHHHHHHHHHcCCeeEEeec
Q psy1871 91 VVSERLKVRGSLARKALEELLQKGLIKQVVKH 122 (139)
Q Consensus 91 vlseRlkI~~SLARkaLreL~~kGlIk~Vskh 122 (139)
-|-.+|+ |.|..+|||...|+|-=|.+.
T Consensus 32 gvir~fg----l~R~~FRe~A~~G~ipGv~Ka 59 (61)
T PRK08061 32 SVYRKFG----LCRICFRELAYKGQIPGVKKA 59 (61)
T ss_pred ceeccCC----ccHHHHHHHHHcCcCCCeeec
Confidence 3445555 899999999999999767654
No 375
>PHA01748 hypothetical protein
Probab=20.38 E-value=2.6e+02 Score=18.42 Aligned_cols=36 Identities=17% Similarity=0.205 Sum_probs=24.0
Q ss_pred ceeeCHHHHHHHHhhCCCCeeechHHHHhhhccchH-HHHHHHHHHHHc
Q psy1871 66 QVLFDKASYDKLLKEVPAYKLITPSVVSERLKVRGS-LARKALEELLQK 113 (139)
Q Consensus 66 ~Vl~Dk~tydKl~KEVpk~KlITPsvlseRlkI~~S-LARkaLreL~~k 113 (139)
.|-+|++++++|- .++++.+++-| +-|.+|+++...
T Consensus 6 SvrLp~el~~eld------------~~a~~~g~~RSE~Ir~Ai~~~~~~ 42 (60)
T PHA01748 6 TFKIEEDLLELLD------------RYAIKHGLNRSEAIRKAIEKMVKD 42 (60)
T ss_pred EEECCHHHHHHHH------------HHHHHhCCCHHHHHHHHHHHHHHH
Confidence 3567888888774 46777777644 567777776644
No 376
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=20.32 E-value=1.7e+02 Score=18.55 Aligned_cols=28 Identities=36% Similarity=0.482 Sum_probs=16.4
Q ss_pred HHHHhhhccchHHHH----HHHHHHHHcCCee
Q psy1871 90 SVVSERLKVRGSLAR----KALEELLQKGLIK 117 (139)
Q Consensus 90 svlseRlkI~~SLAR----kaLreL~~kGlIk 117 (139)
..|+++|.+.-.-++ ..|.+|.+.|+|.
T Consensus 37 ~~l~~~y~~~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 37 DALAEEYDVDPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp HHHHHHTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHHHCcCcC
Confidence 456777877777555 3577888899873
Done!