Query 033932
Match_columns 108
No_of_seqs 104 out of 216
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 07:56:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033932.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033932hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1767 40S ribosomal protein 100.0 2.7E-49 5.8E-54 279.4 6.8 106 1-107 2-107 (110)
2 PF03297 Ribosomal_S25: S25 ri 100.0 2.6E-49 5.7E-54 278.8 6.5 105 1-106 1-105 (105)
3 COG4901 Ribosomal protein S25 100.0 1.3E-37 2.8E-42 219.5 4.6 106 1-107 1-106 (107)
4 PRK09334 30S ribosomal protein 100.0 4.6E-36 1E-40 205.5 8.4 81 25-105 6-86 (86)
5 PF13412 HTH_24: Winged helix- 97.2 0.00034 7.4E-09 41.4 2.9 42 50-91 7-48 (48)
6 PF00392 GntR: Bacterial regul 97.1 0.0031 6.7E-08 39.4 6.3 50 46-95 4-59 (64)
7 PF08220 HTH_DeoR: DeoR-like h 97.0 0.0012 2.5E-08 41.2 4.0 46 49-94 3-48 (57)
8 smart00345 HTH_GNTR helix_turn 97.0 0.0036 7.7E-08 37.0 5.7 38 57-94 17-54 (60)
9 cd07377 WHTH_GntR Winged helix 96.9 0.0039 8.5E-08 37.5 5.7 49 45-93 4-58 (66)
10 PF14502 HTH_41: Helix-turn-he 96.9 0.0019 4.1E-08 40.3 4.1 41 57-97 3-43 (48)
11 PF01978 TrmB: Sugar-specific 96.8 0.0047 1E-07 38.8 5.2 44 59-104 21-64 (68)
12 smart00418 HTH_ARSR helix_turn 96.6 0.007 1.5E-07 35.4 5.0 44 59-103 9-52 (66)
13 PF04703 FaeA: FaeA-like prote 96.6 0.0045 9.8E-08 40.0 4.3 38 60-97 15-52 (62)
14 PF08222 HTH_CodY: CodY helix- 96.5 0.0096 2.1E-07 38.8 5.3 46 60-106 4-49 (61)
15 PF02082 Rrf2: Transcriptional 96.5 0.013 2.7E-07 38.4 6.0 51 54-104 19-69 (83)
16 PF12802 MarR_2: MarR family; 96.3 0.011 2.3E-07 35.8 4.4 34 61-94 22-55 (62)
17 TIGR02018 his_ut_repres histid 96.2 0.017 3.6E-07 43.7 6.1 39 56-94 21-59 (230)
18 cd00090 HTH_ARSR Arsenical Res 96.1 0.018 4E-07 34.3 5.0 42 61-103 21-62 (78)
19 PF13463 HTH_27: Winged helix 96.1 0.019 4E-07 35.3 5.1 47 57-103 15-63 (68)
20 TIGR02325 C_P_lyase_phnF phosp 96.1 0.015 3.3E-07 43.6 5.5 40 56-95 28-67 (238)
21 TIGR02404 trehalos_R_Bsub treh 96.1 0.016 3.4E-07 43.8 5.5 40 56-95 20-59 (233)
22 PRK13509 transcriptional repre 96.1 0.011 2.3E-07 46.3 4.6 50 45-94 4-53 (251)
23 smart00419 HTH_CRP helix_turn_ 96.0 0.013 2.8E-07 33.5 3.8 33 61-93 9-41 (48)
24 PRK09764 DNA-binding transcrip 96.0 0.022 4.7E-07 43.5 5.9 40 56-95 25-64 (240)
25 PRK11534 DNA-binding transcrip 96.0 0.015 3.3E-07 43.6 4.9 54 43-96 8-66 (224)
26 TIGR02787 codY_Gpos GTP-sensin 95.9 0.024 5.1E-07 45.8 5.9 59 36-94 173-232 (251)
27 smart00420 HTH_DEOR helix_turn 95.9 0.044 9.6E-07 31.4 5.6 46 46-95 4-49 (53)
28 PRK10906 DNA-binding transcrip 95.8 0.015 3.3E-07 45.5 4.7 48 46-93 5-52 (252)
29 PRK10225 DNA-binding transcrip 95.8 0.027 5.8E-07 43.1 5.9 51 45-95 12-68 (257)
30 PRK03837 transcriptional regul 95.8 0.019 4.1E-07 43.2 4.9 51 45-95 16-72 (241)
31 PF09012 FeoC: FeoC like trans 95.8 0.0062 1.3E-07 38.8 1.9 47 51-97 5-51 (69)
32 PF01325 Fe_dep_repress: Iron 95.8 0.016 3.5E-07 36.6 3.7 37 57-93 19-55 (60)
33 cd00092 HTH_CRP helix_turn_hel 95.7 0.026 5.6E-07 34.3 4.5 37 58-94 23-59 (67)
34 PHA02943 hypothetical protein; 95.7 0.031 6.6E-07 42.7 5.7 54 49-103 14-67 (165)
35 PRK11402 DNA-binding transcrip 95.7 0.021 4.5E-07 43.5 4.7 39 56-94 29-67 (241)
36 PRK14165 winged helix-turn-hel 95.6 0.029 6.3E-07 43.9 5.2 50 54-103 15-64 (217)
37 PRK14999 histidine utilization 95.5 0.028 6.1E-07 42.8 4.8 39 56-94 32-70 (241)
38 PF01047 MarR: MarR family; I 95.4 0.028 6.1E-07 33.9 3.8 33 61-93 18-50 (59)
39 PRK10434 srlR DNA-bindng trans 95.4 0.023 5E-07 44.5 4.2 48 46-93 5-52 (256)
40 PF09339 HTH_IclR: IclR helix- 95.4 0.033 7.2E-07 33.5 4.0 32 61-92 19-50 (52)
41 PRK10421 DNA-binding transcrip 95.4 0.048 1E-06 41.7 5.8 50 45-94 5-60 (253)
42 smart00843 Ftsk_gamma This dom 95.4 0.02 4.3E-07 37.3 3.1 54 44-97 3-56 (63)
43 TIGR03338 phnR_burk phosphonat 95.4 0.041 8.9E-07 40.7 5.2 49 45-94 14-68 (212)
44 PF09397 Ftsk_gamma: Ftsk gamm 95.4 0.013 2.7E-07 38.3 2.1 58 45-102 5-62 (65)
45 smart00550 Zalpha Z-DNA-bindin 95.3 0.055 1.2E-06 34.6 5.0 34 61-94 23-56 (68)
46 PF12840 HTH_20: Helix-turn-he 95.3 0.024 5.1E-07 35.1 3.1 50 46-95 10-59 (61)
47 PRK11014 transcriptional repre 95.2 0.053 1.2E-06 38.6 5.2 45 55-99 20-64 (141)
48 COG1349 GlpR Transcriptional r 95.2 0.027 5.9E-07 44.1 4.1 49 46-94 5-53 (253)
49 PRK04984 fatty acid metabolism 95.2 0.039 8.4E-07 41.6 4.7 50 45-94 10-65 (239)
50 COG2188 PhnF Transcriptional r 95.2 0.038 8.2E-07 42.5 4.7 41 56-96 27-67 (236)
51 PRK09990 DNA-binding transcrip 95.2 0.066 1.4E-06 40.8 5.9 52 44-95 9-66 (251)
52 COG1522 Lrp Transcriptional re 95.1 0.053 1.1E-06 38.1 4.9 47 43-93 9-55 (154)
53 TIGR02812 fadR_gamma fatty aci 95.0 0.049 1.1E-06 41.1 4.8 51 45-95 9-65 (235)
54 TIGR02337 HpaR homoprotocatech 95.0 0.05 1.1E-06 37.2 4.5 52 51-102 33-86 (118)
55 TIGR03337 phnR transcriptional 95.0 0.075 1.6E-06 39.7 5.7 40 56-95 21-60 (231)
56 TIGR02702 SufR_cyano iron-sulf 95.0 0.048 1E-06 41.0 4.6 43 61-103 16-62 (203)
57 PRK11523 DNA-binding transcrip 94.9 0.05 1.1E-06 41.6 4.7 52 44-95 10-67 (253)
58 PF13730 HTH_36: Helix-turn-he 94.9 0.036 7.8E-07 33.2 3.1 31 60-90 25-55 (55)
59 PRK09802 DNA-binding transcrip 94.8 0.042 9.2E-07 43.4 4.2 49 46-94 17-65 (269)
60 PRK10079 phosphonate metabolis 94.7 0.051 1.1E-06 41.4 4.3 50 46-95 20-70 (241)
61 COG3355 Predicted transcriptio 94.7 0.12 2.7E-06 37.7 6.0 58 43-104 28-90 (126)
62 PRK09464 pdhR transcriptional 94.7 0.068 1.5E-06 40.8 4.9 52 44-95 12-69 (254)
63 PF01726 LexA_DNA_bind: LexA D 94.6 0.067 1.4E-06 34.4 4.1 35 62-96 27-62 (65)
64 smart00346 HTH_ICLR helix_turn 94.4 0.095 2.1E-06 33.7 4.4 34 60-93 20-53 (91)
65 TIGR02010 IscR iron-sulfur clu 94.3 0.097 2.1E-06 37.1 4.6 41 57-97 22-62 (135)
66 PRK11414 colanic acid/biofilm 94.3 0.068 1.5E-06 40.0 4.0 49 45-94 14-68 (221)
67 PF04157 EAP30: EAP30/Vps36 fa 94.2 0.11 2.4E-06 39.8 5.1 46 46-91 174-221 (223)
68 TIGR00738 rrf2_super rrf2 fami 94.0 0.089 1.9E-06 36.4 3.9 38 56-93 21-58 (132)
69 TIGR01610 phage_O_Nterm phage 93.8 0.13 2.8E-06 34.8 4.3 37 57-93 44-80 (95)
70 TIGR02944 suf_reg_Xantho FeS a 93.7 0.092 2E-06 36.6 3.5 35 59-93 24-58 (130)
71 PRK11512 DNA-binding transcrip 93.6 0.14 3.1E-06 36.1 4.5 36 58-93 52-87 (144)
72 PRK03573 transcriptional regul 93.6 0.16 3.4E-06 35.7 4.7 41 60-100 46-88 (144)
73 COG4465 CodY Pleiotropic trans 93.6 0.14 3E-06 41.3 4.8 54 40-93 183-237 (261)
74 PRK10411 DNA-binding transcrip 93.6 0.14 3.1E-06 39.8 4.7 46 48-93 6-51 (240)
75 PRK10870 transcriptional repre 93.5 0.14 3E-06 38.1 4.4 35 59-93 70-104 (176)
76 PRK04424 fatty acid biosynthes 93.5 0.046 1E-06 41.1 1.8 48 46-93 7-54 (185)
77 PF09756 DDRGK: DDRGK domain; 93.5 0.11 2.4E-06 40.1 3.9 58 47-104 100-157 (188)
78 smart00347 HTH_MARR helix_turn 93.4 0.2 4.4E-06 31.8 4.6 34 60-93 24-57 (101)
79 smart00344 HTH_ASNC helix_turn 93.3 0.2 4.3E-06 33.4 4.5 44 44-91 5-48 (108)
80 PRK04158 transcriptional repre 93.3 0.11 2.4E-06 42.1 3.7 61 33-93 173-234 (256)
81 PF13545 HTH_Crp_2: Crp-like h 93.0 0.24 5.2E-06 30.9 4.4 32 60-91 28-59 (76)
82 smart00529 HTH_DTXR Helix-turn 92.9 0.15 3.2E-06 33.3 3.4 32 63-94 2-33 (96)
83 TIGR01884 cas_HTH CRISPR locus 92.9 0.19 4.1E-06 37.8 4.3 46 50-95 147-192 (203)
84 TIGR01889 Staph_reg_Sar staphy 92.8 0.26 5.7E-06 33.6 4.6 35 59-93 42-76 (109)
85 PF14947 HTH_45: Winged helix- 92.7 0.24 5.3E-06 32.2 4.1 44 48-92 8-51 (77)
86 PRK03902 manganese transport t 92.6 0.27 5.8E-06 34.9 4.7 36 58-93 20-55 (142)
87 cd04761 HTH_MerR-SF Helix-Turn 92.4 0.17 3.7E-06 29.1 2.9 40 61-104 1-40 (49)
88 COG1959 Predicted transcriptio 92.3 0.25 5.4E-06 36.2 4.2 46 58-103 23-68 (150)
89 PF01022 HTH_5: Bacterial regu 92.1 0.31 6.8E-06 28.7 3.8 33 59-91 14-46 (47)
90 PRK11920 rirA iron-responsive 92.0 0.31 6.8E-06 35.6 4.5 41 59-99 23-63 (153)
91 PF08279 HTH_11: HTH domain; 91.9 0.61 1.3E-05 27.7 5.0 28 61-88 16-43 (55)
92 PF00325 Crp: Bacterial regula 91.9 0.31 6.7E-06 27.8 3.4 30 61-90 3-32 (32)
93 PRK11050 manganese transport r 91.9 0.32 6.9E-06 35.4 4.3 34 59-92 50-83 (152)
94 COG1802 GntR Transcriptional r 91.8 0.27 5.9E-06 37.1 4.1 55 40-94 14-73 (230)
95 COG1846 MarR Transcriptional r 91.8 0.4 8.7E-06 31.2 4.4 30 64-93 40-69 (126)
96 PF10007 DUF2250: Uncharacteri 91.6 0.25 5.4E-06 34.2 3.4 47 50-96 11-57 (92)
97 COG1725 Predicted transcriptio 91.6 0.41 9E-06 34.8 4.7 46 56-104 31-76 (125)
98 PF00376 MerR: MerR family reg 91.5 0.27 5.9E-06 28.5 3.0 37 62-102 1-38 (38)
99 smart00422 HTH_MERR helix_turn 91.5 0.19 4.2E-06 30.9 2.5 40 61-104 1-41 (70)
100 cd07153 Fur_like Ferric uptake 91.5 0.49 1.1E-05 31.9 4.7 45 59-103 15-64 (116)
101 COG1321 TroR Mn-dependent tran 91.4 0.49 1.1E-05 35.0 5.0 49 46-94 10-58 (154)
102 cd01105 HTH_GlnR-like Helix-Tu 91.4 0.2 4.3E-06 33.4 2.6 41 60-104 1-42 (88)
103 TIGR00122 birA_repr_reg BirA b 91.3 0.61 1.3E-05 29.2 4.7 35 60-94 13-47 (69)
104 COG2512 Predicted membrane-ass 91.2 0.62 1.3E-05 37.3 5.7 80 25-104 175-254 (258)
105 PRK09954 putative kinase; Prov 91.1 0.25 5.4E-06 39.5 3.4 42 50-91 7-48 (362)
106 PRK06266 transcription initiat 91.0 0.25 5.4E-06 37.4 3.1 50 44-93 20-69 (178)
107 TIGR00498 lexA SOS regulatory 91.0 0.34 7.4E-06 35.9 3.8 53 44-96 8-62 (199)
108 PRK10857 DNA-binding transcrip 90.9 0.47 1E-05 35.3 4.5 42 56-97 21-62 (164)
109 cd04766 HTH_HspR Helix-Turn-He 90.9 0.28 6E-06 32.6 3.0 41 60-104 1-41 (91)
110 cd01279 HTH_HspR-like Helix-Tu 90.8 0.26 5.6E-06 33.5 2.8 41 60-104 1-41 (98)
111 PF05158 RNA_pol_Rpc34: RNA po 90.8 0.49 1.1E-05 38.9 4.9 67 36-104 78-146 (327)
112 PRK15481 transcriptional regul 90.7 0.43 9.3E-06 38.9 4.4 50 45-94 8-63 (431)
113 PF01475 FUR: Ferric uptake re 90.6 1.1 2.3E-05 30.7 5.8 54 51-106 16-74 (120)
114 PF08784 RPA_C: Replication pr 90.5 0.39 8.5E-06 32.3 3.5 33 58-90 63-95 (102)
115 PRK11169 leucine-responsive tr 90.2 0.61 1.3E-05 34.0 4.5 43 50-92 18-60 (164)
116 TIGR02698 CopY_TcrY copper tra 90.2 0.74 1.6E-05 32.8 4.8 44 61-105 19-66 (130)
117 PRK13777 transcriptional regul 90.0 0.53 1.1E-05 35.9 4.2 36 58-93 57-92 (185)
118 cd04789 HTH_Cfa Helix-Turn-Hel 89.6 0.31 6.8E-06 33.2 2.4 40 61-104 2-41 (102)
119 cd04775 HTH_Cfa-like Helix-Tur 89.4 0.38 8.2E-06 32.8 2.7 40 61-104 2-41 (102)
120 PRK11179 DNA-binding transcrip 89.0 0.74 1.6E-05 33.1 4.2 46 43-92 10-55 (153)
121 PRK11753 DNA-binding transcrip 89.0 0.88 1.9E-05 32.9 4.5 41 60-102 168-208 (211)
122 COG0789 SoxR Predicted transcr 88.9 0.39 8.4E-06 32.7 2.5 41 61-105 1-42 (124)
123 COG2186 FadR Transcriptional r 88.9 0.78 1.7E-05 35.6 4.4 57 45-104 13-75 (241)
124 cd04770 HTH_HMRTR Helix-Turn-H 88.7 0.32 7E-06 33.7 2.0 40 61-104 1-41 (123)
125 cd04768 HTH_BmrR-like Helix-Tu 88.7 0.43 9.4E-06 32.1 2.6 40 61-104 1-41 (96)
126 PRK15090 DNA-binding transcrip 88.6 1.1 2.4E-05 34.5 5.2 36 60-95 28-63 (257)
127 cd04767 HTH_HspR-like_MBC Heli 88.1 0.52 1.1E-05 33.9 2.8 40 60-104 1-40 (120)
128 PRK09834 DNA-binding transcrip 88.1 1.1 2.3E-05 34.9 4.7 36 61-96 27-62 (263)
129 PF03965 Penicillinase_R: Peni 87.8 1.8 3.9E-05 29.7 5.3 45 61-106 18-66 (115)
130 PRK15002 redox-sensitivie tran 87.8 0.58 1.3E-05 34.7 3.0 42 59-104 10-51 (154)
131 PF13411 MerR_1: MerR HTH fami 87.7 0.66 1.4E-05 28.5 2.8 40 61-104 1-40 (69)
132 PF12728 HTH_17: Helix-turn-he 87.6 0.77 1.7E-05 27.0 2.9 40 60-104 1-40 (51)
133 TIGR02054 MerD mercuric resist 87.6 0.49 1.1E-05 33.8 2.4 43 58-104 1-44 (120)
134 cd04769 HTH_MerR2 Helix-Turn-H 87.6 0.6 1.3E-05 32.4 2.8 39 62-104 2-40 (116)
135 PRK09462 fur ferric uptake reg 87.5 1.4 3E-05 31.6 4.7 43 61-103 34-81 (148)
136 PF13601 HTH_34: Winged helix 87.4 2.2 4.7E-05 28.1 5.3 34 60-93 14-47 (80)
137 PF05732 RepL: Firmicute plasm 87.1 1.2 2.7E-05 33.2 4.4 37 57-93 72-108 (165)
138 cd04781 HTH_MerR-like_sg6 Heli 87.1 0.6 1.3E-05 32.5 2.6 39 62-104 2-40 (120)
139 COG0735 Fur Fe2+/Zn2+ uptake r 87.1 1.7 3.6E-05 31.6 5.0 45 45-103 40-84 (145)
140 PRK11886 bifunctional biotin-- 87.0 1.3 2.7E-05 35.4 4.7 42 51-92 9-51 (319)
141 PRK12423 LexA repressor; Provi 86.8 1.1 2.3E-05 33.9 4.0 49 45-93 9-59 (202)
142 PRK09333 30S ribosomal protein 86.6 0.98 2.1E-05 34.0 3.6 34 61-94 68-115 (150)
143 TIGR01764 excise DNA binding d 86.5 1 2.2E-05 25.3 2.9 40 60-104 1-40 (49)
144 cd04762 HTH_MerR-trunc Helix-T 86.4 0.72 1.6E-05 25.7 2.2 40 61-104 1-40 (49)
145 cd01282 HTH_MerR-like_sg3 Heli 86.2 0.7 1.5E-05 31.9 2.5 39 62-104 2-40 (112)
146 PRK13918 CRP/FNR family transc 85.8 1.7 3.8E-05 31.2 4.5 32 60-91 149-180 (202)
147 cd01107 HTH_BmrR Helix-Turn-He 85.7 0.67 1.5E-05 31.8 2.2 39 62-104 2-42 (108)
148 PRK05472 redox-sensing transcr 85.6 1.3 2.8E-05 33.4 3.9 53 37-89 7-61 (213)
149 TIGR00373 conserved hypothetic 85.5 2.2 4.8E-05 31.5 5.0 42 50-91 18-59 (158)
150 cd04774 HTH_YfmP Helix-Turn-He 85.4 0.98 2.1E-05 30.6 2.9 39 62-104 2-40 (96)
151 cd00592 HTH_MerR-like Helix-Tu 85.4 0.73 1.6E-05 30.5 2.2 40 61-104 1-40 (100)
152 PRK13749 transcriptional regul 85.4 0.65 1.4E-05 33.3 2.1 43 58-104 1-44 (121)
153 PF05331 DUF742: Protein of un 85.1 0.85 1.8E-05 32.7 2.6 34 60-93 55-88 (114)
154 PRK11569 transcriptional repre 84.8 1.7 3.7E-05 34.0 4.4 35 60-94 43-77 (274)
155 PRK13752 putative transcriptio 84.7 1 2.2E-05 32.8 2.9 46 56-105 3-49 (144)
156 PRK00215 LexA repressor; Valid 84.6 1.7 3.7E-05 32.3 4.1 39 61-99 24-63 (205)
157 TIGR01950 SoxR redox-sensitive 84.1 1.2 2.5E-05 32.4 3.0 40 61-104 2-41 (142)
158 cd04782 HTH_BltR Helix-Turn-He 84.1 0.85 1.8E-05 30.8 2.1 40 61-104 1-41 (97)
159 cd04787 HTH_HMRTR_unk Helix-Tu 84.0 1 2.2E-05 32.0 2.6 39 62-104 2-41 (133)
160 cd04783 HTH_MerR1 Helix-Turn-H 83.8 1 2.2E-05 31.5 2.5 40 61-104 1-41 (126)
161 PF01090 Ribosomal_S19e: Ribos 83.7 1.6 3.4E-05 32.4 3.6 27 72-98 92-118 (139)
162 cd01110 HTH_SoxR Helix-Turn-He 83.5 1.3 2.7E-05 32.0 2.9 40 61-104 2-41 (139)
163 PF02002 TFIIE_alpha: TFIIE al 83.4 0.83 1.8E-05 30.9 1.8 35 59-93 26-60 (105)
164 cd04772 HTH_TioE_rpt1 First He 83.4 1.2 2.5E-05 30.3 2.5 39 62-104 2-41 (99)
165 TIGR02044 CueR Cu(I)-responsiv 83.3 1.1 2.3E-05 31.5 2.4 39 62-104 2-41 (127)
166 COG1414 IclR Transcriptional r 83.2 2.2 4.8E-05 33.2 4.4 36 61-96 20-55 (246)
167 cd04777 HTH_MerR-like_sg1 Heli 83.2 1 2.3E-05 30.6 2.3 39 61-104 1-39 (107)
168 PF12793 SgrR_N: Sugar transpo 83.1 4.1 8.9E-05 28.8 5.3 48 46-93 4-52 (115)
169 PRK10163 DNA-binding transcrip 83.0 2.4 5.2E-05 33.2 4.5 35 59-93 39-73 (271)
170 COG1733 Predicted transcriptio 82.9 2 4.4E-05 30.5 3.7 35 47-95 38-72 (120)
171 TIGR02431 pcaR_pcaU beta-ketoa 82.7 1.7 3.7E-05 33.2 3.5 33 60-92 24-56 (248)
172 COG2390 DeoR Transcriptional r 82.6 1.9 4.2E-05 35.6 4.0 37 61-97 27-63 (321)
173 PRK06474 hypothetical protein; 82.6 4 8.6E-05 30.6 5.4 44 61-104 27-75 (178)
174 KOG2760 Vacuolar sorting prote 82.5 3.1 6.7E-05 36.0 5.3 51 43-93 364-414 (432)
175 cd04765 HTH_MlrA-like_sg2 Heli 82.4 1.4 3.1E-05 30.0 2.7 40 61-104 1-41 (99)
176 cd04776 HTH_GnyR Helix-Turn-He 82.2 1.1 2.5E-05 31.3 2.2 39 61-104 1-39 (118)
177 cd04763 HTH_MlrA-like Helix-Tu 82.1 1.2 2.5E-05 27.7 2.0 39 62-104 2-41 (68)
178 cd04784 HTH_CadR-PbrR Helix-Tu 81.9 1.4 3E-05 30.9 2.5 39 62-104 2-41 (127)
179 PF13814 Replic_Relax: Replica 81.8 2.3 5E-05 30.7 3.8 49 56-104 5-62 (191)
180 PF07848 PaaX: PaaX-like prote 81.8 4.2 9.1E-05 26.5 4.6 39 64-103 27-65 (70)
181 cd04773 HTH_TioE_rpt2 Second H 81.8 1.5 3.3E-05 30.1 2.7 40 61-104 1-41 (108)
182 PRK05638 threonine synthase; V 81.6 2.6 5.6E-05 35.4 4.5 65 33-103 363-429 (442)
183 TIGR02043 ZntR Zn(II)-responsi 81.4 1.4 3.1E-05 31.2 2.5 40 61-104 2-42 (131)
184 COG3177 Fic family protein [Fu 81.4 2.4 5.3E-05 34.7 4.2 58 46-103 289-347 (348)
185 PF14394 DUF4423: Domain of un 81.3 3.1 6.7E-05 31.1 4.4 45 51-95 29-76 (171)
186 PRK11161 fumarate/nitrate redu 81.3 2.3 5E-05 31.5 3.7 33 61-93 185-217 (235)
187 COG3432 Predicted transcriptio 81.1 3.8 8.1E-05 28.7 4.5 41 58-98 29-69 (95)
188 TIGR03697 NtcA_cyano global ni 80.8 2.6 5.7E-05 29.9 3.8 32 61-92 144-175 (193)
189 PRK09514 zntR zinc-responsive 80.6 1.7 3.7E-05 31.3 2.7 40 61-104 2-42 (140)
190 cd04788 HTH_NolA-AlbR Helix-Tu 80.0 2 4.4E-05 28.8 2.8 39 62-104 2-41 (96)
191 cd04779 HTH_MerR-like_sg4 Heli 79.9 2 4.4E-05 31.1 2.9 40 61-104 1-40 (134)
192 PRK10681 DNA-binding transcrip 79.6 1.9 4.2E-05 33.6 2.9 44 45-88 6-49 (252)
193 cd04790 HTH_Cfa-like_unk Helix 79.3 1.4 3.1E-05 32.8 2.0 40 61-104 2-42 (172)
194 PF01399 PCI: PCI domain; Int 79.2 13 0.00027 23.7 6.3 47 57-103 57-103 (105)
195 COG3398 Uncharacterized protei 79.0 3.7 7.9E-05 33.1 4.3 59 46-105 101-159 (240)
196 PF13384 HTH_23: Homeodomain-l 78.8 1.6 3.4E-05 25.4 1.7 30 60-89 17-46 (50)
197 COG2345 Predicted transcriptio 78.6 2.7 5.9E-05 33.2 3.4 47 47-93 12-58 (218)
198 PRK09391 fixK transcriptional 78.5 4.4 9.6E-05 30.4 4.5 32 61-92 180-211 (230)
199 cd04785 HTH_CadR-PbrR-like Hel 78.5 1.8 3.8E-05 30.5 2.2 40 61-104 1-41 (126)
200 cd01111 HTH_MerD Helix-Turn-He 78.0 2.3 4.9E-05 29.4 2.6 40 61-104 1-41 (107)
201 cd01108 HTH_CueR Helix-Turn-He 77.8 2.3 5E-05 29.9 2.6 40 61-104 1-41 (127)
202 PF09286 Pro-kuma_activ: Pro-k 77.7 12 0.00025 26.4 6.3 50 44-93 25-80 (143)
203 cd01106 HTH_TipAL-Mta Helix-Tu 77.3 2.7 5.9E-05 28.3 2.8 40 61-104 1-41 (103)
204 PF03444 HrcA_DNA-bdg: Winged 77.2 2.9 6.3E-05 28.3 2.8 36 58-93 21-56 (78)
205 cd01104 HTH_MlrA-CarA Helix-Tu 76.9 2.5 5.4E-05 25.8 2.3 40 61-104 1-41 (68)
206 COG2865 Predicted transcriptio 76.6 2.3 4.9E-05 37.1 2.7 55 50-104 406-460 (467)
207 PF03428 RP-C: Replication pro 76.6 4.1 8.9E-05 31.0 3.8 33 61-93 71-104 (177)
208 COG1339 Transcriptional regula 76.2 3.9 8.4E-05 32.5 3.7 47 54-101 14-60 (214)
209 cd04780 HTH_MerR-like_sg5 Heli 76.0 2.8 6.2E-05 28.3 2.6 39 62-104 2-41 (95)
210 PRK04172 pheS phenylalanyl-tRN 75.9 7.1 0.00015 33.4 5.5 44 51-94 11-54 (489)
211 PRK10263 DNA translocase FtsK; 75.9 3.5 7.7E-05 40.2 4.0 61 44-104 1291-1351(1355)
212 COG2238 RPS19A Ribosomal prote 75.4 3.2 7E-05 31.2 2.9 25 72-96 93-117 (147)
213 PF13518 HTH_28: Helix-turn-he 75.2 3.1 6.7E-05 23.9 2.3 34 62-95 14-47 (52)
214 PTZ00095 40S ribosomal protein 74.9 4.2 9.2E-05 31.2 3.5 23 72-94 117-139 (169)
215 smart00351 PAX Paired Box doma 74.7 4.1 8.8E-05 28.7 3.2 49 44-94 19-67 (125)
216 cd04778 HTH_MerR-like_sg2 Heli 74.5 2.4 5.2E-05 33.0 2.1 40 61-104 2-41 (219)
217 KOG3054 Uncharacterized conser 73.7 8 0.00017 31.9 5.0 58 47-104 201-258 (299)
218 PRK15431 ferrous iron transpor 73.4 6.8 0.00015 26.6 3.9 37 58-94 14-50 (78)
219 PF05158 RNA_pol_Rpc34: RNA po 73.4 13 0.00027 30.7 6.2 60 43-104 10-70 (327)
220 PF12651 RHH_3: Ribbon-helix-h 72.7 10 0.00023 22.4 4.2 36 40-87 6-42 (44)
221 PRK10402 DNA-binding transcrip 72.6 5.9 0.00013 29.6 3.8 32 61-92 170-201 (226)
222 PRK11639 zinc uptake transcrip 72.4 12 0.00027 27.6 5.4 39 60-98 41-84 (169)
223 COG3888 Predicted transcriptio 72.3 4.2 9.1E-05 33.9 3.1 46 48-93 6-53 (321)
224 COG1378 Predicted transcriptio 72.3 5.7 0.00012 31.4 3.8 44 58-103 28-71 (247)
225 TIGR02051 MerR Hg(II)-responsi 72.2 4.6 9.9E-05 28.3 2.9 39 62-104 1-40 (124)
226 cd01109 HTH_YyaN Helix-Turn-He 72.1 2.9 6.3E-05 28.6 1.9 39 62-104 2-41 (113)
227 smart00753 PAM PCI/PINT associ 72.0 16 0.00035 23.2 5.4 46 58-103 22-67 (88)
228 smart00088 PINT motif in prote 72.0 16 0.00035 23.2 5.4 46 58-103 22-67 (88)
229 PRK10227 DNA-binding transcrip 71.8 3.3 7.1E-05 29.8 2.2 39 62-104 2-41 (135)
230 TIGR00331 hrcA heat shock gene 71.6 4.3 9.2E-05 33.4 3.1 37 57-93 18-56 (337)
231 PRK15043 transcriptional regul 71.6 4 8.8E-05 32.6 2.8 43 58-104 1-44 (243)
232 COG4565 CitB Response regulato 71.4 8.6 0.00019 30.8 4.6 51 43-93 155-206 (224)
233 PRK04214 rbn ribonuclease BN/u 71.4 8.9 0.00019 32.0 4.9 47 47-93 297-343 (412)
234 TIGR02047 CadR-PbrR Cd(II)/Pb( 71.3 3.1 6.8E-05 29.3 1.9 39 62-104 2-41 (127)
235 COG1675 TFA1 Transcription ini 71.1 8.1 0.00017 29.6 4.3 50 48-97 20-70 (176)
236 cd04764 HTH_MlrA-like_sg1 Heli 70.2 5.1 0.00011 24.6 2.6 40 61-104 1-40 (67)
237 PRK10141 DNA-binding transcrip 70.0 13 0.00028 26.5 4.9 45 60-105 30-74 (117)
238 PRK09392 ftrB transcriptional 69.9 8.1 0.00018 28.6 4.0 27 63-89 176-202 (236)
239 cd00131 PAX Paired Box domain 69.6 5.8 0.00013 28.2 3.1 51 43-95 18-68 (128)
240 PF06163 DUF977: Bacterial pro 69.3 8.2 0.00018 28.4 3.8 54 47-103 13-66 (127)
241 PF05584 Sulfolobus_pRN: Sulfo 68.5 11 0.00023 25.3 3.9 54 48-102 7-63 (72)
242 PF01638 HxlR: HxlR-like helix 68.0 18 0.00039 23.7 5.0 32 63-94 21-53 (90)
243 PHA03103 double-strand RNA-bin 68.0 16 0.00034 28.3 5.3 54 46-99 13-66 (183)
244 PRK10265 chaperone-modulator p 67.1 8.9 0.00019 26.3 3.5 41 60-104 7-47 (101)
245 TIGR02716 C20_methyl_CrtF C-20 66.8 7.8 0.00017 30.4 3.5 42 46-92 14-55 (306)
246 PRK00135 scpB segregation and 66.2 11 0.00024 28.8 4.2 43 58-103 102-147 (188)
247 cd04786 HTH_MerR-like_sg7 Heli 65.0 6.4 0.00014 28.2 2.5 39 62-104 2-41 (131)
248 PF09507 CDC27: DNA polymerase 64.7 6.5 0.00014 31.8 2.8 29 59-87 1-29 (430)
249 PRK00082 hrcA heat-inducible t 64.5 7.1 0.00015 32.1 3.0 39 55-93 20-60 (339)
250 PF01316 Arg_repressor: Argini 64.4 26 0.00057 22.9 5.1 53 35-104 12-64 (70)
251 PF04182 B-block_TFIIIC: B-blo 64.1 14 0.0003 23.8 3.8 45 51-95 7-53 (75)
252 PF04492 Phage_rep_O: Bacterio 63.9 14 0.0003 25.7 3.9 35 57-91 51-85 (100)
253 TIGR02147 Fsuc_second hypothet 63.3 10 0.00023 30.5 3.7 53 42-94 110-173 (271)
254 COG1386 scpB Chromosome segreg 63.1 13 0.00029 28.4 4.1 41 60-103 106-149 (184)
255 COG5340 Predicted transcriptio 62.9 7 0.00015 31.9 2.6 41 57-97 27-67 (269)
256 PHA00738 putative HTH transcri 62.8 22 0.00047 25.5 4.8 44 60-104 26-69 (108)
257 PF08461 HTH_12: Ribonuclease 62.5 9.1 0.0002 24.4 2.6 37 59-95 12-53 (66)
258 smart00531 TFIIE Transcription 62.5 7.2 0.00016 28.2 2.4 34 59-92 14-47 (147)
259 PF01402 RHH_1: Ribbon-helix-h 62.4 20 0.00043 19.7 3.8 35 40-86 3-38 (39)
260 PRK15418 transcriptional regul 62.2 13 0.00029 30.2 4.1 39 59-97 28-66 (318)
261 TIGR00635 ruvB Holliday juncti 62.0 12 0.00026 28.9 3.7 46 47-93 243-289 (305)
262 PF09743 DUF2042: Uncharacteri 61.7 12 0.00026 30.2 3.7 66 37-105 103-173 (272)
263 PF03551 PadR: Transcriptional 61.1 23 0.0005 22.2 4.3 34 70-103 27-64 (75)
264 PF09106 SelB-wing_2: Elongati 60.6 22 0.00047 21.8 4.0 47 46-92 3-52 (59)
265 PF06413 Neugrin: Neugrin; In 59.3 14 0.00029 29.3 3.6 35 46-82 17-51 (225)
266 TIGR01529 argR_whole arginine 59.3 29 0.00063 25.3 5.1 21 82-103 40-60 (146)
267 KOG3341 RNA polymerase II tran 59.2 11 0.00024 30.5 3.1 33 60-92 190-222 (249)
268 cd04371 DEP DEP domain, named 58.9 20 0.00044 22.4 3.8 42 40-95 27-68 (81)
269 PF13551 HTH_29: Winged helix- 58.9 6.8 0.00015 25.5 1.6 33 62-94 14-46 (112)
270 PF04433 SWIRM: SWIRM domain; 58.8 14 0.00031 24.1 3.1 34 58-91 51-85 (86)
271 PF06969 HemN_C: HemN C-termin 58.5 20 0.00043 21.8 3.6 33 61-93 21-54 (66)
272 PF01710 HTH_Tnp_IS630: Transp 58.5 20 0.00043 24.9 4.0 38 43-83 57-94 (119)
273 PF15436 PGBA_N: Plasminogen-b 58.4 13 0.00028 29.5 3.3 60 38-97 93-158 (218)
274 PF09202 Rio2_N: Rio2, N-termi 58.3 34 0.00074 22.9 5.0 46 47-92 11-56 (82)
275 TIGR00281 segregation and cond 57.1 19 0.0004 27.6 4.0 41 61-104 102-145 (186)
276 PF07106 TBPIP: Tat binding pr 56.9 31 0.00066 25.1 5.0 46 60-106 16-63 (169)
277 PF13404 HTH_AsnC-type: AsnC-t 56.4 17 0.00036 21.3 2.9 39 43-85 4-42 (42)
278 PF13591 MerR_2: MerR HTH fami 56.1 21 0.00046 23.5 3.6 32 61-96 1-32 (84)
279 PF04079 DUF387: Putative tran 56.0 19 0.00042 26.8 3.8 40 61-103 97-139 (159)
280 KOG3233 RNA polymerase III, su 55.1 5.5 0.00012 33.1 0.8 50 54-103 94-145 (297)
281 TIGR03879 near_KaiC_dom probab 54.2 6.2 0.00013 26.3 0.8 32 61-92 33-64 (73)
282 TIGR03433 padR_acidobact trans 54.1 23 0.00049 23.8 3.6 34 70-103 35-72 (100)
283 PF09107 SelB-wing_3: Elongati 53.8 31 0.00068 21.1 3.9 38 58-95 8-45 (50)
284 PF12298 Bot1p: Eukaryotic mit 53.3 17 0.00036 27.7 3.1 46 41-87 15-60 (172)
285 PF13011 LZ_Tnp_IS481: leucine 53.2 20 0.00043 24.6 3.2 38 61-98 26-63 (85)
286 COG0640 ArsR Predicted transcr 52.9 44 0.00095 20.1 4.5 36 59-94 38-73 (110)
287 PF14579 HHH_6: Helix-hairpin- 52.8 6.3 0.00014 26.1 0.7 54 43-99 35-88 (90)
288 PRK15466 carboxysome structura 52.7 12 0.00027 28.6 2.3 55 39-93 102-157 (166)
289 TIGR01714 phage_rep_org_N phag 52.0 29 0.00064 24.9 4.1 40 62-104 53-92 (119)
290 COG1497 Predicted transcriptio 51.9 27 0.00058 28.6 4.2 56 46-103 10-66 (260)
291 PF05043 Mga: Mga helix-turn-h 51.7 14 0.00031 23.7 2.2 37 50-86 20-56 (87)
292 PHA01747 putative ATP-dependen 51.3 16 0.00035 31.7 3.1 42 44-87 328-371 (425)
293 cd04449 DEP_DEPDC5-like DEP (D 51.3 18 0.00039 23.8 2.7 48 37-97 25-72 (83)
294 PF00126 HTH_1: Bacterial regu 51.1 19 0.00042 21.8 2.7 42 62-103 15-56 (60)
295 COG1167 ARO8 Transcriptional r 51.1 20 0.00044 30.2 3.6 50 46-95 8-63 (459)
296 cd04448 DEP_PIKfyve DEP (Dishe 51.0 19 0.00041 23.9 2.8 24 74-97 47-70 (81)
297 TIGR02277 PaaX_trns_reg phenyl 50.8 24 0.00053 28.2 3.9 38 64-102 24-61 (280)
298 PF08438 MMR_HSR1_C: GTPase of 50.6 9.4 0.0002 27.1 1.3 45 44-98 10-54 (109)
299 COG3398 Uncharacterized protei 50.2 38 0.00083 27.4 4.8 59 45-104 173-231 (240)
300 PLN02853 Probable phenylalanyl 49.9 37 0.0008 30.0 5.1 49 48-96 5-54 (492)
301 PF00610 DEP: Domain found in 49.2 28 0.0006 21.6 3.2 30 69-98 33-62 (74)
302 PRK04280 arginine repressor; P 49.0 72 0.0016 23.4 5.8 53 34-103 10-62 (148)
303 PRK05066 arginine repressor; P 48.7 76 0.0016 23.6 6.0 55 33-103 14-68 (156)
304 PF09114 MotA_activ: Transcrip 48.6 25 0.00054 24.8 3.2 39 54-92 24-64 (96)
305 PF09681 Phage_rep_org_N: N-te 46.9 37 0.00081 24.2 4.0 42 61-105 54-95 (121)
306 smart00421 HTH_LUXR helix_turn 46.9 26 0.00056 19.5 2.6 26 61-86 19-44 (58)
307 PF11972 HTH_13: HTH DNA bindi 46.9 23 0.00049 22.5 2.5 30 57-86 10-39 (54)
308 PF04545 Sigma70_r4: Sigma-70, 46.4 28 0.00061 20.1 2.8 27 59-85 19-45 (50)
309 TIGR02844 spore_III_D sporulat 45.3 13 0.00029 24.9 1.4 33 49-82 9-41 (80)
310 COG4109 Predicted transcriptio 45.0 28 0.00062 30.2 3.6 49 56-104 15-63 (432)
311 PTZ00326 phenylalanyl-tRNA syn 44.9 54 0.0012 28.9 5.3 39 59-97 20-58 (494)
312 PF06224 HTH_42: Winged helix 44.8 37 0.00081 26.6 4.0 53 44-96 164-217 (327)
313 PF13542 HTH_Tnp_ISL3: Helix-t 44.5 43 0.00092 19.3 3.4 40 43-84 12-51 (52)
314 PF04760 IF2_N: Translation in 44.2 30 0.00065 20.6 2.7 29 59-90 2-31 (54)
315 PF02022 Integrase_Zn: Integra 44.1 27 0.00058 20.6 2.4 23 62-84 11-33 (40)
316 cd06171 Sigma70_r4 Sigma70, re 43.6 34 0.00073 18.5 2.7 26 61-86 27-52 (55)
317 KOG4068 Uncharacterized conser 43.3 37 0.00081 26.2 3.6 34 72-105 66-100 (174)
318 TIGR03453 partition_RepA plasm 43.3 24 0.00051 28.9 2.8 43 58-104 31-74 (387)
319 PF02796 HTH_7: Helix-turn-hel 43.2 12 0.00027 21.7 0.9 22 61-82 22-43 (45)
320 PF06971 Put_DNA-bind_N: Putat 43.0 20 0.00044 22.1 1.8 34 47-80 13-48 (50)
321 smart00049 DEP Domain found in 42.9 45 0.00098 20.8 3.5 43 39-95 18-60 (77)
322 PF14330 DUF4387: Domain of un 42.8 26 0.00057 24.7 2.6 28 44-75 26-53 (99)
323 cd06170 LuxR_C_like C-terminal 42.4 33 0.00073 19.2 2.6 26 61-86 16-41 (57)
324 PF06224 HTH_42: Winged helix 41.9 58 0.0013 25.5 4.7 59 47-105 86-153 (327)
325 COG1654 BirA Biotin operon rep 41.8 66 0.0014 21.5 4.3 43 56-98 15-57 (79)
326 cd04450 DEP_RGS7-like DEP (Dis 41.7 51 0.0011 21.8 3.8 27 72-98 45-71 (88)
327 PF13613 HTH_Tnp_4: Helix-turn 41.3 33 0.0007 20.5 2.5 27 60-86 19-45 (53)
328 PF03374 ANT: Phage antirepres 40.2 55 0.0012 21.8 3.8 41 46-92 13-53 (111)
329 PF10557 Cullin_Nedd8: Cullin 39.6 96 0.0021 19.4 5.3 27 69-95 39-65 (68)
330 PRK00080 ruvB Holliday junctio 39.3 44 0.00095 26.6 3.7 51 44-95 261-312 (328)
331 cd00569 HTH_Hin_like Helix-tur 39.0 42 0.00092 15.9 2.4 18 62-79 23-40 (42)
332 PF00292 PAX: 'Paired box' dom 38.5 31 0.00067 25.1 2.5 35 60-94 33-67 (125)
333 PRK13824 replication initiatio 38.0 40 0.00087 28.7 3.4 35 60-94 80-117 (404)
334 PF05595 DUF771: Domain of unk 37.9 34 0.00074 23.0 2.5 43 40-82 3-46 (91)
335 PRK13182 racA polar chromosome 36.9 40 0.00087 25.5 3.0 38 62-104 2-40 (175)
336 PRK10046 dpiA two-component re 36.8 62 0.0013 23.8 3.9 34 61-94 178-211 (225)
337 PF03397 Rhabdo_matrix: Rhabdo 35.6 22 0.00047 27.2 1.3 21 62-82 34-54 (168)
338 PF09824 ArsR: ArsR transcript 34.4 30 0.00065 26.4 1.9 47 41-91 12-58 (160)
339 PF02319 E2F_TDP: E2F/DP famil 34.3 1.2E+02 0.0027 19.2 5.8 46 51-97 16-66 (71)
340 smart00342 HTH_ARAC helix_turn 34.2 49 0.0011 19.6 2.6 25 61-85 2-26 (84)
341 cd00073 H15 linker histone 1 a 33.6 89 0.0019 20.6 3.9 29 74-102 45-73 (88)
342 PRK10512 selenocysteinyl-tRNA- 33.1 78 0.0017 28.2 4.6 60 36-95 538-601 (614)
343 PRK13626 transcriptional regul 33.0 95 0.0021 26.6 5.0 47 47-93 9-56 (552)
344 KOG3411 40S ribosomal protein 32.8 51 0.0011 24.8 2.9 24 73-96 96-119 (143)
345 COG0664 Crp cAMP-binding prote 32.6 64 0.0014 22.4 3.3 36 59-94 170-205 (214)
346 PRK03341 arginine repressor; P 32.4 1.5E+02 0.0031 22.4 5.3 53 47-103 16-74 (168)
347 KOG4062 6-O-methylguanine-DNA 31.9 81 0.0018 24.5 3.9 64 33-97 75-142 (178)
348 PRK10512 selenocysteinyl-tRNA- 31.4 94 0.002 27.7 4.8 47 48-95 495-541 (614)
349 PF05119 Terminase_4: Phage te 31.3 80 0.0017 20.5 3.4 46 45-90 2-49 (100)
350 PRK09751 putative ATP-dependen 31.2 51 0.0011 32.8 3.3 47 46-92 975-1021(1490)
351 PF01381 HTH_3: Helix-turn-hel 30.9 50 0.0011 18.9 2.2 41 35-75 13-53 (55)
352 COG1510 Predicted transcriptio 30.2 29 0.00064 26.9 1.3 35 59-93 40-74 (177)
353 cd04441 DEP_2_DEP6 DEP (Dishev 30.2 59 0.0013 22.0 2.7 24 74-97 51-74 (85)
354 TIGR03826 YvyF flagellar opero 30.2 46 0.001 24.5 2.3 46 44-93 28-75 (137)
355 PF06239 ECSIT: Evolutionarily 29.8 1.1E+02 0.0023 24.6 4.4 50 41-90 83-135 (228)
356 cd04442 DEP_1_DEP6 DEP (Dishev 29.7 64 0.0014 21.6 2.7 25 73-97 46-70 (82)
357 PF09743 DUF2042: Uncharacteri 29.7 97 0.0021 25.0 4.2 66 37-105 164-234 (272)
358 PLN03083 E3 UFM1-protein ligas 29.6 66 0.0014 30.2 3.6 64 39-105 109-176 (803)
359 PF02831 gpW: gpW; InterPro: 29.4 1E+02 0.0023 20.1 3.6 33 74-106 7-39 (68)
360 PF05871 ESCRT-II: ESCRT-II co 29.1 73 0.0016 23.4 3.1 35 71-105 60-95 (139)
361 PF00538 Linker_histone: linke 28.6 69 0.0015 20.5 2.7 24 75-98 46-69 (77)
362 PF07900 DUF1670: Protein of u 28.3 74 0.0016 25.4 3.3 37 59-95 104-141 (220)
363 PF13034 DUF3895: Protein of u 28.0 92 0.002 21.1 3.3 34 69-103 43-77 (78)
364 PF13812 PPR_3: Pentatricopept 28.0 76 0.0017 15.9 2.4 16 74-89 17-32 (34)
365 TIGR00475 selB selenocysteine- 27.6 1.1E+02 0.0024 26.9 4.6 48 47-95 476-523 (581)
366 PRK04217 hypothetical protein; 27.3 67 0.0015 22.7 2.6 23 61-83 59-81 (110)
367 PF04967 HTH_10: HTH DNA bindi 26.9 82 0.0018 19.5 2.7 27 60-86 23-49 (53)
368 PF09940 DUF2172: Domain of un 26.8 76 0.0017 27.3 3.3 30 62-91 357-386 (386)
369 COG3682 Predicted transcriptio 26.7 82 0.0018 22.9 3.0 34 70-104 34-67 (123)
370 cd04439 DEP_1_P-Rex DEP (Dishe 26.6 78 0.0017 21.0 2.7 23 75-97 48-70 (81)
371 PLN00158 histone H2B; Provisio 26.6 1E+02 0.0023 22.3 3.5 41 43-83 57-105 (116)
372 PF05402 PqqD: Coenzyme PQQ sy 26.4 1E+02 0.0022 18.6 3.1 27 65-91 38-68 (68)
373 COG1763 MobB Molybdopterin-gua 26.3 76 0.0016 23.7 2.9 26 74-99 16-41 (161)
374 PRK13239 alkylmercury lyase; P 26.1 78 0.0017 24.8 3.0 41 45-85 21-61 (206)
375 PF10543 ORF6N: ORF6N domain; 26.0 78 0.0017 21.0 2.6 30 54-83 6-35 (88)
376 smart00427 H2B Histone H2B. 25.6 1.1E+02 0.0025 21.1 3.4 43 42-84 30-80 (89)
377 PF00196 GerE: Bacterial regul 25.6 82 0.0018 18.7 2.5 27 61-87 19-45 (58)
378 PF08721 Tn7_Tnp_TnsA_C: TnsA 25.6 1.7E+02 0.0036 17.9 4.2 41 48-91 32-76 (79)
379 PRK09775 putative DNA-binding 25.3 1.2E+02 0.0026 26.0 4.3 40 61-103 14-53 (442)
380 PRK08061 rpsN 30S ribosomal pr 25.2 49 0.0011 21.3 1.5 28 65-96 32-59 (61)
381 PRK05590 hypothetical protein; 25.0 56 0.0012 25.0 2.0 35 40-74 27-61 (166)
382 cd04438 DEP_dishevelled DEP (D 24.9 85 0.0018 20.9 2.7 23 75-97 50-72 (84)
383 PF08100 Dimerisation: Dimeris 24.8 86 0.0019 19.2 2.5 36 48-85 12-51 (51)
384 TIGR02937 sigma70-ECF RNA poly 24.6 88 0.0019 20.2 2.7 26 61-86 127-152 (158)
385 KOG0488 Transcription factor B 24.5 58 0.0012 26.8 2.1 46 20-75 166-214 (309)
386 PF14217 DUF4327: Domain of un 23.9 23 0.0005 23.5 -0.3 22 77-103 7-28 (68)
387 COG1533 SplB DNA repair photol 23.6 1.9E+02 0.004 23.6 4.9 59 39-97 60-126 (297)
388 PF00165 HTH_AraC: Bacterial r 23.6 97 0.0021 17.2 2.4 24 61-84 9-32 (42)
389 PF03205 MobB: Molybdopterin g 23.5 92 0.002 22.1 2.8 23 74-96 14-36 (140)
390 PF06218 NPR2: Nitrogen permea 23.3 1.2E+02 0.0025 26.3 3.8 58 46-105 206-263 (428)
391 PRK00441 argR arginine repress 23.0 1.6E+02 0.0035 21.6 4.0 52 48-103 6-62 (149)
392 PF12627 PolyA_pol_RNAbd: Prob 23.0 74 0.0016 19.0 1.9 52 42-93 3-56 (64)
393 KOG2165 Anaphase-promoting com 22.9 1.2E+02 0.0025 28.4 3.9 58 48-105 604-661 (765)
394 PF11625 DUF3253: Protein of u 22.8 2.6E+02 0.0056 19.0 6.1 51 47-97 11-66 (83)
395 PF12844 HTH_19: Helix-turn-he 22.3 82 0.0018 18.6 2.1 42 34-75 15-56 (64)
396 PF01886 DUF61: Protein of unk 22.3 1.9E+02 0.004 21.0 4.2 50 41-90 42-101 (132)
397 PHA02593 62 clamp loader small 22.2 1.4E+02 0.0031 23.4 3.8 54 42-95 93-160 (191)
398 COG4800 Predicted transcriptio 22.2 1.3E+02 0.0028 23.1 3.4 32 45-80 18-49 (170)
399 PRK12543 RNA polymerase sigma 22.2 97 0.0021 22.0 2.7 18 61-78 134-151 (179)
400 COG3415 Transposase and inacti 21.8 85 0.0018 23.1 2.4 30 61-90 22-51 (138)
401 PRK03911 heat-inducible transc 21.7 66 0.0014 26.3 1.9 36 58-93 20-57 (260)
402 PRK10736 hypothetical protein; 21.7 1.3E+02 0.0029 25.5 3.8 37 60-96 321-357 (374)
403 PHA01623 hypothetical protein 21.6 2.1E+02 0.0046 17.7 4.2 38 37-86 14-52 (56)
404 PF13443 HTH_26: Cro/C1-type H 21.5 73 0.0016 18.8 1.7 22 61-82 11-32 (63)
405 PRK09413 IS2 repressor TnpA; R 21.4 1.2E+02 0.0025 21.0 2.9 31 61-91 30-60 (121)
406 PF07836 DmpG_comm: DmpG-like 21.1 99 0.0021 20.3 2.3 24 64-90 26-49 (66)
407 cd08768 Cdc6_C Winged-helix do 21.0 2.2E+02 0.0049 17.7 4.3 22 73-94 45-66 (87)
408 PF00178 Ets: Ets-domain; Int 21.0 2.7E+02 0.0058 18.6 5.0 40 58-97 31-77 (85)
409 PF01976 DUF116: Protein of un 20.9 60 0.0013 24.1 1.4 30 62-91 77-112 (158)
410 PF09639 YjcQ: YjcQ protein; 20.9 1E+02 0.0023 20.4 2.5 19 75-93 25-43 (88)
411 TIGR02928 orc1/cdc6 family rep 20.8 2.3E+02 0.005 22.3 4.8 23 72-94 329-351 (365)
412 PF08765 Mor: Mor transcriptio 20.5 1.2E+02 0.0027 20.6 2.9 35 50-87 65-99 (108)
413 PF14629 ORC4_C: Origin recogn 20.4 98 0.0021 22.8 2.5 22 71-92 150-171 (203)
414 PF08281 Sigma70_r4_2: Sigma-7 20.4 1.3E+02 0.0027 17.3 2.5 23 61-83 27-49 (54)
415 COG2452 Predicted site-specifi 20.3 1.1E+02 0.0024 24.0 2.8 32 60-95 1-32 (193)
416 PF01498 HTH_Tnp_Tc3_2: Transp 20.2 1.1E+02 0.0024 18.8 2.4 41 50-91 3-46 (72)
No 1
>KOG1767 consensus 40S ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.7e-49 Score=279.44 Aligned_cols=106 Identities=67% Similarity=0.965 Sum_probs=101.3
Q ss_pred CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033932 1 MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKA 80 (108)
Q Consensus 1 M~pk~~~~k~~~~~~~~~~~~k~~KKKWsKgk~keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~ 80 (108)
||+++|.++++++. ++.+||+++|||||||+++||+||+|+||++|||||++|||+|+|||||+|+|||+|||||||.+
T Consensus 2 ~~~k~q~sK~~k~~-~~~~ggk~~KKKWskGk~kdkvnn~Vlfdqatydkl~kevp~~k~it~svl~dRlkIngsLAr~a 80 (110)
T KOG1767|consen 2 MPKKQQLSKEKKAP-AASSGGKAKKKKWSKGKVKDKVNNAVLFDQATYDKLLKEVPKYKLITPSVLSDRLKINGSLARAA 80 (110)
T ss_pred CccccccCchhccc-cccCCCcccccccccchHHHHhhhheeecHHHHHHHHHhcccceeecHHHhhhhhhhchHHHHHH
Confidence 78888888877776 45899999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCeeEeccccceEEEecccC
Q 033932 81 IRELMARGLIRMVSAHASQQIYTRATN 107 (108)
Q Consensus 81 Lr~L~~kGlIk~V~k~~~q~IYtr~~~ 107 (108)
||||..+|+|++|++||+|.||||+++
T Consensus 81 lr~L~~kG~Ik~Vs~h~~q~IYTrat~ 107 (110)
T KOG1767|consen 81 LRELSNKGVIKQVSKHSKQVIYTRATA 107 (110)
T ss_pred HHHHHhcchHHHHhhcchheeeccccc
Confidence 999999999999999999999999986
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=2.6e-49 Score=278.84 Aligned_cols=105 Identities=68% Similarity=0.995 Sum_probs=79.0
Q ss_pred CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033932 1 MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKA 80 (108)
Q Consensus 1 M~pk~~~~k~~~~~~~~~~~~k~~KKKWsKgk~keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~ 80 (108)
||||.++++++.++ ++++||++++||||||+++|++||+|+||+++||+|++|||+|++||||+|||||+|++||||++
T Consensus 1 M~pK~~~~k~~k~~-~~~~~~k~~KKKwsKgk~kek~~~~v~~d~~~~~kl~kEV~~~K~ITp~~lserlkI~~SlAr~~ 79 (105)
T PF03297_consen 1 MPPKKQKSKKQKAK-KAKSGGKAKKKKWSKGKVKEKLNNAVLFDKETYDKLLKEVPKMKLITPSVLSERLKINGSLARKA 79 (105)
T ss_dssp ----------------TT------SSS--SS-SCHHHCCCSCCTCHHHHHHHHHCTTSSCECHHHHHHHHCCSCHHHHHH
T ss_pred CCCCcccchhhHHH-HHhccCccccccccccchHHHHhcceEecHHHHHHHHHHhccCcEeeHHHHHHhHhhHHHHHHHH
Confidence 99999888777666 45889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCeeEeccccceEEEeccc
Q 033932 81 IRELMARGLIRMVSAHASQQIYTRAT 106 (108)
Q Consensus 81 Lr~L~~kGlIk~V~k~~~q~IYtr~~ 106 (108)
||||+++|+|++|++||+|.||||+|
T Consensus 80 Lr~L~~kG~Ik~V~k~~~~~IYtr~~ 105 (105)
T PF03297_consen 80 LRELESKGLIKPVSKHHRQRIYTRAT 105 (105)
T ss_dssp HHHHHHCCSSEEEECCTTCEEEEES-
T ss_pred HHHHHHCCCEEEEeccCCeEEEecCC
Confidence 99999999999999999999999986
No 3
>COG4901 Ribosomal protein S25 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-37 Score=219.48 Aligned_cols=106 Identities=40% Similarity=0.638 Sum_probs=101.4
Q ss_pred CCCCCCCCCCCCCCccccCCCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033932 1 MAPKKDKAPPPSSKPAKSGGGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKA 80 (108)
Q Consensus 1 M~pk~~~~k~~~~~~~~~~~~k~~KKKWsKgk~keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~ 80 (108)
|||+.|.+++.++.++ .+|+.+.+|||++++.+|...++|+||+++||++++|||++++||||+|++||+|++||||.+
T Consensus 1 m~pk~qlsK~~Ka~~~-~a~~~k~kKK~~~k~~k~~~~~av~vdee~~~ki~KEV~~~r~VTpy~la~r~gI~~SvAr~v 79 (107)
T COG4901 1 MAPKSQLSKEKKAEKA-KAGTAKDKKKWSKKKKKEEARRAVTVDEELLDKIRKEVPRERVVTPYVLASRYGINGSVARIV 79 (107)
T ss_pred CcchhHHHHHHHHHHH-HhhhhhhhhccccccccchhhhhhhccHHHHHHHHHhcccceeecHHHHHHHhccchHHHHHH
Confidence 9999999998888755 678899999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCeeEeccccceEEEecccC
Q 033932 81 IRELMARGLIRMVSAHASQQIYTRATN 107 (108)
Q Consensus 81 Lr~L~~kGlIk~V~k~~~q~IYtr~~~ 107 (108)
||+|+++|+|++|++||+|.||+++.+
T Consensus 80 LR~LeeeGvv~lvsknrR~~IY~~a~a 106 (107)
T COG4901 80 LRHLEEEGVVQLVSKNRRQAIYTRAKA 106 (107)
T ss_pred HHHHHhCCceeeeccCccceeeecccC
Confidence 999999999999999999999999765
No 4
>PRK09334 30S ribosomal protein S25e; Provisional
Probab=100.00 E-value=4.6e-36 Score=205.45 Aligned_cols=81 Identities=31% Similarity=0.454 Sum_probs=76.5
Q ss_pred ccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 25 KKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 25 KKKWsKgk~keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|+-.++..++.+||+|+||+++||||++|||+|++||||+|||||+|++||||++||||+++|+|++|++||+|.|||+
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 44456667999999999999999999999999999999999999999999999999999999999999999999999997
Q ss_pred c
Q 033932 105 A 105 (108)
Q Consensus 105 ~ 105 (108)
+
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=97.23 E-value=0.00034 Score=41.37 Aligned_cols=42 Identities=29% Similarity=0.417 Sum_probs=32.7
Q ss_pred HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
+|+..+-...-+|...||++++++.+-+...|++|+++|+|+
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 333333334449999999999999999999999999999985
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=97.07 E-value=0.0031 Score=39.37 Aligned_cols=50 Identities=26% Similarity=0.371 Sum_probs=37.2
Q ss_pred HHHHHHHhhCCC-----Ceee-chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 46 ATYDKLLSEAPK-----YKLI-TPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 46 ~t~dKl~KEVpk-----~k~I-Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
..|+.|..+|-. -..+ |...||++|+|+-+.+|.+|+.|++.|+|....+
T Consensus 4 ~i~~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~ 59 (64)
T PF00392_consen 4 QIYDQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPG 59 (64)
T ss_dssp HHHHHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECC
Confidence 344555444433 3455 9999999999999999999999999999987654
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=97.03 E-value=0.0012 Score=41.15 Aligned_cols=46 Identities=15% Similarity=0.289 Sum_probs=38.9
Q ss_pred HHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 49 DKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 49 dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
++|+.-+.....+|...||+.|+|+-+-+|+=|.+|+++|+|..+.
T Consensus 3 ~~Il~~l~~~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~ 48 (57)
T PF08220_consen 3 QQILELLKEKGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRTH 48 (57)
T ss_pred HHHHHHHHHcCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 3455555556789999999999999999999999999999987653
No 8
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=96.98 E-value=0.0036 Score=37.01 Aligned_cols=38 Identities=26% Similarity=0.347 Sum_probs=32.9
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+..+-|...||++|+++-+-.+++|+.|++.|+|..+.
T Consensus 17 ~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~ 54 (60)
T smart00345 17 GDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRP 54 (60)
T ss_pred CCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 33444999999999999999999999999999987653
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=96.94 E-value=0.0039 Score=37.50 Aligned_cols=49 Identities=27% Similarity=0.350 Sum_probs=38.7
Q ss_pred HHHHHHHHhhCC------CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 45 QATYDKLLSEAP------KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 45 k~t~dKl~KEVp------k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+++++.|...+. .-.+.|...||+.|+|+-+-++++|..|++.|+|...
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
>PF14502 HTH_41: Helix-turn-helix domain
Probab=96.91 E-value=0.0019 Score=40.27 Aligned_cols=41 Identities=20% Similarity=0.240 Sum_probs=37.7
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
.-++=|.+.+|++|++....-..+|+.|++.|.|.+.+++|
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 45677999999999999999999999999999999998766
No 11
>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=96.76 E-value=0.0047 Score=38.79 Aligned_cols=44 Identities=20% Similarity=0.364 Sum_probs=37.9
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.=.|+..||+.++|.-+-+..+|+.|+++|+|...... ..+|..
T Consensus 21 ~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~--~~~Y~a 64 (68)
T PF01978_consen 21 GPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGR--PKVYRA 64 (68)
T ss_dssp CHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEEC--CEEEEE
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCc--eEEEEE
Confidence 44899999999999999999999999999999988743 456653
No 12
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=96.61 E-value=0.007 Score=35.40 Aligned_cols=44 Identities=16% Similarity=0.240 Sum_probs=36.9
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
.-+|...|++.++++-+-++.+|+.|.++|+|.....++ ...|.
T Consensus 9 ~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~~~-~~~~~ 52 (66)
T smart00418 9 GELCVCELAEILGLSQSTVSHHLKKLREAGLVESRREGK-RVYYS 52 (66)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeecCC-EEEEE
Confidence 357999999999999999999999999999999775544 44454
No 13
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=96.59 E-value=0.0045 Score=39.99 Aligned_cols=38 Identities=16% Similarity=0.173 Sum_probs=31.9
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
-+|...|||.++|+.+-||..|..|+..|.|+.+--.+
T Consensus 15 p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~r 52 (62)
T PF04703_consen 15 PLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRR 52 (62)
T ss_dssp -EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SS
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCC
Confidence 38889999999999999999999999999999864333
No 14
>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=96.48 E-value=0.0096 Score=38.76 Aligned_cols=46 Identities=26% Similarity=0.380 Sum_probs=32.8
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT 106 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~ 106 (108)
++|.|.|||+++|+-|+--.+||-|++-|+|.--|- .--..|.+..
T Consensus 4 ~lvas~iAd~~GiTRSvIVNALRKleSaGvIesrSl-GmKGT~ikvl 49 (61)
T PF08222_consen 4 RLVASKIADRVGITRSVIVNALRKLESAGVIESRSL-GMKGTYIKVL 49 (61)
T ss_dssp EE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEET-TSS-EEEEE-
T ss_pred eehHHHHHHHhCccHHHHHHHHHHHHhcCceeeccc-CCCceeeeee
Confidence 689999999999999999999999999999984432 1123555443
No 15
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=96.47 E-value=0.013 Score=38.43 Aligned_cols=51 Identities=25% Similarity=0.357 Sum_probs=39.0
Q ss_pred hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 54 EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
..+....+|...||++++++-+..+++|+.|.+.|+|.-....+......+
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 445555699999999999999999999999999999987765444443334
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=96.26 E-value=0.011 Score=35.83 Aligned_cols=34 Identities=29% Similarity=0.466 Sum_probs=31.3
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+|++.||+.+++.-+-.-++++.|+++|+|....
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 6999999999999999999999999999998873
No 17
>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=96.18 E-value=0.017 Score=43.65 Aligned_cols=39 Identities=21% Similarity=0.292 Sum_probs=35.7
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
|+.++=|-..||++|+|+-...|+||.+|+.+|+|..+-
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 567888999999999999999999999999999997754
No 18
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=96.14 E-value=0.018 Score=34.30 Aligned_cols=42 Identities=24% Similarity=0.394 Sum_probs=36.3
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
++...+++.++|..+-++++|+.|.+.|+|...... +...|.
T Consensus 21 ~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~-~~~~~~ 62 (78)
T cd00090 21 LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG-RRVYYS 62 (78)
T ss_pred cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec-cEEEEE
Confidence 999999999999999999999999999999987544 344554
No 19
>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=96.13 E-value=0.019 Score=35.26 Aligned_cols=47 Identities=26% Similarity=0.343 Sum_probs=35.1
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--cccceEEEe
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS--AHASQQIYT 103 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~IYt 103 (108)
...-+|+..||+.+++.-+-+.++|+.|+++|+|.... .++|...|.
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 44568999999999999999999999999999997773 335544443
No 20
>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=96.09 E-value=0.015 Score=43.60 Aligned_cols=40 Identities=30% Similarity=0.419 Sum_probs=36.6
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
|+.+|=|=..||++|+|+-...|+||.+|+.+|+|....+
T Consensus 28 ~G~~LPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~G 67 (238)
T TIGR02325 28 AGDYLPAEMQLAERFGVNRHTVRRAIAALVERGLLRAEQG 67 (238)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 6678999999999999999999999999999999987643
No 21
>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=96.09 E-value=0.016 Score=43.83 Aligned_cols=40 Identities=23% Similarity=0.225 Sum_probs=36.5
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
|+.+|=|=..||++|+|+-...|+||++|+++|+|..+.+
T Consensus 20 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~G 59 (233)
T TIGR02404 20 EGDYLPSEHELMDQYGASRETVRKALNLLTEAGYIQKIQG 59 (233)
T ss_pred CCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 5678889999999999999999999999999999987643
No 22
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=96.05 E-value=0.011 Score=46.25 Aligned_cols=50 Identities=24% Similarity=0.307 Sum_probs=44.7
Q ss_pred HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
.+-.++|+..+-....+|...||++|+|+.+-+|+=|++|+++|+|..+-
T Consensus 4 ~~R~~~Il~~l~~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 4 AQRHQILLELLAQLGFVTVEKVIERLGISPATARRDINKLDESGKLKKVR 53 (251)
T ss_pred HHHHHHHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence 45567788888888999999999999999999999999999999998753
No 23
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=96.01 E-value=0.013 Score=33.51 Aligned_cols=33 Identities=18% Similarity=0.329 Sum_probs=30.7
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+|...||+.++++-+-+.++|+.|++.|+|...
T Consensus 9 ~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~ 41 (48)
T smart00419 9 LTRQEIAELLGLTRETVSRTLKRLEKEGLISRE 41 (48)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEe
Confidence 688999999999999999999999999999753
No 24
>PRK09764 DNA-binding transcriptional repressor MngR; Provisional
Probab=95.98 E-value=0.022 Score=43.51 Aligned_cols=40 Identities=23% Similarity=0.391 Sum_probs=36.1
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
|+.++=|=..||++|+|+-.-.|+||.+|+.+|+|..+-+
T Consensus 25 ~G~~LPsE~eL~~~~~VSR~TvR~Al~~L~~eGli~r~~G 64 (240)
T PRK09764 25 PGDALPTESALQTEFGVSRVTVRQALRQLVEQQILESIQG 64 (240)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 5567889999999999999999999999999999987654
No 25
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=95.97 E-value=0.015 Score=43.56 Aligned_cols=54 Identities=20% Similarity=0.271 Sum_probs=43.4
Q ss_pred eCHHHHHHHHhhCCCC-----eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 43 FDQATYDKLLSEAPKY-----KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~-----k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
+-...|+.|...|-.- ..|+...||++|+|+-+--|-||+.|+..|+|..+-+.
T Consensus 8 ~~~~vy~~i~~~I~~g~l~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~ 66 (224)
T PRK11534 8 TALDGYRWLKNDIIRGNFQPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQK 66 (224)
T ss_pred hhHHHHHHHHHHHHhCCCCCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCC
Confidence 3456788888776442 23477899999999999999999999999999876543
No 26
>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=95.87 E-value=0.024 Score=45.78 Aligned_cols=59 Identities=24% Similarity=0.369 Sum_probs=50.9
Q ss_pred hhhccceeCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 36 KVNNMVLFDQATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 36 K~nn~Vl~dk~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
.++..-+-.-+..++|+.+.... -.++-+.||++++|+-|..|.+|+.|++.|+|.--+
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 899999999999999999999999999999998654
No 27
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=95.86 E-value=0.044 Score=31.40 Aligned_cols=46 Identities=17% Similarity=0.291 Sum_probs=37.7
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
..++-|..+ ..+|...+++.|++.-+-+++.|..|++.|+|....+
T Consensus 4 ~il~~l~~~----~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQ----GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHc----CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 455555543 3489999999999999999999999999999986543
No 28
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=95.85 E-value=0.015 Score=45.52 Aligned_cols=48 Identities=10% Similarity=0.195 Sum_probs=43.0
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+-.++|+..+.....+|...||++|+|+-+-+|+=|.+|+++|+|..+
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 456777777777889999999999999999999999999999999775
No 29
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=95.83 E-value=0.027 Score=43.15 Aligned_cols=51 Identities=16% Similarity=0.186 Sum_probs=41.9
Q ss_pred HHHHHHHHhhCC------CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 45 QATYDKLLSEAP------KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 45 k~t~dKl~KEVp------k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
...|+.|...|- +.++-|-..||++|+|+-+-.|.||+.|+..|+|...-+
T Consensus 12 ~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 68 (257)
T PRK10225 12 QEVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRG 68 (257)
T ss_pred HHHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 456777776664 445557889999999999999999999999999997654
No 30
>PRK03837 transcriptional regulator NanR; Provisional
Probab=95.82 E-value=0.019 Score=43.18 Aligned_cols=51 Identities=16% Similarity=0.241 Sum_probs=41.6
Q ss_pred HHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 45 QATYDKLLSEAPK------YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 45 k~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
...|+.|...|-. .++-+-..||++|+|+-+..|.||+.|+..|+|...-+
T Consensus 16 ~~v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~ 72 (241)
T PRK03837 16 EEVEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHG 72 (241)
T ss_pred HHHHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4566666666543 44558999999999999999999999999999988643
No 31
>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=95.80 E-value=0.0062 Score=38.84 Aligned_cols=47 Identities=15% Similarity=0.232 Sum_probs=36.5
Q ss_pred HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
|..-+-....+|...||.+|++.-+..+..|..|+.+|.|..+..+.
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 33334455789999999999999999999999999999999986543
No 32
>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=95.77 E-value=0.016 Score=36.60 Aligned_cols=37 Identities=14% Similarity=0.301 Sum_probs=33.0
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
.-..|++..||++|+|+-+-+-..|+.|.++|+|...
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 4567999999999999999999999999999999764
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=95.75 E-value=0.026 Score=34.33 Aligned_cols=37 Identities=22% Similarity=0.295 Sum_probs=33.7
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
.--+|...||+.++++-+-+.++|+.|++.|+|....
T Consensus 23 ~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~ 59 (67)
T cd00092 23 QLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRG 59 (67)
T ss_pred cCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 3458999999999999999999999999999998765
No 34
>PHA02943 hypothetical protein; Provisional
Probab=95.74 E-value=0.031 Score=42.66 Aligned_cols=54 Identities=22% Similarity=0.207 Sum_probs=45.1
Q ss_pred HHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 49 DKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 49 dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
+.|+.-+ +.-.-|.+.||++++++-|-|+-+|.-||++|.|+.|..+.....+.
T Consensus 14 ~eILE~L-k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~tyw~l 67 (165)
T PHA02943 14 IKTLRLL-ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRAAIWCL 67 (165)
T ss_pred HHHHHHH-hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecceEEEEE
Confidence 3445444 77788999999999999999999999999999999998776665444
No 35
>PRK11402 DNA-binding transcriptional regulator FrlR; Provisional
Probab=95.69 E-value=0.021 Score=43.45 Aligned_cols=39 Identities=23% Similarity=0.289 Sum_probs=35.8
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
|+.++=|=..||++|+|+-...|+||.+|+++|+|....
T Consensus 29 ~g~kLPsE~eLa~~~~VSR~TvR~Al~~L~~eGli~r~~ 67 (241)
T PRK11402 29 AGQQIPTENELCTQYNVSRITIRKAISDLVADGVLIRWQ 67 (241)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 457999999999999999999999999999999998754
No 36
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=95.57 E-value=0.029 Score=43.91 Aligned_cols=50 Identities=16% Similarity=0.163 Sum_probs=42.2
Q ss_pred hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 54 EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
.+.+.--||.+.||++++++-+-+-++|+.|+++|+|......+.+.||.
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 34444569999999999999999999999999999998886556676664
No 37
>PRK14999 histidine utilization repressor; Provisional
Probab=95.49 E-value=0.028 Score=42.82 Aligned_cols=39 Identities=18% Similarity=0.303 Sum_probs=35.4
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
|+.+|=|-..||++|+|+-...|+||.+|+.+|+|...-
T Consensus 32 ~G~~LPsE~eLa~~~gVSR~TVR~Al~~L~~eGli~r~~ 70 (241)
T PRK14999 32 PHDRIPSEAELVAQYGFSRMTINRALRELTDEGWLVRLQ 70 (241)
T ss_pred CCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEec
Confidence 567888999999999999999999999999999997643
No 38
>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=95.41 E-value=0.028 Score=33.87 Aligned_cols=33 Identities=36% Similarity=0.493 Sum_probs=30.8
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+|++.||+.+++.-|-.-++++.|+.+|+|..-
T Consensus 18 ~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~ 50 (59)
T PF01047_consen 18 ITQSELAEKLGISRSTVTRIIKRLEKKGLIERE 50 (59)
T ss_dssp EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEec
Confidence 899999999999999999999999999999876
No 39
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=95.40 E-value=0.023 Score=44.50 Aligned_cols=48 Identities=17% Similarity=0.123 Sum_probs=42.9
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+=.++|+..+.....||+..||+.|+|+.+-.|+=|++|+++|+|..+
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 345677878888888999999999999999999999999999999775
No 40
>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=95.39 E-value=0.033 Score=33.51 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=29.5
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
+|.+.||+++++.-|-+.++|+.|++.|++..
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 41
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=95.38 E-value=0.048 Score=41.72 Aligned_cols=50 Identities=18% Similarity=0.243 Sum_probs=41.5
Q ss_pred HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+..|+.|...| |+.++-|-..||++|+|+-+-.|-||+.|+..|+|...-
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 45677777775 344555789999999999999999999999999998654
No 42
>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=95.38 E-value=0.02 Score=37.31 Aligned_cols=54 Identities=22% Similarity=0.332 Sum_probs=48.6
Q ss_pred CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
+.++|+....=|....-+++|-|=-+|+|-..-|-+++.+|++.|+|-+...+.
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 467899988888888999999999999999999999999999999999975444
No 43
>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=95.36 E-value=0.041 Score=40.67 Aligned_cols=49 Identities=29% Similarity=0.370 Sum_probs=39.9
Q ss_pred HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
...|+.|...| |+.++ +-..||++|+|+-+--|.||+.|+..|+|...-
T Consensus 14 ~~v~~~l~~~I~~g~l~pG~~L-~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~ 68 (212)
T TIGR03338 14 TLVQDEIERAILSGELPPGAKL-NESDIAARLGVSRGPVREAFRALEEAGLVRNEK 68 (212)
T ss_pred HHHHHHHHHHHHcCCCCCCCEe-cHHHHHHHhCCChHHHHHHHHHHHHCCCEEEec
Confidence 45666666654 44555 889999999999999999999999999997643
No 44
>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=95.35 E-value=0.013 Score=38.33 Aligned_cols=58 Identities=16% Similarity=0.265 Sum_probs=43.2
Q ss_pred HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932 45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY 102 (108)
Q Consensus 45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY 102 (108)
.++|++...=|-...-++.|-|--+|+|-..-|-+++..|++.|+|-+-..+..-.|+
T Consensus 5 D~ly~~a~~~V~~~~~~S~S~lQR~~rIGynrAariid~LE~~GiVs~~~~~~~R~Vl 62 (65)
T PF09397_consen 5 DPLYEEAVEFVIEEGKASISLLQRKFRIGYNRAARIIDQLEEEGIVSPANGSKPREVL 62 (65)
T ss_dssp STTHHHHHHHHHHCTCECHHHHHHHHT--HHHHHHHHHHHHHCTSBE---TTSEEEB-
T ss_pred cHHHHHHHHHHHHcCCccHHHHHHHhCCCHHHHHHHHHHHHHCCCCCCCCCCCCCeec
Confidence 4567777766667788999999999999999999999999999999998655433343
No 45
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=95.30 E-value=0.055 Score=34.64 Aligned_cols=34 Identities=15% Similarity=0.155 Sum_probs=32.2
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+|...||+.++|.-+-++++|..|+++|+|....
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 9999999999999999999999999999997754
No 46
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=95.26 E-value=0.024 Score=35.09 Aligned_cols=50 Identities=24% Similarity=0.243 Sum_probs=40.9
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
++--+|+..+....=.|.+.||+.+++.-+-+..=|+.|++-|+|..+..
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 55556666665556689999999999999999999999999999988754
No 47
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=95.21 E-value=0.053 Score=38.63 Aligned_cols=45 Identities=16% Similarity=0.233 Sum_probs=38.2
Q ss_pred CCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccce
Q 033932 55 APKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQ 99 (108)
Q Consensus 55 Vpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q 99 (108)
.+.-..++...||++++|+-+-.|++|+.|...|+|..+.+.+..
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 333458899999999999999999999999999999988655433
No 48
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=95.21 E-value=0.027 Score=44.12 Aligned_cols=49 Identities=18% Similarity=0.251 Sum_probs=44.3
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+=.++|+..+.....|++..||++|+|+-.-.|+=|++|+++|++..+.
T Consensus 5 eR~~~Il~~l~~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~h 53 (253)
T COG1349 5 ERHQKILELLKEKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRVH 53 (253)
T ss_pred HHHHHHHHHHHHcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEEe
Confidence 3457888888889999999999999999999999999999999998754
No 49
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=95.21 E-value=0.039 Score=41.64 Aligned_cols=50 Identities=14% Similarity=0.228 Sum_probs=40.3
Q ss_pred HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+..|+.|...| |+.++-|-..||++|+|+-+..|.||+.|+..|+|...-
T Consensus 10 ~~~~~~l~~~I~~g~l~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 10 GFAEEYIIESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 34556665555 345566899999999999999999999999999998653
No 50
>COG2188 PhnF Transcriptional regulators [Transcription]
Probab=95.18 E-value=0.038 Score=42.54 Aligned_cols=41 Identities=29% Similarity=0.405 Sum_probs=37.0
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
|+.++=|=..||++|+|+-...|+||++|++.|+|....+.
T Consensus 27 ~G~~LPsE~eLa~~f~VSR~TvRkAL~~L~~eGli~r~~G~ 67 (236)
T COG2188 27 PGDKLPSERELAEQFGVSRMTVRKALDELVEEGLIVRRQGK 67 (236)
T ss_pred CCCCCCCHHHHHHHHCCcHHHHHHHHHHHHHCCcEEEEecC
Confidence 45789999999999999999999999999999999886543
No 51
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=95.16 E-value=0.066 Score=40.75 Aligned_cols=52 Identities=17% Similarity=0.237 Sum_probs=43.4
Q ss_pred CHHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 44 DQATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 44 dk~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
....|+.|...| |+.++=|-..||++|+|+-+--|-||+.|+..|+|...-+
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 356777777776 4455558899999999999999999999999999987654
No 52
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=95.09 E-value=0.053 Score=38.09 Aligned_cols=47 Identities=23% Similarity=0.354 Sum_probs=42.7
Q ss_pred eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+|...++-|+.+.+ ++...||++++++.+-.+.-++.|++.|+|+-+
T Consensus 9 ~D~~IL~~L~~d~r----~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 9 IDRRILRLLQEDAR----ISNAELAERVGLSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred HHHHHHHHHHHhCC----CCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeE
Confidence 56778888888887 999999999999999999999999999999876
No 53
>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=95.03 E-value=0.049 Score=41.08 Aligned_cols=51 Identities=14% Similarity=0.221 Sum_probs=41.6
Q ss_pred HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
+..|+.|...| |+.++-|-..||++|+|+-+-.|-||+.|+..|+|...-+
T Consensus 9 ~~v~~~l~~~I~~g~l~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~~ 65 (235)
T TIGR02812 9 GFAEEYIVESIWNNRFPPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 65 (235)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeCC
Confidence 45666666665 3445558999999999999999999999999999987654
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=95.03 E-value=0.05 Score=37.17 Aligned_cols=52 Identities=12% Similarity=0.089 Sum_probs=39.9
Q ss_pred HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--cccceEEE
Q 033932 51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS--AHASQQIY 102 (108)
Q Consensus 51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~IY 102 (108)
++-.+-...-+|++.||+.+++.-+..-++|+.|+++|+|.... .++|...|
T Consensus 33 iL~~l~~~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~~~~D~R~~~v 86 (118)
T TIGR02337 33 ILRILAEQGSMEFTQLANQACILRPSLTGILARLERDGLVTRLKASNDQRRVYI 86 (118)
T ss_pred HHHHHHHcCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEeccCCCCCCeeEE
Confidence 33334344468999999999999999999999999999999873 34444443
No 55
>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=94.98 E-value=0.075 Score=39.70 Aligned_cols=40 Identities=30% Similarity=0.363 Sum_probs=36.7
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
|+.++=|...||++|+|+-...|++|++|+.+|+|.....
T Consensus 21 ~g~~lPsE~eLa~~~~Vsr~Tvr~Al~~L~~eGli~~~~g 60 (231)
T TIGR03337 21 PGDKLPSERDLGERFNTTRVTIREALQQLEAEGLIYREDR 60 (231)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCeEEEeCC
Confidence 6678889999999999999999999999999999987654
No 56
>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=94.98 E-value=0.048 Score=41.03 Aligned_cols=43 Identities=26% Similarity=0.400 Sum_probs=36.7
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec----cccceEEEe
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS----AHASQQIYT 103 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~----k~~~q~IYt 103 (108)
+|...||++++|+-+-.++.|+.|++.|+|.... .+++..+|.
T Consensus 16 ~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~~~~~~~gRp~~~y~ 62 (203)
T TIGR02702 16 ATAAALAEALAISPQAVRRHLKDLETEGLIEYEAVVQGMGRPQYHYQ 62 (203)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEeecccCCCCCceEEE
Confidence 8999999999999999999999999999998762 345555554
No 57
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=94.90 E-value=0.05 Score=41.62 Aligned_cols=52 Identities=19% Similarity=0.238 Sum_probs=41.8
Q ss_pred CHHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 44 DQATYDKLLSEAPK------YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 44 dk~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
-...|+.|...|-. .++-|-..||++|+|+-+-.|.||+.|+..|+|...-+
T Consensus 10 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~ 67 (253)
T PRK11523 10 YQQLAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKG 67 (253)
T ss_pred HHHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34566666666543 46667899999999999999999999999999986543
No 58
>PF13730 HTH_36: Helix-turn-helix domain
Probab=94.90 E-value=0.036 Score=33.18 Aligned_cols=31 Identities=29% Similarity=0.500 Sum_probs=28.5
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLI 90 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlI 90 (108)
+-+-..||+.+++.-+-.+++|++|++.|+|
T Consensus 25 ~pS~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 25 FPSQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 3367899999999999999999999999987
No 59
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=94.82 E-value=0.042 Score=43.42 Aligned_cols=49 Identities=10% Similarity=0.094 Sum_probs=43.1
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+=+++|+..+.....+|...||+.|+|+..-+|+=|.+|+++|++..+.
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 4566777777777779999999999999999999999999999999765
No 60
>PRK10079 phosphonate metabolism transcriptional regulator PhnF; Provisional
Probab=94.74 E-value=0.051 Score=41.40 Aligned_cols=50 Identities=20% Similarity=0.220 Sum_probs=39.9
Q ss_pred HHHHHHHhhC-CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 46 ATYDKLLSEA-PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 46 ~t~dKl~KEV-pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
.+.++|..+. |+.++=|=..||++|+|+-...|+||.+|+.+|+|...-+
T Consensus 20 ~L~~~I~~~~~~G~~LPsE~eLa~~~~VSR~TVR~Al~~L~~eGli~r~~G 70 (241)
T PRK10079 20 KLEQELRQHYRCGDYLPAEQQLAARYEVNRHTLRRAIDQLVEKGWVQRRQG 70 (241)
T ss_pred HHHHHHhcccCCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 3444444333 4568889999999999999999999999999999987543
No 61
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=94.70 E-value=0.12 Score=37.72 Aligned_cols=58 Identities=22% Similarity=0.391 Sum_probs=48.0
Q ss_pred eCHHHHHHHHh-hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe----ccccceEEEec
Q 033932 43 FDQATYDKLLS-EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV----SAHASQQIYTR 104 (108)
Q Consensus 43 ~dk~t~dKl~K-EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V----~k~~~q~IYtr 104 (108)
.|-+.|..|+. +-| .|.-.|||++++.-|.+.++|+-|.+.|+|... -+++.-.||-+
T Consensus 28 ~Dv~v~~~LL~~~~~----~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~~~Ggy~yiY~~ 90 (126)
T COG3355 28 LDVEVYKALLEENGP----LTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNLKGGGYYYLYKP 90 (126)
T ss_pred HHHHHHHHHHhhcCC----cCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeeccCCCceeEEEec
Confidence 57889999994 444 699999999999999999999999999999876 34455567754
No 62
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=94.67 E-value=0.068 Score=40.75 Aligned_cols=52 Identities=21% Similarity=0.203 Sum_probs=42.7
Q ss_pred CHHHHHHHHhhCCC------CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 44 DQATYDKLLSEAPK------YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 44 dk~t~dKl~KEVpk------~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
.+..|+.|...|-. .++-|-..||++|+|+-+..|-||+.|+..|+|...-+
T Consensus 12 ~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~ 69 (254)
T PRK09464 12 SDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG 69 (254)
T ss_pred HHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 35567777776644 45558899999999999999999999999999997653
No 63
>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=94.64 E-value=0.067 Score=34.43 Aligned_cols=35 Identities=20% Similarity=0.340 Sum_probs=30.8
Q ss_pred chhhhhhhhccc-HHHHHHHHHHHHHcCCeeEeccc
Q 033932 62 TPSILSDRLRIN-GSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 62 Tps~vserlkI~-~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
|..+|++.|+++ -|-+..-|+.|+++|+|.....-
T Consensus 27 t~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~~~ 62 (65)
T PF01726_consen 27 TVREIAEALGLKSTSTVQRHLKALERKGYIRRDPGK 62 (65)
T ss_dssp -HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGCCS
T ss_pred CHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCCCC
Confidence 778999999998 99999999999999999886543
No 64
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=94.39 E-value=0.095 Score=33.71 Aligned_cols=34 Identities=24% Similarity=0.300 Sum_probs=32.3
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
-+|++.||+.+++.-+-+++.|..|++.|+|...
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 5999999999999999999999999999999874
No 65
>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=94.29 E-value=0.097 Score=37.10 Aligned_cols=41 Identities=22% Similarity=0.242 Sum_probs=35.7
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
.-..+|...||++++|.....+++|+.|...|+|.-+...+
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 34579999999999999999999999999999998754433
No 66
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=94.28 E-value=0.068 Score=40.04 Aligned_cols=49 Identities=16% Similarity=0.251 Sum_probs=40.6
Q ss_pred HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+..|+.|...| |+.++ +...||++|+|+-+-.|-||+.|+..|+|....
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 55777777766 44566 568999999999999999999999999998654
No 67
>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=94.15 E-value=0.11 Score=39.85 Aligned_cols=46 Identities=26% Similarity=0.294 Sum_probs=40.2
Q ss_pred HHHHHHHhhC--CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 46 ATYDKLLSEA--PKYKLITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 46 ~t~dKl~KEV--pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
....+|+.=+ .....+|+..|++.++++..+|+..|.+|+..|++.
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 5567777777 778999999999999999999999999999999984
No 68
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=93.99 E-value=0.089 Score=36.36 Aligned_cols=38 Identities=26% Similarity=0.380 Sum_probs=34.4
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
++-..+|...||+.++|+.+..+++|+.|...|+|.-.
T Consensus 21 ~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 21 PDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 44558899999999999999999999999999998764
No 69
>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=93.79 E-value=0.13 Score=34.83 Aligned_cols=37 Identities=19% Similarity=0.283 Sum_probs=34.0
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
...-+|++.||+.+++.=+-..++|.+|+++|+|..-
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 3568999999999999999999999999999999864
No 70
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=93.65 E-value=0.092 Score=36.61 Aligned_cols=35 Identities=11% Similarity=0.289 Sum_probs=32.7
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
..+|...||++++|+-+..+++|+.|++.|+|.-+
T Consensus 24 ~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 24 QPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred CCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 46899999999999999999999999999999765
No 71
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=93.64 E-value=0.14 Score=36.13 Aligned_cols=36 Identities=19% Similarity=0.322 Sum_probs=33.9
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
..-+|++.||+++++.-|-.=++|..|+++|+|...
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~ 87 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERL 87 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 446999999999999999999999999999999988
No 72
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=93.62 E-value=0.16 Score=35.69 Aligned_cols=41 Identities=15% Similarity=0.210 Sum_probs=35.3
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec--cccceE
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS--AHASQQ 100 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~--k~~~q~ 100 (108)
-+|++.||+++++.-|-.-+++..|+++|+|.... .++|..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~~~~DrR~~ 88 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQTCASDRRAK 88 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeecCCCCcCee
Confidence 46899999999999999999999999999999983 344443
No 73
>COG4465 CodY Pleiotropic transcriptional repressor [Transcription]
Probab=93.61 E-value=0.14 Score=41.35 Aligned_cols=54 Identities=22% Similarity=0.338 Sum_probs=46.3
Q ss_pred cceeCHHHHHHHHhhCCC-CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 40 MVLFDQATYDKLLSEAPK-YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 40 ~Vl~dk~t~dKl~KEVpk-~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
.-+-+-+.++-|..|.-. .=+++.|.||||.+|+-|+-=.|||.|++-|+|.-=
T Consensus 183 LSYSEleAve~I~eELdG~EG~lvASkiADrvGITRSVIVNALRKlESAGvIeSR 237 (261)
T COG4465 183 LSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESR 237 (261)
T ss_pred ccHHHHHHHHHHHHhcCCccceeeehhhhhhhCchHHHHHHHHHHhhhcCceeec
Confidence 334456778888888876 479999999999999999999999999999999754
No 74
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=93.56 E-value=0.14 Score=39.82 Aligned_cols=46 Identities=17% Similarity=0.255 Sum_probs=40.4
Q ss_pred HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
.++|+..+.....+|...|++.|+|+-+-+|+-|.+|+++|+|..+
T Consensus 6 ~~~Il~~l~~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~ 51 (240)
T PRK10411 6 QQAIVDLLLNHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRN 51 (240)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 4556666767789999999999999999999999999999999763
No 75
>PRK10870 transcriptional repressor MprA; Provisional
Probab=93.53 E-value=0.14 Score=38.07 Aligned_cols=35 Identities=34% Similarity=0.298 Sum_probs=33.5
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
.-+|++.||+.+++..+-.-++|..|+++|+|...
T Consensus 70 ~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~ 104 (176)
T PRK10870 70 HSIQPSELSCALGSSRTNATRIADELEKRGWIERR 104 (176)
T ss_pred CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 46899999999999999999999999999999998
No 76
>PRK04424 fatty acid biosynthesis transcriptional regulator; Provisional
Probab=93.49 E-value=0.046 Score=41.13 Aligned_cols=48 Identities=17% Similarity=0.096 Sum_probs=42.0
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+=.+.|+..+.....+|...||+.|+++.+-+|+=|.+|++.|++..+
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 345667777777889999999999999999999999999999998764
No 77
>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=93.47 E-value=0.11 Score=40.11 Aligned_cols=58 Identities=17% Similarity=0.204 Sum_probs=45.3
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
++..+..-|...+++....||..|+++..-+-.-|++|+..|.|.-|.-.++..||+-
T Consensus 100 lL~~Fi~yIK~~Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIyIs 157 (188)
T PF09756_consen 100 LLQEFINYIKEHKVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIYIS 157 (188)
T ss_dssp HHHHHHHHHHH-SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE--
T ss_pred HHHHHHHHHHHcceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEEec
Confidence 6778888888889999999999999999999999999999999999988899999974
No 78
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=93.44 E-value=0.2 Score=31.84 Aligned_cols=34 Identities=29% Similarity=0.448 Sum_probs=32.2
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
-+|+..|++.++++-+-..++|+.|++.|+|...
T Consensus 24 ~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 24 PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 4899999999999999999999999999999877
No 79
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=93.28 E-value=0.2 Score=33.45 Aligned_cols=44 Identities=18% Similarity=0.380 Sum_probs=37.0
Q ss_pred CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
|...+.-|..+ .-+|.+.||+.++++-+-+++.|+.|++.|+|.
T Consensus 5 D~~il~~L~~~----~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~ 48 (108)
T smart00344 5 DRKILEELQKD----ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIK 48 (108)
T ss_pred HHHHHHHHHHh----CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCee
Confidence 45555555544 248999999999999999999999999999998
No 80
>PRK04158 transcriptional repressor CodY; Validated
Probab=93.27 E-value=0.11 Score=42.05 Aligned_cols=61 Identities=21% Similarity=0.334 Sum_probs=52.6
Q ss_pred hHHhhhccceeCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 33 QKEKVNNMVLFDQATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 33 ~keK~nn~Vl~dk~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+++-++..-+-.-+..+-|..|.... =+++.|-||||.+|+-||-=.|||-||+-|+|.-=
T Consensus 173 V~~Ai~tLSySEleAv~hIf~eL~g~EG~lvASkiADrvgITRSVIVNALRK~ESAGvIESr 234 (256)
T PRK04158 173 VQMAINTLSYSELEAVEHIFEELDGNEGLLVASKIADRVGITRSVIVNALRKLESAGVIESR 234 (256)
T ss_pred HHHHHHhcCHhHHHHHHHHHHhcCCCcceEEeeecccccCCchhhhhhhhhhhhcccceeec
Confidence 45556666666778889999999885 79999999999999999999999999999999743
No 81
>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=93.05 E-value=0.24 Score=30.91 Aligned_cols=32 Identities=19% Similarity=0.379 Sum_probs=30.6
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
-+|...||+-++++-.-.-++|++|+++|+|.
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 47899999999999999999999999999998
No 82
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=92.92 E-value=0.15 Score=33.27 Aligned_cols=32 Identities=19% Similarity=0.395 Sum_probs=29.5
Q ss_pred hhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 63 PSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 63 ps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+..+|+.++|+-|-..++|+.|+++|+|....
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 56899999999999999999999999998754
No 83
>TIGR01884 cas_HTH CRISPR locus-related DNA-binding protein. Most but not all examples of this family are associated with CRISPR loci, a combination of DNA repeats and characteristic proteins encoded near the repeat cluster. The C-terminal region of this protein is homologous to DNA-binding helix-turn-helix domains with predicted transcriptional regulatory activity.
Probab=92.89 E-value=0.19 Score=37.80 Aligned_cols=46 Identities=20% Similarity=0.192 Sum_probs=38.1
Q ss_pred HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
.++..+-...-+|...+|+.+++.-|.+++.|..|++.|+|.....
T Consensus 147 ~IL~~l~~~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 147 KVLEVLKAEGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHHHcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 4444443334589999999999999999999999999999998863
No 84
>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=92.77 E-value=0.26 Score=33.60 Aligned_cols=35 Identities=20% Similarity=0.215 Sum_probs=33.4
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
.-+|++.||+.+++.-|-.-++++.|+++|+|..+
T Consensus 42 ~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~ 76 (109)
T TIGR01889 42 GKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKE 76 (109)
T ss_pred CcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEecc
Confidence 46999999999999999999999999999999987
No 85
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=92.65 E-value=0.24 Score=32.22 Aligned_cols=44 Identities=20% Similarity=0.189 Sum_probs=31.5
Q ss_pred HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
+-.|++.+. ..-.+++.|+...+++.+.+.+.|++|+++|+|..
T Consensus 8 i~~IL~~l~-~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~ 51 (77)
T PF14947_consen 8 IFDILKILS-KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK 51 (77)
T ss_dssp HHHHHHHH--TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHHHH-cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC
Confidence 334454443 34567899999999999999999999999999943
No 86
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=92.64 E-value=0.27 Score=34.88 Aligned_cols=36 Identities=14% Similarity=0.104 Sum_probs=32.6
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
...+|.+.||+.++|+-+-+..+|+.|+.+|+|...
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 87
>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=92.43 E-value=0.17 Score=29.07 Aligned_cols=40 Identities=18% Similarity=0.228 Sum_probs=30.9
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|+..+|+.++|+-+ -|+.++++|+|.+....++...|+.
T Consensus 1 ~~~~e~a~~~gv~~~----tlr~~~~~g~l~~~~~~~~~~~y~~ 40 (49)
T cd04761 1 YTIGELAKLTGVSPS----TLRYYERIGLLSPARTEGGYRLYSD 40 (49)
T ss_pred CcHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCEEeCH
Confidence 378899999998766 5788899999986544457778874
No 88
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=92.29 E-value=0.25 Score=36.18 Aligned_cols=46 Identities=17% Similarity=0.238 Sum_probs=39.1
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
...+|...||++++|+-+.-+++|..|.+.|+|+-+-....-..-.
T Consensus 23 ~~~~s~~~IA~~~~is~~~L~kil~~L~kaGlV~S~rG~~GGy~La 68 (150)
T COG1959 23 GGPVSSAEIAERQGISPSYLEKILSKLRKAGLVKSVRGKGGGYRLA 68 (150)
T ss_pred CCcccHHHHHHHhCcCHHHHHHHHHHHHHcCCEEeecCCCCCccCC
Confidence 3489999999999999999999999999999999987655544333
No 89
>PF01022 HTH_5: Bacterial regulatory protein, arsR family; InterPro: IPR001845 Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis. The HTH motif is thought to be located in the central part of these proteins []. The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) []. It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA []. The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers []. The dimer interface is formed by helix 5 and an N-terminal part []. Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N terminus, called the alpha3(N) site []. The second metal-binding site is located in helix 5 (and C terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites [, ]. Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognised by multimeric arsR-type metalloregulators. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3CUO_A 1U2W_C 3F72_C 3F6V_A 3JTH_B 2P4W_B 1KU9_B 2LKP_B 1SMT_A 1R22_B ....
Probab=92.07 E-value=0.31 Score=28.71 Aligned_cols=33 Identities=24% Similarity=0.371 Sum_probs=29.7
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
.=.|+..|++.+++.-|....=|+.|.+.|+|.
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 347899999999999999999999999999985
No 90
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=91.99 E-value=0.31 Score=35.62 Aligned_cols=41 Identities=17% Similarity=0.238 Sum_probs=36.1
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccce
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQ 99 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q 99 (108)
..+|..+||++++|+-+.-+++|..|...|+|.-+...+.-
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 46799999999999999999999999999999987654433
No 91
>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=91.94 E-value=0.61 Score=27.71 Aligned_cols=28 Identities=32% Similarity=0.487 Sum_probs=26.7
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcC
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARG 88 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kG 88 (108)
||...||+.|+|+-...++-|.+|.+.|
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 92
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=91.88 E-value=0.31 Score=27.80 Aligned_cols=30 Identities=23% Similarity=0.418 Sum_probs=25.8
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLI 90 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlI 90 (108)
+|-..||+-++.+....-++|..|+++|+|
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 577889999999999999999999999997
No 93
>PRK11050 manganese transport regulator MntR; Provisional
Probab=91.86 E-value=0.32 Score=35.38 Aligned_cols=34 Identities=21% Similarity=0.317 Sum_probs=31.5
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
.-+|+..||++|+|+-|-..++|+.|++.|+|..
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 3479999999999999999999999999999865
No 94
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=91.85 E-value=0.27 Score=37.08 Aligned_cols=55 Identities=20% Similarity=0.319 Sum_probs=45.6
Q ss_pred cceeCHHHHHHHHhhCCCCe-----eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 40 MVLFDQATYDKLLSEAPKYK-----LITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 40 ~Vl~dk~t~dKl~KEVpk~k-----~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
........|+.|...|-.-. -|+...||++|+|+-.--|.||..|+..|+|...-
T Consensus 14 ~~~~~~~vy~~Lr~~Il~g~l~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p 73 (230)
T COG1802 14 PDTLADQVYEELREAILSGELAPGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEP 73 (230)
T ss_pred cccHHHHHHHHHHHHHHhCCCCCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecC
Confidence 34455667888877776654 48899999999999999999999999999999874
No 95
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=91.82 E-value=0.4 Score=31.17 Aligned_cols=30 Identities=27% Similarity=0.496 Sum_probs=29.3
Q ss_pred hhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 64 SILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 64 s~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+.||+++++..|-.-++|+.|+++|+|...
T Consensus 40 ~~la~~l~i~~~~vt~~l~~Le~~glv~r~ 69 (126)
T COG1846 40 KELAERLGLDRSTVTRLLKRLEDKGLIERL 69 (126)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHCCCeeec
Confidence 999999999999999999999999999987
No 96
>PF10007 DUF2250: Uncharacterized protein conserved in archaea (DUF2250); InterPro: IPR019254 Members of this family of hypothetical archaeal proteins have no known function.
Probab=91.65 E-value=0.25 Score=34.23 Aligned_cols=47 Identities=26% Similarity=0.287 Sum_probs=37.5
Q ss_pred HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
+|+.-.-.+-.=+|-.+|-++++...-.+.+|++|++.|||..|...
T Consensus 11 ~IL~hl~~~~~Dy~k~ia~~l~~~~~~v~~~l~~Le~~GLler~~g~ 57 (92)
T PF10007_consen 11 KILQHLKKAGPDYAKSIARRLKIPLEEVREALEKLEEMGLLERVEGK 57 (92)
T ss_pred HHHHHHHHHCCCcHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCc
Confidence 34444444444468899999999999999999999999999998743
No 97
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=91.59 E-value=0.41 Score=34.83 Aligned_cols=46 Identities=22% Similarity=0.354 Sum_probs=39.7
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
|..+|=|.-.+|..++||.-...++.++|++.|+|.- .++...|..
T Consensus 31 pGdkLPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t---~rg~G~fV~ 76 (125)
T COG1725 31 PGDKLPSVRELAKDLGVNPNTVQRAYQELEREGIVET---KRGKGTFVT 76 (125)
T ss_pred CCCCCCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE---ecCeeEEEc
Confidence 6689999999999999999999999999999999965 345556654
No 98
>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=91.53 E-value=0.27 Score=28.53 Aligned_cols=37 Identities=16% Similarity=0.203 Sum_probs=25.5
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCe-eEeccccceEEE
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLI-RMVSAHASQQIY 102 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlI-k~V~k~~~q~IY 102 (108)
|+..+|+.++|+.+ .||..+++||| .+....+....|
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 56788999988764 69999999999 555433444444
No 99
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=91.53 E-value=0.19 Score=30.87 Aligned_cols=40 Identities=13% Similarity=0.140 Sum_probs=30.9
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-ccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV-SAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V-~k~~~q~IYtr 104 (108)
.|+..+|+.++|+-+. |+.++++|+|.+. ...++...|+.
T Consensus 1 ~s~~eva~~~gvs~~t----lr~~~~~gli~~~~~~~~g~r~y~~ 41 (70)
T smart00422 1 YTIGEVAKLAGVSVRT----LRYYERIGLLPPPIRTEGGYRLYSD 41 (70)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHCCCCCCCccCCCCCEecCH
Confidence 4788999999987654 6788899999987 44556677864
No 100
>cd07153 Fur_like Ferric uptake regulator(Fur) and related metalloregulatory proteins; typically iron-dependent, DNA-binding repressors and activators. Ferric uptake regulator (Fur) and related metalloregulatory proteins are iron-dependent, DNA-binding repressors and activators mainly involved in iron metabolism. A general model for Fur repression under iron-rich conditions is that activated Fur (a dimer having one Fe2+ coordinated per monomer) binds to specific DNA sequences (Fur boxes) in the promoter region of iron-responsive genes, hindering access of RNA polymerase, and repressing transcription. Positive regulation by Fur can be direct or indirect, as in the Fur repression of an anti-sense regulatory small RNA. Some members sense metal ions other than Fe2+. For example, the zinc uptake regulator (Zur) responds to Zn2+, the manganese uptake regulator (Mur) responds to Mn2+, and the nickel uptake regulator (Nur) responds to Ni2+. Other members sense signals other than metal ions.
Probab=91.48 E-value=0.49 Score=31.91 Aligned_cols=45 Identities=20% Similarity=0.296 Sum_probs=36.7
Q ss_pred eeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 59 KLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 59 k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
.-+|+..|.+++ +|+.+-.-+.|+.|++.|+|..+.-..+...|-
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 688889999999999999999996544445553
No 101
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=91.39 E-value=0.49 Score=35.05 Aligned_cols=49 Identities=10% Similarity=0.213 Sum_probs=39.2
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+.+.-|..-.-+--.++...||++|+|.-+-+..+|+.|++.|+|..+-
T Consensus 10 dYL~~Iy~l~~~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~ 58 (154)
T COG1321 10 DYLETIYELLEEKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEP 58 (154)
T ss_pred HHHHHHHHHHhccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEec
Confidence 3344444333356789999999999999999999999999999998753
No 102
>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=91.37 E-value=0.2 Score=33.36 Aligned_cols=41 Identities=20% Similarity=0.291 Sum_probs=32.9
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc-ceEEEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA-SQQIYTR 104 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~-~q~IYtr 104 (108)
+.|+..+|+.++|+.+- ||..+++|+|.+..... +...|+.
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 46899999999988765 78889999999875443 7778874
No 103
>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=91.32 E-value=0.61 Score=29.18 Aligned_cols=35 Identities=17% Similarity=0.213 Sum_probs=31.1
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
.+|...||++++|+-+..++.|+.|++.|+.....
T Consensus 13 ~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~ 47 (69)
T TIGR00122 13 PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTV 47 (69)
T ss_pred CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 36789999999999999999999999999965544
No 104
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=91.17 E-value=0.62 Score=37.33 Aligned_cols=80 Identities=19% Similarity=0.172 Sum_probs=58.8
Q ss_pred ccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 25 KKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 25 KKKWsKgk~keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.-.|+.+=..+-..+-.-|+++..+=|.=..-+-=-||.++|...+++.=+-.-++|++||++|+|+..-+++...|-.+
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 34577754444455545555554444333333445899999999999999999999999999999999988888877554
No 105
>PRK09954 putative kinase; Provisional
Probab=91.09 E-value=0.25 Score=39.53 Aligned_cols=42 Identities=29% Similarity=0.409 Sum_probs=36.3
Q ss_pred HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
+|+..+.....||.+.||++|+|+-+-++..|+.|+++|+|.
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 455555555689999999999999999999999999999984
No 106
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=91.01 E-value=0.25 Score=37.41 Aligned_cols=50 Identities=16% Similarity=0.092 Sum_probs=43.4
Q ss_pred CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+.++...|+.-++....+|-..||+.++|+..-.|++|..|.+.|||...
T Consensus 20 ~~~~~~~Vl~~L~~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~ 69 (178)
T PRK06266 20 GDEEGFEVLKALIKKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYK 69 (178)
T ss_pred CCccHhHHHHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEe
Confidence 45666777777777778999999999999999999999999999999843
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=90.98 E-value=0.34 Score=35.90 Aligned_cols=53 Identities=13% Similarity=0.135 Sum_probs=39.4
Q ss_pred CHHHHHHHHhhCCCC-eeechhhhhhhhccc-HHHHHHHHHHHHHcCCeeEeccc
Q 033932 44 DQATYDKLLSEAPKY-KLITPSILSDRLRIN-GSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 44 dk~t~dKl~KEVpk~-k~ITps~vserlkI~-~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
+.+.++-|...+-.. --.|...||+++++. -|.....|+.|+++|+|......
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 445566666432211 126677999999999 89999999999999999987543
No 108
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=90.94 E-value=0.47 Score=35.30 Aligned_cols=42 Identities=19% Similarity=0.199 Sum_probs=36.2
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
+.-..+|...||++++|.....+++|+.|.+.|+|.-....+
T Consensus 21 ~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~rG~~ 62 (164)
T PRK10857 21 SEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSVRGPG 62 (164)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeCCCCC
Confidence 344679999999999999999999999999999999754433
No 109
>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=90.91 E-value=0.28 Score=32.58 Aligned_cols=41 Identities=12% Similarity=0.183 Sum_probs=32.7
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+.|++.+|+.++|+.+. |+..++.|+|.+.-..+....|+.
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 36899999999998765 788899999998754456677864
No 110
>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=90.81 E-value=0.26 Score=33.47 Aligned_cols=41 Identities=20% Similarity=0.271 Sum_probs=32.7
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+.|.+.+|+.++|+.+. ||..++.|+|.+.-..++...|+.
T Consensus 1 ~~~i~eva~~~gVs~~t----LR~ye~~Gli~p~r~~~g~R~Ys~ 41 (98)
T cd01279 1 LYPISVAAELLGIHPQT----LRVYDRLGLVSPARTNGGGRRYSN 41 (98)
T ss_pred CcCHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCeeECH
Confidence 46889999999988765 678899999998644557788874
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=90.76 E-value=0.49 Score=38.95 Aligned_cols=67 Identities=16% Similarity=0.255 Sum_probs=43.6
Q ss_pred hhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--ccccceEEEec
Q 033932 36 KVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV--SAHASQQIYTR 104 (108)
Q Consensus 36 K~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V--~k~~~q~IYtr 104 (108)
|++..---+.-.|+-|. + -+.+=|....|-.+.++.-+.-.++|+.|++++||+.| .+|+...||.-
T Consensus 78 k~~~l~~~e~lvy~~I~-~-ag~~GIw~~~i~~~t~l~~~~~~k~lk~Le~k~lIK~vksv~~~~rK~Yml 146 (327)
T PF05158_consen 78 KLKGLSDEERLVYQLIE-E-AGNKGIWTKDIKKKTNLHQTQLTKILKSLESKKLIKSVKSVKNPNRKVYML 146 (327)
T ss_dssp ---SSSCCHHHHHHHHH-H-HTTT-EEHHHHHHHCT--HHHHHHHHHHHHHTTSEEEE--SS-SS--EEEE
T ss_pred hhcCCCHHHHHHHHHHH-H-hCCCCCcHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEecCcCCCCeEEEEE
Confidence 34444334444555554 2 23456778899999999999999999999999999999 55667778863
No 112
>PRK15481 transcriptional regulatory protein PtsJ; Provisional
Probab=90.66 E-value=0.43 Score=38.95 Aligned_cols=50 Identities=20% Similarity=0.272 Sum_probs=39.5
Q ss_pred HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
...|+.|..+| |..++=+.-.||+.|+|+-+..++++++|+++|+|....
T Consensus 8 ~~~~~~i~~~i~~g~l~~g~~lps~r~la~~~~vsr~tv~~a~~~L~~~g~i~~~~ 63 (431)
T PRK15481 8 NEIFDSIRQLIQAGRLRPGDSLPPVRELASELGVNRNTVAAAYKRLVTAGLAQSQG 63 (431)
T ss_pred HHHHHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 34455555554 345666788999999999999999999999999997543
No 113
>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=90.61 E-value=1.1 Score=30.68 Aligned_cols=54 Identities=30% Similarity=0.427 Sum_probs=39.8
Q ss_pred HHhhCCCCeeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932 51 LLSEAPKYKLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT 106 (108)
Q Consensus 51 l~KEVpk~k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~ 106 (108)
++.+-+. -+|+..|-+++ .|+.|---+.|+.|++.|+|..+...++...|-.+.
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 3444455 67888888877 466667789999999999999998777777776543
No 114
>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=90.50 E-value=0.39 Score=32.28 Aligned_cols=33 Identities=21% Similarity=0.237 Sum_probs=29.5
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLI 90 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlI 90 (108)
-.=|....|+++|++...=-|.+|++|.+.|.|
T Consensus 63 ~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 63 EEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred CCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 355899999999999999999999999999987
No 115
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=90.25 E-value=0.61 Score=34.04 Aligned_cols=43 Identities=26% Similarity=0.333 Sum_probs=35.7
Q ss_pred HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
+|+.....--=+|.+.||++++++-+-.++=++.|++.|+|.-
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 4444444445578899999999999999999999999999974
No 116
>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=90.17 E-value=0.74 Score=32.85 Aligned_cols=44 Identities=16% Similarity=0.170 Sum_probs=34.9
Q ss_pred echhhhhhh----hcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932 61 ITPSILSDR----LRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA 105 (108)
Q Consensus 61 ITps~vser----lkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~ 105 (108)
+|+..|.+. +++.-+.....|+.|+++|+|... +.++..+|++.
T Consensus 19 ~t~~eI~~~l~~~~~~~~tTv~T~L~rL~~KG~v~~~-k~gr~~~Y~p~ 66 (130)
T TIGR02698 19 TTSRDIIRILAEKKDWSDSTIKTLLGRLVDKGCLTTE-KEGRKFIYTAL 66 (130)
T ss_pred CCHHHHHHHHhhccCCcHHHHHHHHHHHHHCCceeee-cCCCcEEEEec
Confidence 488885544 578999999999999999999775 44567789864
No 117
>PRK13777 transcriptional regulator Hpr; Provisional
Probab=90.03 E-value=0.53 Score=35.89 Aligned_cols=36 Identities=19% Similarity=0.084 Sum_probs=32.9
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
..-+|++.||+.+.+..|-.-++|..|+++|+|...
T Consensus 57 ~~~itq~eLa~~l~l~~sTvtr~l~rLE~kGlI~R~ 92 (185)
T PRK13777 57 LKGASISEIAKFGVMHVSTAFNFSKKLEERGYLTFS 92 (185)
T ss_pred CCCcCHHHHHHHHCCCHhhHHHHHHHHHHCCCEEec
Confidence 345899999999999988888999999999999987
No 118
>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=89.58 E-value=0.31 Score=33.23 Aligned_cols=40 Identities=23% Similarity=0.210 Sum_probs=32.8
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+|...||++++|+.+. ||.-++.|+|.+....+...+|+.
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 779999999998655567778874
No 119
>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=89.45 E-value=0.38 Score=32.76 Aligned_cols=40 Identities=20% Similarity=0.300 Sum_probs=31.8
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|...||++++|+.+ .||..++.|+|.+.-..++...|+.
T Consensus 2 ~~i~eva~~~gvs~~----tLR~ye~~Gll~~~r~~~g~R~Y~~ 41 (102)
T cd04775 2 YTIGQMSRKFGVSRS----TLLYYESIGLIPSARSEANYRLYSE 41 (102)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCCeeeCH
Confidence 588999999998876 5799999999955544456778874
No 120
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=89.05 E-value=0.74 Score=33.15 Aligned_cols=46 Identities=11% Similarity=0.238 Sum_probs=39.2
Q ss_pred eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
+|...++-|+.+ -=++.+.||++++++-+-.+.=++.|++.|+|.-
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 466667777766 3478999999999999999999999999999973
No 121
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=88.97 E-value=0.88 Score=32.94 Aligned_cols=41 Identities=17% Similarity=0.259 Sum_probs=34.1
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY 102 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY 102 (108)
-+|...||+.++++-.-.-++|++|+++|+|..- ++...||
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~--~~~i~i~ 208 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAH--GKTIVVY 208 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEec--CCEEEEe
Confidence 4888999999999999999999999999999742 3345555
No 122
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=88.89 E-value=0.39 Score=32.70 Aligned_cols=41 Identities=15% Similarity=0.176 Sum_probs=33.5
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc-cceEEEecc
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH-ASQQIYTRA 105 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~-~~q~IYtr~ 105 (108)
.|...||+.++|+. +.||.-++.|||.|.... ++.++|+..
T Consensus 1 ~~I~eva~~~gvs~----~tLRyYE~~GLl~p~~~~~~gyR~Ys~~ 42 (124)
T COG0789 1 YTIGEVAKLTGVSV----RTLRFYERKGLLSPERRDEGGYRYYTPE 42 (124)
T ss_pred CcHHHHHHHhCCCH----HHHHHHHHcCCCCCcccCCCCceecCHH
Confidence 36788999997765 569999999999999666 588999853
No 123
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=88.87 E-value=0.78 Score=35.59 Aligned_cols=57 Identities=19% Similarity=0.420 Sum_probs=43.4
Q ss_pred HHHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 45 QATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 45 k~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
...+++|...| |+-++=|-..|||+|+|+=++-|-+|+.|+..|+|.. .++-.+|.+
T Consensus 13 ~~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~---r~G~Gt~V~ 75 (241)
T COG2186 13 DEVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEI---RQGSGTFVR 75 (241)
T ss_pred HHHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeee---cCCCceEec
Confidence 44555555554 4567888899999999999999999999999999965 233345553
No 124
>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=88.72 E-value=0.32 Score=33.68 Aligned_cols=40 Identities=15% Similarity=0.194 Sum_probs=31.8
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
.|...||++++|+.+ .||.-++.|||.+..+ .++.+.|+.
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 378899999998865 6899999999997644 456677874
No 125
>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=88.67 E-value=0.43 Score=32.14 Aligned_cols=40 Identities=13% Similarity=0.169 Sum_probs=32.6
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
+|.+.||+.++|+.+ .||.-++.|+|.++.. .++...|+.
T Consensus 1 ~ti~eva~~~gvs~~----tLRyye~~Gll~p~~~~~~gyR~Y~~ 41 (96)
T cd04768 1 LTIGEFAKLAGVSIR----TLRHYDDIGLFKPAKIAENGYRYYSY 41 (96)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCeeeCCH
Confidence 378899999999876 5899999999999854 566778874
No 126
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=88.63 E-value=1.1 Score=34.48 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=32.9
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
-+|.+.||++++++-|-+.++|+.|++.|++.....
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 489999999999999999999999999999977543
No 127
>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=88.10 E-value=0.52 Score=33.90 Aligned_cols=40 Identities=23% Similarity=0.423 Sum_probs=33.3
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+.|...||++++|+.+ .||..+++|+|.+.. .++++.|+.
T Consensus 1 lysI~eVA~~~GVs~~----TLR~wE~~GLl~p~r-~~G~R~Ys~ 40 (120)
T cd04767 1 LYPIGVVAELLNIHPE----TLRIWERHGLIKPAR-RNGQRLYSN 40 (120)
T ss_pred CCCHHHHHHHHCcCHH----HHHHHHHCCCCCCcC-CCCcEEECH
Confidence 3688999999998877 467999999999964 478889975
No 128
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=88.06 E-value=1.1 Score=34.88 Aligned_cols=36 Identities=17% Similarity=0.341 Sum_probs=33.1
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
+|.+.||+++++.-|-+.++|..|++.|+|......
T Consensus 27 ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~ 62 (263)
T PRK09834 27 ATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASD 62 (263)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCC
Confidence 899999999999999999999999999999876433
No 129
>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=87.78 E-value=1.8 Score=29.70 Aligned_cols=45 Identities=13% Similarity=0.191 Sum_probs=34.9
Q ss_pred echhhhhhhhc----ccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932 61 ITPSILSDRLR----INGSLARKAIRELMARGLIRMVSAHASQQIYTRAT 106 (108)
Q Consensus 61 ITps~vserlk----I~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~ 106 (108)
+|...|.+.+. +.-|-.+..|+.|+++|+|..-. .++..+|.+..
T Consensus 18 ~t~~eI~~~l~~~~~~~~sTv~t~L~rL~~Kg~l~~~~-~gr~~~Y~p~i 66 (115)
T PF03965_consen 18 ATVREIHEALPEERSWAYSTVQTLLNRLVEKGFLTREK-IGRAYVYSPLI 66 (115)
T ss_dssp EEHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEE-ETTCEEEEESS
T ss_pred CCHHHHHHHHHhccccchhHHHHHHHHHHhCCceeEee-cCCceEEEeCC
Confidence 67777776665 66899999999999999999864 46788998653
No 130
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=87.77 E-value=0.58 Score=34.71 Aligned_cols=42 Identities=29% Similarity=0.444 Sum_probs=35.7
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.++|...||.+++|+.+ .||.-++.|||.+.-..+..+.|+.
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 68999999999999876 5899999999999755566788874
No 131
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=87.72 E-value=0.66 Score=28.50 Aligned_cols=40 Identities=18% Similarity=0.216 Sum_probs=31.3
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|...||+.++|+.+ .||..+++|+|.+.-..+....|+.
T Consensus 1 yti~eva~~~gvs~~----tlr~y~~~gll~~~~~~~g~r~y~~ 40 (69)
T PF13411_consen 1 YTIKEVAKLLGVSPS----TLRYYEREGLLPPPRDENGYRYYSE 40 (69)
T ss_dssp EEHHHHHHHTTTTHH----HHHHHHHTTSSTTBESTTSSEEE-H
T ss_pred CcHHHHHHHHCcCHH----HHHHHHHhcCcccccccCceeeccH
Confidence 378899999998655 5899999999888775666688874
No 132
>PF12728 HTH_17: Helix-turn-helix domain
Probab=87.58 E-value=0.77 Score=26.98 Aligned_cols=40 Identities=15% Similarity=0.131 Sum_probs=30.2
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
++|+..+|+-|+|+-+- ++.+..+|.|.++. ..+...|.+
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 57999999999986655 66777899998884 555555543
No 133
>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=87.56 E-value=0.49 Score=33.77 Aligned_cols=43 Identities=21% Similarity=0.332 Sum_probs=35.4
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
|..+|...||++++|+.+ .||.-++.|||.|... .++..+|+.
T Consensus 1 m~~~tI~elA~~~gvs~~----tlR~Ye~~GLL~p~~r~~~gyR~Y~~ 44 (120)
T TIGR02054 1 MNAYTISRLAEDAGVSVH----VVRDYLLRGLLHPVRRTTSGYGIFDD 44 (120)
T ss_pred CCCCcHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeeCCH
Confidence 346799999999999875 5899999999999844 467888875
No 134
>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=87.55 E-value=0.6 Score=32.35 Aligned_cols=39 Identities=18% Similarity=0.230 Sum_probs=32.2
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
|...+|++++|+.+ .||.-++.|||.|+..+....+|+.
T Consensus 2 ~ige~a~~~gvs~~----tLryYe~~GLi~p~~~~~~yR~Y~~ 40 (116)
T cd04769 2 YIGELAQQTGVTIK----AIRLYEEKGLLPSPKRSGNYRVYDA 40 (116)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCCCCCceeeCH
Confidence 67789999998765 5899999999999866667788874
No 135
>PRK09462 fur ferric uptake regulator; Provisional
Probab=87.49 E-value=1.4 Score=31.57 Aligned_cols=43 Identities=12% Similarity=0.274 Sum_probs=28.7
Q ss_pred echhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 61 ITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 61 ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
+|+..|-+++ .|+.+-.-+.|+.|++.|+|..+.-......|-
T Consensus 34 ~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~~~~~~~~y~ 81 (148)
T PRK09462 34 VSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHNFEGGKSVFE 81 (148)
T ss_pred CCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEEcCCCcEEEE
Confidence 4555555544 244555668999999999999986544445554
No 136
>PF13601 HTH_34: Winged helix DNA-binding domain; PDB: 1UB9_A.
Probab=87.37 E-value=2.2 Score=28.08 Aligned_cols=34 Identities=21% Similarity=0.242 Sum_probs=29.6
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
=+|++.|.+.++++-|-..+-|+.|++.|+|..-
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 137
>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=87.13 E-value=1.2 Score=33.23 Aligned_cols=37 Identities=22% Similarity=0.401 Sum_probs=33.8
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+.=+.|-..||+.++++-+--.++|.+|++.|+|..+
T Consensus 72 N~v~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~ 108 (165)
T PF05732_consen 72 NAVVATQKEIAEKLGISKPTVSRAIKELEEKNIIKKI 108 (165)
T ss_pred CeEEeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEc
Confidence 4567899999999999999999999999999999876
No 138
>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=87.13 E-value=0.6 Score=32.52 Aligned_cols=39 Identities=15% Similarity=0.258 Sum_probs=33.3
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
|...+|++++|+.+ .||.-++.|||.++-.+++...|+.
T Consensus 2 ~IgevA~~~gvs~~----tlRyYe~~GLl~p~~~~~gyR~Y~~ 40 (120)
T cd04781 2 DIAEVARQSGLPAS----TLRYYEEKGLIASIGRRGLRRQYDP 40 (120)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCceecCH
Confidence 67889999998865 5899999999999866678888975
No 139
>COG0735 Fur Fe2+/Zn2+ uptake regulation proteins [Inorganic ion transport and metabolism]
Probab=87.12 E-value=1.7 Score=31.61 Aligned_cols=45 Identities=22% Similarity=0.401 Sum_probs=33.9
Q ss_pred HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
+++|+.|..+.|...+-|+ -++|+.|++.|+|..+.-..+...|-
T Consensus 40 eei~~~l~~~~p~islaTV--------------Yr~L~~l~e~Glv~~~~~~~~~~~y~ 84 (145)
T COG0735 40 EELYEELREEGPGISLATV--------------YRTLKLLEEAGLVHRLEFEGGKTRYE 84 (145)
T ss_pred HHHHHHHHHhCCCCCHhHH--------------HHHHHHHHHCCCEEEEEeCCCEEEEe
Confidence 5677777777777665554 47899999999999997666555564
No 140
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=87.01 E-value=1.3 Score=35.40 Aligned_cols=42 Identities=29% Similarity=0.253 Sum_probs=34.5
Q ss_pred HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCC-eeE
Q 033932 51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGL-IRM 92 (108)
Q Consensus 51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGl-Ik~ 92 (108)
|+..+..-..++...||++|+|+-+-.++.|+.|++.|+ |.-
T Consensus 9 il~~L~~~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~ 51 (319)
T PRK11886 9 LLSLLADGDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFS 51 (319)
T ss_pred HHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEE
Confidence 333333457889999999999999999999999999999 543
No 141
>PRK12423 LexA repressor; Provisional
Probab=86.78 E-value=1.1 Score=33.88 Aligned_cols=49 Identities=20% Similarity=0.255 Sum_probs=37.3
Q ss_pred HHHHHHHHhhCCCCee-echhhhhhhhcc-cHHHHHHHHHHHHHcCCeeEe
Q 033932 45 QATYDKLLSEAPKYKL-ITPSILSDRLRI-NGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 45 k~t~dKl~KEVpk~k~-ITps~vserlkI-~~SlAr~~Lr~L~~kGlIk~V 93 (108)
.+.++.|...+-..-+ =|...||+.|++ +-+..+..|+.|+++|+|..-
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 4566666654333322 388899999995 788889999999999999864
No 142
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=86.62 E-value=0.98 Score=33.97 Aligned_cols=34 Identities=24% Similarity=0.338 Sum_probs=28.7
Q ss_pred echhhhhhhhcc--------------cHHHHHHHHHHHHHcCCeeEec
Q 033932 61 ITPSILSDRLRI--------------NGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 61 ITps~vserlkI--------------~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
|....|+..|+. ++|+.|.+|+.||+-|+|....
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 566677777777 5899999999999999999765
No 143
>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=86.50 E-value=1 Score=25.26 Aligned_cols=40 Identities=13% Similarity=0.169 Sum_probs=29.1
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
++|+..+|+.|+|+-+ -|+.|.+.|.|..+..+ +...|.+
T Consensus 1 ~lt~~e~a~~lgis~~----ti~~~~~~g~i~~~~~g-~~~~~~~ 40 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKD----TVYRLIHEGELPAYRVG-RHYRIPR 40 (49)
T ss_pred CCCHHHHHHHHCCCHH----HHHHHHHcCCCCeEEeC-CeEEEeH
Confidence 4789999999987544 57777889998876443 4455543
No 144
>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=86.37 E-value=0.72 Score=25.65 Aligned_cols=40 Identities=13% Similarity=0.324 Sum_probs=28.4
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+|...+|+.|+|+-+ -|+.+.++|.+.......+...|..
T Consensus 1 ~s~~e~a~~lgvs~~----tl~~~~~~g~~~~~~~~~~~~~~~~ 40 (49)
T cd04762 1 LTTKEAAELLGVSPS----TLRRWVKEGKLKAIRTPGGHRRFPE 40 (49)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHcCCCCceeCCCCceecCH
Confidence 377889999988655 4677788899876644446666754
No 145
>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=86.24 E-value=0.7 Score=31.95 Aligned_cols=39 Identities=15% Similarity=0.169 Sum_probs=32.4
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
|...||+.++|+.+ .||.-++.|||.+.-..++.+.|+.
T Consensus 2 ~i~eva~~~gvs~~----tlR~Ye~~GLl~p~r~~~g~R~Y~~ 40 (112)
T cd01282 2 RIGELAARTGVSVR----SLRYYEEQGLLVPERSANGYRDYDE 40 (112)
T ss_pred CHHHHHHHHCCCHH----HHHHHHHCCCCCCCcCCCCCeecCH
Confidence 67889999998865 5899999999999755667788875
No 146
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=85.82 E-value=1.7 Score=31.25 Aligned_cols=32 Identities=28% Similarity=0.260 Sum_probs=30.4
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
-+|-..||+-++++-.-.-++|.+|+++|+|.
T Consensus 149 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~ 180 (202)
T PRK13918 149 YATHDELAAAVGSVRETVTKVIGELSREGYIR 180 (202)
T ss_pred cCCHHHHHHHhCccHHHHHHHHHHHHHCCCEE
Confidence 37999999999999999999999999999997
No 147
>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=85.73 E-value=0.67 Score=31.77 Aligned_cols=39 Identities=15% Similarity=0.165 Sum_probs=31.6
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc--ccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA--HASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k--~~~q~IYtr 104 (108)
|...||++++|+.+ .||.-+++|+|.+.-. .+....|+.
T Consensus 2 ~i~eva~~~gis~~----tlR~ye~~GLi~p~~~~~~ngyR~Y~~ 42 (108)
T cd01107 2 TIGEFAKLSNLSIK----ALRYYDKIGLLKPAYVDPDTGYRYYSA 42 (108)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHcCCCCCCcCCCCCCccccCH
Confidence 67899999998876 5899999999999643 256778875
No 148
>PRK05472 redox-sensing transcriptional repressor Rex; Provisional
Probab=85.58 E-value=1.3 Score=33.39 Aligned_cols=53 Identities=15% Similarity=0.204 Sum_probs=44.2
Q ss_pred hhccceeCHHHHHHHHhhCCCCe--eechhhhhhhhcccHHHHHHHHHHHHHcCC
Q 033932 37 VNNMVLFDQATYDKLLSEAPKYK--LITPSILSDRLRINGSLARKAIRELMARGL 89 (108)
Q Consensus 37 ~nn~Vl~dk~t~dKl~KEVpk~k--~ITps~vserlkI~~SlAr~~Lr~L~~kGl 89 (108)
+..+++---+.|.+|++.+.... .||...||+.++|+.+..|+=|..|+..|.
T Consensus 7 ~~~~~~~r~~~~~~il~~l~~~~~~~vs~~~L~~~~~v~~~tirrDl~~l~~~G~ 61 (213)
T PRK05472 7 IPEATIKRLPLYYRYLKELKEEGVERVSSKELAEALGVDSAQIRKDLSYFGEFGK 61 (213)
T ss_pred CCHHHHHHhHHHHHHHHHHHHcCCcEEeHHHHHHHhCcCHHHHHHHHHHHHhcCC
Confidence 33344444677888888888877 999999999999999999999999999885
No 149
>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=85.54 E-value=2.2 Score=31.53 Aligned_cols=42 Identities=26% Similarity=0.139 Sum_probs=36.5
Q ss_pred HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
.+..-++....+|.-.||+.++|+..--|++|..|.+.|||.
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 345556656679999999999999999999999999999995
No 150
>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=85.43 E-value=0.98 Score=30.62 Aligned_cols=39 Identities=13% Similarity=0.253 Sum_probs=31.6
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
|+..+|++++|+.+. ||.-++.|+|.++-..++..+|+.
T Consensus 2 ~I~e~a~~~gvs~~t----LR~ye~~Gll~p~r~~~g~R~Y~~ 40 (96)
T cd04774 2 KVDEVAKRLGLTKRT----LKYYEEIGLVSPERSEGRYRLYSE 40 (96)
T ss_pred CHHHHHHHHCcCHHH----HHHHHHCCCCCCCcCCCCCEEECH
Confidence 788999999887664 788899999998765667778874
No 151
>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=85.41 E-value=0.73 Score=30.54 Aligned_cols=40 Identities=15% Similarity=0.233 Sum_probs=30.9
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|+..+|+.++|+-+. |+..++.|+|.+....++..+|+.
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 3788999999988665 678899999987654456677875
No 152
>PRK13749 transcriptional regulator MerD; Provisional
Probab=85.38 E-value=0.65 Score=33.34 Aligned_cols=43 Identities=21% Similarity=0.310 Sum_probs=34.9
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
|...|...||.+++|+.. .||.-++.|||.++.+ .++...|+.
T Consensus 1 M~~~tIgelA~~~gvS~~----tiR~YE~~GLl~p~~r~~~gyR~Y~~ 44 (121)
T PRK13749 1 MSAYTVSRLALDAGVSVH----IVRDYLLRGLLRPVACTTGGYGLFDD 44 (121)
T ss_pred CCCCcHHHHHHHHCCCHH----HHHHHHHCCCCCCCCcCCCCCccCCH
Confidence 345789999999998875 6899999999999844 367778875
No 153
>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=85.15 E-value=0.85 Score=32.66 Aligned_cols=34 Identities=21% Similarity=0.369 Sum_probs=31.8
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
..+.++||.++++-.+++|-++-+|.+.|+|.--
T Consensus 55 ~~SVAEiAA~L~lPlgVvrVLvsDL~~~G~v~v~ 88 (114)
T PF05331_consen 55 PLSVAEIAARLGLPLGVVRVLVSDLADAGLVRVR 88 (114)
T ss_pred CccHHHHHHhhCCCchhhhhhHHHHHhCCCEEEe
Confidence 7899999999999999999999999999999653
No 154
>PRK11569 transcriptional repressor IclR; Provisional
Probab=84.80 E-value=1.7 Score=34.00 Aligned_cols=35 Identities=14% Similarity=0.326 Sum_probs=32.3
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
-+|.+.||+++++.-|-+-++|..|++.|++....
T Consensus 43 ~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~ 77 (274)
T PRK11569 43 SVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVG 77 (274)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcC
Confidence 48999999999999999999999999999997643
No 155
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=84.72 E-value=1 Score=32.84 Aligned_cols=46 Identities=20% Similarity=0.229 Sum_probs=36.1
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEecc
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTRA 105 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr~ 105 (108)
|....+|...||.+++|+.+ .||.-++.|||.+..+ .++.++|+..
T Consensus 3 ~~~~~~~IgevAk~~Gvs~~----TLRyYE~~GLl~p~~r~~~gyR~Y~~~ 49 (144)
T PRK13752 3 NNLENLTIGVFAKAAGVNVE----TIRFYQRKGLLPEPDKPYGSIRRYGEA 49 (144)
T ss_pred CCCCcccHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCeecCHH
Confidence 34456899999999998875 5999999999987643 4567889753
No 156
>PRK00215 LexA repressor; Validated
Probab=84.61 E-value=1.7 Score=32.30 Aligned_cols=39 Identities=18% Similarity=0.299 Sum_probs=33.7
Q ss_pred echhhhhhhhcc-cHHHHHHHHHHHHHcCCeeEeccccce
Q 033932 61 ITPSILSDRLRI-NGSLARKAIRELMARGLIRMVSAHASQ 99 (108)
Q Consensus 61 ITps~vserlkI-~~SlAr~~Lr~L~~kGlIk~V~k~~~q 99 (108)
+|...||+.+++ .-|-+-+.|+.|+++|+|.......|.
T Consensus 24 ~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~r~ 63 (205)
T PRK00215 24 PSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRSRA 63 (205)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCCcce
Confidence 688899999999 889999999999999999887554443
No 157
>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=84.11 E-value=1.2 Score=32.45 Aligned_cols=40 Identities=28% Similarity=0.376 Sum_probs=32.8
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+|...||+.++|+.+ .||.-++.|||.+.-..++...|+.
T Consensus 2 ~~IgevA~~~Gvs~~----tLRyYE~~GLl~~~r~~~g~R~Y~~ 41 (142)
T TIGR01950 2 LTVGELAKRSGVAVS----ALHFYESKGLITSIRNSGNQRRYKR 41 (142)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCEEECH
Confidence 478899999998875 5899999999998654566788874
No 158
>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=84.10 E-value=0.85 Score=30.76 Aligned_cols=40 Identities=15% Similarity=0.127 Sum_probs=31.2
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
.|...||+.++|+.+ .||..++.|+|.|... .+....|+.
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 377899999998765 5899999999999743 355677764
No 159
>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=84.03 E-value=1 Score=31.95 Aligned_cols=39 Identities=15% Similarity=0.259 Sum_probs=31.8
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc-cceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAH-ASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~-~~q~IYtr 104 (108)
|...+|..++|+.+ .||.-++.|||.+.... ++.+.|+.
T Consensus 2 ~IgE~A~~~gvs~~----TLRyYE~~GLl~p~r~~~~gyR~Y~~ 41 (133)
T cd04787 2 KVKELANAAGVTPD----TVRFYTRIGLLRPTRDPVNGYRLYSE 41 (133)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCeeeCCH
Confidence 67889999998865 68999999999997543 67788874
No 160
>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=83.82 E-value=1 Score=31.51 Aligned_cols=40 Identities=23% Similarity=0.272 Sum_probs=31.4
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-ccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV-SAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V-~k~~~q~IYtr 104 (108)
+|...+|.+++|+.+ .||..++.|||.+. -..++.+.|+.
T Consensus 1 m~I~e~a~~~gvs~~----tlR~Ye~~GLl~~~~r~~~gyR~Y~~ 41 (126)
T cd04783 1 LTIGELAKAAGVNVE----TIRYYQRRGLLPEPPRPEGGYRRYPE 41 (126)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCH
Confidence 377899999999876 57999999999954 43556778874
No 161
>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=83.72 E-value=1.6 Score=32.44 Aligned_cols=27 Identities=26% Similarity=0.417 Sum_probs=22.5
Q ss_pred ccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932 72 INGSLARKAIRELMARGLIRMVSAHAS 98 (108)
Q Consensus 72 I~~SlAr~~Lr~L~~kGlIk~V~k~~~ 98 (108)
=++|++|.+|++||+-|+|....++.|
T Consensus 92 asg~iiR~~LqqLE~~glv~k~~~~GR 118 (139)
T PF01090_consen 92 ASGSIIRKILQQLEKAGLVEKDPKGGR 118 (139)
T ss_dssp CHHHHHHHHHHHHHHTTSEEEETTTEE
T ss_pred CCcHHHHHHHHHHHHCCCEEecCCCCC
Confidence 358899999999999999998854443
No 162
>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=83.47 E-value=1.3 Score=32.02 Aligned_cols=40 Identities=23% Similarity=0.283 Sum_probs=33.3
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+|.+.||++++|+.+ .||.-++.|||.+.-..++...|+.
T Consensus 2 ~~I~EvA~~~Gvs~~----tLRyYE~~GLl~p~r~~~g~R~Y~~ 41 (139)
T cd01110 2 LSVGEVAKRSGVAVS----ALHFYEQKGLIASWRNAGNQRRYPR 41 (139)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCeEECH
Confidence 478899999998876 5899999999998755667788975
No 163
>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=83.39 E-value=0.83 Score=30.90 Aligned_cols=35 Identities=23% Similarity=0.305 Sum_probs=27.6
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
..+|-..||+.++++..-.|++|..|.+.|+|...
T Consensus 26 ~~l~de~la~~~~l~~~~vRkiL~~L~~~~lv~~~ 60 (105)
T PF02002_consen 26 GELTDEDLAKKLGLKPKEVRKILYKLYEDGLVSYR 60 (105)
T ss_dssp --B-HHHHHHTT-S-HHHHHHHHHHHHHHSS-EEE
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeEEE
Confidence 57899999999999999999999999999999665
No 164
>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=83.37 E-value=1.2 Score=30.31 Aligned_cols=39 Identities=21% Similarity=0.280 Sum_probs=31.2
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-ccccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMV-SAHASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V-~k~~~q~IYtr 104 (108)
|++.+|+.++|+.+. ||..++.|+|.++ ...+....|+.
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 7899999999986 33456778874
No 165
>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=83.29 E-value=1.1 Score=31.55 Aligned_cols=39 Identities=18% Similarity=0.212 Sum_probs=31.4
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
|...||++++|+.+ .||.-++.|||.+..+ .++.+.|+.
T Consensus 2 ~I~e~a~~~gvs~~----tlRyYe~~GLl~p~~r~~~gyR~Y~~ 41 (127)
T TIGR02044 2 NIGQVAKLTGLSSK----MIRYYEEKGLIPPPLRSEGGYRTYTQ 41 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCH
Confidence 67889999888765 6899999999998743 567788875
No 166
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=83.25 E-value=2.2 Score=33.21 Aligned_cols=36 Identities=17% Similarity=0.320 Sum_probs=33.0
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
+|.+.||+++++.-|-+.++|..|++.|++..-..+
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 899999999999999999999999999999875433
No 167
>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=83.24 E-value=1 Score=30.57 Aligned_cols=39 Identities=13% Similarity=0.232 Sum_probs=30.4
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|...+|++++|+.+ .||.-++.|||.|.. .++...|+.
T Consensus 1 m~Ige~a~~~gvs~~----tlRyYe~~GLl~p~~-~~g~r~Y~~ 39 (107)
T cd04777 1 MKIGKFAKKNNITID----TVRHYIDLGLLIPEK-KGGQYFFDE 39 (107)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCcCCcc-CCCccccCH
Confidence 367889999998865 799999999999954 345556763
No 168
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=83.11 E-value=4.1 Score=28.78 Aligned_cols=48 Identities=19% Similarity=0.214 Sum_probs=42.6
Q ss_pred HHHHHHHhhCCCCe-eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 46 ATYDKLLSEAPKYK-LITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 46 ~t~dKl~KEVpk~k-~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+.|.+|..-.+... -||...||+.|..+-==||.+|+.|.+.|.|.-.
T Consensus 4 ~~y~~L~~~~~~~~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~W~ 52 (115)
T PF12793_consen 4 EQYQRLWQHYGGQPVEVTLDELAELLFCSRRNARTLLKKMQEEGWITWQ 52 (115)
T ss_pred HHHHHHHHHcCCCCcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCeeee
Confidence 46888888888654 4899999999999999999999999999999876
No 169
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=83.00 E-value=2.4 Score=33.18 Aligned_cols=35 Identities=17% Similarity=0.034 Sum_probs=32.3
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
.-+|.+.||+++++.-|-+-++|..|++.|++..-
T Consensus 39 ~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~ 73 (271)
T PRK10163 39 GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQD 73 (271)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEc
Confidence 34899999999999999999999999999999764
No 170
>COG1733 Predicted transcriptional regulators [Transcription]
Probab=82.91 E-value=2 Score=30.52 Aligned_cols=35 Identities=34% Similarity=0.548 Sum_probs=30.6
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
=|..|..++|. ||+-+|+++| ++|++.|+|....-
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 57889999998 9999999985 89999999988754
No 171
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family. Member of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.
Probab=82.74 E-value=1.7 Score=33.23 Aligned_cols=33 Identities=15% Similarity=0.233 Sum_probs=31.2
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
=+|.++||+++++.-|-+-++|..|++.|++..
T Consensus 24 ~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~ 56 (248)
T TIGR02431 24 RLTLTDVAEATGLTRAAARRFLLTLVELGYVTS 56 (248)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEe
Confidence 479999999999999999999999999999975
No 172
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=82.63 E-value=1.9 Score=35.56 Aligned_cols=37 Identities=16% Similarity=0.358 Sum_probs=33.8
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
+|.+.||++|+|+=....+.|....++|+|+.-..++
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 6999999999999999999999999999998766544
No 173
>PRK06474 hypothetical protein; Provisional
Probab=82.62 E-value=4 Score=30.57 Aligned_cols=44 Identities=18% Similarity=0.375 Sum_probs=36.7
Q ss_pred echhhhhhhh-cccHHHHHHHHHHHHHcCCeeEecc----ccceEEEec
Q 033932 61 ITPSILSDRL-RINGSLARKAIRELMARGLIRMVSA----HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V~k----~~~q~IYtr 104 (108)
.|+..|++.+ +|..+..-+-|+.|++-|+|..+.. +.+..+|.-
T Consensus 27 ~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~~~~~~~~~ek~y~~ 75 (178)
T PRK06474 27 LTPLELVKILKDVPQATLYRHLQTMVDSGILHVVKEKKVRSVSEKYYAI 75 (178)
T ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEeecccccCceeEEEEe
Confidence 8999999999 7988999999999999999999864 234456654
No 174
>KOG2760 consensus Vacuolar sorting protein VPS36 [Intracellular trafficking, secretion, and vesicular transport]
Probab=82.47 E-value=3.1 Score=36.03 Aligned_cols=51 Identities=24% Similarity=0.268 Sum_probs=47.2
Q ss_pred eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
-|++.+-.++-+|++....|.+.+|.+++|...||+--|-..+..|+|..=
T Consensus 364 ~~~e~l~~~l~~V~~~etl~a~e~A~~l~is~~lakErLl~AE~~G~lcRD 414 (432)
T KOG2760|consen 364 SDEEKLVDALEDVSKSETLTASELAKKLGISLGLAKERLLNAEDEGLLCRD 414 (432)
T ss_pred chHHHHHHHHHhccCcchhhHHHHHHHhCchHHHHHHHHHHHHhcCCeeec
Confidence 478888899999999999999999999999999999999999999999753
No 175
>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=82.37 E-value=1.4 Score=30.03 Aligned_cols=40 Identities=10% Similarity=0.174 Sum_probs=31.6
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHc-CCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMAR-GLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~k-GlIk~V~k~~~q~IYtr 104 (108)
.|+..+|+.++|+-+. ||..+.+ |++.+....++...|+.
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 176
>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=82.16 E-value=1.1 Score=31.31 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=31.6
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|+..||+.++|+.+ .||.-++.|||.|.. ..+...|+.
T Consensus 1 ~~Igeva~~~gvs~~----tlRyYe~~GLl~p~r-~~gyR~Y~~ 39 (118)
T cd04776 1 YTISELAREFDVTPR----TLRFYEDKGLLSPER-RGQTRVYSR 39 (118)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCcC-CCCccccCH
Confidence 367889999988875 589999999999964 447888875
No 177
>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=82.12 E-value=1.2 Score=27.71 Aligned_cols=39 Identities=13% Similarity=0.229 Sum_probs=28.8
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHc-CCeeEeccccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMAR-GLIRMVSAHASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~k-GlIk~V~k~~~q~IYtr 104 (108)
|.+.+|+.++|+-+. ||..+.+ |++.+....++...|+.
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 788999999998775 5677876 98876543445567864
No 178
>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=81.87 E-value=1.4 Score=30.88 Aligned_cols=39 Identities=15% Similarity=0.204 Sum_probs=31.6
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
|...||.+++|+.+ .||.-++.|||.+..+ .++.+.|+.
T Consensus 2 ~IgevA~~~gvs~~----tLRyYe~~GLl~p~~r~~~gyR~Y~~ 41 (127)
T cd04784 2 KIGELAKKTGCSVE----TIRYYEKEGLLPAPARSANNYRLYDE 41 (127)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCH
Confidence 67889999998765 6999999999997643 467788875
No 179
>PF13814 Replic_Relax: Replication-relaxation
Probab=81.82 E-value=2.3 Score=30.75 Aligned_cols=49 Identities=16% Similarity=0.275 Sum_probs=41.0
Q ss_pred CCCeeechhhhhhhhcccHH---HHHHHHHHHHHcCCeeEecc------ccceEEEec
Q 033932 56 PKYKLITPSILSDRLRINGS---LARKAIRELMARGLIRMVSA------HASQQIYTR 104 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~S---lAr~~Lr~L~~kGlIk~V~k------~~~q~IYtr 104 (108)
-.+.++|...|+.-+..... -+++.|+.|.+.|+|..... .+...||.-
T Consensus 5 ~~~r~lt~~Qi~~l~~~~~~~~~~~~rrL~~L~~~glv~~~~~~~~~~~g~~~~vy~L 62 (191)
T PF13814_consen 5 ARHRFLTTDQIARLLFPSSKSERTARRRLKRLRELGLVDRFRRRVGARGGSQPYVYYL 62 (191)
T ss_pred HHhcCcCHHHHHHHHcCCCcchHHHHHHHHHHhhCCcEEeecccccccCCCcceEEEE
Confidence 35688999999999999987 79999999999999998865 356678763
No 180
>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=81.77 E-value=4.2 Score=26.50 Aligned_cols=39 Identities=21% Similarity=0.292 Sum_probs=30.2
Q ss_pred hhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 64 SILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 64 s~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
-.+.+.|+|+-+-+|.+|--|.++|++...-.+ +...|.
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 356789999999999999999999999986544 455664
No 181
>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=81.77 E-value=1.5 Score=30.11 Aligned_cols=40 Identities=20% Similarity=0.272 Sum_probs=31.8
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc-cceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH-ASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~-~~q~IYtr 104 (108)
.|+..+|+.++|+.+ .||..++.|+|.+.... ++...|+.
T Consensus 1 ~~i~eva~~~gvs~~----tlR~ye~~Gll~p~~~~~~g~R~Y~~ 41 (108)
T cd04773 1 MTIGELAHLLGVPPS----TLRHWEKEGLLSPDREPETGYRVYDP 41 (108)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCcCCCCCceeeCH
Confidence 378899999988765 58889999999987543 56778875
No 182
>PRK05638 threonine synthase; Validated
Probab=81.59 E-value=2.6 Score=35.40 Aligned_cols=65 Identities=17% Similarity=0.105 Sum_probs=44.6
Q ss_pred hHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhc--ccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 33 QKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLR--INGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 33 ~keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlk--I~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
.+|.+...-+ .-..+.-|..+ | .+.+.|++.++ ++-+...+.|+.|++.|||....+..+...|.
T Consensus 363 ~~~~~~~~~~-r~~IL~~L~~~-~----~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~~~~g~~~~Y~ 429 (442)
T PRK05638 363 GREKFTIGGT-KLEILKILSER-E----MYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEAYRKGRRVYYK 429 (442)
T ss_pred chhhhcccch-HHHHHHHHhhC-C----ccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEeecCCCcEEEE
Confidence 4566554422 34444444432 3 68999999998 88889999999999999998653444443453
No 183
>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=81.45 E-value=1.4 Score=31.24 Aligned_cols=40 Identities=18% Similarity=0.276 Sum_probs=32.6
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
.|...||++++|+.+ .||.-++.|||.+..+ .++.+.|+.
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 578999999998876 6899999999999644 456778874
No 184
>COG3177 Fic family protein [Function unknown]
Probab=81.36 E-value=2.4 Score=34.73 Aligned_cols=58 Identities=16% Similarity=0.269 Sum_probs=46.8
Q ss_pred HHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 46 ATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 46 ~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
..++++...+-.. .++|...++--++|.-+-|++-|.+|.+.|++..+..+.+...|.
T Consensus 289 ~~~~~l~~~~~~~~~~~t~~~~~~~~~~s~~Ta~r~l~~l~~~g~l~~~~~~~r~~~~~ 347 (348)
T COG3177 289 ERIGQLNVLLFGQEGYLTAAEIEAILGVSKATATRDLKELLELGILEEVKGRGRSKLYS 347 (348)
T ss_pred hhHHHHHHHHhccCCCccHHHHHHHhCccHHHHHHHHHHHHhCCCeeecCCCCCceecc
Confidence 3344344455543 899999999999999999999999999999999998777766653
No 185
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=81.33 E-value=3.1 Score=31.12 Aligned_cols=45 Identities=22% Similarity=0.338 Sum_probs=37.0
Q ss_pred HHhhCCCCeee-chhhhhhhh--cccHHHHHHHHHHHHHcCCeeEecc
Q 033932 51 LLSEAPKYKLI-TPSILSDRL--RINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 51 l~KEVpk~k~I-Tps~vserl--kI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
|+.=+|-+.+- +|..||.++ +|+..=++.+|+-|++-|+|+.-..
T Consensus 29 ir~l~~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~ 76 (171)
T PF14394_consen 29 IRELLPLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGD 76 (171)
T ss_pred HHHHhhcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCC
Confidence 33334444555 999999999 9999999999999999999998644
No 186
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=81.31 E-value=2.3 Score=31.48 Aligned_cols=33 Identities=9% Similarity=0.212 Sum_probs=30.4
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+|...||+-++++-.-.-++|++|.++|+|..-
T Consensus 185 lt~~~iA~~lG~sr~tvsR~l~~l~~~g~I~~~ 217 (235)
T PRK11161 185 MTRGDIGNYLGLTVETISRLLGRFQKSGMLAVK 217 (235)
T ss_pred ccHHHHHHHhCCcHHHHHHHHHHHHHCCCEEec
Confidence 788999999999999888899999999999863
No 187
>COG3432 Predicted transcriptional regulator [Transcription]
Probab=81.12 E-value=3.8 Score=28.68 Aligned_cols=41 Identities=22% Similarity=0.091 Sum_probs=31.2
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHAS 98 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~ 98 (108)
..-+.|.-|.=.-|++..+|+..|++|++.|+|.....+++
T Consensus 29 ~~~~~~Tri~y~aNlny~~~~~yi~~L~~~Gli~~~~~~~~ 69 (95)
T COG3432 29 EGGIGITRIIYGANLNYKRAQKYIEMLVEKGLIIKQDNGRR 69 (95)
T ss_pred CCCCCceeeeeecCcCHHHHHHHHHHHHhCCCEEeccCCcc
Confidence 34455566666778999999999999999997777654433
No 188
>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=80.82 E-value=2.6 Score=29.90 Aligned_cols=32 Identities=9% Similarity=0.258 Sum_probs=30.6
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
+|...||+-++++-...=++|++|+++|+|..
T Consensus 144 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~ 175 (193)
T TIGR03697 144 LSHQAIAEAIGSTRVTITRLLGDLRKKKLISI 175 (193)
T ss_pred CCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEe
Confidence 79999999999999999999999999999976
No 189
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=80.56 E-value=1.7 Score=31.30 Aligned_cols=40 Identities=15% Similarity=0.203 Sum_probs=32.5
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
.|.+.||++++|+.+ .||.-++.|||.+..+ .++.+.|+.
T Consensus 2 ~~I~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~ 42 (140)
T PRK09514 2 YRIGELAKLAEVTPD----TLRFYEKQGLMDPEVRTEGGYRLYTE 42 (140)
T ss_pred CcHHHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCCeeeCH
Confidence 578999999998765 6899999999999643 456788875
No 190
>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=80.02 E-value=2 Score=28.81 Aligned_cols=39 Identities=15% Similarity=0.264 Sum_probs=31.4
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEec-cccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVS-AHASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~-k~~~q~IYtr 104 (108)
|...||+.++|+.+ .||.-++.|+|.+.. ..++...|+.
T Consensus 2 ~i~eva~~~gvs~~----tlR~ye~~Gll~p~~r~~~gyR~Y~~ 41 (96)
T cd04788 2 KIGELARRTGLSVR----TLHHYDHIGLLSPSQRTEGGHRLYDR 41 (96)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCceeeCH
Confidence 67889999998765 589999999999863 3466788875
No 191
>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=79.85 E-value=2 Score=31.07 Aligned_cols=40 Identities=13% Similarity=0.142 Sum_probs=32.3
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|++.+|+.++|+.+ .||.-++.|+|.|.-..+....|+.
T Consensus 1 y~I~e~a~~~gvs~~----TLR~Ye~~GLl~p~r~~~g~R~Y~~ 40 (134)
T cd04779 1 YRIGQLAHLAGVSKR----TIDYYTNLGLLTPERSDSNYRYYDE 40 (134)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCccCCCCCeeECH
Confidence 378899999998865 6889999999998755567778874
No 192
>PRK10681 DNA-binding transcriptional repressor DeoR; Provisional
Probab=79.58 E-value=1.9 Score=33.56 Aligned_cols=44 Identities=11% Similarity=0.070 Sum_probs=37.9
Q ss_pred HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcC
Q 033932 45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARG 88 (108)
Q Consensus 45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kG 88 (108)
.+=.++|+.-+.....||+..||+.|+|+..-.|+=|++|+..|
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 34566777777788899999999999999999999999999654
No 193
>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=79.31 E-value=1.4 Score=32.78 Aligned_cols=40 Identities=18% Similarity=0.261 Sum_probs=32.4
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
+|.+.||+.++|+.+ .||..++.|||.|..+ .+..+.|+.
T Consensus 2 ~~I~evA~~~gvs~~----tLRyYe~~GLl~p~~r~~~gyR~Y~~ 42 (172)
T cd04790 2 LTISQLARQFGLSRS----TLLYYERIGLLSPSARSESNYRLYGE 42 (172)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCCccCCH
Confidence 688999999998764 5899999999999643 456778874
No 194
>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=79.19 E-value=13 Score=23.75 Aligned_cols=47 Identities=17% Similarity=0.287 Sum_probs=41.1
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
.|.-|+.+.+|+.+++...-+...|.+|-..|.|.-..-|..+.|+.
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 68999999999999999999999999999999999886666666654
No 195
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=79.01 E-value=3.7 Score=33.15 Aligned_cols=59 Identities=24% Similarity=0.158 Sum_probs=43.8
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA 105 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~ 105 (108)
.+-+.|.+-|.-..=-.-+++++-+.|+-|-||=-||.|++.++|.-++-|.+.. |.++
T Consensus 101 s~R~~Iy~~i~~nPG~~lsEl~~nl~i~R~TlRyhlriLe~~~li~a~~~~g~~~-yfpa 159 (240)
T COG3398 101 SKRDGIYNYIKPNPGFSLSELRANLYINRSTLRYHLRILESNPLIEAGRVGGALR-YFPA 159 (240)
T ss_pred hhHHHHHHHhccCCCccHHHHHHhcCCChHHHHHHHHHHHhCcchhhhccCCceE-EccC
Confidence 3344444444333334568999999999999999999999999999998777664 4444
No 196
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=78.78 E-value=1.6 Score=25.37 Aligned_cols=30 Identities=20% Similarity=0.220 Sum_probs=19.0
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCC
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGL 89 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGl 89 (108)
=.|+..||+.|+|+-+-.++.++...+.|+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-------
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence 358899999999999999999999998885
No 197
>COG2345 Predicted transcriptional regulator [Transcription]
Probab=78.58 E-value=2.7 Score=33.20 Aligned_cols=47 Identities=23% Similarity=0.367 Sum_probs=36.8
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
|=++|+-=..+.-=+|...+|++|+|+.--+|+=|..|+++|++.-.
T Consensus 12 tr~~il~lL~~~g~~sa~elA~~Lgis~~avR~HL~~Le~~Glv~~~ 58 (218)
T COG2345 12 TRERILELLKKSGPVSADELAEELGISPMAVRRHLDDLEAEGLVEVE 58 (218)
T ss_pred HHHHHHHHHhccCCccHHHHHHHhCCCHHHHHHHHHHHHhCcceeee
Confidence 33444433333445789999999999999999999999999999766
No 198
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=78.53 E-value=4.4 Score=30.45 Aligned_cols=32 Identities=25% Similarity=0.415 Sum_probs=29.3
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
+|-..||+.++++-.-.-++|++|+++|+|..
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~ 211 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGL 211 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEe
Confidence 68889999999999988899999999999954
No 199
>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=78.49 E-value=1.8 Score=30.45 Aligned_cols=40 Identities=20% Similarity=0.266 Sum_probs=31.6
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
+|.+.||+.++|+.+ .||.-++.|+|.+..+ .++...|+.
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 367899999998775 5899999999987643 456778874
No 200
>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=77.99 E-value=2.3 Score=29.41 Aligned_cols=40 Identities=18% Similarity=0.296 Sum_probs=31.9
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
.|...||..++|+.. .||..++.|+|.++.+ .++...|+.
T Consensus 1 y~Ige~A~~~gvs~~----tlR~ye~~GLl~p~~r~~~g~R~Y~~ 41 (107)
T cd01111 1 YSISQLALDAGVSVH----IVRDYLLRGLLHPVARTEGGYGLFDD 41 (107)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCeecCH
Confidence 367889999998875 5899999999999733 457778875
No 201
>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=77.79 E-value=2.3 Score=29.89 Aligned_cols=40 Identities=18% Similarity=0.198 Sum_probs=31.6
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
.|...||++++|+.+ .||.-++.|||.+..+ .++.+.|+.
T Consensus 1 m~I~e~a~~~gvs~~----tlRyYe~~GLl~~~~r~~~g~R~Y~~ 41 (127)
T cd01108 1 MNIGEAAKLTGLSAK----MIRYYEEIGLIPPPSRSDNGYRVYNQ 41 (127)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCH
Confidence 377899999988765 6899999999986533 567788875
No 202
>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=77.71 E-value=12 Score=26.39 Aligned_cols=50 Identities=20% Similarity=0.290 Sum_probs=34.6
Q ss_pred CHHHHHHHHhhC-----CCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 44 DQATYDKLLSEA-----PKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 44 dk~t~dKl~KEV-----pk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+.+.++..+.|| |+| +++|+..++++|.-.-.-...+..-|.+.|+-...
T Consensus 25 n~~~L~~~l~~vsdP~s~~Ygk~Lt~~e~~~~~~p~~~~v~~V~~wL~~~G~~~~~ 80 (143)
T PF09286_consen 25 NLDALEQYLAEVSDPGSPNYGKYLTPEEFAALFAPSPEDVAAVKSWLKSHGLTVVE 80 (143)
T ss_dssp THHHHHHHHHHHHTTTSTTTT----HHHHHHHHS--HHHHHHHHHHHHHCT-EEEE
T ss_pred CHHHHHHHHHhCcCCCCcccccCCCHHHHHHHHCCCHHHHHHHHHHHHHcCCceeE
Confidence 456667777776 444 99999999999999999999999999999975443
No 203
>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=77.34 E-value=2.7 Score=28.31 Aligned_cols=40 Identities=13% Similarity=0.158 Sum_probs=30.4
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
.|+..+|+.++|+-+ .||..++.|+|.+... .++...|+.
T Consensus 1 ~ti~eva~~~gvs~~----tlR~ye~~Gll~~~~~~~~g~R~y~~ 41 (103)
T cd01106 1 YTVGEVAKLTGVSVR----TLHYYDEIGLLKPSRRTENGYRLYTE 41 (103)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCccCCCCceeeCH
Confidence 378899999988765 4788999999987532 345677875
No 204
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=77.20 E-value=2.9 Score=28.32 Aligned_cols=36 Identities=14% Similarity=0.222 Sum_probs=32.2
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
-.-|...+||+.++++-.-.|..+.+|++-|||.-+
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 356888899999999999999999999999999644
No 205
>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=76.88 E-value=2.5 Score=25.78 Aligned_cols=40 Identities=15% Similarity=0.197 Sum_probs=28.8
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHc-CCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMAR-GLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~k-GlIk~V~k~~~q~IYtr 104 (108)
.|+..+|+.++|+-+.-|. .+.+ |++.+....++...|+.
T Consensus 1 ~s~~eva~~~gvs~~tlr~----w~~~~g~~~~~r~~~~~r~yt~ 41 (68)
T cd01104 1 YTIGAVARLTGVSPDTLRA----WERRYGLPAPQRTDGGHRLYSE 41 (68)
T ss_pred CCHHHHHHHHCcCHHHHHH----HHHhCCCCCCCcCCCCCeecCH
Confidence 3788999999998887655 4443 88876554456677874
No 206
>COG2865 Predicted transcriptional regulator containing an HTH domain and an uncharacterized domain shared with the mammalian protein Schlafen [Transcription]
Probab=76.64 E-value=2.3 Score=37.07 Aligned_cols=55 Identities=24% Similarity=0.385 Sum_probs=46.9
Q ss_pred HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
++..=++--.-+|+..|.+.|+|+-..|++.|.+|.+.|+++.+-.+.+...|.+
T Consensus 406 ~il~~~~en~~~T~~~L~~~l~is~~~i~r~i~~Lv~~g~~~~~g~~~~g~~~v~ 460 (467)
T COG2865 406 KILELIKENGKVTARELREILGISSETIRRRIANLVKRGLLKQLGSSGRGTWYVK 460 (467)
T ss_pred HHHHHHhhccccCHHHHHHHhCcchhhHHHHHHHHhcccHHHHhCcCCCCcEEec
Confidence 4554445556899999999999999999999999999999999977777777775
No 207
>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=76.57 E-value=4.1 Score=31.03 Aligned_cols=33 Identities=24% Similarity=0.362 Sum_probs=29.8
Q ss_pred echhhhhhhh-cccHHHHHHHHHHHHHcCCeeEe
Q 033932 61 ITPSILSDRL-RINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 61 ITps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
.+-..||+++ ++..+--|+.|++|.+-|||..=
T Consensus 71 pSN~~La~r~~G~s~~tlrR~l~~LveaGLI~rr 104 (177)
T PF03428_consen 71 PSNAQLAERLNGMSERTLRRHLARLVEAGLIVRR 104 (177)
T ss_pred cCHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeec
Confidence 3445899999 99999999999999999999885
No 208
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=76.19 E-value=3.9 Score=32.51 Aligned_cols=47 Identities=26% Similarity=0.322 Sum_probs=39.1
Q ss_pred hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEE
Q 033932 54 EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQI 101 (108)
Q Consensus 54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~I 101 (108)
++-+ =.+|-+.+|+++.++.--|-+.|.+|+..|+|..-.-...|.|
T Consensus 14 a~~~-~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i 60 (214)
T COG1339 14 AVRG-VKVTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLI 60 (214)
T ss_pred hhcC-ccccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEE
Confidence 4445 4589999999999999999999999999999987654556655
No 209
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=75.98 E-value=2.8 Score=28.34 Aligned_cols=39 Identities=23% Similarity=0.253 Sum_probs=29.9
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc-cceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAH-ASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~-~~q~IYtr 104 (108)
|...||+.++|+.+ .||..++.|+|.+..++ ...+.|+.
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 56789999998776 68999999999997443 33467764
No 210
>PRK04172 pheS phenylalanyl-tRNA synthetase subunit alpha; Provisional
Probab=75.88 E-value=7.1 Score=33.43 Aligned_cols=44 Identities=20% Similarity=0.268 Sum_probs=36.3
Q ss_pred HHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 51 LLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 51 l~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
++..+....-+|+..||+++++.-+-.-.++.-|+++|+|....
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 33333334468999999999999999999999999999998764
No 211
>PRK10263 DNA translocase FtsK; Provisional
Probab=75.86 E-value=3.5 Score=40.19 Aligned_cols=61 Identities=13% Similarity=0.222 Sum_probs=52.2
Q ss_pred CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
++++|+....=|-...-.+.|-|=.||+|-..-|.+++..||++|+|-+...+..-.|+.+
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 4688999998888889999999999999999999999999999999999755544445554
No 212
>COG2238 RPS19A Ribosomal protein S19E (S16A) [Translation, ribosomal structure and biogenesis]
Probab=75.38 E-value=3.2 Score=31.25 Aligned_cols=25 Identities=28% Similarity=0.448 Sum_probs=21.6
Q ss_pred ccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 72 INGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 72 I~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
=.+|+.|.+|++|++-|+|..+-++
T Consensus 93 gsgsI~RkilqqLE~~G~V~k~~~G 117 (147)
T COG2238 93 GSGSIIRKVLQQLEKAGLVEKTPKG 117 (147)
T ss_pred CCchHHHHHHHHHHHCCceeecCCC
Confidence 4689999999999999999887633
No 213
>PF13518 HTH_28: Helix-turn-helix domain
Probab=75.23 E-value=3.1 Score=23.93 Aligned_cols=34 Identities=12% Similarity=0.151 Sum_probs=29.5
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
|...+|..|+|+-+-.+..++...+.|+--+..+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~G~~~l~~~ 47 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREGGIEGLKPK 47 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhcCHHHhccC
Confidence 8999999999999999999999999996544433
No 214
>PTZ00095 40S ribosomal protein S19; Provisional
Probab=74.93 E-value=4.2 Score=31.19 Aligned_cols=23 Identities=22% Similarity=0.299 Sum_probs=20.7
Q ss_pred ccHHHHHHHHHHHHHcCCeeEec
Q 033932 72 INGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 72 I~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
=++|++|.+|++||+-|+|....
T Consensus 117 aSg~iiR~~LQqLE~~glVek~~ 139 (169)
T PTZ00095 117 ASGKILRWICQQLEKLGLVEQGP 139 (169)
T ss_pred CchHHHHHHHHHHHHCCCEEecC
Confidence 57899999999999999999863
No 215
>smart00351 PAX Paired Box domain.
Probab=74.68 E-value=4.1 Score=28.73 Aligned_cols=49 Identities=16% Similarity=0.216 Sum_probs=37.1
Q ss_pred CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
..++-.+|..-+- .=.|...||++|+|+-+.+.+.++...+.|.+.+..
T Consensus 19 s~~~R~riv~~~~--~G~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~ 67 (125)
T smart00351 19 PDEERQRIVELAQ--NGVRPCDISRQLCVSHGCVSKILGRYYETGSIRPGA 67 (125)
T ss_pred CHHHHHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcC
Confidence 3444455543221 124889999999999999999999999999998863
No 216
>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=74.47 E-value=2.4 Score=33.00 Aligned_cols=40 Identities=18% Similarity=0.179 Sum_probs=33.1
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|+..||++.+|+.+ .||.++++|||.+....++..+|+.
T Consensus 2 y~i~elA~~~Gvs~~----tIR~Ye~~GLL~p~r~~~~~r~Y~~ 41 (219)
T cd04778 2 YRIDDLARAAGTTVR----NVRAYQDRGLLPPPRRRGRVAIYND 41 (219)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCcccCH
Confidence 467889999998876 5899999999998766666778875
No 217
>KOG3054 consensus Uncharacterized conserved protein [Function unknown]
Probab=73.71 E-value=8 Score=31.90 Aligned_cols=58 Identities=21% Similarity=0.281 Sum_probs=50.8
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
++..+..-|...|+|-.-.||.-|+++--.+=.=|++|...|+|.=|.-.+.-.||+-
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 4555555667789999999999999999988889999999999999998999999973
No 218
>PRK15431 ferrous iron transport protein FeoC; Provisional
Probab=73.44 E-value=6.8 Score=26.56 Aligned_cols=37 Identities=11% Similarity=0.152 Sum_probs=33.8
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
..-.+...||..|+...++-+..|..|+.+|-|..|.
T Consensus 14 ~gr~s~~~Ls~~~~~p~~~VeaMLe~l~~kGkverv~ 50 (78)
T PRK15431 14 RGRMEAAQISQTLNTPQPMINAMLQQLESMGKAVRIQ 50 (78)
T ss_pred cCcccHHHHHHHHCcCHHHHHHHHHHHHHCCCeEeec
Confidence 4456788999999999999999999999999999985
No 219
>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=73.43 E-value=13 Score=30.72 Aligned_cols=60 Identities=18% Similarity=0.248 Sum_probs=45.6
Q ss_pred eCHHHHHHHHhhCCCCeeechhhhhhh-hcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 43 FDQATYDKLLSEAPKYKLITPSILSDR-LRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~k~ITps~vser-lkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+.+.+|+.+..- |.-+.+|...|.+. .+.....--.+|+.|.+.|+|.++.. ....+|--
T Consensus 10 ~~~~l~~~~~~~-~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~~-~~~l~~~~ 70 (327)
T PF05158_consen 10 LEKKLLELCREN-PSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLKK-GGGLSYKA 70 (327)
T ss_dssp HHHHHHHHHHH----SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE--SSSEEEEE
T ss_pred HHHHHHHHHHHh-cCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEEc-CCEEEEEE
Confidence 456788888877 88899999999999 68899999999999999999999984 44466753
No 220
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=72.72 E-value=10 Score=22.43 Aligned_cols=36 Identities=31% Similarity=0.472 Sum_probs=29.4
Q ss_pred cceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHH-HHHHHHHHHHHc
Q 033932 40 MVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGS-LARKAIRELMAR 87 (108)
Q Consensus 40 ~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~S-lAr~~Lr~L~~k 87 (108)
.+.+|++++++|. .+|+..+|..| |-+.||++|.++
T Consensus 6 t~~l~~el~~~L~------------~ls~~t~i~~S~Ll~eAle~~l~k 42 (44)
T PF12651_consen 6 TFSLDKELYEKLK------------ELSEETGIPKSKLLREALEDYLEK 42 (44)
T ss_pred EEecCHHHHHHHH------------HHHHHHCCCHHHHHHHHHHHHHHh
Confidence 5678999999986 68899998876 778888888764
No 221
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=72.56 E-value=5.9 Score=29.56 Aligned_cols=32 Identities=6% Similarity=0.115 Sum_probs=29.7
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
.|...||+.++++-.---++|++|+++|+|..
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 222
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=72.36 E-value=12 Score=27.56 Aligned_cols=39 Identities=26% Similarity=0.318 Sum_probs=26.3
Q ss_pred eechhhhhhhhc-----ccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932 60 LITPSILSDRLR-----INGSLARKAIRELMARGLIRMVSAHAS 98 (108)
Q Consensus 60 ~ITps~vserlk-----I~~SlAr~~Lr~L~~kGlIk~V~k~~~ 98 (108)
-+|+..|-+++. |+.+-.-+.|+.|++.|+|..+....+
T Consensus 41 hlSa~eI~~~L~~~~~~is~aTVYRtL~~L~e~Glv~~~~~~~~ 84 (169)
T PRK11639 41 AISAYDLLDLLREAEPQAKPPTVYRALDFLLEQGFVHKVESTNS 84 (169)
T ss_pred CCCHHHHHHHHHhhCCCCCcchHHHHHHHHHHCCCEEEEecCCc
Confidence 455555555542 444555689999999999999964443
No 223
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=72.35 E-value=4.2 Score=33.86 Aligned_cols=46 Identities=20% Similarity=0.330 Sum_probs=40.6
Q ss_pred HHHHHhhCCCCee--echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 48 YDKLLSEAPKYKL--ITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 48 ~dKl~KEVpk~k~--ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
-|+|..|..+..= |..+.|.+=+++.=|.+--+|.+||++|.|+.=
T Consensus 6 reklir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~Rr 53 (321)
T COG3888 6 REKLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRR 53 (321)
T ss_pred HHHHHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeee
Confidence 4677778777766 999999999999999999999999999999754
No 224
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=72.30 E-value=5.7 Score=31.39 Aligned_cols=44 Identities=16% Similarity=0.274 Sum_probs=37.1
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
+.--|+..||+..+|--+=.-.+|+-|+.+|++.... ++-..|.
T Consensus 28 ~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~--g~P~~y~ 71 (247)
T COG1378 28 LGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIE--GRPKKYR 71 (247)
T ss_pred hCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeC--CCCceEE
Confidence 4456999999999999999999999999999999873 4445554
No 225
>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=72.19 E-value=4.6 Score=28.32 Aligned_cols=39 Identities=21% Similarity=0.228 Sum_probs=30.6
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
|...+|++++|+.+ .||.-++.|+|.+..+ .++.+.|+.
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 56789999999876 5789999999986533 467778874
No 226
>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=72.08 E-value=2.9 Score=28.63 Aligned_cols=39 Identities=15% Similarity=0.247 Sum_probs=30.1
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
|...+|+.++|+.+ .||..++.|+|.+..+ .++.+.|+.
T Consensus 2 ~i~e~a~~~gvs~~----tlr~ye~~gll~~~~r~~~gyR~Y~~ 41 (113)
T cd01109 2 TIKEVAEKTGLSAD----TLRYYEKEGLLPPVKRDENGIRDFTE 41 (113)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCccCCH
Confidence 67889999988765 5889999999976533 346677875
No 227
>smart00753 PAM PCI/PINT associated module.
Probab=72.02 E-value=16 Score=23.20 Aligned_cols=46 Identities=17% Similarity=0.143 Sum_probs=38.8
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
|.-||...||+.+++...-+-..|.++...|.|.--.-|....++.
T Consensus 22 y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~ 67 (88)
T smart00753 22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEF 67 (88)
T ss_pred hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEE
Confidence 7889999999999999999999999999999997665455555543
No 228
>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=72.02 E-value=16 Score=23.20 Aligned_cols=46 Identities=17% Similarity=0.143 Sum_probs=38.8
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
|.-||...||+.+++...-+-..|.++...|.|.--.-|....++.
T Consensus 22 y~~i~~~~i~~~~~l~~~~vE~~i~~~i~~~~l~~~ID~~~~~v~~ 67 (88)
T smart00088 22 YSSISLSDLAKLLGLSVPEVEKLVSKAIRDGEISAKIDQVNGIVEF 67 (88)
T ss_pred hceeeHHHHHHHhCcCHHHHHHHHHHHHHCCCeEEEEcCcCCEEEE
Confidence 7889999999999999999999999999999997665455555543
No 229
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=71.83 E-value=3.3 Score=29.79 Aligned_cols=39 Identities=21% Similarity=0.220 Sum_probs=31.3
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
|...||++++|+.+ .||.-++.|||.+..+ .+..++|+.
T Consensus 2 ~Ige~a~~~gvs~~----tlRyYE~~GLl~p~~r~~~gyR~Y~~ 41 (135)
T PRK10227 2 NISDVAKITGLTSK----AIRFYEEKGLVTPPMRSENGYRTYTQ 41 (135)
T ss_pred CHHHHHHHHCcCHH----HHHHHHHCCCCCCcccCCCCcccCCH
Confidence 56789999988765 6999999999998744 466778874
No 230
>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=71.63 E-value=4.3 Score=33.37 Aligned_cols=37 Identities=16% Similarity=0.269 Sum_probs=33.4
Q ss_pred CCeeechhhhhhh--hcccHHHHHHHHHHHHHcCCeeEe
Q 033932 57 KYKLITPSILSDR--LRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 57 k~k~ITps~vser--lkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
...-|+...|+++ ++++.+-+|+-|.+|++.|+|..+
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 4578999999999 888899999999999999999774
No 231
>PRK15043 transcriptional regulator MirA; Provisional
Probab=71.55 E-value=4 Score=32.62 Aligned_cols=43 Identities=16% Similarity=0.227 Sum_probs=35.2
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHH-cCCeeEeccccceEEEec
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMA-RGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~-kGlIk~V~k~~~q~IYtr 104 (108)
|.+.|...+|++++|+.. .||.-++ .|+|.+.-..++.+.|+.
T Consensus 1 m~~ytIgeVA~~~GVs~~----TLR~wErr~GLL~P~Rt~~G~R~Ys~ 44 (243)
T PRK15043 1 MALYTIGEVALLCDINPV----TLRAWQRRYGLLKPQRTDGGHRLFND 44 (243)
T ss_pred CCCCCHHHHHHHHCcCHH----HHHHHHHhcCCCCCccCCCCCEEECH
Confidence 447899999999999876 5888986 699999765677888875
No 232
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=71.40 E-value=8.6 Score=30.77 Aligned_cols=51 Identities=22% Similarity=0.307 Sum_probs=45.1
Q ss_pred eCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 43 FDQATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+|.-|+++|...+.-. --.|.-++|+.++|+-.-||+=|..|++.|+|..=
T Consensus 155 i~~~Tl~~i~~~~~~~~~~~Taeela~~~giSRvTaRRYLeyl~~~~~l~a~ 206 (224)
T COG4565 155 LDELTLQKVREALKEPDQELTAEELAQALGISRVTARRYLEYLVSNGILEAE 206 (224)
T ss_pred cCHHHHHHHHHHHhCcCCccCHHHHHHHhCccHHHHHHHHHHHHhcCeeeEE
Confidence 7999999999877622 56799999999999999999999999999999764
No 233
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=71.37 E-value=8.9 Score=32.00 Aligned_cols=47 Identities=15% Similarity=0.047 Sum_probs=37.3
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
++..+.+....-+-+|+..+++++++...+.+.+|.+|++-|+|...
T Consensus 297 iL~~l~~~~~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~ 343 (412)
T PRK04214 297 LLGRLDQARKHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRG 343 (412)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEec
Confidence 34444433334457799999999999999999999999999999753
No 234
>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=71.25 E-value=3.1 Score=29.33 Aligned_cols=39 Identities=18% Similarity=0.241 Sum_probs=30.7
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
|.+.||++++|+.+ .||.-++.|||.+..+ .++...|+.
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 6899999999987533 456778864
No 235
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=71.07 E-value=8.1 Score=29.65 Aligned_cols=50 Identities=18% Similarity=0.165 Sum_probs=41.7
Q ss_pred HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe-cccc
Q 033932 48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV-SAHA 97 (108)
Q Consensus 48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V-~k~~ 97 (108)
.=.+.+.++.--.+|--.+|++++|....-|++|.-|-+.|+|... .++.
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 5566667777448999999999999999999999999999999955 4443
No 236
>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=70.23 E-value=5.1 Score=24.61 Aligned_cols=40 Identities=13% Similarity=0.110 Sum_probs=28.1
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.|+..+|+.++|+-+- ||..+++|.+......++...|+.
T Consensus 1 ~~i~evA~~~gvs~~t----lR~~~~~g~l~~~~~~~g~R~y~~ 40 (67)
T cd04764 1 YTIKEVSEIIGVKPHT----LRYYEKEFNLYIPRTENGRRYYTD 40 (67)
T ss_pred CCHHHHHHHHCcCHHH----HHHHHHhcCCCCCCCCCCceeeCH
Confidence 3788999999998774 678888766553333445677875
No 237
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=69.97 E-value=13 Score=26.45 Aligned_cols=45 Identities=13% Similarity=0.038 Sum_probs=37.2
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA 105 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~ 105 (108)
-.|+..|++.+++.-|..-+=|+.|.+-|||...-.+ +...|.-+
T Consensus 30 ~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~G-r~~~Y~l~ 74 (117)
T PRK10141 30 ELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQG-KWVHYRLS 74 (117)
T ss_pred CcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEc-CEEEEEEC
Confidence 3788999999999999999999999999999886554 44556543
No 238
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=69.88 E-value=8.1 Score=28.64 Aligned_cols=27 Identities=19% Similarity=0.313 Sum_probs=25.1
Q ss_pred hhhhhhhhcccHHHHHHHHHHHHHcCC
Q 033932 63 PSILSDRLRINGSLARKAIRELMARGL 89 (108)
Q Consensus 63 ps~vserlkI~~SlAr~~Lr~L~~kGl 89 (108)
...||+-++++-.-.-++|++|+++|+
T Consensus 176 ~~~iA~~lG~tretvsR~l~~L~~~gl 202 (236)
T PRK09392 176 KRVLASYLGMTPENLSRAFAALASHGV 202 (236)
T ss_pred HHHHHHHhCCChhHHHHHHHHHHhCCe
Confidence 467999999999999999999999995
No 239
>cd00131 PAX Paired Box domain
Probab=69.58 E-value=5.8 Score=28.19 Aligned_cols=51 Identities=20% Similarity=0.274 Sum_probs=39.4
Q ss_pred eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
+..++-.+|..=+- .=.++..+|.+|+|+-+...++++...+.|.+.+...
T Consensus 18 lS~d~R~rIv~~~~--~G~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~ 68 (128)
T cd00131 18 LPDSIRQRIVELAQ--SGIRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAI 68 (128)
T ss_pred CCHHHHHHHHHHHH--cCCCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCC
Confidence 44455555553322 2369999999999999999999999999999988643
No 240
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=69.34 E-value=8.2 Score=28.43 Aligned_cols=54 Identities=19% Similarity=0.265 Sum_probs=42.5
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
+..+|..=|-..--+|...++..++++-..+++.|++|.+.|.|-. |..-.||.
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 4445555555567799999999999999999999999999999855 44445654
No 241
>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=68.49 E-value=11 Score=25.27 Aligned_cols=54 Identities=20% Similarity=0.159 Sum_probs=40.0
Q ss_pred HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe---ccccceEEE
Q 033932 48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV---SAHASQQIY 102 (108)
Q Consensus 48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V---~k~~~q~IY 102 (108)
+++|+-=+... .+|--.|-++.+|+=+..-..|..|.++|+|..= ..+....+|
T Consensus 7 ~~~IL~~ls~~-c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rkw~~~~gkk~R~Y 63 (72)
T PF05584_consen 7 TQKILIILSKR-CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERKWRKFGGKKYREY 63 (72)
T ss_pred HHHHHHHHHhc-cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeeEEecCeEEEEE
Confidence 34444333333 8999999999999999999999999999999753 223344455
No 242
>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=67.97 E-value=18 Score=23.68 Aligned_cols=32 Identities=28% Similarity=0.334 Sum_probs=20.1
Q ss_pred hhhhhhhh-cccHHHHHHHHHHHHHcCCeeEec
Q 033932 63 PSILSDRL-RINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 63 ps~vserl-kI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
.+.+.+++ +|+-.+--.-|++|++.|+|....
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 34444444 444444445569999999998863
No 243
>PHA03103 double-strand RNA-binding protein; Provisional
Probab=67.97 E-value=16 Score=28.26 Aligned_cols=54 Identities=20% Similarity=0.210 Sum_probs=45.8
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccce
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQ 99 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q 99 (108)
++..++..+.+--..+|.-.||-+|+|.=|=+-+.|=.|.+.|.+..+..+.--
T Consensus 13 ~lv~~~~~~l~~~~~~~a~~i~~~l~~~k~~vNr~LY~l~~~~~v~~~~~~pp~ 66 (183)
T PHA03103 13 ELVKKEVKNLGLGEGITAIEISRKLNIEKSEVNKQLYKLQREGMVYMSDSNPPK 66 (183)
T ss_pred HHHHHHHHHhccCCCccHHHHHHHhCCCHHHHHHHHHHHHhcCceecCCCCCCC
Confidence 355677777777799999999999999999999999999999999887655433
No 244
>PRK10265 chaperone-modulator protein CbpM; Provisional
Probab=67.09 E-value=8.9 Score=26.28 Aligned_cols=41 Identities=10% Similarity=0.169 Sum_probs=32.9
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
-+|-..+|+..+|.-++ |.+|.+-|+|.+...+..++.|..
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 47888999999877655 899999999999876666777753
No 245
>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=66.78 E-value=7.8 Score=30.40 Aligned_cols=42 Identities=7% Similarity=0.030 Sum_probs=35.4
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
.++|.|.. - -.|+..||++++++-...++.|+.|..-|++..
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 246
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=66.25 E-value=11 Score=28.80 Aligned_cols=43 Identities=26% Similarity=0.374 Sum_probs=32.9
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc---ccceEEEe
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA---HASQQIYT 103 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k---~~~q~IYt 103 (108)
..=||-+.|++..+++. -.+|++|.++|||..+-+ .++-.+|.
T Consensus 102 ~qPiTr~eI~~irGv~~---~~ii~~L~~~gLI~e~gr~~~~Grp~ly~ 147 (188)
T PRK00135 102 KQPITRIEIDEIRGVNS---DGALQTLLAKGLIKEVGRKEVPGRPILYG 147 (188)
T ss_pred cCCcCHHHHHHHHCCCH---HHHHHHHHHCCCeEEcCcCCCCCCCeeee
Confidence 34589999999999995 799999999999987622 22445563
No 247
>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=65.01 E-value=6.4 Score=28.16 Aligned_cols=39 Identities=26% Similarity=0.253 Sum_probs=30.6
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
+...||++++|+.+ .||.-++.|||.+..+ .++...|+.
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 56789999988876 5899999999998633 456677864
No 248
>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=64.71 E-value=6.5 Score=31.84 Aligned_cols=29 Identities=28% Similarity=0.348 Sum_probs=23.5
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHc
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMAR 87 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~k 87 (108)
++||---||-.|+|.+..|+++|.++..+
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 249
>PRK00082 hrcA heat-inducible transcription repressor; Provisional
Probab=64.48 E-value=7.1 Score=32.11 Aligned_cols=39 Identities=21% Similarity=0.296 Sum_probs=33.8
Q ss_pred CCCCeeechhhhhhh--hcccHHHHHHHHHHHHHcCCeeEe
Q 033932 55 APKYKLITPSILSDR--LRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 55 Vpk~k~ITps~vser--lkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+-...-|+...|+++ |+++-+-.|.-|.+|++.|+|...
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 345677899999977 999999999999999999999854
No 250
>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=64.40 E-value=26 Score=22.87 Aligned_cols=53 Identities=21% Similarity=0.296 Sum_probs=28.9
Q ss_pred HhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 35 EKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 35 eK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+-+.+..+-+++-+-..+.+- ++. ||.++|| |+|.+-|+++.- ......+|.-
T Consensus 12 ~li~~~~i~sQ~eL~~~L~~~-Gi~-vTQaTiS--------------RDLkeL~~vKv~-~~~g~~~Y~l 64 (70)
T PF01316_consen 12 ELISEHEISSQEELVELLEEE-GIE-VTQATIS--------------RDLKELGAVKVP-DGNGKYRYVL 64 (70)
T ss_dssp HHHHHS---SHHHHHHHHHHT-T-T---HHHHH--------------HHHHHHT-EEEE-CTTSSEEEE-
T ss_pred HHHHHCCcCCHHHHHHHHHHc-CCC-cchhHHH--------------HHHHHcCcEEee-CCCCCEEEEe
Confidence 334444445554444444443 666 7888877 889999999954 4566778874
No 251
>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=64.05 E-value=14 Score=23.78 Aligned_cols=45 Identities=33% Similarity=0.341 Sum_probs=37.3
Q ss_pred HHhhCCC--CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 51 LLSEAPK--YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 51 l~KEVpk--~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
++.+|.+ +.=||.+.|+..+++...-.-..++.|++.|||....-
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 4445554 45689999999999999999999999999999987644
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=63.90 E-value=14 Score=25.67 Aligned_cols=35 Identities=29% Similarity=0.410 Sum_probs=32.6
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
++..||-+.+++.-++.-+-..++|.+|.+.|+|.
T Consensus 51 k~d~Is~sq~~e~tg~~~~~V~~al~~Li~~~vI~ 85 (100)
T PF04492_consen 51 KMDRISNSQIAEMTGLSRDHVSKALNELIRRGVII 85 (100)
T ss_pred ccceeeHHHHHHHHCcCHHHHHHHHHHHHHCCCEE
Confidence 46789999999999999999999999999999993
No 253
>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=63.32 E-value=10 Score=30.48 Aligned_cols=53 Identities=15% Similarity=0.226 Sum_probs=40.5
Q ss_pred eeCHHHHH--------HHHhhCCCCeee-chhhhhhhhc--ccHHHHHHHHHHHHHcCCeeEec
Q 033932 42 LFDQATYD--------KLLSEAPKYKLI-TPSILSDRLR--INGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 42 l~dk~t~d--------Kl~KEVpk~k~I-Tps~vserlk--I~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
.+|.+.|+ -|+.=+|-+..= +|..||++++ |+..=++.+|+-|++-|+|+...
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 46777766 233333445555 7889999999 88888999999999999999853
No 254
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=63.06 E-value=13 Score=28.39 Aligned_cols=41 Identities=29% Similarity=0.390 Sum_probs=30.2
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc---ccceEEEe
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSA---HASQQIYT 103 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k---~~~q~IYt 103 (108)
=||-+.|.+-.+++.+ .+++.|.++|+|+.+-+ -++-.+|.
T Consensus 106 PiTR~eI~~iRGv~~~---~~i~~L~e~glI~~~g~~~~~Grp~ly~ 149 (184)
T COG1386 106 PVTRSEIEEIRGVAVS---QVISTLLERGLIREVGRRDTPGRPYLYG 149 (184)
T ss_pred CccHHHHHHHhCccHH---HHHHHHHHCCCeEecCCCCCCCCceeee
Confidence 3778888877777665 49999999999999863 23444554
No 255
>COG5340 Predicted transcriptional regulator [Transcription]
Probab=62.92 E-value=7 Score=31.87 Aligned_cols=41 Identities=17% Similarity=0.215 Sum_probs=37.3
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
..++||.-.++|-+.+.-+..|.++..|+++|.|..+-++.
T Consensus 27 ~hkiiTirdvae~~ev~~n~lr~lasrLekkG~LeRi~rG~ 67 (269)
T COG5340 27 GHKIITIRDVAETLEVAPNTLRELASRLEKKGWLERILRGR 67 (269)
T ss_pred hCceEEeHHhhhhccCCHHHHHHHHhhhhhcchhhhhcCcc
Confidence 46999999999999999999999999999999998877654
No 256
>PHA00738 putative HTH transcription regulator
Probab=62.83 E-value=22 Score=25.51 Aligned_cols=44 Identities=14% Similarity=0.243 Sum_probs=35.6
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
-.+...|++.|++.-+-.-+=|+-|++-|||.--- ..+...|.-
T Consensus 26 ~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK-~Gr~vyY~L 69 (108)
T PHA00738 26 ILSASLISHTLLLSYTTVLRHLKILNEQGYIELYK-EGRTLYAKI 69 (108)
T ss_pred CccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEE-ECCEEEEEE
Confidence 37889999999999999999999999999998643 344444543
No 257
>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=62.52 E-value=9.1 Score=24.39 Aligned_cols=37 Identities=27% Similarity=0.490 Sum_probs=27.9
Q ss_pred eeechhhhhhhhcccH-----HHHHHHHHHHHHcCCeeEecc
Q 033932 59 KLITPSILSDRLRING-----SLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 59 k~ITps~vserlkI~~-----SlAr~~Lr~L~~kGlIk~V~k 95 (108)
.-++...|++.|..++ .--|+-|++|++.|++..+..
T Consensus 12 ~P~g~~~l~~~L~~~g~~~se~avRrrLr~me~~Glt~~~g~ 53 (66)
T PF08461_consen 12 KPLGRKQLAEELKLRGEELSEEAVRRRLRAMERDGLTRKVGR 53 (66)
T ss_pred CCCCHHHHHHHHHhcChhhhHHHHHHHHHHHHHCCCccccCC
Confidence 3577788888886553 556899999999998876543
No 258
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=62.50 E-value=7.2 Score=28.21 Aligned_cols=34 Identities=26% Similarity=0.295 Sum_probs=30.7
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
..+|--.||+.++|+..--|++|..|.+.+++..
T Consensus 14 ~~~~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~ 47 (147)
T smart00531 14 GCVTEEDLAELLGIKQKQLRKILYLLYDEKLIKI 47 (147)
T ss_pred CCcCHHHHHHHhCCCHHHHHHHHHHHHhhhcchh
Confidence 4699999999999999999999999999777643
No 259
>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=62.42 E-value=20 Score=19.74 Aligned_cols=35 Identities=31% Similarity=0.449 Sum_probs=25.7
Q ss_pred cceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHH-HHHHHHHHHHH
Q 033932 40 MVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGS-LARKAIRELMA 86 (108)
Q Consensus 40 ~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~S-lAr~~Lr~L~~ 86 (108)
.|-+|++++++|. .+|++.+++.| +-|.+|+++.+
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 3668888888887 46788887765 66777777654
No 260
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=62.18 E-value=13 Score=30.16 Aligned_cols=39 Identities=18% Similarity=0.233 Sum_probs=34.9
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
.=.|.+.||++|+|+-+..-++|.+-.++|++..-.+|.
T Consensus 28 ~g~tQ~eIA~~lgiSR~~VsRlL~~Ar~~GiV~I~I~~~ 66 (318)
T PRK15418 28 DGLTQSEIGERLGLTRLKVSRLLEKGRQSGIIRVQINSR 66 (318)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHcCcEEEEEeCC
Confidence 346999999999999999999999999999998877654
No 261
>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=62.01 E-value=12 Score=28.93 Aligned_cols=46 Identities=11% Similarity=0.107 Sum_probs=36.7
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHH-HHHHcCCeeEe
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIR-ELMARGLIRMV 93 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr-~L~~kGlIk~V 93 (108)
.+.-+.+.+... -++...+|+++++..+-+..+++ .|.+.|+|...
T Consensus 243 ~L~al~~~~~~~-~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~ 289 (305)
T TIGR00635 243 LLSVLIEQFQGG-PVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRT 289 (305)
T ss_pred HHHHHHHHhCCC-cccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccC
Confidence 444355655554 37899999999999999999999 69999999643
No 262
>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=61.66 E-value=12 Score=30.18 Aligned_cols=66 Identities=17% Similarity=0.177 Sum_probs=50.7
Q ss_pred hhccceeCHHHHHHHHhhCCCC----eeechhhhhhhhcccHHHHH-HHHHHHHHcCCeeEeccccceEEEecc
Q 033932 37 VNNMVLFDQATYDKLLSEAPKY----KLITPSILSDRLRINGSLAR-KAIRELMARGLIRMVSAHASQQIYTRA 105 (108)
Q Consensus 37 ~nn~Vl~dk~t~dKl~KEVpk~----k~ITps~vserlkI~~SlAr-~~Lr~L~~kGlIk~V~k~~~q~IYtr~ 105 (108)
+.+.-+|+.+-+|.|..|+-.. -.||.+.+|.+|++.+.+.. .++.. .-.++|.-+..+. .|||.+
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 3455689999999999998774 89999999999999999988 44444 4456666664444 899863
No 263
>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=61.11 E-value=23 Score=22.23 Aligned_cols=34 Identities=21% Similarity=0.287 Sum_probs=26.0
Q ss_pred hcccHHHHHHHHHHHHHcCCeeEeccc----cceEEEe
Q 033932 70 LRINGSLARKAIRELMARGLIRMVSAH----ASQQIYT 103 (108)
Q Consensus 70 lkI~~SlAr~~Lr~L~~kGlIk~V~k~----~~q~IYt 103 (108)
+.|+-+---.+|+.|+++|+|...... +...+|.
T Consensus 27 ~~i~~g~lY~~L~~Le~~gli~~~~~~~~~~~~rk~Y~ 64 (75)
T PF03551_consen 27 WKISPGSLYPALKRLEEEGLIESRWEEEGNGRPRKYYR 64 (75)
T ss_dssp EETTHHHHHHHHHHHHHTTSEEEEEEEETTSSEEEEEE
T ss_pred cccChhHHHHHHHHHHhCCCEEEeeeccCCCCCCEEEE
Confidence 456677778999999999999988543 4555665
No 264
>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=60.56 E-value=22 Score=21.75 Aligned_cols=47 Identities=21% Similarity=0.294 Sum_probs=37.3
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhh---cccHHHHHHHHHHHHHcCCeeE
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRL---RINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserl---kI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
+.++...++-|--.=+....|-.|+ ++..-+...+|+.|+++|.|+.
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 3556667777777778888999898 8899999999999999999975
No 265
>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=59.34 E-value=14 Score=29.25 Aligned_cols=35 Identities=17% Similarity=0.288 Sum_probs=28.9
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHH
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIR 82 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr 82 (108)
+.+--|.++.|. ..|+..|||.|+|.-...|+||+
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 57999999999999999999996
No 266
>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=59.32 E-value=29 Score=25.29 Aligned_cols=21 Identities=19% Similarity=0.480 Sum_probs=15.9
Q ss_pred HHHHHcCCeeEeccccceEEEe
Q 033932 82 RELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 82 r~L~~kGlIk~V~k~~~q~IYt 103 (108)
|+|.+-|+++... .+.+..|.
T Consensus 40 RdL~elglvk~~~-~~g~~~Y~ 60 (146)
T TIGR01529 40 RDLRELGAVKVRD-EDGSYVYS 60 (146)
T ss_pred HHHHHcCCEEEEC-CCCcEEEe
Confidence 4888999998766 55666785
No 267
>KOG3341 consensus RNA polymerase II transcription factor complex subunit [Transcription]
Probab=59.17 E-value=11 Score=30.53 Aligned_cols=33 Identities=30% Similarity=0.375 Sum_probs=30.6
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
++|.+.+-+.|+..-+-|+.+|.+|.++||.=.
T Consensus 190 yvt~s~l~~~l~We~~Ra~qaLe~lv~egL~Wi 222 (249)
T KOG3341|consen 190 YVTISLLKANLGWERSRAIQALEHLVKEGLAWI 222 (249)
T ss_pred ceeHHHHHHhccchHHHHHHHHHHHHhccceee
Confidence 599999999999999999999999999999644
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=58.89 E-value=20 Score=22.40 Aligned_cols=42 Identities=26% Similarity=0.228 Sum_probs=33.6
Q ss_pred cceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 40 MVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 40 ~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
.++.-.+..+=|+...+. ...+-|..+.++|.+.|+|..|..
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 455577777777766543 677899999999999999999986
No 269
>PF13551 HTH_29: Winged helix-turn helix
Probab=58.86 E-value=6.8 Score=25.48 Aligned_cols=33 Identities=15% Similarity=0.237 Sum_probs=29.9
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
|+..+|+.++|+-+...+.++.+.+.|+-.++.
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~ 46 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLP 46 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHh
Confidence 899999999999999999999999999655554
No 270
>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=58.75 E-value=14 Score=24.07 Aligned_cols=34 Identities=24% Similarity=0.236 Sum_probs=28.2
Q ss_pred Ceeechhhhhhhhc-ccHHHHHHHHHHHHHcCCee
Q 033932 58 YKLITPSILSDRLR-INGSLARKAIRELMARGLIR 91 (108)
Q Consensus 58 ~k~ITps~vserlk-I~~SlAr~~Lr~L~~kGlIk 91 (108)
...+|....-+-++ +..+++.++..-|+..|+|.
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 46789999988888 99999999999999999984
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=58.54 E-value=20 Score=21.78 Aligned_cols=33 Identities=27% Similarity=0.374 Sum_probs=24.8
Q ss_pred echhhhhhhhcccHHHH-HHHHHHHHHcCCeeEe
Q 033932 61 ITPSILSDRLRINGSLA-RKAIRELMARGLIRMV 93 (108)
Q Consensus 61 ITps~vserlkI~~SlA-r~~Lr~L~~kGlIk~V 93 (108)
|....+.++|+....-. ...|+.|.+.|++..-
T Consensus 21 i~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~ 54 (66)
T PF06969_consen 21 IDLSEFEQRFGIDFAEEFQKELEELQEDGLLEID 54 (66)
T ss_dssp EEHHHHHHHTT--THHH-HHHHHHHHHTTSEEE-
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHCCCEEEe
Confidence 66788899999875444 8889999999999764
No 272
>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=58.45 E-value=20 Score=24.87 Aligned_cols=38 Identities=24% Similarity=0.303 Sum_probs=26.6
Q ss_pred eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHH
Q 033932 43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRE 83 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~ 83 (108)
+|.+.+..+..+ +.=+|..++|++|+|..|..-.+|..
T Consensus 57 id~~~L~~~v~~---~pd~tl~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 57 IDRDELKALVEE---NPDATLRELAERLGVSPSTIWRALKR 94 (119)
T ss_pred ccHHHHHHHHHH---CCCcCHHHHHHHcCCCHHHHHHHHHH
Confidence 366666666666 45578899999999977765555543
No 273
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=58.44 E-value=13 Score=29.54 Aligned_cols=60 Identities=32% Similarity=0.543 Sum_probs=44.8
Q ss_pred hcccee--CHHHHHHHHhhCCCCeeechhhhhhhhcccH-HHHHHHHHHHHHc---CCeeEecccc
Q 033932 38 NNMVLF--DQATYDKLLSEAPKYKLITPSILSDRLRING-SLARKAIRELMAR---GLIRMVSAHA 97 (108)
Q Consensus 38 nn~Vl~--dk~t~dKl~KEVpk~k~ITps~vserlkI~~-SlAr~~Lr~L~~k---GlIk~V~k~~ 97 (108)
|+++++ |+++|++|....|+..+|.|-.++.-|.-++ .=-|.-||.++.. |+|-.|..++
T Consensus 93 ~rallIAPn~e~Y~~i~~~~~~i~fihpDl~aa~L~~~g~~P~~~dfrkfc~~~svGli~iv~~n~ 158 (218)
T PF15436_consen 93 NRALLIAPNQETYEKIKSSYPNINFIHPDLFAAFLSENGHDPTREDFRKFCNQYSVGLIFIVLKNK 158 (218)
T ss_pred cceEEEcCCHHHHHHHHHhCCCceEecHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCEEEEEEcCc
Confidence 344444 9999999999999999999999998884322 3347778888874 7766665544
No 274
>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=58.27 E-value=34 Score=22.87 Aligned_cols=46 Identities=7% Similarity=0.099 Sum_probs=38.6
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
++.-|.....++.+|....|...-+++.+-+...|..|...|+|..
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 4556777788899999999999999999999999999999999977
No 275
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=57.08 E-value=19 Score=27.61 Aligned_cols=41 Identities=17% Similarity=0.346 Sum_probs=28.1
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc---ccceEEEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA---HASQQIYTR 104 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k---~~~q~IYtr 104 (108)
||-+.|-+--+++ +..+|+.|.++|||..+-+ .++-.+|.-
T Consensus 102 ITr~eIe~IRGv~---s~~~l~~L~ergLI~~~Gr~~~~Grp~ly~T 145 (186)
T TIGR00281 102 ITRARINEIRGVK---SYQIVDDLVEKGLVVELGRKDTPGRSFIYET 145 (186)
T ss_pred cCHHHHHHHcCCC---HHHHHHHHHHCCCeEecCcCCCCCCCeeehh
Confidence 4555555555555 6789999999999999822 345566753
No 276
>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=56.91 E-value=31 Score=25.15 Aligned_cols=46 Identities=22% Similarity=0.290 Sum_probs=35.6
Q ss_pred eechhhhhhhh--cccHHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932 60 LITPSILSDRL--RINGSLARKAIRELMARGLIRMVSAHASQQIYTRAT 106 (108)
Q Consensus 60 ~ITps~vserl--kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~ 106 (108)
=.+...|++=| +|.=+.+-++|..|.++|.|..=. -+.|.||..+.
T Consensus 16 Pys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~-~GKqkiY~~~Q 63 (169)
T PF07106_consen 16 PYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKE-YGKQKIYFANQ 63 (169)
T ss_pred CCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeee-ecceEEEeeCc
Confidence 34555677777 477799999999999999997643 46789998654
No 277
>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=56.42 E-value=17 Score=21.27 Aligned_cols=39 Identities=23% Similarity=0.290 Sum_probs=27.9
Q ss_pred eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHH
Q 033932 43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELM 85 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~ 85 (108)
+|...++-|+.+ + =.+...||+.++++.+-...=++.|+
T Consensus 4 ~D~~Il~~Lq~d-~---r~s~~~la~~lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 4 LDRKILRLLQED-G---RRSYAELAEELGLSESTVRRRIRRLE 42 (42)
T ss_dssp HHHHHHHHHHH--T---TS-HHHHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHc-C---CccHHHHHHHHCcCHHHHHHHHHHhC
Confidence 466667777766 2 36889999999999998888887774
No 278
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=56.09 E-value=21 Score=23.50 Aligned_cols=32 Identities=25% Similarity=0.381 Sum_probs=26.3
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
||-..+|+.++|.-+. |.+|.+.|+|.+....
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 8999999999998655
No 279
>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=55.99 E-value=19 Score=26.76 Aligned_cols=40 Identities=28% Similarity=0.442 Sum_probs=26.2
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc---ccceEEEe
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSA---HASQQIYT 103 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k---~~~q~IYt 103 (108)
||-+.|-+--+++ +..+|+.|.++|+|..+-+ .++-.+|.
T Consensus 97 iTr~eIe~IRGv~---s~~~i~~L~e~glI~~~gr~~~~Grp~ly~ 139 (159)
T PF04079_consen 97 ITRAEIEEIRGVN---SDSVIKTLLERGLIEEVGRKDTPGRPILYG 139 (159)
T ss_dssp EEHHHHHHHHTS-----HCHHHHHHHTTSEEEEEE-TTTT--EEEE
T ss_pred cCHHHHHHHcCCC---hHHHHHHHHHCCCEEecCcCCCCCCCeEee
Confidence 5555555555544 8899999999999999853 34555665
No 280
>KOG3233 consensus RNA polymerase III, subunit C34 [Transcription]
Probab=55.08 E-value=5.5 Score=33.05 Aligned_cols=50 Identities=16% Similarity=0.296 Sum_probs=42.8
Q ss_pred hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe--ccccceEEEe
Q 033932 54 EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV--SAHASQQIYT 103 (108)
Q Consensus 54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V--~k~~~q~IYt 103 (108)
|...-+=|+--+|=.+-++...+-.++|+-|+++.||+-| .++.+-.||.
T Consensus 94 e~sg~~GIW~k~ik~ksnLp~~~v~K~LkSLEsKkLIKsVKsv~n~~~KvYm 145 (297)
T KOG3233|consen 94 EESGNEGIWSKEIKRKSNLPQTVVNKILKSLESKKLIKSVKSVKNSRKKVYM 145 (297)
T ss_pred HHcCCCceeeehhhhccCCCHHHHHHHHHHHHHHHHHHHHHhhcCCCceEEE
Confidence 4556677888899999999999999999999999999999 5666667774
No 281
>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=54.24 E-value=6.2 Score=26.26 Aligned_cols=32 Identities=16% Similarity=0.139 Sum_probs=28.7
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
.|...||+.++|+-+-.+..+..+...|.+..
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~~~~~~~~~~ 64 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKGETKAGGLVK 64 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhcCcccchHHH
Confidence 58899999999999999999999999887643
No 282
>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=54.14 E-value=23 Score=23.77 Aligned_cols=34 Identities=24% Similarity=0.341 Sum_probs=25.0
Q ss_pred hcccHHHHHHHHHHHHHcCCeeEe---c-cccceEEEe
Q 033932 70 LRINGSLARKAIRELMARGLIRMV---S-AHASQQIYT 103 (108)
Q Consensus 70 lkI~~SlAr~~Lr~L~~kGlIk~V---~-k~~~q~IYt 103 (108)
+.|+-+---.+|+.|+++|+|... + .+++..+|.
T Consensus 35 ~~i~~gtlY~~L~rLe~~GlI~~~~~~~~~~~~rk~y~ 72 (100)
T TIGR03433 35 LQVEEGSLYPALHRLERRGWIAAEWGESENNRRAKFYR 72 (100)
T ss_pred cccCCCcHHHHHHHHHHCCCeEEEeeecCCCCCceEEE
Confidence 467777788899999999999984 2 234445664
No 283
>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=53.84 E-value=31 Score=21.08 Aligned_cols=38 Identities=24% Similarity=0.201 Sum_probs=33.8
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
...||++.+=|.++++=-.|-.+|+.|...|+.+.+..
T Consensus 8 ~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~gd 45 (50)
T PF09107_consen 8 NGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVGD 45 (50)
T ss_dssp TSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred CCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeCC
Confidence 56799999999999999999999999999999988753
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=53.27 E-value=17 Score=27.68 Aligned_cols=46 Identities=7% Similarity=0.044 Sum_probs=36.6
Q ss_pred ceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHc
Q 033932 41 VLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMAR 87 (108)
Q Consensus 41 Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~k 87 (108)
-.+++++=+.|..++-.-.. |+-.||.+|+|..+--.+|||--+-+
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 34677777888877766555 99999999999999999998855443
No 285
>PF13011 LZ_Tnp_IS481: leucine-zipper of insertion element IS481
Probab=53.25 E-value=20 Score=24.58 Aligned_cols=38 Identities=11% Similarity=0.052 Sum_probs=33.5
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHAS 98 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~ 98 (108)
.+++.+|+.|+|+-..|.+-+.-..+.|.-=+...+++
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 46899999999999999999999999988877776664
No 286
>COG0640 ArsR Predicted transcriptional regulators [Transcription]
Probab=52.87 E-value=44 Score=20.08 Aligned_cols=36 Identities=19% Similarity=0.287 Sum_probs=31.8
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
.-.++..+++.++++.+....-|..|.+.|+|....
T Consensus 38 ~~~~~~~l~~~~~~~~~~v~~hL~~L~~~glv~~~~ 73 (110)
T COG0640 38 GELTVGELAEALGLSQSTVSHHLKVLREAGLVELRR 73 (110)
T ss_pred CCccHHHHHHHHCCChhHHHHHHHHHHHCCCeEEEe
Confidence 345689999999999999999999999999999943
No 287
>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=52.75 E-value=6.3 Score=26.10 Aligned_cols=54 Identities=13% Similarity=0.239 Sum_probs=42.3
Q ss_pred eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccce
Q 033932 43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQ 99 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q 99 (108)
+..++.++|..|-.+-.+-+...+.+|+. .+-+..|+.|..-|.+.....|+|+
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 56889999999998888999999999995 4557889999999988877665543
No 288
>PRK15466 carboxysome structural protein EutK; Provisional
Probab=52.69 E-value=12 Score=28.64 Aligned_cols=55 Identities=18% Similarity=0.213 Sum_probs=44.1
Q ss_pred ccceeCHHHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 39 NMVLFDQATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 39 n~Vl~dk~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
.++..+.+.-|-|+-++-.. .=.|.-.++.+|+....-||.+|+.|.+.|-+..-
T Consensus 102 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 157 (166)
T PRK15466 102 DAPVIVAESADELLALLTSVRQGMTAGEVAAHFGWPLEKARNALEQLFSAGTLRKR 157 (166)
T ss_pred CCCCCChhhHHHHHHHHHHHHccccHHHHHHHhCCcHHHHHHHHHHHHhccchhhc
Confidence 45556666677777666554 45799999999999999999999999999988653
No 289
>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=51.99 E-value=29 Score=24.93 Aligned_cols=40 Identities=20% Similarity=0.263 Sum_probs=34.7
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
|+-+||..++-....-|.||.-|..-|+|.....+ .||..
T Consensus 53 ~~e~LA~~~~~~~~~V~~Al~~f~k~glIe~~d~g---~i~i~ 92 (119)
T TIGR01714 53 NAEMLATMFNRNVGDIRITLQTLESLGLIEKKNNG---DIFLE 92 (119)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC---cEEeh
Confidence 88999999999999999999999999999988532 46654
No 290
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=51.90 E-value=27 Score=28.59 Aligned_cols=56 Identities=23% Similarity=0.235 Sum_probs=42.2
Q ss_pred HHHHHHHhhCCCC-eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 46 ATYDKLLSEAPKY-KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 46 ~t~dKl~KEVpk~-k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
.|--.|+-|+--+ .-+-|..||+.++|+.-----=|++|.+.|+|.. ++|.-..-|
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 3445566666544 6788999999999999888888999999999987 444333434
No 291
>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=51.67 E-value=14 Score=23.69 Aligned_cols=37 Identities=22% Similarity=0.229 Sum_probs=28.1
Q ss_pred HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHH
Q 033932 50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMA 86 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~ 86 (108)
.|...+-..+.+|...+|+.+.|+-|-.++.|++|..
T Consensus 20 ~ll~~ll~~~~~s~~~la~~~~iS~sti~~~i~~l~~ 56 (87)
T PF05043_consen 20 QLLKLLLNNEYVSIEDLAEELFISRSTIYRDIKKLNK 56 (87)
T ss_dssp HHHHHHHH-SEEEHHHHHHHHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHcCCCcCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4555555678899999999999999999999988765
No 292
>PHA01747 putative ATP-dependent protease
Probab=51.33 E-value=16 Score=31.71 Aligned_cols=42 Identities=17% Similarity=0.114 Sum_probs=37.7
Q ss_pred CHHHHHHHHhhCCCC--eeechhhhhhhhcccHHHHHHHHHHHHHc
Q 033932 44 DQATYDKLLSEAPKY--KLITPSILSDRLRINGSLARKAIRELMAR 87 (108)
Q Consensus 44 dk~t~dKl~KEVpk~--k~ITps~vserlkI~~SlAr~~Lr~L~~k 87 (108)
|.+.+|||. +|.. +-||...++.-+.+..+++|..++.+.++
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 889999999 7764 67899999999999999999999999875
No 293
>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=51.29 E-value=18 Score=23.85 Aligned_cols=48 Identities=21% Similarity=0.207 Sum_probs=32.9
Q ss_pred hhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 37 ~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
.-..+++-.+..|=|....+. + .+-.=|-.+.+.|.+.|+|..|+.+|
T Consensus 25 ~~~~cF~G~e~VdWL~~~~~~--~-----------~~r~eAv~lgq~Ll~~g~I~hv~~~~ 72 (83)
T cd04449 25 LPSNCFIGSEAVSWLINNFED--V-----------DTREEAVELGQELMNEGLIEHVSGRH 72 (83)
T ss_pred cCCcceEhHHHHHHHHHhCCC--C-----------CCHHHHHHHHHHHHHCCCEEecCCCC
Confidence 344556667777776665442 1 22345888899999999999998644
No 294
>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=51.11 E-value=19 Score=21.77 Aligned_cols=42 Identities=17% Similarity=0.144 Sum_probs=31.7
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
+.+..|+.++|+-|-..+.|++||+.=-+.++.++++...-|
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 567789999999999999999999965555666655555544
No 295
>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=51.07 E-value=20 Score=30.24 Aligned_cols=50 Identities=26% Similarity=0.300 Sum_probs=41.1
Q ss_pred HHHHHHHhhC------CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 46 ATYDKLLSEA------PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 46 ~t~dKl~KEV------pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
.+++.|..+| |..++=+.-.+|+.|+|+.+.--++.++|+.+|+|.-..+
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 4468889999999999999999999999999999977644
No 296
>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=51.00 E-value=19 Score=23.87 Aligned_cols=24 Identities=25% Similarity=0.181 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHcCCeeEecccc
Q 033932 74 GSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 74 ~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
-.=|-.+-+.|.+.|+|.+|..+|
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 297
>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=50.79 E-value=24 Score=28.23 Aligned_cols=38 Identities=26% Similarity=0.377 Sum_probs=31.3
Q ss_pred hhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932 64 SILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIY 102 (108)
Q Consensus 64 s~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY 102 (108)
..+.+.++|+-+..|-+|.-|+++|+|......+ ...|
T Consensus 24 i~l~~~~gi~~~~vr~al~RL~~~G~l~~~~~gr-r~~Y 61 (280)
T TIGR02277 24 IEFLAGLGINERLVRTAVSRLVAQGWLQSERKGR-RSFY 61 (280)
T ss_pred HHHHHhcCCCcchHHHHHHHHHHCCCEEeeecCC-CCEE
Confidence 4678999999999999999999999999864433 3455
No 298
>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=50.65 E-value=9.4 Score=27.14 Aligned_cols=45 Identities=20% Similarity=0.353 Sum_probs=27.1
Q ss_pred CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932 44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHAS 98 (108)
Q Consensus 44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~ 98 (108)
..+.++||..+.|...+|-.|..+| -+||.+.+.|+|..+.....
T Consensus 10 a~~ni~kl~~~~~~~~vVp~SA~aE----------l~Lr~a~k~g~I~Y~pGd~~ 54 (109)
T PF08438_consen 10 ADENIEKLKEKYPDEPVVPTSAAAE----------LALRKAAKAGLIDYIPGDSD 54 (109)
T ss_dssp -HHHHHHHHHHHTT-EEEEE-HHHH----------HHHHS-SSS----S------
T ss_pred cHhHHHHHHHhCCCCceeeccHHHH----------HHHHHHHHCCCEEeCCCCCc
Confidence 6789999999999999998887665 57999999999987665443
No 299
>COG3398 Uncharacterized protein conserved in archaea [Function unknown]
Probab=50.16 E-value=38 Score=27.40 Aligned_cols=59 Identities=17% Similarity=0.200 Sum_probs=49.6
Q ss_pred HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
.+|-..|.-|+.+.+.-|.-.||-++++++..-+=.+..|++-|+|..=. ..+-.||.=
T Consensus 173 n~~~k~I~~eiq~~~~~t~~~ia~~l~ls~aTV~~~lk~l~~~Gii~~~~-~Gr~iiy~i 231 (240)
T COG3398 173 NETSKAIIYEIQENKCNTNLLIAYELNLSVATVAYHLKKLEELGIIPEDR-EGRSIIYSI 231 (240)
T ss_pred chhHHHHHHHHhcCCcchHHHHHHHcCccHHHHHHHHHHHHHcCCCcccc-cCceEEEEe
Confidence 34667888999999999999999999999999999999999999998743 344456653
No 300
>PLN02853 Probable phenylalanyl-tRNA synthetase alpha chain
Probab=49.86 E-value=37 Score=29.96 Aligned_cols=49 Identities=8% Similarity=0.091 Sum_probs=38.9
Q ss_pred HHHHHhhCCCCe-eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 48 YDKLLSEAPKYK-LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 48 ~dKl~KEVpk~k-~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
-.+|+....... .+++..+|+.+++.-.-.-.++..|+++|+|..-..-
T Consensus 5 e~~iL~~l~~~~~~~~~~~la~~~g~~~~~v~~~~~~L~~kg~v~~~~~~ 54 (492)
T PLN02853 5 EEALLGALSNNEEISDSGQFAASHGLDHNEVVGVIKSLHGFRYVDAQDIK 54 (492)
T ss_pred HHHHHHHHHhcCCCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEE
Confidence 345555555544 4799999999999999999999999999988765433
No 301
>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=49.16 E-value=28 Score=21.60 Aligned_cols=30 Identities=23% Similarity=0.251 Sum_probs=25.6
Q ss_pred hhcccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932 69 RLRINGSLARKAIRELMARGLIRMVSAHAS 98 (108)
Q Consensus 69 rlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~ 98 (108)
.+..+-+-|..+.++|.+.|+|..|..++.
T Consensus 33 ~~~~~r~eA~~l~q~Ll~~g~i~~v~~~~~ 62 (74)
T PF00610_consen 33 GFVRDREEAVQLGQELLDHGFIEHVSDKSK 62 (74)
T ss_dssp TSTSSHHHHHHHHHHHHHCTSEEESSSSSH
T ss_pred ccccCHHHHHHHHHHHHHCCCEEECCCCCC
Confidence 445677889999999999999999988774
No 302
>PRK04280 arginine repressor; Provisional
Probab=49.01 E-value=72 Score=23.42 Aligned_cols=53 Identities=19% Similarity=0.284 Sum_probs=31.7
Q ss_pred HHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 34 KEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 34 keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
++-+++..+=.++-+-..+++- ++. +|.++|| |+|.+-|+++.-. .+.+..|.
T Consensus 10 ~~iI~~~~I~tQeeL~~~L~~~-Gi~-vTQATiS--------------RDikeL~lvKv~~-~~G~~~Y~ 62 (148)
T PRK04280 10 REIITNNEIETQDELVDRLREE-GFN-VTQATVS--------------RDIKELHLVKVPL-PDGRYKYS 62 (148)
T ss_pred HHHHHhCCCCCHHHHHHHHHHc-CCC-eehHHHH--------------HHHHHcCCEEeec-CCCcEEEe
Confidence 3444444444554444444343 555 7777777 7888889998433 34456775
No 303
>PRK05066 arginine repressor; Provisional
Probab=48.71 E-value=76 Score=23.58 Aligned_cols=55 Identities=22% Similarity=0.208 Sum_probs=34.2
Q ss_pred hHHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 33 QKEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 33 ~keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
.++-+++..+=+++-+-..++|- ++..+|.++|| |+|.+=|+++.-. ...+.+|.
T Consensus 14 I~~iI~~~~I~tQeeL~~~L~~~-Gi~~vTQATiS--------------RDikeL~lvKv~~-~~G~~~Y~ 68 (156)
T PRK05066 14 FKALLKEEKFGSQGEIVTALQEQ-GFDNINQSKVS--------------RMLTKFGAVRTRN-AKMEMVYC 68 (156)
T ss_pred HHHHHhhCCCCCHHHHHHHHHHC-CCCeecHHHHH--------------HHHHHcCCEEeeC-CCCCEEEE
Confidence 34555555555555555555554 66667777776 7888888888433 34456775
No 304
>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=48.57 E-value=25 Score=24.79 Aligned_cols=39 Identities=28% Similarity=0.414 Sum_probs=29.7
Q ss_pred hCCCCeeechhhhhhhh--cccHHHHHHHHHHHHHcCCeeE
Q 033932 54 EAPKYKLITPSILSDRL--RINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 54 EVpk~k~ITps~vserl--kI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
-|-+-.|||++.|+|-+ ..+-+.--.-+--|..+|+|..
T Consensus 24 ~v~Kk~Fit~~ev~e~l~~~~~~~~V~SNIGvLIKkglIEK 64 (96)
T PF09114_consen 24 QVAKKNFITASEVREALATEMNKASVNSNIGVLIKKGLIEK 64 (96)
T ss_dssp HHHHSTTB-HHHHHH-T-TTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHccCCHHHHHHHHHHHhhhhHHHHhHHHHHHcCcccc
Confidence 45667899999999987 6677777777889999999965
No 305
>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=46.94 E-value=37 Score=24.23 Aligned_cols=42 Identities=21% Similarity=0.218 Sum_probs=35.0
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA 105 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~ 105 (108)
.|+-+||..++-....-+.+|.-|.+-|+|.... ...||..+
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 4788999999999999999999999999998743 24566543
No 306
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=46.90 E-value=26 Score=19.47 Aligned_cols=26 Identities=19% Similarity=0.400 Sum_probs=22.7
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMA 86 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~ 86 (108)
.|...+|+.|+|+-+-.+..++.+..
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 58999999999999999998887654
No 307
>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=46.88 E-value=23 Score=22.47 Aligned_cols=30 Identities=20% Similarity=0.324 Sum_probs=26.8
Q ss_pred CCeeechhhhhhhhcccHHHHHHHHHHHHH
Q 033932 57 KYKLITPSILSDRLRINGSLARKAIRELMA 86 (108)
Q Consensus 57 k~k~ITps~vserlkI~~SlAr~~Lr~L~~ 86 (108)
...+||...+++.++|+-.-|.+.+++|..
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 308
>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=46.43 E-value=28 Score=20.11 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=21.5
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHH
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELM 85 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~ 85 (108)
.=.|-..||+.|+++-+-.+..++...
T Consensus 19 ~~~t~~eIa~~lg~s~~~V~~~~~~al 45 (50)
T PF04545_consen 19 EGLTLEEIAERLGISRSTVRRILKRAL 45 (50)
T ss_dssp ST-SHHHHHHHHTSCHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHCCcHHHHHHHHHHHH
Confidence 345889999999999999988776654
No 309
>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=45.33 E-value=13 Score=24.89 Aligned_cols=33 Identities=9% Similarity=-0.036 Sum_probs=25.6
Q ss_pred HHHHhhCCCCeeechhhhhhhhcccHHHHHHHHH
Q 033932 49 DKLLSEAPKYKLITPSILSDRLRINGSLARKAIR 82 (108)
Q Consensus 49 dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr 82 (108)
..|..-+-. .-+|...||+.++|+.+..++.|.
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 344444445 677999999999999999999774
No 310
>COG4109 Predicted transcriptional regulator containing CBS domains [Transcription]
Probab=45.01 E-value=28 Score=30.18 Aligned_cols=49 Identities=20% Similarity=0.261 Sum_probs=41.7
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+==+=|+.--+|..|+++-..|-+|++|.+..|++.-..+....+|=.+
T Consensus 15 ~vG~kISVR~Ia~~l~VSeGTAYRAIKeAen~G~V~Ti~RvGTvRIekk 63 (432)
T COG4109 15 EVGKKISVRGIAKHLKVSEGTAYRAIKEAENLGLVSTIPRVGTVRIEKK 63 (432)
T ss_pred cccceeehHHhhhhCCcccchHHHHHHHHHhcCceEecccceeEEEEec
Confidence 3346789999999999999999999999999999998887777666443
No 311
>PTZ00326 phenylalanyl-tRNA synthetase alpha chain; Provisional
Probab=44.86 E-value=54 Score=28.91 Aligned_cols=39 Identities=18% Similarity=0.261 Sum_probs=33.7
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
..+++..+|+.+++.-.-.-.++..|+++|+|..-..-.
T Consensus 20 ~~~~~~~la~~~~~~~~~v~~~~~~L~~kg~v~~~~~~~ 58 (494)
T PTZ00326 20 EIVNSLALAESLNIDHQKVVGAIKSLESANYITTEMKKS 58 (494)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHHHhCCCEEEEEEEE
Confidence 458999999999999999999999999999887655433
No 312
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=44.82 E-value=37 Score=26.62 Aligned_cols=53 Identities=17% Similarity=0.173 Sum_probs=42.5
Q ss_pred CHHHHHHHH-hhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 44 DQATYDKLL-SEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 44 dk~t~dKl~-KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
+.+.+..|. .-+..+=..|+..++.-++++.+.+|.+|.+|.+.|-|..|.-.
T Consensus 164 ~~ea~~~Lv~Ryl~~~GPat~~d~a~w~gl~~~~~r~~l~~l~~~~~L~~v~~~ 217 (327)
T PF06224_consen 164 REEALAELVRRYLRAYGPATLADFAWWSGLPKTQARRALAQLVEEGELVEVEVE 217 (327)
T ss_pred HHHHHHHHHHHHHHHcCCccHHHHHHHhccCHHHHHHHHHhhccCCcEEEEEEc
Confidence 344444444 34455788999999999999999999999999999999999655
No 313
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=44.52 E-value=43 Score=19.26 Aligned_cols=40 Identities=10% Similarity=0.038 Sum_probs=31.3
Q ss_pred eCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHH
Q 033932 43 FDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIREL 84 (108)
Q Consensus 43 ~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L 84 (108)
+...+-..|+.+.-.. .|...||..++|.-+-.++++.+.
T Consensus 12 ~T~~~~~~i~~~~~~~--~s~~~vA~~~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 12 ITKRLEQYILKLLRES--RSFKDVARELGVSWSTVRRIFDRY 51 (52)
T ss_pred HHHHHHHHHHHHHhhc--CCHHHHHHHHCCCHHHHHHHHHhh
Confidence 3455556666666665 799999999999999999998764
No 314
>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=44.18 E-value=30 Score=20.60 Aligned_cols=29 Identities=24% Similarity=0.409 Sum_probs=22.0
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHH-HHcCCe
Q 033932 59 KLITPSILSDRLRINGSLARKAIREL-MARGLI 90 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L-~~kGlI 90 (108)
.-||.+.||+.|++.. ..+|+.| .+.|+-
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 4589999999999985 5788999 448987
No 315
>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=44.06 E-value=27 Score=20.62 Aligned_cols=23 Identities=13% Similarity=0.280 Sum_probs=17.1
Q ss_pred chhhhhhhhcccHHHHHHHHHHH
Q 033932 62 TPSILSDRLRINGSLARKAIREL 84 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L 84 (108)
.+-.|+++|+|.-.+||.|++..
T Consensus 11 n~~~L~~~f~ip~~vAk~IV~~C 33 (40)
T PF02022_consen 11 NAKALRHKFGIPRLVAKQIVNQC 33 (40)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHS
T ss_pred CHHHHHHHHccCHHHHHHHHHHC
Confidence 35678999999999999998753
No 316
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=43.58 E-value=34 Score=18.47 Aligned_cols=26 Identities=15% Similarity=0.276 Sum_probs=22.0
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMA 86 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~ 86 (108)
.|+..||+.++++.+..+..+.....
T Consensus 27 ~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 27 LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 58999999999999998888876543
No 317
>KOG4068 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.27 E-value=37 Score=26.22 Aligned_cols=34 Identities=21% Similarity=0.314 Sum_probs=26.7
Q ss_pred ccHHHHHHHHHHHHHcCCeeEecccc-ceEEEecc
Q 033932 72 INGSLARKAIRELMARGLIRMVSAHA-SQQIYTRA 105 (108)
Q Consensus 72 I~~SlAr~~Lr~L~~kGlIk~V~k~~-~q~IYtr~ 105 (108)
+..++-+.+|.+|+.+|++.+..+++ +-.||=|.
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 45678899999999999999998764 33467654
No 318
>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=43.25 E-value=24 Score=28.91 Aligned_cols=43 Identities=19% Similarity=0.227 Sum_probs=32.2
Q ss_pred CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 58 YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 58 ~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
+...|...+|++++|+-+. ||..+.+|++-.+.+ .++.+.|+.
T Consensus 31 ~~~~~i~eva~~~gv~~~t----lr~~e~~~~~~~~~r~~~g~r~yt~ 74 (387)
T TIGR03453 31 LRKFTSGEVAKLLGVSDSY----LRQLSLEGKGPEPETLSNGRRSYTL 74 (387)
T ss_pred cccCCHHHHHHHHCcCHHH----HHHHHHcCCCCCCCcCCCCceeeCH
Confidence 3678999999999998776 566899998766533 445667763
No 319
>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=43.19 E-value=12 Score=21.71 Aligned_cols=22 Identities=5% Similarity=0.191 Sum_probs=16.9
Q ss_pred echhhhhhhhcccHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIR 82 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr 82 (108)
+|...||+.|+|.-+--.++|+
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 7899999999999998887775
No 320
>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=43.00 E-value=20 Score=22.06 Aligned_cols=34 Identities=21% Similarity=0.307 Sum_probs=23.6
Q ss_pred HHHHHHhhCCC--CeeechhhhhhhhcccHHHHHHH
Q 033932 47 TYDKLLSEAPK--YKLITPSILSDRLRINGSLARKA 80 (108)
Q Consensus 47 t~dKl~KEVpk--~k~ITps~vserlkI~~SlAr~~ 80 (108)
.|-+++++... ...|+-..||+.++|+.+.-|+=
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 45555555543 58999999999999999988863
No 321
>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=42.86 E-value=45 Score=20.77 Aligned_cols=43 Identities=21% Similarity=0.173 Sum_probs=31.8
Q ss_pred ccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 39 NMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 39 n~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
..++.=.+..+=|..... -.+-+-|..+.+.|.+.|+|.+|..
T Consensus 18 ~~~F~G~e~v~wL~~~~~--------------~~~r~eA~~l~~~ll~~g~i~~v~~ 60 (77)
T smart00049 18 PNCFTGSELVDWLMDNLE--------------IIDREEAVHLGQLLLDEGLIHHVNG 60 (77)
T ss_pred cceeEcHHHHHHHHHcCC--------------cCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 344555666666665553 1456889999999999999999984
No 322
>PF14330 DUF4387: Domain of unknown function (DUF4387)
Probab=42.85 E-value=26 Score=24.67 Aligned_cols=28 Identities=18% Similarity=0.485 Sum_probs=24.0
Q ss_pred CHHHHHHHHhhCCCCeeechhhhhhhhcccHH
Q 033932 44 DQATYDKLLSEAPKYKLITPSILSDRLRINGS 75 (108)
Q Consensus 44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~S 75 (108)
|++.|+++.. ..++|+..+|+-|+|.-+
T Consensus 26 ~~e~Y~~vk~----s~~l~~~~ia~Ly~i~~~ 53 (99)
T PF14330_consen 26 DKEAYERVKA----SGVLTPELIARLYGIDPE 53 (99)
T ss_pred CHHHHHHHHH----cCccCHHHHHHHHCCCHH
Confidence 8999999874 568999999999998754
No 323
>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=42.36 E-value=33 Score=19.21 Aligned_cols=26 Identities=23% Similarity=0.335 Sum_probs=22.5
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMA 86 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~ 86 (108)
.|...+|+.++++-+..+..++.+..
T Consensus 16 ~s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 16 KTNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 58999999999999999988887644
No 324
>PF06224 HTH_42: Winged helix DNA-binding domain; InterPro: IPR009351 This is a family of conserved bacterial proteins with unknown function.
Probab=41.90 E-value=58 Score=25.54 Aligned_cols=59 Identities=17% Similarity=0.133 Sum_probs=46.4
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhccc--------HHHHHHHHHHHHHcCCeeEeccc-cceEEEecc
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRIN--------GSLARKAIRELMARGLIRMVSAH-ASQQIYTRA 105 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~--------~SlAr~~Lr~L~~kGlIk~V~k~-~~q~IYtr~ 105 (108)
..+.|+..+-.-.-+|...|.+.+... .+....+|+.|...|.|...-.. ..+..|...
T Consensus 86 ~~~~v~~~L~~~gplt~~eL~~~l~~~~~~~~~~~~~~~~~~l~~l~~~G~l~~~~~~~g~~~~y~l~ 153 (327)
T PF06224_consen 86 LAEAVLDALRADGPLTRAELREALAEAGWWGWGGPSSPWKHLLEYLWYRGLLCVGPRPRGRWRTYDLT 153 (327)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHhhhccccCCCCCCchHHHHHHHHHhCCeEEEeccCCCceEEEech
Confidence 345566666566789999999998775 45889999999999999998755 667888753
No 325
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=41.78 E-value=66 Score=21.51 Aligned_cols=43 Identities=16% Similarity=0.158 Sum_probs=37.0
Q ss_pred CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932 56 PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHAS 98 (108)
Q Consensus 56 pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~ 98 (108)
-...+++-..|++.|+|+-.---+.++.|.+.|+=...++++.
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 4456888999999999999999999999999999887776654
No 326
>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=41.70 E-value=51 Score=21.75 Aligned_cols=27 Identities=33% Similarity=0.320 Sum_probs=22.1
Q ss_pred ccHHHHHHHHHHHHHcCCeeEeccccc
Q 033932 72 INGSLARKAIRELMARGLIRMVSAHAS 98 (108)
Q Consensus 72 I~~SlAr~~Lr~L~~kGlIk~V~k~~~ 98 (108)
++..=|..+-.+|...|+|.+|..++.
T Consensus 45 ~~~~EA~~~~~~ll~~gli~~V~~~~~ 71 (88)
T cd04450 45 VDPSEALEIAALFVKYGLITPVSDHRS 71 (88)
T ss_pred CCHHHHHHHHHHHHHCCCEEEecCCcc
Confidence 445568888899999999999987654
No 327
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=41.26 E-value=33 Score=20.53 Aligned_cols=27 Identities=22% Similarity=0.209 Sum_probs=23.1
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHH
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMA 86 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~ 86 (108)
..|-..+|.+|+|+-|-+-+++.+++.
T Consensus 19 ~~~~~~La~~FgIs~stvsri~~~~~~ 45 (53)
T PF13613_consen 19 NLTFQDLAYRFGISQSTVSRIFHEWIP 45 (53)
T ss_pred CCcHhHHhhheeecHHHHHHHHHHHHH
Confidence 457788999999999999999988754
No 328
>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=40.20 E-value=55 Score=21.85 Aligned_cols=41 Identities=22% Similarity=0.238 Sum_probs=32.4
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
+.||.+...- .++|...+|.-|+|. .+...+.|.+.|+|-.
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 4566666433 689999999999888 7778888888999866
No 329
>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=39.58 E-value=96 Score=19.43 Aligned_cols=27 Identities=22% Similarity=0.202 Sum_probs=20.9
Q ss_pred hhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 69 RLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 69 rlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
.|....+.-+..|+.|.++|.|..-..
T Consensus 39 ~f~~~~~~ik~~Ie~LIekeyi~Rd~~ 65 (68)
T PF10557_consen 39 RFPPSVSDIKKRIESLIEKEYIERDED 65 (68)
T ss_dssp TS---HHHHHHHHHHHHHTTSEEEESS
T ss_pred CcCCCHHHHHHHHHHHHHhhhhhcCCC
Confidence 777889999999999999999987543
No 330
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=39.30 E-value=44 Score=26.55 Aligned_cols=51 Identities=12% Similarity=0.132 Sum_probs=40.4
Q ss_pred CHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHH-HHHHcCCeeEecc
Q 033932 44 DQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIR-ELMARGLIRMVSA 95 (108)
Q Consensus 44 dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr-~L~~kGlIk~V~k 95 (108)
|.+.+.-+.+.++.- -++..++|+.++...+-+...++ .|...|+|....+
T Consensus 261 ~~~~l~~~~~~~~~~-~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~ 312 (328)
T PRK00080 261 DRKYLRTIIEKFGGG-PVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPR 312 (328)
T ss_pred HHHHHHHHHHHcCCC-ceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCc
Confidence 344554466665554 59999999999999999999999 9999999975443
No 331
>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=39.00 E-value=42 Score=15.92 Aligned_cols=18 Identities=17% Similarity=0.242 Sum_probs=14.5
Q ss_pred chhhhhhhhcccHHHHHH
Q 033932 62 TPSILSDRLRINGSLARK 79 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~ 79 (108)
|...+++.++|.-+....
T Consensus 23 s~~~ia~~~~is~~tv~~ 40 (42)
T cd00569 23 SVAEIARRLGVSRSTLYR 40 (42)
T ss_pred CHHHHHHHHCCCHHHHHH
Confidence 889999999988776544
No 332
>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=38.52 E-value=31 Score=25.15 Aligned_cols=35 Identities=23% Similarity=0.288 Sum_probs=25.9
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
=+.|..||-+|.|.-+...++|....+-|.|.|=.
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 46899999999999999999999999999998764
No 333
>PRK13824 replication initiation protein RepC; Provisional
Probab=37.98 E-value=40 Score=28.67 Aligned_cols=35 Identities=29% Similarity=0.417 Sum_probs=30.0
Q ss_pred eech--hhhhhh-hcccHHHHHHHHHHHHHcCCeeEec
Q 033932 60 LITP--SILSDR-LRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 60 ~ITp--s~vser-lkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+|=| ..||+| +++..+--|+.|+.|++-|||..=+
T Consensus 80 IVfpSN~~La~r~~Gms~~tlrRhla~LveaGLI~rrD 117 (404)
T PRK13824 80 VVFPSNAQLSLRAHGMAGATLRRHLAALVEAGLIIRRD 117 (404)
T ss_pred eechhHHHHHHHHcCCCHHHHHHHHHHHHHCCCeEeec
Confidence 4444 479999 5999999999999999999998764
No 334
>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=37.93 E-value=34 Score=22.97 Aligned_cols=43 Identities=16% Similarity=0.162 Sum_probs=36.4
Q ss_pred cceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHH-HHHHH
Q 033932 40 MVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLA-RKAIR 82 (108)
Q Consensus 40 ~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlA-r~~Lr 82 (108)
.|+++++-|+.|.+....-...|-..|.++++.+-+-. ..+|.
T Consensus 3 ~vii~k~ey~el~~~~~~~~~W~~~dl~k~~~~s~~wi~~~il~ 46 (91)
T PF05595_consen 3 KVIIDKEEYEELKKKDLEGKWWDMKDLRKRTGKSREWIKENILY 46 (91)
T ss_pred eEEeeHHHHHHHHHHhhccceeeHHHHHHHHCCCHHHHHHHccc
Confidence 58999999999999999999999999999998665554 35555
No 335
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=36.92 E-value=40 Score=25.54 Aligned_cols=38 Identities=8% Similarity=0.180 Sum_probs=28.7
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc-ccceEEEec
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIRMVSA-HASQQIYTR 104 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr 104 (108)
|++.+|++++|+.+.. |.-+++|.|. +.+ .++.++|+.
T Consensus 2 ti~evA~~lGVS~~TL----Rrw~k~g~L~-~~R~~~G~R~y~~ 40 (175)
T PRK13182 2 KTPFVAKKLGVSPKTV----QRWVKQLNLP-CEKNEYGHYIFTE 40 (175)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHcCCCC-CCcCCCCCEEECH
Confidence 7899999999998764 5566788885 544 456788874
No 336
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=36.78 E-value=62 Score=23.77 Aligned_cols=34 Identities=24% Similarity=0.225 Sum_probs=31.6
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
.|-.+||++++|+-.-++.=++.|++.|++..--
T Consensus 178 ~s~~eIa~~l~iS~~Tv~~~~~~~~~~~~~~~~~ 211 (225)
T PRK10046 178 HTAETVAQALTISRTTARRYLEYCASRHLIIAEI 211 (225)
T ss_pred cCHHHHHHHhCccHHHHHHHHHHHHhCCeEEEEe
Confidence 5889999999999999999999999999998764
No 337
>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=35.64 E-value=22 Score=27.21 Aligned_cols=21 Identities=19% Similarity=0.319 Sum_probs=19.4
Q ss_pred chhhhhhhhcccHHHHHHHHH
Q 033932 62 TPSILSDRLRINGSLARKAIR 82 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr 82 (108)
+|+++-|++...++||++||-
T Consensus 34 ~P~~l~eKi~~aM~LA~AIlg 54 (168)
T PF03397_consen 34 RPTNLTEKIYYAMKLAAAILG 54 (168)
T ss_pred CCCchhhHHHHHHHHHHHHHC
Confidence 699999999999999999973
No 338
>PF09824 ArsR: ArsR transcriptional regulator; InterPro: IPR014517 Members of this family of archaeal proteins are conserved transcriptional regulators belonging to the ArsR family.
Probab=34.42 E-value=30 Score=26.43 Aligned_cols=47 Identities=26% Similarity=0.378 Sum_probs=39.7
Q ss_pred ceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 41 VLFDQATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 41 Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
..|+-++|.++..++.+ .-+|-.+|.|+++-.+ +.+|.-|..-|||.
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 46888999999866654 5789999999999888 88899999999885
No 339
>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=34.29 E-value=1.2e+02 Score=19.20 Aligned_cols=46 Identities=28% Similarity=0.376 Sum_probs=34.5
Q ss_pred HHhhCCCCeeechhhhhhhh---ccc--HHHHHHHHHHHHHcCCeeEecccc
Q 033932 51 LLSEAPKYKLITPSILSDRL---RIN--GSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 51 l~KEVpk~k~ITps~vserl---kI~--~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
++...|. ..|+...+|+.| ++. -==---++.=|++=|+|....++.
T Consensus 16 ~~~~~~~-~~i~l~~ia~~l~~~~~k~~~RRlYDI~NVLealgli~K~~k~~ 66 (71)
T PF02319_consen 16 LFESSPD-KSISLNEIADKLISENVKTQRRRLYDIINVLEALGLIEKQSKNS 66 (71)
T ss_dssp HHHHCCC-TEEEHHHHHHHCHHHCCHHHCHHHHHHHHHHHHCTSEEEEETTE
T ss_pred HHHHCCC-CcccHHHHHHHHcccccccccchhhHHHHHHHHhCceeecCCCc
Confidence 5556677 899999999999 773 222334678899999999876654
No 340
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=34.16 E-value=49 Score=19.61 Aligned_cols=25 Identities=12% Similarity=0.170 Sum_probs=18.1
Q ss_pred echhhhhhhhcccHHHHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIRELM 85 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~ 85 (108)
+|...||+.++++.+.-.+++++..
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 4677888888888777766666553
No 341
>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=33.55 E-value=89 Score=20.59 Aligned_cols=29 Identities=17% Similarity=0.316 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHcCCeeEeccccceEEE
Q 033932 74 GSLARKAIRELMARGLIRMVSAHASQQIY 102 (108)
Q Consensus 74 ~SlAr~~Lr~L~~kGlIk~V~k~~~q~IY 102 (108)
-++-+.+|+.|.++|.|..+..+....-|
T Consensus 45 ~~~l~~aLkk~v~~G~l~~~kG~g~~gsf 73 (88)
T cd00073 45 NKLLKLALKKGVAKGKLVQVKGTGASGSF 73 (88)
T ss_pred HHHHHHHHHHHHHCCCeEeecCCCCccce
Confidence 46778899999999999999865443334
No 342
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=33.11 E-value=78 Score=28.19 Aligned_cols=60 Identities=12% Similarity=0.104 Sum_probs=49.9
Q ss_pred hhhccceeCHHHHHHHHhhCC----CCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 36 KVNNMVLFDQATYDKLLSEAP----KYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 36 K~nn~Vl~dk~t~dKl~KEVp----k~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
++++..+|+.+.|+++...+- ...-||++.+=|.++++-=.|-.+|++|.+.|+.+.+..
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 456678899998885554443 357899999999999999999999999999999988753
No 343
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=32.98 E-value=95 Score=26.62 Aligned_cols=47 Identities=17% Similarity=0.186 Sum_probs=39.0
Q ss_pred HHHHHHhhC-CCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 47 TYDKLLSEA-PKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 47 t~dKl~KEV-pk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
-|.+|..-. ..---+|-..||+.|..+-==||.+|+.|+++|.|.=-
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 366666555 33347899999999999999999999999999999865
No 344
>KOG3411 consensus 40S ribosomal protein S19 [Translation, ribosomal structure and biogenesis]
Probab=32.81 E-value=51 Score=24.76 Aligned_cols=24 Identities=25% Similarity=0.465 Sum_probs=20.1
Q ss_pred cHHHHHHHHHHHHHcCCeeEeccc
Q 033932 73 NGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 73 ~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
.++++|++|+.|+.-|+|..=-++
T Consensus 96 s~~i~rkvlQ~Le~~~~ve~hp~g 119 (143)
T KOG3411|consen 96 SGGIARKVLQALEKMGIVEKHPKG 119 (143)
T ss_pred ccHHHHHHHHHHHhCCceeeCCCC
Confidence 579999999999999999775443
No 345
>COG0664 Crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
Probab=32.58 E-value=64 Score=22.37 Aligned_cols=36 Identities=22% Similarity=0.313 Sum_probs=32.5
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEec
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
-.+|...+|+-++++..-.-++|.+|...|+|..-.
T Consensus 170 ~~~~~~~ia~~~g~~~~~vsr~l~~l~~~g~i~~~~ 205 (214)
T COG0664 170 LPLTHKDLAEYLGLSRETVSRILKELRKDGLISVRG 205 (214)
T ss_pred ccCCHHHHHHHhCCchhhHHHHHHHHHhCCcEeeCC
Confidence 468999999999999999999999999999997643
No 346
>PRK03341 arginine repressor; Provisional
Probab=32.38 E-value=1.5e+02 Score=22.40 Aligned_cols=53 Identities=13% Similarity=0.255 Sum_probs=33.1
Q ss_pred HHHHHHhhCCCCeeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceE-EEe
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQ-IYT 103 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~-IYt 103 (108)
-.+.|..-+....+.|...|++.| .++-+--+ |+|.+-|++|.-.. ..+. +|.
T Consensus 16 R~~~I~~li~~~~i~tQ~eL~~~L~~~Gi~vTQaTiS---RDl~eL~~~Kv~~~-~G~~~~Y~ 74 (168)
T PRK03341 16 RQARIVAILSRQSVRSQAELAALLADEGIEVTQATLS---RDLDELGAVKLRGA-DGGLGVYV 74 (168)
T ss_pred HHHHHHHHHHHCCCccHHHHHHHHHHcCCcccHHHHH---HHHHHhcCEeeecC-CCCEEEEE
Confidence 344555555667788888998888 44444433 56666688884333 3444 775
No 347
>KOG4062 consensus 6-O-methylguanine-DNA methyltransferase MGMT/MGT1, involved in DNA repair [Replication, recombination and repair]
Probab=31.94 E-value=81 Score=24.48 Aligned_cols=64 Identities=22% Similarity=0.200 Sum_probs=49.3
Q ss_pred hHHhhh-ccceeCHHHHHHHHh---hCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 33 QKEKVN-NMVLFDQATYDKLLS---EAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 33 ~keK~n-n~Vl~dk~t~dKl~K---EVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
..+.++ +.++++.+-+-++.+ +||.=.++|=+.||.+.+ +=|-||++=+.+....+--+|-.||
T Consensus 75 ~~~~~p~~~~~~~t~F~~kVw~al~~i~~Gev~tY~~iA~~iG-~PsaaRaVg~A~~~n~la~lvPcHR 142 (178)
T KOG4062|consen 75 AIEEFPVHPVMRGTDFQRKVWDALCEIPYGEVSTYGQIARRIG-NPSAARAVGSAMAHNNLAILVPCHR 142 (178)
T ss_pred hcccCCccceeccchHHHHHHHHHhccCCCceeeHHHHHHHhC-CcHHHHHHHHHHccCCCcEEeccee
Confidence 445566 577777777666554 566669999999999988 6788999999998888877776655
No 348
>PRK10512 selenocysteinyl-tRNA-specific translation factor; Provisional
Probab=31.41 E-value=94 Score=27.67 Aligned_cols=47 Identities=13% Similarity=0.085 Sum_probs=34.3
Q ss_pred HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
.++|..-.+ +.--+...+++.+++.-...+.+|+.|.+.|.+..++.
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 22223345788889999999999999999999988874
No 349
>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=31.32 E-value=80 Score=20.45 Aligned_cols=46 Identities=17% Similarity=0.273 Sum_probs=39.6
Q ss_pred HHHHHHHHhhCCCCeeechhhh--hhhhcccHHHHHHHHHHHHHcCCe
Q 033932 45 QATYDKLLSEAPKYKLITPSIL--SDRLRINGSLARKAIRELMARGLI 90 (108)
Q Consensus 45 k~t~dKl~KEVpk~k~ITps~v--serlkI~~SlAr~~Lr~L~~kGlI 90 (108)
++.|++|..+.....++++..+ -++|=...+.-+.+-++|.+.|++
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 4678889888888888888764 478888899999999999999999
No 350
>PRK09751 putative ATP-dependent helicase Lhr; Provisional
Probab=31.20 E-value=51 Score=32.80 Aligned_cols=47 Identities=17% Similarity=0.267 Sum_probs=36.8
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeE
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
++-+=+..=...+==+|...++++|++-.+++..+|+.|+..|.+..
T Consensus 975 ~~~~l~~r~~~~~gp~~~~~~a~~~gl~~~~~~~~l~~l~~~g~~~~ 1021 (1490)
T PRK09751 975 PLRDLFLRYLRAHALVTAEQLAHEFSLGIAIVEEQLQQLREQGLVMN 1021 (1490)
T ss_pred HHHHHHHHHHhccCCCcHHHHHHHhCCCHHHHHHHHHHHHhCCCEEe
Confidence 33333333333445589999999999999999999999999999876
No 351
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=30.92 E-value=50 Score=18.94 Aligned_cols=41 Identities=10% Similarity=0.118 Sum_probs=27.8
Q ss_pred HhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHH
Q 033932 35 EKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGS 75 (108)
Q Consensus 35 eK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~S 75 (108)
.-+...+=++..++.+++.......+=+...||+-|++..+
T Consensus 13 ~~la~~~gis~~~i~~~~~g~~~~~~~~~~~ia~~l~~~~~ 53 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENGKRNPSLDTLKKIAKALGVSPE 53 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTTSSTSBHHHHHHHHHHHTSEHH
T ss_pred HHHHHHhCCCcchhHHHhcCCCCCCHHHHHHHHHHHCCCHH
Confidence 44555555888888888888666666677777777776643
No 352
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=30.17 E-value=29 Score=26.87 Aligned_cols=35 Identities=20% Similarity=0.299 Sum_probs=32.3
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+=+|-+.++|-++++-|=--.+|++|+.-|++..|
T Consensus 40 ~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 40 KPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred CCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhh
Confidence 45799999999999999999999999999999998
No 353
>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=30.16 E-value=59 Score=21.99 Aligned_cols=24 Identities=29% Similarity=0.373 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHcCCeeEecccc
Q 033932 74 GSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 74 ~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
-.-|..+.+.|.+.|+|..|...|
T Consensus 51 R~eAv~lgq~Ll~~gii~HV~~~h 74 (85)
T cd04441 51 RREAVQLCRRLLEHGIIQHVSNKH 74 (85)
T ss_pred HHHHHHHHHHHHHCCCEEecCCCC
Confidence 356888899999999999997544
No 354
>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=30.16 E-value=46 Score=24.46 Aligned_cols=46 Identities=15% Similarity=0.213 Sum_probs=31.8
Q ss_pred CHHHHHHHHhhCCCCee--echhhhhhhhcccHHHHHHHHHHHHHcCCeeEe
Q 033932 44 DQATYDKLLSEAPKYKL--ITPSILSDRLRINGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 44 dk~t~dKl~KEVpk~k~--ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V 93 (108)
+.+.|+++..=+-...- -|.+.|||.++|...+-.+- ..+|=|...
T Consensus 28 ~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~----IreGRL~~~ 75 (137)
T TIGR03826 28 EEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKF----IREGRLQLK 75 (137)
T ss_pred HHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHH----HHcCCeecc
Confidence 46677777665555544 79999999999998875444 445655543
No 355
>PF06239 ECSIT: Evolutionarily conserved signalling intermediate in Toll pathway; InterPro: IPR010418 Activation of NF-kappaB as a consequence of signalling through the Toll and IL-1 receptors is a major element of innate immune responses. ECSIT plays an important role in signalling to NF-kappaB, functioning as the intermediate in the signalling pathways between TRAF-6 and MEKK-1 [].
Probab=29.80 E-value=1.1e+02 Score=24.64 Aligned_cols=50 Identities=20% Similarity=0.284 Sum_probs=40.8
Q ss_pred ceeCHHHHHHHHhhCCCCeeechhhhhh---hhcccHHHHHHHHHHHHHcCCe
Q 033932 41 VLFDQATYDKLLSEAPKYKLITPSILSD---RLRINGSLARKAIRELMARGLI 90 (108)
Q Consensus 41 Vl~dk~t~dKl~KEVpk~k~ITps~vse---rlkI~~SlAr~~Lr~L~~kGlI 90 (108)
|--|=++|++|+.=.|+-++|+-+.+=. .|--...+|-.+|+++|.-|++
T Consensus 83 v~kDL~~Y~~LLDvFPKg~fvp~n~fQ~~F~hyp~Qq~c~i~lL~qME~~gV~ 135 (228)
T PF06239_consen 83 VEKDLEVYKALLDVFPKGKFVPRNFFQAEFMHYPRQQECAIDLLEQMENNGVM 135 (228)
T ss_pred CcccHHHHHHHHHhCCCCCcccccHHHHHhccCcHHHHHHHHHHHHHHHcCCC
Confidence 4568999999999999999985544432 3556788999999999999987
No 356
>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=29.69 E-value=64 Score=21.61 Aligned_cols=25 Identities=20% Similarity=0.323 Sum_probs=20.5
Q ss_pred cHHHHHHHHHHHHHcCCeeEecccc
Q 033932 73 NGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 73 ~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
+-.=|-.+-+.|.+.|+|..|...|
T Consensus 46 sR~eAv~lgq~Ll~~gvi~HV~~~h 70 (82)
T cd04442 46 DRETAIKIMQKLLDHSIIHHVCDEH 70 (82)
T ss_pred CHHHHHHHHHHHHHCCCEEeccCCc
Confidence 3456888899999999999997654
No 357
>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=29.66 E-value=97 Score=24.96 Aligned_cols=66 Identities=17% Similarity=0.172 Sum_probs=51.0
Q ss_pred hhccceeCHHHHHHHHhhCCC-----CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932 37 VNNMVLFDQATYDKLLSEAPK-----YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA 105 (108)
Q Consensus 37 ~nn~Vl~dk~t~dKl~KEVpk-----~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~ 105 (108)
++..+++.+.-.++..--|-. .+-+..+.|.+++++...+.-.+|.+|.+.|-|.=...+ .+|++.
T Consensus 164 ~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 164 LDGDVLYTEAYVARQKARIRGALSAITRPTPLSSLLKRYGFEEKLFQSILEELIKSGELPGSIVG---ASYVPD 234 (272)
T ss_pred EeCCEEecHHHHHHHHHHHHHHHhcCccceEHHHHHHHhCCcHHHHHHHHHHHHhcCcceEEEEC---CEEech
Confidence 344477787777776655444 367778899999999999999999999999988766555 567664
No 358
>PLN03083 E3 UFM1-protein ligase 1 homolog; Provisional
Probab=29.59 E-value=66 Score=30.17 Aligned_cols=64 Identities=17% Similarity=0.295 Sum_probs=49.1
Q ss_pred ccceeCHHHHHHHHhhCCC----CeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932 39 NMVLFDQATYDKLLSEAPK----YKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA 105 (108)
Q Consensus 39 n~Vl~dk~t~dKl~KEVpk----~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~ 105 (108)
+--+|+..-+|.|..||-. .-.|+.+.||.+|.+..-+.+.+|+.... ++|.=.. .+..+||.+
T Consensus 109 ~GeLit~~Yld~iaeEIne~LqE~G~isI~eLa~~~~Lpsefl~~~l~~rlG-~iI~g~~--~g~~lyT~a 176 (803)
T PLN03083 109 QGEIISQSYWDSIAEEINERLQECSQIALAELARQLQVGSELVTSMLEPRLG-TIVKARL--EGGQLYTPA 176 (803)
T ss_pred cCEecchHHHHHHHHHHHHHHHHcCcChHHHHHHhcCChHHHHHHHHHHHhc-cceEEEe--cCCEEecHH
Confidence 4467889999999888754 57899999999999999999999987644 4554433 344579853
No 359
>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=29.43 E-value=1e+02 Score=20.10 Aligned_cols=33 Identities=24% Similarity=0.265 Sum_probs=26.9
Q ss_pred HHHHHHHHHHHHHcCCeeEeccccceEEEeccc
Q 033932 74 GSLARKAIRELMARGLIRMVSAHASQQIYTRAT 106 (108)
Q Consensus 74 ~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~~ 106 (108)
+.-|+.|+.+|..=.-.+-|+.+.+..=|+.+.
T Consensus 7 L~~a~~A~h~L~tG~~vvsv~~dgrsV~Yt~a~ 39 (68)
T PF02831_consen 7 LAEARAAYHDLLTGQRVVSVQGDGRSVTYTQAN 39 (68)
T ss_dssp HHHHHHHHHHHHCS-SEEEEEETTEEEEEEGGG
T ss_pred HHHHHHHHHHHHhCCceeEeecCCeEEEEecCC
Confidence 346999999999987788899888888899753
No 360
>PF05871 ESCRT-II: ESCRT-II complex subunit; InterPro: IPR008570 This entry represents the vps25 subunit (vacuolar protein sorting-associated protein 25) of the endosome-associated complex ESCRT-II (Endosomal Sorting Complexes Required for Transport protein II). ESCRT (ESCRT-I, -II, -III) complexes orchestrate efficient sorting of ubiquitinated transmembrane receptors to lysosomes via multivesicular bodies (MVBs) []. ESCRT-II recruits the transport machinery for protein sorting at MVB []. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. ESCRT-II transiently associates with the endosomal membrane and thereby initiates the formation of ESCRT-III, a membrane-associated protein complex that functions immediately downstream of ESCRT-II during sorting of MVB cargo. ESCRT-II in turn functions downstream of ESCRT-I, a protein complex that binds to ubiquitinated endosomal cargo []. ESCRT-II is a trilobal complex composed of two copies of vps25, one copy of vps22 and the C-terminal region of vps36. The crystal structure of vps25 revealed two winged-helix domains, the N-terminal domain of vps25 interacting with vps22 and vps35 [].; PDB: 1W7P_B 1U5T_D 1XB4_D 3HTU_E 3CUQ_C 2ZME_D.
Probab=29.07 E-value=73 Score=23.35 Aligned_cols=35 Identities=23% Similarity=0.415 Sum_probs=24.9
Q ss_pred cccHHHHHHHHHHHHHcCCeeEecc-ccceEEEecc
Q 033932 71 RINGSLARKAIRELMARGLIRMVSA-HASQQIYTRA 105 (108)
Q Consensus 71 kI~~SlAr~~Lr~L~~kGlIk~V~k-~~~q~IYtr~ 105 (108)
.++.+..+.+|.+|.++|.+..+.+ ..+-.||-|.
T Consensus 60 ~L~~e~~~~Il~~Lv~~g~aew~~~~~~~~~I~Wrt 95 (139)
T PF05871_consen 60 RLSPEFIREILDELVQKGNAEWIDKSKTRCLIYWRT 95 (139)
T ss_dssp E--HHHHHHHHHHHHCTTSEEECSTTSCEEEE-SS-
T ss_pred CCCHHHHHHHHHHHHhcCCeEEeeCCCCEEEEEeCC
Confidence 4567889999999999999999944 4456677664
No 361
>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=28.64 E-value=69 Score=20.46 Aligned_cols=24 Identities=17% Similarity=0.320 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHcCCeeEeccccc
Q 033932 75 SLARKAIRELMARGLIRMVSAHAS 98 (108)
Q Consensus 75 SlAr~~Lr~L~~kGlIk~V~k~~~ 98 (108)
++-+++|+.+.++|.+..|..+..
T Consensus 46 ~~l~~aLk~~v~~G~l~~~kg~G~ 69 (77)
T PF00538_consen 46 SRLKRALKRGVEKGKLVQVKGKGA 69 (77)
T ss_dssp HHHHHHHHHHHHCTSEEECSCSTT
T ss_pred HHHHHHHHHHHHCCcEEeecccCC
Confidence 567899999999999999874443
No 362
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=28.29 E-value=74 Score=25.39 Aligned_cols=37 Identities=24% Similarity=0.251 Sum_probs=34.1
Q ss_pred eeechhhhhhhhcccHHHHHHHHHHHHHc-CCeeEecc
Q 033932 59 KLITPSILSDRLRINGSLARKAIRELMAR-GLIRMVSA 95 (108)
Q Consensus 59 k~ITps~vserlkI~~SlAr~~Lr~L~~k-GlIk~V~k 95 (108)
=+.|...||-=|+++...-++-+++++++ |.+.|...
T Consensus 104 glLT~~Dla~LL~~S~~TI~~~i~~yq~e~g~vvPtrG 141 (220)
T PF07900_consen 104 GLLTQEDLAMLLGISPRTISKDIKEYQKEHGVVVPTRG 141 (220)
T ss_pred CcccHHHHHHHHCCCHHHHHHHHHHHHHHcCceeccCC
Confidence 58999999999999999999999999999 99988743
No 363
>PF13034 DUF3895: Protein of unknown function (DUF3895)
Probab=28.00 E-value=92 Score=21.12 Aligned_cols=34 Identities=15% Similarity=0.337 Sum_probs=24.4
Q ss_pred hhcccHHHHHHHHHHHHHcCCeeEec-cccceEEEe
Q 033932 69 RLRINGSLARKAIRELMARGLIRMVS-AHASQQIYT 103 (108)
Q Consensus 69 rlkI~~SlAr~~Lr~L~~kGlIk~V~-k~~~q~IYt 103 (108)
|++|=+.|+ ..|+.|+.+|.|..+. ..-+-+||.
T Consensus 43 KpkiY~~Vc-~yLe~L~~eg~l~~i~~~~~~dRiY~ 77 (78)
T PF13034_consen 43 KPKIYPYVC-NYLEYLVKEGKLSFIENDGTRDRIYK 77 (78)
T ss_pred CceeHHHHH-HHHHHHHHCCeEEEEecCcchhhhhc
Confidence 455555555 5799999999999994 444556664
No 364
>PF13812 PPR_3: Pentatricopeptide repeat domain
Probab=27.96 E-value=76 Score=15.89 Aligned_cols=16 Identities=19% Similarity=0.289 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHcCC
Q 033932 74 GSLARKAIRELMARGL 89 (108)
Q Consensus 74 ~SlAr~~Lr~L~~kGl 89 (108)
...|..+++++.+.|+
T Consensus 17 ~~~a~~~~~~M~~~gv 32 (34)
T PF13812_consen 17 PDAALQLFDEMKEQGV 32 (34)
T ss_pred HHHHHHHHHHHHHhCC
Confidence 4568899999999884
No 365
>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=27.56 E-value=1.1e+02 Score=26.90 Aligned_cols=48 Identities=13% Similarity=0.081 Sum_probs=38.4
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
..++|..... +..-+...+++.+++.-...+.+|+.|...|.+..++.
T Consensus 476 ~~~~i~~~~~-~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~g~~~~~~~ 523 (581)
T TIGR00475 476 IWQKIKGTFG-TKGAWVREFAEEVNGDEKVMLKRVRKAGHRGGETLIVK 523 (581)
T ss_pred HHHHHHHHHh-cCCCCHHHHHhhhCCCHHHHHHHHHHHHhCCCEEEEeC
Confidence 3566665443 55567778888999999999999999999999888875
No 366
>PRK04217 hypothetical protein; Provisional
Probab=27.34 E-value=67 Score=22.70 Aligned_cols=23 Identities=13% Similarity=0.253 Sum_probs=18.6
Q ss_pred echhhhhhhhcccHHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIRE 83 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~ 83 (108)
+|...||+.|+|+-+-.+..|..
T Consensus 59 lS~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 59 LTQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 48999999999998877666554
No 367
>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=26.94 E-value=82 Score=19.49 Aligned_cols=27 Identities=26% Similarity=0.246 Sum_probs=21.5
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHH
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMA 86 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~ 86 (108)
=+|-..||+.|+|.-|-.-.-||.-++
T Consensus 23 ~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 23 RITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 578899999999999887766665544
No 368
>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=26.83 E-value=76 Score=27.34 Aligned_cols=30 Identities=20% Similarity=0.327 Sum_probs=24.3
Q ss_pred chhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 62 TPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 62 Tps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
+.-.||||.++....-..+++.|.+.|||+
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 445799999999999999999999999986
No 369
>COG3682 Predicted transcriptional regulator [Transcription]
Probab=26.73 E-value=82 Score=22.94 Aligned_cols=34 Identities=15% Similarity=0.209 Sum_probs=24.5
Q ss_pred hcccHHHHHHHHHHHHHcCCeeEeccccceEEEec
Q 033932 70 LRINGSLARKAIRELMARGLIRMVSAHASQQIYTR 104 (108)
Q Consensus 70 lkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr 104 (108)
+-+.-|--+-+|+.|..+|+|...- .++..+|.+
T Consensus 34 ~ews~sTV~TLl~RL~KKg~l~~~k-dgr~~~y~p 67 (123)
T COG3682 34 REWSYSTVKTLLNRLVKKGLLTRKK-DGRAFRYSP 67 (123)
T ss_pred ccccHHHHHHHHHHHHhccchhhhh-cCCeeeeec
Confidence 4455566677899999999998864 455566664
No 370
>cd04439 DEP_1_P-Rex DEP (Dishevelled, Egl-10, and Pleckstrin) domain 1 found in P-Rex-like proteins. The P-Rex family is the guanine-nucleotide exchange factor (GEF) for the small GTPase Rac that contains an N-terminal RhoGEF domain, two DEP and PDZ domains. Rac-GEF activity is stimulated by phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3), a lipid second messenger, and by the G beta-gamma subunits of heterotrimeric G proteins. The DEP domains are not involved in mediating these stimuli, but may be of importance for basal and stimulated levels Rac-GEF activity.
Probab=26.62 E-value=78 Score=20.99 Aligned_cols=23 Identities=22% Similarity=0.254 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHcCCeeEecccc
Q 033932 75 SLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 75 SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
+=|-.+-+.|.+.|+|..|..+|
T Consensus 48 ~eAv~lg~~Ll~~G~i~HV~~~h 70 (81)
T cd04439 48 EEGVNLGQALLENGIIHHVSDKH 70 (81)
T ss_pred HHHHHHHHHHHHCCCEEecCCCC
Confidence 34667778999999999998765
No 371
>PLN00158 histone H2B; Provisional
Probab=26.61 E-value=1e+02 Score=22.32 Aligned_cols=41 Identities=32% Similarity=0.476 Sum_probs=32.8
Q ss_pred eCHHHHHHHHhhCC------CCeeechhhh--hhhhcccHHHHHHHHHH
Q 033932 43 FDQATYDKLLSEAP------KYKLITPSIL--SDRLRINGSLARKAIRE 83 (108)
Q Consensus 43 ~dk~t~dKl~KEVp------k~k~ITps~v--serlkI~~SlAr~~Lr~ 83 (108)
|..++|++|..|-. +-.-||+-+| |=||=+.|.||+-++.|
T Consensus 57 fvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvLpgELaKhAvsE 105 (116)
T PLN00158 57 FINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLILPGELAKHAVSE 105 (116)
T ss_pred HHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhccHHHHHHHHHH
Confidence 88999999999853 4467777776 56788889999988876
No 372
>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=26.43 E-value=1e+02 Score=18.60 Aligned_cols=27 Identities=22% Similarity=0.431 Sum_probs=15.8
Q ss_pred hhhhhhcccHHHHH----HHHHHHHHcCCee
Q 033932 65 ILSDRLRINGSLAR----KAIRELMARGLIR 91 (108)
Q Consensus 65 ~vserlkI~~SlAr----~~Lr~L~~kGlIk 91 (108)
.|+++|.+.-.-++ ..|.+|.+.|+|.
T Consensus 38 ~l~~~y~~~~~~~~~dv~~fl~~L~~~glIe 68 (68)
T PF05402_consen 38 ALAEEYDVDPEEAEEDVEEFLEQLREKGLIE 68 (68)
T ss_dssp HHHHHTT--HHHHHHHHHHHHHHHHHTT---
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHHHCcCcC
Confidence 46677877777554 4677888899873
No 373
>COG1763 MobB Molybdopterin-guanine dinucleotide biosynthesis protein [Coenzyme metabolism]
Probab=26.35 E-value=76 Score=23.70 Aligned_cols=26 Identities=35% Similarity=0.439 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHHHcCCeeEeccccce
Q 033932 74 GSLARKAIRELMARGLIRMVSAHASQ 99 (108)
Q Consensus 74 ~SlAr~~Lr~L~~kGlIk~V~k~~~q 99 (108)
-+|..++++.|.++|+-.-+.+|+.-
T Consensus 16 TTLie~lv~~L~~~G~rVa~iKH~hh 41 (161)
T COG1763 16 TTLIEKLVRKLKARGYRVATVKHAHH 41 (161)
T ss_pred hhHHHHHHHHHHhCCcEEEEEEecCC
Confidence 46889999999999998888776643
No 374
>PRK13239 alkylmercury lyase; Provisional
Probab=26.06 E-value=78 Score=24.81 Aligned_cols=41 Identities=12% Similarity=0.046 Sum_probs=35.6
Q ss_pred HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHH
Q 033932 45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELM 85 (108)
Q Consensus 45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~ 85 (108)
..++--|+.++-+=+=+|++.||+.++....-++++|++|.
T Consensus 21 ~~~~~~llr~la~G~pvt~~~lA~~~~~~~~~v~~~L~~l~ 61 (206)
T PRK13239 21 ATLLVPLLRLLAKGRPVSVTTLAAALGWPVEEVEAVLEAMP 61 (206)
T ss_pred hHHHHHHHHHHHcCCCCCHHHHHHHhCCCHHHHHHHHHhCC
Confidence 44666777887788899999999999999999999999974
No 375
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=25.97 E-value=78 Score=20.97 Aligned_cols=30 Identities=10% Similarity=0.171 Sum_probs=26.8
Q ss_pred hCCCCeeechhhhhhhhcccHHHHHHHHHH
Q 033932 54 EAPKYKLITPSILSDRLRINGSLARKAIRE 83 (108)
Q Consensus 54 EVpk~k~ITps~vserlkI~~SlAr~~Lr~ 83 (108)
|+.+.++||-..||+=|++...-+++++..
T Consensus 6 e~rg~rV~t~~~lA~~yg~~~~~i~~~~~r 35 (88)
T PF10543_consen 6 EYRGQRVMTDEDLAELYGVETKTINRNFKR 35 (88)
T ss_pred EEcCEEEEEHHHHHHHhCcCHHHHHHHHHH
Confidence 677889999999999999999998888764
No 376
>smart00427 H2B Histone H2B.
Probab=25.64 E-value=1.1e+02 Score=21.07 Aligned_cols=43 Identities=26% Similarity=0.414 Sum_probs=33.5
Q ss_pred eeCHHHHHHHHhhCC------CCeeechhhh--hhhhcccHHHHHHHHHHH
Q 033932 42 LFDQATYDKLLSEAP------KYKLITPSIL--SDRLRINGSLARKAIREL 84 (108)
Q Consensus 42 l~dk~t~dKl~KEVp------k~k~ITps~v--serlkI~~SlAr~~Lr~L 84 (108)
.|..++|++|..|-. +-+-||+-.| |=||=+.|.||+-++.|=
T Consensus 30 SfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~LpgeLakhAvsEg 80 (89)
T smart00427 30 SFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLILPGELAKHAVSEG 80 (89)
T ss_pred HHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHccHHHHHHHHHHH
Confidence 578899999998854 3457777766 567888899999888764
No 377
>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=25.59 E-value=82 Score=18.67 Aligned_cols=27 Identities=15% Similarity=0.342 Sum_probs=21.4
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHc
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMAR 87 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~k 87 (108)
-|+..||+.++|+.+--+.-++.+..+
T Consensus 19 ~~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 19 MSNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp S-HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred CCcchhHHhcCcchhhHHHHHHHHHHH
Confidence 378899999999999888887777653
No 378
>PF08721 Tn7_Tnp_TnsA_C: TnsA endonuclease C terminal; InterPro: IPR014832 The Tn7 transposase is composed of proteins TnsA and TnsB. DNA breakage at the 5'-end of the transposon is carried out by TnsA, and breakage and joining at the 3'-end is carried out by TnsB. The C-terminal domain of TnsA binds DNA. ; PDB: 1F1Z_B 1T0F_B.
Probab=25.56 E-value=1.7e+02 Score=17.87 Aligned_cols=41 Identities=24% Similarity=0.268 Sum_probs=30.2
Q ss_pred HHHHHhhCCCCeeechhhhhhhh----cccHHHHHHHHHHHHHcCCee
Q 033932 48 YDKLLSEAPKYKLITPSILSDRL----RINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 48 ~dKl~KEVpk~k~ITps~vserl----kI~~SlAr~~Lr~L~~kGlIk 91 (108)
+-..+.+.|. .|+..++..+ ++..+-+=..|++|.+.+.|.
T Consensus 32 i~~~l~~~~~---~tl~~l~~~~d~~~~l~~g~~L~~l~~LiA~k~i~ 76 (79)
T PF08721_consen 32 ILARLRKNPT---MTLRDLCKELDKDYELEPGTALPLLRHLIATKRIK 76 (79)
T ss_dssp HHHHHHHTTT---SBHHHHHHHHHHHCT--TTHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHcCC---CCHHHHHHHHHHhcCCCcCChHHHHHHHHhCChhc
Confidence 3444455555 7888888776 899999999999999998875
No 379
>PRK09775 putative DNA-binding transcriptional regulator; Provisional
Probab=25.28 E-value=1.2e+02 Score=26.03 Aligned_cols=40 Identities=15% Similarity=0.257 Sum_probs=32.3
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
.|++.|+++++|+-+.--+.|+.| .|+|.-.- ..+...|.
T Consensus 14 ~~~~eL~~~l~~sq~~~s~~L~~L--~~~V~~~~-~gr~~~Y~ 53 (442)
T PRK09775 14 LSAAELAARLGVSQATLSRLLAAL--GDQVVRFG-KARATRYA 53 (442)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHh--hcceeEec-cCceEEEE
Confidence 589999999999999999999999 78876654 44555665
No 380
>PRK08061 rpsN 30S ribosomal protein S14; Reviewed
Probab=25.24 E-value=49 Score=21.35 Aligned_cols=28 Identities=29% Similarity=0.348 Sum_probs=21.8
Q ss_pred hhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 65 ILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 65 ~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
-+-.+|+ |.|..+|||...|+|-=|.+.
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 899999999999999766654
No 381
>PRK05590 hypothetical protein; Provisional
Probab=25.00 E-value=56 Score=25.05 Aligned_cols=35 Identities=11% Similarity=0.118 Sum_probs=28.2
Q ss_pred cceeCHHHHHHHHhhCCCCeeechhhhhhhhcccH
Q 033932 40 MVLFDQATYDKLLSEAPKYKLITPSILSDRLRING 74 (108)
Q Consensus 40 ~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~ 74 (108)
-..+.+..|++|+.+-...-==|...||++|++..
T Consensus 27 y~~~ek~iy~~iL~~~~~~~~gtv~ela~k~~~~~ 61 (166)
T PRK05590 27 YGSVEKNIYTQILANHKEVVEGTVKELAEKFGTSV 61 (166)
T ss_pred HHHHHHHHHHHHHcCCCceeeeeHHHHHHHhCCCh
Confidence 34568899999998887766668999999998654
No 382
>cd04438 DEP_dishevelled DEP (Dishevelled, Egl-10, and Pleckstrin) domain found in dishevelled-like proteins. Dishevelled-like proteins play a key role in the transduction of the Wnt signal from the cell surface to the nucleus, which in turn is an important regulatory pathway for cellular development and growth. They contain an N-terminal DIX domain, a central PDZ domain, and a C-terminal DEP domain.
Probab=24.89 E-value=85 Score=20.95 Aligned_cols=23 Identities=30% Similarity=0.306 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHcCCeeEecccc
Q 033932 75 SLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 75 SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
.-|...-+.|.+.|+|..|...|
T Consensus 50 ~eAv~~g~~Ll~~G~i~HV~~~h 72 (84)
T cd04438 50 REARKYASSLLKLGYIRHTVNKI 72 (84)
T ss_pred HHHHHHHHHHHHCCcEEecCCCc
Confidence 47888899999999999996554
No 383
>PF08100 Dimerisation: Dimerisation domain; InterPro: IPR012967 This domain is found at the N terminus of a variety of plant O-methyltransferases. It has been shown to mediate dimerisation of these proteins [].; GO: 0008168 methyltransferase activity, 0046983 protein dimerization activity; PDB: 1ZGJ_A 1ZG3_A 1ZHF_A 1ZGA_A 2QYO_A 1KYW_A 1KYZ_A 3REO_D 1FPX_A 1FP2_A ....
Probab=24.80 E-value=86 Score=19.19 Aligned_cols=36 Identities=17% Similarity=0.161 Sum_probs=24.4
Q ss_pred HHHHHhhCCCCeeechhhhhhhhc----ccHHHHHHHHHHHH
Q 033932 48 YDKLLSEAPKYKLITPSILSDRLR----INGSLARKAIRELM 85 (108)
Q Consensus 48 ~dKl~KEVpk~k~ITps~vserlk----I~~SlAr~~Lr~L~ 85 (108)
+|-|.+.- -.-+|+++|+.++. -..++=+++||-|.
T Consensus 12 ~dii~~~g--~~~ls~~eia~~l~~~~p~~~~~L~RimR~L~ 51 (51)
T PF08100_consen 12 PDIIHNAG--GGPLSLSEIAARLPTSNPSAPPMLDRIMRLLV 51 (51)
T ss_dssp HHHHHHHT--TS-BEHHHHHHTSTCT-TTHHHHHHHHHHHHH
T ss_pred HHHHHHcC--CCCCCHHHHHHHcCCCCcchHHHHHHHHHHhC
Confidence 44454444 26799999999999 44556688888763
No 384
>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=24.60 E-value=88 Score=20.23 Aligned_cols=26 Identities=8% Similarity=0.181 Sum_probs=22.1
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMA 86 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~ 86 (108)
.|...||+.|+++-+-.+..+.....
T Consensus 127 ~s~~eIA~~l~~s~~~v~~~~~~~~~ 152 (158)
T TIGR02937 127 LSYKEIAEILGISVGTVKRRLKRARK 152 (158)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 58899999999999999888877644
No 385
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=24.49 E-value=58 Score=26.78 Aligned_cols=46 Identities=20% Similarity=0.227 Sum_probs=36.1
Q ss_pred CCcccccccCchhhHHhhhccceeCHHHHHHHHhhCCCCeeechh---hhhhhhcccHH
Q 033932 20 GGKQKKKKWSKGKQKEKVNNMVLFDQATYDKLLSEAPKYKLITPS---ILSDRLRINGS 75 (108)
Q Consensus 20 ~~k~~KKKWsKgk~keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps---~vserlkI~~S 75 (108)
.+..+|.+|+.+ .|..-.+..|+|.+-.-|||++. .||.+|+++-.
T Consensus 166 ~~~pkK~RksRT----------aFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTda 214 (309)
T KOG0488|consen 166 RSTPKKRRKSRT----------AFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDA 214 (309)
T ss_pred cCCCcccccchh----------hhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchh
Confidence 344467778887 78888999999999999999986 47777776654
No 386
>PF14217 DUF4327: Domain of unknown function (DUF4327)
Probab=23.88 E-value=23 Score=23.48 Aligned_cols=22 Identities=32% Similarity=0.582 Sum_probs=16.0
Q ss_pred HHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 77 ARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 77 Ar~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
-+.=-|+|.++|+| ++.|.||+
T Consensus 7 iq~ear~LV~~g~v-----~r~qpI~~ 28 (68)
T PF14217_consen 7 IQDEARSLVESGVV-----SRQQPIYT 28 (68)
T ss_pred HHHHHHHHHHcCCC-----CccCcHHH
Confidence 34445889999998 46677776
No 387
>COG1533 SplB DNA repair photolyase [DNA replication, recombination, and repair]
Probab=23.62 E-value=1.9e+02 Score=23.56 Aligned_cols=59 Identities=25% Similarity=0.327 Sum_probs=47.6
Q ss_pred ccceeCHHHHHHHHhhC----CCCeeechhhhhhhhcc---cHHHHHHHHHHHHHcCC-eeEecccc
Q 033932 39 NMVLFDQATYDKLLSEA----PKYKLITPSILSDRLRI---NGSLARKAIRELMARGL-IRMVSAHA 97 (108)
Q Consensus 39 n~Vl~dk~t~dKl~KEV----pk~k~ITps~vserlkI---~~SlAr~~Lr~L~~kGl-Ik~V~k~~ 97 (108)
--|.+.+..++.|.+|+ ++--+|-.++++|=|-. ...|-|.+|+-|...|. +..+.++.
T Consensus 60 ~~v~vk~n~~e~l~~el~~~~~k~~~i~is~~TDpyqp~E~~~~ltR~ilei~~~~~~~v~I~TKS~ 126 (297)
T COG1533 60 TKVNVKENLLELLERELRKPGPKRTVIAISSVTDPYQPIEKEYRLTRKILEILLKYGFPVSIVTKSA 126 (297)
T ss_pred ceeeechhHHHHHHHHHhhccCCceEEEEecCCCCCCcchHHHHHHHHHHHHHHHcCCcEEEEECCc
Confidence 34667777999999996 56688888999998887 99999999999999987 44445544
No 388
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=23.57 E-value=97 Score=17.18 Aligned_cols=24 Identities=8% Similarity=0.126 Sum_probs=17.9
Q ss_pred echhhhhhhhcccHHHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIREL 84 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L 84 (108)
+|...||+.++++.+--++++++.
T Consensus 9 ~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 9 LTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 788999999999888888877764
No 389
>PF03205 MobB: Molybdopterin guanine dinucleotide synthesis protein B; PDB: 2F1R_B 1P9N_A 1NP6_B 2NPI_A 1XJC_A.
Probab=23.53 E-value=92 Score=22.10 Aligned_cols=23 Identities=43% Similarity=0.488 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHcCCeeEeccc
Q 033932 74 GSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 74 ~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
-+|++.++++|.++|.=..+.+|
T Consensus 14 TTl~~~Li~~l~~~g~~v~~ik~ 36 (140)
T PF03205_consen 14 TTLIRKLINELKRRGYRVAVIKH 36 (140)
T ss_dssp HHHHHHHHHHHHHTT--EEEEEE
T ss_pred HHHHHHHHHHHhHcCCceEEEEE
Confidence 37999999999999986664333
No 390
>PF06218 NPR2: Nitrogen permease regulator 2; InterPro: IPR009348 This family of regulators are involved in post-translational control of nitrogen permease.
Probab=23.25 E-value=1.2e+02 Score=26.28 Aligned_cols=58 Identities=16% Similarity=0.229 Sum_probs=47.7
Q ss_pred HHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932 46 ATYDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA 105 (108)
Q Consensus 46 ~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~ 105 (108)
-|+.+|.--|-+. =+...||.--.+..+|.+.+||+|.==|.|.++.-=.-..||+..
T Consensus 206 lT~qkIlP~IdGv--n~V~rIa~ladvd~~Lv~~ci~hL~yYg~v~lidiFqfsNiY~~t 263 (428)
T PF06218_consen 206 LTMQKILPYIDGV--NHVRRIAQLADVDYELVKECIQHLLYYGCVILIDIFQFSNIYAPT 263 (428)
T ss_pred HHHHHhhhhccCc--cHHHHHHHHHcCCHHHHHHHHHHHHhhCeeEEeeehhccceeecc
Confidence 3667777777664 367889999999999999999999999999999766666788754
No 391
>PRK00441 argR arginine repressor; Provisional
Probab=23.04 E-value=1.6e+02 Score=21.56 Aligned_cols=52 Identities=19% Similarity=0.293 Sum_probs=36.0
Q ss_pred HHHHHhhCCCCeeechhhhhhhh-----cccHHHHHHHHHHHHHcCCeeEeccccceEEEe
Q 033932 48 YDKLLSEAPKYKLITPSILSDRL-----RINGSLARKAIRELMARGLIRMVSAHASQQIYT 103 (108)
Q Consensus 48 ~dKl~KEVpk~k~ITps~vserl-----kI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYt 103 (108)
.+.|..-+....+.|...|++.| .++-+-.|+-|+ +-|+++.-+.++ ...|.
T Consensus 6 ~~~I~~ll~~~~~~~q~eL~~~L~~~G~~vSqaTisRDl~---~L~lvKv~~~~G-~~~Y~ 62 (149)
T PRK00441 6 HAKILEIINSKEIETQEELAEELKKMGFDVTQATVSRDIK---ELKLIKVLSNDG-KYKYA 62 (149)
T ss_pred HHHHHHHHHHcCCCcHHHHHHHHHhcCCCcCHHHHHHHHH---HcCcEEeECCCC-CEEEE
Confidence 44566666677899999999997 888777775555 457887544433 45665
No 392
>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=23.01 E-value=74 Score=19.03 Aligned_cols=52 Identities=15% Similarity=0.252 Sum_probs=39.1
Q ss_pred eeCHHHHHHHHhhCCCCeeechhhhhhhhc--ccHHHHHHHHHHHHHcCCeeEe
Q 033932 42 LFDQATYDKLLSEAPKYKLITPSILSDRLR--INGSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 42 l~dk~t~dKl~KEVpk~k~ITps~vserlk--I~~SlAr~~Lr~L~~kGlIk~V 93 (108)
-+|++|.+-|.+.++...-|++.-|.+-+. +.++-+..+++.|.+-|++..+
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 479999999999988778888877776654 3566678889999998887554
No 393
>KOG2165 consensus Anaphase-promoting complex (APC), subunit 2 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=22.93 E-value=1.2e+02 Score=28.45 Aligned_cols=58 Identities=16% Similarity=0.127 Sum_probs=45.0
Q ss_pred HHHHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccccceEEEecc
Q 033932 48 YDKLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMARGLIRMVSAHASQQIYTRA 105 (108)
Q Consensus 48 ~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~~~q~IYtr~ 105 (108)
+.-|.--+..-.-.|-..+||.++|..++-|+-|.-...+|+|..----+...+||+.
T Consensus 604 qA~iI~~Fqek~twt~eelse~l~ip~~~lrrrL~fWi~~GvL~e~~~~s~tgt~T~i 661 (765)
T KOG2165|consen 604 QAAIINLFQEKNTWTLEELSESLGIPVPALRRRLSFWIQKGVLREEPIISDTGTLTVI 661 (765)
T ss_pred HHHHHHHhcCcccccHHHHHHHhCCCHHHHHHHHHHHHHcCeeecCCCCCCCceeeec
Confidence 3333333444444899999999999999999999999999999876544677888864
No 394
>PF11625 DUF3253: Protein of unknown function (DUF3253); InterPro: IPR021660 This bacterial family of proteins has no known function. ; PDB: 2NS0_A.
Probab=22.76 E-value=2.6e+02 Score=19.05 Aligned_cols=51 Identities=25% Similarity=0.169 Sum_probs=35.1
Q ss_pred HHHHHHhhCCCCeeechhhhhhhhc-----ccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 47 TYDKLLSEAPKYKLITPSILSDRLR-----INGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 47 t~dKl~KEVpk~k~ITps~vserlk-----I~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
+.-.|+.+-.--+-|-||.+|--+. =-+.-.|.+-.+|...|.|...-++.
T Consensus 11 ~Il~ll~~R~~~ktiCPSevARal~~~~WR~lm~~vR~~A~~L~~~G~i~I~qkG~ 66 (83)
T PF11625_consen 11 AILALLAARGPGKTICPSEVARALGPDDWRDLMPPVRAAARRLARAGRIEITQKGK 66 (83)
T ss_dssp HHHHHHHHS-TT--B-HHHHHHHH-TTS-GGGHHHHHHHHHHHHHTTSEEEEETTE
T ss_pred HHHHHHHhcCCCCccCHHHHHHHHCchhhHHHHHHHHHHHHHHHHCCcEEEEECCE
Confidence 3445556666678999999987664 33678999999999999998876543
No 395
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=22.35 E-value=82 Score=18.65 Aligned_cols=42 Identities=12% Similarity=0.141 Sum_probs=23.9
Q ss_pred HHhhhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHH
Q 033932 34 KEKVNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGS 75 (108)
Q Consensus 34 keK~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~S 75 (108)
.+.+...+-++..++.++...--...+-+...||+-|+|...
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~~~~~~~l~~i~~~~~v~~~ 56 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKRKPSVSTLKKIAEALGVSLD 56 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS--BHHHHHHHHHHHTS-HH
T ss_pred HHHHHHHHCcCHHHHHHHHCCCcCCCHHHHHHHHHHhCCCHH
Confidence 444555556677777777776555555556666777766543
No 396
>PF01886 DUF61: Protein of unknown function DUF61; InterPro: IPR002746 The proteins in this entry are functionally uncharacterised.
Probab=22.26 E-value=1.9e+02 Score=21.04 Aligned_cols=50 Identities=28% Similarity=0.484 Sum_probs=40.1
Q ss_pred ceeCHHHHHHHHhhCCCC---ee-------echhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033932 41 VLFDQATYDKLLSEAPKY---KL-------ITPSILSDRLRINGSLARKAIRELMARGLI 90 (108)
Q Consensus 41 Vl~dk~t~dKl~KEVpk~---k~-------ITps~vserlkI~~SlAr~~Lr~L~~kGlI 90 (108)
-.||++-++.|..=+|.+ ++ ++|+.=..-+.|+|+++.++++.+...+.-
T Consensus 42 h~f~k~ELe~L~~~lp~~~~~~lrLPIile~~~~~~~g~~~V~g~~e~k~i~~ilg~~~~ 101 (132)
T PF01886_consen 42 HRFDKEELERLAEILPEYEWSKLRLPIILEIDPTLGEGSYRVRGKEEVKAISKILGKERE 101 (132)
T ss_pred EEEcHHHHHHHHHhCCHHHHhceeccEEEEEeccCCCceEEEeCHHHHHHHHHHhCCCcc
Confidence 369999999999988886 22 344423688999999999999999987765
No 397
>PHA02593 62 clamp loader small subunit; Provisional
Probab=22.20 E-value=1.4e+02 Score=23.36 Aligned_cols=54 Identities=28% Similarity=0.281 Sum_probs=41.7
Q ss_pred eeCHHHHHHHHhhCCCCeeec--------------hhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 42 LFDQATYDKLLSEAPKYKLIT--------------PSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 42 l~dk~t~dKl~KEVpk~k~IT--------------ps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
|-|+.-|+=++--||+.|... ...|++.|+|+..=|+..|+.|..+|-+..+.+
T Consensus 93 L~dqmhydYll~sVrkgKRy~~WAKl~ed~e~~~~i~ll~~~Y~vn~~kA~eyl~iltk~~~l~~~lk 160 (191)
T PHA02593 93 LSDQAHFNYLLASVRKGKRYGKWAKLTEDSEEKLIIKLLAKAYSVNTDDAREYLDILKKKGKLPDVLK 160 (191)
T ss_pred CCHHHHHHHHHHhccCcccCchhhccCcchHHHHHHHHHHHHhCCCHHHHHHHHHHhccccchHHHHH
Confidence 456777777777777755432 267999999999999999999999996655433
No 398
>COG4800 Predicted transcriptional regulator with an HTH domain [Transcription]
Probab=22.18 E-value=1.3e+02 Score=23.07 Aligned_cols=32 Identities=34% Similarity=0.294 Sum_probs=24.4
Q ss_pred HHHHHHHHhhCCCCeeechhhhhhhhcccHHHHHHH
Q 033932 45 QATYDKLLSEAPKYKLITPSILSDRLRINGSLARKA 80 (108)
Q Consensus 45 k~t~dKl~KEVpk~k~ITps~vserlkI~~SlAr~~ 80 (108)
.+++.++++| -=.||+.+|+|-||-.|---++
T Consensus 18 ~~~l~~~l~E----lglt~~eFak~anIP~StLYKi 49 (170)
T COG4800 18 GSCLQKLLDE----LGLTPSEFAKRANIPLSTLYKI 49 (170)
T ss_pred HHHHHHHHHH----cCCCHHHHHHHcCCCHHHHHHH
Confidence 3567788888 3479999999999988765444
No 399
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=22.16 E-value=97 Score=22.03 Aligned_cols=18 Identities=11% Similarity=0.126 Sum_probs=15.7
Q ss_pred echhhhhhhhcccHHHHH
Q 033932 61 ITPSILSDRLRINGSLAR 78 (108)
Q Consensus 61 ITps~vserlkI~~SlAr 78 (108)
.|...||+.|+|+.+..+
T Consensus 134 ~s~~EIA~~lgis~~tV~ 151 (179)
T PRK12543 134 YSQEEIAQLLQIPIGTVK 151 (179)
T ss_pred CCHHHHHHHHCCCHHHHH
Confidence 689999999999998843
No 400
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.80 E-value=85 Score=23.07 Aligned_cols=30 Identities=17% Similarity=0.172 Sum_probs=27.9
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLI 90 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlI 90 (108)
.+...+|.+|+|..|....-++...+.|+.
T Consensus 22 ~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~ 51 (138)
T COG3415 22 LSCREAAKRFGVSISTVYRWVRRYRETGLD 51 (138)
T ss_pred ccHHHHHHHhCccHHHHHHHHHHhcccccc
Confidence 456789999999999999999999999998
No 401
>PRK03911 heat-inducible transcription repressor; Provisional
Probab=21.75 E-value=66 Score=26.33 Aligned_cols=36 Identities=17% Similarity=0.302 Sum_probs=28.2
Q ss_pred Ceeechhhhhhhhccc--HHHHHHHHHHHHHcCCeeEe
Q 033932 58 YKLITPSILSDRLRIN--GSLARKAIRELMARGLIRMV 93 (108)
Q Consensus 58 ~k~ITps~vserlkI~--~SlAr~~Lr~L~~kGlIk~V 93 (108)
-.=|.-.+|+++++++ .+.-|..+.+|++.|+|..-
T Consensus 20 ~~PVGSk~L~~~~~l~~SsATIRn~m~~LE~~G~L~qp 57 (260)
T PRK03911 20 NEPIGSNELKSLMNLKISAATIRNYFKKLSDEGLLTQL 57 (260)
T ss_pred CCccCHHHHHHHcCCCCCcHHHHHHHHHHHHCcCccCC
Confidence 3456677899998755 55669999999999998653
No 402
>PRK10736 hypothetical protein; Provisional
Probab=21.73 E-value=1.3e+02 Score=25.47 Aligned_cols=37 Identities=16% Similarity=0.152 Sum_probs=33.6
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEeccc
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSAH 96 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k~ 96 (108)
-++.-+|+++.++..+-.-.+|-+||-+|+|.....+
T Consensus 321 ~~~iD~L~~~~~l~~~~v~~~L~~LEl~G~v~~~~g~ 357 (374)
T PRK10736 321 VTPVDVVAERAGQPVPEVVTQLLELELAGWIAAVPGG 357 (374)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHhCCcEEEcCCc
Confidence 3578999999999999999999999999999998665
No 403
>PHA01623 hypothetical protein
Probab=21.55 E-value=2.1e+02 Score=17.66 Aligned_cols=38 Identities=13% Similarity=0.155 Sum_probs=25.5
Q ss_pred hhccceeCHHHHHHHHhhCCCCeeechhhhhhhhcccHH-HHHHHHHHHHH
Q 033932 37 VNNMVLFDQATYDKLLSEAPKYKLITPSILSDRLRINGS-LARKAIRELMA 86 (108)
Q Consensus 37 ~nn~Vl~dk~t~dKl~KEVpk~k~ITps~vserlkI~~S-lAr~~Lr~L~~ 86 (108)
..=.|-+|++++++|.. .|+..+++.| +-|.||+++..
T Consensus 14 ~r~sVrldeel~~~Ld~------------y~~~~g~~rSe~IreAI~~yL~ 52 (56)
T PHA01623 14 AVFGIYMDKDLKTRLKV------------YCAKNNLQLTQAIEEAIKEYLQ 52 (56)
T ss_pred eeEEEEeCHHHHHHHHH------------HHHHcCCCHHHHHHHHHHHHHH
Confidence 33467889999999873 4555555533 55777777764
No 404
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=21.50 E-value=73 Score=18.83 Aligned_cols=22 Identities=23% Similarity=0.247 Sum_probs=13.5
Q ss_pred echhhhhhhhcccHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIR 82 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr 82 (108)
||++.||++.+|.-+.-.+++.
T Consensus 11 it~~~La~~~gis~~tl~~~~~ 32 (63)
T PF13443_consen 11 ITQKDLARKTGISRSTLSRILN 32 (63)
T ss_dssp --HHHHHHHHT--HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHh
Confidence 5899999999887776555543
No 405
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=21.44 E-value=1.2e+02 Score=20.97 Aligned_cols=31 Identities=13% Similarity=0.071 Sum_probs=27.0
Q ss_pred echhhhhhhhcccHHHHHHHHHHHHHcCCee
Q 033932 61 ITPSILSDRLRINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~L~~kGlIk 91 (108)
.|++.||.+|+|+-++-.+=++++...|+..
T Consensus 30 ~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~ 60 (121)
T PRK09413 30 MTVSLVARQHGVAASQLFLWRKQYQEGSLTA 60 (121)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhhccccc
Confidence 3889999999999999999999998877643
No 406
>PF07836 DmpG_comm: DmpG-like communication domain; InterPro: IPR012425 This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain []. The communication domain is thought to play an important role in the heterodimerisation of the enzyme []. Members of this entry heterodimerise with members of IPR003361 from INTERPRO to form a bifunctional aldolase-dehydrogenase [].; GO: 0016833 oxo-acid-lyase activity, 0019439 aromatic compound catabolic process; PDB: 1NVM_E.
Probab=21.10 E-value=99 Score=20.31 Aligned_cols=24 Identities=25% Similarity=0.405 Sum_probs=17.0
Q ss_pred hhhhhhhcccHHHHHHHHHHHHHcCCe
Q 033932 64 SILSDRLRINGSLARKAIRELMARGLI 90 (108)
Q Consensus 64 s~vserlkI~~SlAr~~Lr~L~~kGlI 90 (108)
-..|+||+|. +|.+|.||-+++++
T Consensus 26 ~raa~~ygVd---~r~il~elgrR~~V 49 (66)
T PF07836_consen 26 ERAAERYGVD---PRDILVELGRRKLV 49 (66)
T ss_dssp HHHHHHHT-----HHHHHHHHHHCT--
T ss_pred HHHHHHhCcC---HHHHHHHHhccccc
Confidence 3578999887 68999999999876
No 407
>cd08768 Cdc6_C Winged-helix domain of essential DNA replication protein Cell division control protein (Cdc6), which mediates DNA binding. This model characterizes the winged-helix, C-terminal domain of the Cell division control protein (Cdc6_C). Cdc6 (also known as Cell division cycle 6 or Cdc18) functions as a regulator at the early stages of DNA replication, by helping to recruit and load the Minichromosome Maintenance Complex (MCM) onto DNA and may have additional roles in the control of mitotic entry. Precise duplication of chromosomal DNA is required for genomic stability during replication. Cdc6 has an essential role in DNA replication and irregular expression of Cdc6 may lead to genomic instability. Cdc6 over-expression is observed in many cancerous lesions. DNA replication begins when an origin recognition complex (ORC) binds to a replication origin site on the chromatin. Studies indicate that Cdc6 interacts with ORC through the Orc1 subunit, and that this association increases
Probab=21.05 E-value=2.2e+02 Score=17.72 Aligned_cols=22 Identities=18% Similarity=0.169 Sum_probs=17.2
Q ss_pred cHHHHHHHHHHHHHcCCeeEec
Q 033932 73 NGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 73 ~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+..-...+|.+|+..|+|..=.
T Consensus 45 ~~~~~~~~l~~L~~~gli~~~~ 66 (87)
T cd08768 45 TQRRISDLLSELEMLGLLETEV 66 (87)
T ss_pred cHHHHHHHHHHHHHcCCeEEEE
Confidence 4455677899999999998753
No 408
>PF00178 Ets: Ets-domain; InterPro: IPR000418 Transcription factors are protein molecules that bind to specific DNA sequences in the genome, resulting in the induction or inhibition of gene transcription []. The ets oncogene is such a factor, possessing a region of 85-90 amino acids known as the ETS (erythroblast transformation specific) domain [, , ]. This domain is rich in positively-charged and aromatic residues, and binds to purine-rich segments of DNA. The ETS domain has been identified in other transcription factors such as PU.1, human erg, human elf-1, human elk-1, GA binding protein, and a number of others [, , ]. It is generally localized at the C terminus of the protein, with the exception of ELF-1, ELK-1, ELK-3, ELK-4 and ERF where it is found at the N terminus. NMR-analysis of the structure of the Ets domains revealed that it contains three alpha-helixes (1-3) and four-stranded beta-sheets (1-4) arranged in the order alpha1-beta1-beta2-alpha2-alpha3-beta3-beta4 forming a winged helix-turn-helix (wHTH) topology []. The third alpha-helix is responsive to contact to the major groove of the DNA. Different members of the Ets family proteins display distinct DNA binding specificities. The Ets domains and the flanking amino acid sequences of the proteins influence the binding affinity, and the alteration of a single amino acid in the Ets domain can change its DNA binding specificities. Avian leukemia virus E26 is a replication defective retrovirus that induces a mixed erythroid/myeloid leukemia in chickens.This virus carries two distinct oncogenes: v-myb and v-ets. The ets portion of this oncogene is required for the induction of erythroblastosis. V-ets and c-ets-1, its cellular progenitor, have been shown [] to be nuclear DNA-binding proteins. Ets-1 differs slightly from v-ets at its carboxy-terminal region. In most species where it has been sequenced, c-ets-1 exists in various isoforms generated by alternative splicing and differential phosphorylation.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1DUX_F 4AVP_B 1HBX_G 1BC7_C 1K6O_A 1BC8_C 1PUE_E 1FLI_A 2DAO_A 1WWX_A ....
Probab=21.01 E-value=2.7e+02 Score=18.64 Aligned_cols=40 Identities=18% Similarity=0.401 Sum_probs=28.1
Q ss_pred Ceeechhhhhhhh-------cccHHHHHHHHHHHHHcCCeeEecccc
Q 033932 58 YKLITPSILSDRL-------RINGSLARKAIRELMARGLIRMVSAHA 97 (108)
Q Consensus 58 ~k~ITps~vserl-------kI~~SlAr~~Lr~L~~kGlIk~V~k~~ 97 (108)
++++.|-.||+.. ..+..-..++||..-++|++..|...+
T Consensus 31 Fki~d~~~vA~lWG~~k~~~~m~yeklsR~LR~yy~k~il~kv~g~r 77 (85)
T PF00178_consen 31 FKIVDPEAVARLWGKHKNRPNMNYEKLSRALRYYYKKGILEKVKGQR 77 (85)
T ss_dssp EEESSHHHHHHHHHHHTTSTT-SHHHHHHHHHHHHHTTSEEEETTST
T ss_pred EEecCHHHHHHHHHHHcCCccccHHHHHHHHHHHhhCCeEEecCCcE
Confidence 4666666666543 345566678899999999999996544
No 409
>PF01976 DUF116: Protein of unknown function DUF116; InterPro: IPR002829 These archaeal and bacterial proteins have no known function. Members of this family contain seven conserved cysteines and may also be an integral membrane protein.
Probab=20.90 E-value=60 Score=24.08 Aligned_cols=30 Identities=30% Similarity=0.499 Sum_probs=23.6
Q ss_pred chhhhhhhhccc------HHHHHHHHHHHHHcCCee
Q 033932 62 TPSILSDRLRIN------GSLARKAIRELMARGLIR 91 (108)
Q Consensus 62 Tps~vserlkI~------~SlAr~~Lr~L~~kGlIk 91 (108)
.-..++|+|++. +|+||+++++..-+|+|-
T Consensus 77 ~l~~lae~~g~~v~i~~Ggt~ar~~ik~~~p~~iig 112 (158)
T PF01976_consen 77 DLKKLAEKYGYKVYIATGGTLARKIIKEYRPKAIIG 112 (158)
T ss_pred HHHHHHHHcCCEEEEEcChHHHHHHHHHhCCCEEEE
Confidence 346788888875 799999999998886653
No 410
>PF09639 YjcQ: YjcQ protein; InterPro: IPR018597 YjcQ is a protein of approx. 100 residues containing four alpha helices and three beta strands. It is found in bacteria and also in the Lactococcus phage Tuc2009. In bacteria it appears to be under the regulation of SigD RNA polymerase which is responsible for the expression of many genes encoding cell-surface proteins related to flagellar assembly, motility, chemotaxis and autolysis in the late exponential growth phase. The exact function of YjcQ is unknown []. However, it is thought to be the major head protein in viruses [] and is found in prophage in bacteria. ; PDB: 2HGC_A.
Probab=20.88 E-value=1e+02 Score=20.38 Aligned_cols=19 Identities=32% Similarity=0.350 Sum_probs=14.8
Q ss_pred HHHHHHHHHHHHcCCeeEe
Q 033932 75 SLARKAIRELMARGLIRMV 93 (108)
Q Consensus 75 SlAr~~Lr~L~~kGlIk~V 93 (108)
+---.+|+.|.+.|+|+=|
T Consensus 25 ~~~~~il~~L~d~GyI~G~ 43 (88)
T PF09639_consen 25 SYWSDILRMLQDEGYIKGV 43 (88)
T ss_dssp HHHHHHHHHHHHHTSEE--
T ss_pred HHHHHHHHHHHHCCCccce
Confidence 5667899999999999643
No 411
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=20.78 E-value=2.3e+02 Score=22.26 Aligned_cols=23 Identities=17% Similarity=0.215 Sum_probs=19.8
Q ss_pred ccHHHHHHHHHHHHHcCCeeEec
Q 033932 72 INGSLARKAIRELMARGLIRMVS 94 (108)
Q Consensus 72 I~~SlAr~~Lr~L~~kGlIk~V~ 94 (108)
+..+-.+.+|.+|+..|+|....
T Consensus 329 ~~~~~~~~~l~~l~~~gli~~~~ 351 (365)
T TIGR02928 329 LTQRRISDLLNELDMLGLVEAEE 351 (365)
T ss_pred CcHHHHHHHHHHHHhcCCeEEEE
Confidence 55677889999999999999984
No 412
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=20.47 E-value=1.2e+02 Score=20.56 Aligned_cols=35 Identities=11% Similarity=0.142 Sum_probs=23.5
Q ss_pred HHHhhCCCCeeechhhhhhhhcccHHHHHHHHHHHHHc
Q 033932 50 KLLSEAPKYKLITPSILSDRLRINGSLARKAIRELMAR 87 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserlkI~~SlAr~~Lr~L~~k 87 (108)
.|..|.-++ +...||.+|+++..-.++||++...+
T Consensus 65 ~I~~~f~G~---n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 65 EIRREFNGM---NVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp HHHHH--SS----HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred HHHHHhCCC---CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 455555544 57899999999999999999987653
No 413
>PF14629 ORC4_C: Origin recognition complex (ORC) subunit 4 C-terminus
Probab=20.40 E-value=98 Score=22.82 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=19.5
Q ss_pred cccHHHHHHHHHHHHHcCCeeE
Q 033932 71 RINGSLARKAIRELMARGLIRM 92 (108)
Q Consensus 71 kI~~SlAr~~Lr~L~~kGlIk~ 92 (108)
-..-.+++++.++|.+-|+|.+
T Consensus 150 ~~~k~v~~~a~E~L~~l~Ll~~ 171 (203)
T PF14629_consen 150 VWSKPVALKAWEHLLSLELLKP 171 (203)
T ss_pred cCCHHHHHHHHHHHHHCCCcee
Confidence 3456789999999999999999
No 414
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=20.37 E-value=1.3e+02 Score=17.33 Aligned_cols=23 Identities=17% Similarity=0.353 Sum_probs=16.9
Q ss_pred echhhhhhhhcccHHHHHHHHHH
Q 033932 61 ITPSILSDRLRINGSLARKAIRE 83 (108)
Q Consensus 61 ITps~vserlkI~~SlAr~~Lr~ 83 (108)
.|...||+.++++.+-.+..|..
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHH
Confidence 57789999999999988877754
No 415
>COG2452 Predicted site-specific integrase-resolvase [DNA replication, recombination, and repair]
Probab=20.31 E-value=1.1e+02 Score=24.02 Aligned_cols=32 Identities=28% Similarity=0.344 Sum_probs=24.0
Q ss_pred eechhhhhhhhcccHHHHHHHHHHHHHcCCeeEecc
Q 033932 60 LITPSILSDRLRINGSLARKAIRELMARGLIRMVSA 95 (108)
Q Consensus 60 ~ITps~vserlkI~~SlAr~~Lr~L~~kGlIk~V~k 95 (108)
+.+|.++|++++|+.+.+ ..-...|.|.++..
T Consensus 1 ~m~~~e~~~~lgis~~Tl----~rw~r~G~i~~~~~ 32 (193)
T COG2452 1 LLRPKEACQLLGISYSTL----LRWIREGKIRVVTT 32 (193)
T ss_pred CCCHHHHHHHhCcCHHHH----HHHHHcCcccceEe
Confidence 368999999999876665 45556799987743
No 416
>PF01498 HTH_Tnp_Tc3_2: Transposase; InterPro: IPR002492 Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in []. Tc3 is a member of the Tc1/mariner family of transposable elements. This entry also includes histone-lysine N-methyltransferase SETMAR, which is a SET domain and mariner transposase fusion gene-containing protein. This histone methyltransferase has sequence-specific DNA-binding activity and recognises the 19-mer core of the 5'-terminal inverted repeats (TIRs) of the Hsmar1 element. This protein has DNA nicking activity, and has in vivo end joining activity and may mediate genomic integration of foreign DNA [, , , ]. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration; PDB: 3K9K_B 3F2K_B 3K9J_B 1U78_A.
Probab=20.23 E-value=1.1e+02 Score=18.76 Aligned_cols=41 Identities=20% Similarity=0.248 Sum_probs=15.0
Q ss_pred HHHhhCCCCeeechhhhhhhh---cccHHHHHHHHHHHHHcCCee
Q 033932 50 KLLSEAPKYKLITPSILSDRL---RINGSLARKAIRELMARGLIR 91 (108)
Q Consensus 50 Kl~KEVpk~k~ITps~vserl---kI~~SlAr~~Lr~L~~kGlIk 91 (108)
.|...|-.-..+|...|+..+ ++++|. .-+.+.|.+.|+-.
T Consensus 3 ~I~~~v~~~p~~s~~~i~~~l~~~~~~vS~-~TI~r~L~~~g~~~ 46 (72)
T PF01498_consen 3 RIVRMVRRNPRISAREIAQELQEAGISVSK-STIRRRLREAGLKK 46 (72)
T ss_dssp -------------HHHHHHHT---T--S-H-HHHHHHHHHT-EEE
T ss_pred HHHHHHHHCCCCCHHHHHHHHHHccCCcCH-HHHHHHHHHcCccc
Confidence 345556666779999999988 554442 33444555567544
Done!