Query 012778
Match_columns 456
No_of_seqs 206 out of 461
Neff 3.8
Searched_HMMs 46136
Date Fri Mar 29 06:12:50 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/012778.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/012778hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2577 Transcription factor E 100.0 1E-64 2.3E-69 508.2 26.5 271 127-418 61-334 (354)
2 PF02319 E2F_TDP: E2F/DP famil 99.9 1.4E-22 3E-27 163.0 5.6 66 134-199 1-71 (71)
3 KOG2578 Transcription factor E 99.8 2E-19 4.3E-24 179.2 4.9 88 126-218 13-100 (388)
4 KOG2578 Transcription factor E 99.0 1.4E-09 3.1E-14 109.5 7.8 74 130-203 152-241 (388)
5 KOG2829 E2F-like protein [Tran 98.7 2.7E-07 5.9E-12 92.7 13.9 127 147-289 51-208 (326)
6 PF01978 TrmB: Sugar-specific 94.4 0.047 1E-06 42.8 3.6 46 154-199 19-64 (68)
7 PF08279 HTH_11: HTH domain; 92.3 0.25 5.5E-06 36.9 4.4 41 144-185 3-43 (55)
8 cd00092 HTH_CRP helix_turn_hel 91.5 0.41 8.9E-06 36.4 4.8 54 142-195 5-63 (67)
9 smart00420 HTH_DEOR helix_turn 91.4 0.28 6.1E-06 35.1 3.7 45 145-191 4-48 (53)
10 smart00346 HTH_ICLR helix_turn 91.2 1.1 2.3E-05 36.2 7.2 47 144-191 8-54 (91)
11 smart00550 Zalpha Z-DNA-bindin 89.6 0.54 1.2E-05 37.7 4.1 55 144-198 9-63 (68)
12 COG1378 Predicted transcriptio 89.3 1.4 3E-05 43.7 7.6 52 146-200 22-73 (247)
13 PF09339 HTH_IclR: IclR helix- 88.3 0.46 1E-05 35.7 2.7 45 145-190 7-51 (52)
14 COG3355 Predicted transcriptio 86.7 3.3 7.1E-05 37.9 7.7 86 146-245 33-120 (126)
15 PF12802 MarR_2: MarR family; 86.5 0.98 2.1E-05 34.0 3.7 46 145-190 9-54 (62)
16 PF13412 HTH_24: Winged helix- 86.3 1.1 2.3E-05 32.9 3.6 43 144-188 6-48 (48)
17 smart00418 HTH_ARSR helix_turn 86.2 0.86 1.9E-05 33.1 3.1 38 155-192 8-45 (66)
18 PF13463 HTH_27: Winged helix 82.9 1.7 3.7E-05 33.2 3.7 38 153-190 14-51 (68)
19 PF02082 Rrf2: Transcriptional 82.1 2 4.4E-05 35.1 4.0 49 142-190 9-58 (83)
20 PF13730 HTH_36: Helix-turn-he 80.9 1.9 4E-05 32.2 3.1 29 159-187 27-55 (55)
21 TIGR02944 suf_reg_Xantho FeS a 80.7 2.1 4.6E-05 37.4 3.9 46 145-190 13-58 (130)
22 PF01047 MarR: MarR family; I 80.5 1.7 3.7E-05 32.6 2.8 43 147-191 9-51 (59)
23 PF14394 DUF4423: Domain of un 80.4 18 0.00039 34.0 10.2 44 153-196 35-80 (171)
24 PF09079 Cdc6_C: CDC6, C termi 79.9 0.86 1.9E-05 37.2 1.1 29 162-190 27-58 (85)
25 cd00090 HTH_ARSR Arsenical Res 79.4 4.2 9E-05 30.1 4.6 47 144-193 10-56 (78)
26 smart00345 HTH_GNTR helix_turn 78.7 3.2 6.9E-05 30.4 3.7 41 153-193 15-56 (60)
27 cd08768 Cdc6_C Winged-helix do 78.0 1.3 2.9E-05 35.7 1.7 22 169-190 44-65 (87)
28 PF00392 GntR: Bacterial regul 76.3 6.5 0.00014 30.5 5.0 50 144-193 7-60 (64)
29 cd00890 Prefoldin Prefoldin is 76.0 8.7 0.00019 33.1 6.2 55 191-245 68-122 (129)
30 smart00419 HTH_CRP helix_turn_ 74.4 3.2 7E-05 29.4 2.7 38 157-195 8-45 (48)
31 TIGR00122 birA_repr_reg BirA b 73.5 3.1 6.6E-05 32.7 2.6 53 145-200 4-57 (69)
32 PF08784 RPA_C: Replication pr 73.4 4 8.6E-05 34.5 3.4 50 138-187 44-95 (102)
33 PRK10163 DNA-binding transcrip 73.4 12 0.00025 37.1 7.1 54 145-199 29-82 (271)
34 PHA02943 hypothetical protein; 70.9 16 0.00034 35.0 7.0 48 144-194 14-61 (165)
35 PF01022 HTH_5: Bacterial regu 69.5 4.8 0.0001 29.7 2.7 42 145-189 6-47 (47)
36 PF08220 HTH_DeoR: DeoR-like h 69.4 6.6 0.00014 30.4 3.5 45 144-190 3-47 (57)
37 PF04182 B-block_TFIIIC: B-blo 68.9 6.4 0.00014 32.0 3.5 49 144-192 5-53 (75)
38 TIGR02702 SufR_cyano iron-sulf 65.6 40 0.00087 31.9 8.7 45 144-190 4-48 (203)
39 TIGR02147 Fsuc_second hypothet 65.4 55 0.0012 33.2 10.1 40 154-193 134-175 (271)
40 TIGR00738 rrf2_super rrf2 fami 65.4 9.5 0.00021 33.0 4.1 37 154-190 22-58 (132)
41 cd00584 Prefoldin_alpha Prefol 65.4 17 0.00037 31.8 5.8 54 192-245 69-122 (129)
42 cd04766 HTH_HspR Helix-Turn-He 63.9 19 0.00041 29.9 5.5 27 158-188 2-28 (91)
43 PRK03947 prefoldin subunit alp 63.7 22 0.00047 31.8 6.2 51 193-243 77-127 (140)
44 PF09012 FeoC: FeoC like trans 63.6 3.8 8.2E-05 32.6 1.2 41 154-194 11-51 (69)
45 PF12840 HTH_20: Helix-turn-he 63.6 5.9 0.00013 30.5 2.2 45 145-191 14-58 (61)
46 PRK09834 DNA-binding transcrip 63.0 28 0.0006 34.1 7.3 50 146-196 16-66 (263)
47 cd07377 WHTH_GntR Winged helix 62.2 14 0.00031 27.4 4.1 38 154-191 21-59 (66)
48 PRK03573 transcriptional regul 61.9 70 0.0015 28.1 9.0 35 157-191 46-80 (144)
49 smart00344 HTH_ASNC helix_turn 61.8 9.3 0.0002 31.9 3.3 47 142-190 4-50 (108)
50 COG1474 CDC6 Cdc6-related prot 60.5 6 0.00013 41.4 2.3 30 159-188 303-332 (366)
51 PRK10870 transcriptional repre 60.3 50 0.0011 30.8 8.2 41 151-191 65-105 (176)
52 PRK11414 colanic acid/biofilm 60.1 17 0.00038 34.2 5.2 56 138-193 11-70 (221)
53 TIGR02231 conserved hypothetic 59.9 60 0.0013 35.1 9.8 98 210-324 138-241 (525)
54 smart00347 HTH_MARR helix_turn 59.8 16 0.00035 29.0 4.3 45 144-190 13-57 (101)
55 PF01325 Fe_dep_repress: Iron 59.7 18 0.00039 28.5 4.4 42 149-191 15-56 (60)
56 TIGR01610 phage_O_Nterm phage 59.7 14 0.00031 31.3 4.1 46 154-201 44-89 (95)
57 cd04770 HTH_HMRTR Helix-Turn-H 59.3 17 0.00037 31.6 4.6 37 159-199 2-40 (123)
58 PRK10411 DNA-binding transcrip 59.0 45 0.00097 32.7 8.0 53 144-198 7-59 (240)
59 cd04775 HTH_Cfa-like Helix-Tur 58.9 27 0.00059 29.8 5.7 37 158-198 2-39 (102)
60 smart00529 HTH_DTXR Helix-turn 58.7 8.6 0.00019 31.4 2.5 33 160-192 2-34 (96)
61 TIGR02337 HpaR homoprotocatech 58.5 7.9 0.00017 33.1 2.4 37 155-191 40-76 (118)
62 TIGR00293 prefoldin, archaeal 57.5 35 0.00075 29.8 6.3 54 192-245 68-121 (126)
63 cd04783 HTH_MerR1 Helix-Turn-H 55.8 31 0.00068 30.3 5.8 37 159-199 2-40 (126)
64 COG1510 Predicted transcriptio 55.8 21 0.00045 34.6 4.9 37 154-190 38-74 (177)
65 PRK05014 hscB co-chaperone Hsc 55.4 1E+02 0.0022 29.1 9.4 54 134-189 12-82 (171)
66 PRK09954 putative kinase; Prov 55.3 11 0.00025 38.0 3.3 47 142-190 4-50 (362)
67 cd04789 HTH_Cfa Helix-Turn-Hel 54.9 31 0.00067 29.5 5.4 38 158-199 2-40 (102)
68 PF08280 HTH_Mga: M protein tr 54.8 13 0.00028 28.9 2.8 36 145-182 9-44 (59)
69 PRK06474 hypothetical protein; 54.7 97 0.0021 29.2 9.2 47 144-191 14-61 (178)
70 TIGR02716 C20_methyl_CrtF C-20 54.7 8.3 0.00018 38.2 2.2 37 155-191 21-57 (306)
71 COG1414 IclR Transcriptional r 54.3 56 0.0012 32.1 7.8 53 145-199 8-61 (246)
72 PF13518 HTH_28: Helix-turn-he 54.0 9.9 0.00021 27.6 2.0 38 145-186 4-41 (52)
73 PRK09413 IS2 repressor TnpA; R 54.0 88 0.0019 27.4 8.2 31 156-186 28-58 (121)
74 PF05732 RepL: Firmicute plasm 54.0 30 0.00065 32.5 5.6 39 157-195 75-113 (165)
75 PF12329 TMF_DNA_bd: TATA elem 53.9 33 0.00071 28.4 5.2 37 209-245 11-47 (74)
76 PF01726 LexA_DNA_bind: LexA D 53.7 12 0.00027 30.0 2.6 46 146-191 14-60 (65)
77 PRK11569 transcriptional repre 53.7 52 0.0011 32.5 7.5 46 146-192 33-78 (274)
78 COG2739 Uncharacterized protei 53.0 10 0.00022 33.9 2.2 40 140-179 16-55 (105)
79 PF01920 Prefoldin_2: Prefoldi 52.8 34 0.00075 28.3 5.3 80 161-243 15-102 (106)
80 cd00632 Prefoldin_beta Prefold 52.5 22 0.00047 30.6 4.1 77 163-243 21-103 (105)
81 cd04784 HTH_CadR-PbrR Helix-Tu 52.0 36 0.00078 29.9 5.5 79 158-245 1-100 (127)
82 TIGR01889 Staph_reg_Sar staphy 52.0 18 0.00039 30.9 3.5 45 147-191 31-77 (109)
83 PF14257 DUF4349: Domain of un 52.0 59 0.0013 31.9 7.5 87 137-234 59-156 (262)
84 KOG1318 Helix loop helix trans 51.5 12 0.00026 40.4 2.8 76 168-245 239-318 (411)
85 PF04977 DivIC: Septum formati 51.3 37 0.0008 26.8 5.0 36 211-246 18-53 (80)
86 TIGR01764 excise DNA binding d 50.9 8.7 0.00019 27.0 1.2 22 158-179 2-23 (49)
87 PRK15090 DNA-binding transcrip 50.4 85 0.0019 30.5 8.3 53 145-199 18-70 (257)
88 PRK00215 LexA repressor; Valid 50.0 19 0.00042 33.7 3.7 42 152-193 18-60 (205)
89 TIGR02047 CadR-PbrR Cd(II)/Pb( 49.9 43 0.00094 29.7 5.7 37 159-199 2-40 (127)
90 PF13545 HTH_Crp_2: Crp-like h 49.1 16 0.00034 28.5 2.5 51 142-192 3-63 (76)
91 COG1777 Predicted transcriptio 49.0 98 0.0021 31.0 8.4 43 144-189 18-60 (217)
92 TIGR02338 gimC_beta prefoldin, 48.8 42 0.00092 29.1 5.4 83 161-244 20-108 (110)
93 PRK14165 winged helix-turn-hel 48.8 53 0.0012 32.4 6.6 50 143-192 6-56 (217)
94 PRK11534 DNA-binding transcrip 48.5 58 0.0013 30.6 6.7 47 153-199 26-72 (224)
95 TIGR02431 pcaR_pcaU beta-ketoa 48.4 24 0.00053 34.0 4.2 44 146-190 14-57 (248)
96 TIGR02010 IscR iron-sulfur clu 48.4 24 0.00051 31.4 3.8 38 152-189 20-57 (135)
97 KOG2420 Phosphatidylserine dec 48.3 7.6 0.00016 41.1 0.8 12 29-40 235-246 (382)
98 COG1382 GimC Prefoldin, chaper 47.4 47 0.001 30.3 5.5 99 141-247 10-114 (119)
99 PRK00888 ftsB cell division pr 47.3 23 0.00049 31.1 3.5 28 210-237 34-61 (105)
100 cd01109 HTH_YyaN Helix-Turn-He 47.2 46 0.00099 28.7 5.3 35 159-197 2-38 (113)
101 PRK11511 DNA-binding transcrip 46.8 27 0.00058 30.7 3.9 42 139-180 7-48 (127)
102 COG1802 GntR Transcriptional r 46.6 41 0.0009 31.9 5.4 41 153-193 35-75 (230)
103 TIGR01884 cas_HTH CRISPR locus 46.2 29 0.00062 32.8 4.3 45 145-191 147-191 (203)
104 TIGR03338 phnR_burk phosphonat 46.0 44 0.00096 31.0 5.4 41 153-193 30-70 (212)
105 PF09940 DUF2172: Domain of un 45.9 16 0.00036 39.0 2.8 46 139-188 341-386 (386)
106 COG1846 MarR Transcriptional r 45.6 24 0.00052 28.7 3.2 44 146-191 27-70 (126)
107 PRK11050 manganese transport r 45.3 35 0.00075 31.2 4.5 39 155-193 49-87 (152)
108 PRK13509 transcriptional repre 44.9 21 0.00045 35.2 3.2 45 144-190 8-52 (251)
109 COG4189 Predicted transcriptio 44.6 24 0.00053 36.1 3.6 52 137-190 18-70 (308)
110 TIGR00498 lexA SOS regulatory 44.5 28 0.00062 32.4 3.9 48 144-191 9-60 (199)
111 KOG3863 bZIP transcription fac 44.0 42 0.00091 37.9 5.6 69 175-246 479-554 (604)
112 PRK10219 DNA-binding transcrip 44.0 28 0.0006 29.2 3.4 40 141-180 5-44 (107)
113 COG2894 MinD Septum formation 43.8 9.3 0.0002 38.8 0.6 31 155-185 38-68 (272)
114 PRK09343 prefoldin subunit bet 43.1 56 0.0012 29.1 5.4 74 171-245 34-113 (121)
115 PF05565 Sipho_Gp157: Siphovir 43.0 1.5E+02 0.0033 27.6 8.4 31 138-168 2-32 (162)
116 PLN02938 phosphatidylserine de 42.8 9 0.0002 41.4 0.3 11 29-39 260-270 (428)
117 PRK13626 transcriptional regul 42.4 52 0.0011 35.7 6.0 49 140-188 4-54 (552)
118 PF07106 TBPIP: Tat binding pr 42.4 2.8E+02 0.006 25.6 10.4 53 146-199 6-62 (169)
119 PRK10857 DNA-binding transcrip 42.2 32 0.0007 32.2 3.8 39 152-190 20-58 (164)
120 PF05377 FlaC_arch: Flagella a 40.9 77 0.0017 25.5 5.2 39 207-245 4-42 (55)
121 COG1522 Lrp Transcriptional re 40.5 36 0.00077 29.9 3.7 50 139-190 6-55 (154)
122 PRK09464 pdhR transcriptional 40.3 1.8E+02 0.0039 27.9 8.8 54 138-191 10-68 (254)
123 TIGR02297 HpaA 4-hydroxyphenyl 40.2 24 0.00052 34.0 2.8 44 141-184 186-229 (287)
124 PF14947 HTH_45: Winged helix- 39.5 33 0.00072 27.9 3.1 41 155-196 17-57 (77)
125 PF05491 RuvB_C: Holliday junc 39.1 55 0.0012 27.8 4.4 58 138-195 5-64 (76)
126 TIGR02043 ZntR Zn(II)-responsi 38.9 92 0.002 27.8 6.1 81 158-245 2-102 (131)
127 PF10779 XhlA: Haemolysin XhlA 38.5 89 0.0019 25.3 5.4 35 211-245 14-48 (71)
128 PRK11014 transcriptional repre 38.5 36 0.00077 30.4 3.4 40 152-191 20-59 (141)
129 TIGR02366 DHAK_reg probable di 38.1 34 0.00073 30.5 3.2 36 140-175 6-41 (176)
130 cd04762 HTH_MerR-trunc Helix-T 37.3 29 0.00063 24.0 2.1 23 158-180 1-23 (49)
131 PF12793 SgrR_N: Sugar transpo 36.8 1.4E+02 0.0029 26.6 6.7 47 142-188 2-50 (115)
132 PF04111 APG6: Autophagy prote 36.7 61 0.0013 33.4 5.2 35 212-246 59-93 (314)
133 KOG3026 Splicing factor SPF30 36.5 1.3E+02 0.0028 30.8 7.2 89 220-313 26-124 (262)
134 PRK10225 DNA-binding transcrip 36.4 1.6E+02 0.0035 28.4 7.7 51 141-191 13-67 (257)
135 PF01638 HxlR: HxlR-like helix 35.9 33 0.00071 28.5 2.6 43 149-191 10-53 (90)
136 cd07153 Fur_like Ferric uptake 35.8 51 0.0011 27.8 3.8 45 146-191 6-55 (116)
137 PRK03902 manganese transport t 35.7 88 0.0019 27.8 5.4 38 154-191 19-56 (142)
138 TIGR02044 CueR Cu(I)-responsiv 35.3 97 0.0021 27.3 5.6 37 159-199 2-40 (127)
139 COG4519 Uncharacterized protei 35.1 51 0.0011 28.8 3.6 36 153-188 18-53 (95)
140 PF03444 HrcA_DNA-bdg: Winged 34.9 64 0.0014 27.5 4.1 47 143-190 10-56 (78)
141 PRK00080 ruvB Holliday junctio 34.8 48 0.001 33.3 4.0 57 137-193 255-313 (328)
142 TIGR02928 orc1/cdc6 family rep 34.0 39 0.00084 33.8 3.2 31 162-192 319-352 (365)
143 cd04787 HTH_HMRTR_unk Helix-Tu 33.9 1.1E+02 0.0025 27.2 5.9 81 158-245 1-100 (133)
144 KOG2747 Histone acetyltransfer 33.8 1E+02 0.0022 33.4 6.3 57 138-199 304-366 (396)
145 PF04977 DivIC: Septum formati 33.6 49 0.0011 26.0 3.2 31 207-237 21-51 (80)
146 PRK11512 DNA-binding transcrip 33.6 32 0.0007 30.5 2.3 37 155-191 52-88 (144)
147 PRK10869 recombination and rep 33.4 44 0.00096 36.8 3.8 102 134-245 258-362 (553)
148 cd01108 HTH_CueR Helix-Turn-He 33.3 1.2E+02 0.0026 26.8 5.9 37 159-199 2-40 (127)
149 PHA00738 putative HTH transcri 32.6 1.2E+02 0.0027 27.3 5.7 72 144-222 15-86 (108)
150 PRK09391 fixK transcriptional 32.4 86 0.0019 29.8 5.1 39 158-196 180-218 (230)
151 cd04790 HTH_Cfa-like_unk Helix 32.4 72 0.0016 29.9 4.5 38 158-201 2-43 (172)
152 PF03374 ANT: Phage antirepres 32.2 40 0.00086 28.6 2.6 42 145-190 13-54 (111)
153 PRK09514 zntR zinc-responsive 31.7 1.3E+02 0.0027 27.4 5.8 81 158-245 2-102 (140)
154 PF04703 FaeA: FaeA-like prote 31.5 61 0.0013 26.2 3.3 43 146-189 5-47 (62)
155 PF05930 Phage_AlpA: Prophage 31.0 27 0.00058 26.4 1.2 24 156-179 2-25 (51)
156 PRK10130 transcriptional regul 30.9 40 0.00087 35.0 2.8 40 140-179 239-278 (350)
157 cd04785 HTH_CadR-PbrR-like Hel 30.7 1.2E+02 0.0025 26.9 5.3 81 158-245 1-100 (126)
158 PF08781 DP: Transcription fac 30.4 95 0.0021 29.1 4.9 33 271-310 59-91 (142)
159 PTZ00403 phosphatidylserine de 30.1 16 0.00035 38.5 -0.2 11 29-39 189-199 (353)
160 PF02295 z-alpha: Adenosine de 30.1 93 0.002 25.2 4.2 57 142-198 5-61 (66)
161 TIGR02051 MerR Hg(II)-responsi 29.8 1.4E+02 0.0031 26.3 5.7 79 160-245 2-97 (124)
162 PRK13922 rod shape-determining 29.7 1.3E+02 0.0029 29.6 6.1 41 208-249 74-114 (276)
163 PRK03837 transcriptional regul 29.6 96 0.0021 29.3 4.9 50 142-191 18-71 (241)
164 KOG0804 Cytoplasmic Zn-finger 29.4 36 0.00078 37.4 2.2 60 173-246 390-450 (493)
165 PHA01750 hypothetical protein 29.0 1.2E+02 0.0027 25.5 4.7 30 211-240 43-72 (75)
166 PRK09802 DNA-binding transcrip 29.0 3.2E+02 0.0069 27.3 8.6 50 142-193 18-67 (269)
167 cd04772 HTH_TioE_rpt1 First He 28.9 95 0.0021 26.5 4.3 37 159-199 2-40 (99)
168 PRK09990 DNA-binding transcrip 28.8 89 0.0019 30.0 4.6 40 153-192 26-66 (251)
169 PF01853 MOZ_SAS: MOZ/SAS fami 28.8 68 0.0015 31.3 3.8 55 138-195 124-185 (188)
170 PF04297 UPF0122: Putative hel 28.6 34 0.00074 30.2 1.6 40 141-180 17-56 (101)
171 PRK11169 leucine-responsive tr 28.5 87 0.0019 28.7 4.3 51 137-189 10-60 (164)
172 smart00338 BRLZ basic region l 28.5 1.8E+02 0.0038 22.8 5.5 35 211-245 27-61 (65)
173 PF13551 HTH_29: Winged helix- 28.3 41 0.00089 27.6 2.0 27 159-185 14-40 (112)
174 PRK11886 bifunctional biotin-- 28.2 85 0.0018 31.7 4.5 52 144-197 7-59 (319)
175 PF02954 HTH_8: Bacterial regu 28.1 59 0.0013 23.6 2.5 37 139-177 2-38 (42)
176 PF13384 HTH_23: Homeodomain-l 27.8 48 0.001 24.1 2.0 36 146-185 10-45 (50)
177 cd04777 HTH_MerR-like_sg1 Heli 27.7 1.8E+02 0.0039 24.8 5.8 19 159-177 2-22 (107)
178 PF12728 HTH_17: Helix-turn-he 27.1 34 0.00074 25.1 1.2 22 158-179 2-23 (51)
179 COG1497 Predicted transcriptio 27.0 6.6E+02 0.014 26.0 10.4 141 154-319 22-170 (260)
180 PRK13752 putative transcriptio 26.9 1.7E+02 0.0036 26.9 5.8 81 158-245 8-105 (144)
181 COG2919 Septum formation initi 26.2 72 0.0016 28.3 3.2 32 208-239 55-86 (117)
182 COG1321 TroR Mn-dependent tran 26.2 1E+02 0.0022 28.8 4.3 42 154-195 21-62 (154)
183 cd04782 HTH_BltR Helix-Turn-He 26.2 1.6E+02 0.0035 24.8 5.2 36 159-198 2-39 (97)
184 PF05103 DivIVA: DivIVA protei 26.2 31 0.00068 29.8 0.9 48 195-245 13-60 (131)
185 PRK06266 transcription initiat 26.0 3E+02 0.0066 26.2 7.5 42 145-188 26-67 (178)
186 cd04776 HTH_GnyR Helix-Turn-He 25.9 1.5E+02 0.0032 26.2 5.1 9 144-152 45-53 (118)
187 PF01475 FUR: Ferric uptake re 25.8 69 0.0015 27.5 3.0 49 144-193 11-64 (120)
188 PRK15121 right oriC-binding tr 25.7 71 0.0015 31.5 3.4 44 141-184 5-48 (289)
189 PRK13729 conjugal transfer pil 25.7 1.1E+02 0.0023 34.0 4.9 34 212-245 85-118 (475)
190 PF09756 DDRGK: DDRGK domain; 25.6 70 0.0015 31.1 3.2 46 142-189 100-145 (188)
191 PF09107 SelB-wing_3: Elongati 25.6 96 0.0021 24.0 3.4 41 154-194 7-47 (50)
192 COG3093 VapI Plasmid maintenan 25.6 33 0.00072 30.7 1.0 33 141-179 13-45 (104)
193 PF02996 Prefoldin: Prefoldin 25.5 1.5E+02 0.0032 25.3 4.9 69 174-243 42-110 (120)
194 PF10018 Med4: Vitamin-D-recep 25.4 1.8E+02 0.0039 27.6 6.0 30 213-242 25-54 (188)
195 PRK10803 tol-pal system protei 25.4 1.3E+02 0.0027 30.2 5.1 35 209-243 60-94 (263)
196 TIGR00373 conserved hypothetic 25.3 2.7E+02 0.0058 25.9 6.9 35 154-188 25-59 (158)
197 PF15358 TSKS: Testis-specific 25.3 1.1E+02 0.0023 33.8 4.8 65 176-245 108-181 (558)
198 TIGR02338 gimC_beta prefoldin, 25.2 1.2E+02 0.0026 26.3 4.3 32 213-244 70-101 (110)
199 cd04788 HTH_NolA-AlbR Helix-Tu 25.1 2.3E+02 0.005 23.9 5.9 37 159-199 2-40 (96)
200 COG2512 Predicted membrane-ass 24.8 99 0.0022 31.3 4.3 61 137-198 191-251 (258)
201 PF13851 GAS: Growth-arrest sp 24.6 1.4E+02 0.0029 29.0 5.0 36 210-245 27-62 (201)
202 cd01279 HTH_HspR-like Helix-Tu 24.5 2.5E+02 0.0053 23.9 6.0 28 158-189 2-29 (98)
203 PF15513 DUF4651: Domain of un 24.4 47 0.001 27.3 1.5 23 304-326 16-38 (62)
204 PRK04984 fatty acid metabolism 24.4 61 0.0013 30.8 2.6 39 153-191 26-65 (239)
205 PRK00888 ftsB cell division pr 24.3 1.6E+02 0.0036 25.8 5.0 61 211-277 28-90 (105)
206 PF03836 RasGAP_C: RasGAP C-te 24.2 26 0.00055 31.9 0.0 26 170-197 5-30 (142)
207 PRK09333 30S ribosomal protein 24.1 80 0.0017 29.9 3.2 37 155-191 65-115 (150)
208 cd01106 HTH_TipAL-Mta Helix-Tu 24.0 2.3E+02 0.005 23.9 5.8 17 159-175 2-18 (103)
209 PF10141 ssDNA-exonuc_C: Singl 23.7 3.7E+02 0.0081 25.6 7.7 46 145-190 102-149 (195)
210 TIGR00635 ruvB Holliday juncti 23.7 92 0.002 30.5 3.7 55 139-193 236-292 (305)
211 PF10779 XhlA: Haemolysin XhlA 23.6 2.1E+02 0.0046 23.1 5.2 39 208-246 4-42 (71)
212 PF10018 Med4: Vitamin-D-recep 23.6 1.7E+02 0.0037 27.8 5.4 55 208-262 27-88 (188)
213 PF09340 NuA4: Histone acetylt 23.5 1.2E+02 0.0026 25.6 3.9 27 217-243 2-28 (80)
214 PF00170 bZIP_1: bZIP transcri 23.3 2.6E+02 0.0056 21.8 5.5 34 211-244 27-60 (64)
215 PRK03578 hscB co-chaperone Hsc 23.2 6E+02 0.013 24.2 8.9 51 134-186 17-84 (176)
216 PRK00044 psd phosphatidylserin 23.2 25 0.00054 35.6 -0.3 11 29-39 139-149 (288)
217 PRK10402 DNA-binding transcrip 23.1 74 0.0016 30.0 2.9 54 142-196 151-207 (226)
218 PF04218 CENP-B_N: CENP-B N-te 23.0 61 0.0013 24.9 1.9 32 147-179 13-44 (53)
219 TIGR02894 DNA_bind_RsfA transc 23.0 2E+02 0.0043 27.7 5.6 36 211-246 105-140 (161)
220 PRK00723 phosphatidylserine de 22.9 26 0.00056 35.9 -0.3 14 26-40 159-172 (297)
221 PRK11753 DNA-binding transcrip 22.8 1.2E+02 0.0027 27.6 4.2 39 157-196 168-206 (211)
222 cd00592 HTH_MerR-like Helix-Tu 22.6 1.3E+02 0.0028 25.0 3.9 21 159-179 2-22 (100)
223 PRK09393 ftrA transcriptional 22.4 94 0.002 31.0 3.6 42 141-182 218-259 (322)
224 COG1373 Predicted ATPase (AAA+ 22.2 97 0.0021 32.7 3.8 49 141-189 220-269 (398)
225 PLN03239 histone acetyltransfe 22.2 2E+02 0.0044 30.7 6.1 49 138-189 257-313 (351)
226 PRK13503 transcriptional activ 22.2 1E+02 0.0022 29.5 3.6 39 141-179 171-209 (278)
227 cd04768 HTH_BmrR-like Helix-Tu 22.0 1.8E+02 0.0038 24.6 4.6 38 159-200 2-41 (96)
228 KOG3501 Molecular chaperone Pr 22.0 2.1E+02 0.0046 26.0 5.2 40 207-246 71-110 (114)
229 PF09904 HTH_43: Winged helix- 21.9 94 0.002 27.3 3.0 30 159-188 23-52 (90)
230 PF11853 DUF3373: Protein of u 21.3 68 0.0015 35.5 2.5 25 211-235 32-56 (489)
231 PF05158 RNA_pol_Rpc34: RNA po 21.2 1.5E+02 0.0032 31.0 4.8 63 138-200 6-71 (327)
232 TIGR02063 RNase_R ribonuclease 20.9 1.2E+02 0.0025 34.5 4.3 55 144-198 5-63 (709)
233 PRK11642 exoribonuclease R; Pr 20.8 1.2E+02 0.0026 35.4 4.4 51 145-196 23-77 (813)
234 PRK13182 racA polar chromosome 20.8 2.4E+02 0.0052 27.0 5.8 28 219-246 87-114 (175)
235 PF10805 DUF2730: Protein of u 20.8 5.7E+02 0.012 22.3 8.0 81 145-247 22-102 (106)
236 PF03428 RP-C: Replication pro 20.7 2.2E+02 0.0047 27.4 5.5 33 159-191 72-105 (177)
237 PRK11179 DNA-binding transcrip 20.7 1.2E+02 0.0027 27.4 3.7 50 139-190 7-56 (153)
238 KOG3990 Uncharacterized conser 20.6 1.2E+02 0.0026 31.4 3.8 40 211-250 226-265 (305)
239 PHA02047 phage lambda Rz1-like 20.6 57 0.0012 29.1 1.4 7 195-201 26-32 (101)
240 PRK04214 rbn ribonuclease BN/u 20.6 1.4E+02 0.003 31.6 4.5 44 153-196 306-349 (412)
241 PF14712 Snapin_Pallidin: Snap 20.3 2.7E+02 0.0059 23.0 5.4 37 209-245 13-49 (92)
242 cd00890 Prefoldin Prefoldin is 20.2 2.6E+02 0.0057 23.9 5.5 36 208-243 92-127 (129)
243 PF13600 DUF4140: N-terminal d 20.2 2.6E+02 0.0056 23.6 5.3 35 209-243 69-103 (104)
244 PF11932 DUF3450: Protein of u 20.0 1.8E+02 0.0039 28.6 4.9 36 210-245 56-91 (251)
No 1
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=100.00 E-value=1e-64 Score=508.25 Aligned_cols=271 Identities=44% Similarity=0.636 Sum_probs=213.5
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCCC
Q 012778 127 LTPTGPCRYDSSLGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRPG 206 (456)
Q Consensus 127 ~tp~~~~R~d~SLglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~~ 206 (456)
..|.+++|+|+|||+||||||.|+++++||++|||+||+.|+|||||||||||||||||||+|++||+|+|+|.+....+
T Consensus 61 ~s~~~~~R~d~SLglLTkKFv~Llq~s~dGvldLn~aA~~L~VqKRRIYDITNVLEGI~LIeKksKN~IqW~G~~~~~~~ 140 (354)
T KOG2577|consen 61 SSPSESTRSDTSLGLLTKKFVDLLQESPDGVLDLNKAAEVLNVQKRRIYDITNVLEGIGLIEKKSKNNIQWIGGDFNSTG 140 (354)
T ss_pred cCCCCcccchhhHHHHHHHHHHHHHhCCCceeeHHHHHHHhccccceeeehhhhhhcccceeeccccceeeecCCCcccc
Confidence 45678999999999999999999999999999999999999999999999999999999999999999999999987767
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccchhhhccCCCCCCCeEEEeeCCCCCeEEecC
Q 012778 207 EADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSEDENNQKWLFVTEDDIKSLPCFQNETLIAIKAPHGTTLEVPD 286 (456)
Q Consensus 207 ~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP~gT~LEVPd 286 (456)
+..++.+.|++|++.|.++|+.||++|.+|+++|+.|++|..|++|+|||++||++|+.|++|||||||||++|+||||+
T Consensus 141 ~~~e~~~~l~~e~~~L~~~E~~LD~~i~~~q~~L~~lted~~n~~laYVT~eDI~~i~~f~~q~vi~vkap~et~levp~ 220 (354)
T KOG2577|consen 141 GVPERLNGLEAEVEDLSQEEDDLDQLIRDCQQNLRLLTEDVENRRLAYVTYEDIRSIPGFDEQTVIAVKAPPETRLEVPD 220 (354)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchhcccceeeeHHHHhhccccCCceEEEEecCCcceEeccc
Confidence 78888999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCcccCCCCCceEEEEecCCCceEEEEecCcchhhhhccCCCCCCCCCCCCCCCCCcccceeeecccccccccccccccc
Q 012778 287 PDEAVDYPQRRYRIVLRSTMGPIDVYLVSQFEEKFEEIHGAEAPPNLPSNSGFNENQTATVITEESRGKEIEVQEQDSQR 366 (456)
Q Consensus 287 Pde~~~~~qr~YqI~LkS~~GPIdVyL~~~~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 366 (456)
+++ .+|+|+|+|++||||||||+.++... ......++. +++..+..... +.. ...+.+.
T Consensus 221 ~~~------~~~~i~L~s~~GpI~v~l~~~e~~~~--~~~~~~~~~---~~~~~~~~~~~-----sp~-----~~~~~~~ 279 (354)
T KOG2577|consen 221 PDE------DRYQIRLKSNQGPIDVYLCSEEEGEE--SEPTAKPVG---SSSSSEDTISP-----SPY-----LPEQPAS 279 (354)
T ss_pred CCC------CceEEEeccCCCceeEEeccccccCc--cCCCCCCCC---CccccccCCCC-----CCC-----cCCchhh
Confidence 984 47999999999999999999877522 222222211 11111110000 000 0000001
Q ss_pred ccCCCCCccc--ccCCceeecCCCC-CCCCCeeeecCCCCccccccCCCCCCCCC
Q 012778 367 ICTDLSSSQD--FVSGIMKIVPSEV-DSDADYWLLSDAGVSITDIWRTEPGVEWN 418 (456)
Q Consensus 367 ~~~~~~~s~~--~~~g~~ki~psd~-~~d~dywl~sd~~vsitd~w~t~~~~~w~ 418 (456)
..++|..+-+ +++-.....+++. -...|+|+....+++...+|-+.+-.+|+
T Consensus 280 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~i~l~~~~~~~d 334 (354)
T KOG2577|consen 280 LALNPQQSEELLDSSNLLSFFPSTSASGSSDIRESFSDDLSEPLISLSPPPRQED 334 (354)
T ss_pred hhcCcccccchhhcccccccCccccccCCcceeccccccccCCcccCCCCccccc
Confidence 1111110000 0111111112222 35689999999999999999999988888
No 2
>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=99.87 E-value=1.4e-22 Score=163.03 Aligned_cols=66 Identities=53% Similarity=0.863 Sum_probs=63.0
Q ss_pred CCCCcHHHHHHHHHHHHhhCCCCcccHHHHHhhh---cc--eeeehhhhHHhhhhccceecccCCeEEEee
Q 012778 134 RYDSSLGLLTKKFINLIKHAEDGILDLNKAADTL---EV--QKRRIYDITNVLEGIGLIEKKLKNRIQWKG 199 (456)
Q Consensus 134 R~d~SLglLTkKFI~Ll~~apdg~idLn~aA~~L---~V--qKRRIYDItNVLEGIGLIeK~sKN~i~W~G 199 (456)
|+++||+.||++||++|...+++.++|+++|+.| ++ +|||||||+||||++|||+|..|+.|+|+|
T Consensus 1 r~~~sL~~lt~~fi~~~~~~~~~~i~l~~ia~~l~~~~~k~~~RRlYDI~NVLealgli~K~~k~~~~W~G 71 (71)
T PF02319_consen 1 RKEKSLKLLTQRFIQLFESSPDKSISLNEIADKLISENVKTQRRRLYDIINVLEALGLIEKQSKNSYKWIG 71 (71)
T ss_dssp TTTTHHHHHHHHHHHHHHHCCCTEEEHHHHHHHCHHHCCHHHCHHHHHHHHHHHHCTSEEEEETTEEEE--
T ss_pred CCcCCHHHHHHHHHHHHHHCCCCcccHHHHHHHHcccccccccchhhHHHHHHHHhCceeecCCCceEecC
Confidence 7899999999999999999999999999999999 99 999999999999999999999999999998
No 3
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.77 E-value=2e-19 Score=179.17 Aligned_cols=88 Identities=38% Similarity=0.612 Sum_probs=77.8
Q ss_pred CCCCCCCCCCCCcHHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCC
Q 012778 126 NLTPTGPCRYDSSLGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRP 205 (456)
Q Consensus 126 ~~tp~~~~R~d~SLglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~ 205 (456)
...+.-++|+++|||+||.+|+.++....-..+-|+.||.+|||.|||||||+||||+||++.|.+||.|.|+|+..
T Consensus 13 ~l~lqvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkGf~a--- 89 (388)
T KOG2578|consen 13 DLDLQVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKGFGA--- 89 (388)
T ss_pred hccchhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccchhh---
Confidence 35677899999999999999999998877778999999999999999999999999999999999999999999874
Q ss_pred CchhHHHHHHHHH
Q 012778 206 GEADENASSLQAE 218 (456)
Q Consensus 206 ~~~~~~~~~Lq~E 218 (456)
+..-+..||+|
T Consensus 90 --iPral~eLqeE 100 (388)
T KOG2578|consen 90 --IPRALFELQEE 100 (388)
T ss_pred --hhHHHHHHHHH
Confidence 34445566553
No 4
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=98.96 E-value=1.4e-09 Score=109.50 Aligned_cols=74 Identities=36% Similarity=0.581 Sum_probs=64.0
Q ss_pred CCCCCCCCcHHHHHHHHHHHHhhCCCC-cccHHHHHhhhc----------ceeeehhhhHHhhhhccceecc-----cCC
Q 012778 130 TGPCRYDSSLGLLTKKFINLIKHAEDG-ILDLNKAADTLE----------VQKRRIYDITNVLEGIGLIEKK-----LKN 193 (456)
Q Consensus 130 ~~~~R~d~SLglLTkKFI~Ll~~apdg-~idLn~aA~~L~----------VqKRRIYDItNVLEGIGLIeK~-----sKN 193 (456)
.--.|+++||++||++||.++-.+++- .|.|+.||..|= -.-||||||.|||-++|||+|. .|.
T Consensus 152 k~DnrkekSL~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trkP 231 (388)
T KOG2578|consen 152 KRDNRKEKSLWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRKP 231 (388)
T ss_pred cccchhhhHHHHHHHHHHHheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhcccccccc
Confidence 446789999999999999999888877 899999998873 3569999999999999999995 478
Q ss_pred eEEEeecCCC
Q 012778 194 RIQWKGLDVS 203 (456)
Q Consensus 194 ~i~W~G~d~s 203 (456)
.|+|.|....
T Consensus 232 afrwlG~~~~ 241 (388)
T KOG2578|consen 232 AFRWLGSKPI 241 (388)
T ss_pred hhheeCCCcc
Confidence 8999997643
No 5
>KOG2829 consensus E2F-like protein [Transcription]
Probab=98.69 E-value=2.7e-07 Score=92.66 Aligned_cols=127 Identities=26% Similarity=0.449 Sum_probs=83.0
Q ss_pred HHHH-hhCCCCcccHHHHHhhhc----------------------ceeeehhhhHHhhhhccceecccCCeEEEeecCCC
Q 012778 147 INLI-KHAEDGILDLNKAADTLE----------------------VQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVS 203 (456)
Q Consensus 147 I~Ll-~~apdg~idLn~aA~~L~----------------------VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s 203 (456)
+..| +....|....|++|+.|- -.|||+||..|||.++.+|.|. |..|+|+|....
T Consensus 51 ~kVCeKve~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd-KKEIrW~GLP~~ 129 (326)
T KOG2829|consen 51 MKVCEKVERKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD-KKEIRWIGLPAT 129 (326)
T ss_pred HHHHHHHHhcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc-cceeeeeccCcc
Confidence 3455 345778888999988872 3699999999999999999999 667999999865
Q ss_pred CCCchhHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHhhhhccccccccccc----hhhhccCCCCCCCeEEEee
Q 012778 204 RPGEADENASSLQAEVESL----TIQERRLDEQIRIMQERLRDLSEDENNQKWLFVT----EDDIKSLPCFQNETLIAIK 275 (456)
Q Consensus 204 ~~~~~~~~~~~Lq~El~~L----~~eE~~LDelI~~~~q~Lr~Lted~~n~~~aYVT----~eDI~~l~~f~~qTvIAIK 275 (456)
.. +.+.+|+.|...+ .++-..|.+||... -.++.|.+ .| +.++.+ .++| .| ..|.|.
T Consensus 130 ss----~dv~~le~Er~k~~erI~kK~a~lqEl~~q~-~~fknLV~--RN-~~~e~~~~~P~~~i-~L------PFiiin 194 (326)
T KOG2829|consen 130 SS----QDVSELEEERKKRMERIKKKAAQLQELIEQV-SAFKNLVQ--RN-RHAESQGQPPSENI-HL------PFIIIN 194 (326)
T ss_pred ch----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHH--hh-hhhhhccCCCCccc-cc------ceEEEe
Confidence 33 3345555444333 33444455555432 44555544 12 223333 2222 12 378899
Q ss_pred CCCCCeEEecCCCc
Q 012778 276 APHGTTLEVPDPDE 289 (456)
Q Consensus 276 AP~gT~LEVPdPde 289 (456)
.-+.|.|++-...+
T Consensus 195 T~k~a~IeceiseD 208 (326)
T KOG2829|consen 195 TSKKAVIECEISED 208 (326)
T ss_pred cCCCceEEEEeccc
Confidence 99999999987654
No 6
>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=94.43 E-value=0.047 Score=42.77 Aligned_cols=46 Identities=20% Similarity=0.389 Sum_probs=41.2
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEee
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKG 199 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G 199 (456)
..|.....++|+.+++.|..+|++++-|+..|||++...+.+.|.-
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~a 64 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYRA 64 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEEE
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEEE
Confidence 5678999999999999999999999999999999999877666653
No 7
>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=92.27 E-value=0.25 Score=36.92 Aligned_cols=41 Identities=22% Similarity=0.359 Sum_probs=35.2
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhcc
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIG 185 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIG 185 (456)
++++.+|..+.+. +...++|+.|+|++|-||--++.|+..|
T Consensus 3 ~~il~~L~~~~~~-it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 3 KQILKLLLESKEP-ITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHHHHHHHHTTTS-BEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHcCCC-cCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 4677777666666 9999999999999999999999999998
No 8
>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=91.49 E-value=0.41 Score=36.35 Aligned_cols=54 Identities=22% Similarity=0.245 Sum_probs=42.7
Q ss_pred HHHHHHHHHhhC-----CCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeE
Q 012778 142 LTKKFINLIKHA-----EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRI 195 (456)
Q Consensus 142 LTkKFI~Ll~~a-----pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i 195 (456)
+..-|+.++... ..+.+...++|+.+++.+.-++-+++.|+.-|+|++.....|
T Consensus 5 ia~~l~~l~~~~~~~~~~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~g~i~~~~~~~~ 63 (67)
T cd00092 5 LASFLLNLSLRYGAGDLVQLPLTRQEIADYLGLTRETVSRTLKELEEEGLISRRGRGKY 63 (67)
T ss_pred HHHHHHHHHHHcCCCccccCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCeE
Confidence 444555555432 456789999999999999999999999999999998764444
No 9
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=91.41 E-value=0.28 Score=35.12 Aligned_cols=45 Identities=24% Similarity=0.366 Sum_probs=38.6
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.++.++.+. +.+.+.++|+.|++.++.+|-+++-|+..|+|.+..
T Consensus 4 ~il~~l~~~--~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 4 QILELLAQQ--GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 466666553 459999999999999999999999999999999764
No 10
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=91.21 E-value=1.1 Score=36.18 Aligned_cols=47 Identities=21% Similarity=0.321 Sum_probs=39.7
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.+.++++.+.+ +.+.+.++|+.+++.+.-+|-+++.|+..|+|++..
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~ 54 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDG 54 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecC
Confidence 34566665543 479999999999999999999999999999999864
No 11
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=89.61 E-value=0.54 Score=37.66 Aligned_cols=55 Identities=20% Similarity=0.306 Sum_probs=46.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEe
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWK 198 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~ 198 (456)
.+.+.+|+.+.+..+.+.++|+.||+.|+-+.-++.-|+.-|+|++.+-+-=.|.
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~ 63 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWK 63 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceE
Confidence 5788888876553599999999999999999999999999999999865433563
No 12
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=89.30 E-value=1.4 Score=43.72 Aligned_cols=52 Identities=19% Similarity=0.374 Sum_probs=41.0
Q ss_pred HHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeec
Q 012778 146 FINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGL 200 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~ 200 (456)
++.|+. -|...-.++|+..||.+=|+|||++.||+=|+|+....+--+++-.
T Consensus 22 Y~aLl~---~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av 73 (247)
T COG1378 22 YLALLC---LGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAV 73 (247)
T ss_pred HHHHHH---hCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeC
Confidence 444443 3567778999999999999999999999999999986555555543
No 13
>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=88.27 E-value=0.46 Score=35.70 Aligned_cols=45 Identities=18% Similarity=0.337 Sum_probs=36.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
+.++++..++.+ +.+.++|+.+++.|=-+|-+.+.|+..|+|+|.
T Consensus 7 ~iL~~l~~~~~~-~t~~eia~~~gl~~stv~r~L~tL~~~g~v~~d 51 (52)
T PF09339_consen 7 RILEALAESGGP-LTLSEIARALGLPKSTVHRLLQTLVEEGYVERD 51 (52)
T ss_dssp HHHHCHHCTBSC-EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEC
T ss_pred HHHHHHHcCCCC-CCHHHHHHHHCcCHHHHHHHHHHHHHCcCeecC
Confidence 345555555444 799999999999999999999999999999874
No 14
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=86.69 E-value=3.3 Score=37.88 Aligned_cols=86 Identities=21% Similarity=0.307 Sum_probs=57.3
Q ss_pred HHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCCCchh--HHHHHHHHHHHHHH
Q 012778 146 FINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRPGEAD--ENASSLQAEVESLT 223 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~~~~~--~~~~~Lq~El~~L~ 223 (456)
|..|++ +.+.++.+++|+.|+..|=.+|=.+|=|...|||.|.--+. .|.. +.-+. -...+++..
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~---~~Gg---y~yiY~~i~~ee~k~~----- 99 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL---KGGG---YYYLYKPIDPEEIKKK----- 99 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc---CCCc---eeEEEecCCHHHHHHH-----
Confidence 455554 68889999999999999999999999999999999974442 2221 10000 011223222
Q ss_pred HHHHHHHHHHHHHHHHHHhhhh
Q 012778 224 IQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 224 ~eE~~LDelI~~~~q~Lr~Lte 245 (456)
.++.||++-..+.+.|.++..
T Consensus 100 -i~~~l~~w~~~~~~~i~~~~~ 120 (126)
T COG3355 100 -ILKDLDEWYDKMKQLIEEFEK 120 (126)
T ss_pred -HHHHHHHHHHHHHHHHHHHhc
Confidence 344577777777777766644
No 15
>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=86.53 E-value=0.98 Score=34.01 Aligned_cols=46 Identities=22% Similarity=0.344 Sum_probs=40.2
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
..+.++...++..+.+.++|+.|++.|=.+--+++-||.-|||+|.
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~Glv~r~ 54 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKKGLVERE 54 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 4555667777778999999999999999999999999999999987
No 16
>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=86.27 E-value=1.1 Score=32.89 Aligned_cols=43 Identities=23% Similarity=0.408 Sum_probs=35.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
++.+.++.+. +.+...++|+.+++.+..++.+++-|+.-|+|+
T Consensus 6 ~~Il~~l~~~--~~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLREN--PRITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHC--TTS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHc--CCCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 5677777774 449999999999999999999999999999985
No 17
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=86.18 E-value=0.86 Score=33.09 Aligned_cols=38 Identities=21% Similarity=0.329 Sum_probs=34.5
Q ss_pred CCcccHHHHHhhhcceeeehhhhHHhhhhccceecccC
Q 012778 155 DGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLK 192 (456)
Q Consensus 155 dg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sK 192 (456)
.+.+.++++++.|++.+..++.+++.|+.-|+|++..+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 56689999999999999999999999999999997653
No 18
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=82.94 E-value=1.7 Score=33.17 Aligned_cols=38 Identities=32% Similarity=0.470 Sum_probs=31.9
Q ss_pred CCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 153 AEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 153 apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
..++.+.+.++|+.|++.+--+..+++-|+..|||+|.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 37889999999999999999999999999999999887
No 19
>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=82.13 E-value=2 Score=35.08 Aligned_cols=49 Identities=20% Similarity=0.325 Sum_probs=39.2
Q ss_pred HHHHHHHHHhhCCCC-cccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 142 LTKKFINLIKHAEDG-ILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 142 LTkKFI~Ll~~apdg-~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
.+-+++.+|...+++ .+.+.++|+.+++..+.+..|++-|+--|||+..
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 344566666555554 4999999999999999999999999999999854
No 20
>PF13730 HTH_36: Helix-turn-helix domain
Probab=80.86 E-value=1.9 Score=32.24 Aligned_cols=29 Identities=31% Similarity=0.386 Sum_probs=27.9
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhccce
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLI 187 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLI 187 (456)
....+|+.+++.+|.|+-.++.||-.|+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 79999999999999999999999999986
No 21
>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=80.74 E-value=2.1 Score=37.42 Aligned_cols=46 Identities=11% Similarity=0.181 Sum_probs=40.2
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
+.+.++....++.+.+.++|+.|++.+..++.|++.|+.-|+|+..
T Consensus 13 ~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 13 LVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 4555665666788999999999999999999999999999999864
No 22
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=80.52 E-value=1.7 Score=32.60 Aligned_cols=43 Identities=21% Similarity=0.385 Sum_probs=35.5
Q ss_pred HHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 147 INLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 147 I~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
+.++.+.++ +.+.++|+.+++.+--+-.+++-||.-|+|+|..
T Consensus 9 L~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 9 LRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 344444444 9999999999999999999999999999999873
No 23
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=80.44 E-value=18 Score=34.02 Aligned_cols=44 Identities=23% Similarity=0.215 Sum_probs=38.6
Q ss_pred CCCCcccHHHHHhhh--cceeeehhhhHHhhhhccceecccCCeEE
Q 012778 153 AEDGILDLNKAADTL--EVQKRRIYDITNVLEGIGLIEKKLKNRIQ 196 (456)
Q Consensus 153 apdg~idLn~aA~~L--~VqKRRIYDItNVLEGIGLIeK~sKN~i~ 196 (456)
-.++.-|..++|++| +|.--.+=+.++.|+-+|||+|...+.|.
T Consensus 35 l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~ 80 (171)
T PF14394_consen 35 LMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYV 80 (171)
T ss_pred cCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEE
Confidence 356667999999999 99999999999999999999999774443
No 24
>PF09079 Cdc6_C: CDC6, C terminal ; InterPro: IPR015163 The C-terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity []. ; PDB: 2QBY_A 2V1U_A 1W5T_A 1W5S_B 1FNN_B.
Probab=79.90 E-value=0.86 Score=37.24 Aligned_cols=29 Identities=38% Similarity=0.529 Sum_probs=22.9
Q ss_pred HHHhhhcc---eeeehhhhHHhhhhccceecc
Q 012778 162 KAADTLEV---QKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 162 ~aA~~L~V---qKRRIYDItNVLEGIGLIeK~ 190 (456)
.+|+.+++ ..|||||+++-|+-+|||+..
T Consensus 27 ~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~ 58 (85)
T PF09079_consen 27 ELCESLGVDPLSYRRFSDYLSELEMLGLIESE 58 (85)
T ss_dssp HHHHHTTS----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEE
Confidence 34555554 789999999999999999866
No 25
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=79.40 E-value=4.2 Score=30.12 Aligned_cols=47 Identities=19% Similarity=0.354 Sum_probs=38.4
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCC
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
.+++..+...+ +.+.++++.|++.+.-++-+++.|+.-|+|.+....
T Consensus 10 ~~il~~l~~~~---~~~~ei~~~~~i~~~~i~~~l~~L~~~g~i~~~~~~ 56 (78)
T cd00090 10 LRILRLLLEGP---LTVSELAERLGLSQSTVSRHLKKLEEAGLVESRREG 56 (78)
T ss_pred HHHHHHHHHCC---cCHHHHHHHHCcCHhHHHHHHHHHHHCCCeEEEEec
Confidence 34555555433 999999999999999999999999999999976443
No 26
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=78.67 E-value=3.2 Score=30.36 Aligned_cols=41 Identities=20% Similarity=0.284 Sum_probs=35.8
Q ss_pred CCCCcc-cHHHHHhhhcceeeehhhhHHhhhhccceecccCC
Q 012778 153 AEDGIL-DLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 153 apdg~i-dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
.++..+ ...++|+.++|++=-+...++.|+.-|+|.+....
T Consensus 15 ~~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 15 RPGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 356667 89999999999999999999999999999876543
No 27
>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=78.03 E-value=1.3 Score=35.67 Aligned_cols=22 Identities=41% Similarity=0.685 Sum_probs=20.0
Q ss_pred ceeeehhhhHHhhhhccceecc
Q 012778 169 VQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 169 VqKRRIYDItNVLEGIGLIeK~ 190 (456)
...|||+||+|-||..|||+-.
T Consensus 44 l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEEE
Confidence 4789999999999999999865
No 28
>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=76.31 E-value=6.5 Score=30.50 Aligned_cols=50 Identities=20% Similarity=0.258 Sum_probs=38.6
Q ss_pred HHHHHHHhh---CCCCcc-cHHHHHhhhcceeeehhhhHHhhhhccceecccCC
Q 012778 144 KKFINLIKH---AEDGIL-DLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 144 kKFI~Ll~~---apdg~i-dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
..+.+.+.. .++..+ ...++|+.++|++.=+...++.|+.-|+|++..+.
T Consensus 7 ~~l~~~I~~g~~~~g~~lps~~~la~~~~vsr~tvr~al~~L~~~g~i~~~~~~ 60 (64)
T PF00392_consen 7 DQLRQAILSGRLPPGDRLPSERELAERYGVSRTTVREALRRLEAEGLIERRPGR 60 (64)
T ss_dssp HHHHHHHHTTSS-TTSBE--HHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTT
T ss_pred HHHHHHHHcCCCCCCCEeCCHHHHHHHhccCCcHHHHHHHHHHHCCcEEEECCc
Confidence 344454433 366688 99999999999999999999999999999987554
No 29
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=76.01 E-value=8.7 Score=33.06 Aligned_cols=55 Identities=22% Similarity=0.280 Sum_probs=31.8
Q ss_pred cCCeEEEeecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 191 LKNRIQWKGLDVSRPGEADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 191 sKN~i~W~G~d~s~~~~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
...-+.|+|.+..-....++-...|+..++.|...-..|++.|..+++++..+..
T Consensus 68 ~~~v~v~iG~~~~ve~~~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~ 122 (129)
T cd00890 68 DDKVLVDLGTGVYVEKSLEEAIEFLKKRLETLEKQIEKLEKQLEKLQDQITELQE 122 (129)
T ss_pred CCEEEEEecCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556888996643222334445555556666666666666666666666655543
No 30
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=74.43 E-value=3.2 Score=29.39 Aligned_cols=38 Identities=26% Similarity=0.326 Sum_probs=33.3
Q ss_pred cccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeE
Q 012778 157 ILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRI 195 (456)
Q Consensus 157 ~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i 195 (456)
.+...++|+.+++.+..++.+++.|+.-|+|++.. +.|
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~-~~~ 45 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG-GRI 45 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC-CEE
Confidence 36788999999999999999999999999999864 444
No 31
>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=73.46 E-value=3.1 Score=32.71 Aligned_cols=53 Identities=11% Similarity=0.094 Sum_probs=37.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccce-ecccCCeEEEeec
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLI-EKKLKNRIQWKGL 200 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLI-eK~sKN~i~W~G~ 200 (456)
+.+.++.+ +.+..+++|+.|+|+++-|+--++.|+.-|++ ....+..+.+.+.
T Consensus 4 ~il~~L~~---~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~~ 57 (69)
T TIGR00122 4 RLLALLAD---NPFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTVGKGYRLPPPI 57 (69)
T ss_pred HHHHHHHc---CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCCceEecCcc
Confidence 45666553 34669999999999999999999999888883 3334443333333
No 32
>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=73.41 E-value=4 Score=34.47 Aligned_cols=50 Identities=22% Similarity=0.362 Sum_probs=40.7
Q ss_pred cHHHHHHHHHHHHhhC--CCCcccHHHHHhhhcceeeehhhhHHhhhhccce
Q 012778 138 SLGLLTKKFINLIKHA--EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLI 187 (456)
Q Consensus 138 SLglLTkKFI~Ll~~a--pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLI 187 (456)
+|..+.++.+++|++. .+.=+.+++++++|++....|.+++.-|..-|+|
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 7899999999999872 2223999999999999999999999999999987
No 33
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=73.41 E-value=12 Score=37.05 Aligned_cols=54 Identities=9% Similarity=0.202 Sum_probs=42.0
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEee
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKG 199 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G 199 (456)
..++++.... ..+.|.++|+.|++.|=.+|-+++-|+..|++++.....--+.|
T Consensus 29 ~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG 82 (271)
T PRK10163 29 AILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIG 82 (271)
T ss_pred HHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEec
Confidence 4555664433 45899999999999999999999999999999986544333455
No 34
>PHA02943 hypothetical protein; Provisional
Probab=70.91 E-value=16 Score=35.00 Aligned_cols=48 Identities=23% Similarity=0.243 Sum_probs=42.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCe
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNR 194 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~ 194 (456)
..+++++ ..|.....++|+.||++--....++-|||.-|.|++.....
T Consensus 14 ~eILE~L---k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~ 61 (165)
T PHA02943 14 IKTLRLL---ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGR 61 (165)
T ss_pred HHHHHHH---hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecc
Confidence 4577887 67888999999999999999999999999999999976543
No 35
>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=69.47 E-value=4.8 Score=29.70 Aligned_cols=42 Identities=24% Similarity=0.472 Sum_probs=35.1
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceec
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK 189 (456)
+.+.++. ++...+.++|+.|++.+=-++==+++|+..|+|+|
T Consensus 6 ~Il~~L~---~~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 6 RILKLLS---EGPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHHT---TSSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHH---hCCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 3444443 37899999999999999999999999999999986
No 36
>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=69.37 E-value=6.6 Score=30.39 Aligned_cols=45 Identities=27% Similarity=0.440 Sum_probs=39.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
++.++++++ .+.+.+.++|+.|+|+..-|.==+|.|+.-|+|.|.
T Consensus 3 ~~Il~~l~~--~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 3 QQILELLKE--KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHHH--cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 356677765 588999999999999999888888999999999987
No 37
>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=68.89 E-value=6.4 Score=32.01 Aligned_cols=49 Identities=20% Similarity=0.205 Sum_probs=39.7
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccC
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLK 192 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sK 192 (456)
.++++.+-.+...=+.-.+++..+++..|-|+=++++|+..|||.|+.-
T Consensus 5 ~~~Le~I~rsR~~Gi~q~~L~~~~~~D~r~i~~~~k~L~~~gLI~k~~~ 53 (75)
T PF04182_consen 5 YCLLERIARSRYNGITQSDLSKLLGIDPRSIFYRLKKLEKKGLIVKQSV 53 (75)
T ss_pred HHHHHHHHhcCCCCEehhHHHHHhCCCchHHHHHHHHHHHCCCEEEEEe
Confidence 3567777655444456667889999999999999999999999999865
No 38
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=65.58 E-value=40 Score=31.86 Aligned_cols=45 Identities=20% Similarity=0.281 Sum_probs=38.5
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
++.+.++... +.+...++|+.|+|.+=-+.-.++.||.-|||++.
T Consensus 4 ~~IL~~L~~~--~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQ--GQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 4566667654 34999999999999999999999999999999976
No 39
>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=65.41 E-value=55 Score=33.23 Aligned_cols=40 Identities=20% Similarity=0.207 Sum_probs=35.9
Q ss_pred CCCcccHHHHHhhhc--ceeeehhhhHHhhhhccceecccCC
Q 012778 154 EDGILDLNKAADTLE--VQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 154 pdg~idLn~aA~~L~--VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
.++.-|..++|++|+ |.--.+=|.++.|+-+|||+|.+.+
T Consensus 134 ~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g 175 (271)
T TIGR02147 134 MPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDG 175 (271)
T ss_pred CCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCC
Confidence 567778999999999 8899999999999999999998655
No 40
>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=65.37 E-value=9.5 Score=33.02 Aligned_cols=37 Identities=19% Similarity=0.390 Sum_probs=33.9
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
..+.+...++|+.+++.++.+++|+..|+.-|+|...
T Consensus 22 ~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 22 DEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 3458999999999999999999999999999999864
No 41
>cd00584 Prefoldin_alpha Prefoldin alpha subunit; Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=65.35 E-value=17 Score=31.82 Aligned_cols=54 Identities=17% Similarity=0.249 Sum_probs=32.6
Q ss_pred CCeEEEeecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 192 KNRIQWKGLDVSRPGEADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 192 KN~i~W~G~d~s~~~~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
+.-+.|+|.+..-...+.+-+.-++..++.|...-..|.+.|..+++++..+.+
T Consensus 69 ~~v~v~iG~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~ 122 (129)
T cd00584 69 DKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEA 122 (129)
T ss_pred CEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345788887654322344445566666666666666666666666666665543
No 42
>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=63.87 E-value=19 Score=29.94 Aligned_cols=27 Identities=19% Similarity=0.263 Sum_probs=21.6
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
+.+.++|+.+||+.+-|.-. |..|+|.
T Consensus 2 ~~i~e~A~~~gvs~~tLr~y----e~~Gli~ 28 (91)
T cd04766 2 YVISVAAELSGMHPQTLRLY----ERLGLLS 28 (91)
T ss_pred cCHHHHHHHHCcCHHHHHHH----HHCCCcC
Confidence 46789999999999877765 5568886
No 43
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=63.75 E-value=22 Score=31.77 Aligned_cols=51 Identities=24% Similarity=0.284 Sum_probs=27.2
Q ss_pred CeEEEeecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012778 193 NRIQWKGLDVSRPGEADENASSLQAEVESLTIQERRLDEQIRIMQERLRDL 243 (456)
Q Consensus 193 N~i~W~G~d~s~~~~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~L 243 (456)
.-+.|.|.+..-...+++-+..|+..++.|...-..|.+.|..+++++..+
T Consensus 77 kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~ 127 (140)
T PRK03947 77 KVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQL 127 (140)
T ss_pred eEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346688866432223344455555555555555555555555555555444
No 44
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=63.63 E-value=3.8 Score=32.57 Aligned_cols=41 Identities=20% Similarity=0.212 Sum_probs=34.4
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCe
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNR 194 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~ 194 (456)
..+.+++.++|..|+++..-+=.++.+|+..|.|+|...+.
T Consensus 11 ~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~ 51 (69)
T PF09012_consen 11 ERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSS 51 (69)
T ss_dssp HS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE-
T ss_pred HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCC
Confidence 47889999999999999999999999999999999986554
No 45
>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=63.57 E-value=5.9 Score=30.53 Aligned_cols=45 Identities=24% Similarity=0.416 Sum_probs=37.8
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
+.+.++ ..++.+.+.++|+.|++.+=-+|-=+++|+..|||+...
T Consensus 14 ~Il~~L--~~~~~~t~~ela~~l~~~~~t~s~hL~~L~~aGli~~~~ 58 (61)
T PF12840_consen 14 RILRLL--ASNGPMTVSELAEELGISQSTVSYHLKKLEEAGLIEVER 58 (61)
T ss_dssp HHHHHH--HHCSTBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHH--hcCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEec
Confidence 455555 357789999999999999999999999999999999763
No 46
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=62.99 E-value=28 Score=34.14 Aligned_cols=50 Identities=10% Similarity=0.260 Sum_probs=39.6
Q ss_pred HHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc-CCeEE
Q 012778 146 FINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL-KNRIQ 196 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s-KN~i~ 196 (456)
.++++... ++.+.+.++|+.|++.|=-+|-+++-|+..|+|++.. .+.|.
T Consensus 16 iL~~l~~~-~~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~ 66 (263)
T PRK09834 16 VLRALNRL-DGGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFR 66 (263)
T ss_pred HHHHHHhc-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence 44555443 3349999999999999999999999999999999863 34443
No 47
>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=62.19 E-value=14 Score=27.39 Aligned_cols=38 Identities=24% Similarity=0.348 Sum_probs=32.9
Q ss_pred CCCcc-cHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 154 EDGIL-DLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 154 pdg~i-dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.+..+ ...++|+.+++.+=.+...++-|+.-|+|++..
T Consensus 21 ~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 21 PGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 34444 499999999999999999999999999998764
No 48
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=61.87 E-value=70 Score=28.12 Aligned_cols=35 Identities=17% Similarity=0.244 Sum_probs=32.4
Q ss_pred cccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 157 ILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 157 ~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.+...++|+.+++.+--+--+++.||.-|+|+|..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 35789999999999999999999999999999973
No 49
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=61.85 E-value=9.3 Score=31.95 Aligned_cols=47 Identities=15% Similarity=0.280 Sum_probs=40.9
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 142 LTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 142 LTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
+-++++.+|++. +.+..+++|+.|++.+.-++..++-|+.-|+|.+.
T Consensus 4 ~D~~il~~L~~~--~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKD--ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHh--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeece
Confidence 346788888764 56899999999999999999999999999999953
No 50
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=60.50 E-value=6 Score=41.39 Aligned_cols=30 Identities=30% Similarity=0.571 Sum_probs=27.4
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
-+..+++.+++++||+|||+|-|+++|+|.
T Consensus 303 ~y~~~~~~~~~~~~~~~~ii~~L~~lgiv~ 332 (366)
T COG1474 303 VYESLCERLRTSQRRFSDIISELEGLGIVS 332 (366)
T ss_pred HHHHHHhhhCchHHHHHHHHHHHHhcCeEE
Confidence 466788888899999999999999999998
No 51
>PRK10870 transcriptional repressor MprA; Provisional
Probab=60.26 E-value=50 Score=30.83 Aligned_cols=41 Identities=20% Similarity=0.258 Sum_probs=36.4
Q ss_pred hhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 151 KHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 151 ~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
...+++.+...++|+.|++.+=-+-=+++-||.-|||+|..
T Consensus 65 ~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 65 ESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred hcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 34457789999999999999999999999999999999973
No 52
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=60.07 E-value=17 Score=34.18 Aligned_cols=56 Identities=13% Similarity=0.100 Sum_probs=43.3
Q ss_pred cHHH-HHHHHHHHHhh---CCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCC
Q 012778 138 SLGL-LTKKFINLIKH---AEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 138 SLgl-LTkKFI~Ll~~---apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
++.. +..++.+.+.. .|+..+.-.++|+.|||+|=-+=+.+..|+..|||+.....
T Consensus 11 ~~~e~v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~ 70 (221)
T PRK11414 11 SLTLQVENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQ 70 (221)
T ss_pred CHHHHHHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCC
Confidence 3443 33444444432 48888999999999999999999999999999999976544
No 53
>TIGR02231 conserved hypothetical protein. This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown.
Probab=59.90 E-value=60 Score=35.12 Aligned_cols=98 Identities=16% Similarity=0.239 Sum_probs=57.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccchhhhccCCCCCCCeEEEeeCCCCC--eEEecCC
Q 012778 210 ENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSEDENNQKWLFVTEDDIKSLPCFQNETLIAIKAPHGT--TLEVPDP 287 (456)
Q Consensus 210 ~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP~gT--~LEVPdP 287 (456)
.++..+..++.+|..+.++|++.|..++++|..+...... ......+.|.++.+. .|+|-.-
T Consensus 138 ~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~~~~----------------~~~~v~v~l~~~~~g~~~l~lsY~ 201 (525)
T TIGR02231 138 SEIERLLTEDREAERRIRELEKQLSELQNELNALLTGKSQ----------------RSHTVLVRLEAPEDAEAELNLTYQ 201 (525)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccCCcc----------------ceEEEEEEEeccCCceEEEEEEEE
Confidence 3455666666777777777777777777777776553111 111345566665544 3444332
Q ss_pred CcccCCCCCceEEEEecCCCceEEE----EecCcchhhhhc
Q 012778 288 DEAVDYPQRRYRIVLRSTMGPIDVY----LVSQFEEKFEEI 324 (456)
Q Consensus 288 de~~~~~qr~YqI~LkS~~GPIdVy----L~~~~~~~~e~~ 324 (456)
-.+.. =+-.|.|.|.+..+++++. +....++.+.+.
T Consensus 202 v~~a~-W~P~Ydlrl~~~~~~~~l~~~A~V~Q~TGeDW~~V 241 (525)
T TIGR02231 202 VGNAS-WTPSYDARLDTGAPTVELTYLAEIRQSTGEDWSDI 241 (525)
T ss_pred eCCCc-EeeeeEEEecCCCceEEEEEEEEEEeCCCCCCCCC
Confidence 11111 1357999999999988764 345556655544
No 54
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=59.79 E-value=16 Score=29.00 Aligned_cols=45 Identities=22% Similarity=0.330 Sum_probs=37.4
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
.+.+.++... +.+...++|+.+++.+.-|+-+++-|+.-|+|++.
T Consensus 13 ~~il~~l~~~--~~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 13 FLVLRILYEE--GPLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHc--CCcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 3444555443 35889999999999999999999999999999976
No 55
>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=59.72 E-value=18 Score=28.54 Aligned_cols=42 Identities=21% Similarity=0.303 Sum_probs=36.9
Q ss_pred HHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 149 LIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 149 Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.+.+ .++.+...++|+.|+|.+=-..+.++-|+.-|||++..
T Consensus 15 ~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 15 ELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 3444 88999999999999999999999999999999999874
No 56
>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=59.67 E-value=14 Score=31.27 Aligned_cols=46 Identities=11% Similarity=0.140 Sum_probs=37.5
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecC
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLD 201 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d 201 (456)
....+.-.++|+.+++.|--+.-+++.||--|+|++..+ ..|.|..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~--~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM--MGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC--CceeecC
Confidence 455688899999999999999999999999999997643 3344543
No 57
>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=59.29 E-value=17 Score=31.58 Aligned_cols=37 Identities=24% Similarity=0.372 Sum_probs=27.2
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEEee
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQWKG 199 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W~G 199 (456)
.+.++|+.+||..|-| --.|-.|||. +...|.|+|-.
T Consensus 2 ~I~eva~~~gvs~~tL----RyYe~~GLl~p~~r~~~gyR~Y~ 40 (123)
T cd04770 2 KIGELAKAAGVSPDTI----RYYERIGLLPPPQRSENGYRLYG 40 (123)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCCCCCCCCccCC
Confidence 5788999999988855 3467888886 44567777754
No 58
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=59.04 E-value=45 Score=32.71 Aligned_cols=53 Identities=21% Similarity=0.204 Sum_probs=42.8
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEe
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWK 198 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~ 198 (456)
++.++++++ .+.+.+.++|+.|+|+.+.|.--++.|+.-|+|.+....-+.+.
T Consensus 7 ~~Il~~l~~--~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~ 59 (240)
T PRK10411 7 QAIVDLLLN--HTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHGRAKYIH 59 (240)
T ss_pred HHHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCeEEEec
Confidence 345667764 56899999999999999999999999999999988644444444
No 59
>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=58.88 E-value=27 Score=29.80 Aligned_cols=37 Identities=16% Similarity=0.292 Sum_probs=25.0
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhcccee-cccCCeEEEe
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLIE-KKLKNRIQWK 198 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLIe-K~sKN~i~W~ 198 (456)
+.+.++|+.+||+.+-| -..|-.|||. +...|.++.-
T Consensus 2 ~~i~eva~~~gvs~~tL----R~ye~~Gll~~~r~~~g~R~Y 39 (102)
T cd04775 2 YTIGQMSRKFGVSRSTL----LYYESIGLIPSARSEANYRLY 39 (102)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCCCCCCCeee
Confidence 46789999999998876 4456678883 3334555543
No 60
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=58.68 E-value=8.6 Score=31.39 Aligned_cols=33 Identities=24% Similarity=0.292 Sum_probs=30.5
Q ss_pred HHHHHhhhcceeeehhhhHHhhhhccceecccC
Q 012778 160 LNKAADTLEVQKRRIYDITNVLEGIGLIEKKLK 192 (456)
Q Consensus 160 Ln~aA~~L~VqKRRIYDItNVLEGIGLIeK~sK 192 (456)
+.++|+.|+|.+=-++-++..|+.-|||.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 578999999999999999999999999999853
No 61
>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=58.47 E-value=7.9 Score=33.12 Aligned_cols=37 Identities=19% Similarity=0.306 Sum_probs=34.1
Q ss_pred CCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 155 DGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 155 dg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.+.+.+.++|+.+++.+--++=+++-||.-|||+|..
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence 4568899999999999999999999999999999973
No 62
>TIGR00293 prefoldin, archaeal alpha subunit/eukaryotic subunit 5. This model finds a set of small proteins from the Archaea and from Aquifex aeolicus that may represent two orthologous groups. The proteins are predicted to be mostly coiled coil, and may hit large numbers of proteins that contain coiled coil regions.
Probab=57.47 E-value=35 Score=29.80 Aligned_cols=54 Identities=19% Similarity=0.234 Sum_probs=37.6
Q ss_pred CCeEEEeecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 192 KNRIQWKGLDVSRPGEADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 192 KN~i~W~G~d~s~~~~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
.+-+.|+|.+..-....++-+.-|+..++.|...-+.|.+.|.++++++..+.+
T Consensus 68 ~~v~v~iG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~l~~~~~~i~~ 121 (126)
T TIGR00293 68 DKVLVSIGSGYYVEKDAEEAIEFLKKRIEELEKAIEKLQEALAELASRAQQLEQ 121 (126)
T ss_pred CEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456789987754333455556777777788877777788878877777776644
No 63
>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=55.83 E-value=31 Score=30.32 Aligned_cols=37 Identities=14% Similarity=0.161 Sum_probs=27.0
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEEee
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQWKG 199 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W~G 199 (456)
.+.++|+.+||..|-| --.|.+|||. +...|.|++-+
T Consensus 2 ~I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~ 40 (126)
T cd04783 2 TIGELAKAAGVNVETI----RYYQRRGLLPEPPRPEGGYRRYP 40 (126)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCCeecC
Confidence 5778999999988754 3448899997 44566777754
No 64
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=55.82 E-value=21 Score=34.61 Aligned_cols=37 Identities=22% Similarity=0.240 Sum_probs=34.8
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
....+.|.++++.||++|=++-=.+-+|++.||++|+
T Consensus 38 s~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~ 74 (177)
T COG1510 38 SRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKV 74 (177)
T ss_pred cCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhh
Confidence 3677899999999999999999999999999999987
No 65
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=55.37 E-value=1e+02 Score=29.07 Aligned_cols=54 Identities=31% Similarity=0.474 Sum_probs=39.0
Q ss_pred CCCCcHHHHHHHHHHHHhh-CCCCcc---------------cHHHHHhhhcc-eeeehhhhHHhhhhccceec
Q 012778 134 RYDSSLGLLTKKFINLIKH-AEDGIL---------------DLNKAADTLEV-QKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 134 R~d~SLglLTkKFI~Ll~~-apdg~i---------------dLn~aA~~L~V-qKRRIYDItNVLEGIGLIeK 189 (456)
.++-+...|.++|..+.+. .||... -||+|-+.|.= .+|..|++ -|.|+.+...
T Consensus 12 ~~~~d~~~L~~~yr~l~~~~HPDk~~~~~~~~~~~a~~~s~~iN~AY~~L~dp~~Ra~Yll--~l~g~~~~~~ 82 (171)
T PRK05014 12 RYDIDTQLLASRYQELQRQFHPDKFANASERERLLAVQQAATINDAYQTLKHPLKRAEYLL--SLHGFDLAHE 82 (171)
T ss_pred CCCCCHHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHHHHHHHHHHHHCChhHHHHHHH--HhcCCccccc
Confidence 4567788999999998754 566532 37788888876 78999985 5567766544
No 66
>PRK09954 putative kinase; Provisional
Probab=55.27 E-value=11 Score=37.99 Aligned_cols=47 Identities=21% Similarity=0.340 Sum_probs=40.6
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 142 LTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 142 LTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
.-++.++++++. +.+...++|+.|+|.|..++..++-|+.-|+|++.
T Consensus 4 ~~~~il~~l~~~--~~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~ 50 (362)
T PRK09954 4 REKEILAILRRN--PLIQQNEIADILQISRSRVAAHIMDLMRKGRIKGK 50 (362)
T ss_pred HHHHHHHHHHHC--CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCc
Confidence 345788888764 48999999999999999999999999999999754
No 67
>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=54.92 E-value=31 Score=29.52 Aligned_cols=38 Identities=16% Similarity=0.288 Sum_probs=24.3
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhcccee-cccCCeEEEee
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLIE-KKLKNRIQWKG 199 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLIe-K~sKN~i~W~G 199 (456)
+.+.++|+.+||..+-|- -.|-.|||. ....|.+++-.
T Consensus 2 ~~i~eva~~~gvs~~tlR----~ye~~Gll~~~r~~~g~R~Y~ 40 (102)
T cd04789 2 YTISELAEKAGISRSTLL----YYEKLGLITGTRNANGYRLYP 40 (102)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCcCCCCCeeCC
Confidence 568899999999887442 345567775 23345566543
No 68
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=54.80 E-value=13 Score=28.86 Aligned_cols=36 Identities=25% Similarity=0.413 Sum_probs=28.2
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhh
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLE 182 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLE 182 (456)
+.+++|-. .+.+.+.++|+.|+++.|-|.--++-|.
T Consensus 9 ~Ll~~L~~--~~~~~~~ela~~l~~S~rti~~~i~~L~ 44 (59)
T PF08280_consen 9 KLLELLLK--NKWITLKELAKKLNISERTIKNDINELN 44 (59)
T ss_dssp HHHHHHHH--HTSBBHHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHHHHHc--CCCCcHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46676655 6778999999999999999877777665
No 69
>PRK06474 hypothetical protein; Provisional
Probab=54.74 E-value=97 Score=29.24 Aligned_cols=47 Identities=15% Similarity=0.282 Sum_probs=38.8
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhh-cceeeehhhhHHhhhhccceeccc
Q 012778 144 KKFINLIKHAEDGILDLNKAADTL-EVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L-~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.+.+++|...+.. +...++++.| ++.+=-+|=.+++|+-.|||++..
T Consensus 14 ~~Il~~L~~~~~~-~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 14 MKICQVLMRNKEG-LTPLELVKILKDVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHHhCCCC-CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence 3566777665443 9999999999 789999999999999999999754
No 70
>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=54.74 E-value=8.3 Score=38.19 Aligned_cols=37 Identities=19% Similarity=0.171 Sum_probs=34.5
Q ss_pred CCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 155 DGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 155 dg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
++...+.++|+++++..|.++-+.+.|.++||+++..
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~ 57 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED 57 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC
Confidence 4688999999999999999999999999999999864
No 71
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=54.27 E-value=56 Score=32.14 Aligned_cols=53 Identities=23% Similarity=0.441 Sum_probs=43.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCC-eEEEee
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKN-RIQWKG 199 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN-~i~W~G 199 (456)
..++++...+.+ +.+.++|+++++.|=-.|=+.+.|+-.|++++...+ +| +.|
T Consensus 8 ~iL~~l~~~~~~-l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y-~Lg 61 (246)
T COG1414 8 AILDLLAEGPGG-LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRY-RLG 61 (246)
T ss_pred HHHHHHHhCCCC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcE-eeh
Confidence 466777664444 899999999999999999999999999999999865 44 344
No 72
>PF13518 HTH_28: Helix-turn-helix domain
Probab=54.04 E-value=9.9 Score=27.57 Aligned_cols=38 Identities=13% Similarity=0.331 Sum_probs=30.6
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccc
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGL 186 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGL 186 (456)
+.|.++. +|. .+.++|..++|.++.||.+++-++.-|+
T Consensus 4 ~iv~~~~---~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 4 QIVELYL---EGE-SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHHH---cCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 3455554 244 9999999999999999999999988664
No 73
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=54.03 E-value=88 Score=27.43 Aligned_cols=31 Identities=10% Similarity=0.034 Sum_probs=26.4
Q ss_pred CcccHHHHHhhhcceeeehhhhHHhhhhccc
Q 012778 156 GILDLNKAADTLEVQKRRIYDITNVLEGIGL 186 (456)
Q Consensus 156 g~idLn~aA~~L~VqKRRIYDItNVLEGIGL 186 (456)
+-..+.++|..|+|+.--||-+.+-+..-|+
T Consensus 28 ~g~sv~evA~e~gIs~~tl~~W~r~y~~~~~ 58 (121)
T PRK09413 28 PGMTVSLVARQHGVAASQLFLWRKQYQEGSL 58 (121)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHHhhccc
Confidence 3468999999999999999999999875444
No 74
>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=53.96 E-value=30 Score=32.55 Aligned_cols=39 Identities=18% Similarity=0.221 Sum_probs=35.0
Q ss_pred cccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeE
Q 012778 157 ILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRI 195 (456)
Q Consensus 157 ~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i 195 (456)
.+...++|+.|+++++-++-.+..|+--++|.|...+.|
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y 113 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAY 113 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeE
Confidence 568889999999999999999999999999999865544
No 75
>PF12329 TMF_DNA_bd: TATA element modulatory factor 1 DNA binding; InterPro: IPR022092 This is the middle region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes that contains at its N-terminal section a number of leucine zippers that could potentially form coiled coil structures. The whole proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant [] cells.
Probab=53.93 E-value=33 Score=28.39 Aligned_cols=37 Identities=27% Similarity=0.521 Sum_probs=31.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 209 DENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 209 ~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
+..|..|..|.+.|...|..+...|+.++.++.++-.
T Consensus 11 De~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~ 47 (74)
T PF12329_consen 11 DEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEK 47 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 5678899999999999999999999998888877643
No 76
>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=53.71 E-value=12 Score=30.02 Aligned_cols=46 Identities=17% Similarity=0.201 Sum_probs=35.1
Q ss_pred HHHHHhhCCCCcccHHHHHhhhcce-eeehhhhHHhhhhccceeccc
Q 012778 146 FINLIKHAEDGILDLNKAADTLEVQ-KRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~Vq-KRRIYDItNVLEGIGLIeK~s 191 (456)
||.-+....+-.-.+.++|+.||+. ..-+++.+..||.-|+|++..
T Consensus 14 ~I~~~~~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~kG~I~r~~ 60 (65)
T PF01726_consen 14 FIREYIEENGYPPTVREIAEALGLKSTSTVQRHLKALERKGYIRRDP 60 (65)
T ss_dssp HHHHHHHHHSS---HHHHHHHHTSSSHHHHHHHHHHHHHTTSEEEGC
T ss_pred HHHHHHHHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCcCccCCC
Confidence 4433334456677999999999996 999999999999999999874
No 77
>PRK11569 transcriptional repressor IclR; Provisional
Probab=53.67 E-value=52 Score=32.48 Aligned_cols=46 Identities=11% Similarity=0.253 Sum_probs=38.3
Q ss_pred HHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccC
Q 012778 146 FINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLK 192 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sK 192 (456)
.++++.. ....+.|.++|+.|++.|=.+|=+++-|+..|++++...
T Consensus 33 IL~~l~~-~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~ 78 (274)
T PRK11569 33 LLEWIAE-SNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGE 78 (274)
T ss_pred HHHHHHh-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCC
Confidence 4455544 355689999999999999999999999999999998643
No 78
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.00 E-value=10 Score=33.92 Aligned_cols=40 Identities=33% Similarity=0.374 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHH
Q 012778 140 GLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITN 179 (456)
Q Consensus 140 glLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItN 179 (456)
++||+|=..++.--=..-+.|.++|+.++|+|-.|||=|+
T Consensus 16 sLLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIK 55 (105)
T COG2739 16 SLLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIK 55 (105)
T ss_pred HHHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHH
Confidence 4788776665554444558999999999999999999765
No 79
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=52.78 E-value=34 Score=28.34 Aligned_cols=80 Identities=16% Similarity=0.349 Sum_probs=35.4
Q ss_pred HHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCC-Cc-------hhHHHHHHHHHHHHHHHHHHHHHHH
Q 012778 161 NKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRP-GE-------ADENASSLQAEVESLTIQERRLDEQ 232 (456)
Q Consensus 161 n~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~-~~-------~~~~~~~Lq~El~~L~~eE~~LDel 232 (456)
..+...+.--++.+..+.-|++-|..+.- +...|++.+..-. .. +...+..++.+++.|..+...|...
T Consensus 15 ~~~~~q~~~l~~~~~~~~~~~~eL~~l~~---~~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~ 91 (106)
T PF01920_consen 15 QQLEQQIQQLERQLRELELTLEELEKLDD---DRKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKK 91 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTSST---T-EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCC---cchhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333333333444445555544433 3555655443210 11 2233444455555555555555555
Q ss_pred HHHHHHHHHhh
Q 012778 233 IRIMQERLRDL 243 (456)
Q Consensus 233 I~~~~q~Lr~L 243 (456)
+..++..|+.+
T Consensus 92 l~~~~~~l~~~ 102 (106)
T PF01920_consen 92 LKELKKKLYEL 102 (106)
T ss_dssp HHHHHHHHHCC
T ss_pred HHHHHHHHHHH
Confidence 55555555443
No 80
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=52.46 E-value=22 Score=30.57 Aligned_cols=77 Identities=18% Similarity=0.249 Sum_probs=43.8
Q ss_pred HHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCC------CchhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012778 163 AADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRP------GEADENASSLQAEVESLTIQERRLDEQIRIM 236 (456)
Q Consensus 163 aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~------~~~~~~~~~Lq~El~~L~~eE~~LDelI~~~ 236 (456)
.-..|..+++...++++-|+.+. ...+.|+=+|.-.... ..+...+..+..+++.|..+...|...+..+
T Consensus 21 ~~~~l~~~~~E~~~v~~EL~~l~----~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~el 96 (105)
T cd00632 21 QRQKVEAQLNENKKALEELEKLA----DDAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKEL 96 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHcCC----CcchHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445567788888888887775 2233333345322211 0133445556666666666666666666666
Q ss_pred HHHHHhh
Q 012778 237 QERLRDL 243 (456)
Q Consensus 237 ~q~Lr~L 243 (456)
+.+|+++
T Consensus 97 k~~l~~~ 103 (105)
T cd00632 97 QEKIQQA 103 (105)
T ss_pred HHHHHHH
Confidence 6666654
No 81
>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=51.97 E-value=36 Score=29.94 Aligned_cols=79 Identities=18% Similarity=0.235 Sum_probs=0.0
Q ss_pred ccHHHHHhhhcceee--ehhhhHHhhhhcccee--cccCCeEEEeecCCCCCCchhHHHHHHH------HHHHHHHHH--
Q 012778 158 LDLNKAADTLEVQKR--RIYDITNVLEGIGLIE--KKLKNRIQWKGLDVSRPGEADENASSLQ------AEVESLTIQ-- 225 (456)
Q Consensus 158 idLn~aA~~L~VqKR--RIYDItNVLEGIGLIe--K~sKN~i~W~G~d~s~~~~~~~~~~~Lq------~El~~L~~e-- 225 (456)
+.+.++|+.+||+++ |.| |.+|||. +...|.|++-..+.. ..-..+..|+ +|++.+-..
T Consensus 1 m~IgevA~~~gvs~~tLRyY------e~~GLl~p~~r~~~gyR~Y~~~~l---~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYY------EKEGLLPAPARSANNYRLYDEEHL---ERLLFIRRCRSLDMSLDEIRTLLQLQD 71 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHH------HHCCCCCCCCcCCCCCeecCHHHH---HHHHHHHHHHHcCCCHHHHHHHHHhhh
Q ss_pred ---------HHHHHHHHHHHHHHHHhhhh
Q 012778 226 ---------ERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 226 ---------E~~LDelI~~~~q~Lr~Lte 245 (456)
...|.+++..+.+++.+|..
T Consensus 72 ~~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd04784 72 DPEASCAEVNALIDEHLAHVRARIAELQA 100 (127)
T ss_pred cCCCcHHHHHHHHHHHHHHHHHHHHHHHH
No 82
>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=51.97 E-value=18 Score=30.91 Aligned_cols=45 Identities=16% Similarity=0.319 Sum_probs=39.5
Q ss_pred HHHHh--hCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 147 INLIK--HAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 147 I~Ll~--~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
+.++. .++++.+.+.++|+.|++.+=.+-=+++-||--|+|.|..
T Consensus 31 L~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 31 LYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred HHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 44444 5577899999999999999999999999999999999874
No 83
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=51.96 E-value=59 Score=31.92 Aligned_cols=87 Identities=21% Similarity=0.251 Sum_probs=53.8
Q ss_pred CcHHHHHHHHHHHHhhCCCCcccHHH-----------HHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCC
Q 012778 137 SSLGLLTKKFINLIKHAEDGILDLNK-----------AADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRP 205 (456)
Q Consensus 137 ~SLglLTkKFI~Ll~~apdg~idLn~-----------aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~ 205 (456)
..+....++..+++....+.+...+. +.-.+.|..-++-+.++-|+++|-|....-+ .
T Consensus 59 ~d~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~g~v~~~~~~-----~------ 127 (262)
T PF14257_consen 59 KDVEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSELGKVTSRNIS-----S------ 127 (262)
T ss_pred CCHHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhccCceeeeecc-----c------
Confidence 44556667777788776655544443 2445667888999999999999977655222 1
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012778 206 GEADENASSLQAEVESLTIQERRLDEQIR 234 (456)
Q Consensus 206 ~~~~~~~~~Lq~El~~L~~eE~~LDelI~ 234 (456)
.++..+...+++.++.|+.++++|-++++
T Consensus 128 ~DvT~~y~D~~arl~~l~~~~~rl~~ll~ 156 (262)
T PF14257_consen 128 EDVTEQYVDLEARLKNLEAEEERLLELLE 156 (262)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 23334444555556666666665555544
No 84
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=51.51 E-value=12 Score=40.37 Aligned_cols=76 Identities=18% Similarity=0.282 Sum_probs=47.6
Q ss_pred cceeeehhhhHHhhhhc-cceecccCCeEEEeecCCCCCCchhHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHhh
Q 012778 168 EVQKRRIYDITNVLEGI-GLIEKKLKNRIQWKGLDVSRPGEADENASSLQAEVE---SLTIQERRLDEQIRIMQERLRDL 243 (456)
Q Consensus 168 ~VqKRRIYDItNVLEGI-GLIeK~sKN~i~W~G~d~s~~~~~~~~~~~Lq~El~---~L~~eE~~LDelI~~~~q~Lr~L 243 (456)
.|.|||=|-|=+-.--| .||-|..-+..+|. ...+-. ...+-+..||++.+ ++....+.|+.-++.+.+++++|
T Consensus 239 eVERRRR~nIN~~IkeLg~liP~~~~~~~~~n-KgtILk-~s~dYIr~Lqq~~q~~~E~~~rqk~le~~n~~L~~rieeL 316 (411)
T KOG1318|consen 239 EVERRRRENINDRIKELGQLIPKCNSEDMKSN-KGTILK-ASCDYIRELQQTLQRARELENRQKKLESTNQELALRIEEL 316 (411)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCcchhhcc-cchhhH-HHHHHHHHHHHHHHHHHHHHhhhhHHHhHHHHHHHHHHHH
Confidence 47888866555443333 47888888888885 222211 22334666665554 55666677777788888887777
Q ss_pred hh
Q 012778 244 SE 245 (456)
Q Consensus 244 te 245 (456)
..
T Consensus 317 k~ 318 (411)
T KOG1318|consen 317 KS 318 (411)
T ss_pred HH
Confidence 54
No 85
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=51.27 E-value=37 Score=26.79 Aligned_cols=36 Identities=19% Similarity=0.304 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 012778 211 NASSLQAEVESLTIQERRLDEQIRIMQERLRDLSED 246 (456)
Q Consensus 211 ~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted 246 (456)
....++.++..|+.+-+.|.+.+..+++++..|..|
T Consensus 18 ~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~ 53 (80)
T PF04977_consen 18 RYYQLNQEIAELQKEIEELKKENEELKEEIERLKND 53 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 355677778888888888888888888888888333
No 86
>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=50.86 E-value=8.7 Score=27.02 Aligned_cols=22 Identities=32% Similarity=0.561 Sum_probs=20.2
Q ss_pred ccHHHHHhhhcceeeehhhhHH
Q 012778 158 LDLNKAADTLEVQKRRIYDITN 179 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItN 179 (456)
+++.++|+.|+|.++.||-.++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999986
No 87
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=50.37 E-value=85 Score=30.52 Aligned_cols=53 Identities=6% Similarity=0.207 Sum_probs=41.4
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEee
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKG 199 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G 199 (456)
+.++++.. .+.+.+.++|+.|++.|=-+|-+++.|+..|++++...+.--..|
T Consensus 18 ~IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG 70 (257)
T PRK15090 18 GILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLT 70 (257)
T ss_pred HHHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEec
Confidence 45555543 346899999999999999999999999999999987544323345
No 88
>PRK00215 LexA repressor; Validated
Probab=50.02 E-value=19 Score=33.68 Aligned_cols=42 Identities=17% Similarity=0.165 Sum_probs=36.9
Q ss_pred hCCCCcccHHHHHhhhcc-eeeehhhhHHhhhhccceecccCC
Q 012778 152 HAEDGILDLNKAADTLEV-QKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 152 ~apdg~idLn~aA~~L~V-qKRRIYDItNVLEGIGLIeK~sKN 193 (456)
...+....+.++|+.|++ .|=-++.+++-||.-|+|++....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 445667899999999999 999999999999999999987544
No 89
>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=49.85 E-value=43 Score=29.73 Aligned_cols=37 Identities=19% Similarity=0.232 Sum_probs=25.4
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEEee
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQWKG 199 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W~G 199 (456)
.+.++|+.+||..+-| -..|.+||+. +...|.|++-.
T Consensus 2 ~I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~ 40 (127)
T TIGR02047 2 KIGELAQKTGVSVETI----RFYEKQGLLPPPARTDNNYRVYT 40 (127)
T ss_pred cHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCCCcCC
Confidence 4778899999987744 2346778884 45567777654
No 90
>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=49.07 E-value=16 Score=28.51 Aligned_cols=51 Identities=25% Similarity=0.289 Sum_probs=40.4
Q ss_pred HHHHHHHHHhhCC----------CCcccHHHHHhhhcceeeehhhhHHhhhhccceecccC
Q 012778 142 LTKKFINLIKHAE----------DGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLK 192 (456)
Q Consensus 142 LTkKFI~Ll~~ap----------dg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sK 192 (456)
|+.-|+.++.... ...+...++|+.+|+.++.+--+++-|+.-|+|+...+
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 5566666665432 12467899999999999999999999999999997644
No 91
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=48.97 E-value=98 Score=31.01 Aligned_cols=43 Identities=19% Similarity=0.411 Sum_probs=32.6
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceec
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK 189 (456)
++.+.+|.+.| .=..+++..|||....|-+=.-.||--|||+-
T Consensus 18 R~Il~lLt~~p---~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS 60 (217)
T COG1777 18 RRILQLLTRRP---CYVSEISRELGVSQKAVLKHLRILERAGLVES 60 (217)
T ss_pred HHHHHHHhcCc---hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchh
Confidence 46777877766 44567788899988888888888888887764
No 92
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=48.84 E-value=42 Score=29.12 Aligned_cols=83 Identities=20% Similarity=0.268 Sum_probs=45.7
Q ss_pred HHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCC------CchhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012778 161 NKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRP------GEADENASSLQAEVESLTIQERRLDEQIR 234 (456)
Q Consensus 161 n~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~------~~~~~~~~~Lq~El~~L~~eE~~LDelI~ 234 (456)
..++..+..-.+-+=....|++.|.-+. .+.+.|+=.|.=.... ..+..++..+...++.|..+...|.+.+.
T Consensus 20 ~~l~~q~~~le~~~~E~~~v~~eL~~l~-~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~ 98 (110)
T TIGR02338 20 QAVATQKQQVEAQLKEAEKALEELERLP-DDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLK 98 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCC-CcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333333444555665555554 3344455555322211 12344556666777777777777777788
Q ss_pred HHHHHHHhhh
Q 012778 235 IMQERLRDLS 244 (456)
Q Consensus 235 ~~~q~Lr~Lt 244 (456)
.++.+|+.+.
T Consensus 99 e~q~~l~~~~ 108 (110)
T TIGR02338 99 ELQEKIQEAL 108 (110)
T ss_pred HHHHHHHHHh
Confidence 8887777764
No 93
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=48.79 E-value=53 Score=32.41 Aligned_cols=50 Identities=16% Similarity=0.169 Sum_probs=40.2
Q ss_pred HHHHHHHHhh-CCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccC
Q 012778 143 TKKFINLIKH-AEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLK 192 (456)
Q Consensus 143 TkKFI~Ll~~-apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sK 192 (456)
+-|.|.++.. .....+...++|+.|++.+..+.-+++-||--|+|+|...
T Consensus 6 ~Lk~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~ 56 (217)
T PRK14165 6 ALKKLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIV 56 (217)
T ss_pred HHHHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEc
Confidence 3344444433 4455689999999999999999999999999999999754
No 94
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=48.50 E-value=58 Score=30.65 Aligned_cols=47 Identities=9% Similarity=0.026 Sum_probs=40.0
Q ss_pred CCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEee
Q 012778 153 AEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKG 199 (456)
Q Consensus 153 apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G 199 (456)
.|+..+...++|+.|||+|==|=+.+..|+.-|||+...+.-+.-..
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~ 72 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVAS 72 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCC
Confidence 47888999999999999999999999999999999977555444443
No 95
>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=48.45 E-value=24 Score=34.01 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=37.3
Q ss_pred HHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 146 FINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
.++++..+ ...+.+.++|+.|++.|=.+|-+++-|+..|++++.
T Consensus 14 IL~~l~~~-~~~~~l~eia~~lglpksT~~RlL~tL~~~G~l~~~ 57 (248)
T TIGR02431 14 VIEAFGAE-RPRLTLTDVAEATGLTRAAARRFLLTLVELGYVTSD 57 (248)
T ss_pred HHHHHhcC-CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 44455443 456899999999999999999999999999999985
No 96
>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=48.40 E-value=24 Score=31.41 Aligned_cols=38 Identities=18% Similarity=0.299 Sum_probs=34.0
Q ss_pred hCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceec
Q 012778 152 HAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 152 ~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK 189 (456)
+..++.+.+.++|+.+++..+-+..|+..|.--|||.-
T Consensus 20 ~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 20 NAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 33455899999999999999999999999999999974
No 97
>KOG2420 consensus Phosphatidylserine decarboxylase [Lipid transport and metabolism]
Probab=48.27 E-value=7.6 Score=41.15 Aligned_cols=12 Identities=50% Similarity=0.988 Sum_probs=10.5
Q ss_pred CCCCCccCCCCC
Q 012778 29 PGGDYHRFAAEP 40 (456)
Q Consensus 29 ~~~~yh~f~~~~ 40 (456)
+|||||||.++.
T Consensus 235 aPGDYH~fHSP~ 246 (382)
T KOG2420|consen 235 APGDYHRFHSPA 246 (382)
T ss_pred cCCcccccCChH
Confidence 799999998873
No 98
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=47.36 E-value=47 Score=30.34 Aligned_cols=99 Identities=18% Similarity=0.265 Sum_probs=56.9
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCC------CchhHHHHH
Q 012778 141 LLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRP------GEADENASS 214 (456)
Q Consensus 141 lLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~------~~~~~~~~~ 214 (456)
.+..+|-.|-.+...-.+....+...| -+|.-||+-+..|.--. .-|+=.|.=.... .++..+...
T Consensus 10 ~~l~q~QqLq~ql~~~~~qk~~le~qL-------~E~~~al~Ele~l~eD~-~vYk~VG~llvk~~k~~~~~eL~er~E~ 81 (119)
T COG1382 10 AQLAQLQQLQQQLQKVILQKQQLEAQL-------KEIEKALEELEKLDEDA-PVYKKVGNLLVKVSKEEAVDELEERKET 81 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHhcCCccc-HHHHHhhhHHhhhhHHHHHHHHHHHHHH
Confidence 344555555544333333444444333 35777777777665432 2233344222111 134455666
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcc
Q 012778 215 LQAEVESLTIQERRLDEQIRIMQERLRDLSEDE 247 (456)
Q Consensus 215 Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted~ 247 (456)
|.-+++-|+.+|+.|++.+..++..|+.+..+.
T Consensus 82 Le~ri~tLekQe~~l~e~l~eLq~~i~~~l~~~ 114 (119)
T COG1382 82 LELRIKTLEKQEEKLQERLEELQSEIQKALGDA 114 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 677777888888888888888888888776554
No 99
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=47.34 E-value=23 Score=31.08 Aligned_cols=28 Identities=14% Similarity=0.201 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012778 210 ENASSLQAEVESLTIQERRLDEQIRIMQ 237 (456)
Q Consensus 210 ~~~~~Lq~El~~L~~eE~~LDelI~~~~ 237 (456)
+++..+++|++.|+.+.+.|...|..++
T Consensus 34 ~q~~~~~~e~~~l~~~n~~L~~eI~~L~ 61 (105)
T PRK00888 34 DQVAAQQQTNAKLKARNDQLFAEIDDLK 61 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3444455555555555555555555443
No 100
>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=47.24 E-value=46 Score=28.70 Aligned_cols=35 Identities=20% Similarity=0.245 Sum_probs=23.2
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEE
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQW 197 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W 197 (456)
.+.++|+.+||..|-|--. |..|||. ....|.+++
T Consensus 2 ~i~e~a~~~gvs~~tlr~y----e~~gll~~~~r~~~gyR~ 38 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYY----EKEGLLPPVKRDENGIRD 38 (113)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCcc
Confidence 4788999999998865322 5678883 334455554
No 101
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=46.78 E-value=27 Score=30.75 Aligned_cols=42 Identities=12% Similarity=0.171 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHh
Q 012778 139 LGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNV 180 (456)
Q Consensus 139 LglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNV 180 (456)
-.....++++++.+.....++|.++|+.+++.+|.|.-+..-
T Consensus 7 ~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 7 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred cHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 355667999999998888999999999999999988776653
No 102
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=46.57 E-value=41 Score=31.93 Aligned_cols=41 Identities=24% Similarity=0.291 Sum_probs=38.1
Q ss_pred CCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCC
Q 012778 153 AEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 153 apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
.|+..++.+++|+.|||+|=-|=+.+..|+.-|||+.....
T Consensus 35 ~pG~~l~e~~La~~~gvSrtPVReAL~rL~~eGlv~~~p~r 75 (230)
T COG1802 35 APGERLSEEELAEELGVSRTPVREALRRLEAEGLVEIEPNR 75 (230)
T ss_pred CCCCCccHHHHHHHhCCCCccHHHHHHHHHHCCCeEecCCC
Confidence 58999999999999999999999999999999999998443
No 103
>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=46.23 E-value=29 Score=32.83 Aligned_cols=45 Identities=27% Similarity=0.316 Sum_probs=37.9
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
+.+.++.+ .+.+.+.++|+.|++.+-.++-.++-||..|+|++..
T Consensus 147 ~IL~~l~~--~g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~ 191 (203)
T TIGR01884 147 KVLEVLKA--EGEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKG 191 (203)
T ss_pred HHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEc
Confidence 34444443 2568999999999999999999999999999999986
No 104
>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=46.00 E-value=44 Score=31.02 Aligned_cols=41 Identities=20% Similarity=0.280 Sum_probs=37.2
Q ss_pred CCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCC
Q 012778 153 AEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 153 apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
.++..+.-.++|+.|||+|==+=+.+..|+.-|||+...+.
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~ 70 (212)
T TIGR03338 30 PPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNR 70 (212)
T ss_pred CCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCC
Confidence 48888999999999999999999999999999999976543
No 105
>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=45.95 E-value=16 Score=39.03 Aligned_cols=46 Identities=20% Similarity=0.221 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 139 LGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 139 LglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
...+...|+.+ .||..+|.++|+++++.-++++|+.+.|...|||+
T Consensus 341 ~~~~~l~~L~~----~DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 341 QQMAMLWVLNY----SDGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp -HHHHHHHHHH-----EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHHh----ccCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 33444455555 48999999999999999999999999999999985
No 106
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=45.56 E-value=24 Score=28.75 Aligned_cols=44 Identities=20% Similarity=0.271 Sum_probs=35.8
Q ss_pred HHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 146 FINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
++..+...++... .++|+.|++.+=-+.-+++-||.-|+|+|..
T Consensus 27 ~L~~l~~~~~~~~--~~la~~l~i~~~~vt~~l~~Le~~glv~r~~ 70 (126)
T COG1846 27 VLLALYEAGGITV--KELAERLGLDRSTVTRLLKRLEDKGLIERLR 70 (126)
T ss_pred HHHHHHHhCCCcH--HHHHHHHCCCHHHHHHHHHHHHHCCCeeecC
Confidence 4444445444444 9999999999999999999999999999874
No 107
>PRK11050 manganese transport regulator MntR; Provisional
Probab=45.31 E-value=35 Score=31.20 Aligned_cols=39 Identities=21% Similarity=0.170 Sum_probs=35.0
Q ss_pred CCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCC
Q 012778 155 DGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 155 dg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
++.+.++++|+.|+|.+--+..+++-||.-|+|.+....
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~~ 87 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYR 87 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 466899999999999999999999999999999986533
No 108
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=44.91 E-value=21 Score=35.16 Aligned_cols=45 Identities=18% Similarity=0.300 Sum_probs=38.3
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
++.+++++ ..+.+.+.++|+.|+|++.-|+=-++.||..|+|.|.
T Consensus 8 ~~Il~~l~--~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~ 52 (251)
T PRK13509 8 QILLELLA--QLGFVTVEKVIERLGISPATARRDINKLDESGKLKKV 52 (251)
T ss_pred HHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEe
Confidence 34556665 4789999999999999999888889999999999885
No 109
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=44.58 E-value=24 Score=36.07 Aligned_cols=52 Identities=25% Similarity=0.434 Sum_probs=41.4
Q ss_pred CcHHHHHH-HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 137 SSLGLLTK-KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 137 ~SLglLTk-KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
++|+..++ +.+++|. ..+.+++|++|+.|+...--+--=+.|||-.|||+-.
T Consensus 18 kalaS~vRv~Il~lL~--~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 18 KALASKVRVAILQLLH--RKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHH--HhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeee
Confidence 45666663 4555654 4577999999999999999999999999999999854
No 110
>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=44.53 E-value=28 Score=32.42 Aligned_cols=48 Identities=17% Similarity=0.250 Sum_probs=38.8
Q ss_pred HHHHHHHhh---CCCCcccHHHHHhhhcce-eeehhhhHHhhhhccceeccc
Q 012778 144 KKFINLIKH---AEDGILDLNKAADTLEVQ-KRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 144 kKFI~Ll~~---apdg~idLn~aA~~L~Vq-KRRIYDItNVLEGIGLIeK~s 191 (456)
++.++++.+ ..+....+.++|+.|++. +=-++..++.||..|+|++..
T Consensus 9 ~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 9 QEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence 345555543 344458899999999998 999999999999999999974
No 111
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=43.97 E-value=42 Score=37.95 Aligned_cols=69 Identities=26% Similarity=0.422 Sum_probs=49.3
Q ss_pred hhhH-HhhhhccceecccCCeEEEeecCCCCCC------chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 012778 175 YDIT-NVLEGIGLIEKKLKNRIQWKGLDVSRPG------EADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSED 246 (456)
Q Consensus 175 YDIt-NVLEGIGLIeK~sKN~i~W~G~d~s~~~------~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted 246 (456)
|+.+ +-|..|.=|.|++||++- ..+-+-+ .++..+..|+.|-+.|..+...+|.-+..+.++|..|..+
T Consensus 479 ~~lte~QLslIrDIRRRgKNkvA---AQnCRKRKLd~I~nLE~ev~~l~~eKeqLl~Er~~~d~~L~~~kqqls~L~~~ 554 (604)
T KOG3863|consen 479 YKLTEEQLSLIRDIRRRGKNKVA---AQNCRKRKLDCILNLEDEVEKLQKEKEQLLRERDELDSTLGVMKQQLSELYQE 554 (604)
T ss_pred cccCHHHHHHhhccccccccchh---ccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444 678889999999999873 2221111 2445566777777788888888899999999998887654
No 112
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=43.95 E-value=28 Score=29.17 Aligned_cols=40 Identities=15% Similarity=0.162 Sum_probs=34.1
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHh
Q 012778 141 LLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNV 180 (456)
Q Consensus 141 lLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNV 180 (456)
.+..+++.++.+.....+++.++|+.+++++|.+.=+.+=
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4567888899888888899999999999999998876653
No 113
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=43.78 E-value=9.3 Score=38.80 Aligned_cols=31 Identities=26% Similarity=0.442 Sum_probs=25.2
Q ss_pred CCcccHHHHHhhhcceeeehhhhHHhhhhcc
Q 012778 155 DGILDLNKAADTLEVQKRRIYDITNVLEGIG 185 (456)
Q Consensus 155 dg~idLn~aA~~L~VqKRRIYDItNVLEGIG 185 (456)
|.-+-|..+=-.||..+|=+||.+||+||=-
T Consensus 38 D~DiGLRNLDlimGlE~RiVYd~vdVi~g~~ 68 (272)
T COG2894 38 DFDIGLRNLDLIMGLENRIVYDLVDVIEGEA 68 (272)
T ss_pred ecCcCchhhhhhhcccceeeeeehhhhcCcc
Confidence 4455666666779999999999999999854
No 114
>PRK09343 prefoldin subunit beta; Provisional
Probab=43.07 E-value=56 Score=29.14 Aligned_cols=74 Identities=18% Similarity=0.283 Sum_probs=46.5
Q ss_pred eeehhhhHHhhhhccceecccCCeEEEeecCCCCC------CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 012778 171 KRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRP------GEADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLS 244 (456)
Q Consensus 171 KRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~------~~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lt 244 (456)
.+.+=..-.|++.|..+.-- -.-|+=.|.=.... .++..++..+..+++.|+.++..|.+.+..++.+|+.+.
T Consensus 34 e~q~~e~~~~~~EL~~L~~d-~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~~l~~ll 112 (121)
T PRK09343 34 DLELREINKALEELEKLPDD-TPIYKIVGNLLVKVDKTKVEKELKERKELLELRSRTLEKQEKKLREKLKELQAKINEML 112 (121)
T ss_pred HHHHHHHHHHHHHHHcCCCc-chhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444566677777666522 22233334221111 124455667778888899999999999999999999886
Q ss_pred h
Q 012778 245 E 245 (456)
Q Consensus 245 e 245 (456)
.
T Consensus 113 ~ 113 (121)
T PRK09343 113 S 113 (121)
T ss_pred H
Confidence 5
No 115
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=43.03 E-value=1.5e+02 Score=27.57 Aligned_cols=31 Identities=42% Similarity=0.550 Sum_probs=23.3
Q ss_pred cHHHHHHHHHHHHhhCCCCcccHHHHHhhhc
Q 012778 138 SLGLLTKKFINLIKHAEDGILDLNKAADTLE 168 (456)
Q Consensus 138 SLglLTkKFI~Ll~~apdg~idLn~aA~~L~ 168 (456)
+|..|+..|.+++.-..++.+|-..+++.|.
T Consensus 2 ~LYel~~~~~~l~~~~e~~~~d~e~~~dtLe 32 (162)
T PF05565_consen 2 KLYELTDEYLELLELLEEGDLDEEAIADTLE 32 (162)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCHHHHHHHHH
Confidence 6888999999999776666677776655554
No 116
>PLN02938 phosphatidylserine decarboxylase
Probab=42.78 E-value=9 Score=41.36 Aligned_cols=11 Identities=45% Similarity=0.830 Sum_probs=10.0
Q ss_pred CCCCCccCCCC
Q 012778 29 PGGDYHRFAAE 39 (456)
Q Consensus 29 ~~~~yh~f~~~ 39 (456)
+|+|||||.++
T Consensus 260 sP~DYHR~HsP 270 (428)
T PLN02938 260 GPGDYHRIHSP 270 (428)
T ss_pred CccccceEeec
Confidence 79999999886
No 117
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=42.44 E-value=52 Score=35.69 Aligned_cols=49 Identities=24% Similarity=0.403 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHhhCC--CCcccHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 140 GLLTKKFINLIKHAE--DGILDLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 140 glLTkKFI~Ll~~ap--dg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
..|-+.|+.|++... ...+.|.++|+.|++++|-.==|+|-|+..|.|+
T Consensus 4 ~~~~~~~~~L~~~~~~~~~~~~l~~la~~l~cs~R~~~~~l~~~~~~gwl~ 54 (552)
T PRK13626 4 ARLQQQFIRLWQCCEGKSQETTLNELAELLNCSRRHMRTLLNTMQQRGWLT 54 (552)
T ss_pred hHHHHHHHHHHHhcCCCcceeeHHHHHHHhcCChhHHHHHHHHHHHCCCee
Confidence 357788999987653 5578999999999999999999999999999987
No 118
>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=42.41 E-value=2.8e+02 Score=25.57 Aligned_cols=53 Identities=23% Similarity=0.298 Sum_probs=28.3
Q ss_pred HHHHHhhCCCCcccHHHHHhhhc--ceeeehhhhHHhhhhccce-ecc-cCCeEEEee
Q 012778 146 FINLIKHAEDGILDLNKAADTLE--VQKRRIYDITNVLEGIGLI-EKK-LKNRIQWKG 199 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~--VqKRRIYDItNVLEGIGLI-eK~-sKN~i~W~G 199 (456)
.++||+. .+.++..+.+...|+ |.|=-+==+..-|..=|.| .|. +|-.|-|.-
T Consensus 6 Il~y~~~-qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~ 62 (169)
T PF07106_consen 6 ILEYMKE-QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFAN 62 (169)
T ss_pred HHHHHHH-cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeecceEEEeeC
Confidence 3455644 566777888888884 5553333333333333433 343 455666643
No 119
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=42.17 E-value=32 Score=32.18 Aligned_cols=39 Identities=15% Similarity=0.239 Sum_probs=34.9
Q ss_pred hCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 152 HAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 152 ~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
...++.+.+.++|+.+++.++-+..|++-|.--|||.-.
T Consensus 20 ~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 20 NSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 344568999999999999999999999999999999953
No 120
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=40.88 E-value=77 Score=25.47 Aligned_cols=39 Identities=13% Similarity=0.414 Sum_probs=29.6
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 207 EADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 207 ~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
+++.++.++...+..++.+-+.|-+-|..+.+.++.|..
T Consensus 4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ll~ 42 (55)
T PF05377_consen 4 ELENELPRIESSINTVKKENEEISESVEKIEENVKDLLS 42 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677777777888888888888888888888877654
No 121
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=40.52 E-value=36 Score=29.95 Aligned_cols=50 Identities=16% Similarity=0.294 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 139 LGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 139 LglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
|-.+=++.+++|+. ++.+.+.++|++||++...+...+.-||.-|+|.+.
T Consensus 6 lD~~D~~IL~~L~~--d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~ 55 (154)
T COG1522 6 LDDIDRRILRLLQE--DARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGY 55 (154)
T ss_pred ccHHHHHHHHHHHH--hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeE
Confidence 34455778888865 455999999999999999999999999999999986
No 122
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=40.33 E-value=1.8e+02 Score=27.91 Aligned_cols=54 Identities=19% Similarity=0.247 Sum_probs=42.8
Q ss_pred cHHH-HHHHHHHHHhh---CCCCcc-cHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 138 SLGL-LTKKFINLIKH---AEDGIL-DLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 138 SLgl-LTkKFI~Ll~~---apdg~i-dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
+|.. +...+.+.+.. .|+..+ .-.++|+.|||+|=-+-+.+..|+..|||+...
T Consensus 10 ~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~ 68 (254)
T PRK09464 10 KLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQ 68 (254)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 4543 44555555533 477778 899999999999999999999999999998653
No 123
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=40.15 E-value=24 Score=33.96 Aligned_cols=44 Identities=27% Similarity=0.369 Sum_probs=37.3
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhc
Q 012778 141 LLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGI 184 (456)
Q Consensus 141 lLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGI 184 (456)
.+..+|+.++.+.....+.|.++|+.+++++|.|..+..-..|+
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G~ 229 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSAL 229 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhCC
Confidence 46688999998888889999999999999999999887654443
No 124
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=39.49 E-value=33 Score=27.94 Aligned_cols=41 Identities=17% Similarity=0.174 Sum_probs=32.3
Q ss_pred CCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEE
Q 012778 155 DGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQ 196 (456)
Q Consensus 155 dg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~ 196 (456)
.+.....+++...++.-+++..+++-|+.-|||++ ..+.|.
T Consensus 17 ~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~-~~~~Y~ 57 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK-KDGKYR 57 (77)
T ss_dssp TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE-ETTEEE
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC-CCCEEE
Confidence 67788999999999999999999999999999966 455554
No 125
>PF05491 RuvB_C: Holliday junction DNA helicase ruvB C-terminus; InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein []. This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 3PFI_B 1IXR_C 1HQC_B 1IXS_B 1IN8_A 1IN4_A 1IN5_A 1J7K_A 1IN6_A 1IN7_A.
Probab=39.08 E-value=55 Score=27.76 Aligned_cols=58 Identities=24% Similarity=0.450 Sum_probs=45.1
Q ss_pred cHHHHHHHHHHHHhhC-CCCcccHHHHHhhhcceeeehhhhHH-hhhhccceecccCCeE
Q 012778 138 SLGLLTKKFINLIKHA-EDGILDLNKAADTLEVQKRRIYDITN-VLEGIGLIEKKLKNRI 195 (456)
Q Consensus 138 SLglLTkKFI~Ll~~a-pdg~idLn~aA~~L~VqKRRIYDItN-VLEGIGLIeK~sKN~i 195 (456)
-|-.+=++++..+.+. .+|.+-|+.+|..|+..+.-|=|++- -|--+|+|+|+.+.++
T Consensus 5 GLd~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT~rGR~ 64 (76)
T PF05491_consen 5 GLDELDRRYLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRTPRGRV 64 (76)
T ss_dssp S-BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEETTEEE
T ss_pred cCCHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhCccHHH
Confidence 4556778899977554 89999999999999999999888775 5778999999988764
No 126
>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=38.89 E-value=92 Score=27.80 Aligned_cols=81 Identities=14% Similarity=0.199 Sum_probs=0.0
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEEeecCCCCCCchhHHHHHHH------HHHHHHHHHH---
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQWKGLDVSRPGEADENASSLQ------AEVESLTIQE--- 226 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W~G~d~s~~~~~~~~~~~Lq------~El~~L~~eE--- 226 (456)
+.+.++|+.+||+.+ -+-..|..|||. +...|.|++-+.+.. ..-..+..|+ +|+..+-...
T Consensus 2 ~~I~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l---~~l~~I~~lr~~G~sl~eI~~~l~~~~~~ 74 (131)
T TIGR02043 2 FQIGELAKLCGVTSD----TLRFYEKNGLIKPAGRTDSGYRLYTDEDQ---KRLRFILKAKELGFTLDEIKELLSIKLDA 74 (131)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHHHH---HHHHHHHHHHHcCCCHHHHHHHHHhhccC
Q ss_pred ---------HHHHHHHHHHHHHHHhhhh
Q 012778 227 ---------RRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 227 ---------~~LDelI~~~~q~Lr~Lte 245 (456)
..|++.+..+++++.+|..
T Consensus 75 ~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (131)
T TIGR02043 75 TEHSCAEVKAIVDAKLELVDEKINELTK 102 (131)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
No 127
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=38.54 E-value=89 Score=25.33 Aligned_cols=35 Identities=9% Similarity=0.304 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 211 NASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 211 ~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
++..+...+..|+.....++..|..+..+|..+.+
T Consensus 14 ~l~~~~~~i~~lE~~~~~~e~~i~~~~~~l~~I~~ 48 (71)
T PF10779_consen 14 KLDNHEERIDKLEKRDAANEKDIKNLNKQLEKIKS 48 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566667777777788888888888888765
No 128
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=38.47 E-value=36 Score=30.43 Aligned_cols=40 Identities=15% Similarity=0.275 Sum_probs=35.6
Q ss_pred hCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 152 HAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 152 ~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
..++..+...++|+.++|.+.-+-.|+..|+.-|||+...
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~ 59 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVR 59 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEec
Confidence 3456689999999999999999999999999999998664
No 129
>TIGR02366 DHAK_reg probable dihydroxyacetone kinase regulator. The seed alignment for this family was built from a set of closely related uncharacterized proteins associated with operons for the type of bacterial dihydroxyacetone kinase that transfers PEP-derived phosphate from a phosphoprotein, as in phosphotransferase system transport, rather than from ATP. Members have a TetR transcriptional regulator domain (pfam00440) at the N-terminus and sequence homology throughout.
Probab=38.08 E-value=34 Score=30.55 Aligned_cols=36 Identities=14% Similarity=0.328 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehh
Q 012778 140 GLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIY 175 (456)
Q Consensus 140 glLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIY 175 (456)
..+..-|++|++..+=..+.++++|++-||.|.-+|
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY 41 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHH
Confidence 346677999999999999999999999999999887
No 130
>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=37.32 E-value=29 Score=24.04 Aligned_cols=23 Identities=22% Similarity=0.212 Sum_probs=19.9
Q ss_pred ccHHHHHhhhcceeeehhhhHHh
Q 012778 158 LDLNKAADTLEVQKRRIYDITNV 180 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNV 180 (456)
+.+.++|+.|+|.++-||..+.-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999999988774
No 131
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=36.79 E-value=1.4e+02 Score=26.65 Aligned_cols=47 Identities=19% Similarity=0.290 Sum_probs=40.3
Q ss_pred HHHHHHHHHhhCCCC--cccHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 142 LTKKFINLIKHAEDG--ILDLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 142 LTkKFI~Ll~~apdg--~idLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
|...|..|++.-.++ .+.|.++|+.|.+++|-.==|++-|+..|.|+
T Consensus 2 l~~~y~~L~~~~~~~~~~vtl~elA~~l~cS~Rn~r~lLkkm~~~gWi~ 50 (115)
T PF12793_consen 2 LLEQYQRLWQHYGGQPVEVTLDELAELLFCSRRNARTLLKKMQEEGWIT 50 (115)
T ss_pred HHHHHHHHHHHcCCCCcceeHHHHHHHhCCCHHHHHHHHHHHHHCCCee
Confidence 456788888776644 57999999999999999999999999999876
No 132
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=36.73 E-value=61 Score=33.38 Aligned_cols=35 Identities=29% Similarity=0.529 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 012778 212 ASSLQAEVESLTIQERRLDEQIRIMQERLRDLSED 246 (456)
Q Consensus 212 ~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted 246 (456)
...|.+|++.|+.++..|++.|..++.++..+.+.
T Consensus 59 e~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~e 93 (314)
T PF04111_consen 59 EEELLQELEELEKEREELDQELEELEEELEELDEE 93 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555777778888888888888888777776554
No 133
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=36.52 E-value=1.3e+02 Score=30.80 Aligned_cols=89 Identities=19% Similarity=0.240 Sum_probs=62.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccchhhhccCC---------CCCCCeEEEeeCCCCCeEEecCCCcc
Q 012778 220 ESLTIQERRLDEQIRIMQERLRDLSEDENNQKWLFVTEDDIKSLP---------CFQNETLIAIKAPHGTTLEVPDPDEA 290 (456)
Q Consensus 220 ~~L~~eE~~LDelI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~l~---------~f~~qTvIAIKAP~gT~LEVPdPde~ 290 (456)
++|...|..|+++|.--.+-|..-.++..+..+++|+.+-+++-+ .|.+..|-|++=+.|+++.++-+|..
T Consensus 26 eEllkLe~DLkEvIsLTedLlqT~~ee~~sss~a~~ssq~~h~s~~~~~~~~~~l~~~~~i~a~~w~vg~K~~A~~~ddg 105 (262)
T KOG3026|consen 26 EELLKLEKDLKEVISLTEDLLQTQKEEDKSSSDAFVSSQPTHSSFTPRWVSGDYLFYPSRITAVGWKVGDKVQAVFSDDG 105 (262)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccccCccccCCCchhhhhhhhccccccchhcccccCCEEEEeecCCC
Confidence 467788899999998666666655555567779999888777622 24567788889999999999988643
Q ss_pred cCCCCCceEEEEecCCC-ceEEEE
Q 012778 291 VDYPQRRYRIVLRSTMG-PIDVYL 313 (456)
Q Consensus 291 ~~~~qr~YqI~LkS~~G-PIdVyL 313 (456)
.-|...|..-.. ++.|-+
T Consensus 106 -----~~y~AtIe~ita~~~~~ai 124 (262)
T KOG3026|consen 106 -----QIYDATIEHITAMEGTVAI 124 (262)
T ss_pred -----ceEEeehhhccCCCCceeE
Confidence 146666655433 344433
No 134
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=36.36 E-value=1.6e+02 Score=28.41 Aligned_cols=51 Identities=22% Similarity=0.221 Sum_probs=40.7
Q ss_pred HHHHHHHHHHhh---CCCCcc-cHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 141 LLTKKFINLIKH---AEDGIL-DLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 141 lLTkKFI~Ll~~---apdg~i-dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.+...+.+.+.. .|+..+ .-.++|+.|||+|==+=+.+..|+.-|||+...
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 334444444422 488889 699999999999999999999999999998664
No 135
>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=35.89 E-value=33 Score=28.46 Aligned_cols=43 Identities=16% Similarity=0.359 Sum_probs=36.3
Q ss_pred HHhhCCCCcccHHHHHhhh-cceeeehhhhHHhhhhccceeccc
Q 012778 149 LIKHAEDGILDLNKAADTL-EVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 149 Ll~~apdg~idLn~aA~~L-~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
++..-..|...++++.+.+ +++++=+.+=...|+..|||+|..
T Consensus 10 IL~~l~~g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 10 ILRALFQGPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHHHHTTSSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHhCCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhccc
Confidence 3344445899999999999 899999999999999999999974
No 136
>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=35.79 E-value=51 Score=27.83 Aligned_cols=45 Identities=20% Similarity=0.406 Sum_probs=37.8
Q ss_pred HHHHHhhCCCCcccHHHHHhhh-----cceeeehhhhHHhhhhccceeccc
Q 012778 146 FINLIKHAEDGILDLNKAADTL-----EVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L-----~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.++++..+ ++.++..++.+.| .+.+=-+|=+++.|+..|+|.|..
T Consensus 6 Il~~l~~~-~~~~sa~ei~~~l~~~~~~i~~~TVYR~L~~L~~~Gli~~~~ 55 (116)
T cd07153 6 ILEVLLES-DGHLTAEEIYERLRKKGPSISLATVYRTLELLEEAGLVREIE 55 (116)
T ss_pred HHHHHHhC-CCCCCHHHHHHHHHhcCCCCCHHHHHHHHHHHHhCCCEEEEE
Confidence 45666665 6778999999888 588999999999999999999864
No 137
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=35.74 E-value=88 Score=27.84 Aligned_cols=38 Identities=16% Similarity=0.227 Sum_probs=34.1
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.++.+.+.++|+.|+|.+=-+--+++-|+.-|+|.+..
T Consensus 19 ~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 19 EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec
Confidence 45677899999999999999999999999999999663
No 138
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=35.33 E-value=97 Score=27.35 Aligned_cols=37 Identities=16% Similarity=0.184 Sum_probs=26.4
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhccceec--ccCCeEEEee
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIEK--KLKNRIQWKG 199 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK--~sKN~i~W~G 199 (456)
.+.++|+.+||..+-|. ..|-.|||.. ...|.|++-.
T Consensus 2 ~I~e~a~~~gvs~~tlR----yYe~~GLl~p~~r~~~gyR~Y~ 40 (127)
T TIGR02044 2 NIGQVAKLTGLSSKMIR----YYEEKGLIPPPLRSEGGYRTYT 40 (127)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCCeecC
Confidence 57889999999887553 4567888853 4467777754
No 139
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.10 E-value=51 Score=28.75 Aligned_cols=36 Identities=14% Similarity=0.285 Sum_probs=32.1
Q ss_pred CCCCcccHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 153 AEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 153 apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
......++-++.+.-|-.||-+-|++..|+|||++-
T Consensus 18 ~S~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~l 53 (95)
T COG4519 18 DSGETANVPELMAATGWPRRTAQDVIKALPGLGIVL 53 (95)
T ss_pred hccccCChHHHHHHcCCchhHHHHHHHhCcCCCeEE
Confidence 356678899999999999999999999999999864
No 140
>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=34.90 E-value=64 Score=27.52 Aligned_cols=47 Identities=21% Similarity=0.264 Sum_probs=37.8
Q ss_pred HHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 143 TKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 143 TkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
.+-.|+++.+ .+..|-=.++|+.|++.-=-|..+.-.||.+|||+++
T Consensus 10 L~alV~~Y~~-~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 10 LKALVELYIE-TGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHh-cCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 3445565544 4777888889999999888899999999999999975
No 141
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=34.80 E-value=48 Score=33.34 Aligned_cols=57 Identities=21% Similarity=0.377 Sum_probs=47.7
Q ss_pred CcHHHHHHHHHH-HHhhCCCCcccHHHHHhhhcceeeehhhhHH-hhhhccceecccCC
Q 012778 137 SSLGLLTKKFIN-LIKHAEDGILDLNKAADTLEVQKRRIYDITN-VLEGIGLIEKKLKN 193 (456)
Q Consensus 137 ~SLglLTkKFI~-Ll~~apdg~idLn~aA~~L~VqKRRIYDItN-VLEGIGLIeK~sKN 193 (456)
..|...-++++. +++.-.++.+.+..+|..|+.....+-|++. .|-..|||++....
T Consensus 255 ~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 313 (328)
T PRK00080 255 LGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRG 313 (328)
T ss_pred CCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCch
Confidence 455667778887 6677788899999999999999999998888 89999999877543
No 142
>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=34.02 E-value=39 Score=33.83 Aligned_cols=31 Identities=29% Similarity=0.575 Sum_probs=25.8
Q ss_pred HHHhhhc---ceeeehhhhHHhhhhccceecccC
Q 012778 162 KAADTLE---VQKRRIYDITNVLEGIGLIEKKLK 192 (456)
Q Consensus 162 ~aA~~L~---VqKRRIYDItNVLEGIGLIeK~sK 192 (456)
.+|+.++ +..|++|++++-||.+|||+-..+
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~ 352 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEER 352 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEE
Confidence 5666666 578999999999999999997643
No 143
>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=33.94 E-value=1.1e+02 Score=27.17 Aligned_cols=81 Identities=12% Similarity=0.216 Sum_probs=0.0
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhccceecccC--CeEEEeecCCCCCCchhHHHHHHH------HHHHHHHHH----
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLK--NRIQWKGLDVSRPGEADENASSLQ------AEVESLTIQ---- 225 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sK--N~i~W~G~d~s~~~~~~~~~~~Lq------~El~~L~~e---- 225 (456)
+.+.++|+.+||..|-| =-.|-+|||.-... |.|+.-..+.. ..-..+..|+ +|+..+-..
T Consensus 1 m~IgE~A~~~gvs~~TL----RyYE~~GLl~p~r~~~~gyR~Y~~~~~---~~l~~I~~lr~~G~sL~eI~~~l~~~~~~ 73 (133)
T cd04787 1 MKVKELANAAGVTPDTV----RFYTRIGLLRPTRDPVNGYRLYSEKDL---SRLRFILSARQLGFSLKDIKEILSHADQG 73 (133)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCcCCCCCeeeCCHHHH---HHHHHHHHHHHcCCCHHHHHHHHhhhccC
Q ss_pred -------HHHHHHHHHHHHHHHHhhhh
Q 012778 226 -------ERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 226 -------E~~LDelI~~~~q~Lr~Lte 245 (456)
..-|.+++..+++++..|..
T Consensus 74 ~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (133)
T cd04787 74 ESPCPMVRRLIEQRLAETERRIKELLK 100 (133)
T ss_pred CCcHHHHHHHHHHHHHHHHHHHHHHHH
No 144
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=33.78 E-value=1e+02 Score=33.39 Aligned_cols=57 Identities=18% Similarity=0.332 Sum_probs=45.3
Q ss_pred cHHHHHHH------HHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEee
Q 012778 138 SLGLLTKK------FINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKG 199 (456)
Q Consensus 138 SLglLTkK------FI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G 199 (456)
-||+|+-+ .+++|....+..|.|+++|+.-++. .-||++.|+.+++|... |. +.|..
T Consensus 304 DLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~---~~DIisTL~~L~m~~y~-k~-~~~~~ 366 (396)
T KOG2747|consen 304 DLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIR---PDDIISTLQSLNMIKYY-KG-YIISI 366 (396)
T ss_pred hhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCC---HHHHHHHHHhhCCcccc-CC-eeEEE
Confidence 47888844 6777777666669999999999984 57999999999999866 33 66665
No 145
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=33.62 E-value=49 Score=26.05 Aligned_cols=31 Identities=26% Similarity=0.475 Sum_probs=25.7
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012778 207 EADENASSLQAEVESLTIQERRLDEQIRIMQ 237 (456)
Q Consensus 207 ~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~ 237 (456)
.+...+..|+.+++.|..+.+.|.+.|+.++
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~ 51 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERLK 51 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3456788899999999999999999998883
No 146
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=33.55 E-value=32 Score=30.47 Aligned_cols=37 Identities=14% Similarity=0.121 Sum_probs=34.3
Q ss_pred CCcccHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 155 DGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 155 dg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.+.+...++|+.|++.|=-+--+++-||.-|+|+|..
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 4568999999999999999999999999999999974
No 147
>PRK10869 recombination and repair protein; Provisional
Probab=33.37 E-value=44 Score=36.82 Aligned_cols=102 Identities=17% Similarity=0.222 Sum_probs=52.7
Q ss_pred CCCCcHHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCCCchhHHHH
Q 012778 134 RYDSSLGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRPGEADENAS 213 (456)
Q Consensus 134 R~d~SLglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~~~~~~~~~ 213 (456)
++|.+|..+...+-+.+-.-.+-.-+|....+.+.+.--|+-.|-+=|.-|.=+.|+ | |.+ ..++-...+
T Consensus 258 ~~d~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~~dp~~l~~ie~Rl~~l~~L~rK----y---g~~---~~~~~~~~~ 327 (553)
T PRK10869 258 GMDSKLSGVLDMLEEALIQIQEASDELRHYLDRLDLDPNRLAELEQRLSKQISLARK----H---HVS---PEELPQHHQ 327 (553)
T ss_pred hhCHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHH----h---CCC---HHHHHHHHH
Confidence 344444444444444433333444445555555556555666666666665555555 2 422 224555667
Q ss_pred HHHHHHHHHHHHHHHHHHH---HHHHHHHHHhhhh
Q 012778 214 SLQAEVESLTIQERRLDEQ---IRIMQERLRDLSE 245 (456)
Q Consensus 214 ~Lq~El~~L~~eE~~LDel---I~~~~q~Lr~Lte 245 (456)
++++|++.|...+..+.++ +..+.+++..+.+
T Consensus 328 ~l~~eL~~L~~~e~~l~~Le~e~~~l~~~l~~~A~ 362 (553)
T PRK10869 328 QLLEEQQQLDDQEDDLETLALAVEKHHQQALETAQ 362 (553)
T ss_pred HHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 7777777776655444433 4444445544443
No 148
>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=33.33 E-value=1.2e+02 Score=26.81 Aligned_cols=37 Identities=24% Similarity=0.323 Sum_probs=24.6
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEEee
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQWKG 199 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W~G 199 (456)
.+.++|+.+||+.+-| --.|-.||+. +...|.|++-.
T Consensus 2 ~I~e~a~~~gvs~~tl----RyYe~~GLl~~~~r~~~g~R~Y~ 40 (127)
T cd01108 2 NIGEAAKLTGLSAKMI----RYYEEIGLIPPPSRSDNGYRVYN 40 (127)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCceecC
Confidence 4678889999887643 2446778885 34556666643
No 149
>PHA00738 putative HTH transcription regulator
Probab=32.59 E-value=1.2e+02 Score=27.33 Aligned_cols=72 Identities=21% Similarity=0.306 Sum_probs=49.6
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCCCchhHHHHHHHHHHHHH
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRPGEADENASSLQAEVESL 222 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~~~~~~~~~~Lq~El~~L 222 (456)
++.+.+|.. ++.+-..++++.|++.+=.|-==+.||+..|||+.....+..+.-.... ...++.|..|++..
T Consensus 15 r~IL~lL~~--~e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~-----~~~~~l~~~~~~~~ 86 (108)
T PHA00738 15 RKILELIAE--NYILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIREN-----SKEIQILNSELEGF 86 (108)
T ss_pred HHHHHHHHH--cCCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCC-----ccHHHHHhhHHHHH
Confidence 356666754 3347888999999999999999999999999999776555444433321 12355565665544
No 150
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=32.41 E-value=86 Score=29.79 Aligned_cols=39 Identities=21% Similarity=0.220 Sum_probs=33.9
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEE
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQ 196 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~ 196 (456)
+.-.++|..||++|..+.=+++-|+--|+|++...++|.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 455899999999999999999999999999877655554
No 151
>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=32.37 E-value=72 Score=29.95 Aligned_cols=38 Identities=18% Similarity=0.388 Sum_probs=27.3
Q ss_pred ccHHHHHhhhcceee--ehhhhHHhhhhcccee--cccCCeEEEeecC
Q 012778 158 LDLNKAADTLEVQKR--RIYDITNVLEGIGLIE--KKLKNRIQWKGLD 201 (456)
Q Consensus 158 idLn~aA~~L~VqKR--RIYDItNVLEGIGLIe--K~sKN~i~W~G~d 201 (456)
+.+.++|+.+||.++ |.|| .+|||. +...|.|++-+.+
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe------~~GLl~p~~r~~~gyR~Y~~~ 43 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYE------RIGLLSPSARSESNYRLYGER 43 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHH------HCCCCCCCccCCCCCccCCHH
Confidence 467899999999988 5564 567775 3456778876543
No 152
>PF03374 ANT: Phage antirepressor protein KilAC domain; InterPro: IPR005039 This entry is represented by Bacteriophage P1, Ant1 C-terminal domain, which represents the processed Ant2 chain. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=32.19 E-value=40 Score=28.65 Aligned_cols=42 Identities=19% Similarity=0.491 Sum_probs=33.6
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
.|.+-+-+ .++.+.+.++|..|++.+++++++ |...|++-|.
T Consensus 13 ~~~d~~~~-~~~~~ti~~~AK~L~i~~~~l~~~---Lr~~g~l~~~ 54 (111)
T PF03374_consen 13 EFYDAFVD-SDGLYTIREAAKLLGIGRNKLFQW---LREKGWLYRR 54 (111)
T ss_pred HHHHHHHc-CCCCccHHHHHHHhCCCHHHHHHH---HHhCCceEEC
Confidence 35665544 459999999999999999999876 6668888884
No 153
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=31.67 E-value=1.3e+02 Score=27.36 Aligned_cols=81 Identities=15% Similarity=0.155 Sum_probs=0.0
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhccce--ecccCCeEEEeecCCCCCCchhHHHHHHH------HHHHHHHH-----
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLI--EKKLKNRIQWKGLDVSRPGEADENASSLQ------AEVESLTI----- 224 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLI--eK~sKN~i~W~G~d~s~~~~~~~~~~~Lq------~El~~L~~----- 224 (456)
+.+.++|+.+||+.|-|--. |-.||| .+...|.|++-..... ..-..+..|+ +|+..+-.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Y----e~~GLl~p~~r~~~gyR~Y~~~~l---~~l~~I~~lr~~G~sL~eI~~~l~~~~~~ 74 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFY----EKQGLMDPEVRTEGGYRLYTEQDL---QRLRFIRRAKQLGFTLEEIRELLSIRLDP 74 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCCeeeCHHHH---HHHHHHHHHHHcCCCHHHHHHHHHhcccC
Q ss_pred -------HHHHHHHHHHHHHHHHHhhhh
Q 012778 225 -------QERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 225 -------eE~~LDelI~~~~q~Lr~Lte 245 (456)
....|++++..+.+++.+|..
T Consensus 75 ~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (140)
T PRK09514 75 EHHTCQEVKGIVDEKLAEVEAKIAELQH 102 (140)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHH
No 154
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=31.45 E-value=61 Score=26.22 Aligned_cols=43 Identities=26% Similarity=0.329 Sum_probs=34.3
Q ss_pred HHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceec
Q 012778 146 FINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK 189 (456)
.+++++.. ++.+.-.++|+.+++.+-..-=+.+.||.-|.|++
T Consensus 5 Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~ 47 (62)
T PF04703_consen 5 ILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVER 47 (62)
T ss_dssp HHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEE
T ss_pred HHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEE
Confidence 45556553 55688899999999998888889999999999996
No 155
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=30.97 E-value=27 Score=26.36 Aligned_cols=24 Identities=25% Similarity=0.526 Sum_probs=19.8
Q ss_pred CcccHHHHHhhhcceeeehhhhHH
Q 012778 156 GILDLNKAADTLEVQKRRIYDITN 179 (456)
Q Consensus 156 g~idLn~aA~~L~VqKRRIYDItN 179 (456)
..|+++++++.+++++.-||..++
T Consensus 2 rll~~~ev~~~~g~s~~ti~~~~k 25 (51)
T PF05930_consen 2 RLLRIKEVAELLGVSRSTIYRLIK 25 (51)
T ss_dssp -EE-HHHHHHHHSS-HHHHHHHHH
T ss_pred ccccHHHHHHHHCCCHHHHHHHHh
Confidence 458899999999999999999988
No 156
>PRK10130 transcriptional regulator EutR; Provisional
Probab=30.89 E-value=40 Score=35.03 Aligned_cols=40 Identities=10% Similarity=0.119 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHH
Q 012778 140 GLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITN 179 (456)
Q Consensus 140 glLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItN 179 (456)
..+.+++++++.+..+..+++.++|+.++|++|.|+-...
T Consensus 239 ~~~v~~~~~~i~~~~~~~ltv~~lA~~~gvS~r~L~r~Fk 278 (350)
T PRK10130 239 RRLLSRAREYVLENMSEPVTVLDLCNQLHVSRRTLQNAFH 278 (350)
T ss_pred HHHHHHHHHHHHhhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 4677888899988888889999999999999999987664
No 157
>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=30.70 E-value=1.2e+02 Score=26.86 Aligned_cols=81 Identities=19% Similarity=0.219 Sum_probs=0.0
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEEeecCCCCCCchhHHHHHHH------HHHHHHHHH----
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQWKGLDVSRPGEADENASSLQ------AEVESLTIQ---- 225 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W~G~d~s~~~~~~~~~~~Lq------~El~~L~~e---- 225 (456)
+.+.++|+.+||+.+-|- -.|.+|||. +...|.|+|-..+.. ..-..+..|+ +|+..+-..
T Consensus 1 ~~I~e~a~~~gvs~~tlR----~Ye~~Gll~~~~r~~~g~R~Y~~~~l---~~l~~I~~lr~~G~sL~eI~~~l~~~~~~ 73 (126)
T cd04785 1 LSIGELARRTGVNVETIR----YYESIGLLPEPARTAGGYRLYGAAHV---ERLRFIRRARDLGFSLEEIRALLALSDRP 73 (126)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCccccCHHHH---HHHHHHHHHHHCCCCHHHHHHHHhhhhcC
Q ss_pred -------HHHHHHHHHHHHHHHHhhhh
Q 012778 226 -------ERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 226 -------E~~LDelI~~~~q~Lr~Lte 245 (456)
..-|.+++..+++++++|..
T Consensus 74 ~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (126)
T cd04785 74 DRSCAEADAIARAHLADVRARIADLRR 100 (126)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
No 158
>PF08781 DP: Transcription factor DP; InterPro: IPR014889 DP forms a heterodimer with E2F and regulates genes involved in cell cycle progression. The transcriptional activity of E2F is inhibited by the retinoblastoma protein which binds to the E2F-DP heterodimer [] and negatively regulates the G1-S transition. ; PDB: 2AZE_A.
Probab=30.37 E-value=95 Score=29.14 Aligned_cols=33 Identities=9% Similarity=0.217 Sum_probs=18.3
Q ss_pred EEEeeCCCCCeEEecCCCcccCCCCCceEEEEecCCCceE
Q 012778 271 LIAIKAPHGTTLEVPDPDEAVDYPQRRYRIVLRSTMGPID 310 (456)
Q Consensus 271 vIAIKAP~gT~LEVPdPde~~~~~qr~YqI~LkS~~GPId 310 (456)
.|.|+.-+.|+|+|-..++. ..++.+-..-|..
T Consensus 59 FIlV~T~~~a~I~ceiS~D~-------~~~~F~Fn~~pFe 91 (142)
T PF08781_consen 59 FILVNTSKKAVIECEISEDK-------SEYHFDFNSTPFE 91 (142)
T ss_dssp -EEEEEESS--EEEEE-TTS-------SEEEEEESS--EE
T ss_pred EEEEEecCCcEEEEEEcCCc-------cEEEEEcCCCcee
Confidence 68999999999999765432 2355555554444
No 159
>PTZ00403 phosphatidylserine decarboxylase; Provisional
Probab=30.15 E-value=16 Score=38.53 Aligned_cols=11 Identities=36% Similarity=0.628 Sum_probs=10.0
Q ss_pred CCCCCccCCCC
Q 012778 29 PGGDYHRFAAE 39 (456)
Q Consensus 29 ~~~~yh~f~~~ 39 (456)
.|+|||||.++
T Consensus 189 sP~DYHR~HsP 199 (353)
T PTZ00403 189 SPKKYHHFHAP 199 (353)
T ss_pred CcceeeEEecc
Confidence 79999999886
No 160
>PF02295 z-alpha: Adenosine deaminase z-alpha domain; InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase (3.5 from EC) converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1OYI_A 3EYI_A 2L4M_A 2HEO_D 1J75_A 1SFU_B 3IRR_B 2ACJ_C 3F22_B 2L54_A ....
Probab=30.11 E-value=93 Score=25.20 Aligned_cols=57 Identities=21% Similarity=0.272 Sum_probs=47.5
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEe
Q 012778 142 LTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWK 198 (456)
Q Consensus 142 LTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~ 198 (456)
+-.+.+++|....+...---..+..|.+.|+.|==+..=|+.=|.|.|.+-+--.|.
T Consensus 5 ~ee~Il~~L~~~g~~~a~~ia~~~~L~~~kk~VN~~LY~L~k~g~v~k~~~~PP~W~ 61 (66)
T PF02295_consen 5 LEEKILDFLKELGGSTATAIAKALGLSVPKKEVNRVLYRLEKQGKVCKEGGTPPKWS 61 (66)
T ss_dssp HHHHHHHHHHHHTSSEEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEECSSSTEEE
T ss_pred HHHHHHHHHHhcCCccHHHHHHHhCcchhHHHHHHHHHHHHHCCCEeeCCCCCCceE
Confidence 446778888776677778888889999999999999999999999999988888885
No 161
>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=29.84 E-value=1.4e+02 Score=26.32 Aligned_cols=79 Identities=15% Similarity=0.128 Sum_probs=0.0
Q ss_pred HHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEEeecCCCCCCchhHHHHHHH------HHHHHHHH-------
Q 012778 160 LNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQWKGLDVSRPGEADENASSLQ------AEVESLTI------- 224 (456)
Q Consensus 160 Ln~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W~G~d~s~~~~~~~~~~~Lq------~El~~L~~------- 224 (456)
+.++|+.+||..+-|--. |.+|||. +...|.|++-+.+.. .--..+..|+ +|+..+-.
T Consensus 2 I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~g~R~Y~~~~l---~~l~~I~~l~~~G~sl~eI~~~l~~~~~~~~ 74 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYY----ERKGLLPEPDRPEGGYRRYPEETV---KRLRFIKRAQELGFSLEEIGGLLGLVDGTHC 74 (124)
T ss_pred HHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCEeECHHHH---HHHHHHHHHHHCCCCHHHHHHHHhcccCCCH
Q ss_pred --HHHHHHHHHHHHHHHHHhhhh
Q 012778 225 --QERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 225 --eE~~LDelI~~~~q~Lr~Lte 245 (456)
....|.+++..+++++.+|..
T Consensus 75 ~~~~~~l~~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 75 REMYELASRKLKSVQAKMADLLR 97 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
No 162
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=29.69 E-value=1.3e+02 Score=29.63 Aligned_cols=41 Identities=22% Similarity=0.271 Sum_probs=26.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcccc
Q 012778 208 ADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSEDENN 249 (456)
Q Consensus 208 ~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted~~n 249 (456)
+.++.+.|++|+..|+.+..+++++..+ .++|++|.+-...
T Consensus 74 l~~en~~L~~e~~~l~~~~~~~~~l~~e-n~~L~~lL~~~~~ 114 (276)
T PRK13922 74 LREENEELKKELLELESRLQELEQLEAE-NARLRELLNLKES 114 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCccc
Confidence 4455667777777777777777654443 5677777654433
No 163
>PRK03837 transcriptional regulator NanR; Provisional
Probab=29.56 E-value=96 Score=29.34 Aligned_cols=50 Identities=12% Similarity=0.222 Sum_probs=41.1
Q ss_pred HHHHHHHHHhh---CCCCcc-cHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 142 LTKKFINLIKH---AEDGIL-DLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 142 LTkKFI~Ll~~---apdg~i-dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
+-+.+.+.+.. .++..+ ..+++|+.|+|+|-=+=+.+..||.-|||+...
T Consensus 18 v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~ 71 (241)
T PRK03837 18 VEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISH 71 (241)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 44555554433 477788 899999999999999999999999999999764
No 164
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=29.39 E-value=36 Score=37.36 Aligned_cols=60 Identities=30% Similarity=0.303 Sum_probs=39.0
Q ss_pred ehhhhHHhhhhccceecc-cCCeEEEeecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 012778 173 RIYDITNVLEGIGLIEKK-LKNRIQWKGLDVSRPGEADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSED 246 (456)
Q Consensus 173 RIYDItNVLEGIGLIeK~-sKN~i~W~G~d~s~~~~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted 246 (456)
++-++.|-|+++.=+.|. -||.-.|+| .|++..+.+...-...|+.|.++++||++|+--
T Consensus 390 k~~k~~kel~~~~E~n~~l~knq~vw~~--------------kl~~~~e~~~~~~~s~d~~I~dLqEQlrDlmf~ 450 (493)
T KOG0804|consen 390 KLKKCQKELKEEREENKKLIKNQDVWRG--------------KLKELEEREKEALGSKDEKITDLQEQLRDLMFF 450 (493)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhee
Confidence 455666666666544433 255555554 333444555666677899999999999998653
No 165
>PHA01750 hypothetical protein
Probab=29.01 E-value=1.2e+02 Score=25.49 Aligned_cols=30 Identities=27% Similarity=0.541 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012778 211 NASSLQAEVESLTIQERRLDEQIRIMQERL 240 (456)
Q Consensus 211 ~~~~Lq~El~~L~~eE~~LDelI~~~~q~L 240 (456)
.+.+|+.|++++....++|.+++.++...+
T Consensus 43 ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 43 ELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 455666666666666666666666665544
No 166
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=28.96 E-value=3.2e+02 Score=27.34 Aligned_cols=50 Identities=16% Similarity=0.242 Sum_probs=38.6
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCC
Q 012778 142 LTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 142 LTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
--.+.++++++ .+.+.++++|+.|+|+.+=|.==++.||.-|++.|.-..
T Consensus 18 R~~~Il~~L~~--~~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GG 67 (269)
T PRK09802 18 RREQIIQRLRQ--QGSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGG 67 (269)
T ss_pred HHHHHHHHHHH--cCCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCC
Confidence 33456677766 345999999999999988776556679999999987544
No 167
>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=28.89 E-value=95 Score=26.46 Aligned_cols=37 Identities=16% Similarity=0.215 Sum_probs=24.2
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEEee
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQWKG 199 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W~G 199 (456)
.+.++|+.+||+.+-|- -.|-.||+. +...|.+++-.
T Consensus 2 ~i~e~A~~~gvs~~tlR----~Ye~~Gll~~~~r~~~g~R~Y~ 40 (99)
T cd04772 2 RTVDLARAIGLSPQTVR----NYESLGLIPPAERTANGYRIYT 40 (99)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHcCCCCCCCcCCCCCeecC
Confidence 46788999999776332 226778875 34566676644
No 168
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=28.80 E-value=89 Score=29.96 Aligned_cols=40 Identities=20% Similarity=0.273 Sum_probs=36.6
Q ss_pred CCCCcc-cHHHHHhhhcceeeehhhhHHhhhhccceecccC
Q 012778 153 AEDGIL-DLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLK 192 (456)
Q Consensus 153 apdg~i-dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sK 192 (456)
.|+..+ .-.++|+.|||+|==+-+.+..|+..|||+....
T Consensus 26 ~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 26 KVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred CCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 488889 8999999999999999999999999999987643
No 169
>PF01853 MOZ_SAS: MOZ/SAS family; InterPro: IPR002717 Moz is a monocytic leukemia Zn_finger protein and the SAS protein from Saccharomyces cerevisiae (Baker's yeast) is involved in silencing the Hmr locus. These proteins were reported to be homologous to acetyltransferases [] but this similarity is not supported by standard sequence analysis.; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3TO6_A 1MJA_A 1MJ9_A 3TO7_A 3TO9_A 1MJB_A 1FY7_A 2OZU_A 2RC4_A 2OU2_A ....
Probab=28.75 E-value=68 Score=31.35 Aligned_cols=55 Identities=15% Similarity=0.321 Sum_probs=40.0
Q ss_pred cHHHHH------HHHHHHHhhCCCC-cccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeE
Q 012778 138 SLGLLT------KKFINLIKHAEDG-ILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRI 195 (456)
Q Consensus 138 SLglLT------kKFI~Ll~~apdg-~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i 195 (456)
-||.++ ...++.|....+. .++++++++..++.+ -||+..|+.+|+|.....+++
T Consensus 124 dlG~~sY~sYW~~~i~~~L~~~~~~~~isi~~is~~Tgi~~---~DIi~tL~~l~~l~~~~~~~~ 185 (188)
T PF01853_consen 124 DLGRLSYRSYWRRVILEYLLEFKGKKSISIKDISQETGIRP---EDIISTLQQLGMLKYYKGQHI 185 (188)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHTSSE--EEHHHHHHHH-BTH---HHHHHHHHHTT-EEEETTEEE
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCeEEHHHHHHHHCCCH---HHHHHHHHHCCCEEEECCcEE
Confidence 467776 3366666665554 899999999999965 699999999999988765544
No 170
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=28.65 E-value=34 Score=30.25 Aligned_cols=40 Identities=25% Similarity=0.383 Sum_probs=26.1
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHh
Q 012778 141 LLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNV 180 (456)
Q Consensus 141 lLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNV 180 (456)
+||.|=-.++.--=..-+.|.++|+.++|+|=-+||.+.-
T Consensus 17 LLT~kQ~~~l~lyy~eDlSlsEIAe~~~iSRqaV~d~ikr 56 (101)
T PF04297_consen 17 LLTEKQREILELYYEEDLSLSEIAEELGISRQAVYDSIKR 56 (101)
T ss_dssp GS-HHHHHHHHHHCTS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 5665544444444556799999999999999999998764
No 171
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=28.51 E-value=87 Score=28.73 Aligned_cols=51 Identities=16% Similarity=0.290 Sum_probs=44.7
Q ss_pred CcHHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceec
Q 012778 137 SSLGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 137 ~SLglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK 189 (456)
..|-.+=++.|.+|+ .++.+...++|+++|++.--++.=++=||.-|+|++
T Consensus 10 ~~lD~~D~~IL~~Lq--~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 10 KDLDRIDRNILNELQ--KDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred hhHHHHHHHHHHHhc--cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 446677788998885 578899999999999999999999999999999986
No 172
>smart00338 BRLZ basic region leucin zipper.
Probab=28.49 E-value=1.8e+02 Score=22.83 Aligned_cols=35 Identities=26% Similarity=0.463 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 211 NASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 211 ~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
.+..|+.++..|..+-..|-..+..+..++..|.+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35566777777777777777777777776666543
No 173
>PF13551 HTH_29: Winged helix-turn helix
Probab=28.26 E-value=41 Score=27.60 Aligned_cols=27 Identities=19% Similarity=0.329 Sum_probs=25.7
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhcc
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIG 185 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIG 185 (456)
.+.++|..|||.++-+|.+++-++.=|
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 799999999999999999999998877
No 174
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=28.22 E-value=85 Score=31.66 Aligned_cols=52 Identities=15% Similarity=0.238 Sum_probs=40.1
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccc-eecccCCeEEE
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGL-IEKKLKNRIQW 197 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGL-IeK~sKN~i~W 197 (456)
.+.+.++.+ +..+...++|+.|+|+|.-++-.+..|+.-|+ |.......|..
T Consensus 7 ~~il~~L~~--~~~~s~~~LA~~lgvsr~tV~~~l~~L~~~G~~i~~~~~~Gy~L 59 (319)
T PRK11886 7 LQLLSLLAD--GDFHSGEQLGEELGISRAAIWKHIQTLEEWGLDIFSVKGKGYRL 59 (319)
T ss_pred HHHHHHHHc--CCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCceEEecCCeEEe
Confidence 466677754 56788889999999999999999999999999 54433223544
No 175
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=28.11 E-value=59 Score=23.63 Aligned_cols=37 Identities=27% Similarity=0.411 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhh
Q 012778 139 LGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDI 177 (456)
Q Consensus 139 LglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDI 177 (456)
|..+=+.+|.-.-...+| ++..+|+.|||.|+-||-=
T Consensus 2 l~~~E~~~i~~aL~~~~g--n~~~aA~~Lgisr~tL~~k 38 (42)
T PF02954_consen 2 LEEFEKQLIRQALERCGG--NVSKAARLLGISRRTLYRK 38 (42)
T ss_dssp HHHHHHHHHHHHHHHTTT---HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHHHHHhCC--CHHHHHHHHCCCHHHHHHH
Confidence 444556666633333333 4689999999999998853
No 176
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.83 E-value=48 Score=24.08 Aligned_cols=36 Identities=19% Similarity=0.338 Sum_probs=22.1
Q ss_pred HHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhcc
Q 012778 146 FINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIG 185 (456)
Q Consensus 146 FI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIG 185 (456)
.|.++.+ -....++|+.|||.++-+|-|++=.+.-|
T Consensus 10 ii~l~~~----G~s~~~ia~~lgvs~~Tv~~w~kr~~~~G 45 (50)
T PF13384_consen 10 IIRLLRE----GWSIREIAKRLGVSRSTVYRWIKRYREEG 45 (50)
T ss_dssp HHHHHHH----T--HHHHHHHHTS-HHHHHHHHT------
T ss_pred HHHHHHC----CCCHHHHHHHHCcCHHHHHHHHHHccccc
Confidence 4455544 47789999999999999999988764433
No 177
>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=27.66 E-value=1.8e+02 Score=24.79 Aligned_cols=19 Identities=21% Similarity=0.158 Sum_probs=13.3
Q ss_pred cHHHHHhhhcceee--ehhhh
Q 012778 159 DLNKAADTLEVQKR--RIYDI 177 (456)
Q Consensus 159 dLn~aA~~L~VqKR--RIYDI 177 (456)
.+.++|+.+||+.| |.||=
T Consensus 2 ~Ige~a~~~gvs~~tlRyYe~ 22 (107)
T cd04777 2 KIGKFAKKNNITIDTVRHYID 22 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 46788888888777 44543
No 178
>PF12728 HTH_17: Helix-turn-helix domain
Probab=27.10 E-value=34 Score=25.10 Aligned_cols=22 Identities=23% Similarity=0.475 Sum_probs=20.3
Q ss_pred ccHHHHHhhhcceeeehhhhHH
Q 012778 158 LDLNKAADTLEVQKRRIYDITN 179 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItN 179 (456)
+++.++|+.|+|.+..||.+++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999986
No 179
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=27.01 E-value=6.6e+02 Score=26.00 Aligned_cols=141 Identities=19% Similarity=0.238 Sum_probs=81.6
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEE--eecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHH
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQW--KGLDVSRPGEADENASSLQAEVESLTIQERRLDE 231 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W--~G~d~s~~~~~~~~~~~Lq~El~~L~~eE~~LDe 231 (456)
....+...++|++|+|.---+-+=+-=|-.=|||++.+..+|.- +| .+.|...+.+|..
T Consensus 22 ~qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~gR~~Y~iTkkG------------~e~l~~~~~dlr~------- 82 (260)
T COG1497 22 RQPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEGRGEYEITKKG------------AEWLLEQLSDLRR------- 82 (260)
T ss_pred hCCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecCCeeEEEehhH------------HHHHHHHHHHHHH-------
Confidence 34568999999999998777777777777889999966555543 22 2223222222221
Q ss_pred HHHHHHHHHHhhhhccccccccccchhhhccCC----CCCCCeEEEeeCCCC--CeEEecCCCcccCCCCCceEEEEecC
Q 012778 232 QIRIMQERLRDLSEDENNQKWLFVTEDDIKSLP----CFQNETLIAIKAPHG--TTLEVPDPDEAVDYPQRRYRIVLRST 305 (456)
Q Consensus 232 lI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~l~----~f~~qTvIAIKAP~g--T~LEVPdPde~~~~~qr~YqI~LkS~ 305 (456)
.+.+...-|... .-|.-+..+||+.=. .+++-.+.|=+.+.| |-.-+-+-.++.+.+-..+.=.+--+
T Consensus 83 f~~ev~~~l~~~------~vw~AIA~edI~~Gd~V~L~M~dG~LyA~~~~kg~A~g~A~~dA~~GedV~it~i~G~Id~e 156 (260)
T COG1497 83 FSEEVELVLDYV------MVWTAIAKEDIKEGDTVYLRMKDGYLYASRSAKGGATGVALTDAEKGEDVGITEIGGMIDVE 156 (260)
T ss_pred HHHHHHHHHhhH------HHHHHhhHhhhccCCEEEEEecCcEEEEeccCCCcceeEEecccccCCeeeeeeccCcccCC
Confidence 111111111111 135566777776511 357888999999998 54555555554443322222223345
Q ss_pred CCceEEEEecCcch
Q 012778 306 MGPIDVYLVSQFEE 319 (456)
Q Consensus 306 ~GPIdVyL~~~~~~ 319 (456)
.|.|.++.++.-.+
T Consensus 157 ~G~v~i~~vP~~~~ 170 (260)
T COG1497 157 KGEVTIVKVPGVAE 170 (260)
T ss_pred CCeEEEEECCCccc
Confidence 67888888875543
No 180
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=26.92 E-value=1.7e+02 Score=26.93 Aligned_cols=81 Identities=20% Similarity=0.220 Sum_probs=0.0
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhcccee--cccCCeEEEeecCCCCCCchhHHHHHHH------HHHHHHHH-----
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLIE--KKLKNRIQWKGLDVSRPGEADENASSLQ------AEVESLTI----- 224 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLIe--K~sKN~i~W~G~d~s~~~~~~~~~~~Lq------~El~~L~~----- 224 (456)
+.+.++|+.+||+.|-| -..|-+|||. +...|.|++-..... .--..+..|+ +|+..+-.
T Consensus 8 ~~IgevAk~~Gvs~~TL----RyYE~~GLl~p~~r~~~gyR~Y~~~~l---~rl~~I~~lr~~G~sL~eI~~ll~~~~~~ 80 (144)
T PRK13752 8 LTIGVFAKAAGVNVETI----RFYQRKGLLPEPDKPYGSIRRYGEADV---TRVRFVKSAQRLGFSLDEIAELLRLEDGT 80 (144)
T ss_pred ccHHHHHHHHCcCHHHH----HHHHHCCCCCCCccCCCCCeecCHHHH---HHHHHHHHHHHcCCCHHHHHHHHhccCCC
Q ss_pred ----HHHHHHHHHHHHHHHHHhhhh
Q 012778 225 ----QERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 225 ----eE~~LDelI~~~~q~Lr~Lte 245 (456)
...-|.+.+..+.+++.+|..
T Consensus 81 ~~~~~~~ll~~k~~~l~~~i~~L~~ 105 (144)
T PRK13752 81 HCEEASSLAEHKLKDVREKMADLAR 105 (144)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHH
No 181
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=26.24 E-value=72 Score=28.33 Aligned_cols=32 Identities=22% Similarity=0.401 Sum_probs=25.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 012778 208 ADENASSLQAEVESLTIQERRLDEQIRIMQER 239 (456)
Q Consensus 208 ~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~ 239 (456)
+..++..+++|++.|.+.+..|...|+.+++.
T Consensus 55 l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 55 LQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34456677888888888888888888888777
No 182
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=26.23 E-value=1e+02 Score=28.79 Aligned_cols=42 Identities=24% Similarity=0.392 Sum_probs=37.8
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeE
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRI 195 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i 195 (456)
.+|.+-..++|+.|+|..--.-..+|=|+..|||++.....|
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi 62 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGV 62 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCe
Confidence 789999999999999999999999999999999998644433
No 183
>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=26.21 E-value=1.6e+02 Score=24.84 Aligned_cols=36 Identities=17% Similarity=0.296 Sum_probs=23.2
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhccceec--ccCCeEEEe
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIEK--KLKNRIQWK 198 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK--~sKN~i~W~ 198 (456)
.+.++|+.+||..+-|- -.|..|||.- ...|.|++-
T Consensus 2 ~i~eva~~~gvs~~tlR----~ye~~Gll~p~~~~~~gyR~Y 39 (97)
T cd04782 2 TTGEFAKLCGISKQTLF----HYDKIGLFKPEIVKENGYRYY 39 (97)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCCccC
Confidence 46788999999877553 3366788743 334555544
No 184
>PF05103 DivIVA: DivIVA protein; InterPro: IPR007793 The Bacillus subtilis divIVA1 mutation causes misplacement of the septum during cell division, resulting in the formation of small, circular, anucleate minicells []. Inactivation of divIVA produces a minicell phenotype, whereas overproduction of DivIVA results in a filamentation phenotype []. These proteins appear to contain coiled-coils.; PDB: 2WUK_C 2WUJ_A.
Probab=26.21 E-value=31 Score=29.85 Aligned_cols=48 Identities=31% Similarity=0.463 Sum_probs=33.4
Q ss_pred EEEeecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 195 IQWKGLDVSRPGEADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 195 i~W~G~d~s~~~~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
..|+|.+. .+++..+..|..++..|..+-..|...|..++.+|..+..
T Consensus 13 ~~~rGYd~---~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~ 60 (131)
T PF05103_consen 13 KSMRGYDP---DEVDDFLDELAEELERLQRENAELKEEIEELQAQLEELRE 60 (131)
T ss_dssp EEEEEEEH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT------
T ss_pred CCCCCcCH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Confidence 56788775 3677788888888888888888888888877777766644
No 185
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.95 E-value=3e+02 Score=26.22 Aligned_cols=42 Identities=12% Similarity=0.173 Sum_probs=35.0
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
+++..|. ..|.+.-.++|..||+++.-+=-+.+-|+.-|||.
T Consensus 26 ~Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 26 EVLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 3444443 34679999999999999999999999999999999
No 186
>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=25.89 E-value=1.5e+02 Score=26.17 Aligned_cols=9 Identities=33% Similarity=0.047 Sum_probs=3.9
Q ss_pred HHHHHHHhh
Q 012778 144 KKFINLIKH 152 (456)
Q Consensus 144 kKFI~Ll~~ 152 (456)
-+||..++.
T Consensus 45 l~~I~~lr~ 53 (118)
T cd04776 45 LKLILRGKR 53 (118)
T ss_pred HHHHHHHHH
Confidence 344444443
No 187
>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=25.76 E-value=69 Score=27.47 Aligned_cols=49 Identities=24% Similarity=0.371 Sum_probs=38.5
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhc-----ceeeehhhhHHhhhhccceecccCC
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLE-----VQKRRIYDITNVLEGIGLIEKKLKN 193 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~-----VqKRRIYDItNVLEGIGLIeK~sKN 193 (456)
+..++++.++++ .++.+++.+.|. +.+=-||-.++.|+..|+|.|...+
T Consensus 11 ~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 11 LAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 346778887777 899999999886 3444599999999999999997643
No 188
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=25.75 E-value=71 Score=31.49 Aligned_cols=44 Identities=14% Similarity=0.158 Sum_probs=36.4
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhc
Q 012778 141 LLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGI 184 (456)
Q Consensus 141 lLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGI 184 (456)
.+..+.+.++.......++|.++|+.+++++|.|.=+..-.-|+
T Consensus 5 ~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~ 48 (289)
T PRK15121 5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGH 48 (289)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCc
Confidence 35578889999999999999999999999999988777654443
No 189
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=25.74 E-value=1.1e+02 Score=34.00 Aligned_cols=34 Identities=18% Similarity=0.220 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 212 ASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 212 ~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
+..|+.|++.|..+.+.+++.|+.+++.++.|.+
T Consensus 85 LaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~ 118 (475)
T PRK13729 85 YEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAE 118 (475)
T ss_pred HHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHH
Confidence 3344444433334444555555565555555543
No 190
>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=25.65 E-value=70 Score=31.11 Aligned_cols=46 Identities=24% Similarity=0.413 Sum_probs=32.9
Q ss_pred HHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceec
Q 012778 142 LTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 142 LTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK 189 (456)
|...||++++.+ .++.|+.+|..+++..==+-|-|+-|+.-|.|.=
T Consensus 100 lL~~Fi~yIK~~--Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltG 145 (188)
T PF09756_consen 100 LLQEFINYIKEH--KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTG 145 (188)
T ss_dssp HHHHHHHHHHH---SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-E
T ss_pred HHHHHHHHHHHc--ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCcee
Confidence 778999999874 6899999999999966655566677777776653
No 191
>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=25.61 E-value=96 Score=24.02 Aligned_cols=41 Identities=15% Similarity=0.294 Sum_probs=36.2
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCe
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNR 194 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~ 194 (456)
.++.+++.++=+.|+++|+-.-=|..-|...|+..|.+-.+
T Consensus 7 ~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~gd~R 47 (50)
T PF09107_consen 7 KNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVGDKR 47 (50)
T ss_dssp TTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTEE
T ss_pred cCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeCCEE
Confidence 38899999999999999999999999999999999986433
No 192
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=25.60 E-value=33 Score=30.67 Aligned_cols=33 Identities=24% Similarity=0.450 Sum_probs=27.5
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHH
Q 012778 141 LLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITN 179 (456)
Q Consensus 141 lLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItN 179 (456)
.|..+|++.+ -++.+.+|+.|||++.+|-.|+|
T Consensus 13 iL~eeflep~------glt~~~lA~~lgV~r~~is~lin 45 (104)
T COG3093 13 ILREEFLEPL------GLTQTELAEALGVTRNTISELIN 45 (104)
T ss_pred HHHHHHhccc------cCCHHHHHHHhCCCHHHHHHHHc
Confidence 4556777644 37899999999999999999998
No 193
>PF02996 Prefoldin: Prefoldin subunit; InterPro: IPR004127 This entry comprises of several prefoldin subunits. Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal alpha subunit, eukaryotic prefoldin subunits 3 and 5 and the UXT (ubiquitously expressed transcript) family. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 1FXK_C 2ZDI_C.
Probab=25.54 E-value=1.5e+02 Score=25.33 Aligned_cols=69 Identities=14% Similarity=0.160 Sum_probs=33.6
Q ss_pred hhhhHHhhhhccceecccCCeEEEeecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012778 174 IYDITNVLEGIGLIEKKLKNRIQWKGLDVSRPGEADENASSLQAEVESLTIQERRLDEQIRIMQERLRDL 243 (456)
Q Consensus 174 IYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~~~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~L 243 (456)
+-+|...+-.=|-|... ..-+.|.|.+..-....++-+.-++..++.|+..-+.|.+.+..++.++..+
T Consensus 42 lvplg~~~~v~g~i~~~-~~vlV~lG~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~ 110 (120)
T PF02996_consen 42 LVPLGSGVFVPGKIPDT-DKVLVSLGAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQL 110 (120)
T ss_dssp EEEECTTEEEEEE-SST-TEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred eecCCCCeEEEEEeCCC-CEEEEEeeCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444433333444333 3467788866432112333344555555555555555555555555555544
No 194
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=25.41 E-value=1.8e+02 Score=27.57 Aligned_cols=30 Identities=33% Similarity=0.485 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 012778 213 SSLQAEVESLTIQERRLDEQIRIMQERLRD 242 (456)
Q Consensus 213 ~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~ 242 (456)
+.++.+|..|..+-..||+.|+.+..+|..
T Consensus 25 q~~~~~I~~L~~e~~~ld~~i~~~~~~L~~ 54 (188)
T PF10018_consen 25 QENQARIQQLRAEIEELDEQIRDILKQLKE 54 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666666666666666555555443
No 195
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=25.38 E-value=1.3e+02 Score=30.22 Aligned_cols=35 Identities=23% Similarity=0.285 Sum_probs=17.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012778 209 DENASSLQAEVESLTIQERRLDEQIRIMQERLRDL 243 (456)
Q Consensus 209 ~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~L 243 (456)
..++..||.||..|+.+-+++.-.|..++++-+++
T Consensus 60 ~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~ 94 (263)
T PRK10803 60 QQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQI 94 (263)
T ss_pred HHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555554444444444444444444
No 196
>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=25.34 E-value=2.7e+02 Score=25.95 Aligned_cols=35 Identities=14% Similarity=0.153 Sum_probs=32.5
Q ss_pred CCCcccHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 154 EDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 154 pdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
..+.+.-.++|..||++++-+=-|.+.|...|||.
T Consensus 25 ~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 25 IKGEFTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 36679999999999999999999999999999995
No 197
>PF15358 TSKS: Testis-specific serine kinase substrate
Probab=25.30 E-value=1.1e+02 Score=33.75 Aligned_cols=65 Identities=26% Similarity=0.452 Sum_probs=40.6
Q ss_pred hhHHhhhhc--cceecccCCeEEEeecCCCCCCchhHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHhhhh
Q 012778 176 DITNVLEGI--GLIEKKLKNRIQWKGLDVSRPGEADENASSLQAEVESLT-------IQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 176 DItNVLEGI--GLIeK~sKN~i~W~G~d~s~~~~~~~~~~~Lq~El~~L~-------~eE~~LDelI~~~~q~Lr~Lte 245 (456)
||+.+|+|+ ||+ +.|++|.=.-.. ...+.++++.||.|..-|. ++-.+|++.-..+.+..+.++.
T Consensus 108 Di~~~l~gvnSGLv--rAKDSItSlKek---t~~vnQHVq~LQseCsvlsEnLErrrQEaeELEgyCsqLk~nCrkVt~ 181 (558)
T PF15358_consen 108 DITELLEGVNSGLV--RAKDSITSLKEK---TSRVNQHVQTLQSECSVLSENLERRRQEAEELEGYCSQLKENCRKVTR 181 (558)
T ss_pred cHHHHHhhhcccce--ecccchhhHHHh---hHHHHHHHHHHHHHhHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhh
Confidence 677777776 677 567776532211 2256788999998876543 3334566666666666666654
No 198
>TIGR02338 gimC_beta prefoldin, beta subunit, archaeal. Chaperonins are cytosolic, ATP-dependent molecular chaperones, with a conserved toroidal architecture, that assist in the folding of nascent and/or denatured polypeptide chains. The group I chaperonin system consists of GroEL and GroES, and is found (usually) in bacteria and organelles of bacterial origin. The group II chaperonin system, called the thermosome in Archaea and TRiC or CCT in the Eukaryota, is structurally similar but only distantly related. Prefoldin, also called GimC, is a complex in Archaea and Eukaryota, that works with group II chaperonins. Members of this protein family are the archaeal clade of the beta class of prefoldin subunit. Closely related, but outside the scope of this family are the eukaryotic beta-class prefoldin subunits, Gim-1,3,4 and 6. The alpha class prefoldin subunits are more distantly related.
Probab=25.20 E-value=1.2e+02 Score=26.34 Aligned_cols=32 Identities=25% Similarity=0.476 Sum_probs=19.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 012778 213 SSLQAEVESLTIQERRLDEQIRIMQERLRDLS 244 (456)
Q Consensus 213 ~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lt 244 (456)
..|+..++.|+..-..|++.+..++.+|.++-
T Consensus 70 ~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q 101 (110)
T TIGR02338 70 QELKEKKETLELRVKTLQRQEERLREQLKELQ 101 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555556666666666666666666666653
No 199
>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=25.09 E-value=2.3e+02 Score=23.88 Aligned_cols=37 Identities=14% Similarity=0.216 Sum_probs=23.9
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhccceec--ccCCeEEEee
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIEK--KLKNRIQWKG 199 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK--~sKN~i~W~G 199 (456)
.+.++|+.+||..+-|- -.|..|||.. ...|.++.-.
T Consensus 2 ~i~eva~~~gvs~~tlR----~ye~~Gll~p~~r~~~gyR~Y~ 40 (96)
T cd04788 2 KIGELARRTGLSVRTLH----HYDHIGLLSPSQRTEGGHRLYD 40 (96)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCceeeC
Confidence 46789999999877432 2356788854 3346565544
No 200
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=24.80 E-value=99 Score=31.28 Aligned_cols=61 Identities=28% Similarity=0.342 Sum_probs=50.1
Q ss_pred CcHHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEe
Q 012778 137 SSLGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWK 198 (456)
Q Consensus 137 ~SLglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~ 198 (456)
..|-.-=+.-|+++.. .+|.+.-+++.+.||..|=-++=|+-=||-.|||+|..++.=.|.
T Consensus 191 ~~L~~~e~~il~~i~~-~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V 251 (258)
T COG2512 191 YDLNEDEKEILDLIRE-RGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIV 251 (258)
T ss_pred CCCCHHHHHHHHHHHH-hCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEE
Confidence 3444555677777766 699999999999999999999999999999999999877655443
No 201
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=24.63 E-value=1.4e+02 Score=29.01 Aligned_cols=36 Identities=25% Similarity=0.353 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 210 ENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 210 ~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
.-|+.|++|+..+...+...+.++..+.++.+.|++
T Consensus 27 ~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~e 62 (201)
T PF13851_consen 27 ELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSE 62 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 347889999999999999988888888877777665
No 202
>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=24.54 E-value=2.5e+02 Score=23.90 Aligned_cols=28 Identities=18% Similarity=0.369 Sum_probs=20.4
Q ss_pred ccHHHHHhhhcceeeehhhhHHhhhhccceec
Q 012778 158 LDLNKAADTLEVQKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 158 idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK 189 (456)
+.+.++|+.+||+.+-|--. |..|+|.-
T Consensus 2 ~~i~eva~~~gVs~~tLR~y----e~~Gli~p 29 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVY----DRLGLVSP 29 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHH----HHCCCCCC
Confidence 56889999999988765444 45667653
No 203
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=24.38 E-value=47 Score=27.28 Aligned_cols=23 Identities=30% Similarity=0.580 Sum_probs=18.4
Q ss_pred cCCCceEEEEecCcchhhhhccC
Q 012778 304 STMGPIDVYLVSQFEEKFEEIHG 326 (456)
Q Consensus 304 S~~GPIdVyL~~~~~~~~e~~~~ 326 (456)
|..|+|+|+.+..++...+.+.|
T Consensus 16 s~lG~I~vLYvn~~eS~~~~~~G 38 (62)
T PF15513_consen 16 SQLGEIAVLYVNPYESDEDRLTG 38 (62)
T ss_pred HhcCcEEEEEEcccccCCCeEec
Confidence 78999999999988876555544
No 204
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=24.37 E-value=61 Score=30.78 Aligned_cols=39 Identities=13% Similarity=0.217 Sum_probs=35.5
Q ss_pred CCCCcc-cHHHHHhhhcceeeehhhhHHhhhhccceeccc
Q 012778 153 AEDGIL-DLNKAADTLEVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 153 apdg~i-dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.++..+ .-.++|++|||+|=-|-+-+..|+.-|||+...
T Consensus 26 ~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 477788 799999999999999999999999999999653
No 205
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=24.35 E-value=1.6e+02 Score=25.78 Aligned_cols=61 Identities=15% Similarity=0.168 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccccccccchhhhcc-CC-CCCCCeEEEeeCC
Q 012778 211 NASSLQAEVESLTIQERRLDEQIRIMQERLRDLSEDENNQKWLFVTEDDIKS-LP-CFQNETLIAIKAP 277 (456)
Q Consensus 211 ~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~-l~-~f~~qTvIAIKAP 277 (456)
....++++++.++.+-++|.+....++.++..|.++. .||.+. .+. +- .-.|+++|-|.-|
T Consensus 28 ~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~-----dyiEe~-AR~~Lg~vk~gEivy~~~~~ 90 (105)
T PRK00888 28 DYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQ-----EAIEER-ARNELGMVKPGETFYRIVPD 90 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcH-----HHHHHH-HHHHcCCCCCCCEEEEeCCC
Confidence 4678889999999999999999999999999997753 243322 221 11 2256777655544
No 206
>PF03836 RasGAP_C: RasGAP C-terminus; InterPro: IPR000593 Ras GTPase-activating protein (rasGAP) is a major contributor to the down-regulation of ras by facilitating GTP hydrolysis of activated ras. In addition, GAP participates in the down-stream effector system of the ras signalling pathway. Abnormal signal transduction involving activated ras genes plays a major role in the development of a variety of tumours. Depending on the precise genetic alteration, its location within the gene and the effects it exerts on protein function, rasGAP can theoretically function as either an oncogene or as a tumour suppressor gene [].; GO: 0005099 Ras GTPase activator activity, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 3ISU_A 3IEZ_A 4EZA_B 1X0H_A.
Probab=24.16 E-value=26 Score=31.88 Aligned_cols=26 Identities=27% Similarity=0.459 Sum_probs=0.0
Q ss_pred eeeehhhhHHhhhhccceecccCCeEEE
Q 012778 170 QKRRIYDITNVLEGIGLIEKKLKNRIQW 197 (456)
Q Consensus 170 qKRRIYDItNVLEGIGLIeK~sKN~i~W 197 (456)
-|+++-+-+..||.+|+|.+. |.|+=
T Consensus 5 lk~~~l~~l~~LE~~G~v~~~--n~yQ~ 30 (142)
T PF03836_consen 5 LKKKILENLKELESLGIVSRS--NNYQD 30 (142)
T ss_dssp ----------------------------
T ss_pred HHHHHHHHHHHHHHCCCCCCc--ccHHH
Confidence 467888889999999999998 66654
No 207
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=24.13 E-value=80 Score=29.89 Aligned_cols=37 Identities=32% Similarity=0.444 Sum_probs=31.0
Q ss_pred CCcccHHHHHhhhcceeee--------------hhhhHHhhhhccceeccc
Q 012778 155 DGILDLNKAADTLEVQKRR--------------IYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 155 dg~idLn~aA~~L~VqKRR--------------IYDItNVLEGIGLIeK~s 191 (456)
.+.+-+..++..+|..||| |=-|+.+||.+|||+|..
T Consensus 65 ~gpvGV~~L~~~yGg~k~~G~~P~h~~~~sg~iiR~~LqqLE~~glVek~~ 115 (150)
T PRK09333 65 DGPVGVERLRTAYGGRKNRGVRPEHFVKGSGSIIRKILQQLEKAGLVEKTK 115 (150)
T ss_pred cCCccHHHHHHHHCCCcCCCCCCCccccCccHHHHHHHHHHHHCCCeeeCC
Confidence 5567788888999996664 778999999999999864
No 208
>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=24.00 E-value=2.3e+02 Score=23.93 Aligned_cols=17 Identities=18% Similarity=0.198 Sum_probs=11.6
Q ss_pred cHHHHHhhhcceeeehh
Q 012778 159 DLNKAADTLEVQKRRIY 175 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIY 175 (456)
.+.++|+.+||..+-|-
T Consensus 2 ti~eva~~~gvs~~tlR 18 (103)
T cd01106 2 TVGEVAKLTGVSVRTLH 18 (103)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 46677788887766554
No 209
>PF10141 ssDNA-exonuc_C: Single-strand DNA-specific exonuclease, C terminal domain; InterPro: IPR018779 This entry represents a domain found at the C terminus of a set of single-stranded DNA-specific exonucleases, including RecJ. Its function has not, as yet, been determined.
Probab=23.69 E-value=3.7e+02 Score=25.57 Aligned_cols=46 Identities=17% Similarity=0.242 Sum_probs=36.6
Q ss_pred HHHHHHhhCCCCcc--cHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 145 KFINLIKHAEDGIL--DLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 145 KFI~Ll~~apdg~i--dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
++..++.+.+.-.+ .+..+|..|++.++-|-=+++|+.-+|+|+-.
T Consensus 102 ~~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~VF~EL~FVti~ 149 (195)
T PF10141_consen 102 KLYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLKVFFELGFVTIE 149 (195)
T ss_pred HHHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCcEEEe
Confidence 45555555544432 56899999999999999999999999999866
No 210
>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=23.67 E-value=92 Score=30.49 Aligned_cols=55 Identities=24% Similarity=0.408 Sum_probs=42.2
Q ss_pred HHHHHHHHHH-HHhhCCCCcccHHHHHhhhcceeeehhhhHH-hhhhccceecccCC
Q 012778 139 LGLLTKKFIN-LIKHAEDGILDLNKAADTLEVQKRRIYDITN-VLEGIGLIEKKLKN 193 (456)
Q Consensus 139 LglLTkKFI~-Ll~~apdg~idLn~aA~~L~VqKRRIYDItN-VLEGIGLIeK~sKN 193 (456)
|...-+.|+. +++.-.++.+.+.++|..||+..+.+..++- .|-..|||++....
T Consensus 236 l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 292 (305)
T TIGR00635 236 LDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRG 292 (305)
T ss_pred CCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCch
Confidence 3334455666 5565566678899999999999999999888 79899999876544
No 211
>PF10779 XhlA: Haemolysin XhlA; InterPro: IPR019715 Haemolysin XhlA is a cell-surface associated haemolysin that lyses the two most prevalent types of insect immune cells (granulocytes and plasmatocytes) as well as rabbit and horse erythrocytes [].
Probab=23.63 E-value=2.1e+02 Score=23.12 Aligned_cols=39 Identities=8% Similarity=0.268 Sum_probs=31.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 012778 208 ADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSED 246 (456)
Q Consensus 208 ~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted 246 (456)
+.+++..++..++++....+.|+........++.++.++
T Consensus 4 i~e~l~~ie~~l~~~~~~i~~lE~~~~~~e~~i~~~~~~ 42 (71)
T PF10779_consen 4 IKEKLNRIETKLDNHEERIDKLEKRDAANEKDIKNLNKQ 42 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456677888888888888888888888888888887665
No 212
>PF10018 Med4: Vitamin-D-receptor interacting Mediator subunit 4; InterPro: IPR019258 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. Members of this family represent the Med4 subunit of the Mediator (Med) complex [, ]. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=23.62 E-value=1.7e+02 Score=27.77 Aligned_cols=55 Identities=24% Similarity=0.286 Sum_probs=37.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc-------cccccccccchhhhcc
Q 012778 208 ADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSED-------ENNQKWLFVTEDDIKS 262 (456)
Q Consensus 208 ~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted-------~~n~~~aYVT~eDI~~ 262 (456)
...++..|++|++.|..+-+.+=..+..|...|..+... .....-.=|+++||.+
T Consensus 27 ~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~~~~~~~~~~~~~~~~~~v~~~eLL~ 88 (188)
T PF10018_consen 27 NQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLPDQADEKLKSIPKAEKRPVDYEELLS 88 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccCCCCHHHHHH
Confidence 345688888888888888888888888888888887621 1111122367777765
No 213
>PF09340 NuA4: Histone acetyltransferase subunit NuA4; InterPro: IPR015418 The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast []. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control [].
Probab=23.51 E-value=1.2e+02 Score=25.56 Aligned_cols=27 Identities=15% Similarity=0.449 Sum_probs=21.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012778 217 AEVESLTIQERRLDEQIRIMQERLRDL 243 (456)
Q Consensus 217 ~El~~L~~eE~~LDelI~~~~q~Lr~L 243 (456)
++|.+|.+.-+.|++.+..++++|-++
T Consensus 2 ~~L~~l~~~k~~Le~~L~~lE~qIy~~ 28 (80)
T PF09340_consen 2 KELKELLQKKKKLEKDLAALEKQIYDK 28 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567777888888888888888888776
No 214
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=23.27 E-value=2.6e+02 Score=21.85 Aligned_cols=34 Identities=18% Similarity=0.406 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 012778 211 NASSLQAEVESLTIQERRLDEQIRIMQERLRDLS 244 (456)
Q Consensus 211 ~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lt 244 (456)
.+..|+.++..|..+-..|-..+..+...+..|.
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~ 60 (64)
T PF00170_consen 27 YIEELEEKVEELESENEELKKELEQLKKEIQSLK 60 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566777777777777777777777777776664
No 215
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=23.25 E-value=6e+02 Score=24.21 Aligned_cols=51 Identities=24% Similarity=0.303 Sum_probs=36.8
Q ss_pred CCCCcHHHHHHHHHHHHhh-CCCCc---------------ccHHHHHhhhcc-eeeehhhhHHhhhhccc
Q 012778 134 RYDSSLGLLTKKFINLIKH-AEDGI---------------LDLNKAADTLEV-QKRRIYDITNVLEGIGL 186 (456)
Q Consensus 134 R~d~SLglLTkKFI~Ll~~-apdg~---------------idLn~aA~~L~V-qKRRIYDItNVLEGIGL 186 (456)
+++-+...|.++|..+.+. .||.. --||+|=..|.- .+|..|++ .|.|+.+
T Consensus 17 ~f~~d~~~L~~~yr~lq~~~HPD~~~~~~~~e~~~a~~~s~~iN~AY~tL~~p~~Ra~Yll--~l~G~~~ 84 (176)
T PRK03578 17 RFALDEAALDAAYRTVQAQVHPDRFAAAGDAEKRVAMQWATRANEAYQTLRDPLKRARYLL--HLRGVDV 84 (176)
T ss_pred CCCCCHHHHHHHHHHHHHHHCcCCCCCCCHHHHHHHHHHHHHHHHHHHHhCChhhHHHHHH--HhcCCCC
Confidence 4667788999999998743 56542 367777777777 57889988 5557665
No 216
>PRK00044 psd phosphatidylserine decarboxylase; Reviewed
Probab=23.21 E-value=25 Score=35.63 Aligned_cols=11 Identities=36% Similarity=0.579 Sum_probs=9.9
Q ss_pred CCCCCccCCCC
Q 012778 29 PGGDYHRFAAE 39 (456)
Q Consensus 29 ~~~~yh~f~~~ 39 (456)
.|.|||||.+|
T Consensus 139 sp~DYHr~HsP 149 (288)
T PRK00044 139 SPRDYHRVHMP 149 (288)
T ss_pred CcceeeEEecc
Confidence 79999999876
No 217
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=23.12 E-value=74 Score=29.99 Aligned_cols=54 Identities=19% Similarity=0.157 Sum_probs=39.9
Q ss_pred HHHHHHHHHhhC-CC--CcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEE
Q 012778 142 LTKKFINLIKHA-ED--GILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQ 196 (456)
Q Consensus 142 LTkKFI~Ll~~a-pd--g~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~ 196 (456)
+..|+..+|... .. ..+.-.++|+.||++|+-+.=+++-|+--|+|++.. ++|.
T Consensus 151 ~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~-~~i~ 207 (226)
T PRK10402 151 LENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSK-RGYL 207 (226)
T ss_pred HHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeC-CEEE
Confidence 345555654322 12 235678999999999999999999999999999874 3443
No 218
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=23.05 E-value=61 Score=24.93 Aligned_cols=32 Identities=22% Similarity=0.371 Sum_probs=22.2
Q ss_pred HHHHhhCCCCcccHHHHHhhhcceeeehhhhHH
Q 012778 147 INLIKHAEDGILDLNKAADTLEVQKRRIYDITN 179 (456)
Q Consensus 147 I~Ll~~apdg~idLn~aA~~L~VqKRRIYDItN 179 (456)
+++++....|. ...++|..+||.+.-|++|..
T Consensus 13 ~~iI~~~e~g~-s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 13 LEIIKRLEEGE-SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HHHHHHHHCTT--HHHHHHHHT--CCHHHHHHH
T ss_pred HHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHH
Confidence 34444445555 899999999999999999986
No 219
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=23.00 E-value=2e+02 Score=27.72 Aligned_cols=36 Identities=25% Similarity=0.489 Sum_probs=18.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 012778 211 NASSLQAEVESLTIQERRLDEQIRIMQERLRDLSED 246 (456)
Q Consensus 211 ~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted 246 (456)
..+.|+.|+..|..+-..|..-+..+.+++..+.+|
T Consensus 105 e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eD 140 (161)
T TIGR02894 105 ENERLKNQNESLQKRNEELEKELEKLRQRLSTIEED 140 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555555555555555555555555444443
No 220
>PRK00723 phosphatidylserine decarboxylase; Provisional
Probab=22.86 E-value=26 Score=35.91 Aligned_cols=14 Identities=43% Similarity=0.498 Sum_probs=11.5
Q ss_pred CCCCCCCCccCCCCC
Q 012778 26 FLAPGGDYHRFAAEP 40 (456)
Q Consensus 26 f~~~~~~yh~f~~~~ 40 (456)
|. .|.|||||.+|-
T Consensus 159 yL-sp~DYHR~HsPv 172 (297)
T PRK00723 159 RL-CPTDYHRFHFPD 172 (297)
T ss_pred EE-CCCeEEEEEccC
Confidence 55 899999998863
No 221
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=22.84 E-value=1.2e+02 Score=27.57 Aligned_cols=39 Identities=15% Similarity=0.210 Sum_probs=33.5
Q ss_pred cccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEE
Q 012778 157 ILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQ 196 (456)
Q Consensus 157 ~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~ 196 (456)
.+...++|..||+.++.+.=+.+-|+.-|+|+... ++|.
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~-~~i~ 206 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHG-KTIV 206 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecC-CEEE
Confidence 46679999999999999999999999999998774 3343
No 222
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.60 E-value=1.3e+02 Score=24.96 Aligned_cols=21 Identities=19% Similarity=0.224 Sum_probs=15.6
Q ss_pred cHHHHHhhhcceeeehhhhHH
Q 012778 159 DLNKAADTLEVQKRRIYDITN 179 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItN 179 (456)
.+.++|+.+||..+.|--..+
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567888888888877665544
No 223
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=22.44 E-value=94 Score=31.02 Aligned_cols=42 Identities=7% Similarity=-0.028 Sum_probs=35.6
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhh
Q 012778 141 LLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLE 182 (456)
Q Consensus 141 lLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLE 182 (456)
....++++++.......++|.++|+.+++++|.|+-.++-.-
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~ 259 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAAT 259 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 345788999999888999999999999999999987776443
No 224
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=22.24 E-value=97 Score=32.74 Aligned_cols=49 Identities=18% Similarity=0.177 Sum_probs=45.9
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhhh-cceeeehhhhHHhhhhccceec
Q 012778 141 LLTKKFINLIKHAEDGILDLNKAADTL-EVQKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 141 lLTkKFI~Ll~~apdg~idLn~aA~~L-~VqKRRIYDItNVLEGIGLIeK 189 (456)
.+.++|+.++-...+..++++.+|..+ ++.++-++.-++.||..-|+-.
T Consensus 220 ~~~k~i~~~l~~~~g~~~s~~~la~~l~~is~~Ti~~Yl~~le~~fll~~ 269 (398)
T COG1373 220 DLMKRILRFLASNIGSPISYSSLARELKGISKDTIRKYLSYLEDAFLLFL 269 (398)
T ss_pred HHHHHHHHHHHhhcCCccCHHHHHHHHhccchHHHHHHHHHHHHhhheEE
Confidence 577899999999999999999999999 7999999999999999999984
No 225
>PLN03239 histone acetyltransferase; Provisional
Probab=22.19 E-value=2e+02 Score=30.70 Aligned_cols=49 Identities=18% Similarity=0.338 Sum_probs=37.2
Q ss_pred cHHHHH------HHHHHHHhhCC--CCcccHHHHHhhhcceeeehhhhHHhhhhccceec
Q 012778 138 SLGLLT------KKFINLIKHAE--DGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEK 189 (456)
Q Consensus 138 SLglLT------kKFI~Ll~~ap--dg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK 189 (456)
-||++. ...+++|.... +..+.|++++...++. .-||+..|+.+|++..
T Consensus 257 dlG~~sY~~YW~~~il~~L~~~~~~~~~~si~dis~~Tgi~---~~DIi~tL~~l~~l~~ 313 (351)
T PLN03239 257 DLGQQAYIPYWGSTIVDFLLNHSGNDSSLSIMDIAKKTSIM---AEDIVFALNQLGILKF 313 (351)
T ss_pred HHHHHHHHHHHHHHHHHHHHhccCCCCCccHHHHHHHhCCC---HHHHHHHHHHCCcEEE
Confidence 467766 23556554443 3579999999999994 5799999999999954
No 226
>PRK13503 transcriptional activator RhaS; Provisional
Probab=22.18 E-value=1e+02 Score=29.51 Aligned_cols=39 Identities=8% Similarity=0.101 Sum_probs=33.7
Q ss_pred HHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHH
Q 012778 141 LLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITN 179 (456)
Q Consensus 141 lLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItN 179 (456)
...+++++++.+.....+.|.++|+.++++++.+.-+..
T Consensus 171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 457889999988888899999999999999999877654
No 227
>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=21.96 E-value=1.8e+02 Score=24.60 Aligned_cols=38 Identities=18% Similarity=0.261 Sum_probs=25.4
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhccceec--ccCCeEEEeec
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIEK--KLKNRIQWKGL 200 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIeK--~sKN~i~W~G~ 200 (456)
.+.++|+.+||..+-|- -.|..|||.- ...|.|++-+.
T Consensus 2 ti~eva~~~gvs~~tLR----yye~~Gll~p~~~~~~gyR~Y~~ 41 (96)
T cd04768 2 TIGEFAKLAGVSIRTLR----HYDDIGLFKPAKIAENGYRYYSY 41 (96)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCeeeCCH
Confidence 57889999999887542 2356688853 34567776553
No 228
>KOG3501 consensus Molecular chaperone Prefoldin, subunit 1 [Posttranslational modification, protein turnover, chaperones]
Probab=21.95 E-value=2.1e+02 Score=26.05 Aligned_cols=40 Identities=18% Similarity=0.352 Sum_probs=34.8
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 012778 207 EADENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSED 246 (456)
Q Consensus 207 ~~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted 246 (456)
..+..++.+++.++.|+.+...|+....++.+.|++|.+.
T Consensus 71 ~leak~k~see~IeaLqkkK~YlEk~v~eaE~nLrellqs 110 (114)
T KOG3501|consen 71 HLEAKMKSSEEKIEALQKKKTYLEKTVSEAEQNLRELLQS 110 (114)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4566677888899999999999999999999999999764
No 229
>PF09904 HTH_43: Winged helix-turn helix; InterPro: IPR017162 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.; PDB: 3KE2_B.
Probab=21.93 E-value=94 Score=27.28 Aligned_cols=30 Identities=17% Similarity=0.296 Sum_probs=23.2
Q ss_pred cHHHHHhhhcceeeehhhhHHhhhhcccee
Q 012778 159 DLNKAADTLEVQKRRIYDITNVLEGIGLIE 188 (456)
Q Consensus 159 dLn~aA~~L~VqKRRIYDItNVLEGIGLIe 188 (456)
++..+.+..|..||-+.|.++.|.++|+.-
T Consensus 23 nvp~L~~~TGmPrRT~Qd~i~aL~~~~I~~ 52 (90)
T PF09904_consen 23 NVPALMEATGMPRRTIQDTIKALPELGIEC 52 (90)
T ss_dssp -HHHHHHHH---HHHHHHHHHGGGGGT-EE
T ss_pred cHHHHHHHhCCCHhHHHHHHHHhhcCCeEE
Confidence 889999999999999999999999999754
No 230
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=21.33 E-value=68 Score=35.49 Aligned_cols=25 Identities=20% Similarity=0.426 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 012778 211 NASSLQAEVESLTIQERRLDEQIRI 235 (456)
Q Consensus 211 ~~~~Lq~El~~L~~eE~~LDelI~~ 235 (456)
++++|++||++|+++-..|++.|..
T Consensus 32 kie~L~kql~~Lk~q~~~l~~~v~k 56 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDLNDRVDK 56 (489)
T ss_pred HHHHHHHHHHHHHHhhcccccccch
Confidence 4555555555555554444444433
No 231
>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=21.20 E-value=1.5e+02 Score=30.97 Aligned_cols=63 Identities=17% Similarity=0.236 Sum_probs=46.1
Q ss_pred cHHHHHHHHHHHHhhC-CCCcccHHHHHhh-hcceeeehhhhHHhhhhccceec-ccCCeEEEeec
Q 012778 138 SLGLLTKKFINLIKHA-EDGILDLNKAADT-LEVQKRRIYDITNVLEGIGLIEK-KLKNRIQWKGL 200 (456)
Q Consensus 138 SLglLTkKFI~Ll~~a-pdg~idLn~aA~~-L~VqKRRIYDItNVLEGIGLIeK-~sKN~i~W~G~ 200 (456)
.|..+.++++++|..+ ....+...++... .++...-+-.++|-|..-|+|+= +..+.+.|+-.
T Consensus 6 ~~~~~~~~l~~~~~~~~~~~~~~~~~L~~~~~~~~~~~~~~~in~Ll~~~~~~~~~~~~~l~~~~~ 71 (327)
T PF05158_consen 6 KLSELEKKLLELCRENPSPKGFSQEDLQQLIPGLDLQELVKAINELLSSGLLKLLKKGGGLSYKAV 71 (327)
T ss_dssp -HHHHHHHHHHHHHH---SS-EEHHHHHHH-TTS-HHHHHHHHHHHHHHTSEEEEE-SSSEEEEE-
T ss_pred hHHHHHHHHHHHHHHhcCCCCcCHHHHHhhcCCCCHHHHHHHHHHHHhCCCEEEEEcCCEEEEEEe
Confidence 7889999999999887 6667777777777 67788999999999999998873 24566777654
No 232
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=20.92 E-value=1.2e+02 Score=34.51 Aligned_cols=55 Identities=15% Similarity=0.272 Sum_probs=45.9
Q ss_pred HHHHHHHhhCCCCcccHHHHHhhhccee----eehhhhHHhhhhccceecccCCeEEEe
Q 012778 144 KKFINLIKHAEDGILDLNKAADTLEVQK----RRIYDITNVLEGIGLIEKKLKNRIQWK 198 (456)
Q Consensus 144 kKFI~Ll~~apdg~idLn~aA~~L~VqK----RRIYDItNVLEGIGLIeK~sKN~i~W~ 198 (456)
.+.+++++......+.+++++..|++.+ .-|+.+++-|+.-|.|.|..++.|...
T Consensus 5 ~~il~~l~~~~~~~~~~~~l~~~l~~~~~~~~~~l~~~l~~l~~~g~l~~~~~~~~~~~ 63 (709)
T TIGR02063 5 ELILEFLKSKKGKPISLKELAKAFHLKGADEKKALRKRLRALEDDGLVKKNRRGLYALP 63 (709)
T ss_pred HHHHHHHHhCCCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEecC
Confidence 3577888888889999999999999953 459999999999999998777766543
No 233
>PRK11642 exoribonuclease R; Provisional
Probab=20.78 E-value=1.2e+02 Score=35.45 Aligned_cols=51 Identities=8% Similarity=0.048 Sum_probs=41.4
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcce----eeehhhhHHhhhhccceecccCCeEE
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQ----KRRIYDITNVLEGIGLIEKKLKNRIQ 196 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~Vq----KRRIYDItNVLEGIGLIeK~sKN~i~ 196 (456)
+.+++|.. .+..+.+++++..|++. +..|..+++-|+..|.|.+..++.|.
T Consensus 23 ~Il~~l~~-~~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~~~~~~ 77 (813)
T PRK11642 23 FILEHLTK-REKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYA 77 (813)
T ss_pred HHHHHHHh-cCCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEe
Confidence 35666665 34899999999999996 35599999999999999987767663
No 234
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=20.77 E-value=2.4e+02 Score=27.03 Aligned_cols=28 Identities=18% Similarity=0.367 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 012778 219 VESLTIQERRLDEQIRIMQERLRDLSED 246 (456)
Q Consensus 219 l~~L~~eE~~LDelI~~~~q~Lr~Lted 246 (456)
++-|..+.+.|++.|..+++.|..+.++
T Consensus 87 ~~lLe~~~~~l~~ri~eLe~~l~~kad~ 114 (175)
T PRK13182 87 FEQLEAQLNTITRRLDELERQLQQKADD 114 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3556666677777777777777766655
No 235
>PF10805 DUF2730: Protein of unknown function (DUF2730); InterPro: IPR020269 This entry represents a family of various hypothetical proteins. The proteins, which include HI1498 and Gp25, from phage Mu, are currently uncharacterised.
Probab=20.75 E-value=5.7e+02 Score=22.32 Aligned_cols=81 Identities=22% Similarity=0.343 Sum_probs=58.0
Q ss_pred HHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEEEeecCCCCCCchhHHHHHHHHHHHHHHH
Q 012778 145 KFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQWKGLDVSRPGEADENASSLQAEVESLTI 224 (456)
Q Consensus 145 KFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~W~G~d~s~~~~~~~~~~~Lq~El~~L~~ 224 (456)
-|.-++...---.-++..+.+++.-..+|+-.|=+.|+.+ | ..+++..|+-++..++.
T Consensus 22 ~~~~~l~~~~a~~~~~~~l~~~~~~~~~Rl~~lE~~l~~L--------------------P--t~~dv~~L~l~l~el~G 79 (106)
T PF10805_consen 22 IFWLWLRRTYAKREDIEKLEERLDEHDRRLQALETKLEHL--------------------P--TRDDVHDLQLELAELRG 79 (106)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHhC--------------------C--CHHHHHHHHHHHHHHHh
Confidence 3444444332334678888888888888887766655432 1 13468889999999999
Q ss_pred HHHHHHHHHHHHHHHHHhhhhcc
Q 012778 225 QERRLDEQIRIMQERLRDLSEDE 247 (456)
Q Consensus 225 eE~~LDelI~~~~q~Lr~Lted~ 247 (456)
+=+.|...|+-+..++.-|.|.+
T Consensus 80 ~~~~l~~~l~~v~~~~~lLlE~~ 102 (106)
T PF10805_consen 80 ELKELSARLQGVSHQLDLLLENE 102 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999988888754
No 236
>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=20.74 E-value=2.2e+02 Score=27.43 Aligned_cols=33 Identities=21% Similarity=0.230 Sum_probs=29.4
Q ss_pred cHHHHHhhh-cceeeehhhhHHhhhhccceeccc
Q 012778 159 DLNKAADTL-EVQKRRIYDITNVLEGIGLIEKKL 191 (456)
Q Consensus 159 dLn~aA~~L-~VqKRRIYDItNVLEGIGLIeK~s 191 (456)
.=..+|+.+ |+.-|.|.=.+..|...|||.+..
T Consensus 72 SN~~La~r~~G~s~~tlrR~l~~LveaGLI~rrD 105 (177)
T PF03428_consen 72 SNAQLAERLNGMSERTLRRHLARLVEAGLIVRRD 105 (177)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHCCCeeecc
Confidence 346889999 999999999999999999999864
No 237
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=20.66 E-value=1.2e+02 Score=27.38 Aligned_cols=50 Identities=12% Similarity=0.168 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHhhCCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecc
Q 012778 139 LGLLTKKFINLIKHAEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKK 190 (456)
Q Consensus 139 LglLTkKFI~Ll~~apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~ 190 (456)
|-.+=++.+.+|+. ++.....++|+.||++.-.+..=++=|+.-|+|.+.
T Consensus 7 lD~~D~~Il~~Lq~--d~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 7 IDNLDRGILEALME--NARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred cCHHHHHHHHHHHH--cCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 44566788998876 489999999999999999999999999999999864
No 238
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.55 E-value=1.2e+02 Score=31.42 Aligned_cols=40 Identities=20% Similarity=0.277 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhccccc
Q 012778 211 NASSLQAEVESLTIQERRLDEQIRIMQERLRDLSEDENNQ 250 (456)
Q Consensus 211 ~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lted~~n~ 250 (456)
.++.|++||..|...-..-|++|-+-..+|-+|.-|++++
T Consensus 226 ~i~~lkeeia~Lkk~L~qkdq~ileKdkqisnLKad~e~~ 265 (305)
T KOG3990|consen 226 KIQKLKEEIARLKKLLHQKDQLILEKDKQISNLKADKEYQ 265 (305)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHhhhhhhhccCcchhHH
Confidence 5889999999999999999999999999999998885554
No 239
>PHA02047 phage lambda Rz1-like protein
Probab=20.55 E-value=57 Score=29.07 Aligned_cols=7 Identities=14% Similarity=0.202 Sum_probs=4.2
Q ss_pred EEEeecC
Q 012778 195 IQWKGLD 201 (456)
Q Consensus 195 i~W~G~d 201 (456)
|+|.|..
T Consensus 26 ~r~~g~~ 32 (101)
T PHA02047 26 YRALGIA 32 (101)
T ss_pred HHHHHHH
Confidence 5676643
No 240
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=20.55 E-value=1.4e+02 Score=31.63 Aligned_cols=44 Identities=14% Similarity=0.188 Sum_probs=38.1
Q ss_pred CCCCcccHHHHHhhhcceeeehhhhHHhhhhccceecccCCeEE
Q 012778 153 AEDGILDLNKAADTLEVQKRRIYDITNVLEGIGLIEKKLKNRIQ 196 (456)
Q Consensus 153 apdg~idLn~aA~~L~VqKRRIYDItNVLEGIGLIeK~sKN~i~ 196 (456)
..+..+...++++++++.-+.+-+|..-|+..|||.+...+.|.
T Consensus 306 ~~g~~~t~~~La~~l~~~~~~v~~iL~~L~~agLI~~~~~g~~~ 349 (412)
T PRK04214 306 KHGKALDVDEIRRLEPMGYDELGELLCELARIGLLRRGERGQWV 349 (412)
T ss_pred hcCCCCCHHHHHHHhCCCHHHHHHHHHHHHhCCCeEecCCCceE
Confidence 35568899999999999999999999999999999987656443
No 241
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=20.29 E-value=2.7e+02 Score=22.95 Aligned_cols=37 Identities=24% Similarity=0.466 Sum_probs=32.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 209 DENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 209 ~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
...+..+++.+.+|......|-..|......|+++.+
T Consensus 13 ~P~l~~~~~~l~el~~sQ~~L~~~i~~~~~~L~~~~~ 49 (92)
T PF14712_consen 13 EPDLDRLDQQLQELRQSQEELLQQIDRLNEKLKELNE 49 (92)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457888899999999999999999999999998877
No 242
>cd00890 Prefoldin Prefoldin is a hexameric molecular chaperone complex, found in both eukaryotes and archaea, that binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The complex contains two alpha and four beta subunits, the two subunits being evolutionarily related. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the structure of the hexamer. The structure of the complex consists of a double beta barrel assembly with six protruding coiled-coils.
Probab=20.22 E-value=2.6e+02 Score=23.88 Aligned_cols=36 Identities=31% Similarity=0.475 Sum_probs=23.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012778 208 ADENASSLQAEVESLTIQERRLDEQIRIMQERLRDL 243 (456)
Q Consensus 208 ~~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~L 243 (456)
+..++..|+.+++.|...-..+.+.|..+...|+.+
T Consensus 92 l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~~ 127 (129)
T cd00890 92 LKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQL 127 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445566666666666666666666666666666554
No 243
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=20.21 E-value=2.6e+02 Score=23.59 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=26.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 012778 209 DENASSLQAEVESLTIQERRLDEQIRIMQERLRDL 243 (456)
Q Consensus 209 ~~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~L 243 (456)
...+..|+++++.|+.+...+...+.-+..++.-|
T Consensus 69 ~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~L 103 (104)
T PF13600_consen 69 SPELKELEEELEALEDELAALQDEIQALEAQIAFL 103 (104)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34677888888888888888888888777776544
No 244
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=20.01 E-value=1.8e+02 Score=28.55 Aligned_cols=36 Identities=22% Similarity=0.429 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 012778 210 ENASSLQAEVESLTIQERRLDEQIRIMQERLRDLSE 245 (456)
Q Consensus 210 ~~~~~Lq~El~~L~~eE~~LDelI~~~~q~Lr~Lte 245 (456)
..+..|++|++.|+...+.|..++...+++|..|.+
T Consensus 56 ~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~ 91 (251)
T PF11932_consen 56 AEYRQLEREIENLEVYNEQLERQVASQEQELASLEQ 91 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455555555555555555555555555544433
Done!