Query 015878
Match_columns 399
No_of_seqs 212 out of 459
Neff 3.9
Searched_HMMs 46136
Date Fri Mar 29 01:44:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015878.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015878hhsearch_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 5.2E-66 1.1E-70 510.4 26.3 187 121-313 61-247 (354)
2 PF02319 E2F_TDP: E2F/DP famil 99.9 7.4E-23 1.6E-27 162.1 5.5 66 128-193 1-71 (71)
3 KOG2578 Transcription factor E 99.8 4.7E-20 1E-24 181.0 4.8 87 121-212 14-100 (388)
4 KOG2578 Transcription factor E 99.0 3.6E-10 7.7E-15 112.1 6.7 73 124-196 152-240 (388)
5 KOG2829 E2F-like protein [Tran 99.0 8.5E-09 1.8E-13 101.7 13.0 122 146-283 57-208 (326)
6 PF01978 TrmB: Sugar-specific 94.9 0.033 7.2E-07 42.9 3.7 45 148-192 19-63 (68)
7 COG1378 Predicted transcriptio 93.0 0.66 1.4E-05 45.2 9.3 53 140-195 22-74 (247)
8 PF08279 HTH_11: HTH domain; 92.9 0.18 3.9E-06 37.1 4.2 41 138-179 3-43 (55)
9 smart00346 HTH_ICLR helix_turn 92.4 0.77 1.7E-05 36.4 7.5 48 138-186 8-55 (91)
10 smart00420 HTH_DEOR helix_turn 91.8 0.27 5.9E-06 34.6 3.9 46 139-186 4-49 (53)
11 cd00092 HTH_CRP helix_turn_hel 91.5 0.42 9.2E-06 35.6 4.9 54 136-189 5-63 (67)
12 smart00550 Zalpha Z-DNA-bindin 90.5 0.45 9.8E-06 37.4 4.3 54 138-191 9-62 (68)
13 PF09339 HTH_IclR: IclR helix- 89.3 0.37 8.1E-06 35.5 2.8 45 139-184 7-51 (52)
14 COG3355 Predicted transcriptio 88.6 2.9 6.3E-05 37.6 8.4 87 140-239 33-120 (126)
15 PF13412 HTH_24: Winged helix- 87.4 0.92 2E-05 32.6 3.8 43 138-182 6-48 (48)
16 PF12802 MarR_2: MarR family; 87.2 0.92 2E-05 33.6 3.8 46 139-184 9-54 (62)
17 smart00418 HTH_ARSR helix_turn 86.7 0.82 1.8E-05 32.6 3.2 38 149-186 8-45 (66)
18 PF14394 DUF4423: Domain of un 85.4 10 0.00023 35.0 10.5 98 147-244 35-158 (171)
19 PF13463 HTH_27: Winged helix 83.6 1.6 3.5E-05 32.7 3.7 45 140-184 6-51 (68)
20 PF02082 Rrf2: Transcriptional 82.8 2 4.3E-05 34.5 4.1 49 136-184 9-58 (83)
21 PF01047 MarR: MarR family; I 81.9 1.6 3.4E-05 32.3 3.0 43 141-185 9-51 (59)
22 TIGR02944 suf_reg_Xantho FeS a 81.3 2.1 4.5E-05 36.8 4.0 46 139-184 13-58 (130)
23 PF09079 Cdc6_C: CDC6, C termi 80.5 0.83 1.8E-05 36.7 1.2 31 155-185 26-59 (85)
24 PF13730 HTH_36: Helix-turn-he 80.4 2.1 4.6E-05 31.4 3.2 29 153-181 27-55 (55)
25 cd00090 HTH_ARSR Arsenical Res 79.8 4.2 9.1E-05 29.6 4.7 47 138-187 10-56 (78)
26 cd08768 Cdc6_C Winged-helix do 77.8 1.4 3E-05 35.0 1.7 22 163-184 44-65 (87)
27 smart00345 HTH_GNTR helix_turn 77.7 3.3 7.2E-05 29.7 3.5 41 147-187 15-56 (60)
28 PRK10163 DNA-binding transcrip 77.6 9.7 0.00021 36.9 7.7 55 139-194 29-83 (271)
29 cd00890 Prefoldin Prefoldin is 76.8 10 0.00022 32.0 6.8 55 185-239 68-122 (129)
30 smart00419 HTH_CRP helix_turn_ 76.4 2.7 6E-05 29.2 2.7 38 151-189 8-45 (48)
31 PF00392 GntR: Bacterial regul 75.1 7.5 0.00016 29.6 5.0 50 138-187 7-60 (64)
32 PF04182 B-block_TFIIIC: B-blo 73.7 4.6 9.9E-05 32.3 3.6 49 138-186 5-53 (75)
33 TIGR02147 Fsuc_second hypothet 73.7 33 0.00071 34.2 10.3 94 148-243 134-255 (271)
34 TIGR00122 birA_repr_reg BirA b 72.5 3.7 8E-05 31.7 2.8 53 139-194 4-57 (69)
35 PRK11414 colanic acid/biofilm 71.2 36 0.00078 31.5 9.5 51 138-188 18-71 (221)
36 PF01022 HTH_5: Bacterial regu 70.9 4.7 0.0001 29.2 2.8 34 150-183 14-47 (47)
37 TIGR02231 conserved hypothetic 70.5 29 0.00064 36.8 9.8 99 204-319 138-242 (525)
38 PRK09834 DNA-binding transcrip 68.6 24 0.00053 33.9 8.0 50 140-190 16-66 (263)
39 TIGR00738 rrf2_super rrf2 fami 67.2 8.4 0.00018 32.8 4.1 36 149-184 23-58 (132)
40 cd04766 HTH_HspR Helix-Turn-He 67.1 17 0.00036 29.7 5.6 27 152-182 2-28 (91)
41 PF08220 HTH_DeoR: DeoR-like h 66.6 8.6 0.00019 29.2 3.6 45 138-184 3-47 (57)
42 PHA02943 hypothetical protein; 66.6 15 0.00032 34.5 5.8 49 138-189 14-62 (165)
43 PF09012 FeoC: FeoC like trans 65.9 3.3 7.2E-05 32.3 1.3 42 148-189 11-52 (69)
44 cd00584 Prefoldin_alpha Prefol 65.8 22 0.00047 30.6 6.4 54 186-239 69-122 (129)
45 PF12329 TMF_DNA_bd: TATA elem 65.7 17 0.00038 29.5 5.4 38 202-239 10-47 (74)
46 PF12840 HTH_20: Helix-turn-he 65.7 5.3 0.00012 30.2 2.3 45 139-185 14-58 (61)
47 PRK03947 prefoldin subunit alp 65.6 25 0.00054 30.8 6.8 52 186-237 76-127 (140)
48 PRK05014 hscB co-chaperone Hsc 65.4 73 0.0016 29.5 10.1 96 128-235 12-127 (171)
49 smart00347 HTH_MARR helix_turn 63.3 14 0.00029 28.9 4.3 45 138-184 13-57 (101)
50 PF08784 RPA_C: Replication pr 63.3 8.4 0.00018 31.9 3.3 51 132-182 44-96 (102)
51 TIGR01610 phage_O_Nterm phage 61.7 13 0.00029 30.8 4.2 45 148-194 44-88 (95)
52 PRK10411 DNA-binding transcrip 61.6 43 0.00092 32.3 8.2 54 138-193 7-60 (240)
53 smart00344 HTH_ASNC helix_turn 61.5 10 0.00022 31.2 3.4 47 136-184 4-50 (108)
54 cd07377 WHTH_GntR Winged helix 61.2 15 0.00032 26.8 4.0 38 148-185 21-59 (66)
55 PRK03573 transcriptional regul 61.2 84 0.0018 27.1 9.3 34 151-184 46-79 (144)
56 TIGR02702 SufR_cyano iron-sulf 60.6 68 0.0015 29.8 9.1 45 138-184 4-48 (203)
57 PRK10870 transcriptional repre 60.2 52 0.0011 30.2 8.1 40 145-184 65-104 (176)
58 KOG1318 Helix loop helix trans 60.1 8.8 0.00019 40.6 3.5 75 162-239 239-318 (411)
59 PRK11569 transcriptional repre 59.7 46 0.001 32.3 8.1 47 140-187 33-79 (274)
60 PRK15090 DNA-binding transcrip 59.2 44 0.00095 31.9 7.8 54 139-194 18-71 (257)
61 TIGR02337 HpaR homoprotocatech 59.1 8 0.00017 32.5 2.5 37 149-185 40-76 (118)
62 PF01726 LexA_DNA_bind: LexA D 58.9 9.9 0.00021 30.0 2.8 46 140-185 14-60 (65)
63 PF01325 Fe_dep_repress: Iron 58.8 20 0.00044 27.7 4.5 39 148-186 19-57 (60)
64 COG1414 IclR Transcriptional r 58.0 14 0.00031 35.6 4.3 55 139-194 8-62 (246)
65 COG1474 CDC6 Cdc6-related prot 58.0 7.2 0.00016 40.1 2.4 30 153-182 303-332 (366)
66 cd00632 Prefoldin_beta Prefold 57.9 18 0.00039 30.5 4.4 76 158-237 22-103 (105)
67 smart00529 HTH_DTXR Helix-turn 57.5 11 0.00024 30.2 3.0 33 154-186 2-34 (96)
68 COG1510 Predicted transcriptio 57.5 25 0.00053 33.5 5.6 38 149-186 39-76 (177)
69 TIGR02716 C20_methyl_CrtF C-20 57.4 7.2 0.00016 38.0 2.2 37 149-185 21-57 (306)
70 PF04977 DivIC: Septum formati 56.8 29 0.00062 26.9 5.1 35 205-239 18-52 (80)
71 TIGR00293 prefoldin, archaeal 56.5 38 0.00081 29.0 6.2 54 186-239 68-121 (126)
72 cd04789 HTH_Cfa Helix-Turn-Hel 56.3 41 0.00088 28.3 6.2 38 152-193 2-40 (102)
73 cd04775 HTH_Cfa-like Helix-Tur 56.2 45 0.00098 27.9 6.5 37 152-192 2-39 (102)
74 PRK09413 IS2 repressor TnpA; R 56.1 86 0.0019 27.0 8.4 31 150-180 28-58 (121)
75 PF05732 RepL: Firmicute plasm 55.9 28 0.00062 32.1 5.7 39 151-189 75-113 (165)
76 PF08280 HTH_Mga: M protein tr 55.5 13 0.00028 28.4 2.9 36 139-176 9-44 (59)
77 PRK14165 winged helix-turn-hel 55.5 41 0.0009 32.6 6.9 54 139-192 8-62 (217)
78 TIGR03338 phnR_burk phosphonat 54.8 78 0.0017 28.9 8.4 41 147-187 30-70 (212)
79 cd04770 HTH_HMRTR Helix-Turn-H 53.6 32 0.0007 29.3 5.3 38 152-193 1-40 (123)
80 TIGR01889 Staph_reg_Sar staphy 53.4 18 0.00038 30.4 3.6 45 141-185 31-77 (109)
81 PRK09954 putative kinase; Prov 52.8 14 0.0003 36.7 3.4 47 136-184 4-50 (362)
82 TIGR01764 excise DNA binding d 52.5 8.1 0.00018 26.7 1.2 22 152-173 2-23 (49)
83 TIGR02338 gimC_beta prefoldin, 52.4 40 0.00087 28.7 5.7 83 155-238 20-108 (110)
84 PF13518 HTH_28: Helix-turn-he 52.1 12 0.00025 26.7 2.1 37 140-180 5-41 (52)
85 COG1802 GntR Transcriptional r 51.9 45 0.00098 31.1 6.5 41 147-187 35-75 (230)
86 PF05565 Sipho_Gp157: Siphovir 51.2 1.2E+02 0.0025 27.8 8.9 32 132-163 2-33 (162)
87 TIGR02431 pcaR_pcaU beta-ketoa 51.0 34 0.00073 32.5 5.5 44 140-184 14-57 (248)
88 PRK11050 manganese transport r 50.6 83 0.0018 28.2 7.7 42 149-190 49-90 (152)
89 PRK00215 LexA repressor; Valid 50.3 20 0.00043 33.0 3.8 42 146-187 18-60 (205)
90 PRK11511 DNA-binding transcrip 50.2 23 0.0005 30.6 3.9 43 132-174 6-48 (127)
91 COG2739 Uncharacterized protei 50.1 13 0.00027 32.8 2.3 40 134-173 16-55 (105)
92 COG1777 Predicted transcriptio 49.8 1.2E+02 0.0026 29.9 9.0 47 134-183 13-60 (217)
93 PF13545 HTH_Crp_2: Crp-like h 49.7 16 0.00035 27.9 2.7 51 136-186 3-63 (76)
94 TIGR00498 lexA SOS regulatory 48.2 24 0.00053 32.3 4.0 49 138-186 9-61 (199)
95 TIGR02010 IscR iron-sulfur clu 47.9 25 0.00054 30.7 3.8 39 146-184 20-58 (135)
96 KOG3026 Splicing factor SPF30 47.8 1.1E+02 0.0024 30.8 8.5 82 213-299 25-115 (262)
97 COG4189 Predicted transcriptio 47.0 20 0.00044 36.0 3.5 52 131-184 18-70 (308)
98 PRK09343 prefoldin subunit bet 47.0 57 0.0012 28.6 5.9 73 166-239 35-113 (121)
99 COG1382 GimC Prefoldin, chaper 46.6 58 0.0012 29.2 5.9 70 170-240 38-113 (119)
100 COG1846 MarR Transcriptional r 46.2 25 0.00054 28.1 3.3 44 140-185 27-70 (126)
101 PRK13626 transcriptional regul 45.8 52 0.0011 35.0 6.5 50 134-183 4-55 (552)
102 PF07106 TBPIP: Tat binding pr 45.7 2.3E+02 0.005 25.6 10.3 55 140-195 6-64 (169)
103 PRK09464 pdhR transcriptional 45.6 2.4E+02 0.0051 26.6 10.3 55 132-186 10-69 (254)
104 TIGR02047 CadR-PbrR Cd(II)/Pb( 45.4 70 0.0015 27.9 6.2 81 152-239 1-100 (127)
105 PRK00888 ftsB cell division pr 45.4 1E+02 0.0022 26.5 7.1 58 207-271 30-90 (105)
106 PRK10219 DNA-binding transcrip 45.0 28 0.0006 28.6 3.5 40 135-174 5-44 (107)
107 PF03428 RP-C: Replication pro 44.9 1.3E+02 0.0027 28.5 8.2 33 153-185 72-105 (177)
108 cd01109 HTH_YyaN Helix-Turn-He 44.9 60 0.0013 27.4 5.6 36 153-192 2-39 (113)
109 PRK10225 DNA-binding transcrip 44.6 1.6E+02 0.0034 27.9 9.0 52 135-186 13-68 (257)
110 cd04783 HTH_MerR1 Helix-Turn-H 44.6 1.2E+02 0.0027 26.1 7.6 38 153-194 2-41 (126)
111 PRK11534 DNA-binding transcrip 43.4 99 0.0021 28.6 7.2 48 147-194 26-73 (224)
112 COG3093 VapI Plasmid maintenan 43.2 14 0.0003 32.5 1.4 33 135-173 13-45 (104)
113 TIGR02297 HpaA 4-hydroxyphenyl 42.9 21 0.00047 33.7 2.9 43 135-177 186-228 (287)
114 PRK13922 rod shape-determining 42.8 66 0.0014 31.2 6.2 41 202-243 74-114 (276)
115 PF04111 APG6: Autophagy prote 42.4 59 0.0013 32.9 6.0 35 207-241 60-94 (314)
116 PRK13509 transcriptional repre 42.4 25 0.00054 34.0 3.3 47 138-186 8-54 (251)
117 PF10779 XhlA: Haemolysin XhlA 42.2 89 0.0019 24.8 5.9 36 204-239 13-48 (71)
118 PRK00888 ftsB cell division pr 42.2 37 0.00081 29.2 4.0 54 200-254 30-83 (105)
119 PRK13752 putative transcriptio 42.1 74 0.0016 28.6 6.0 79 152-239 8-105 (144)
120 TIGR01884 cas_HTH CRISPR locus 41.2 36 0.00078 31.6 4.0 45 140-186 148-192 (203)
121 PRK10857 DNA-binding transcrip 40.8 28 0.0006 32.0 3.2 39 146-184 20-58 (164)
122 PF12793 SgrR_N: Sugar transpo 40.8 1.3E+02 0.0029 26.2 7.2 47 136-182 2-50 (115)
123 PF10018 Med4: Vitamin-D-recep 40.6 85 0.0018 29.2 6.4 30 207-236 25-54 (188)
124 PRK09802 DNA-binding transcrip 40.3 1.8E+02 0.0039 28.6 8.8 53 135-189 17-69 (269)
125 PF04977 DivIC: Septum formati 39.8 86 0.0019 24.2 5.4 30 201-230 21-50 (80)
126 cd04787 HTH_HMRTR_unk Helix-Tu 39.4 1.8E+02 0.004 25.4 7.9 80 152-237 1-112 (133)
127 PHA01750 hypothetical protein 38.9 78 0.0017 26.2 5.0 31 204-234 42-72 (75)
128 PRK03902 manganese transport t 38.8 90 0.0019 27.3 5.9 47 138-186 11-57 (142)
129 COG2894 MinD Septum formation 38.6 13 0.00028 37.2 0.6 27 153-179 42-68 (272)
130 PRK11014 transcriptional repre 38.6 38 0.00082 29.7 3.5 42 146-187 20-61 (141)
131 TIGR02366 DHAK_reg probable di 38.6 34 0.00073 30.0 3.2 36 134-169 6-41 (176)
132 PF05377 FlaC_arch: Flagella a 38.5 1.1E+02 0.0024 24.1 5.7 39 201-239 4-42 (55)
133 PF01920 Prefoldin_2: Prefoldi 38.4 65 0.0014 26.2 4.7 78 157-237 17-95 (106)
134 cd07153 Fur_like Ferric uptake 38.2 48 0.001 27.5 3.9 45 140-185 6-55 (116)
135 PRK03837 transcriptional regul 37.7 3E+02 0.0065 25.5 9.5 52 136-187 18-73 (241)
136 cd04762 HTH_MerR-trunc Helix-T 37.0 31 0.00067 23.4 2.2 23 152-174 1-23 (49)
137 PF05103 DivIVA: DivIVA protei 36.5 16 0.00035 31.1 0.9 48 189-239 13-60 (131)
138 PRK09990 DNA-binding transcrip 36.3 85 0.0018 29.5 5.7 50 138-187 14-67 (251)
139 KOG3990 Uncharacterized conser 36.3 51 0.0011 33.4 4.3 46 199-244 220-265 (305)
140 PF14947 HTH_45: Winged helix- 36.0 35 0.00076 27.3 2.7 42 149-191 17-58 (77)
141 PF01638 HxlR: HxlR-like helix 35.5 34 0.00074 27.8 2.6 40 146-185 13-53 (90)
142 PF09756 DDRGK: DDRGK domain; 35.5 41 0.00089 32.1 3.4 47 136-184 100-146 (188)
143 PF03374 ANT: Phage antirepres 34.9 34 0.00075 28.5 2.6 41 140-184 14-54 (111)
144 COG4519 Uncharacterized protei 34.8 53 0.0012 28.1 3.6 36 147-182 18-53 (95)
145 PHA00738 putative HTH transcri 34.6 1.2E+02 0.0025 26.9 5.8 73 138-217 15-87 (108)
146 PF13851 GAS: Growth-arrest sp 34.5 80 0.0017 30.0 5.2 36 204-239 27-62 (201)
147 PRK11512 DNA-binding transcrip 34.3 32 0.0007 29.9 2.4 37 149-185 52-88 (144)
148 KOG3863 bZIP transcription fac 34.2 87 0.0019 35.0 6.1 69 169-240 479-554 (604)
149 PRK00080 ruvB Holliday junctio 34.1 53 0.0012 32.4 4.2 57 131-187 255-313 (328)
150 PF01920 Prefoldin_2: Prefoldi 34.0 1.6E+02 0.0034 24.0 6.3 39 201-239 66-104 (106)
151 COG1522 Lrp Transcriptional re 33.6 58 0.0013 28.1 3.9 50 133-184 6-55 (154)
152 PRK03578 hscB co-chaperone Hsc 33.3 4.1E+02 0.0088 24.8 9.7 51 128-180 17-84 (176)
153 smart00338 BRLZ basic region l 33.2 1.5E+02 0.0033 22.7 5.8 34 206-239 28-61 (65)
154 PF05491 RuvB_C: Holliday junc 33.2 83 0.0018 26.2 4.4 59 131-189 4-64 (76)
155 TIGR02928 orc1/cdc6 family rep 33.1 44 0.00094 32.9 3.4 31 156-186 319-352 (365)
156 cd04772 HTH_TioE_rpt1 First He 33.1 92 0.002 26.0 4.9 35 153-193 2-40 (99)
157 PF03444 HrcA_DNA-bdg: Winged 33.0 77 0.0017 26.5 4.2 46 138-184 11-56 (78)
158 PF01853 MOZ_SAS: MOZ/SAS fami 32.3 64 0.0014 31.0 4.2 56 131-189 123-185 (188)
159 PF08781 DP: Transcription fac 32.0 1.7E+02 0.0037 27.0 6.7 34 265-305 59-92 (142)
160 cd00592 HTH_MerR-like Helix-Tu 31.8 90 0.002 25.4 4.5 21 153-173 2-22 (100)
161 PF02295 z-alpha: Adenosine de 31.4 97 0.0021 24.6 4.4 57 136-192 5-61 (66)
162 PF15513 DUF4651: Domain of un 31.4 34 0.00074 27.5 1.9 23 298-320 16-38 (62)
163 PF05930 Phage_AlpA: Prophage 30.8 28 0.0006 25.7 1.2 24 150-173 2-25 (51)
164 PRK09391 fixK transcriptional 30.6 90 0.0019 29.1 4.9 39 152-190 180-218 (230)
165 PRK13729 conjugal transfer pil 30.6 92 0.002 33.8 5.4 38 202-239 81-118 (475)
166 PF14257 DUF4349: Domain of un 30.4 77 0.0017 30.5 4.5 87 131-228 59-156 (262)
167 PRK10130 transcriptional regul 30.3 43 0.00094 34.2 2.9 40 134-173 239-278 (350)
168 PF04703 FaeA: FaeA-like prote 30.3 71 0.0015 25.3 3.5 52 140-192 5-59 (62)
169 KOG2747 Histone acetyltransfer 29.9 1.1E+02 0.0023 32.6 5.7 58 132-194 304-367 (396)
170 PRK11886 bifunctional biotin-- 29.6 81 0.0017 31.3 4.6 52 138-191 7-59 (319)
171 PF02954 HTH_8: Bacterial regu 29.3 59 0.0013 23.2 2.7 37 133-171 2-38 (42)
172 PF12728 HTH_17: Helix-turn-he 29.3 31 0.00066 24.9 1.2 22 152-173 2-23 (51)
173 PF13384 HTH_23: Homeodomain-l 29.0 47 0.001 23.6 2.2 36 140-179 10-45 (50)
174 PRK10803 tol-pal system protei 28.9 1.2E+02 0.0027 29.7 5.7 32 208-239 58-89 (263)
175 cd04769 HTH_MerR2 Helix-Turn-H 28.9 1.9E+02 0.0041 24.6 6.2 86 152-239 1-114 (116)
176 PRK09514 zntR zinc-responsive 28.9 1.8E+02 0.004 25.8 6.3 81 152-239 2-102 (140)
177 PF10018 Med4: Vitamin-D-recep 28.6 1.4E+02 0.0031 27.7 5.8 54 202-256 27-88 (188)
178 PF11853 DUF3373: Protein of u 28.5 45 0.00099 36.2 2.8 25 205-229 32-56 (489)
179 PF01475 FUR: Ferric uptake re 28.4 63 0.0014 27.2 3.1 48 139-187 12-64 (120)
180 PRK14127 cell division protein 28.4 1.4E+02 0.0031 26.2 5.4 46 191-239 20-65 (109)
181 KOG0804 Cytoplasmic Zn-finger 28.3 1.1E+02 0.0024 33.2 5.5 32 208-239 418-449 (493)
182 cd04790 HTH_Cfa-like_unk Helix 27.9 1.2E+02 0.0026 28.0 5.0 38 152-195 2-43 (172)
183 PF00170 bZIP_1: bZIP transcri 27.4 2.4E+02 0.0052 21.6 6.0 35 205-239 27-61 (64)
184 PF13551 HTH_29: Winged helix- 27.4 46 0.001 26.8 2.1 27 153-179 14-40 (112)
185 COG1321 TroR Mn-dependent tran 27.3 87 0.0019 28.7 4.0 43 148-190 21-63 (154)
186 PRK09863 putative frv operon r 27.2 1.6E+02 0.0034 31.7 6.6 53 138-195 7-65 (584)
187 COG2512 Predicted membrane-ass 27.0 88 0.0019 31.1 4.3 61 131-192 191-251 (258)
188 PRK15121 right oriC-binding tr 27.0 68 0.0015 31.0 3.5 44 135-178 5-48 (289)
189 COG2919 Septum formation initi 27.0 80 0.0017 27.5 3.6 32 202-233 55-86 (117)
190 PF04297 UPF0122: Putative hel 26.9 39 0.00084 29.4 1.6 40 135-174 17-56 (101)
191 cd04779 HTH_MerR-like_sg4 Heli 26.9 49 0.0011 29.6 2.3 82 152-239 1-102 (134)
192 cd04776 HTH_GnyR Helix-Turn-He 26.9 1.4E+02 0.0031 25.7 5.1 8 138-145 45-52 (118)
193 TIGR02044 CueR Cu(I)-responsiv 26.8 3.5E+02 0.0075 23.4 7.5 81 152-236 1-111 (127)
194 PF10046 BLOC1_2: Biogenesis o 26.8 1.4E+02 0.0029 25.3 4.8 34 204-237 66-99 (99)
195 PF06005 DUF904: Protein of un 26.7 2.1E+02 0.0044 23.4 5.7 38 204-241 18-55 (72)
196 cd04782 HTH_BltR Helix-Turn-He 26.7 1.1E+02 0.0024 25.4 4.3 37 153-193 2-40 (97)
197 cd01108 HTH_CueR Helix-Turn-He 26.6 3.3E+02 0.0071 23.6 7.3 81 152-239 1-107 (127)
198 TIGR02338 gimC_beta prefoldin, 26.5 1.4E+02 0.003 25.5 4.9 32 207-238 70-101 (110)
199 PRK10869 recombination and rep 26.3 90 0.002 33.9 4.6 78 153-240 283-363 (553)
200 PRK04984 fatty acid metabolism 26.3 55 0.0012 30.5 2.6 40 147-186 26-66 (239)
201 TIGR01950 SoxR redox-sensitive 26.0 1.6E+02 0.0035 26.5 5.4 36 152-193 2-40 (142)
202 PF10805 DUF2730: Protein of u 25.9 4.2E+02 0.0092 22.7 8.6 80 140-241 23-102 (106)
203 cd04784 HTH_CadR-PbrR Helix-Tu 25.9 1.7E+02 0.0037 25.2 5.4 87 152-241 1-116 (127)
204 PRK09333 30S ribosomal protein 25.9 75 0.0016 29.6 3.3 37 149-185 65-115 (150)
205 PF04218 CENP-B_N: CENP-B N-te 25.9 53 0.0011 24.8 2.0 42 129-173 3-44 (53)
206 PF02996 Prefoldin: Prefoldin 25.7 1.5E+02 0.0033 24.8 5.0 69 168-237 42-110 (120)
207 cd01279 HTH_HspR-like Helix-Tu 25.7 2.3E+02 0.0051 23.6 6.0 28 152-183 2-29 (98)
208 PTZ00454 26S protease regulato 25.7 6.1E+02 0.013 26.6 10.3 35 205-239 23-57 (398)
209 cd01282 HTH_MerR-like_sg3 Heli 25.5 1.6E+02 0.0035 25.0 5.1 14 153-166 2-15 (112)
210 PF10779 XhlA: Haemolysin XhlA 25.3 2.5E+02 0.0053 22.3 5.8 39 202-240 4-42 (71)
211 PRK11169 leucine-responsive tr 25.2 1.2E+02 0.0025 27.4 4.4 52 131-184 10-61 (164)
212 PF03836 RasGAP_C: RasGAP C-te 25.1 24 0.00052 31.5 0.0 27 164-192 5-31 (142)
213 TIGR00635 ruvB Holliday juncti 24.8 92 0.002 29.9 3.9 56 132-187 235-292 (305)
214 PRK06474 hypothetical protein; 24.7 1E+02 0.0022 28.6 4.0 46 139-185 15-61 (178)
215 PF09940 DUF2172: Domain of un 24.7 36 0.00078 36.0 1.2 35 148-182 352-386 (386)
216 cd01106 HTH_TipAL-Mta Helix-Tu 24.7 3E+02 0.0066 22.8 6.5 17 153-169 2-18 (103)
217 PF14817 HAUS5: HAUS augmin-li 24.6 1.3E+02 0.0029 33.7 5.5 49 186-234 56-109 (632)
218 COG1497 Predicted transcriptio 24.6 7.5E+02 0.016 25.1 10.8 135 150-313 24-170 (260)
219 TIGR00714 hscB Fe-S protein as 24.6 3.2E+02 0.007 24.9 7.2 26 153-180 41-67 (157)
220 PRK01194 V-type ATP synthase s 24.5 2.6E+02 0.0055 26.2 6.7 33 208-240 67-99 (185)
221 PRK13503 transcriptional activ 24.4 89 0.0019 29.3 3.7 39 135-173 171-209 (278)
222 PRK13182 racA polar chromosome 24.0 2E+02 0.0043 27.1 5.8 28 213-240 87-114 (175)
223 PF09904 HTH_43: Winged helix- 23.7 89 0.0019 26.9 3.2 30 153-182 23-52 (90)
224 PRK09393 ftrA transcriptional 23.4 92 0.002 30.5 3.7 41 135-175 218-258 (322)
225 COG1373 Predicted ATPase (AAA+ 23.3 93 0.002 32.3 3.9 50 135-184 220-270 (398)
226 PF10141 ssDNA-exonuc_C: Singl 23.1 3.9E+02 0.0084 25.0 7.6 47 138-184 101-149 (195)
227 PF11932 DUF3450: Protein of u 22.8 2.1E+02 0.0046 27.6 5.9 27 212-238 92-118 (251)
228 PF08317 Spc7: Spc7 kinetochor 22.8 1.9E+02 0.0041 29.2 5.8 68 208-280 234-308 (325)
229 PF13600 DUF4140: N-terminal d 22.8 2.3E+02 0.0049 23.4 5.4 35 203-237 69-103 (104)
230 PF03961 DUF342: Protein of un 22.7 7.6E+02 0.016 25.9 10.4 33 264-307 413-446 (451)
231 PRK01356 hscB co-chaperone Hsc 22.7 5.4E+02 0.012 23.8 8.3 50 129-180 14-78 (166)
232 PF09107 SelB-wing_3: Elongati 22.5 1.3E+02 0.0028 22.9 3.5 41 148-188 7-47 (50)
233 PF09340 NuA4: Histone acetylt 22.4 1.4E+02 0.003 24.7 4.0 29 211-239 2-30 (80)
234 TIGR02063 RNase_R ribonuclease 22.3 1.3E+02 0.0028 33.6 4.9 55 138-192 5-63 (709)
235 cd00890 Prefoldin Prefoldin is 22.3 2.5E+02 0.0054 23.6 5.7 36 202-237 92-127 (129)
236 PRK10402 DNA-binding transcrip 22.1 1.1E+02 0.0025 28.2 3.8 54 136-190 151-207 (226)
237 KOG3501 Molecular chaperone Pr 21.9 2.7E+02 0.0059 24.9 5.8 40 201-240 71-110 (114)
238 PHA02047 phage lambda Rz1-like 21.8 67 0.0015 28.1 2.1 35 189-230 26-60 (101)
239 COG1730 GIM5 Predicted prefold 21.7 2.5E+02 0.0055 25.8 5.9 36 202-237 11-46 (145)
240 PRK10572 DNA-binding transcrip 21.2 92 0.002 29.7 3.1 38 136-173 184-221 (290)
241 PF14712 Snapin_Pallidin: Snap 21.1 2.9E+02 0.0064 22.3 5.7 36 204-239 14-49 (92)
242 PRK04214 rbn ribonuclease BN/u 21.1 1.4E+02 0.0029 31.1 4.5 44 147-190 306-349 (412)
243 PRK11642 exoribonuclease R; Pr 21.0 1.2E+02 0.0026 34.8 4.4 51 139-190 23-77 (813)
244 PRK10421 DNA-binding transcrip 21.0 98 0.0021 29.3 3.2 39 147-185 21-60 (253)
245 PRK05638 threonine synthase; V 21.0 1.4E+02 0.003 31.3 4.6 61 121-184 357-419 (442)
246 PRK01203 prefoldin subunit alp 20.9 2.7E+02 0.0059 25.3 5.8 36 202-237 5-40 (130)
247 PF14282 FlxA: FlxA-like prote 20.7 2E+02 0.0044 24.7 4.8 36 203-238 25-71 (106)
248 PRK03963 V-type ATP synthase s 20.6 5.6E+02 0.012 23.5 8.0 30 211-240 71-100 (198)
249 PRK09975 DNA-binding transcrip 20.5 1E+02 0.0022 27.7 3.1 37 134-170 14-50 (213)
250 PRK15002 redox-sensitivie tran 20.4 2.4E+02 0.0051 25.9 5.5 79 152-239 12-118 (154)
251 COG1730 GIM5 Predicted prefold 20.4 3.8E+02 0.0082 24.7 6.7 28 158-185 26-53 (145)
No 1
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=100.00 E-value=5.2e-66 Score=510.42 Aligned_cols=187 Identities=52% Similarity=0.827 Sum_probs=179.6
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCCCCc
Q 015878 121 LNLSNGCRYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTS 200 (399)
Q Consensus 121 ~tp~~~~R~dkSLglLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~ 200 (399)
.+|...+|+++|||+||+|||.|++++|+|++|||+||++|+|+|||||||||||||||||+|++||+|+|+|.+.+..+
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 55678999999999999999999999999999999999999999999999999999999999999999999999987667
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhhcccccccccHhhhccCCCCCCceEEEEeCCCCceEEecC
Q 015878 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDIASLPCFQNQTLIAIKAPQASYIEVPD 280 (399)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP~gT~LEVPd 280 (399)
+..++.+.|++|++.|.++|+.||++|++|+++|+.|++|..|++|+|||++||++|+.|++|||||||||++|+||||+
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 78888899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcchhhcccceEEEEEecCCCCeEEEEecCCCC
Q 015878 281 PDEDISFLKRQYKMIIRSTTGPIDVYLLSKYQS 313 (399)
Q Consensus 281 P~e~~~~~~~~yqI~LkS~~GPIdVyL~~~~~~ 313 (399)
|++ .+|+|+|+|++||||||||+.++.
T Consensus 221 ~~~------~~~~i~L~s~~GpI~v~l~~~e~~ 247 (354)
T KOG2577|consen 221 PDE------DRYQIRLKSNQGPIDVYLCSEEEG 247 (354)
T ss_pred CCC------CceEEEeccCCCceeEEecccccc
Confidence 984 459999999999999999998885
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=7.4e-23 Score=162.07 Aligned_cols=66 Identities=53% Similarity=0.882 Sum_probs=63.0
Q ss_pred CCCCcHHHHHHHHHHHHHhCCCCcccHHHHHHHh---cc--eeeehhhhHHhhhhccceecccCCeeEEec
Q 015878 128 RYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVL---EV--QKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (399)
Q Consensus 128 R~dkSLglLTkkFI~Ll~~ap~g~ldLn~aA~~L---~V--qKRRIYDItNVLEgIgLIeK~sKN~i~W~G 193 (399)
|+++||+.||++||++|...+++.++|+++|+.| ++ +|||||||+||||++|||+|.+|+.|+|+|
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=99.79 E-value=4.7e-20 Score=181.04 Aligned_cols=87 Identities=37% Similarity=0.611 Sum_probs=79.5
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCCCCc
Q 015878 121 LNLSNGCRYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTS 200 (399)
Q Consensus 121 ~tp~~~~R~dkSLglLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~ 200 (399)
+.+.-++|+++|||+||++|+.++....-..+-|+.||.+|||.|||||||+||||+||++.|.+||.|.|+|+.
T Consensus 14 l~lqvysrkekslgvlv~nfl~lynr~dvdlvgLddaA~KlgVErRRIYDiVNvlEsig~var~~KnqYsWkGf~----- 88 (388)
T KOG2578|consen 14 LDLQVYSRKEKSLGVLVQNFLILYNRSDVDLVGLDDAARKLGVERRRIYDIVNVLESIGAVARRGKNQYSWKGFG----- 88 (388)
T ss_pred ccchhhccccchhhHHHHHHHHHhcCCCcceechhhHHHhcCchHHHHHHHHHHHHHHHHHHhcccCcccccchh-----
Confidence 556679999999999999999999877777899999999999999999999999999999999999999999986
Q ss_pred chHHHHHHHHHH
Q 015878 201 KLDDQVARLKAE 212 (399)
Q Consensus 201 ~~~~~~~~Lk~E 212 (399)
++...+.+||+|
T Consensus 89 aiPral~eLqeE 100 (388)
T KOG2578|consen 89 AIPRALFELQEE 100 (388)
T ss_pred hhhHHHHHHHHH
Confidence 466677788876
No 4
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.03 E-value=3.6e-10 Score=112.12 Aligned_cols=73 Identities=40% Similarity=0.627 Sum_probs=64.7
Q ss_pred CCCCCCCCcHHHHHHHHHHHHHhCCCC-cccHHHHHHHhc----------ceeeehhhhHHhhhhccceecc-----cCC
Q 015878 124 SNGCRYDSSLGLLTRKFINLIQEAKDG-TLDLNRTAEVLE----------VQKRRIYDITNVLEGIGLIEKT-----SKN 187 (399)
Q Consensus 124 ~~~~R~dkSLglLTkkFI~Ll~~ap~g-~ldLn~aA~~L~----------VqKRRIYDItNVLEgIgLIeK~-----sKN 187 (399)
....|+++||++||++||.++-++++. .|.|+.||..|= ..-||+|||.|||-+++||+|. .|.
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 456789999999999999999999888 789999999873 3459999999999999999997 688
Q ss_pred eeEEecCCC
Q 015878 188 HIRWKGSDS 196 (399)
Q Consensus 188 ~i~W~G~~~ 196 (399)
.|+|.|...
T Consensus 232 afrwlG~~~ 240 (388)
T KOG2578|consen 232 AFRWLGSKP 240 (388)
T ss_pred hhheeCCCc
Confidence 999999764
No 5
>KOG2829 consensus E2F-like protein [Transcription]
Probab=98.95 E-value=8.5e-09 Score=101.73 Aligned_cols=122 Identities=25% Similarity=0.408 Sum_probs=82.7
Q ss_pred hCCCCcccHHHHHHHhc----------------------ceeeehhhhHHhhhhccceecccCCeeEEecCCCCCCcchH
Q 015878 146 EAKDGTLDLNRTAEVLE----------------------VQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLD 203 (399)
Q Consensus 146 ~ap~g~ldLn~aA~~L~----------------------VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~~~~ 203 (399)
....|....|++|+.|- -.|||+||.+|||.++.+|.|. |..|+|+|..... .
T Consensus 57 ve~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd-KKEIrW~GLP~~s----s 131 (326)
T KOG2829|consen 57 VERKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD-KKEIRWIGLPATS----S 131 (326)
T ss_pred HHhcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc-cceeeeeccCccc----h
Confidence 34667888888888872 4689999999999999999999 7779999997532 3
Q ss_pred HHHHHHHHHHHHH----HHHHHhHHHHHHHHHHHHHHHhhhhccccccccc----HhhhccCCCCCCceEEEEeCCCCce
Q 015878 204 DQVARLKAEIESL----HAEECRIDDSIREKQELIRTLEENENHQKYMFLT----EEDIASLPCFQNQTLIAIKAPQASY 275 (399)
Q Consensus 204 ~~~~~Lk~El~~L----~~~E~~LD~lI~~~~q~Lr~Lted~~n~~~aYVT----~eDI~~l~~f~~qTvIAIKAP~gT~ 275 (399)
+.+++|+.|-..+ .++-..|.++|.. .-.+++|.+- | +.++.+ .+.| . -.+|.|..-+.|.
T Consensus 132 ~dv~~le~Er~k~~erI~kK~a~lqEl~~q-~~~fknLV~R--N-~~~e~~~~~P~~~i-~------LPFiiinT~k~a~ 200 (326)
T KOG2829|consen 132 QDVSELEEERKKRMERIKKKAAQLQELIEQ-VSAFKNLVQR--N-RHAESQGQPPSENI-H------LPFIIINTSKKAV 200 (326)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHh--h-hhhhhccCCCCccc-c------cceEEEecCCCce
Confidence 4566666665443 3344455555554 2456666542 2 334444 1222 1 2368999999999
Q ss_pred EEecCCcc
Q 015878 276 IEVPDPDE 283 (399)
Q Consensus 276 LEVPdP~e 283 (399)
|++...++
T Consensus 201 IeceiseD 208 (326)
T KOG2829|consen 201 IECEISED 208 (326)
T ss_pred EEEEeccc
Confidence 99987643
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=94.90 E-value=0.033 Score=42.89 Aligned_cols=45 Identities=24% Similarity=0.425 Sum_probs=40.7
Q ss_pred CCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEe
Q 015878 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (399)
Q Consensus 148 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~ 192 (399)
..+..+..++|+.+++.|..+|++++-|+.-|||++...+.+.|.
T Consensus 19 ~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~GlV~~~~~~~~~Y~ 63 (68)
T PF01978_consen 19 KNGPATAEEIAEELGISRSTVYRALKSLEEKGLVEREEGRPKVYR 63 (68)
T ss_dssp HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHTTSEEEEEECCEEEE
T ss_pred HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcCceEEEE
Confidence 456799999999999999999999999999999999987776664
No 7
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=92.96 E-value=0.66 Score=45.21 Aligned_cols=53 Identities=21% Similarity=0.404 Sum_probs=42.3
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecCC
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD 195 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~ 195 (399)
++.|+.. |...-.++|+..||.+=|+|||++.||+=|+|+....+--+++-.+
T Consensus 22 Y~aLl~~---g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~ 74 (247)
T COG1378 22 YLALLCL---GEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVP 74 (247)
T ss_pred HHHHHHh---CCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeCC
Confidence 4444433 5677889999999999999999999999999999866656665544
No 8
>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=92.93 E-value=0.18 Score=37.06 Aligned_cols=41 Identities=27% Similarity=0.387 Sum_probs=35.4
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhcc
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIG 179 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIg 179 (399)
.+.+.+|..+.+. +...++|+.|+|++|-||--++.|+..|
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 4677788666666 9999999999999999999999999998
No 9
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.36 E-value=0.77 Score=36.35 Aligned_cols=48 Identities=25% Similarity=0.388 Sum_probs=40.1
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
.+.++++...+ +.+.+.++|+.+++.+.-+|-+++.|+..|+|++...
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 34556665543 4799999999999999999999999999999998743
No 10
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=91.79 E-value=0.27 Score=34.59 Aligned_cols=46 Identities=26% Similarity=0.418 Sum_probs=39.0
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
.++.++... +.+.+.++|+.|++.++.+|-++.-|+..|+|++..+
T Consensus 4 ~il~~l~~~--~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~~ 49 (53)
T smart00420 4 QILELLAQQ--GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVHG 49 (53)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeec
Confidence 456666653 4599999999999999999999999999999998643
No 11
>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=91.55 E-value=0.42 Score=35.62 Aligned_cols=54 Identities=20% Similarity=0.250 Sum_probs=42.4
Q ss_pred HHHHHHHHHHhC-----CCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCee
Q 015878 136 LTRKFINLIQEA-----KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (399)
Q Consensus 136 LTkkFI~Ll~~a-----p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i 189 (399)
++.-|+.+.... ..+.+...++|+.+++.+.-++-+++.|+.-|+|++.....|
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 344455555433 345789999999999999999999999999999999863433
No 12
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=90.53 E-value=0.45 Score=37.42 Aligned_cols=54 Identities=20% Similarity=0.308 Sum_probs=46.0
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEE
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W 191 (399)
.+.+.+|...++..+.+.++|+.||+.|+-+.-++.-|+.-|+|++.+.+-=.|
T Consensus 9 ~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W 62 (68)
T smart00550 9 EKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLW 62 (68)
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCce
Confidence 567888887755459999999999999999999999999999999986543466
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=89.32 E-value=0.37 Score=35.54 Aligned_cols=45 Identities=20% Similarity=0.353 Sum_probs=37.0
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
+.++++..++.+ +.+.++|+.+++.|=-+|-+++.|+..|+++|.
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 345555555544 799999999999999999999999999999874
No 14
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=88.61 E-value=2.9 Score=37.57 Aligned_cols=87 Identities=23% Similarity=0.377 Sum_probs=57.9
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCC-CCcchHHHHHHHHHHHHHHHH
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSL-GTSKLDDQVARLKAEIESLHA 218 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s-~~~~~~~~~~~Lk~El~~L~~ 218 (399)
|..|++ +++.++.+++|+.|+..|=.+|=.+|=|...|||+|..-+. .|..-- -...++ ..+++ ..
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~---~~Ggy~yiY~~i~--~ee~k------~~ 99 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL---KGGGYYYLYKPID--PEEIK------KK 99 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc---CCCceeEEEecCC--HHHHH------HH
Confidence 455554 67889999999999999999999999999999999984442 222100 000011 12233 22
Q ss_pred HHHhHHHHHHHHHHHHHHHhh
Q 015878 219 EECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 219 ~E~~LD~lI~~~~q~Lr~Lte 239 (399)
.++.||++-..+.+-|+++..
T Consensus 100 i~~~l~~w~~~~~~~i~~~~~ 120 (126)
T COG3355 100 ILKDLDEWYDKMKQLIEEFEK 120 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 345677777777777776654
No 15
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=87.44 E-value=0.92 Score=32.61 Aligned_cols=43 Identities=30% Similarity=0.450 Sum_probs=36.0
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhcccee
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe 182 (399)
++.+.++...+ .+...++|+.+++.+..++.+++-|+.-|+|+
T Consensus 6 ~~Il~~l~~~~--~~t~~ela~~~~is~~tv~~~l~~L~~~g~I~ 48 (48)
T PF13412_consen 6 RKILNYLRENP--RITQKELAEKLGISRSTVNRYLKKLEEKGLIE 48 (48)
T ss_dssp HHHHHHHHHCT--TS-HHHHHHHHTS-HHHHHHHHHHHHHTTSEE
T ss_pred HHHHHHHHHcC--CCCHHHHHHHhCCCHHHHHHHHHHHHHCcCcC
Confidence 56677777744 49999999999999999999999999999985
No 16
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=87.24 E-value=0.92 Score=33.56 Aligned_cols=46 Identities=24% Similarity=0.340 Sum_probs=40.5
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
..+..+...++..+.+.++|+.|++.|=.+--+++-||.-|||+|.
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 4556667788878999999999999999999999999999999997
No 17
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=86.66 E-value=0.82 Score=32.60 Aligned_cols=38 Identities=24% Similarity=0.376 Sum_probs=34.5
Q ss_pred CCcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
.+.+.++++++.|++.+..++.+++.|+.-|+|++..+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 45689999999999999999999999999999997653
No 18
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=85.38 E-value=10 Score=35.01 Aligned_cols=98 Identities=19% Similarity=0.235 Sum_probs=62.7
Q ss_pred CCCCcccHHHHHHHh--cceeeehhhhHHhhhhccceecccCCeeEEecCCCCCCcc-hHHHHHHHHHHHHH-----HH-
Q 015878 147 AKDGTLDLNRTAEVL--EVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSK-LDDQVARLKAEIES-----LH- 217 (399)
Q Consensus 147 ap~g~ldLn~aA~~L--~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~~-~~~~~~~Lk~El~~-----L~- 217 (399)
-.++.-|...+|++| +|.--.+=+.++.|+-+|||+|...+.|.=.-...+.+.+ ...-+..++.+.-. |.
T Consensus 35 l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~~~lA~~al~~ 114 (171)
T PF14394_consen 35 LMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEAVRSYHKQMLELAQEALDR 114 (171)
T ss_pred cCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHHHHHHHHHHHHHHHHHHHh
Confidence 356666999999999 9999999999999999999999977544332222222222 22234444444322 22
Q ss_pred -----------------HHHHhHHHHHHHHHHHHHHHhhhhccc
Q 015878 218 -----------------AEECRIDDSIREKQELIRTLEENENHQ 244 (399)
Q Consensus 218 -----------------~~E~~LD~lI~~~~q~Lr~Lted~~n~ 244 (399)
+.=.++-+.|+.++.++..+.+...+.
T Consensus 115 ~p~~~R~~s~~T~~vs~~~~~ki~~~i~~fRk~i~~i~~~~~~~ 158 (171)
T PF14394_consen 115 VPPEERDFSGLTMSVSREDYEKIKKEIREFRKKIIAIAEEDKEP 158 (171)
T ss_pred CCccccceeeeEEEeCHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 112356667777888888777654443
No 19
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=83.60 E-value=1.6 Score=32.73 Aligned_cols=45 Identities=33% Similarity=0.403 Sum_probs=35.0
Q ss_pred HHHHHHhC-CCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 140 FINLIQEA-KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 140 FI~Ll~~a-p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
|.-|..-. .++.+.+.++|+.+++.+--+..+++-|+..|||+|.
T Consensus 6 ~~vL~~l~~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 6 WQVLRALAHSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp HHHHHHHT--TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 44344333 7888999999999999999999999999999999887
No 20
>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=82.81 E-value=2 Score=34.49 Aligned_cols=49 Identities=22% Similarity=0.341 Sum_probs=39.6
Q ss_pred HHHHHHHHHHhCCCC-cccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 136 LTRKFINLIQEAKDG-TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 136 LTkkFI~Ll~~ap~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
.+-+++.+|...+++ .+.+.++|+.+++..+.+..|++-|+.-|||+..
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 445566666655554 4999999999999999999999999999999865
No 21
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=81.88 E-value=1.6 Score=32.25 Aligned_cols=43 Identities=26% Similarity=0.402 Sum_probs=35.7
Q ss_pred HHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceeccc
Q 015878 141 INLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 141 I~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
+.++.+.++ +.+.++|+.+++.+--+-.+++-||.-|+|+|..
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 344455444 8999999999999999999999999999999973
No 22
>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=81.30 E-value=2.1 Score=36.78 Aligned_cols=46 Identities=11% Similarity=0.159 Sum_probs=40.2
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
+.+.+|....++.+.+.++|+.+++.+..++.|++.|+.-|+|+..
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 4555666666788999999999999999999999999999999864
No 23
>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=80.49 E-value=0.83 Score=36.69 Aligned_cols=31 Identities=39% Similarity=0.462 Sum_probs=24.0
Q ss_pred HHHHHHhcc---eeeehhhhHHhhhhccceeccc
Q 015878 155 NRTAEVLEV---QKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 155 n~aA~~L~V---qKRRIYDItNVLEgIgLIeK~s 185 (399)
..+|+.+++ ..|||||+++-|+.+|+|+-..
T Consensus 26 ~~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~~ 59 (85)
T PF09079_consen 26 EELCESLGVDPLSYRRFSDYLSELEMLGLIESER 59 (85)
T ss_dssp HHHHHHTTS----HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEEe
Confidence 344555554 7899999999999999998773
No 24
>PF13730 HTH_36: Helix-turn-helix domain
Probab=80.36 E-value=2.1 Score=31.35 Aligned_cols=29 Identities=31% Similarity=0.356 Sum_probs=27.9
Q ss_pred cHHHHHHHhcceeeehhhhHHhhhhccce
Q 015878 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLI 181 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIgLI 181 (399)
....+|+.+|+.+|.|+-.++.||..|+|
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 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=79.85 E-value=4.2 Score=29.56 Aligned_cols=47 Identities=23% Similarity=0.359 Sum_probs=38.5
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCC
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
.+++..+...+ +...++++.|++.+.-++-+++.|+.-|+|.+....
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 34555555443 899999999999999999999999999999986443
No 26
>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=77.82 E-value=1.4 Score=34.98 Aligned_cols=22 Identities=41% Similarity=0.665 Sum_probs=20.0
Q ss_pred ceeeehhhhHHhhhhccceecc
Q 015878 163 VQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 163 VqKRRIYDItNVLEgIgLIeK~ 184 (399)
...|||+||+|-||..|||+-.
T Consensus 44 l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEEE
Confidence 4789999999999999999865
No 27
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=77.65 E-value=3.3 Score=29.73 Aligned_cols=41 Identities=20% Similarity=0.282 Sum_probs=35.8
Q ss_pred CCCCcc-cHHHHHHHhcceeeehhhhHHhhhhccceecccCC
Q 015878 147 AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 147 ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
.++..+ ...++|+.++|++=-+...++.|+.-|+|++..+.
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 355667 89999999999999999999999999999877544
No 28
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=77.57 E-value=9.7 Score=36.93 Aligned_cols=55 Identities=11% Similarity=0.225 Sum_probs=43.2
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecC
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~ 194 (399)
..+++|.... ..+.+.++|+.|++.|=.+|-+++.|+..|++++.....-.+.|.
T Consensus 29 ~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG~ 83 (271)
T PRK10163 29 AILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIGL 83 (271)
T ss_pred HHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEecH
Confidence 3455665443 458999999999999999999999999999999875554444564
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=76.82 E-value=10 Score=32.01 Aligned_cols=55 Identities=18% Similarity=0.302 Sum_probs=33.1
Q ss_pred cCCeeEEecCCCCCCcchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 185 SKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 185 sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
...-+.|+|.+..-....++-..-|++.++.|..+-..|+..|..+++++..+..
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 4556889996643222334445556666666666666666666666666666543
No 30
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=76.42 E-value=2.7 Score=29.22 Aligned_cols=38 Identities=26% Similarity=0.374 Sum_probs=33.3
Q ss_pred cccHHHHHHHhcceeeehhhhHHhhhhccceecccCCee
Q 015878 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (399)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i 189 (399)
.+...++|+.+++.+..++.+++.|+.-|+|++.. +.|
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 36788999999999999999999999999999874 443
No 31
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=75.14 E-value=7.5 Score=29.57 Aligned_cols=50 Identities=22% Similarity=0.260 Sum_probs=38.4
Q ss_pred HHHHHHHHh---CCCCcc-cHHHHHHHhcceeeehhhhHHhhhhccceecccCC
Q 015878 138 RKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 138 kkFI~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
..+.+.+.. .++..+ ...++|+.++|++.=+...++.|+.-|+|++..+.
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 344444443 356678 99999999999999999999999999999987554
No 32
>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=73.72 E-value=4.6 Score=32.27 Aligned_cols=49 Identities=22% Similarity=0.285 Sum_probs=40.7
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
.++++.+-.+...-+.-.+++..+++..|-++=++++|+..|||.|+.-
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 4567777666655566677889999999999999999999999999865
No 33
>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=73.67 E-value=33 Score=34.21 Aligned_cols=94 Identities=16% Similarity=0.185 Sum_probs=59.9
Q ss_pred CCCcccHHHHHHHhc--ceeeehhhhHHhhhhccceecccCCeeEEecCC--CCCCcch-HHHHHHHHHHHHHHH-----
Q 015878 148 KDGTLDLNRTAEVLE--VQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD--SLGTSKL-DDQVARLKAEIESLH----- 217 (399)
Q Consensus 148 p~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~--~s~~~~~-~~~~~~Lk~El~~L~----- 217 (399)
.++.-|..++|+.|+ |.--.+=|.+..|+-+|||+|...+ .|.-.+ ...+.+. ...+..++.+.-.|.
T Consensus 134 ~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g--~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al~ 211 (271)
T TIGR02147 134 MPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDG--FYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEALD 211 (271)
T ss_pred CCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCC--cEEeecceeecCCccchHHHHHHHHHHHHHHHHHHH
Confidence 567778999999999 8888999999999999999998655 443322 2222222 222444444332221
Q ss_pred ------------------HHHHhHHHHHHHHHHHHHHHhhhhcc
Q 015878 218 ------------------AEECRIDDSIREKQELIRTLEENENH 243 (399)
Q Consensus 218 ------------------~~E~~LD~lI~~~~q~Lr~Lted~~n 243 (399)
..-.++-+.|+.++.++..+.++..+
T Consensus 212 ~~p~~eR~~S~lT~~i~~~~~~~i~~~i~~fRk~i~~i~~~~~~ 255 (271)
T TIGR02147 212 ALPPSERDVSTVTFGISEEAYKEIVKKIQEFRKEVLAIATKDKE 255 (271)
T ss_pred hCCccccccceeeEecCHHHHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 11235566677777777777665544
No 34
>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=72.53 E-value=3.7 Score=31.66 Aligned_cols=53 Identities=11% Similarity=0.170 Sum_probs=38.0
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccc-eecccCCeeEEecC
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL-IEKTSKNHIRWKGS 194 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgL-IeK~sKN~i~W~G~ 194 (399)
+.+.++.+. .+..+++|+.|+|+++-|+--++.|+.-|+ |....+..+-+.+.
T Consensus 4 ~il~~L~~~---~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~~ 57 (69)
T TIGR00122 4 RLLALLADN---PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTVGKGYRLPPPI 57 (69)
T ss_pred HHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCCceEecCcc
Confidence 455665543 466999999999999999999999988888 33334443333443
No 35
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=71.22 E-value=36 Score=31.48 Aligned_cols=51 Identities=10% Similarity=0.058 Sum_probs=41.4
Q ss_pred HHHHHHHHh---CCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCe
Q 015878 138 RKFINLIQE---AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNH 188 (399)
Q Consensus 138 kkFI~Ll~~---ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~ 188 (399)
.++.+.+.. .||..+.-.++|+.|||+|=-+=+.+..|+..|||+.....-
T Consensus 18 ~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g 71 (221)
T PRK11414 18 NDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQA 71 (221)
T ss_pred HHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCc
Confidence 444444432 478889999999999999999999999999999999875543
No 36
>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=70.86 E-value=4.7 Score=29.21 Aligned_cols=34 Identities=29% Similarity=0.427 Sum_probs=31.5
Q ss_pred CcccHHHHHHHhcceeeehhhhHHhhhhccceec
Q 015878 150 GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (399)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK 183 (399)
+...+.++|+.|++.+=-++==++.|+..|+|+|
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 7799999999999999999999999999999986
No 37
>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=70.48 E-value=29 Score=36.79 Aligned_cols=99 Identities=13% Similarity=0.213 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhhcccccccccHhhhccCCCCCCceEEEEeCCCCc--eEEecCC
Q 015878 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDIASLPCFQNQTLIAIKAPQAS--YIEVPDP 281 (399)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~l~~f~~qTvIAIKAP~gT--~LEVPdP 281 (399)
.++.+|..++..|..+.++|++.|..++++|..+...... ......+.|.+|.+. .|+|-.-
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 3445566666666667777777777777777666542111 112345666666544 3444332
Q ss_pred cchhhcccceEEEEEecCCCCeEEEE----ecCCCCCCcccc
Q 015878 282 DEDISFLKRQYKMIIRSTTGPIDVYL----LSKYQSEGKDIT 319 (399)
Q Consensus 282 ~e~~~~~~~~yqI~LkS~~GPIdVyL----~~~~~~~~e~~~ 319 (399)
..+.. =...|.|.|.+..+++++.. .....++..+..
T Consensus 202 v~~a~-W~P~Ydlrl~~~~~~~~l~~~A~V~Q~TGeDW~~V~ 242 (525)
T TIGR02231 202 VGNAS-WTPSYDARLDTGAPTVELTYLAEIRQSTGEDWSDIP 242 (525)
T ss_pred eCCCc-EeeeeEEEecCCCceEEEEEEEEEEeCCCCCCCCCc
Confidence 22211 14579999999999887643 344455554443
No 38
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=68.58 E-value=24 Score=33.92 Aligned_cols=50 Identities=12% Similarity=0.324 Sum_probs=39.6
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceeccc-CCeeE
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS-KNHIR 190 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s-KN~i~ 190 (399)
.+++|...+ ..+.+.++|+.|++.|=-+|-+++-|+..|++++.. .+.|+
T Consensus 16 iL~~l~~~~-~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~ 66 (263)
T PRK09834 16 VLRALNRLD-GGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFR 66 (263)
T ss_pred HHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEE
Confidence 345554443 349999999999999999999999999999999863 34443
No 39
>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=67.18 E-value=8.4 Score=32.77 Aligned_cols=36 Identities=22% Similarity=0.402 Sum_probs=33.5
Q ss_pred CCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
.+.+...++|+.+++.++.+++|+..|..-|+|...
T Consensus 23 ~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 23 EGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 448999999999999999999999999999999864
No 40
>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=67.06 E-value=17 Score=29.74 Aligned_cols=27 Identities=19% Similarity=0.287 Sum_probs=21.4
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhcccee
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe 182 (399)
+.+.++|+.+||+.+-|.-. |..|+|.
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 46789999999998877665 5568886
No 41
>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=66.63 E-value=8.6 Score=29.19 Aligned_cols=45 Identities=31% Similarity=0.471 Sum_probs=38.6
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
++.++++++ .+.+.+.++|+.|+|+..-|.==+|.|+.-|+|.|.
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 345677765 479999999999999998888888999999999987
No 42
>PHA02943 hypothetical protein; Provisional
Probab=66.56 E-value=15 Score=34.54 Aligned_cols=49 Identities=22% Similarity=0.230 Sum_probs=42.4
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCee
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i 189 (399)
..+++++ ..|.....++|+.||++--....++-|||.-|.|++......
T Consensus 14 ~eILE~L---k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~~ 62 (165)
T PHA02943 14 IKTLRLL---ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGRA 62 (165)
T ss_pred HHHHHHH---hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecce
Confidence 4577887 677888999999999999999999999999999999865543
No 43
>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=65.89 E-value=3.3 Score=32.30 Aligned_cols=42 Identities=17% Similarity=0.230 Sum_probs=34.4
Q ss_pred CCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCee
Q 015878 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (399)
Q Consensus 148 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i 189 (399)
..+.+++.++|..|+++..-+=.++.+|+..|.|+|...+.-
T Consensus 11 ~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~~ 52 (69)
T PF09012_consen 11 ERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSSC 52 (69)
T ss_dssp HS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE--
T ss_pred HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCCC
Confidence 457899999999999999999999999999999999866543
No 44
>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=65.79 E-value=22 Score=30.62 Aligned_cols=54 Identities=19% Similarity=0.268 Sum_probs=33.6
Q ss_pred CCeeEEecCCCCCCcchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 186 KNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 186 KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
+.-+.|+|.+..-...+.+-+.-++..++.|...-..|.+.|..+++++..+.+
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 445788887643223344445566666777776666777777777666666543
No 45
>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=65.74 E-value=17 Score=29.46 Aligned_cols=38 Identities=32% Similarity=0.519 Sum_probs=32.5
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
-+.+|..|.+|.+.|...|..+...|+.++.++.++-.
T Consensus 10 KDe~Ia~L~eEGekLSk~el~~~~~IKKLr~~~~e~e~ 47 (74)
T PF12329_consen 10 KDEQIAQLMEEGEKLSKKELKLNNTIKKLRAKIKELEK 47 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 35778999999999999999999999999888877654
No 46
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=65.68 E-value=5.3 Score=30.19 Aligned_cols=45 Identities=27% Similarity=0.427 Sum_probs=37.6
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceeccc
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
+.+.++ ..++.+.+.++|+.|++.+=-+|-=+++|+..|||+...
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 356789999999999999999999999999999999764
No 47
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=65.57 E-value=25 Score=30.83 Aligned_cols=52 Identities=17% Similarity=0.243 Sum_probs=27.6
Q ss_pred CCeeEEecCCCCCCcchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 015878 186 KNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (399)
Q Consensus 186 KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~L 237 (399)
..-+-|.|.+..-...+++.+..|++.++.|...-..|.+.|.++++++..+
T Consensus 76 ~kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~ 127 (140)
T PRK03947 76 DKVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQL 127 (140)
T ss_pred CeEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3446788876432223444455555555555555555555555555554444
No 48
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=65.44 E-value=73 Score=29.49 Aligned_cols=96 Identities=21% Similarity=0.338 Sum_probs=55.9
Q ss_pred CCCCcHHHHHHHHHHHHH-hCCCCcc---------------cHHHHHHHhcc-eeeehhhhHHhhhhccceecccCCeeE
Q 015878 128 RYDSSLGLLTRKFINLIQ-EAKDGTL---------------DLNRTAEVLEV-QKRRIYDITNVLEGIGLIEKTSKNHIR 190 (399)
Q Consensus 128 R~dkSLglLTkkFI~Ll~-~ap~g~l---------------dLn~aA~~L~V-qKRRIYDItNVLEgIgLIeK~sKN~i~ 190 (399)
.++-+...|.++|..+.+ -.||... -+|+|-+.|.- .+|..|++ -|.|+.+......
T Consensus 12 ~~~~d~~~L~~~yr~l~~~~HPDk~~~~~~~~~~~a~~~s~~iN~AY~~L~dp~~Ra~Yll--~l~g~~~~~~~~~---- 85 (171)
T PRK05014 12 RYDIDTQLLASRYQELQRQFHPDKFANASERERLLAVQQAATINDAYQTLKHPLKRAEYLL--SLHGFDLAHEQHT---- 85 (171)
T ss_pred CCCCCHHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHHHHHHHHHHHHCChhHHHHHHH--HhcCCccccccCC----
Confidence 456677899999998874 4565422 37778788876 78999985 5567766544311
Q ss_pred EecCCCCCCcchHHHHHHHHHHHHHHHHH---HHhHHHHHHHHHHHHH
Q 015878 191 WKGSDSLGTSKLDDQVARLKAEIESLHAE---ECRIDDSIREKQELIR 235 (399)
Q Consensus 191 W~G~~~s~~~~~~~~~~~Lk~El~~L~~~---E~~LD~lI~~~~q~Lr 235 (399)
.. +.+.-.++-+++++++.+... +..|+++...+++.++
T Consensus 86 -----~~-d~efLme~me~rE~le~~~~~~d~~~~l~~l~~~~~~~~~ 127 (171)
T PRK05014 86 -----VR-DTAFLMEQMELREELEDIEQSKDPEAALESFIKRVKKMFK 127 (171)
T ss_pred -----cC-CHHHHHHHHHHHHHHHhhccccCHHHHHHHHHHHHHHHHH
Confidence 11 223344455677777655321 3334444444444333
No 49
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=63.25 E-value=14 Score=28.91 Aligned_cols=45 Identities=22% Similarity=0.311 Sum_probs=37.6
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
.+.+.++...+ .+...++|+.+++.+.-|+-+++-|+.-|+|++.
T Consensus 13 ~~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 13 FLVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 34445555443 5889999999999999999999999999999977
No 50
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=63.25 E-value=8.4 Score=31.91 Aligned_cols=51 Identities=20% Similarity=0.333 Sum_probs=41.3
Q ss_pred cHHHHHHHHHHHHHhCC--CCcccHHHHHHHhcceeeehhhhHHhhhhcccee
Q 015878 132 SLGLLTRKFINLIQEAK--DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (399)
Q Consensus 132 SLglLTkkFI~Ll~~ap--~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe 182 (399)
+|..+.++.+++|++.+ ..-+.+++++++|++....|.+++.-|..-|+|=
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~IY 96 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHIY 96 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSEE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeEe
Confidence 78999999999998722 3349999999999999999999999999999874
No 51
>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=61.69 E-value=13 Score=30.84 Aligned_cols=45 Identities=16% Similarity=0.190 Sum_probs=37.5
Q ss_pred CCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecC
Q 015878 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (399)
Q Consensus 148 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~ 194 (399)
....+.-.++|+.+++.|--+.-+++.||.-|+|++..+ ..|.|.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~--~~~~~~ 88 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM--MGIVGV 88 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC--Cceeec
Confidence 345678899999999999999999999999999998743 345554
No 52
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=61.57 E-value=43 Score=32.29 Aligned_cols=54 Identities=22% Similarity=0.217 Sum_probs=43.9
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEec
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G 193 (399)
++.+++++. .+.+...++|+.|+|+.+.|.--++.|+.-|+|.+....-+.+.+
T Consensus 7 ~~Il~~l~~--~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~~ 60 (240)
T PRK10411 7 QAIVDLLLN--HTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHGRAKYIHR 60 (240)
T ss_pred HHHHHHHHH--cCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCeEEEecC
Confidence 345667764 468999999999999999999999999999999887555555544
No 53
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=61.52 E-value=10 Score=31.16 Aligned_cols=47 Identities=19% Similarity=0.310 Sum_probs=41.0
Q ss_pred HHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 136 LTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
+=++.+.+|+.. +.+...++|+.+++...-++..++-|+.-|+|.+.
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 56899999999999999999999999999999954
No 54
>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=61.22 E-value=15 Score=26.78 Aligned_cols=38 Identities=26% Similarity=0.349 Sum_probs=32.9
Q ss_pred CCCcc-cHHHHHHHhcceeeehhhhHHhhhhccceeccc
Q 015878 148 KDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 148 p~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
++..+ ...++|+.+++.+=.+...++-|+.-|+|++..
T Consensus 21 ~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 21 PGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 34444 599999999999999999999999999998774
No 55
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=61.19 E-value=84 Score=27.12 Aligned_cols=34 Identities=18% Similarity=0.275 Sum_probs=32.1
Q ss_pred cccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
.+...++|+.+++.+--+--+++.||.-|+|+|.
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~ 79 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQ 79 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeee
Confidence 4578999999999999999999999999999998
No 56
>TIGR02702 SufR_cyano iron-sulfur cluster biosynthesis transcriptional regulator SufR. All members of this cyanobacterial protein family are the transcriptional regulator SufR and regulate the SUF system, which makes possible iron-sulfur cluster biosynthesis despite exposure to oxygen. In all cases, the sufR gene is encoded near SUF system genes but in the opposite direction. This DNA-binding protein belongs to the the DeoR family of helix-loop-helix proteins. All members also have a probable metal-binding motif C-X(12)-C-X(13)-C-X(14)-C near the C-terminus.
Probab=60.63 E-value=68 Score=29.77 Aligned_cols=45 Identities=22% Similarity=0.288 Sum_probs=38.3
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
.+.+.++... +.+...++|+.|++.+=-+.-.++.||.-|||++.
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 3466667654 34999999999999999999999999999999986
No 57
>PRK10870 transcriptional repressor MprA; Provisional
Probab=60.20 E-value=52 Score=30.19 Aligned_cols=40 Identities=18% Similarity=0.268 Sum_probs=36.0
Q ss_pred HhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 145 QEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 145 ~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
...+++.+...++|+.|++.+=-+-=+++-||.-|||+|.
T Consensus 65 ~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~ 104 (176)
T PRK10870 65 ESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERR 104 (176)
T ss_pred hcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEec
Confidence 3445778999999999999999999999999999999997
No 58
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=60.06 E-value=8.8 Score=40.63 Aligned_cols=75 Identities=20% Similarity=0.328 Sum_probs=49.0
Q ss_pred cceeeehhhhHHhhhhc-cceecccCCeeEEe-cCCCCCCcchHHHHHHHHHHHH---HHHHHHHhHHHHHHHHHHHHHH
Q 015878 162 EVQKRRIYDITNVLEGI-GLIEKTSKNHIRWK-GSDSLGTSKLDDQVARLKAEIE---SLHAEECRIDDSIREKQELIRT 236 (399)
Q Consensus 162 ~VqKRRIYDItNVLEgI-gLIeK~sKN~i~W~-G~~~s~~~~~~~~~~~Lk~El~---~L~~~E~~LD~lI~~~~q~Lr~ 236 (399)
.|.|||=|-|=+-.--+ .||-|..-+..+|. |.-. +...+-+.+||++.+ ++....+.|+.-++.+.+++++
T Consensus 239 eVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtIL---k~s~dYIr~Lqq~~q~~~E~~~rqk~le~~n~~L~~riee 315 (411)
T KOG1318|consen 239 EVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTIL---KASCDYIRELQQTLQRARELENRQKKLESTNQELALRIEE 315 (411)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhh---HHHHHHHHHHHHHHHHHHHHHhhhhHHHhHHHHHHHHHHH
Confidence 37888866655444333 47888888888994 3221 233445677777665 4555667777778888888877
Q ss_pred Hhh
Q 015878 237 LEE 239 (399)
Q Consensus 237 Lte 239 (399)
|..
T Consensus 316 Lk~ 318 (411)
T KOG1318|consen 316 LKS 318 (411)
T ss_pred HHH
Confidence 764
No 59
>PRK11569 transcriptional repressor IclR; Provisional
Probab=59.71 E-value=46 Score=32.28 Aligned_cols=47 Identities=13% Similarity=0.308 Sum_probs=38.7
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCC
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
.+++|.. ....+.|.++|+.|++.|=.+|=+++-|+..|++++....
T Consensus 33 IL~~l~~-~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~ 79 (274)
T PRK11569 33 LLEWIAE-SNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGEL 79 (274)
T ss_pred HHHHHHh-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCC
Confidence 3455544 3456899999999999999999999999999999986443
No 60
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=59.20 E-value=44 Score=31.93 Aligned_cols=54 Identities=7% Similarity=0.236 Sum_probs=42.4
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecC
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~ 194 (399)
+.++++.. .+.+.+.++|+.|++.|=-+|-+++.|+..|++++...+.-...|.
T Consensus 18 ~IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~ 71 (257)
T PRK15090 18 GILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLTL 71 (257)
T ss_pred HHHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEecH
Confidence 34555543 2468999999999999999999999999999999975544344553
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=59.11 E-value=8 Score=32.51 Aligned_cols=37 Identities=19% Similarity=0.337 Sum_probs=34.1
Q ss_pred CCcccHHHHHHHhcceeeehhhhHHhhhhccceeccc
Q 015878 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
.+.+.+.++|+.+++.+--++=+++-||.-|||++..
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
>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=58.88 E-value=9.9 Score=30.03 Aligned_cols=46 Identities=22% Similarity=0.259 Sum_probs=35.1
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcce-eeehhhhHHhhhhccceeccc
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQ-KRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIgLIeK~s 185 (399)
||.-+-...+..-.+.++|+.||+. ..-+++-+..||.-|+|++..
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 3333334456677999999999995 999999999999999999874
No 63
>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=58.83 E-value=20 Score=27.72 Aligned_cols=39 Identities=23% Similarity=0.306 Sum_probs=35.5
Q ss_pred CCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 148 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
.++.+...++|+.|+|.+=-+.+.++-|+.-|||+....
T Consensus 19 ~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~y 57 (60)
T PF01325_consen 19 EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEPY 57 (60)
T ss_dssp CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecCC
Confidence 888999999999999999999999999999999998743
No 64
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=58.05 E-value=14 Score=35.57 Aligned_cols=55 Identities=24% Similarity=0.392 Sum_probs=44.7
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecC
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~ 194 (399)
..+++|...+.+ +.+.++|+.+++.|=-.|=+++.|+..|++++...+.-.+.|.
T Consensus 8 ~iL~~l~~~~~~-l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg~ 62 (246)
T COG1414 8 AILDLLAEGPGG-LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRLGP 62 (246)
T ss_pred HHHHHHHhCCCC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEeehH
Confidence 466777775544 8999999999999999999999999999999998653333443
No 65
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=57.99 E-value=7.2 Score=40.08 Aligned_cols=30 Identities=33% Similarity=0.556 Sum_probs=27.4
Q ss_pred cHHHHHHHhcceeeehhhhHHhhhhcccee
Q 015878 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIgLIe 182 (399)
-+..+++.+++++||+|||+|-|+.+|+|.
T Consensus 303 ~y~~~~~~~~~~~~~~~~ii~~L~~lgiv~ 332 (366)
T COG1474 303 VYESLCERLRTSQRRFSDIISELEGLGIVS 332 (366)
T ss_pred HHHHHHhhhCchHHHHHHHHHHHHhcCeEE
Confidence 367788888899999999999999999998
No 66
>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=57.92 E-value=18 Score=30.51 Aligned_cols=76 Identities=17% Similarity=0.262 Sum_probs=42.7
Q ss_pred HHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCCCC------cchHHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 015878 158 AEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSIREKQ 231 (399)
Q Consensus 158 A~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~ 231 (399)
-..|..+++...|+.+-|+.+. ...+.|+=+|.-.... ..+...+..+..+++.|..+...+...+..++
T Consensus 22 ~~~l~~~~~E~~~v~~EL~~l~----~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk 97 (105)
T cd00632 22 RQKVEAQLNENKKALEELEKLA----DDAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQ 97 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC----CcchHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445567788888888888775 3334444455432111 12333344555556666666666666666666
Q ss_pred HHHHHH
Q 015878 232 ELIRTL 237 (399)
Q Consensus 232 q~Lr~L 237 (399)
..|+++
T Consensus 98 ~~l~~~ 103 (105)
T cd00632 98 EKIQQA 103 (105)
T ss_pred HHHHHH
Confidence 666654
No 67
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=57.50 E-value=11 Score=30.16 Aligned_cols=33 Identities=27% Similarity=0.292 Sum_probs=30.4
Q ss_pred HHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
+.++|+.|++.+=-++-++..|+.-|||.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 568999999999999999999999999999853
No 68
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=57.48 E-value=25 Score=33.55 Aligned_cols=38 Identities=24% Similarity=0.255 Sum_probs=35.2
Q ss_pred CCcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
...+.|.++++.||++|=++-=.+-+|++.||++|+-+
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~~ 76 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVFE 76 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhhc
Confidence 56789999999999999999999999999999999833
No 69
>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=57.42 E-value=7.2 Score=37.96 Aligned_cols=37 Identities=19% Similarity=0.197 Sum_probs=34.3
Q ss_pred CCcccHHHHHHHhcceeeehhhhHHhhhhccceeccc
Q 015878 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
.+..++.++|+++++..|+++-+.+.|.++||+++..
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~ 57 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED 57 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC
Confidence 3678999999999999999999999999999999863
No 70
>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=56.84 E-value=29 Score=26.88 Aligned_cols=35 Identities=26% Similarity=0.296 Sum_probs=26.6
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 205 QVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 205 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
....++.|+..|..+-+.|.+.+..+++++..|..
T Consensus 18 ~~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~ 52 (80)
T PF04977_consen 18 RYYQLNQEIAELQKEIEELKKENEELKEEIERLKN 52 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 34567778888888888888888888888888833
No 71
>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=56.51 E-value=38 Score=29.04 Aligned_cols=54 Identities=19% Similarity=0.235 Sum_probs=38.5
Q ss_pred CCeeEEecCCCCCCcchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 186 KNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 186 KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
++-+.|+|.+..-...+++.+.-|+..++.|...-+.|.+.|.++++++..+.+
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 556889998754323455666777788888888878888888888877776654
No 72
>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=56.26 E-value=41 Score=28.27 Aligned_cols=38 Identities=21% Similarity=0.305 Sum_probs=23.9
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhcccee-cccCCeeEEec
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE-KTSKNHIRWKG 193 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe-K~sKN~i~W~G 193 (399)
+.+.++|+.+||..+-|- -.|-.|||. ....|.+++-.
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 568899999999887332 334566665 22345566644
No 73
>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=56.23 E-value=45 Score=27.94 Aligned_cols=37 Identities=22% Similarity=0.332 Sum_probs=24.6
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhcccee-cccCCeeEEe
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE-KTSKNHIRWK 192 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe-K~sKN~i~W~ 192 (399)
+.+.++|+.+||+.+-| -..|-.||+. +...|.++.-
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 46789999999988866 3455678873 3334555543
No 74
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=56.08 E-value=86 Score=26.98 Aligned_cols=31 Identities=10% Similarity=0.059 Sum_probs=26.3
Q ss_pred CcccHHHHHHHhcceeeehhhhHHhhhhccc
Q 015878 150 GTLDLNRTAEVLEVQKRRIYDITNVLEGIGL 180 (399)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItNVLEgIgL 180 (399)
+-..+.++|.++||+.--||-+.+-+..-|+
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 75
>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=55.89 E-value=28 Score=32.13 Aligned_cols=39 Identities=21% Similarity=0.210 Sum_probs=34.7
Q ss_pred cccHHHHHHHhcceeeehhhhHHhhhhccceecccCCee
Q 015878 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (399)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i 189 (399)
+++..++|+.|+++++-++-.+..|+--++|.|...+.|
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 457889999999999999999999999999999865543
No 76
>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=55.55 E-value=13 Score=28.36 Aligned_cols=36 Identities=25% Similarity=0.389 Sum_probs=28.0
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhh
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLE 176 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLE 176 (399)
+.+++|-. .+.+.+.++|+.|+++.|-|.--++-|.
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 46677766 6788999999999999999877666665
No 77
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=55.52 E-value=41 Score=32.58 Aligned_cols=54 Identities=17% Similarity=0.099 Sum_probs=41.2
Q ss_pred HHHHHHH-hCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEe
Q 015878 139 KFINLIQ-EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (399)
Q Consensus 139 kFI~Ll~-~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~ 192 (399)
+.|.++. ......+...++|+.|++.+..+.-+++-||.-|+|+|.....-+|.
T Consensus 8 k~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v 62 (217)
T PRK14165 8 KKLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLI 62 (217)
T ss_pred HHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEE
Confidence 3444443 33445688999999999999999999999999999999854333443
No 78
>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=54.83 E-value=78 Score=28.88 Aligned_cols=41 Identities=20% Similarity=0.288 Sum_probs=37.3
Q ss_pred CCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCC
Q 015878 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 147 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
.||..+.-.++|+.|||+|=-+=+.+..|+.-|||+...+.
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~ 70 (212)
T TIGR03338 30 PPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNR 70 (212)
T ss_pred CCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCC
Confidence 47888999999999999999999999999999999987554
No 79
>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=53.60 E-value=32 Score=29.32 Aligned_cols=38 Identities=29% Similarity=0.417 Sum_probs=27.0
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhcccee--cccCCeeEEec
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKG 193 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe--K~sKN~i~W~G 193 (399)
+.+.++|+.+||..|-| --.|..|||. +...|.|+|-.
T Consensus 1 ~~I~eva~~~gvs~~tL----RyYe~~GLl~p~~r~~~gyR~Y~ 40 (123)
T cd04770 1 MKIGELAKAAGVSPDTI----RYYERIGLLPPPQRSENGYRLYG 40 (123)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCCCCCCCCccCC
Confidence 35789999999988754 2367788886 34567777754
No 80
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=53.37 E-value=18 Score=30.40 Aligned_cols=45 Identities=18% Similarity=0.352 Sum_probs=39.5
Q ss_pred HHHHH--hCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceeccc
Q 015878 141 INLIQ--EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 141 I~Ll~--~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
+.++. ..+++.+.+.++|+.+++.+=.+-=+++-||.-|+|+|..
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 5677899999999999999999999999999999999973
No 81
>PRK09954 putative kinase; Provisional
Probab=52.85 E-value=14 Score=36.73 Aligned_cols=47 Identities=15% Similarity=0.290 Sum_probs=40.7
Q ss_pred HHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 136 LTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
.-++.+.+|++.+ .+...++|+.|+|.|..++-.++=|+.-|+|++.
T Consensus 4 ~~~~il~~l~~~~--~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~ 50 (362)
T PRK09954 4 REKEILAILRRNP--LIQQNEIADILQISRSRVAAHIMDLMRKGRIKGK 50 (362)
T ss_pred HHHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCc
Confidence 3456788888554 8999999999999999999999999999999755
No 82
>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=52.48 E-value=8.1 Score=26.67 Aligned_cols=22 Identities=32% Similarity=0.548 Sum_probs=20.2
Q ss_pred ccHHHHHHHhcceeeehhhhHH
Q 015878 152 LDLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItN 173 (399)
+++.++|+.|+|.++.||-.++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999986
No 83
>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=52.39 E-value=40 Score=28.72 Aligned_cols=83 Identities=17% Similarity=0.240 Sum_probs=45.6
Q ss_pred HHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCCCC------cchHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 015878 155 NRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSIR 228 (399)
Q Consensus 155 n~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~~E~~LD~lI~ 228 (399)
..++..+..-.+-+=....|++.|.-+. .+.+.|+=+|.=.... .++..++..+...++.|..++..|...+.
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 3333333333333344555555555554 3455566666432211 12344455566667777777777777777
Q ss_pred HHHHHHHHHh
Q 015878 229 EKQELIRTLE 238 (399)
Q Consensus 229 ~~~q~Lr~Lt 238 (399)
+++++|+.+.
T Consensus 99 e~q~~l~~~~ 108 (110)
T TIGR02338 99 ELQEKIQEAL 108 (110)
T ss_pred HHHHHHHHHh
Confidence 7777777664
No 84
>PF13518 HTH_28: Helix-turn-helix domain
Probab=52.10 E-value=12 Score=26.67 Aligned_cols=37 Identities=14% Similarity=0.339 Sum_probs=30.0
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccc
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL 180 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgL 180 (399)
.|.++. .|. .+.++|..++|.++.||.+++-++.-|+
T Consensus 5 iv~~~~---~g~-s~~~~a~~~gis~~tv~~w~~~y~~~G~ 41 (52)
T PF13518_consen 5 IVELYL---EGE-SVREIAREFGISRSTVYRWIKRYREGGI 41 (52)
T ss_pred HHHHHH---cCC-CHHHHHHHHCCCHhHHHHHHHHHHhcCH
Confidence 455554 244 9999999999999999999999988663
No 85
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=51.90 E-value=45 Score=31.09 Aligned_cols=41 Identities=27% Similarity=0.305 Sum_probs=38.3
Q ss_pred CCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCC
Q 015878 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 147 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
.||..++.+++|+.|||+|=-|=+.+..|++-|||+.....
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 58999999999999999999999999999999999999544
No 86
>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=51.22 E-value=1.2e+02 Score=27.80 Aligned_cols=32 Identities=31% Similarity=0.478 Sum_probs=24.0
Q ss_pred cHHHHHHHHHHHHHhCCCCcccHHHHHHHhcc
Q 015878 132 SLGLLTRKFINLIQEAKDGTLDLNRTAEVLEV 163 (399)
Q Consensus 132 SLglLTkkFI~Ll~~ap~g~ldLn~aA~~L~V 163 (399)
+|..|+..|.+++.-...+..|-..+++.|.-
T Consensus 2 ~LYel~~~~~~l~~~~e~~~~d~e~~~dtLe~ 33 (162)
T PF05565_consen 2 KLYELTDEYLELLELLEEGDLDEEAIADTLES 33 (162)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 68889999999997776666777766665543
No 87
>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=51.02 E-value=34 Score=32.47 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=37.2
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
.++++..+ ...+.+.++|+.|++.|=.+|-+++-|+..|++++.
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 34445443 456899999999999999999999999999999985
No 88
>PRK11050 manganese transport regulator MntR; Provisional
Probab=50.59 E-value=83 Score=28.23 Aligned_cols=42 Identities=19% Similarity=0.148 Sum_probs=36.1
Q ss_pred CCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeE
Q 015878 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (399)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~ 190 (399)
++.+.+.++|+.|+|.+--+..+++-||.-|+|.+.....+.
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~~~v~ 90 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGVF 90 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCceE
Confidence 456889999999999999999999999999999986543333
No 89
>PRK00215 LexA repressor; Validated
Probab=50.34 E-value=20 Score=32.99 Aligned_cols=42 Identities=17% Similarity=0.207 Sum_probs=37.0
Q ss_pred hCCCCcccHHHHHHHhcc-eeeehhhhHHhhhhccceecccCC
Q 015878 146 EAKDGTLDLNRTAEVLEV-QKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 146 ~ap~g~ldLn~aA~~L~V-qKRRIYDItNVLEgIgLIeK~sKN 187 (399)
...+....+.++|+.+++ .|=-++.+++-||.-|+|++....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 345667899999999999 999999999999999999998544
No 90
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=50.25 E-value=23 Score=30.60 Aligned_cols=43 Identities=12% Similarity=0.215 Sum_probs=36.4
Q ss_pred cHHHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHh
Q 015878 132 SLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNV 174 (399)
Q Consensus 132 SLglLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 174 (399)
.-.....++++++.......++|.++|+.+|+.+|.|.-+..-
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3456678999999999989999999999999999988776653
No 91
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.14 E-value=13 Score=32.77 Aligned_cols=40 Identities=33% Similarity=0.390 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHH
Q 015878 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 134 glLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 173 (399)
++||.|=..++.--=..-+.|.++|+.++|+|-.|||=++
T Consensus 16 sLLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIK 55 (105)
T COG2739 16 SLLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIK 55 (105)
T ss_pred HHHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHH
Confidence 4778776666554444568999999999999999999765
No 92
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=49.76 E-value=1.2e+02 Score=29.89 Aligned_cols=47 Identities=23% Similarity=0.399 Sum_probs=33.1
Q ss_pred HHHH-HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceec
Q 015878 134 GLLT-RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (399)
Q Consensus 134 glLT-kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK 183 (399)
|.=| ++.|.+|.+.| .=..+++..|||....|-+=.-.||--|||+-
T Consensus 13 GNetRR~Il~lLt~~p---~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS 60 (217)
T COG1777 13 GNETRRRILQLLTRRP---CYVSEISRELGVSQKAVLKHLRILERAGLVES 60 (217)
T ss_pred cCcHHHHHHHHHhcCc---hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchh
Confidence 3334 45777777777 34567778888888888777777777777765
No 93
>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=49.75 E-value=16 Score=27.93 Aligned_cols=51 Identities=24% Similarity=0.313 Sum_probs=40.0
Q ss_pred HHHHHHHHHHhCCC----------CcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 136 LTRKFINLIQEAKD----------GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 136 LTkkFI~Ll~~ap~----------g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
++.-|+.++..... ..+...++|+.+|+.++.+--+++-|+.-|+|+...+
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 45556666654321 2468999999999999999999999999999997644
No 94
>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=48.17 E-value=24 Score=32.27 Aligned_cols=49 Identities=16% Similarity=0.266 Sum_probs=39.4
Q ss_pred HHHHHHHHh---CCCCcccHHHHHHHhcce-eeehhhhHHhhhhccceecccC
Q 015878 138 RKFINLIQE---AKDGTLDLNRTAEVLEVQ-KRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 138 kkFI~Ll~~---ap~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIgLIeK~sK 186 (399)
++.++++.+ ..+....+.++|+.|++. +=-++..++.||..|+|++...
T Consensus 9 ~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~~ 61 (199)
T TIGR00498 9 QEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDPG 61 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCCC
Confidence 445555553 344458899999999998 9999999999999999999843
No 95
>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=47.90 E-value=25 Score=30.67 Aligned_cols=39 Identities=18% Similarity=0.279 Sum_probs=34.4
Q ss_pred hCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 146 EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 146 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
...++.+.+.++|+.+++..+-+..|+..|.--|||.-.
T Consensus 20 ~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s~ 58 (135)
T TIGR02010 20 NAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKSV 58 (135)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEEE
Confidence 334458999999999999999999999999999999743
No 96
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=47.83 E-value=1.1e+02 Score=30.77 Aligned_cols=82 Identities=17% Similarity=0.198 Sum_probs=59.1
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHhhhhcccccccccHhhhccCC---------CCCCceEEEEeCCCCceEEecCCcc
Q 015878 213 IESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDIASLP---------CFQNQTLIAIKAPQASYIEVPDPDE 283 (399)
Q Consensus 213 l~~L~~~E~~LD~lI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~l~---------~f~~qTvIAIKAP~gT~LEVPdP~e 283 (399)
-++|...|..|+++|.--.+-|+.-.++..+..++||+-+-+++-+ .|.+..+-|++=+.|+++.++-++.
T Consensus 25 NeEllkLe~DLkEvIsLTedLlqT~~ee~~sss~a~~ssq~~h~s~~~~~~~~~~l~~~~~i~a~~w~vg~K~~A~~~dd 104 (262)
T KOG3026|consen 25 NEELLKLEKDLKEVISLTEDLLQTQKEEDKSSSDAFVSSQPTHSSFTPRWVSGDYLFYPSRITAVGWKVGDKVQAVFSDD 104 (262)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHhhhhhhcccccccccCccccCCCchhhhhhhhccccccchhcccccCCEEEEeecCC
Confidence 3677888999999998766666665566567779999988776622 2466778888999999999988754
Q ss_pred hhhcccceEEEEEecC
Q 015878 284 DISFLKRQYKMIIRST 299 (399)
Q Consensus 284 ~~~~~~~~yqI~LkS~ 299 (399)
.- -|...|..-
T Consensus 105 g~-----~y~AtIe~i 115 (262)
T KOG3026|consen 105 GQ-----IYDATIEHI 115 (262)
T ss_pred Cc-----eEEeehhhc
Confidence 22 256655543
No 97
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=47.05 E-value=20 Score=36.01 Aligned_cols=52 Identities=29% Similarity=0.458 Sum_probs=41.9
Q ss_pred CcHHHHHH-HHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 131 SSLGLLTR-KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 131 kSLglLTk-kFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
++|+..++ +.+++|.. .+.+++|++|+.|+..+--+--=+.|||-.|||+-.
T Consensus 18 kalaS~vRv~Il~lL~~--k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 18 KALASKVRVAILQLLHR--KGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHHH--hCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeee
Confidence 45666663 45666653 467999999999999999888889999999999865
No 98
>PRK09343 prefoldin subunit beta; Provisional
Probab=46.98 E-value=57 Score=28.60 Aligned_cols=73 Identities=15% Similarity=0.239 Sum_probs=46.6
Q ss_pred eehhhhHHhhhhccceecccCCeeEEecCCCCCC------cchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 166 RRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 166 RRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
+.+=..-.|++.|..+.- .-.-|+=.|.=.... .++..++..+..++..|+.++..|.+.+.+++.+|+.+..
T Consensus 35 ~q~~e~~~~~~EL~~L~~-d~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~~l~~ll~ 113 (121)
T PRK09343 35 LELREINKALEELEKLPD-DTPIYKIVGNLLVKVDKTKVEKELKERKELLELRSRTLEKQEKKLREKLKELQAKINEMLS 113 (121)
T ss_pred HHHHHHHHHHHHHHcCCC-cchhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455667777766652 233344455322111 2344556667778888889999999999999999998865
No 99
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=46.59 E-value=58 Score=29.23 Aligned_cols=70 Identities=17% Similarity=0.301 Sum_probs=41.5
Q ss_pred hhHHhhhhccceecccCCeeEEecCCCCCC------cchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhh
Q 015878 170 DITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (399)
Q Consensus 170 DItNVLEgIgLIeK~sKN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted 240 (399)
+|.-||+-+..+.--. .-|+=.|.-.... .++..+...|.-++..|+.+|+.|++.+..++..|+.+..+
T Consensus 38 E~~~al~Ele~l~eD~-~vYk~VG~llvk~~k~~~~~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq~~i~~~l~~ 113 (119)
T COG1382 38 EIEKALEELEKLDEDA-PVYKKVGNLLVKVSKEEAVDELEERKETLELRIKTLEKQEEKLQERLEELQSEIQKALGD 113 (119)
T ss_pred HHHHHHHHHhcCCccc-HHHHHhhhHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4666777776665442 3344455322111 12334444455566777777888888888888888777654
No 100
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=46.20 E-value=25 Score=28.14 Aligned_cols=44 Identities=27% Similarity=0.326 Sum_probs=35.9
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceeccc
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
++..+...++... .++|+.|++.+=-+.-+++-||.-|+|++..
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 3444455554444 9999999999999999999999999999983
No 101
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=45.77 E-value=52 Score=35.05 Aligned_cols=50 Identities=26% Similarity=0.390 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHhCC--CCcccHHHHHHHhcceeeehhhhHHhhhhccceec
Q 015878 134 GLLTRKFINLIQEAK--DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (399)
Q Consensus 134 glLTkkFI~Ll~~ap--~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK 183 (399)
..|-+.|+.|++... ...+.|.++|+.|++++|-.==|+|-|+..|.|+=
T Consensus 4 ~~~~~~~~~L~~~~~~~~~~~~l~~la~~l~cs~R~~~~~l~~~~~~gwl~w 55 (552)
T PRK13626 4 ARLQQQFIRLWQCCEGKSQETTLNELAELLNCSRRHMRTLLNTMQQRGWLTW 55 (552)
T ss_pred hHHHHHHHHHHHhcCCCcceeeHHHHHHHhcCChhHHHHHHHHHHHCCCeee
Confidence 357788999987653 44789999999999999999999999999888753
No 102
>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=45.71 E-value=2.3e+02 Score=25.60 Aligned_cols=55 Identities=20% Similarity=0.311 Sum_probs=28.5
Q ss_pred HHHHHHhCCCCcccHHHHHHHhc--ceeeehhhhHHhhhhccc-eecc-cCCeeEEecCC
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLE--VQKRRIYDITNVLEGIGL-IEKT-SKNHIRWKGSD 195 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIgL-IeK~-sKN~i~W~G~~ 195 (399)
.++||.. .+.++..+.+..-|+ |.|=-+==+..-|..=|. +.|. +|-.|.|.-.+
T Consensus 6 Il~y~~~-qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 6 ILEYMKE-QNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFANQD 64 (169)
T ss_pred HHHHHHH-cCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeecceEEEeeCcc
Confidence 3455543 455677777777774 455332223333333343 3343 66677775443
No 103
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=45.56 E-value=2.4e+02 Score=26.63 Aligned_cols=55 Identities=20% Similarity=0.254 Sum_probs=43.1
Q ss_pred cHHH-HHHHHHHHHHh---CCCCcc-cHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 132 SLGL-LTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 132 SLgl-LTkkFI~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
++.. +...+.+.+.. .||..+ .-.++|+.|||+|=-+-+.+..|+..|||+...+
T Consensus 10 ~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~~ 69 (254)
T PRK09464 10 KLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQG 69 (254)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 4443 44555555543 467778 8999999999999999999999999999986643
No 104
>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=45.38 E-value=70 Score=27.90 Aligned_cols=81 Identities=17% Similarity=0.212 Sum_probs=0.0
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhcccee--cccCCeeEEecCCCCCCcchHHHHHHHHH------HHHHH-------
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKGSDSLGTSKLDDQVARLKA------EIESL------- 216 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe--K~sKN~i~W~G~~~s~~~~~~~~~~~Lk~------El~~L------- 216 (399)
+.+.++|+.+||..+ -+---|.+||+. +...|.|++-..+.. ..-..+..|++ |+..+
T Consensus 1 m~I~e~a~~~gvs~~----tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l---~~l~~I~~lr~lG~sL~eI~~~l~~~~~~ 73 (127)
T TIGR02047 1 MKIGELAQKTGVSVE----TIRFYEKQGLLPPPARTDNNYRVYTVGHV---ERLAFIRNCRTLDMSLAEIRQLLRYQDKP 73 (127)
T ss_pred CcHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCCCcCCHHHH---HHHHHHHHHHHcCCCHHHHHHHHHhhhCC
Q ss_pred ----HHHHHhHHHHHHHHHHHHHHHhh
Q 015878 217 ----HAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 217 ----~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
......|++++..+.+++.+|..
T Consensus 74 ~~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T TIGR02047 74 EKSCSDVNALLDEHISHVRARIIKLQA 100 (127)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
No 105
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=45.36 E-value=1e+02 Score=26.55 Aligned_cols=58 Identities=10% Similarity=0.160 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhhcccccccccHh---hhccCCCCCCceEEEEeCC
Q 015878 207 ARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEE---DIASLPCFQNQTLIAIKAP 271 (399)
Q Consensus 207 ~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~~n~~~aYVT~e---DI~~l~~f~~qTvIAIKAP 271 (399)
.+++++++.++++-.+|.+....++.++..|.++. .|+.+. ++.= .-.++++|-|.-|
T Consensus 30 ~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~-----dyiEe~AR~~Lg~--vk~gEivy~~~~~ 90 (105)
T PRK00888 30 WRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQ-----EAIEERARNELGM--VKPGETFYRIVPD 90 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcH-----HHHHHHHHHHcCC--CCCCCEEEEeCCC
Confidence 34455555555555555555555555555554431 233322 2211 2356777766655
No 106
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=44.98 E-value=28 Score=28.63 Aligned_cols=40 Identities=18% Similarity=0.207 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHh
Q 015878 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNV 174 (399)
Q Consensus 135 lLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 174 (399)
.+..+++.++.......+++.++|+.+++++|.+.=+..=
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4567888999888888899999999999999988876653
No 107
>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=44.94 E-value=1.3e+02 Score=28.45 Aligned_cols=33 Identities=24% Similarity=0.236 Sum_probs=29.4
Q ss_pred cHHHHHHHh-cceeeehhhhHHhhhhccceeccc
Q 015878 153 DLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 153 dLn~aA~~L-~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
.=..+|..+ |+.-|.|.=.+..|...|||.+..
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 346788899 999999999999999999999973
No 108
>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=44.92 E-value=60 Score=27.43 Aligned_cols=36 Identities=25% Similarity=0.231 Sum_probs=23.3
Q ss_pred cHHHHHHHhcceeeehhhhHHhhhhcccee--cccCCeeEEe
Q 015878 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWK 192 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIgLIe--K~sKN~i~W~ 192 (399)
.+.++|+.+||..|-|.-. |..|||. ....|.+++-
T Consensus 2 ~i~e~a~~~gvs~~tlr~y----e~~gll~~~~r~~~gyR~Y 39 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYY----EKEGLLPPVKRDENGIRDF 39 (113)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCccC
Confidence 5788999999988855322 4678883 2334555543
No 109
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=44.60 E-value=1.6e+02 Score=27.90 Aligned_cols=52 Identities=23% Similarity=0.213 Sum_probs=41.3
Q ss_pred HHHHHHHHHHH---hCCCCcc-cHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 135 LLTRKFINLIQ---EAKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 135 lLTkkFI~Ll~---~ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
.+...+.+.+. =.||..+ .-.++|+.|||+|==+=+.+..|+.-|||+...+
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 68 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRRG 68 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34444444443 3478888 6999999999999999999999999999987643
No 110
>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=44.56 E-value=1.2e+02 Score=26.09 Aligned_cols=38 Identities=16% Similarity=0.175 Sum_probs=26.7
Q ss_pred cHHHHHHHhcceeeehhhhHHhhhhcccee--cccCCeeEEecC
Q 015878 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKGS 194 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIgLIe--K~sKN~i~W~G~ 194 (399)
.+.++|+.+||..|-| =-.|.+|||. +...|.|++-+.
T Consensus 2 ~I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~~ 41 (126)
T cd04783 2 TIGELAKAAGVNVETI----RYYQRRGLLPEPPRPEGGYRRYPE 41 (126)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCCeecCH
Confidence 5788999999987744 3338889987 344566777543
No 111
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=43.39 E-value=99 Score=28.59 Aligned_cols=48 Identities=10% Similarity=0.072 Sum_probs=41.0
Q ss_pred CCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecC
Q 015878 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (399)
Q Consensus 147 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~ 194 (399)
.||..+...++|+.|||+|==|=+.+..|+.-|||+...+.-+.-...
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~ 73 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASM 73 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCC
Confidence 478889999999999999999999999999999999876655554443
No 112
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=43.25 E-value=14 Score=32.48 Aligned_cols=33 Identities=27% Similarity=0.472 Sum_probs=27.9
Q ss_pred HHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHH
Q 015878 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 135 lLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 173 (399)
.|..+|++.+ -++.+.+|+.|||++.+|-.|+|
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 4567777654 37899999999999999999998
No 113
>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=42.91 E-value=21 Score=33.69 Aligned_cols=43 Identities=28% Similarity=0.367 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhh
Q 015878 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEG 177 (399)
Q Consensus 135 lLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEg 177 (399)
.+..+|+.++.+.....+.|.++|+.+++++|.+..++.-..|
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G 228 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSA 228 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 4568899999988888999999999999999999988765443
No 114
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=42.83 E-value=66 Score=31.18 Aligned_cols=41 Identities=20% Similarity=0.242 Sum_probs=27.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhhcc
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENH 243 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~~n 243 (399)
+.++-++|++|++.|+.+..+++++..+ .++|++|.+-...
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 4445567777888877777777766555 5777777655443
No 115
>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=42.38 E-value=59 Score=32.93 Aligned_cols=35 Identities=31% Similarity=0.490 Sum_probs=25.0
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhh
Q 015878 207 ARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (399)
Q Consensus 207 ~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~ 241 (399)
..|.+|++.|+.++.+|++.|..++.++..+.+.+
T Consensus 60 ~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE 94 (314)
T PF04111_consen 60 EELLQELEELEKEREELDQELEELEEELEELDEEE 94 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34556677777788888888888877777776543
No 116
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=42.37 E-value=25 Score=33.96 Aligned_cols=47 Identities=17% Similarity=0.270 Sum_probs=38.7
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
++.+++++ ..+.+.+.++|+.|+|++.-|+=-++.||..|+|.|...
T Consensus 8 ~~Il~~l~--~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~g 54 (251)
T PRK13509 8 QILLELLA--QLGFVTVEKVIERLGISPATARRDINKLDESGKLKKVRN 54 (251)
T ss_pred HHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecC
Confidence 34556666 468999999999999999888878999999999988633
No 117
>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=42.21 E-value=89 Score=24.83 Aligned_cols=36 Identities=8% Similarity=0.289 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
..+..+.+.+..|+.....++..|..+..+|..+.+
T Consensus 13 ~~l~~~~~~i~~lE~~~~~~e~~i~~~~~~l~~I~~ 48 (71)
T PF10779_consen 13 TKLDNHEERIDKLEKRDAANEKDIKNLNKQLEKIKS 48 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556666777777888888888888888888875
No 118
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=42.16 E-value=37 Score=29.20 Aligned_cols=54 Identities=15% Similarity=0.127 Sum_probs=38.1
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhhcccccccccHhhh
Q 015878 200 SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDI 254 (399)
Q Consensus 200 ~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~~n~~~aYVT~eDI 254 (399)
..+.+++..+++|++.|+++.+.|.+.|..++... +..|..--..|-||-..+|
T Consensus 30 ~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~-dyiEe~AR~~Lg~vk~gEi 83 (105)
T PRK00888 30 WRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQ-EAIEERARNELGMVKPGET 83 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcH-HHHHHHHHHHcCCCCCCCE
Confidence 35667788999999999999999999999987642 2333322334556666555
No 119
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=42.13 E-value=74 Score=28.64 Aligned_cols=79 Identities=20% Similarity=0.275 Sum_probs=0.0
Q ss_pred ccHHHHHHHhcceee--ehhhhHHhhhhccce--ecccCCeeEEecCCCCCCcchHHHHHHHHH------HHHHHHH---
Q 015878 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLI--EKTSKNHIRWKGSDSLGTSKLDDQVARLKA------EIESLHA--- 218 (399)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIgLI--eK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~------El~~L~~--- 218 (399)
+.+.++|+..||+.| |.|| -+||| .+...|.|++-..... ..-..+..|++ |+..+-.
T Consensus 8 ~~IgevAk~~Gvs~~TLRyYE------~~GLl~p~~r~~~gyR~Y~~~~l---~rl~~I~~lr~~G~sL~eI~~ll~~~~ 78 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFYQ------RKGLLPEPDKPYGSIRRYGEADV---TRVRFVKSAQRLGFSLDEIAELLRLED 78 (144)
T ss_pred ccHHHHHHHHCcCHHHHHHHH------HCCCCCCCccCCCCCeecCHHHH---HHHHHHHHHHHcCCCHHHHHHHHhccC
Q ss_pred ------HHHhHHHHHHHHHHHHHHHhh
Q 015878 219 ------EECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 219 ------~E~~LD~lI~~~~q~Lr~Lte 239 (399)
....|.+.+..+.+++.+|..
T Consensus 79 ~~~~~~~~~ll~~k~~~l~~~i~~L~~ 105 (144)
T PRK13752 79 GTHCEEASSLAEHKLKDVREKMADLAR 105 (144)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHH
No 120
>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=41.23 E-value=36 Score=31.59 Aligned_cols=45 Identities=20% Similarity=0.307 Sum_probs=37.9
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
.+.++... +.+.+.++|+.|++.+-.++-.++-|+..|+|++..+
T Consensus 148 IL~~l~~~--g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 148 VLEVLKAE--GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 44444432 5689999999999999999999999999999999863
No 121
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=40.85 E-value=28 Score=32.01 Aligned_cols=39 Identities=15% Similarity=0.241 Sum_probs=35.0
Q ss_pred hCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 146 EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 146 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
...++.+.+.++|+.+++.++-+..|++-|.--|||.-.
T Consensus 20 ~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 20 NSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 344568999999999999999999999999999999964
No 122
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=40.76 E-value=1.3e+02 Score=26.21 Aligned_cols=47 Identities=21% Similarity=0.291 Sum_probs=39.9
Q ss_pred HHHHHHHHHHhCCCC--cccHHHHHHHhcceeeehhhhHHhhhhcccee
Q 015878 136 LTRKFINLIQEAKDG--TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (399)
Q Consensus 136 LTkkFI~Ll~~ap~g--~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe 182 (399)
|...|..|++...+. .+.|.++|+.|.+++|-.==|++-|+..|.|+
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 456788888777655 57999999999999999999999999988764
No 123
>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=40.63 E-value=85 Score=29.23 Aligned_cols=30 Identities=27% Similarity=0.399 Sum_probs=16.4
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 015878 207 ARLKAEIESLHAEECRIDDSIREKQELIRT 236 (399)
Q Consensus 207 ~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~ 236 (399)
+.++.+|..|..+-..||+.|+.+..+|..
T Consensus 25 q~~~~~I~~L~~e~~~ld~~i~~~~~~L~~ 54 (188)
T PF10018_consen 25 QENQARIQQLRAEIEELDEQIRDILKQLKE 54 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555566666666666665555444443
No 124
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=40.29 E-value=1.8e+02 Score=28.56 Aligned_cols=53 Identities=15% Similarity=0.238 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCee
Q 015878 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (399)
Q Consensus 135 lLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i 189 (399)
.--.+.+++|++. +.+.+.++|+.|+|+.+-|.==+..||.-|++.|.-...+
T Consensus 17 eR~~~Il~~L~~~--~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GGa~ 69 (269)
T PRK09802 17 ERREQIIQRLRQQ--GSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGAL 69 (269)
T ss_pred HHHHHHHHHHHHc--CCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCCEE
Confidence 3345566777764 3599999999999988777655667899999998865543
No 125
>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=39.77 E-value=86 Score=24.21 Aligned_cols=30 Identities=30% Similarity=0.531 Sum_probs=25.4
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 015878 201 KLDDQVARLKAEIESLHAEECRIDDSIREK 230 (399)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~ 230 (399)
....+++.|+.+++.|..+-+.|.+.|+.+
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 355678889999999999999999998888
No 126
>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=39.41 E-value=1.8e+02 Score=25.38 Aligned_cols=80 Identities=16% Similarity=0.170 Sum_probs=0.0
Q ss_pred ccHHHHHHHhcceee--ehhhhHHhhhhccceecccC--CeeEEe----------------------------cCCCCCC
Q 015878 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLIEKTSK--NHIRWK----------------------------GSDSLGT 199 (399)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIgLIeK~sK--N~i~W~----------------------------G~~~s~~ 199 (399)
+.+.++|+.+||..| |.| |-+|||.-... |.|+.- .......
T Consensus 1 m~IgE~A~~~gvs~~TLRyY------E~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~ 74 (133)
T cd04787 1 MKVKELANAAGVTPDTVRFY------TRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGE 74 (133)
T ss_pred CCHHHHHHHHCcCHHHHHHH------HHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhccCC
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 015878 200 SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (399)
Q Consensus 200 ~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~L 237 (399)
.........|++.++.|+++-.+|.+++..+...+...
T Consensus 75 ~~~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~ 112 (133)
T cd04787 75 SPCPMVRRLIEQRLAETERRIKELLKLRDRMQQAVSQW 112 (133)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 127
>PHA01750 hypothetical protein
Probab=38.87 E-value=78 Score=26.15 Aligned_cols=31 Identities=23% Similarity=0.409 Sum_probs=19.5
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 015878 204 DQVARLKAEIESLHAEECRIDDSIREKQELI 234 (399)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L 234 (399)
+.+.+|+.|++++..+.++|.+++.++...+
T Consensus 42 ~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 42 SELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 3455666777777766666666666665543
No 128
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=38.81 E-value=90 Score=27.28 Aligned_cols=47 Identities=17% Similarity=0.212 Sum_probs=37.6
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
+.|..++. .++.+.+.++|+.|+|.+=-+--+++-|+.-|+|.+...
T Consensus 11 ~~I~~l~~--~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~~ 57 (142)
T PRK03902 11 EQIYLLIE--EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEKY 57 (142)
T ss_pred HHHHHHHh--cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEecC
Confidence 33444443 446778999999999999999999999999999997633
No 129
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=38.62 E-value=13 Score=37.23 Aligned_cols=27 Identities=26% Similarity=0.578 Sum_probs=21.4
Q ss_pred cHHHHHHHhcceeeehhhhHHhhhhcc
Q 015878 153 DLNRTAEVLEVQKRRIYDITNVLEGIG 179 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIg 179 (399)
-|..+=-.||..+|=+||.+||+||=.
T Consensus 42 GLRNLDlimGlE~RiVYd~vdVi~g~~ 68 (272)
T COG2894 42 GLRNLDLIMGLENRIVYDLVDVIEGEA 68 (272)
T ss_pred CchhhhhhhcccceeeeeehhhhcCcc
Confidence 344444558999999999999999854
No 130
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=38.60 E-value=38 Score=29.71 Aligned_cols=42 Identities=17% Similarity=0.265 Sum_probs=36.5
Q ss_pred hCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCC
Q 015878 146 EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 146 ~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
..++..+...++|+.++|.+.-+-.|+..|..-|||+.....
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G~ 61 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRGK 61 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecCC
Confidence 345668899999999999999999999999999999877443
No 131
>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=38.58 E-value=34 Score=30.00 Aligned_cols=36 Identities=8% Similarity=0.314 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehh
Q 015878 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIY 169 (399)
Q Consensus 134 glLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIY 169 (399)
..+..-|++||+..+=..+.++++|++-||.|.-+|
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY 41 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHH
Confidence 356677999999999999999999999999998776
No 132
>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=38.49 E-value=1.1e+02 Score=24.10 Aligned_cols=39 Identities=21% Similarity=0.477 Sum_probs=27.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
+++..+..+...+..++.+-+.|-+-|..+.+.++.|..
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 455566667777777777777777777777777777654
No 133
>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=38.43 E-value=65 Score=26.21 Aligned_cols=78 Identities=13% Similarity=0.290 Sum_probs=32.6
Q ss_pred HHHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCCC-CcchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHH
Q 015878 157 TAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLG-TSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIR 235 (399)
Q Consensus 157 aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~-~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr 235 (399)
+...+.--++.+..+.-|++-|..+.-. ...|.+.+..- ......-+..|+++++.+..+-..|...+..+..++.
T Consensus 17 ~~~q~~~l~~~~~~~~~~~~eL~~l~~~---~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~ 93 (106)
T PF01920_consen 17 LEQQIQQLERQLRELELTLEELEKLDDD---RKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLK 93 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHTSSTT----EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCc---chhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333334444455555444333 44554433210 1122333444555444454444444444444444444
Q ss_pred HH
Q 015878 236 TL 237 (399)
Q Consensus 236 ~L 237 (399)
++
T Consensus 94 ~~ 95 (106)
T PF01920_consen 94 EL 95 (106)
T ss_dssp HH
T ss_pred HH
Confidence 44
No 134
>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=38.20 E-value=48 Score=27.50 Aligned_cols=45 Identities=24% Similarity=0.469 Sum_probs=37.9
Q ss_pred HHHHHHhCCCCcccHHHHHHHh-----cceeeehhhhHHhhhhccceeccc
Q 015878 140 FINLIQEAKDGTLDLNRTAEVL-----EVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L-----~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
.+++|..+ +..++..++.+.| .+.+=-+|=+++.|+..|+|.|..
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 5778999999988 578899999999999999999973
No 135
>PRK03837 transcriptional regulator NanR; Provisional
Probab=37.72 E-value=3e+02 Score=25.53 Aligned_cols=52 Identities=12% Similarity=0.245 Sum_probs=42.1
Q ss_pred HHHHHHHHHHh---CCCCcc-cHHHHHHHhcceeeehhhhHHhhhhccceecccCC
Q 015878 136 LTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 136 LTkkFI~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
+.+.+.+.+.. .||..+ ...++|+.|||+|-=+=+.+..|+.-|||+...+.
T Consensus 18 v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~~ 73 (241)
T PRK03837 18 VEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHGE 73 (241)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 44555555543 477788 89999999999999999999999999999987443
No 136
>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=37.00 E-value=31 Score=23.44 Aligned_cols=23 Identities=22% Similarity=0.232 Sum_probs=19.8
Q ss_pred ccHHHHHHHhcceeeehhhhHHh
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNV 174 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNV 174 (399)
+++.++|+.|+|.++-||..+.-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 46789999999999999988764
No 137
>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=36.51 E-value=16 Score=31.07 Aligned_cols=48 Identities=29% Similarity=0.479 Sum_probs=34.5
Q ss_pred eEEecCCCCCCcchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 189 IRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 189 i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
..|.|.+ +.+++..+..|..+++.|..+-..|...+..++.+|..+.+
T Consensus 13 ~~~rGYd---~~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~ 60 (131)
T PF05103_consen 13 KSMRGYD---PDEVDDFLDELAEELERLQRENAELKEEIEELQAQLEELRE 60 (131)
T ss_dssp EEEEEEE---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT------
T ss_pred CCCCCcC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhh
Confidence 5678877 45788889999999999988888888888888777776643
No 138
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=36.32 E-value=85 Score=29.54 Aligned_cols=50 Identities=24% Similarity=0.329 Sum_probs=40.8
Q ss_pred HHHHHHHHh---CCCCcc-cHHHHHHHhcceeeehhhhHHhhhhccceecccCC
Q 015878 138 RKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 138 kkFI~Ll~~---ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
..+.+.+.. .||..+ .-.++|+.|||+|==+-+.+..|+..|||+...+.
T Consensus 14 ~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~~ 67 (251)
T PRK09990 14 ERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQGR 67 (251)
T ss_pred HHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCCC
Confidence 444444432 478889 89999999999999999999999999999877543
No 139
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=36.30 E-value=51 Score=33.42 Aligned_cols=46 Identities=26% Similarity=0.281 Sum_probs=38.9
Q ss_pred CcchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhhccc
Q 015878 199 TSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQ 244 (399)
Q Consensus 199 ~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~~n~ 244 (399)
+++-.-.++.|++||..|+..-.+-|++|-+-..+|-+|..|.+++
T Consensus 220 ~~dh~V~i~~lkeeia~Lkk~L~qkdq~ileKdkqisnLKad~e~~ 265 (305)
T KOG3990|consen 220 PGDHMVKIQKLKEEIARLKKLLHQKDQLILEKDKQISNLKADKEYQ 265 (305)
T ss_pred CcchHHHHHHHHHHHHHHHHHHhhhHHHHHhhhhhhhccCcchhHH
Confidence 3444556899999999999999999999999999999999885554
No 140
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=35.99 E-value=35 Score=27.26 Aligned_cols=42 Identities=19% Similarity=0.199 Sum_probs=32.7
Q ss_pred CCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEE
Q 015878 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (399)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W 191 (399)
.+.....+++...++.-+++..+++-|+.-|||++ .++.|.-
T Consensus 17 ~~~~~~t~i~~~~~L~~~~~~~yL~~L~~~gLI~~-~~~~Y~l 58 (77)
T PF14947_consen 17 KGGAKKTEIMYKANLNYSTLKKYLKELEEKGLIKK-KDGKYRL 58 (77)
T ss_dssp TT-B-HHHHHTTST--HHHHHHHHHHHHHTTSEEE-ETTEEEE
T ss_pred cCCCCHHHHHHHhCcCHHHHHHHHHHHHHCcCeeC-CCCEEEE
Confidence 67788899999999999999999999999999966 4555554
No 141
>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=35.50 E-value=34 Score=27.84 Aligned_cols=40 Identities=18% Similarity=0.287 Sum_probs=34.7
Q ss_pred hCCCCcccHHHHHHHh-cceeeehhhhHHhhhhccceeccc
Q 015878 146 EAKDGTLDLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 146 ~ap~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
.-..|...++++.+.+ +++++=+.+=...|+..|||+|..
T Consensus 13 ~l~~g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 13 ALFQGPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHTTSSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHhCCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhccc
Confidence 3344889999999999 899999999999999999999983
No 142
>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=35.50 E-value=41 Score=32.11 Aligned_cols=47 Identities=26% Similarity=0.406 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 136 LTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
|...||++++... ++.|+.+|..+++.-==+-|-++-|+..|.|+=.
T Consensus 100 lL~~Fi~yIK~~K--vv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv 146 (188)
T PF09756_consen 100 LLQEFINYIKEHK--VVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGV 146 (188)
T ss_dssp HHHHHHHHHHH-S--EE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EE
T ss_pred HHHHHHHHHHHcc--eeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceee
Confidence 7899999999764 9999999999999665555666777777766543
No 143
>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=34.92 E-value=34 Score=28.49 Aligned_cols=41 Identities=17% Similarity=0.473 Sum_probs=32.9
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
|.+-+-++ ++.+.+.++|..|++.++++|++ |...|++-|.
T Consensus 14 ~~d~~~~~-~~~~ti~~~AK~L~i~~~~l~~~---Lr~~g~l~~~ 54 (111)
T PF03374_consen 14 FYDAFVDS-DGLYTIREAAKLLGIGRNKLFQW---LREKGWLYRR 54 (111)
T ss_pred HHHHHHcC-CCCccHHHHHHHhCCCHHHHHHH---HHhCCceEEC
Confidence 55555443 48999999999999999999876 6668888884
No 144
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.79 E-value=53 Score=28.12 Aligned_cols=36 Identities=17% Similarity=0.303 Sum_probs=31.7
Q ss_pred CCCCcccHHHHHHHhcceeeehhhhHHhhhhcccee
Q 015878 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (399)
Q Consensus 147 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe 182 (399)
......++-++...-|-.||-+-|++..|+|||++-
T Consensus 18 ~S~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~l 53 (95)
T COG4519 18 DSGETANVPELMAATGWPRRTAQDVIKALPGLGIVL 53 (95)
T ss_pred hccccCChHHHHHHcCCchhHHHHHHHhCcCCCeEE
Confidence 345678889999999999999999999999999863
No 145
>PHA00738 putative HTH transcription regulator
Probab=34.61 E-value=1.2e+02 Score=26.95 Aligned_cols=73 Identities=19% Similarity=0.265 Sum_probs=50.5
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCCCCcchHHHHHHHHHHHHHHH
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLH 217 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~ 217 (399)
++.+.+|... +.+...++++.|++.+=.|-==+.||+..|||+........+--... ....++.|..|++...
T Consensus 15 r~IL~lL~~~--e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~-----~~~~~~l~~~~~~~~~ 87 (108)
T PHA00738 15 RKILELIAEN--YILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIRE-----NSKEIQILNSELEGFK 87 (108)
T ss_pred HHHHHHHHHc--CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECC-----CccHHHHHhhHHHHHH
Confidence 3456666543 34888899999999999999999999999999887666544433321 1234566777766554
No 146
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=34.46 E-value=80 Score=30.00 Aligned_cols=36 Identities=25% Similarity=0.338 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
.-|..|++|++.+...+...+..+.++.++.+.|++
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 347889999999999999999998888888777765
No 147
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=34.31 E-value=32 Score=29.92 Aligned_cols=37 Identities=16% Similarity=0.187 Sum_probs=34.3
Q ss_pred CCcccHHHHHHHhcceeeehhhhHHhhhhccceeccc
Q 015878 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
.+.+...++|+.+++.|=-+--+++-||.-|+|+|..
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 4568999999999999999999999999999999983
No 148
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=34.18 E-value=87 Score=34.96 Aligned_cols=69 Identities=25% Similarity=0.358 Sum_probs=46.9
Q ss_pred hhhH-HhhhhccceecccCCeeEEecCCCCCCc------chHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhh
Q 015878 169 YDIT-NVLEGIGLIEKTSKNHIRWKGSDSLGTS------KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (399)
Q Consensus 169 YDIt-NVLEgIgLIeK~sKN~i~W~G~~~s~~~------~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted 240 (399)
|+.+ +-|..|.=|.+.+||++-= ..++-. .++..+..|+.|-+.|..+..++|.-+..+.++|..|..+
T Consensus 479 ~~lte~QLslIrDIRRRgKNkvAA---QnCRKRKLd~I~nLE~ev~~l~~eKeqLl~Er~~~d~~L~~~kqqls~L~~~ 554 (604)
T KOG3863|consen 479 YKLTEEQLSLIRDIRRRGKNKVAA---QNCRKRKLDCILNLEDEVEKLQKEKEQLLRERDELDSTLGVMKQQLSELYQE 554 (604)
T ss_pred cccCHHHHHHhhccccccccchhc---cchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444 6788889999999997632 222222 2344455666666777777778888888888888877654
No 149
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=34.14 E-value=53 Score=32.45 Aligned_cols=57 Identities=25% Similarity=0.436 Sum_probs=47.8
Q ss_pred CcHHHHHHHHHH-HHHhCCCCcccHHHHHHHhcceeeehhhhHH-hhhhccceecccCC
Q 015878 131 SSLGLLTRKFIN-LIQEAKDGTLDLNRTAEVLEVQKRRIYDITN-VLEGIGLIEKTSKN 187 (399)
Q Consensus 131 kSLglLTkkFI~-Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIgLIeK~sKN 187 (399)
..|...-++++. ++..-.++.+.+..+|..|+.....+=|++- .|-..|||++....
T Consensus 255 ~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 313 (328)
T PRK00080 255 LGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRG 313 (328)
T ss_pred CCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCch
Confidence 456667788886 6677788899999999999999999998888 89999999877443
No 150
>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=33.97 E-value=1.6e+02 Score=23.95 Aligned_cols=39 Identities=18% Similarity=0.376 Sum_probs=34.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
.+...+..++.+++.|..+...+...+..++..|+.+..
T Consensus 66 ~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~~~~ 104 (106)
T PF01920_consen 66 ELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYELFG 104 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCS
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 466778899999999999999999999999999987653
No 151
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=33.59 E-value=58 Score=28.09 Aligned_cols=50 Identities=24% Similarity=0.341 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 133 LglLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
|-.+=.+-+++|+. ++.+.+.++|++||++...+...+.-||.-|+|.+.
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 34455777888874 445999999999999999999999999999999987
No 152
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=33.31 E-value=4.1e+02 Score=24.84 Aligned_cols=51 Identities=20% Similarity=0.233 Sum_probs=36.0
Q ss_pred CCCCcHHHHHHHHHHHHH-hCCCCc---------------ccHHHHHHHhcc-eeeehhhhHHhhhhccc
Q 015878 128 RYDSSLGLLTRKFINLIQ-EAKDGT---------------LDLNRTAEVLEV-QKRRIYDITNVLEGIGL 180 (399)
Q Consensus 128 R~dkSLglLTkkFI~Ll~-~ap~g~---------------ldLn~aA~~L~V-qKRRIYDItNVLEgIgL 180 (399)
+++-+...|-++|..+.+ -.||.. --+|+|=..|.- .+|..|++ .|.|+.+
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 456677889999998864 445532 357777777777 57889988 5567765
No 153
>smart00338 BRLZ basic region leucin zipper.
Probab=33.24 E-value=1.5e+02 Score=22.70 Aligned_cols=34 Identities=24% Similarity=0.430 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 206 ~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
+..|+.++..|..+-..|-..+..+..++..|.+
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566667777777777777777776666666543
No 154
>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=33.23 E-value=83 Score=26.23 Aligned_cols=59 Identities=29% Similarity=0.490 Sum_probs=45.3
Q ss_pred CcHHHHHHHHHHHHHhC-CCCcccHHHHHHHhcceeeehhhhHH-hhhhccceecccCCee
Q 015878 131 SSLGLLTRKFINLIQEA-KDGTLDLNRTAEVLEVQKRRIYDITN-VLEGIGLIEKTSKNHI 189 (399)
Q Consensus 131 kSLglLTkkFI~Ll~~a-p~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIgLIeK~sKN~i 189 (399)
.-|..+=++++..+-.. .+|.+-|+.+|..|+..+.-|=|++- -|--+|+|+|..+.++
T Consensus 4 ~GLd~~D~~yL~~l~~~f~ggPvGl~tlA~~l~ed~~Tie~v~EPyLiq~G~I~RT~rGR~ 64 (76)
T PF05491_consen 4 LGLDELDRRYLKTLIENFKGGPVGLDTLAAALGEDKETIEDVIEPYLIQIGFIQRTPRGRV 64 (76)
T ss_dssp TS-BHHHHHHHHHHHHCSTTS-B-HHHHHHHTTS-HHHHHHTTHHHHHHTTSEEEETTEEE
T ss_pred ccCCHHHHHHHHHHHHHcCCCCeeHHHHHHHHCCCHhHHHHHhhHHHHHhhhHhhCccHHH
Confidence 34566778899888654 89999999999999999998887765 5778999999988764
No 155
>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=33.13 E-value=44 Score=32.87 Aligned_cols=31 Identities=32% Similarity=0.562 Sum_probs=25.7
Q ss_pred HHHHHhc---ceeeehhhhHHhhhhccceecccC
Q 015878 156 RTAEVLE---VQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 156 ~aA~~L~---VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
.+++.++ +..|++|++++-||.+|||+-...
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~~ 352 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEER 352 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEEE
Confidence 5666666 577999999999999999998743
No 156
>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=33.09 E-value=92 Score=26.04 Aligned_cols=35 Identities=26% Similarity=0.349 Sum_probs=24.1
Q ss_pred cHHHHHHHhcceee--ehhhhHHhhhhcccee--cccCCeeEEec
Q 015878 153 DLNRTAEVLEVQKR--RIYDITNVLEGIGLIE--KTSKNHIRWKG 193 (399)
Q Consensus 153 dLn~aA~~L~VqKR--RIYDItNVLEgIgLIe--K~sKN~i~W~G 193 (399)
.+.++|+.+||+.+ |.| |-.||+. +...|.++|-.
T Consensus 2 ~i~e~A~~~gvs~~tlR~Y------e~~Gll~~~~r~~~g~R~Y~ 40 (99)
T cd04772 2 RTVDLARAIGLSPQTVRNY------ESLGLIPPAERTANGYRIYT 40 (99)
T ss_pred CHHHHHHHHCcCHHHHHHH------HHcCCCCCCCcCCCCCeecC
Confidence 46789999999775 345 6778875 34566677644
No 157
>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=32.98 E-value=77 Score=26.52 Aligned_cols=46 Identities=24% Similarity=0.303 Sum_probs=36.6
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
+-.|+++.. .+..|-=.++|+.|++.-=-|..+.-.||.+|||+++
T Consensus 11 ~alV~~Y~~-~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 11 KALVELYIE-TGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHh-cCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 334455443 3677888889999999888899999999999999975
No 158
>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=32.34 E-value=64 Score=30.98 Aligned_cols=56 Identities=21% Similarity=0.392 Sum_probs=40.8
Q ss_pred CcHHHHHH------HHHHHHHhCCCC-cccHHHHHHHhcceeeehhhhHHhhhhccceecccCCee
Q 015878 131 SSLGLLTR------KFINLIQEAKDG-TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (399)
Q Consensus 131 kSLglLTk------kFI~Ll~~ap~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i 189 (399)
+-||.++- ..++.|....+. .++++++++..++.+ -||+..|+.+|++.....+++
T Consensus 123 SdlG~~sY~sYW~~~i~~~L~~~~~~~~isi~~is~~Tgi~~---~DIi~tL~~l~~l~~~~~~~~ 185 (188)
T PF01853_consen 123 SDLGRLSYRSYWRRVILEYLLEFKGKKSISIKDISQETGIRP---EDIISTLQQLGMLKYYKGQHI 185 (188)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHTSSE--EEHHHHHHHH-BTH---HHHHHHHHHTT-EEEETTEEE
T ss_pred CHHHHHHHHHHHHHHHHHHHHhcCCCCeEEHHHHHHHHCCCH---HHHHHHHHHCCCEEEECCcEE
Confidence 34677763 366777666664 899999999999964 699999999999998866554
No 159
>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=31.99 E-value=1.7e+02 Score=26.98 Aligned_cols=34 Identities=12% Similarity=0.310 Sum_probs=19.3
Q ss_pred EEEEeCCCCceEEecCCcchhhcccceEEEEEecCCCCeEE
Q 015878 265 LIAIKAPQASYIEVPDPDEDISFLKRQYKMIIRSTTGPIDV 305 (399)
Q Consensus 265 vIAIKAP~gT~LEVPdP~e~~~~~~~~yqI~LkS~~GPIdV 305 (399)
.|.|+.-+.|++++-..++ +..++....+-|..+
T Consensus 59 FIlV~T~~~a~I~ceiS~D-------~~~~~F~Fn~~pFeI 92 (142)
T PF08781_consen 59 FILVNTSKKAVIECEISED-------KSEYHFDFNSTPFEI 92 (142)
T ss_dssp -EEEEEESS--EEEEE-TT-------SSEEEEEESS--EEE
T ss_pred EEEEEecCCcEEEEEEcCC-------ccEEEEEcCCCceee
Confidence 5899999999999965433 234666666666553
No 160
>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=31.79 E-value=90 Score=25.40 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=15.5
Q ss_pred cHHHHHHHhcceeeehhhhHH
Q 015878 153 DLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItN 173 (399)
.+.++|+.+||..+.|--..+
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567888999988776665544
No 161
>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=31.41 E-value=97 Score=24.62 Aligned_cols=57 Identities=23% Similarity=0.315 Sum_probs=47.4
Q ss_pred HHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEe
Q 015878 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (399)
Q Consensus 136 LTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~ 192 (399)
+-.+.+++|....+....--..+..|.+.|+.|==+..=|+.=|.|.|.+-+--.|.
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 446778888777777777788888999999999999999999999999988888884
No 162
>PF15513 DUF4651: Domain of unknown function (DUF4651)
Probab=31.38 E-value=34 Score=27.54 Aligned_cols=23 Identities=30% Similarity=0.449 Sum_probs=19.3
Q ss_pred cCCCCeEEEEecCCCCCCccccc
Q 015878 298 STTGPIDVYLLSKYQSEGKDITL 320 (399)
Q Consensus 298 S~~GPIdVyL~~~~~~~~e~~~~ 320 (399)
|..|+|+|+.+..++...+.+.|
T Consensus 16 s~lG~I~vLYvn~~eS~~~~~~G 38 (62)
T PF15513_consen 16 SQLGEIAVLYVNPYESDEDRLTG 38 (62)
T ss_pred HhcCcEEEEEEcccccCCCeEec
Confidence 78999999999999877666654
No 163
>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=30.82 E-value=28 Score=25.74 Aligned_cols=24 Identities=29% Similarity=0.512 Sum_probs=19.7
Q ss_pred CcccHHHHHHHhcceeeehhhhHH
Q 015878 150 GTLDLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItN 173 (399)
..++++++++.+++++.-||..++
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 468899999999999999999988
No 164
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=30.64 E-value=90 Score=29.12 Aligned_cols=39 Identities=18% Similarity=0.244 Sum_probs=34.0
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeE
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~ 190 (399)
+.-.++|..||+++..+.=+++-|+--|+|++.+.++|.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 456899999999999999999999999999887655554
No 165
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=30.57 E-value=92 Score=33.83 Aligned_cols=38 Identities=16% Similarity=0.225 Sum_probs=20.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
+++++..|+.|++.|..+...+++.|+.++..++.|.+
T Consensus 81 LEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~ 118 (475)
T PRK13729 81 MQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAE 118 (475)
T ss_pred HHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHH
Confidence 34444455555544445555566666666666666644
No 166
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=30.35 E-value=77 Score=30.54 Aligned_cols=87 Identities=16% Similarity=0.240 Sum_probs=54.0
Q ss_pred CcHHHHHHHHHHHHHhCCCCcccHHHH-----------HHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCCCC
Q 015878 131 SSLGLLTRKFINLIQEAKDGTLDLNRT-----------AEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT 199 (399)
Q Consensus 131 kSLglLTkkFI~Ll~~ap~g~ldLn~a-----------A~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~ 199 (399)
..+....++..+++....+.+...+.- .-.+.|..-++-+.++-|.++|-|....-+ .
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 456666677777887776555444432 334567888999999999999977655222 1
Q ss_pred cchHHHHHHHHHHHHHHHHHHHhHHHHHH
Q 015878 200 SKLDDQVARLKAEIESLHAEECRIDDSIR 228 (399)
Q Consensus 200 ~~~~~~~~~Lk~El~~L~~~E~~LD~lI~ 228 (399)
.++..+...+++.++.|+.++++|-+++.
T Consensus 128 ~DvT~~y~D~~arl~~l~~~~~rl~~ll~ 156 (262)
T PF14257_consen 128 EDVTEQYVDLEARLKNLEAEEERLLELLE 156 (262)
T ss_pred cchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 23444444555566666655555555443
No 167
>PRK10130 transcriptional regulator EutR; Provisional
Probab=30.30 E-value=43 Score=34.17 Aligned_cols=40 Identities=13% Similarity=0.144 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHH
Q 015878 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 134 glLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 173 (399)
..+.+++++++....+..+++.++|+.++|++|.|+-.+.
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 4677888899988888899999999999999999987664
No 168
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=30.27 E-value=71 Score=25.33 Aligned_cols=52 Identities=21% Similarity=0.404 Sum_probs=37.4
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc--cCCe-eEEe
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT--SKNH-IRWK 192 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~--sKN~-i~W~ 192 (399)
.+++++.. .+.+.-.++|+.+++.+-..-=+.+.||.-|.|++. .+.. ..|.
T Consensus 5 Il~~i~~~-~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~~~~~~rG~~~~W~ 59 (62)
T PF04703_consen 5 ILEYIKEQ-NGPLKTREIADALGLSIYQARYYLEKLEKEGKVERSPVRRGKSTYWR 59 (62)
T ss_dssp HHHHHHHH-TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEEEES-SSSSS-EEE
T ss_pred HHHHHHHc-CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCCCCcceeee
Confidence 44555543 556888999999999988888899999999999973 2222 4575
No 169
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=29.92 E-value=1.1e+02 Score=32.61 Aligned_cols=58 Identities=16% Similarity=0.311 Sum_probs=46.2
Q ss_pred cHHHHHHH------HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecC
Q 015878 132 SLGLLTRK------FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (399)
Q Consensus 132 SLglLTkk------FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~ 194 (399)
-||+|+-+ .+++|....+..|.++++|+.-++. .=||++.|+.+++|....- +.|...
T Consensus 304 DLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~---~~DIisTL~~L~m~~y~k~--~~~~~~ 367 (396)
T KOG2747|consen 304 DLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIR---PDDIISTLQSLNMIKYYKG--YIISIC 367 (396)
T ss_pred hhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCC---HHHHHHHHHhhCCccccCC--eeEEEe
Confidence 47888855 6778877666669999999999984 5799999999999987733 777653
No 170
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=29.56 E-value=81 Score=31.26 Aligned_cols=52 Identities=19% Similarity=0.270 Sum_probs=40.6
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccc-eecccCCeeEE
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL-IEKTSKNHIRW 191 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgL-IeK~sKN~i~W 191 (399)
.+.+.++.+ +..+...++|+.|+|+|.-++-.+..|+.-|+ |.......|..
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 456677764 46788889999999999999999999999999 54443334555
No 171
>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=29.33 E-value=59 Score=23.16 Aligned_cols=37 Identities=22% Similarity=0.455 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhh
Q 015878 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDI 171 (399)
Q Consensus 133 LglLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDI 171 (399)
|..+=+.+|.-.-...+| ++..+|+.||+.++-||-=
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 444555666443332333 4689999999999988853
No 172
>PF12728 HTH_17: Helix-turn-helix domain
Probab=29.29 E-value=31 Score=24.89 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=20.2
Q ss_pred ccHHHHHHHhcceeeehhhhHH
Q 015878 152 LDLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItN 173 (399)
+++.++|+.|+|.+..||.+++
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 173
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=29.04 E-value=47 Score=23.64 Aligned_cols=36 Identities=22% Similarity=0.372 Sum_probs=22.0
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhcc
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIG 179 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIg 179 (399)
.|.++.+ -....++|+.|||+++-+|-|++=.+.-|
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 4444444 56789999999999999999988764333
No 174
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=28.95 E-value=1.2e+02 Score=29.71 Aligned_cols=32 Identities=16% Similarity=0.268 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
+|+..|+.|..+-.+|-.+|+..+.+|+.+.+
T Consensus 58 ~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~ 89 (263)
T PRK10803 58 QLQQQLSDNQSDIDSLRGQIQENQYQLNQVVE 89 (263)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 34444555555555555555555555555544
No 175
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=28.94 E-value=1.9e+02 Score=24.63 Aligned_cols=86 Identities=12% Similarity=0.145 Sum_probs=0.0
Q ss_pred ccHHHHHHHhccee--------------------eehhhh--------HHhhhhccceecccCCeeEEecCCCCCCcchH
Q 015878 152 LDLNRTAEVLEVQK--------------------RRIYDI--------TNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLD 203 (399)
Q Consensus 152 ldLn~aA~~L~VqK--------------------RRIYDI--------tNVLEgIgLIeK~sKN~i~W~G~~~s~~~~~~ 203 (399)
+.+.++|+.+||++ +|+|+. +..|-.+|+=-+.-+.-+....... .....
T Consensus 1 ~~ige~a~~~gvs~~tLryYe~~GLi~p~~~~~~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~--~~~~~ 78 (116)
T cd04769 1 MYIGELAQQTGVTIKAIRLYEEKGLLPSPKRSGNYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGRA--VLPWP 78 (116)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccCC--cCcHH
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
.....|++.++.|..+-++|.++++.+...+..+.+
T Consensus 79 ~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~~ 114 (116)
T cd04769 79 HLQQALEDKKQEIRAQITELQQLLARLDAFEASLKD 114 (116)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
No 176
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=28.86 E-value=1.8e+02 Score=25.82 Aligned_cols=81 Identities=22% Similarity=0.257 Sum_probs=0.0
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhccce--ecccCCeeEEecCCCCCCcchHHHHHHHHH------HHHHHHH-----
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLI--EKTSKNHIRWKGSDSLGTSKLDDQVARLKA------EIESLHA----- 218 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLI--eK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~------El~~L~~----- 218 (399)
+.+.++|+.+||+.|-|--. |-.||| .+...|.|++-..... ..-..+..|++ |+..+-.
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 015878 219 -------EECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 219 -------~E~~LD~lI~~~~q~Lr~Lte 239 (399)
....|++++..+.+++.+|..
T Consensus 75 ~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (140)
T PRK09514 75 EHHTCQEVKGIVDEKLAEVEAKIAELQH 102 (140)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHH
No 177
>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=28.61 E-value=1.4e+02 Score=27.72 Aligned_cols=54 Identities=26% Similarity=0.369 Sum_probs=39.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhh--------cccccccccHhhhcc
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENE--------NHQKYMFLTEEDIAS 256 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~--------~n~~~aYVT~eDI~~ 256 (399)
...++..|++|++.|..+-+.+-..+..|...|..+.... ...++ =|++++|.+
T Consensus 27 ~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~~~~~~~~~~~~~~~~~-~v~~~eLL~ 88 (188)
T PF10018_consen 27 NQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLPDQADEKLKSIPKAEKR-PVDYEELLS 88 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccC-CCCHHHHHH
Confidence 4567889999999999888888888888999998887211 11122 377788754
No 178
>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=28.48 E-value=45 Score=36.19 Aligned_cols=25 Identities=24% Similarity=0.527 Sum_probs=13.5
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHH
Q 015878 205 QVARLKAEIESLHAEECRIDDSIRE 229 (399)
Q Consensus 205 ~~~~Lk~El~~L~~~E~~LD~lI~~ 229 (399)
++++|++||++|+++-..|++.|..
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 4555555555555555555444443
No 179
>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=28.42 E-value=63 Score=27.23 Aligned_cols=48 Identities=23% Similarity=0.416 Sum_probs=38.4
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhc-----ceeeehhhhHHhhhhccceecccCC
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLE-----VQKRRIYDITNVLEGIGLIEKTSKN 187 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~-----VqKRRIYDItNVLEgIgLIeK~sKN 187 (399)
..+++|.+.+. .++.+++.+.|. +.+=-||-.++.|+..|+|.|...+
T Consensus 12 ~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 12 AILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 36788888777 899999999886 3444599999999999999998543
No 180
>PRK14127 cell division protein GpsB; Provisional
Probab=28.38 E-value=1.4e+02 Score=26.25 Aligned_cols=46 Identities=13% Similarity=0.240 Sum_probs=29.7
Q ss_pred EecCCCCCCcchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 191 WKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 191 W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
++|.+ ..+++.-++.+-.+.+.|..+-.+|.+.+..++++|.++..
T Consensus 20 ~RGYd---~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 20 MRGYD---QDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred CCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45766 34666667766666666666666666666666666666554
No 181
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=28.25 E-value=1.1e+02 Score=33.18 Aligned_cols=32 Identities=28% Similarity=0.218 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
+|++..+.+...-...|+.|.++++||++|+=
T Consensus 418 kl~~~~e~~~~~~~s~d~~I~dLqEQlrDlmf 449 (493)
T KOG0804|consen 418 KLKELEEREKEALGSKDEKITDLQEQLRDLMF 449 (493)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhe
Confidence 34444455666667889999999999999873
No 182
>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=27.85 E-value=1.2e+02 Score=28.00 Aligned_cols=38 Identities=24% Similarity=0.454 Sum_probs=27.3
Q ss_pred ccHHHHHHHhcceee--ehhhhHHhhhhcccee--cccCCeeEEecCC
Q 015878 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLIE--KTSKNHIRWKGSD 195 (399)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIgLIe--K~sKN~i~W~G~~ 195 (399)
+.+.++|+.+||+++ |.|| .+|||. +...|.|++-+.+
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 5665 567774 3456778876543
No 183
>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=27.41 E-value=2.4e+02 Score=21.59 Aligned_cols=35 Identities=17% Similarity=0.397 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 205 QVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 205 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
.+..|+.++..|..+-..|-..+..+.+.+..|..
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~ 61 (64)
T PF00170_consen 27 YIEELEEKVEELESENEELKKELEQLKKEIQSLKS 61 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35567777777777777777777777777666643
No 184
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.36 E-value=46 Score=26.80 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=25.7
Q ss_pred cHHHHHHHhcceeeehhhhHHhhhhcc
Q 015878 153 DLNRTAEVLEVQKRRIYDITNVLEGIG 179 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIg 179 (399)
...++|..||+.+|-+|.+++-++.=|
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 185
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=27.35 E-value=87 Score=28.65 Aligned_cols=43 Identities=23% Similarity=0.334 Sum_probs=38.1
Q ss_pred CCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeE
Q 015878 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (399)
Q Consensus 148 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~ 190 (399)
.++.+...++|+.|+|..--.-..+|=|+..|||++.....|+
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~ 63 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVT 63 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeE
Confidence 7889999999999999999999999999999999997444333
No 186
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=27.19 E-value=1.6e+02 Score=31.73 Aligned_cols=53 Identities=28% Similarity=0.356 Sum_probs=35.0
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhcceeeehh-hhH---Hhhhh--ccceecccCCeeEEecCC
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIY-DIT---NVLEG--IGLIEKTSKNHIRWKGSD 195 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIY-DIt---NVLEg--IgLIeK~sKN~i~W~G~~ 195 (399)
.+.+.+|+ ++.+...++|+.|+|+.|-|+ ||. .+|++ ++++.+ + +-|++.+.+
T Consensus 7 ~~iL~~L~---~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~-~-~Gy~l~~~~ 65 (584)
T PRK09863 7 LKIVDLLE---QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISG-S-AKYHLEILN 65 (584)
T ss_pred HHHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheec-C-CceEEEeCC
Confidence 34555553 357899999999999998775 433 34555 445555 2 358887654
No 187
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=27.05 E-value=88 Score=31.09 Aligned_cols=61 Identities=26% Similarity=0.351 Sum_probs=49.5
Q ss_pred CcHHHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEe
Q 015878 131 SSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (399)
Q Consensus 131 kSLglLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~ 192 (399)
..|-.-=+.-|+++.. .+|.+.-+++.+.||.+|=-++=|+-=||-.|||+|..++.=.|.
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 3444445667777765 688999999999999999999999999999999999977765553
No 188
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=27.00 E-value=68 Score=31.04 Aligned_cols=44 Identities=16% Similarity=0.191 Sum_probs=36.4
Q ss_pred HHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhc
Q 015878 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGI 178 (399)
Q Consensus 135 lLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgI 178 (399)
.+..+.+.++.......++|.++|+.+++++|.|.=+..-.-|+
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 35678889999999999999999999999999888777654433
No 189
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=26.98 E-value=80 Score=27.50 Aligned_cols=32 Identities=28% Similarity=0.454 Sum_probs=24.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQEL 233 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~ 233 (399)
+..++..+++|++.|.+++..|...|+.+++.
T Consensus 55 l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 55 LQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34556677888888888888888888887777
No 190
>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=26.88 E-value=39 Score=29.39 Aligned_cols=40 Identities=28% Similarity=0.397 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHh
Q 015878 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNV 174 (399)
Q Consensus 135 lLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNV 174 (399)
+||.|=-.++.-.=..-+.|.++|+.++|+|=-+||.+.-
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 5665544455444556789999999999999999998763
No 191
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.86 E-value=49 Score=29.58 Aligned_cols=82 Identities=21% Similarity=0.234 Sum_probs=0.0
Q ss_pred ccHHHHHHHhccee--------------------eehhhhHHhhhhccceecccCCeeEEecCCCCCCcchHHHHHHHHH
Q 015878 152 LDLNRTAEVLEVQK--------------------RRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKA 211 (399)
Q Consensus 152 ldLn~aA~~L~VqK--------------------RRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~ 211 (399)
+.+.++|+.+||+. +|.|+. ..++-|.+|..-..- |+....-.++-.....+..
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~GLl~p~r~~~g~R~Y~~-~~l~~l~~I~~lr~~-----G~sL~eI~~~l~~~~~~~~ 74 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNLGLLTPERSDSNYRYYDE-TALDRLQLIEHLKGQ-----RLSLAEIKDQLEEVQRSDK 74 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCccCCCCCeeECH-HHHHHHHHHHHHHHC-----CCCHHHHHHHHHhhccccc
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 212 EIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 212 El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
+.+.+..+.+.+..+|+.++++++.|.+
T Consensus 75 ~~~~~~~~~~~l~~~i~~Le~~l~~L~~ 102 (134)
T cd04779 75 EQREVAQEVQLVCDQIDGLEHRLKQLKP 102 (134)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 192
>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=26.85 E-value=1.4e+02 Score=25.70 Aligned_cols=8 Identities=25% Similarity=-0.048 Sum_probs=3.4
Q ss_pred HHHHHHHH
Q 015878 138 RKFINLIQ 145 (399)
Q Consensus 138 kkFI~Ll~ 145 (399)
-+||..++
T Consensus 45 l~~I~~lr 52 (118)
T cd04776 45 LKLILRGK 52 (118)
T ss_pred HHHHHHHH
Confidence 34444444
No 193
>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=26.85 E-value=3.5e+02 Score=23.41 Aligned_cols=81 Identities=15% Similarity=0.152 Sum_probs=0.0
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhccceec--ccCCeeEEe----------------------------cCCCCCCcc
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK--TSKNHIRWK----------------------------GSDSLGTSK 201 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK--~sKN~i~W~----------------------------G~~~s~~~~ 201 (399)
+.+.++|+.+||..+-|. ..|-.|||.. ...|.|++- .........
T Consensus 1 m~I~e~a~~~gvs~~tlR----yYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~ 76 (127)
T TIGR02044 1 MNIGQVAKLTGLSSKMIR----YYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWNDPNRT 76 (127)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhccCCCC
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHH
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRT 236 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~ 236 (399)
.......|+..++.|+++..+|..+...+...+..
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~ 111 (127)
T TIGR02044 77 SADVKARTLEKVAEIERKISELQSMRDQLEALAQA 111 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
No 194
>PF10046 BLOC1_2: Biogenesis of lysosome-related organelles complex-1 subunit 2 ; InterPro: IPR019269 This entry represents a family of proteins that play a role in cellular proliferation, as well as in the biogenesis of specialised organelles of the endosomal-lysosomal system [].
Probab=26.79 E-value=1.4e+02 Score=25.29 Aligned_cols=34 Identities=15% Similarity=0.366 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 015878 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (399)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~L 237 (399)
+++..+.+++..|+.-=..||+.++.+..+++.|
T Consensus 66 ~~Id~Ie~~V~~LE~~v~~LD~ysk~LE~k~k~l 99 (99)
T PF10046_consen 66 QQIDQIEEQVTELEQTVYELDEYSKELESKFKKL 99 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 4455566677777777778888888877777653
No 195
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=26.75 E-value=2.1e+02 Score=23.40 Aligned_cols=38 Identities=21% Similarity=0.301 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhh
Q 015878 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (399)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~ 241 (399)
+.+..||.|++.|..+-..|.+....+.+....|.++.
T Consensus 18 eti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~ 55 (72)
T PF06005_consen 18 ETIALLQMENEELKEKNNELKEENEELKEENEQLKQER 55 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 45677888888888887788777777777777776543
No 196
>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=26.74 E-value=1.1e+02 Score=25.36 Aligned_cols=37 Identities=19% Similarity=0.366 Sum_probs=23.4
Q ss_pred cHHHHHHHhcceeeehhhhHHhhhhccceec--ccCCeeEEec
Q 015878 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEK--TSKNHIRWKG 193 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK--~sKN~i~W~G 193 (399)
.+.++|+.+||..+-|- -.|..|||.- .+.|.|++-.
T Consensus 2 ~i~eva~~~gvs~~tlR----~ye~~Gll~p~~~~~~gyR~Y~ 40 (97)
T cd04782 2 TTGEFAKLCGISKQTLF----HYDKIGLFKPEIVKENGYRYYT 40 (97)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCCccCC
Confidence 46788999999876542 2366788743 3345555543
No 197
>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=26.64 E-value=3.3e+02 Score=23.63 Aligned_cols=81 Identities=22% Similarity=0.257 Sum_probs=0.0
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhccce--ecccCCeeEEe-----------------cCCCCCCcchHHHHHH----
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLI--EKTSKNHIRWK-----------------GSDSLGTSKLDDQVAR---- 208 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLI--eK~sKN~i~W~-----------------G~~~s~~~~~~~~~~~---- 208 (399)
+.+.++|+.+||+.+-|- -.|-.||+ .+...|.|++- |+... ++..-+..
T Consensus 1 m~I~e~a~~~gvs~~tlR----yYe~~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~---eI~~~l~~~~~~ 73 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIR----YYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLE---EIRELLALWRDP 73 (127)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHH---HHHHHHHHHhCC
Q ss_pred ---HHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 209 ---LKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 209 ---Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
..+-.+-|..+...|++.|..++...+.|..
T Consensus 74 ~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~l~~ 107 (127)
T cd01108 74 SRASADVKALALEHIAELERKIAELQAMRRTLQQ 107 (127)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
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=26.55 E-value=1.4e+02 Score=25.46 Aligned_cols=32 Identities=19% Similarity=0.257 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 015878 207 ARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (399)
Q Consensus 207 ~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lt 238 (399)
..|+..++.++..-..|++.+..++.++.++-
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 34555556666666666666666666666654
No 199
>PRK10869 recombination and repair protein; Provisional
Probab=26.29 E-value=90 Score=33.90 Aligned_cols=78 Identities=12% Similarity=0.181 Sum_probs=37.9
Q ss_pred cHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCCCCcchHHHHHHHHHHHHHHHHHHH---hHHHHHHH
Q 015878 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEEC---RIDDSIRE 229 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~---~LD~lI~~ 229 (399)
+|....+.+.+.--|+-.|-+=|.-|.=+.|+ | |.+ ..++-...+++++|++.|...+. .|.+.+..
T Consensus 283 ~l~~~~~~~~~dp~~l~~ie~Rl~~l~~L~rK----y---g~~---~~~~~~~~~~l~~eL~~L~~~e~~l~~Le~e~~~ 352 (553)
T PRK10869 283 ELRHYLDRLDLDPNRLAELEQRLSKQISLARK----H---HVS---PEELPQHHQQLLEEQQQLDDQEDDLETLALAVEK 352 (553)
T ss_pred HHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHH----h---CCC---HHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHH
Confidence 33333444444444455554444444444443 1 332 23455566777788777665444 33444444
Q ss_pred HHHHHHHHhhh
Q 015878 230 KQELIRTLEEN 240 (399)
Q Consensus 230 ~~q~Lr~Lted 240 (399)
+.+++..+.+.
T Consensus 353 l~~~l~~~A~~ 363 (553)
T PRK10869 353 HHQQALETAQK 363 (553)
T ss_pred HHHHHHHHHHH
Confidence 44455444443
No 200
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=26.26 E-value=55 Score=30.50 Aligned_cols=40 Identities=13% Similarity=0.191 Sum_probs=35.8
Q ss_pred CCCCcc-cHHHHHHHhcceeeehhhhHHhhhhccceecccC
Q 015878 147 AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (399)
Q Consensus 147 ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sK 186 (399)
.|+..+ .-.++|++|||+|=-+-+.+..|+.-|||+...+
T Consensus 26 ~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~g 66 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQHG 66 (239)
T ss_pred CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 467788 7999999999999999999999999999997633
No 201
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=26.00 E-value=1.6e+02 Score=26.46 Aligned_cols=36 Identities=25% Similarity=0.291 Sum_probs=21.0
Q ss_pred ccHHHHHHHhcceee--ehhhhHHhhhhccceecc-cCCeeEEec
Q 015878 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLIEKT-SKNHIRWKG 193 (399)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIgLIeK~-sKN~i~W~G 193 (399)
+.+.++|+.+||..+ |.| |.+|||... ..|.+++-.
T Consensus 2 ~~IgevA~~~Gvs~~tLRyY------E~~GLl~~~r~~~g~R~Y~ 40 (142)
T TIGR01950 2 LTVGELAKRSGVAVSALHFY------ESKGLITSIRNSGNQRRYK 40 (142)
T ss_pred CCHHHHHHHHCcCHHHHHHH------HHCCCCCCccCCCCCEEEC
Confidence 467888888888665 445 455555432 234455543
No 202
>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=25.92 E-value=4.2e+02 Score=22.68 Aligned_cols=80 Identities=23% Similarity=0.321 Sum_probs=57.9
Q ss_pred HHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEEecCCCCCCcchHHHHHHHHHHHHHHHHH
Q 015878 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAE 219 (399)
Q Consensus 140 FI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~ 219 (399)
|.-++...--..-++..+.+++.-..+|+-.|=+.|+.+ | ..+.+..|+-++..+..+
T Consensus 23 ~~~~l~~~~a~~~~~~~l~~~~~~~~~Rl~~lE~~l~~L--------------------P--t~~dv~~L~l~l~el~G~ 80 (106)
T PF10805_consen 23 FWLWLRRTYAKREDIEKLEERLDEHDRRLQALETKLEHL--------------------P--TRDDVHDLQLELAELRGE 80 (106)
T ss_pred HHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHhC--------------------C--CHHHHHHHHHHHHHHHhH
Confidence 333343332234577888888888888887776666532 1 135678899999999999
Q ss_pred HHhHHHHHHHHHHHHHHHhhhh
Q 015878 220 ECRIDDSIREKQELIRTLEENE 241 (399)
Q Consensus 220 E~~LD~lI~~~~q~Lr~Lted~ 241 (399)
=+.+...|+-+..++.-|.|.+
T Consensus 81 ~~~l~~~l~~v~~~~~lLlE~~ 102 (106)
T PF10805_consen 81 LKELSARLQGVSHQLDLLLENE 102 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 9999999999999988888754
No 203
>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=25.90 E-value=1.7e+02 Score=25.23 Aligned_cols=87 Identities=9% Similarity=0.156 Sum_probs=0.0
Q ss_pred ccHHHHHHHhccee---------------------eehhh--------hHHhhhhccceecccCCeeEEecCCCCCCcch
Q 015878 152 LDLNRTAEVLEVQK---------------------RRIYD--------ITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKL 202 (399)
Q Consensus 152 ldLn~aA~~L~VqK---------------------RRIYD--------ItNVLEgIgLIeK~sKN~i~W~G~~~s~~~~~ 202 (399)
+.+.++|+.+||++ +|.|| .+..|..+|+==+.-|.-+.+.... ....
T Consensus 1 m~IgevA~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~---~~~~ 77 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDP---EASC 77 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhcC---CCcH
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhh
Q 015878 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (399)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~ 241 (399)
......|+..++.|+++-++|.++.+.++..+.....+.
T Consensus 78 ~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~~~ 116 (127)
T cd04784 78 AEVNALIDEHLAHVRARIAELQALEKQLQALRERCDGAR 116 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCC
No 204
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=25.90 E-value=75 Score=29.56 Aligned_cols=37 Identities=38% Similarity=0.522 Sum_probs=30.2
Q ss_pred CCcccHHHHHHHhcceeee--------------hhhhHHhhhhccceeccc
Q 015878 149 DGTLDLNRTAEVLEVQKRR--------------IYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRR--------------IYDItNVLEgIgLIeK~s 185 (399)
.+.+-+..++..+|..||| |=-|+.+||.+|||+|..
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 3467778888889986664 778999999999999874
No 205
>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=25.87 E-value=53 Score=24.79 Aligned_cols=42 Identities=19% Similarity=0.309 Sum_probs=24.9
Q ss_pred CCCcHHHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHH
Q 015878 129 YDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 129 ~dkSLglLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 173 (399)
+.++|.+--+ +++++....|. ...++|..+||.+.-||+|..
T Consensus 3 kR~~LTl~eK--~~iI~~~e~g~-s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 3 KRKSLTLEEK--LEIIKRLEEGE-SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp SSSS--HHHH--HHHHHHHHCTT--HHHHHHHHT--CCHHHHHHH
T ss_pred CCccCCHHHH--HHHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHH
Confidence 3444444332 33444444455 899999999999999999985
No 206
>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=25.73 E-value=1.5e+02 Score=24.76 Aligned_cols=69 Identities=19% Similarity=0.211 Sum_probs=32.9
Q ss_pred hhhhHHhhhhccceecccCCeeEEecCCCCCCcchHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 015878 168 IYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (399)
Q Consensus 168 IYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~L 237 (399)
+-+|...+-.=|-|... ..-+.|.|.+..-....++-+.-|+..+..|+.+-+.|.+.+..++.++..+
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 33444443333444333 3467778866321122333444455555555555555555555555555444
No 207
>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=25.72 E-value=2.3e+02 Score=23.56 Aligned_cols=28 Identities=18% Similarity=0.392 Sum_probs=20.2
Q ss_pred ccHHHHHHHhcceeeehhhhHHhhhhccceec
Q 015878 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (399)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK 183 (399)
+.+.++|+.+||+.+-|--. |..|+|.-
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 56889999999987755433 45667653
No 208
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=25.67 E-value=6.1e+02 Score=26.55 Aligned_cols=35 Identities=20% Similarity=0.281 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 205 QVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 205 ~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
...+++.++..|..++..|...++.++++++.+.+
T Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 (398)
T PTZ00454 23 KLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKE 57 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455556666666666666666666555555443
No 209
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.54 E-value=1.6e+02 Score=25.05 Aligned_cols=14 Identities=21% Similarity=0.166 Sum_probs=10.1
Q ss_pred cHHHHHHHhcceee
Q 015878 153 DLNRTAEVLEVQKR 166 (399)
Q Consensus 153 dLn~aA~~L~VqKR 166 (399)
.+.++|+.+||+.+
T Consensus 2 ~i~eva~~~gvs~~ 15 (112)
T cd01282 2 RIGELAARTGVSVR 15 (112)
T ss_pred CHHHHHHHHCCCHH
Confidence 46677888887665
No 210
>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=25.26 E-value=2.5e+02 Score=22.31 Aligned_cols=39 Identities=8% Similarity=0.315 Sum_probs=30.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhh
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted 240 (399)
+.+++..++..+.++....+.|++.......++.++.++
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 456677778888888888888888888888887777665
No 211
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=25.25 E-value=1.2e+02 Score=27.40 Aligned_cols=52 Identities=21% Similarity=0.307 Sum_probs=45.1
Q ss_pred CcHHHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 131 SSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 131 kSLglLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
..|-.+=++.|.+|+ .++.+...++|+++|++.--++.=++=||.-|+|++-
T Consensus 10 ~~lD~~D~~IL~~Lq--~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~~ 61 (164)
T PRK11169 10 KDLDRIDRNILNELQ--KDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQGY 61 (164)
T ss_pred hhHHHHHHHHHHHhc--cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEE
Confidence 446777788998887 5778899999999999999999999999999999863
No 212
>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=25.09 E-value=24 Score=31.48 Aligned_cols=27 Identities=22% Similarity=0.430 Sum_probs=0.0
Q ss_pred eeeehhhhHHhhhhccceecccCCeeEEe
Q 015878 164 QKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (399)
Q Consensus 164 qKRRIYDItNVLEgIgLIeK~sKN~i~W~ 192 (399)
-|+++-+-+..||.+|+|.+. |.|+=+
T Consensus 5 lk~~~l~~l~~LE~~G~v~~~--n~yQ~l 31 (142)
T PF03836_consen 5 LKKKILENLKELESLGIVSRS--NNYQDL 31 (142)
T ss_dssp -----------------------------
T ss_pred HHHHHHHHHHHHHHCCCCCCc--ccHHHH
Confidence 467888889999999999998 666653
No 213
>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=24.80 E-value=92 Score=29.94 Aligned_cols=56 Identities=27% Similarity=0.462 Sum_probs=42.9
Q ss_pred cHHHHHHHHHH-HHHhCCCCcccHHHHHHHhcceeeehhhhHH-hhhhccceecccCC
Q 015878 132 SLGLLTRKFIN-LIQEAKDGTLDLNRTAEVLEVQKRRIYDITN-VLEGIGLIEKTSKN 187 (399)
Q Consensus 132 SLglLTkkFI~-Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIgLIeK~sKN 187 (399)
.|...-+.|+. ++..-.++.+.+.++|..||+..+.+..++- .|-..|||++....
T Consensus 235 ~l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 292 (305)
T TIGR00635 235 GLDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRG 292 (305)
T ss_pred CCCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCch
Confidence 33444555666 5565566678899999999999999999887 79999999876443
No 214
>PRK06474 hypothetical protein; Provisional
Probab=24.70 E-value=1e+02 Score=28.62 Aligned_cols=46 Identities=15% Similarity=0.312 Sum_probs=38.4
Q ss_pred HHHHHHHhCCCCcccHHHHHHHh-cceeeehhhhHHhhhhccceeccc
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
+.+++|...+. .+...++++.| ++.+=-+|=.+++|+-.|||++..
T Consensus 15 ~Il~~L~~~~~-~~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 15 KICQVLMRNKE-GLTPLELVKILKDVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHhCCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence 46677766544 39999999999 789999999999999999999754
No 215
>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=24.68 E-value=36 Score=35.95 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=29.6
Q ss_pred CCCcccHHHHHHHhcceeeehhhhHHhhhhcccee
Q 015878 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (399)
Q Consensus 148 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIe 182 (399)
.||..+|-++|+++++.-++++|+.+-|...|||+
T Consensus 352 ~DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 352 SDGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp -EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred ccCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 57899999999999999999999999999999985
No 216
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=24.67 E-value=3e+02 Score=22.78 Aligned_cols=17 Identities=18% Similarity=0.255 Sum_probs=11.4
Q ss_pred cHHHHHHHhcceeeehh
Q 015878 153 DLNRTAEVLEVQKRRIY 169 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIY 169 (399)
.+.++|+.+||..+-|-
T Consensus 2 ti~eva~~~gvs~~tlR 18 (103)
T cd01106 2 TVGEVAKLTGVSVRTLH 18 (103)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 46677888887766443
No 217
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=24.62 E-value=1.3e+02 Score=33.65 Aligned_cols=49 Identities=20% Similarity=0.388 Sum_probs=31.0
Q ss_pred CCeeEEecCCCCCC----cc-hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 015878 186 KNHIRWKGSDSLGT----SK-LDDQVARLKAEIESLHAEECRIDDSIREKQELI 234 (399)
Q Consensus 186 KN~i~W~G~~~s~~----~~-~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~L 234 (399)
+.++.|.|...... .+ ...+-.+|++||+.|..+-..||..|+.+..++
T Consensus 56 RgNl~~~~~~~~~~~~~~~e~~~~~r~~L~~everLraei~~l~~~I~~~e~e~ 109 (632)
T PF14817_consen 56 RGNLLWYGHQQSKERKKSRENEARRRRELEKEVERLRAEIQELDKEIESREREV 109 (632)
T ss_pred HcceeeccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55689999764320 00 112345677888888888888888777665443
No 218
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=24.60 E-value=7.5e+02 Score=25.12 Aligned_cols=135 Identities=16% Similarity=0.213 Sum_probs=77.7
Q ss_pred CcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeEE--ecCCCCCCcchHHHHHHHHHHHHHHHHH----HHhH
Q 015878 150 GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW--KGSDSLGTSKLDDQVARLKAEIESLHAE----ECRI 223 (399)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~W--~G~~~s~~~~~~~~~~~Lk~El~~L~~~----E~~L 223 (399)
..+...++|++|+|.=--+-+=+-=|-.=|||++.+..+|.- +|+ +.|.+.+.+|..- |..|
T Consensus 24 p~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~gR~~Y~iTkkG~------------e~l~~~~~dlr~f~~ev~~~l 91 (260)
T COG1497 24 PRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEGRGEYEITKKGA------------EWLLEQLSDLRRFSEEVELVL 91 (260)
T ss_pred CCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecCCeeEEEehhHH------------HHHHHHHHHHHHHHHHHHHHH
Confidence 468899999999997666666666677789999976655554 332 2233333333211 1122
Q ss_pred HHHHHHHHHHHHHHhhhhcccccccccHhhhccCC----CCCCceEEEEeCCCC--ceEEecCCcchhhcccceEEEEEe
Q 015878 224 DDSIREKQELIRTLEENENHQKYMFLTEEDIASLP----CFQNQTLIAIKAPQA--SYIEVPDPDEDISFLKRQYKMIIR 297 (399)
Q Consensus 224 D~lI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~l~----~f~~qTvIAIKAP~g--T~LEVPdP~e~~~~~~~~yqI~Lk 297 (399)
+... -|.-+..+||+.=. .|++-.+.|=+.+.| +-.-+.+-.++.+-+-..+.=.+-
T Consensus 92 ~~~~-----------------vw~AIA~edI~~Gd~V~L~M~dG~LyA~~~~kg~A~g~A~~dA~~GedV~it~i~G~Id 154 (260)
T COG1497 92 DYVM-----------------VWTAIAKEDIKEGDTVYLRMKDGYLYASRSAKGGATGVALTDAEKGEDVGITEIGGMID 154 (260)
T ss_pred hhHH-----------------HHHHhhHhhhccCCEEEEEecCcEEEEeccCCCcceeEEecccccCCeeeeeeccCccc
Confidence 2221 34456667776421 257888999999998 444445444433211111212233
Q ss_pred cCCCCeEEEEecCCCC
Q 015878 298 STTGPIDVYLLSKYQS 313 (399)
Q Consensus 298 S~~GPIdVyL~~~~~~ 313 (399)
=+.|.|.++.++...+
T Consensus 155 ~e~G~v~i~~vP~~~~ 170 (260)
T COG1497 155 VEKGEVTIVKVPGVAE 170 (260)
T ss_pred CCCCeEEEEECCCccc
Confidence 3567777777776543
No 219
>TIGR00714 hscB Fe-S protein assembly co-chaperone HscB. This model describes the small subunit, Hsc20 (20K heat shock cognate protein) of a pair of proteins Hsc66-Hsc20, related to the DnaK-DnaJ heat shock proteins, which also serve as molecular chaperones. Hsc20, unlike DnaJ, appears not to have chaperone activity on its own, but to act solely as a regulatory subunit for Hsc66 (i.e., to be a co-chaperone). The gene for Hsc20 in E. coli, hscB, is not induced by heat shock.
Probab=24.56 E-value=3.2e+02 Score=24.92 Aligned_cols=26 Identities=35% Similarity=0.492 Sum_probs=19.1
Q ss_pred cHHHHHHHhcc-eeeehhhhHHhhhhccc
Q 015878 153 DLNRTAEVLEV-QKRRIYDITNVLEGIGL 180 (399)
Q Consensus 153 dLn~aA~~L~V-qKRRIYDItNVLEgIgL 180 (399)
-+|+|=+.|.- .+|..|++. |.|+.+
T Consensus 41 ~iN~AY~~L~~p~~Ra~ylL~--l~g~~~ 67 (157)
T TIGR00714 41 TLNQAYQTLKDPLMRAEYMLS--LHGIDL 67 (157)
T ss_pred HHHHHHHHhCChhhhHHHHHH--hcCCCC
Confidence 46777777876 689999876 557665
No 220
>PRK01194 V-type ATP synthase subunit E; Provisional
Probab=24.47 E-value=2.6e+02 Score=26.16 Aligned_cols=33 Identities=9% Similarity=0.081 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhh
Q 015878 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (399)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted 240 (399)
.|+.....|..++.-|++.+..+.++|.+|..+
T Consensus 67 ~Le~R~~~L~aree~I~~v~~~a~e~L~~l~~~ 99 (185)
T PRK01194 67 NIEARSIKREKRREILKDYLDIAYEHLMNITKS 99 (185)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHcccCC
Confidence 455556778889999999999999999999853
No 221
>PRK13503 transcriptional activator RhaS; Provisional
Probab=24.41 E-value=89 Score=29.31 Aligned_cols=39 Identities=5% Similarity=0.115 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHH
Q 015878 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 135 lLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 173 (399)
...+++++++.+.....++|.++|+.++++++.+.-+..
T Consensus 171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 447889999988888899999999999999998877654
No 222
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=24.00 E-value=2e+02 Score=27.05 Aligned_cols=28 Identities=18% Similarity=0.283 Sum_probs=19.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHhhh
Q 015878 213 IESLHAEECRIDDSIREKQELIRTLEEN 240 (399)
Q Consensus 213 l~~L~~~E~~LD~lI~~~~q~Lr~Lted 240 (399)
++-|..+.+.|++.|.++++.|..+.++
T Consensus 87 ~~lLe~~~~~l~~ri~eLe~~l~~kad~ 114 (175)
T PRK13182 87 FEQLEAQLNTITRRLDELERQLQQKADD 114 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3556667777777777777777777665
No 223
>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=23.72 E-value=89 Score=26.90 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=22.6
Q ss_pred cHHHHHHHhcceeeehhhhHHhhhhcccee
Q 015878 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (399)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIgLIe 182 (399)
++..+.+..|..||-+.|.++.|.++|+.-
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 788888889999999999999999999753
No 224
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=23.35 E-value=92 Score=30.54 Aligned_cols=41 Identities=7% Similarity=-0.019 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHHhh
Q 015878 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVL 175 (399)
Q Consensus 135 lLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItNVL 175 (399)
....++++++.......+++.++|+.+++++|.|+-.++-.
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~ 258 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAA 258 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 45578899999998899999999999999999998777643
No 225
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=23.31 E-value=93 Score=32.29 Aligned_cols=50 Identities=16% Similarity=0.186 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHhCCCCcccHHHHHHHh-cceeeehhhhHHhhhhccceecc
Q 015878 135 LLTRKFINLIQEAKDGTLDLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 135 lLTkkFI~Ll~~ap~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
.+.++|+.++-...+..++++.+|+.+ ++.++-++.-++.||..-|+-..
T Consensus 220 ~~~k~i~~~l~~~~g~~~s~~~la~~l~~is~~Ti~~Yl~~le~~fll~~~ 270 (398)
T COG1373 220 DLMKRILRFLASNIGSPISYSSLARELKGISKDTIRKYLSYLEDAFLLFLV 270 (398)
T ss_pred HHHHHHHHHHHhhcCCccCHHHHHHHHhccchHHHHHHHHHHHHhhheEEe
Confidence 678999999999999999999999999 79999999999999999999843
No 226
>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=23.11 E-value=3.9e+02 Score=25.00 Aligned_cols=47 Identities=15% Similarity=0.273 Sum_probs=37.7
Q ss_pred HHHHHHHHhCCCCcc--cHHHHHHHhcceeeehhhhHHhhhhccceecc
Q 015878 138 RKFINLIQEAKDGTL--DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 138 kkFI~Ll~~ap~g~l--dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~ 184 (399)
+++..++...+.-.+ .+..+|..|++.++-|-=++.|+.-+|+|+-.
T Consensus 101 ~~~Y~~l~~~~~~~l~~~~~~La~~l~i~~~~l~fml~VF~EL~FVti~ 149 (195)
T PF10141_consen 101 KKLYKFLKQHPNFDLKEQLQALAKYLGISPDTLKFMLKVFFELGFVTIE 149 (195)
T ss_pred HHHHHHHHhCCCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHcCcEEEe
Confidence 445566666654433 57899999999999999999999999999876
No 227
>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=22.82 E-value=2.1e+02 Score=27.56 Aligned_cols=27 Identities=7% Similarity=0.158 Sum_probs=11.4
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHh
Q 015878 212 EIESLHAEECRIDDSIREKQELIRTLE 238 (399)
Q Consensus 212 El~~L~~~E~~LD~lI~~~~q~Lr~Lt 238 (399)
+++.+...++.|.-++..+-+.|+.+.
T Consensus 92 qi~~~~~~~~~l~p~m~~m~~~L~~~v 118 (251)
T PF11932_consen 92 QIEQIEETRQELVPLMEQMIDELEQFV 118 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333334444444444444444433
No 228
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=22.80 E-value=1.9e+02 Score=29.16 Aligned_cols=68 Identities=18% Similarity=0.228 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhhhcccccccccHhhhccC-------CCCCCceEEEEeCCCCceEEecC
Q 015878 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDIASL-------PCFQNQTLIAIKAPQASYIEVPD 280 (399)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted~~n~~~aYVT~eDI~~l-------~~f~~qTvIAIKAP~gT~LEVPd 280 (399)
.|+.+++.|..+-+.+...+..++.+|.++....+..+- +|..+|..| ..+.+=.++.+. |+.|++--
T Consensus 234 el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~r~--~t~~Ev~~Lk~~~~~Le~~~gw~~~~~~---~~~l~~~~ 308 (325)
T PF08317_consen 234 ELQEELEELEEKIEELEEQKQELLAEIAEAEKIREECRG--WTRSEVKRLKAKVDALEKLTGWKIVSIS---GSTLEFRY 308 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHHHHHCcEEEEEe---CCeEEEEE
Confidence 444445555555555556666666666665543322221 366666554 233344444444 66666643
No 229
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=22.79 E-value=2.3e+02 Score=23.45 Aligned_cols=35 Identities=26% Similarity=0.398 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 015878 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (399)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~L 237 (399)
...+..|+++++.|+.+...+...+.-+..++.-|
T Consensus 69 ~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~L 103 (104)
T PF13600_consen 69 SPELKELEEELEALEDELAALQDEIQALEAQIAFL 103 (104)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45677888888888888888888888777776543
No 230
>PF03961 DUF342: Protein of unknown function (DUF342); InterPro: IPR005646 This family of bacterial proteins has no known function. The proteins are in the region of 500-600 amino acid residues in length.
Probab=22.71 E-value=7.6e+02 Score=25.93 Aligned_cols=33 Identities=18% Similarity=0.253 Sum_probs=21.0
Q ss_pred eEEEEe-CCCCceEEecCCcchhhcccceEEEEEecCCCCeEEEE
Q 015878 264 TLIAIK-APQASYIEVPDPDEDISFLKRQYKMIIRSTTGPIDVYL 307 (399)
Q Consensus 264 TvIAIK-AP~gT~LEVPdP~e~~~~~~~~yqI~LkS~~GPIdVyL 307 (399)
.+.+=+ +=+|+.+.+.. ....++-+.+++-+|+
T Consensus 413 ~I~v~~~vypgv~i~i~~-----------~~~~i~~~~~~~~f~~ 446 (451)
T PF03961_consen 413 RIKVRKRVYPGVEIHIGN-----------KSYKIKEEYGNVKFYL 446 (451)
T ss_pred EEEECCEEECCEEEEECC-----------EEEEEeeecCCEEEEE
Confidence 333333 46788888763 3455666678887777
No 231
>PRK01356 hscB co-chaperone HscB; Provisional
Probab=22.65 E-value=5.4e+02 Score=23.77 Aligned_cols=50 Identities=26% Similarity=0.429 Sum_probs=33.6
Q ss_pred CCCcHHHHHHHHHHHH-HhCCCCc-------------ccHHHHHHHhcc-eeeehhhhHHhhhhccc
Q 015878 129 YDSSLGLLTRKFINLI-QEAKDGT-------------LDLNRTAEVLEV-QKRRIYDITNVLEGIGL 180 (399)
Q Consensus 129 ~dkSLglLTkkFI~Ll-~~ap~g~-------------ldLn~aA~~L~V-qKRRIYDItNVLEgIgL 180 (399)
++-+...|.++|..+. +-.||.. --+|+|=+.|.- .+|..|++- |.|+.+
T Consensus 14 f~id~~~L~~aYr~lq~~~HPDk~~~~~~k~~~~~~s~~in~AY~~L~dp~~Ra~YlL~--l~g~~~ 78 (166)
T PRK01356 14 YNIDLKILEKQYFAMQVKYHPDKAKTLQEKEQNLIIASELNNAYSTLKDALKRAEYMLL--LQNINL 78 (166)
T ss_pred CCCCHHHHHHHHHHHHHHHCcCCCCCHHHHHHHHHHHHHHHHHHHHhCCHHHHHHHHHH--ccCCCC
Confidence 4566778888998885 4456542 256777777776 679999543 456554
No 232
>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=22.55 E-value=1.3e+02 Score=22.88 Aligned_cols=41 Identities=12% Similarity=0.354 Sum_probs=35.9
Q ss_pred CCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCe
Q 015878 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNH 188 (399)
Q Consensus 148 p~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~ 188 (399)
.++.+++.++=+.|+++|+-.-=|..-|...|+..|.+-.+
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 37899999999999999999999999999999999986433
No 233
>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=22.35 E-value=1.4e+02 Score=24.70 Aligned_cols=29 Identities=14% Similarity=0.267 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 211 AEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 211 ~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
++|..|.++-+.|++.+..++++|-++-.
T Consensus 2 ~~L~~l~~~k~~Le~~L~~lE~qIy~~Et 30 (80)
T PF09340_consen 2 KELKELLQKKKKLEKDLAALEKQIYDKET 30 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56777777778888888888888877643
No 234
>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=22.30 E-value=1.3e+02 Score=33.60 Aligned_cols=55 Identities=15% Similarity=0.293 Sum_probs=46.0
Q ss_pred HHHHHHHHhCCCCcccHHHHHHHhccee----eehhhhHHhhhhccceecccCCeeEEe
Q 015878 138 RKFINLIQEAKDGTLDLNRTAEVLEVQK----RRIYDITNVLEGIGLIEKTSKNHIRWK 192 (399)
Q Consensus 138 kkFI~Ll~~ap~g~ldLn~aA~~L~VqK----RRIYDItNVLEgIgLIeK~sKN~i~W~ 192 (399)
.+.+++|+..+...+.++++++.|++.+ .-++.+++-|+.-|.|.+..++.|...
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 4577888888889999999999999853 459999999999999998877766554
No 235
>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=22.28 E-value=2.5e+02 Score=23.58 Aligned_cols=36 Identities=31% Similarity=0.470 Sum_probs=24.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~L 237 (399)
+..++..|+.+++.|..+-..+.+.+..++..|+.+
T Consensus 92 l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~~ 127 (129)
T cd00890 92 LKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQL 127 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455566677777777777777777777777666654
No 236
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=22.13 E-value=1.1e+02 Score=28.24 Aligned_cols=54 Identities=17% Similarity=0.164 Sum_probs=39.8
Q ss_pred HHHHHHHHHHhC-CC--CcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeE
Q 015878 136 LTRKFINLIQEA-KD--GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (399)
Q Consensus 136 LTkkFI~Ll~~a-p~--g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~ 190 (399)
+..|+..+|... .. ..+.-.++|+.||++|+-+.=+++-|+--|+|++.. ++|.
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 345555555322 11 235679999999999999999999999999999974 3443
No 237
>KOG3501 consensus Molecular chaperone Prefoldin, subunit 1 [Posttranslational modification, protein turnover, chaperones]
Probab=21.87 E-value=2.7e+02 Score=24.91 Aligned_cols=40 Identities=18% Similarity=0.406 Sum_probs=33.8
Q ss_pred chHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhhh
Q 015878 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (399)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lted 240 (399)
..+.....+++.++.|+.+..-|.....+..+.||+|.+.
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 3455666778889999999999999999999999999865
No 238
>PHA02047 phage lambda Rz1-like protein
Probab=21.76 E-value=67 Score=28.14 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=17.8
Q ss_pred eEEecCCCCCCcchHHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 015878 189 IRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREK 230 (399)
Q Consensus 189 i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~ 230 (399)
|+|.|.. .+....|...++.++.+-..+.++...+
T Consensus 26 ~r~~g~~-------h~~a~~la~qLE~a~~r~~~~Q~~V~~l 60 (101)
T PHA02047 26 YRALGIA-------HEEAKRQTARLEALEVRYATLQRHVQAV 60 (101)
T ss_pred HHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6787753 2334455555555555444444444443
No 239
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=21.74 E-value=2.5e+02 Score=25.84 Aligned_cols=36 Identities=39% Similarity=0.494 Sum_probs=23.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~L 237 (399)
+...++.|+++++.|..+-..|...|.+++..+..|
T Consensus 11 l~a~lq~l~~qie~L~~~i~~l~~~~~e~~~~~~tl 46 (145)
T COG1730 11 LAAQLQILQSQIESLQAQIAALNAAISELQTAIETL 46 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566666777777777777777777666665544
No 240
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=21.17 E-value=92 Score=29.71 Aligned_cols=38 Identities=13% Similarity=0.211 Sum_probs=32.5
Q ss_pred HHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhhhHH
Q 015878 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (399)
Q Consensus 136 LTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYDItN 173 (399)
+..+++.++.....+.+.|.++|+.+++++++|.-++.
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk 221 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFR 221 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46778888888888999999999999999998876654
No 241
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=21.13 E-value=2.9e+02 Score=22.32 Aligned_cols=36 Identities=19% Similarity=0.361 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
..+..+++.+.+|......|-..|..+...|+++.+
T Consensus 14 P~l~~~~~~l~el~~sQ~~L~~~i~~~~~~L~~~~~ 49 (92)
T PF14712_consen 14 PDLDRLDQQLQELRQSQEELLQQIDRLNEKLKELNE 49 (92)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788899999999999999999999999999887
No 242
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=21.12 E-value=1.4e+02 Score=31.12 Aligned_cols=44 Identities=14% Similarity=0.241 Sum_probs=37.9
Q ss_pred CCCCcccHHHHHHHhcceeeehhhhHHhhhhccceecccCCeeE
Q 015878 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (399)
Q Consensus 147 ap~g~ldLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~sKN~i~ 190 (399)
..+..+...++++.+++.-+.+-+|..-|+..|+|.+...+.|.
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 35568899999999999999999999999999999987656433
No 243
>PRK11642 exoribonuclease R; Provisional
Probab=21.02 E-value=1.2e+02 Score=34.79 Aligned_cols=51 Identities=10% Similarity=0.090 Sum_probs=41.2
Q ss_pred HHHHHHHhCCCCcccHHHHHHHhccee----eehhhhHHhhhhccceecccCCeeE
Q 015878 139 KFINLIQEAKDGTLDLNRTAEVLEVQK----RRIYDITNVLEGIGLIEKTSKNHIR 190 (399)
Q Consensus 139 kFI~Ll~~ap~g~ldLn~aA~~L~VqK----RRIYDItNVLEgIgLIeK~sKN~i~ 190 (399)
+.+++|... +..+.+++++..|++.+ +.|..+++-|+..|.|.+..++.|.
T Consensus 23 ~Il~~l~~~-~~~~~~~~L~~~l~l~~~~~~~~l~~~L~~L~~~g~l~~~~~~~~~ 77 (813)
T PRK11642 23 FILEHLTKR-EKPASREELAVELNIEGEEQLEALRRRLRAMERDGQLVFTRRQCYA 77 (813)
T ss_pred HHHHHHHhc-CCCCCHHHHHHHhCCCChHHHHHHHHHHHHHHHCCCEEEcCCceEe
Confidence 345666653 48999999999999963 5599999999999999988777664
No 244
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=21.00 E-value=98 Score=29.30 Aligned_cols=39 Identities=15% Similarity=0.119 Sum_probs=35.1
Q ss_pred CCCCcc-cHHHHHHHhcceeeehhhhHHhhhhccceeccc
Q 015878 147 AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 147 ap~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
.|+..+ .-.++|+.|||+|==+=+.+..||..|||+...
T Consensus 21 ~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~ 60 (253)
T PRK10421 21 EAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRR 60 (253)
T ss_pred CCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 477788 699999999999999999999999999998653
No 245
>PRK05638 threonine synthase; Validated
Probab=20.95 E-value=1.4e+02 Score=31.27 Aligned_cols=61 Identities=20% Similarity=0.308 Sum_probs=47.4
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHHhCCCCcccHHHHHHHhc--ceeeehhhhHHhhhhccceecc
Q 015878 121 LNLSNGCRYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLE--VQKRRIYDITNVLEGIGLIEKT 184 (399)
Q Consensus 121 ~tp~~~~R~dkSLglLTkkFI~Ll~~ap~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIgLIeK~ 184 (399)
..+....|-.-.++.+-.+.+.+|.+. .+...++++.|+ +.+--||-.+.+||.-|||+..
T Consensus 357 k~~~~~~~~~~~~~~~r~~IL~~L~~~---~~~~~el~~~l~~~~s~~~v~~hL~~Le~~GLV~~~ 419 (442)
T PRK05638 357 KGYGEGGREKFTIGGTKLEILKILSER---EMYGYEIWKALGKPLKYQAVYQHIKELEELGLIEEA 419 (442)
T ss_pred CCCCCCchhhhcccchHHHHHHHHhhC---CccHHHHHHHHcccCCcchHHHHHHHHHHCCCEEEe
Confidence 444556665656666666667777754 477889999998 8999999999999999999863
No 246
>PRK01203 prefoldin subunit alpha; Provisional
Probab=20.88 E-value=2.7e+02 Score=25.30 Aligned_cols=36 Identities=19% Similarity=0.320 Sum_probs=22.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHH
Q 015878 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (399)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~q~Lr~L 237 (399)
+..+++.++++++.|.++-..|...+.+..+.+..|
T Consensus 5 ~~~~~~~~~~q~e~l~~ql~~L~~a~se~~~~ie~L 40 (130)
T PRK01203 5 VEAQLNYIESLISSVDSQIDSLNKTLSEVQQTISFL 40 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566666777776666666666666655555444
No 247
>PF14282 FlxA: FlxA-like protein
Probab=20.73 E-value=2e+02 Score=24.66 Aligned_cols=36 Identities=19% Similarity=0.345 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHH-----------HHHhHHHHHHHHHHHHHHHh
Q 015878 203 DDQVARLKAEIESLHA-----------EECRIDDSIREKQELIRTLE 238 (399)
Q Consensus 203 ~~~~~~Lk~El~~L~~-----------~E~~LD~lI~~~~q~Lr~Lt 238 (399)
..++..|+++|..|.. +...|...|..++.+|..|-
T Consensus 25 ~~Qi~~Lq~ql~~l~~~~~~~~e~k~~q~q~Lq~QI~~LqaQI~qlq 71 (106)
T PF14282_consen 25 QKQIKQLQEQLQELSQDSDLDAEQKQQQIQLLQAQIQQLQAQIAQLQ 71 (106)
T ss_pred HHHHHHHHHHHHHHHcccCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555555543 12345555555666655554
No 248
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=20.63 E-value=5.6e+02 Score=23.48 Aligned_cols=30 Identities=20% Similarity=0.274 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHhhh
Q 015878 211 AEIESLHAEECRIDDSIREKQELIRTLEEN 240 (399)
Q Consensus 211 ~El~~L~~~E~~LD~lI~~~~q~Lr~Lted 240 (399)
...+.|..+++-+++++..+.++|.++..+
T Consensus 71 ~r~~~l~ar~el~~~v~~~a~~~l~~~~~~ 100 (198)
T PRK03963 71 VRRKRLAVQEELISEVLEAVRERLAELPED 100 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 334567778888899999999999887764
No 249
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=20.52 E-value=1e+02 Score=27.70 Aligned_cols=37 Identities=22% Similarity=0.144 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHhCCCCcccHHHHHHHhcceeeehhh
Q 015878 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYD 170 (399)
Q Consensus 134 glLTkkFI~Ll~~ap~g~ldLn~aA~~L~VqKRRIYD 170 (399)
..|...+++++.+..=.-+.++++|++.||.|+-||-
T Consensus 14 ~~Il~aa~~lf~~~G~~~~ti~~Ia~~agvsk~t~Y~ 50 (213)
T PRK09975 14 QELIETAIAQFALRGVSNTTLNDIADAANVTRGAIYW 50 (213)
T ss_pred HHHHHHHHHHHHHcCcccCCHHHHHHHcCCCHHHHHH
Confidence 4566778888887776789999999999999999995
No 250
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=20.40 E-value=2.4e+02 Score=25.88 Aligned_cols=79 Identities=18% Similarity=0.149 Sum_probs=0.0
Q ss_pred ccHHHHHHHhccee--------------------eehhhhHHhhhhccceecccCCeeEEecCCCCCCcchHHHHHH---
Q 015878 152 LDLNRTAEVLEVQK--------------------RRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVAR--- 208 (399)
Q Consensus 152 ldLn~aA~~L~VqK--------------------RRIYDItNVLEgIgLIeK~sKN~i~W~G~~~s~~~~~~~~~~~--- 208 (399)
+.+.++|+.+||+. .|.|+. ..++-+.+|..-..- |+... ++.+-+..
T Consensus 12 ~~IgevAk~~gvs~~TlRyYE~~GLi~~~r~~~g~R~Y~~-~~i~~L~~I~~lr~l-----G~sL~---eIk~ll~~~~~ 82 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFYESKGLITSIRNSGNQRRYKR-DVLRYVAIIKIAQRI-----GIPLA---TIGEAFGVLPE 82 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHCCCCCCccCCCCCEEECH-HHHHHHHHHHHHHHc-----CCCHH---HHHHHHHHhhc
Q ss_pred -----HHHHHHHHHHHHHhHHHHHHHHHHHHHHHhh
Q 015878 209 -----LKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (399)
Q Consensus 209 -----Lk~El~~L~~~E~~LD~lI~~~~q~Lr~Lte 239 (399)
..+-.+-|..+...|++.|+.++..+..|..
T Consensus 83 ~~~~~~~~~~~ll~~k~~~l~~~I~~L~~~~~~L~~ 118 (154)
T PRK15002 83 GHTLSAKEWKQLSSQWREELDRRIHTLVALRDELDG 118 (154)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 251
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=20.36 E-value=3.8e+02 Score=24.71 Aligned_cols=28 Identities=7% Similarity=0.188 Sum_probs=16.1
Q ss_pred HHHhcceeeehhhhHHhhhhccceeccc
Q 015878 158 AEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (399)
Q Consensus 158 A~~L~VqKRRIYDItNVLEgIgLIeK~s 185 (399)
...++.-...+-.+..+++.|.-++..+
T Consensus 26 ~~~i~~l~~~~~e~~~~~~tl~~lk~~~ 53 (145)
T COG1730 26 QAQIAALNAAISELQTAIETLENLKGAG 53 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3334444556666666666666665554
Done!