Query 022537
Match_columns 295
No_of_seqs 204 out of 459
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 04:17:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022537.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022537hhsearch_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 1.5E-60 3.2E-65 455.3 19.6 175 121-295 61-238 (354)
2 PF02319 E2F_TDP: E2F/DP famil 99.9 1.6E-23 3.5E-28 159.8 6.4 66 128-193 1-71 (71)
3 KOG2578 Transcription factor E 99.8 2.3E-20 4.9E-25 177.1 6.2 87 121-212 14-100 (388)
4 KOG2578 Transcription factor E 99.1 1.1E-10 2.3E-15 111.8 6.0 159 124-282 152-354 (388)
5 KOG2829 E2F-like protein [Tran 99.0 1.1E-08 2.5E-13 97.3 16.5 120 148-283 59-208 (326)
6 PF01978 TrmB: Sugar-specific 95.8 0.022 4.8E-07 42.1 5.0 45 148-192 19-63 (68)
7 COG1378 Predicted transcriptio 94.5 0.31 6.7E-06 45.6 9.6 53 140-195 22-74 (247)
8 PF08279 HTH_11: HTH domain; 93.9 0.16 3.5E-06 35.7 5.2 41 138-179 3-43 (55)
9 smart00346 HTH_ICLR helix_turn 93.8 0.55 1.2E-05 35.7 8.4 49 138-187 8-56 (91)
10 smart00420 HTH_DEOR helix_turn 93.6 0.17 3.7E-06 34.2 4.7 45 139-185 4-48 (53)
11 cd00092 HTH_CRP helix_turn_hel 93.3 0.31 6.6E-06 34.9 5.9 54 136-189 5-63 (67)
12 smart00550 Zalpha Z-DNA-bindin 92.3 0.36 7.9E-06 36.4 5.2 54 138-191 9-62 (68)
13 PF09339 HTH_IclR: IclR helix- 92.2 0.26 5.7E-06 34.9 4.2 45 139-184 7-51 (52)
14 PF12802 MarR_2: MarR family; 91.2 0.6 1.3E-05 33.1 5.1 46 139-184 9-54 (62)
15 COG3355 Predicted transcriptio 91.0 2.2 4.8E-05 36.8 9.2 87 140-239 33-120 (126)
16 PF13412 HTH_24: Winged helix- 90.7 0.62 1.3E-05 32.1 4.7 43 138-182 6-48 (48)
17 smart00418 HTH_ARSR helix_turn 89.0 0.73 1.6E-05 31.5 4.0 38 149-186 8-45 (66)
18 PF14394 DUF4423: Domain of un 88.8 7.8 0.00017 34.3 11.3 98 147-244 35-158 (171)
19 PF02082 Rrf2: Transcriptional 88.2 1.3 2.9E-05 34.0 5.4 59 136-194 9-69 (83)
20 PF01047 MarR: MarR family; I 87.8 1.1 2.3E-05 31.8 4.3 44 140-185 8-51 (59)
21 PF13463 HTH_27: Winged helix 87.6 1.4 3E-05 31.7 4.9 38 147-184 14-51 (68)
22 cd00890 Prefoldin Prefoldin is 87.3 4.5 9.9E-05 32.7 8.3 55 185-239 68-122 (129)
23 TIGR02944 suf_reg_Xantho FeS a 87.3 1.2 2.6E-05 36.7 4.9 47 138-184 12-58 (130)
24 PF13730 HTH_36: Helix-turn-he 87.0 0.93 2E-05 31.9 3.6 29 153-181 27-55 (55)
25 PF09079 Cdc6_C: CDC6, C termi 86.1 0.53 1.2E-05 36.2 2.1 29 156-184 27-58 (85)
26 cd00090 HTH_ARSR Arsenical Res 85.3 2.8 6E-05 29.2 5.4 47 138-187 10-56 (78)
27 TIGR00122 birA_repr_reg BirA b 84.9 1.4 3.1E-05 32.6 3.8 54 139-195 4-58 (69)
28 PF00392 GntR: Bacterial regul 84.3 4.2 9.2E-05 29.6 6.1 50 138-187 7-60 (64)
29 PRK10163 DNA-binding transcrip 83.6 6.2 0.00014 36.7 8.3 55 139-194 29-83 (271)
30 cd08768 Cdc6_C Winged-helix do 83.6 1 2.2E-05 34.3 2.6 22 163-184 44-65 (87)
31 smart00419 HTH_CRP helix_turn_ 83.2 1.8 3.9E-05 28.9 3.4 35 151-185 8-42 (48)
32 smart00345 HTH_GNTR helix_turn 82.6 2.6 5.7E-05 29.0 4.2 40 148-187 16-56 (60)
33 PF01022 HTH_5: Bacterial regu 81.5 3 6.6E-05 28.9 4.2 41 140-183 7-47 (47)
34 TIGR02147 Fsuc_second hypothet 81.4 22 0.00047 34.0 11.1 43 148-192 134-178 (271)
35 PF04182 B-block_TFIIIC: B-blo 80.4 3.1 6.7E-05 31.8 4.2 49 138-186 5-53 (75)
36 cd00584 Prefoldin_alpha Prefol 80.3 12 0.00025 30.9 8.0 53 187-239 70-122 (129)
37 PF09012 FeoC: FeoC like trans 79.2 1.8 3.8E-05 32.4 2.5 42 148-189 11-52 (69)
38 PRK11414 colanic acid/biofilm 78.5 13 0.00027 33.0 8.1 54 136-189 16-72 (221)
39 PRK03947 prefoldin subunit alp 78.2 17 0.00036 30.6 8.4 51 188-238 78-128 (140)
40 TIGR00738 rrf2_super rrf2 fami 77.1 5.6 0.00012 32.4 5.1 44 141-184 14-58 (132)
41 PHA02943 hypothetical protein; 77.0 9.3 0.0002 34.4 6.7 49 138-189 14-62 (165)
42 PF08220 HTH_DeoR: DeoR-like h 76.8 6.3 0.00014 28.6 4.7 45 138-184 3-47 (57)
43 cd04766 HTH_HspR Helix-Turn-He 76.5 13 0.00027 29.1 6.7 27 152-182 2-28 (91)
44 TIGR00293 prefoldin, archaeal 76.3 22 0.00048 29.2 8.4 54 186-239 68-121 (126)
45 PF12840 HTH_20: Helix-turn-he 76.1 4 8.7E-05 29.5 3.6 45 139-185 14-58 (61)
46 cd00632 Prefoldin_beta Prefold 75.3 13 0.00027 30.1 6.6 78 156-237 20-103 (105)
47 PF01726 LexA_DNA_bind: LexA D 74.3 5.1 0.00011 30.3 3.8 46 140-185 14-60 (65)
48 TIGR02702 SufR_cyano iron-sulf 73.9 39 0.00085 30.0 10.0 45 138-184 4-48 (203)
49 PRK09834 DNA-binding transcrip 73.8 19 0.00041 33.2 8.2 50 140-190 16-66 (263)
50 PRK10870 transcriptional repre 73.0 33 0.00071 30.1 9.2 41 145-185 65-105 (176)
51 TIGR01610 phage_O_Nterm phage 72.5 8.9 0.00019 30.5 5.0 46 148-195 44-89 (95)
52 COG1777 Predicted transcriptio 72.2 41 0.00088 31.7 9.9 43 138-183 18-60 (217)
53 TIGR02338 gimC_beta prefoldin, 72.2 18 0.00038 29.6 6.8 84 154-238 19-108 (110)
54 PF12329 TMF_DNA_bd: TATA elem 72.0 13 0.00028 28.9 5.7 38 202-239 10-47 (74)
55 PF08784 RPA_C: Replication pr 72.0 7.8 0.00017 30.7 4.6 51 132-182 44-96 (102)
56 PRK03573 transcriptional regul 71.9 55 0.0012 27.0 9.9 35 151-185 46-80 (144)
57 PF05732 RepL: Firmicute plasm 71.7 19 0.00042 31.8 7.4 45 151-195 75-125 (165)
58 KOG1318 Helix loop helix trans 71.3 7.4 0.00016 39.5 5.3 75 162-239 239-318 (411)
59 PRK11569 transcriptional repre 70.7 30 0.00065 32.1 8.9 53 140-193 33-85 (274)
60 smart00529 HTH_DTXR Helix-turn 70.5 6.9 0.00015 30.0 3.9 32 154-185 2-33 (96)
61 cd07377 WHTH_GntR Winged helix 70.4 11 0.00025 26.2 4.7 38 148-185 21-59 (66)
62 PRK10411 DNA-binding transcrip 70.4 32 0.00069 31.7 8.9 54 138-193 7-60 (240)
63 COG1474 CDC6 Cdc6-related prot 70.4 4.3 9.3E-05 40.0 3.3 29 154-182 304-332 (366)
64 PRK09413 IS2 repressor TnpA; R 70.3 50 0.0011 27.2 9.2 31 150-180 28-58 (121)
65 PF01325 Fe_dep_repress: Iron 70.1 14 0.0003 27.3 5.3 42 143-185 15-56 (60)
66 TIGR03338 phnR_burk phosphonat 69.6 36 0.00078 29.7 8.7 41 147-187 30-70 (212)
67 cd04783 HTH_MerR1 Helix-Turn-H 69.1 47 0.001 27.4 8.9 38 153-194 2-41 (126)
68 COG1802 GntR Transcriptional r 68.2 89 0.0019 27.9 11.5 41 147-187 35-75 (230)
69 cd04789 HTH_Cfa Helix-Turn-Hel 67.3 33 0.00071 27.6 7.3 38 152-193 2-40 (102)
70 PF13545 HTH_Crp_2: Crp-like h 67.0 9.1 0.0002 28.1 3.8 52 135-186 2-63 (76)
71 PF13518 HTH_28: Helix-turn-he 66.9 6.6 0.00014 26.7 2.8 37 140-180 5-41 (52)
72 PRK15090 DNA-binding transcrip 66.9 37 0.0008 31.0 8.5 54 139-194 18-71 (257)
73 smart00347 HTH_MARR helix_turn 66.7 13 0.00028 27.8 4.7 44 139-184 14-57 (101)
74 TIGR02716 C20_methyl_CrtF C-20 66.5 5.2 0.00011 37.3 2.9 37 149-185 21-57 (306)
75 cd04770 HTH_HMRTR Helix-Turn-H 65.9 40 0.00088 27.5 7.8 37 153-193 2-40 (123)
76 cd04775 HTH_Cfa-like Helix-Tur 65.4 34 0.00073 27.4 7.1 37 152-192 2-39 (102)
77 smart00344 HTH_ASNC helix_turn 65.2 11 0.00025 29.5 4.2 47 136-184 4-50 (108)
78 TIGR01764 excise DNA binding d 65.1 5.3 0.00012 26.4 2.0 22 152-173 2-23 (49)
79 PF04977 DivIC: Septum formati 65.0 18 0.00039 26.8 5.1 35 206-240 19-53 (80)
80 PRK05014 hscB co-chaperone Hsc 64.0 1.1E+02 0.0023 27.2 10.9 54 128-183 12-82 (171)
81 TIGR01889 Staph_reg_Sar staphy 63.9 13 0.00028 29.9 4.4 46 140-185 30-77 (109)
82 TIGR02337 HpaR homoprotocatech 63.6 6.9 0.00015 31.5 2.8 37 149-185 40-76 (118)
83 PF08280 HTH_Mga: M protein tr 63.3 12 0.00026 27.3 3.8 36 139-176 9-44 (59)
84 PRK00215 LexA repressor; Valid 62.9 12 0.00027 32.9 4.5 43 146-188 18-61 (205)
85 PRK11534 DNA-binding transcrip 62.9 42 0.0009 29.7 7.8 49 147-195 26-74 (224)
86 COG1510 Predicted transcriptio 62.8 20 0.00044 32.7 5.8 37 149-185 39-75 (177)
87 PRK09954 putative kinase; Prov 62.6 10 0.00023 36.0 4.2 47 136-184 4-50 (362)
88 TIGR02010 IscR iron-sulfur clu 62.5 15 0.00033 30.7 4.7 37 147-183 21-57 (135)
89 PRK11511 DNA-binding transcrip 61.4 16 0.00036 30.1 4.7 41 133-173 7-47 (127)
90 COG2739 Uncharacterized protei 61.0 9.2 0.0002 32.2 3.1 40 134-173 16-55 (105)
91 COG1414 IclR Transcriptional r 60.9 17 0.00037 33.5 5.2 54 139-193 8-61 (246)
92 PRK14165 winged helix-turn-hel 60.7 37 0.0008 31.5 7.3 55 139-193 8-63 (217)
93 PRK06474 hypothetical protein; 59.4 1E+02 0.0023 27.3 9.7 47 138-185 14-61 (178)
94 cd01109 HTH_YyaN Helix-Turn-He 59.4 85 0.0018 25.4 8.5 36 153-192 2-39 (113)
95 PF03428 RP-C: Replication pro 59.3 63 0.0014 29.2 8.3 33 153-185 72-105 (177)
96 PF01920 Prefoldin_2: Prefoldi 59.2 77 0.0017 24.6 8.0 80 156-238 16-96 (106)
97 PRK11050 manganese transport r 59.1 30 0.00065 29.7 6.1 42 149-190 49-90 (152)
98 PRK09802 DNA-binding transcrip 59.1 94 0.002 29.2 9.8 52 135-188 17-68 (269)
99 TIGR02431 pcaR_pcaU beta-ketoa 58.9 29 0.00062 31.5 6.2 44 140-184 14-57 (248)
100 PF05103 DivIVA: DivIVA protei 58.9 4.9 0.00011 32.8 1.1 49 189-240 13-61 (131)
101 cd04784 HTH_CadR-PbrR Helix-Tu 58.7 75 0.0016 26.2 8.2 84 152-241 1-116 (127)
102 COG3093 VapI Plasmid maintenan 58.1 7.5 0.00016 32.6 2.1 33 135-173 13-45 (104)
103 COG1846 MarR Transcriptional r 57.7 17 0.00038 27.8 4.0 44 140-185 27-70 (126)
104 TIGR01884 cas_HTH CRISPR locus 57.7 22 0.00048 31.6 5.2 46 139-186 147-192 (203)
105 PRK10219 DNA-binding transcrip 57.2 22 0.00048 28.0 4.6 39 135-173 5-43 (107)
106 PF05565 Sipho_Gp157: Siphovir 57.0 1.2E+02 0.0026 26.5 9.6 32 132-163 2-33 (162)
107 PRK09343 prefoldin subunit bet 54.6 42 0.00091 28.1 6.0 85 154-239 23-113 (121)
108 PF10779 XhlA: Haemolysin XhlA 54.2 50 0.0011 25.1 5.9 38 203-240 12-49 (71)
109 TIGR00498 lexA SOS regulatory 54.0 21 0.00046 31.3 4.4 49 138-186 9-61 (199)
110 KOG3026 Splicing factor SPF30 53.9 63 0.0014 31.1 7.7 71 213-283 25-104 (262)
111 PRK10857 DNA-binding transcrip 53.0 20 0.00043 31.6 4.0 38 147-184 21-58 (164)
112 PRK00888 ftsB cell division pr 52.7 23 0.00049 29.2 4.1 59 207-272 30-91 (105)
113 PRK13752 putative transcriptio 52.7 1.3E+02 0.0029 25.8 9.0 76 152-239 8-112 (144)
114 PF03374 ANT: Phage antirepres 52.2 18 0.00039 28.9 3.4 41 140-184 14-54 (111)
115 TIGR02297 HpaA 4-hydroxyphenyl 52.2 17 0.00037 32.9 3.6 43 135-177 186-228 (287)
116 PRK13509 transcriptional repre 51.8 21 0.00045 33.1 4.2 48 138-187 8-55 (251)
117 PRK09464 pdhR transcriptional 51.7 1.8E+02 0.004 26.2 12.5 54 132-185 10-68 (254)
118 cd04786 HTH_MerR-like_sg7 Heli 51.5 1.5E+02 0.0032 25.1 9.0 87 152-242 1-116 (131)
119 PF04111 APG6: Autophagy prote 51.2 39 0.00084 32.8 6.0 35 207-241 60-94 (314)
120 PRK11014 transcriptional repre 51.2 26 0.00056 29.4 4.3 41 146-186 20-60 (141)
121 PRK09990 DNA-binding transcrip 51.1 47 0.001 29.9 6.3 50 137-186 13-66 (251)
122 TIGR02366 DHAK_reg probable di 51.0 22 0.00047 29.9 3.8 36 134-169 6-41 (176)
123 COG4189 Predicted transcriptio 50.8 20 0.00044 34.6 3.9 52 131-184 18-70 (308)
124 cd04762 HTH_MerR-trunc Helix-T 50.4 21 0.00045 23.2 2.9 23 152-174 1-23 (49)
125 COG1382 GimC Prefoldin, chaper 50.1 54 0.0012 28.1 6.0 71 169-240 37-113 (119)
126 TIGR02047 CadR-PbrR Cd(II)/Pb( 50.0 1.2E+02 0.0025 25.4 8.0 37 153-193 2-40 (127)
127 PF02295 z-alpha: Adenosine de 49.7 61 0.0013 24.6 5.7 57 136-192 5-61 (66)
128 PF04703 FaeA: FaeA-like prote 49.5 43 0.00093 25.4 4.8 52 140-192 5-59 (62)
129 PF01638 HxlR: HxlR-like helix 49.4 27 0.00059 27.2 3.9 43 143-185 10-53 (90)
130 cd07153 Fur_like Ferric uptake 49.1 34 0.00075 27.1 4.5 45 140-185 6-55 (116)
131 TIGR02044 CueR Cu(I)-responsiv 49.0 1.3E+02 0.0028 24.9 8.1 37 153-193 2-40 (127)
132 PRK14127 cell division protein 48.9 51 0.0011 27.7 5.7 55 180-239 11-65 (109)
133 cd00592 HTH_MerR-like Helix-Tu 48.4 60 0.0013 25.3 5.7 21 153-173 2-22 (100)
134 PF10018 Med4: Vitamin-D-recep 48.3 67 0.0014 28.6 6.7 28 208-235 26-53 (188)
135 PRK09391 fixK transcriptional 47.6 52 0.0011 29.4 5.9 39 152-190 180-218 (230)
136 PF04977 DivIC: Septum formati 47.5 64 0.0014 23.8 5.5 31 201-231 21-51 (80)
137 PF05491 RuvB_C: Holliday junc 47.4 52 0.0011 26.2 5.2 59 131-189 4-64 (76)
138 PF07106 TBPIP: Tat binding pr 47.1 1.9E+02 0.0041 25.0 10.4 55 140-195 6-64 (169)
139 PF09756 DDRGK: DDRGK domain; 46.9 35 0.00075 31.2 4.7 47 136-184 100-146 (188)
140 COG1522 Lrp Transcriptional re 46.8 38 0.00082 28.0 4.6 51 133-185 6-56 (154)
141 PF14257 DUF4349: Domain of un 46.7 71 0.0015 29.5 6.8 86 131-227 59-155 (262)
142 PHA01750 hypothetical protein 46.6 55 0.0012 25.9 5.0 31 204-234 42-72 (75)
143 PF05377 FlaC_arch: Flagella a 46.2 84 0.0018 23.7 5.8 39 201-239 4-42 (55)
144 PRK13626 transcriptional regul 45.9 63 0.0014 33.0 6.9 49 134-182 4-54 (552)
145 PF14947 HTH_45: Winged helix- 45.9 30 0.00066 26.4 3.6 42 149-191 17-58 (77)
146 PRK03837 transcriptional regul 45.9 52 0.0011 29.2 5.6 51 136-186 18-72 (241)
147 PF01475 FUR: Ferric uptake re 45.7 41 0.00089 27.1 4.6 49 138-187 11-64 (120)
148 PRK03902 manganese transport t 45.5 89 0.0019 26.1 6.7 38 148-185 19-56 (142)
149 PF05930 Phage_AlpA: Prophage 45.4 19 0.00042 25.4 2.3 24 150-173 2-25 (51)
150 PF03444 HrcA_DNA-bdg: Winged 44.6 53 0.0012 26.3 4.9 46 138-184 11-56 (78)
151 KOG3990 Uncharacterized conser 44.0 39 0.00084 32.9 4.7 46 199-244 220-265 (305)
152 PF01853 MOZ_SAS: MOZ/SAS fami 43.9 46 0.00099 30.6 5.0 56 131-189 123-185 (188)
153 PHA00738 putative HTH transcri 43.3 1E+02 0.0023 26.1 6.6 72 138-216 15-86 (108)
154 PF02996 Prefoldin: Prefoldin 43.3 59 0.0013 26.1 5.1 52 187-238 60-111 (120)
155 PRK13922 rod shape-determining 43.3 72 0.0016 29.6 6.3 42 201-243 73-114 (276)
156 PRK10225 DNA-binding transcrip 43.0 2.6E+02 0.0056 25.3 12.3 51 135-185 13-67 (257)
157 PF02954 HTH_8: Bacterial regu 42.9 39 0.00085 23.0 3.4 37 133-171 2-38 (42)
158 PF01920 Prefoldin_2: Prefoldi 42.8 56 0.0012 25.4 4.8 83 155-238 18-103 (106)
159 PRK00080 ruvB Holliday junctio 42.8 39 0.00085 32.0 4.6 57 131-187 255-313 (328)
160 COG2894 MinD Septum formation 42.1 8.1 0.00018 37.1 -0.1 28 152-179 41-68 (272)
161 smart00338 BRLZ basic region l 42.1 1E+02 0.0022 22.6 5.8 34 206-239 28-61 (65)
162 PF13384 HTH_23: Homeodomain-l 41.6 37 0.00079 23.1 3.2 36 140-179 10-45 (50)
163 PF12728 HTH_17: Helix-turn-he 41.3 22 0.00047 24.5 2.0 22 152-173 2-23 (51)
164 KOG3863 bZIP transcription fac 41.2 56 0.0012 34.9 5.8 70 168-240 478-554 (604)
165 cd01108 HTH_CueR Helix-Turn-He 41.1 2E+02 0.0043 23.9 8.1 37 153-193 2-40 (127)
166 PF13551 HTH_29: Winged helix- 40.9 29 0.00063 26.7 2.9 27 153-179 14-40 (112)
167 PRK04984 fatty acid metabolism 40.8 31 0.00068 30.8 3.4 39 147-185 26-65 (239)
168 PF12793 SgrR_N: Sugar transpo 40.6 1.7E+02 0.0038 24.3 7.6 47 136-182 2-50 (115)
169 PRK10869 recombination and rep 40.6 54 0.0012 34.1 5.5 85 128-222 258-342 (553)
170 PF09940 DUF2172: Domain of un 40.5 22 0.00048 36.0 2.6 35 148-182 352-386 (386)
171 PRK10130 transcriptional regul 40.5 32 0.00068 33.7 3.7 40 134-173 239-278 (350)
172 PRK01203 prefoldin subunit alp 40.4 1.9E+02 0.0042 25.1 8.0 37 202-238 5-41 (130)
173 cd01279 HTH_HspR-like Helix-Tu 39.9 1.6E+02 0.0034 23.5 7.0 28 152-183 2-29 (98)
174 PRK11512 DNA-binding transcrip 39.8 31 0.00067 28.7 3.1 37 149-185 52-88 (144)
175 TIGR02928 orc1/cdc6 family rep 39.8 21 0.00045 33.6 2.3 30 156-185 319-351 (365)
176 cd01106 HTH_TipAL-Mta Helix-Tu 38.9 2E+02 0.0043 22.8 7.6 25 153-181 2-26 (103)
177 PRK11886 bifunctional biotin-- 38.8 64 0.0014 30.6 5.4 52 138-191 7-59 (319)
178 PF09107 SelB-wing_3: Elongati 38.7 71 0.0015 23.2 4.4 39 148-186 7-45 (50)
179 PRK06266 transcription initiat 38.7 2.2E+02 0.0048 25.5 8.5 41 140-182 27-67 (178)
180 PF04297 UPF0122: Putative hel 38.5 28 0.00061 28.9 2.5 40 135-174 17-56 (101)
181 PHA02047 phage lambda Rz1-like 37.9 29 0.00063 29.0 2.5 36 188-230 25-60 (101)
182 PF09904 HTH_43: Winged helix- 37.7 54 0.0012 27.0 4.0 30 153-182 23-52 (90)
183 KOG0718 Molecular chaperone (D 37.7 1.5E+02 0.0033 31.2 8.1 83 129-227 19-119 (546)
184 PRK15121 right oriC-binding tr 37.5 49 0.0011 30.7 4.3 46 135-180 5-50 (289)
185 PRK09514 zntR zinc-responsive 37.2 2.5E+02 0.0054 23.8 8.2 81 152-239 2-109 (140)
186 cd04776 HTH_GnyR Helix-Turn-He 36.9 85 0.0018 25.9 5.2 11 135-145 42-52 (118)
187 PF13851 GAS: Growth-arrest sp 36.9 76 0.0016 28.9 5.3 35 205-239 28-62 (201)
188 KOG2747 Histone acetyltransfer 36.7 77 0.0017 32.3 5.7 58 132-194 304-367 (396)
189 cd04782 HTH_BltR Helix-Turn-He 36.6 99 0.0021 24.5 5.4 37 153-193 2-40 (97)
190 PRK13729 conjugal transfer pil 36.5 71 0.0015 33.3 5.6 38 203-240 82-119 (475)
191 cd04772 HTH_TioE_rpt1 First He 36.3 1.4E+02 0.0031 23.8 6.2 37 153-193 2-40 (99)
192 PRK11169 leucine-responsive tr 36.2 84 0.0018 27.1 5.2 51 131-183 10-60 (164)
193 cd04790 HTH_Cfa-like_unk Helix 36.1 1.8E+02 0.0039 25.6 7.4 38 152-195 2-43 (172)
194 PRK11523 DNA-binding transcrip 36.1 64 0.0014 29.2 4.7 51 136-186 13-67 (253)
195 PRK10402 DNA-binding transcrip 35.9 45 0.00097 29.6 3.6 53 137-190 152-207 (226)
196 TIGR02051 MerR Hg(II)-responsi 35.9 2.5E+02 0.0054 23.2 8.8 79 154-236 2-108 (124)
197 COG4519 Uncharacterized protei 35.8 60 0.0013 26.6 3.9 42 140-182 12-53 (95)
198 PRK00888 ftsB cell division pr 35.5 96 0.0021 25.5 5.2 53 201-254 31-83 (105)
199 PF00170 bZIP_1: bZIP transcri 35.5 1.7E+02 0.0036 21.5 6.0 34 206-239 28-61 (64)
200 TIGR01063 gyrA DNA gyrase, A s 35.4 89 0.0019 34.2 6.4 16 280-295 493-509 (800)
201 COG1730 GIM5 Predicted prefold 35.4 3E+02 0.0066 24.2 8.6 30 156-185 24-53 (145)
202 PF08781 DP: Transcription fac 35.3 1.1E+02 0.0024 26.9 5.9 20 264-283 58-77 (142)
203 COG2919 Septum formation initi 35.1 51 0.0011 27.5 3.6 32 202-233 55-86 (117)
204 TIGR00373 conserved hypothetic 35.1 1.9E+02 0.0041 25.3 7.3 35 148-182 25-59 (158)
205 cd04787 HTH_HMRTR_unk Helix-Tu 35.0 2.7E+02 0.0058 23.2 9.4 36 153-192 2-39 (133)
206 PRK13503 transcriptional activ 34.5 64 0.0014 29.0 4.4 39 135-173 171-209 (278)
207 PF10018 Med4: Vitamin-D-recep 34.4 1.1E+02 0.0024 27.2 5.9 55 202-256 27-88 (188)
208 PRK10421 DNA-binding transcrip 34.2 54 0.0012 29.7 3.9 39 147-185 21-60 (253)
209 PF11853 DUF3373: Protein of u 34.0 33 0.00072 35.7 2.8 25 205-229 32-56 (489)
210 PF04218 CENP-B_N: CENP-B N-te 33.9 36 0.00079 24.5 2.2 31 142-173 14-44 (53)
211 TIGR02231 conserved hypothetic 33.7 1.8E+02 0.0038 29.7 7.9 37 203-239 137-173 (525)
212 COG1321 TroR Mn-dependent tran 33.3 77 0.0017 27.7 4.6 40 148-187 21-60 (154)
213 PRK09333 30S ribosomal protein 33.1 49 0.0011 29.4 3.3 37 149-185 65-115 (150)
214 PRK13182 racA polar chromosome 32.9 1.6E+02 0.0035 26.5 6.7 28 213-240 87-114 (175)
215 COG1730 GIM5 Predicted prefold 32.8 1.4E+02 0.003 26.3 6.1 38 201-238 10-47 (145)
216 COG2512 Predicted membrane-ass 32.4 80 0.0017 30.0 4.9 60 132-192 192-251 (258)
217 PRK09863 putative frv operon r 32.3 1.8E+02 0.0038 30.1 7.7 52 139-195 8-65 (584)
218 PF10779 XhlA: Haemolysin XhlA 32.2 1.8E+02 0.0039 22.0 5.9 39 202-240 4-42 (71)
219 TIGR02894 DNA_bind_RsfA transc 32.0 1.7E+02 0.0037 26.4 6.6 35 206-240 106-140 (161)
220 PRK09393 ftrA transcriptional 31.8 72 0.0016 29.9 4.4 41 135-175 218-258 (322)
221 PF10805 DUF2730: Protein of u 31.7 2.9E+02 0.0063 22.6 9.8 82 138-241 21-102 (106)
222 PF02796 HTH_7: Helix-turn-hel 31.6 36 0.00078 23.5 1.8 32 138-173 12-43 (45)
223 PRK09975 DNA-binding transcrip 31.4 63 0.0014 27.8 3.7 37 134-170 14-50 (213)
224 TIGR02209 ftsL_broad cell divi 31.3 1.6E+02 0.0035 22.2 5.6 32 208-239 28-59 (85)
225 TIGR00635 ruvB Holliday juncti 31.2 69 0.0015 29.5 4.2 55 133-187 236-292 (305)
226 KOG3501 Molecular chaperone Pr 31.1 1.7E+02 0.0036 25.1 5.9 40 201-240 71-110 (114)
227 PF03836 RasGAP_C: RasGAP C-te 30.9 16 0.00035 31.2 0.0 26 164-191 5-30 (142)
228 PRK04214 rbn ribonuclease BN/u 30.9 94 0.002 30.9 5.3 44 147-190 306-349 (412)
229 PF11932 DUF3450: Protein of u 30.8 1.4E+02 0.003 27.5 6.1 33 207-239 87-119 (251)
230 PRK11753 DNA-binding transcrip 30.7 81 0.0018 27.0 4.3 39 151-190 168-206 (211)
231 PF06005 DUF904: Protein of un 30.4 2.1E+02 0.0045 22.3 6.0 37 204-240 18-54 (72)
232 PRK01203 prefoldin subunit alp 30.3 1.6E+02 0.0035 25.6 5.9 59 208-279 4-62 (130)
233 COG1373 Predicted ATPase (AAA+ 30.2 78 0.0017 31.5 4.6 50 135-184 220-270 (398)
234 COG1382 GimC Prefoldin, chaper 29.8 1.2E+02 0.0026 26.1 5.0 33 207-239 73-105 (119)
235 PF14712 Snapin_Pallidin: Snap 29.8 1.8E+02 0.0039 22.5 5.7 37 203-239 13-49 (92)
236 cd04785 HTH_CadR-PbrR-like Hel 29.6 3.2E+02 0.007 22.5 8.1 86 152-241 1-116 (126)
237 TIGR00714 hscB Fe-S protein as 29.6 3.4E+02 0.0073 23.7 7.9 26 153-180 41-67 (157)
238 PF08222 HTH_CodY: CodY helix- 29.5 58 0.0013 25.0 2.7 36 150-185 3-38 (61)
239 PF10141 ssDNA-exonuc_C: Singl 29.4 3.6E+02 0.0077 24.1 8.3 47 138-184 101-149 (195)
240 TIGR02812 fadR_gamma fatty aci 29.4 3.4E+02 0.0074 24.1 8.2 39 147-185 25-64 (235)
241 KOG0804 Cytoplasmic Zn-finger 29.4 1.1E+02 0.0025 31.8 5.6 59 167-239 390-449 (493)
242 PRK10803 tol-pal system protei 29.3 1.4E+02 0.003 28.2 5.9 44 208-254 58-101 (263)
243 PF01991 vATP-synt_E: ATP synt 28.9 1.5E+02 0.0032 25.5 5.6 31 211-241 62-92 (198)
244 PRK11179 DNA-binding transcrip 28.9 1E+02 0.0022 26.2 4.5 50 133-184 7-56 (153)
245 cd00890 Prefoldin Prefoldin is 28.9 3E+02 0.0066 22.0 8.5 36 203-238 5-40 (129)
246 PF09340 NuA4: Histone acetylt 28.8 96 0.0021 24.5 4.0 29 211-239 2-30 (80)
247 PRK10572 DNA-binding transcrip 28.6 75 0.0016 29.0 3.9 38 136-173 184-221 (290)
248 PF10046 BLOC1_2: Biogenesis o 28.4 1.3E+02 0.0029 24.2 4.9 34 204-237 66-99 (99)
249 PF14389 Lzipper-MIP1: Leucine 28.3 1.9E+02 0.0041 23.1 5.7 37 200-236 50-86 (88)
250 COG2186 FadR Transcriptional r 28.1 51 0.0011 30.3 2.7 56 135-190 14-74 (241)
251 cd04776 HTH_GnyR Helix-Turn-He 28.1 1.2E+02 0.0027 25.0 4.7 12 154-165 3-14 (118)
252 PRK09685 DNA-binding transcrip 27.6 78 0.0017 28.9 3.8 38 136-173 198-236 (302)
253 PRK00411 cdc6 cell division co 27.4 66 0.0014 30.7 3.4 35 150-184 314-358 (394)
254 PF05911 DUF869: Plant protein 27.3 2.3E+02 0.0049 31.3 7.7 102 133-234 514-619 (769)
255 COG2207 AraC AraC-type DNA-bin 27.3 85 0.0019 24.0 3.5 43 139-181 24-66 (127)
256 COG1497 Predicted transcriptio 27.2 5.9E+02 0.013 24.8 9.8 43 149-191 23-65 (260)
257 cd04779 HTH_MerR-like_sg4 Heli 27.1 1.2E+02 0.0027 25.9 4.7 84 152-239 1-102 (134)
258 PF13600 DUF4140: N-terminal d 26.9 1.9E+02 0.0041 22.9 5.5 35 203-237 69-103 (104)
259 PF13542 HTH_Tnp_ISL3: Helix-t 26.7 85 0.0018 21.5 3.0 38 136-173 12-49 (52)
260 PRK11642 exoribonuclease R; Pr 26.2 1.1E+02 0.0024 33.7 5.2 51 139-190 23-77 (813)
261 cd01110 HTH_SoxR Helix-Turn-He 26.1 3E+02 0.0066 23.4 6.9 24 152-175 2-27 (139)
262 smart00342 HTH_ARAC helix_turn 26.1 58 0.0013 23.1 2.2 25 152-176 2-26 (84)
263 PRK10141 DNA-binding transcrip 26.1 4E+02 0.0086 22.4 7.8 51 139-191 20-70 (117)
264 TIGR01062 parC_Gneg DNA topois 26.1 1.9E+02 0.0041 31.7 6.8 54 131-184 337-392 (735)
265 PRK10906 DNA-binding transcrip 26.0 1E+02 0.0022 28.6 4.4 48 138-187 8-55 (252)
266 PRK11920 rirA iron-responsive 26.0 1.2E+02 0.0026 26.2 4.5 43 142-184 15-57 (153)
267 TIGR02063 RNase_R ribonuclease 26.0 1.2E+02 0.0026 32.4 5.3 55 138-192 5-63 (709)
268 PF14817 HAUS5: HAUS augmin-li 25.9 1.6E+02 0.0034 31.7 6.2 49 186-234 56-109 (632)
269 PRK10371 DNA-binding transcrip 25.8 95 0.0021 29.2 4.1 39 136-174 192-230 (302)
270 COG3888 Predicted transcriptio 25.7 1.4E+02 0.003 29.5 5.2 62 134-195 3-67 (321)
271 PF15358 TSKS: Testis-specific 25.6 1.3E+02 0.0028 31.3 5.3 64 170-238 108-180 (558)
272 TIGR01950 SoxR redox-sensitive 25.5 4.3E+02 0.0094 22.6 9.0 38 152-193 2-40 (142)
273 PHA02542 41 41 helicase; Provi 25.1 7.5E+02 0.016 25.4 10.6 113 153-274 86-201 (473)
274 PRK09343 prefoldin subunit bet 24.8 2.8E+02 0.0061 23.2 6.4 32 208-239 75-106 (121)
275 PF04102 SlyX: SlyX; InterPro 24.7 1.8E+02 0.004 22.0 4.8 38 203-240 17-54 (69)
276 PF14830 Haemocyan_bet_s: Haem 24.7 27 0.00059 29.2 0.2 14 168-181 57-70 (103)
277 TIGR00634 recN DNA repair prot 24.7 1.5E+02 0.0032 30.7 5.6 57 151-217 286-342 (563)
278 PTZ00446 vacuolar sorting prot 24.6 2.9E+02 0.0062 25.4 6.8 38 202-239 25-62 (191)
279 PF08317 Spc7: Spc7 kinetochor 24.3 2.3E+02 0.0051 27.3 6.6 70 208-283 234-311 (325)
280 PRK05560 DNA gyrase subunit A; 24.3 1.8E+02 0.004 31.8 6.4 16 280-295 495-511 (805)
281 PRK03963 V-type ATP synthase s 24.3 3.6E+02 0.0077 23.7 7.2 31 210-240 70-100 (198)
282 PRK09462 fur ferric uptake reg 24.2 1.5E+02 0.0032 25.0 4.7 46 140-185 22-72 (148)
283 PF07106 TBPIP: Tat binding pr 24.2 2.5E+02 0.0055 24.2 6.2 8 249-256 142-149 (169)
284 TIGR02787 codY_Gpos GTP-sensin 23.9 1.3E+02 0.0029 28.9 4.7 38 148-185 195-232 (251)
285 PF14178 YppF: YppF-like prote 23.6 1.4E+02 0.0031 22.9 3.9 50 133-182 3-56 (60)
286 TIGR02043 ZntR Zn(II)-responsi 23.5 4.4E+02 0.0095 22.0 9.2 81 152-236 2-113 (131)
287 PF06717 DUF1202: Protein of u 23.4 2.6E+02 0.0055 27.7 6.5 52 178-236 119-177 (308)
288 PF00440 TetR_N: Bacterial reg 23.4 93 0.002 21.2 2.7 30 140-169 5-34 (47)
289 COG2378 Predicted transcriptio 23.4 85 0.0018 30.2 3.4 39 141-181 14-52 (311)
290 PRK10434 srlR DNA-bindng trans 23.3 1.2E+02 0.0027 28.0 4.4 44 139-184 9-52 (256)
291 PRK15185 transcriptional regul 23.3 1.1E+02 0.0024 30.0 4.1 39 135-173 206-244 (309)
292 PF05584 Sulfolobus_pRN: Sulfo 23.3 1.8E+02 0.0039 23.0 4.6 46 136-184 6-51 (72)
293 PF07830 PP2C_C: Protein serin 23.1 78 0.0017 25.4 2.6 42 217-258 18-63 (81)
294 PRK10884 SH3 domain-containing 23.1 1.6E+02 0.0034 27.2 4.9 22 213-234 134-155 (206)
295 TIGR03697 NtcA_cyano global ni 23.1 2.1E+02 0.0045 24.0 5.4 41 151-192 143-183 (193)
296 PF07889 DUF1664: Protein of u 23.1 2.6E+02 0.0056 24.1 5.9 10 188-197 22-31 (126)
297 PF04539 Sigma70_r3: Sigma-70 23.0 1E+02 0.0022 22.8 3.1 47 138-184 7-53 (78)
298 PF14282 FlxA: FlxA-like prote 22.9 1.9E+02 0.004 23.8 4.8 36 203-238 25-71 (106)
299 COG5625 Predicted transcriptio 22.9 2.8E+02 0.006 23.7 5.8 46 149-195 34-79 (113)
300 TIGR00219 mreC rod shape-deter 22.9 2.7E+02 0.0057 26.6 6.6 34 208-241 77-110 (283)
301 PF05225 HTH_psq: helix-turn-h 22.8 1.1E+02 0.0023 21.5 2.9 26 149-174 14-39 (45)
302 TIGR00293 prefoldin, archaeal 22.8 2.7E+02 0.0059 22.7 5.9 35 203-237 5-39 (126)
303 cd04788 HTH_NolA-AlbR Helix-Tu 22.7 3.9E+02 0.0084 21.1 7.4 37 153-193 2-40 (96)
304 PF02996 Prefoldin: Prefoldin 22.6 2.2E+02 0.0048 22.7 5.2 35 203-237 83-117 (120)
305 PF01381 HTH_3: Helix-turn-hel 22.6 67 0.0015 22.0 1.9 23 151-173 9-31 (55)
306 cd04769 HTH_MerR2 Helix-Turn-H 22.6 1.3E+02 0.0029 24.4 3.9 26 153-182 2-27 (116)
307 cd04777 HTH_MerR-like_sg1 Heli 22.6 4E+02 0.0086 21.2 7.7 25 153-183 2-28 (107)
308 KOG2255 Peptidyl-tRNA hydrolas 22.6 39 0.00084 31.8 0.8 29 154-184 64-92 (224)
309 smart00338 BRLZ basic region l 22.5 2.6E+02 0.0057 20.4 5.2 29 211-239 26-54 (65)
310 PRK05638 threonine synthase; V 22.3 1.3E+02 0.0028 30.1 4.5 61 121-184 357-419 (442)
311 COG0497 RecN ATPase involved i 22.2 2.4E+02 0.0052 30.1 6.5 101 129-239 260-363 (557)
312 PRK05771 V-type ATP synthase s 22.1 3.5E+02 0.0077 28.4 7.9 59 170-239 192-250 (646)
313 PRK13502 transcriptional activ 21.9 1.2E+02 0.0026 27.4 3.9 39 135-173 176-214 (282)
314 PRK09039 hypothetical protein; 21.9 2.3E+02 0.0049 27.9 6.0 30 209-238 156-185 (343)
315 PRK15008 HTH-type transcriptio 21.6 2.1E+02 0.0045 25.0 5.2 41 130-170 17-57 (212)
316 PF07716 bZIP_2: Basic region 21.4 3E+02 0.0065 19.6 5.2 26 212-237 26-51 (54)
317 PF12761 End3: Actin cytoskele 21.3 2.5E+02 0.0055 26.0 5.8 17 222-238 136-152 (195)
318 PRK02793 phi X174 lysis protei 21.3 3.9E+02 0.0084 20.6 6.0 36 202-237 6-41 (72)
319 PF11853 DUF3373: Protein of u 21.3 90 0.002 32.6 3.2 37 203-240 24-60 (489)
320 PF11559 ADIP: Afadin- and alp 21.1 3.1E+02 0.0066 23.2 6.0 37 204-240 80-116 (151)
321 PF08181 DegQ: DegQ (SacQ) fam 21.1 2.4E+02 0.0053 20.3 4.4 39 211-249 4-43 (46)
322 PF11972 HTH_13: HTH DNA bindi 21.0 1.9E+02 0.0041 21.7 4.0 47 139-190 3-49 (54)
323 PRK09978 DNA-binding transcrip 21.0 1.3E+02 0.0028 28.9 4.0 38 135-172 142-179 (274)
324 PF04521 Viral_P18: ssRNA posi 21.0 2.3E+02 0.0049 24.6 5.1 31 205-235 73-103 (120)
325 PRK01194 V-type ATP synthase s 21.0 2.6E+02 0.0055 25.0 5.7 32 208-239 67-98 (185)
326 COG5509 Uncharacterized small 20.9 1.1E+02 0.0023 23.8 2.8 25 199-223 27-51 (65)
327 KOG4057 Uncharacterized conser 20.9 1.8E+02 0.0038 26.4 4.6 38 209-246 7-44 (180)
328 PF12269 zf-CpG_bind_C: CpG bi 20.9 1.4E+02 0.0031 28.4 4.2 35 203-237 35-69 (236)
329 PF01710 HTH_Tnp_IS630: Transp 20.9 1.1E+02 0.0024 25.1 3.2 43 138-185 60-102 (119)
330 PRK03578 hscB co-chaperone Hsc 20.9 6.1E+02 0.013 22.6 10.5 51 128-180 17-84 (176)
331 COG3074 Uncharacterized protei 20.9 2.8E+02 0.0061 22.2 5.2 34 205-238 19-52 (79)
332 COG5124 Protein predicted to b 20.8 2.5E+02 0.0053 26.2 5.6 63 167-230 44-108 (209)
333 PRK04406 hypothetical protein; 20.8 3.8E+02 0.0083 20.9 6.0 37 202-238 9-45 (75)
334 PRK13979 DNA topoisomerase IV 20.7 1.9E+02 0.0042 32.5 5.8 16 280-295 513-529 (957)
335 PRK04325 hypothetical protein; 20.7 4E+02 0.0087 20.6 6.0 36 202-237 7-42 (74)
336 PF07061 Swi5: Swi5; InterPro 20.6 1.6E+02 0.0034 23.5 3.8 27 207-233 3-29 (83)
337 PRK00846 hypothetical protein; 20.6 3.5E+02 0.0075 21.5 5.7 24 202-225 11-34 (77)
338 COG1339 Transcriptional regula 20.5 3.1E+02 0.0067 25.9 6.2 48 146-193 14-61 (214)
339 PRK00118 putative DNA-binding 20.5 69 0.0015 26.6 1.9 34 151-184 33-74 (104)
340 PF12844 HTH_19: Helix-turn-he 20.5 80 0.0017 22.4 2.0 23 151-173 12-34 (64)
341 PRK09392 ftrB transcriptional 20.4 2.2E+02 0.0049 25.0 5.2 37 154-192 176-212 (236)
342 PRK13918 CRP/FNR family transc 20.3 3.3E+02 0.0071 23.1 6.1 40 152-192 150-189 (202)
343 TIGR01242 26Sp45 26S proteasom 20.3 2.3E+02 0.0049 27.3 5.6 36 204-239 6-41 (364)
344 PF06320 GCN5L1: GCN5-like pro 20.2 1.7E+02 0.0038 24.7 4.2 54 201-257 51-104 (121)
345 KOG4098 Molecular chaperone Pr 20.1 3.7E+02 0.008 23.8 6.3 100 136-240 16-115 (140)
No 1
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=100.00 E-value=1.5e-60 Score=455.34 Aligned_cols=175 Identities=53% Similarity=0.801 Sum_probs=167.4
Q ss_pred CCCCCCCCCcCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCc
Q 022537 121 LNLSNGCRYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTS 200 (295)
Q Consensus 121 ~tp~~~~R~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~ 200 (295)
..+...+|+++|||+||+|||.|++++|+|++|||.||++|+|||||||||||||||||||+|++||+|+|+|.+.+..+
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 45567899999999999999999999999999999999999999999999999999999999999999999999987667
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccHhhhhcCCCCCCCeEEEEeCCCCCeEEecC
Q 022537 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDIASLPCFQNQTLIAIKAPQASYIEVPD 280 (295)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~n~~~aYVT~eDI~~i~~f~~qTviAIKAP~gT~LEVPd 280 (295)
+..++.+.|++|++.|.++|+.||++|++|+++|+.|++|.+|++||||||+||++|+.|++|||||||||++|+||||+
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 CCCc---eeeeecCCCCC
Q 022537 281 PDEN---RILVSSKGNIK 295 (295)
Q Consensus 281 P~e~---~~l~s~~G~I~ 295 (295)
|+++ ++|+|.+|||.
T Consensus 221 ~~~~~~~i~L~s~~GpI~ 238 (354)
T KOG2577|consen 221 PDEDRYQIRLKSNQGPID 238 (354)
T ss_pred CCCCceEEEeccCCCcee
Confidence 9876 47889999994
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=99.89 E-value=1.6e-23 Score=159.83 Aligned_cols=66 Identities=53% Similarity=0.882 Sum_probs=62.9
Q ss_pred CCcCcHHHHHHHHHHHHHhCCCCceeHHHHHHHh---hh--hhhhhhhhhhHhhhccceeccccCceEEec
Q 022537 128 RYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVL---EV--QKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (295)
Q Consensus 128 R~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L---~V--qKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (295)
|.++||+.||++||++|...+++.++|+++|+.| ++ +|||||||+||||++|||+|.+|+.|+|+|
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=99.81 E-value=2.3e-20 Score=177.10 Aligned_cols=87 Identities=37% Similarity=0.611 Sum_probs=78.8
Q ss_pred CCCCCCCCCcCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCc
Q 022537 121 LNLSNGCRYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTS 200 (295)
Q Consensus 121 ~tp~~~~R~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~ 200 (295)
+.+.-++|+++|||+||++|+.++....-..+-|+.||.+|||.|||||||+||||+||++.|.+||.|.|+|+.
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 666789999999999999999999877778899999999999999999999999999999999999999999987
Q ss_pred hhHHHHHHHHHH
Q 022537 201 KLDDQVARLKAE 212 (295)
Q Consensus 201 ~~~~~~~~Lk~E 212 (295)
.+...+.+||+|
T Consensus 89 aiPral~eLqeE 100 (388)
T KOG2578|consen 89 AIPRALFELQEE 100 (388)
T ss_pred hhhHHHHHHHHH
Confidence 455566677765
No 4
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.09 E-value=1.1e-10 Score=111.79 Aligned_cols=159 Identities=25% Similarity=0.348 Sum_probs=102.7
Q ss_pred CCCCCCcCcHHHHHHHHHHHHHhCCCC-ceeHHHHHHHh----------hhhhhhhhhhhhHhhhccceecc-----ccC
Q 022537 124 SNGCRYDSSLGLLTRKFINLIQEAKDG-TLDLNRTAEVL----------EVQKRRIYDITNVLEGIGLIEKT-----SKN 187 (295)
Q Consensus 124 ~~~~R~d~SLglLTkkFI~ll~~a~~g-~ldLn~aA~~L----------~VqKRRIYDItNVLEgIGLIeK~-----~KN 187 (295)
....|+++||++||++||.++-++++. .|.|+.||..| ...-||+|||.|||-++|||+|. .|.
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 346789999999999999999988887 88999999988 34679999999999999999997 478
Q ss_pred ceEEecCCCCCCch-------h-----------HHHHHHHHHH--HHHHHHHHHHHHHH--------HHHHHHHHHHHhh
Q 022537 188 HIRWKGSDSLGTSK-------L-----------DDQVARLKAE--IESLHAEECRIDDS--------IREKQELIRTLEE 239 (295)
Q Consensus 188 ~i~W~G~~~s~~~~-------~-----------~~~~~~Lk~E--l~~L~~~E~~LD~l--------I~~~~~~L~~Lte 239 (295)
.|+|.|......+. + .-.+.++++. -..-..+|...... ++.-+++..+|.+
T Consensus 232 afrwlG~~~~~t~sf~~gs~sL~~~n~~K~rafgteItnvnakr~kSs~s~~en~~~~~~~~~k~~~e~~~ye~~~~l~~ 311 (388)
T KOG2578|consen 232 AFRWLGSKPIQTGSFFQGSRSLSEQNLPKPRAFGTEITNVNAKRNKSSCSSMENFMFAEVVTKKHAAEKMRYEAFAQLSS 311 (388)
T ss_pred hhheeCCCccccccccccchhHhhcCCCCcccCCccccchhhhhccCcchhhhhHHHHHhhhhhccchhhhhhhhhhhhh
Confidence 99999976432210 0 0011122111 11122233222121 2222444555555
Q ss_pred hccccccccccHhhhhcCCCCCCCeEEEEeCCCCCeEEecCCC
Q 022537 240 NENHQKYMFLTEEDIASLPCFQNQTLIAIKAPQASYIEVPDPD 282 (295)
Q Consensus 240 d~~n~~~aYVT~eDI~~i~~f~~qTviAIKAP~gT~LEVPdP~ 282 (295)
+..-..-+|+----+-.|+..+.+..+--.|+.+-.++||+-.
T Consensus 312 ~~~p~~~~~~~gp~~P~igt~~t~~~~~~~~~srr~f~ie~l~ 354 (388)
T KOG2578|consen 312 RLKPLPMAYLFGPFLPEIGTSQTNKQFNFPATSRRLFNIEALT 354 (388)
T ss_pred ccCCcccccccCCCCCCCCCcchhhccCCCCCccccccchhcc
Confidence 5444445555444444556666666677777777777777544
No 5
>KOG2829 consensus E2F-like protein [Transcription]
Probab=99.03 E-value=1.1e-08 Score=97.27 Aligned_cols=120 Identities=25% Similarity=0.446 Sum_probs=80.9
Q ss_pred CCCceeHHHHHHHh----------------------hhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCchhHHH
Q 022537 148 KDGTLDLNRTAEVL----------------------EVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQ 205 (295)
Q Consensus 148 ~~g~ldLn~aA~~L----------------------~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~ 205 (295)
..|....|++|+.| .-.|||+||.+|||.++.+|.|. |..|+|+|+.... .+.
T Consensus 59 ~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd-KKEIrW~GLP~~s----s~d 133 (326)
T KOG2829|consen 59 RKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD-KKEIRWIGLPATS----SQD 133 (326)
T ss_pred hcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc-cceeeeeccCccc----hHH
Confidence 55677778888777 44799999999999999999999 6779999998532 234
Q ss_pred HHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHhhhcccccccccc----HhhhhcCCCCCCCeEEEEeCCCCCeEE
Q 022537 206 VARLKAEIES----LHAEECRIDDSIREKQELIRTLEENENHQKYMFLT----EEDIASLPCFQNQTLIAIKAPQASYIE 277 (295)
Q Consensus 206 ~~~Lk~El~~----L~~~E~~LD~lI~~~~~~L~~Lted~~n~~~aYVT----~eDI~~i~~f~~qTviAIKAP~gT~LE 277 (295)
+.+|+.|... ..++-..|.++|... -.+++|.+. | +.++.+ .++| --.+|.|..-+.|.|+
T Consensus 134 v~~le~Er~k~~erI~kK~a~lqEl~~q~-~~fknLV~R--N-~~~e~~~~~P~~~i-------~LPFiiinT~k~a~Ie 202 (326)
T KOG2829|consen 134 VSELEEERKKRMERIKKKAAQLQELIEQV-SAFKNLVQR--N-RHAESQGQPPSENI-------HLPFIIINTSKKAVIE 202 (326)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHh--h-hhhhhccCCCCccc-------ccceEEEecCCCceEE
Confidence 5556555433 334444555555432 445666543 2 334444 1221 1358999999999999
Q ss_pred ecCCCC
Q 022537 278 VPDPDE 283 (295)
Q Consensus 278 VPdP~e 283 (295)
+...++
T Consensus 203 ceiseD 208 (326)
T KOG2829|consen 203 CEISED 208 (326)
T ss_pred EEeccc
Confidence 987754
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=95.76 E-value=0.022 Score=42.11 Aligned_cols=45 Identities=24% Similarity=0.425 Sum_probs=40.9
Q ss_pred CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEe
Q 022537 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (295)
..+.....++|+.+++.+..+|++++-|+.-|+|++...+.+.|.
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 567899999999999999999999999999999999987777664
No 7
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=94.45 E-value=0.31 Score=45.58 Aligned_cols=53 Identities=21% Similarity=0.397 Sum_probs=42.0
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCC
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD 195 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~ 195 (295)
++.|++ -|...-.++|+..||.+=|+|||++.||+=|+|+....+--++.-.+
T Consensus 22 Y~aLl~---~g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~ 74 (247)
T COG1378 22 YLALLC---LGEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVP 74 (247)
T ss_pred HHHHHH---hCCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeCC
Confidence 444443 24567789999999999999999999999999999866656665554
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=93.92 E-value=0.16 Score=35.74 Aligned_cols=41 Identities=27% Similarity=0.387 Sum_probs=35.4
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhcc
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIG 179 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIG 179 (295)
.+.+.+|..+.+. +...++|+.|+|++|-||--++.|+..|
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 4577788666666 9999999999999999999999999998
No 9
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=93.84 E-value=0.55 Score=35.67 Aligned_cols=49 Identities=27% Similarity=0.406 Sum_probs=40.7
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccC
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
...++++.+.+ +.+.+.++|+.+++.+.-+|-+++.|+..|+|++...+
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~~ 56 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQN 56 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCCC
Confidence 34566665543 47999999999999999999999999999999987433
No 10
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=93.60 E-value=0.17 Score=34.17 Aligned_cols=45 Identities=27% Similarity=0.435 Sum_probs=38.7
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.++.++.+. +.+.+.++|+.|++.++.+|..+.-|+..|+|.+..
T Consensus 4 ~il~~l~~~--~~~s~~~l~~~l~~s~~tv~~~l~~L~~~g~i~~~~ 48 (53)
T smart00420 4 QILELLAQQ--GKVSVEELAELLGVSEMTIRRDLNKLEEQGLLTRVH 48 (53)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEee
Confidence 466666654 459999999999999999999999999999999764
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=93.32 E-value=0.31 Score=34.89 Aligned_cols=54 Identities=20% Similarity=0.250 Sum_probs=42.7
Q ss_pred HHHHHHHHHHhC-----CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCce
Q 022537 136 LTRKFINLIQEA-----KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (295)
Q Consensus 136 LTkkFI~ll~~a-----~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i 189 (295)
+..-|+.+.... ..+.+...++|+.+++.+.-++.+++.|+.-|+|++.....|
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 445555555543 346789999999999999999999999999999998863433
No 12
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=92.28 E-value=0.36 Score=36.37 Aligned_cols=54 Identities=20% Similarity=0.308 Sum_probs=46.2
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEE
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W 191 (295)
.+.+.+|...++..+.+.++|..||+.++-+.-++.-|+.-|+|++.+.+.=.|
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 567888887755459999999999999999999999999999999987543467
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=92.23 E-value=0.26 Score=34.86 Aligned_cols=45 Identities=20% Similarity=0.353 Sum_probs=37.3
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
..++++..++.+ +.+.++|+.+|+.|=-+|-+++.|+..|++++.
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 345566555554 799999999999999999999999999999874
No 14
>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=91.18 E-value=0.6 Score=33.13 Aligned_cols=46 Identities=24% Similarity=0.340 Sum_probs=40.7
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
..+.++...++..+.+.++|+.|++.|=.+--+++-||.-|+|+|.
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 4566677888888999999999999999999999999999999987
No 15
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=91.02 E-value=2.2 Score=36.75 Aligned_cols=87 Identities=23% Similarity=0.373 Sum_probs=58.2
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCC-CCCchhHHHHHHHHHHHHHHHH
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDS-LGTSKLDDQVARLKAEIESLHA 218 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~-s~~~~~~~~~~~Lk~El~~L~~ 218 (295)
|..|++ +++.++.+++|+.|+..|=.+|=.++=|...|||.|.--+. .|..- .-...++ -.+++. .
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~---~~Ggy~yiY~~i~--~ee~k~------~ 99 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL---KGGGYYYLYKPID--PEEIKK------K 99 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc---CCCceeEEEecCC--HHHHHH------H
Confidence 556665 77889999999999999999999999999999999884442 22110 0000011 122232 2
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 022537 219 EECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 219 ~E~~LD~lI~~~~~~L~~Lte 239 (295)
.++.||++-..+.+-|.++..
T Consensus 100 i~~~l~~w~~~~~~~i~~~~~ 120 (126)
T COG3355 100 ILKDLDEWYDKMKQLIEEFEK 120 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 446677777777777777654
No 16
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=90.72 E-value=0.62 Score=32.11 Aligned_cols=43 Identities=30% Similarity=0.450 Sum_probs=35.9
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
.+.+.++.+.| .+...++|+.+++.+..++.+++-|+.-|+|+
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 56777887744 49999999999999999999999999999985
No 17
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=89.04 E-value=0.73 Score=31.50 Aligned_cols=38 Identities=24% Similarity=0.376 Sum_probs=34.4
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecccc
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (295)
.+.+.+++++..|++.+..++++++.|+.-|+|+...+
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~g~i~~~~~ 45 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREAGLVESRRE 45 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHCCCeeeeec
Confidence 56689999999999999999999999999999997653
No 18
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=88.81 E-value=7.8 Score=34.33 Aligned_cols=98 Identities=20% Similarity=0.278 Sum_probs=61.8
Q ss_pred CCCCceeHHHHHHHh--hhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCchh-HHHHHHHHHHH-----HHH--
Q 022537 147 AKDGTLDLNRTAEVL--EVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKL-DDQVARLKAEI-----ESL-- 216 (295)
Q Consensus 147 a~~g~ldLn~aA~~L--~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~-~~~~~~Lk~El-----~~L-- 216 (295)
-.++.-|...+|.+| +|.--.+=+.++.|+-+|||+|...+.|.=.-...+.+.++ ..-+..++.+. +.|
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 456666999999999 99999999999999999999999774433322111112221 22233333332 122
Q ss_pred ----------------HHHHHHHHHHHHHHHHHHHHHhhhcccc
Q 022537 217 ----------------HAEECRIDDSIREKQELIRTLEENENHQ 244 (295)
Q Consensus 217 ----------------~~~E~~LD~lI~~~~~~L~~Lted~~n~ 244 (295)
.+.-.++-+.|+.++.++..+.+...+.
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 1223456667777777777777654433
No 19
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=88.24 E-value=1.3 Score=34.04 Aligned_cols=59 Identities=19% Similarity=0.241 Sum_probs=43.8
Q ss_pred HHHHHHHHHHhCCCC-ceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc-ccCceEEecC
Q 022537 136 LTRKFINLIQEAKDG-TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT-SKNHIRWKGS 194 (295)
Q Consensus 136 LTkkFI~ll~~a~~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~-~KN~i~W~G~ 194 (295)
.+-+++.++...+++ .+.+.++|+.+++..+.+..|++-|+--|+|+.. +++-=.|...
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~ 69 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLAR 69 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecC
Confidence 445667777655554 4999999999999999999999999999999864 3333334443
No 20
>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=87.81 E-value=1.1 Score=31.76 Aligned_cols=44 Identities=25% Similarity=0.400 Sum_probs=36.3
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
++.++.+.++ +.+.++|+.+++.+--+-.+++-||.-|+|+|..
T Consensus 8 iL~~l~~~~~--~~~~~la~~~~~~~~~~t~~i~~L~~~g~I~r~~ 51 (59)
T PF01047_consen 8 ILRILYENGG--ITQSELAEKLGISRSTVTRIIKRLEKKGLIERER 51 (59)
T ss_dssp HHHHHHHHSS--EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHHcCC--CCHHHHHHHHCCChhHHHHHHHHHHHCCCEEecc
Confidence 3444554444 9999999999999999999999999999999873
No 21
>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=87.59 E-value=1.4 Score=31.69 Aligned_cols=38 Identities=34% Similarity=0.466 Sum_probs=31.9
Q ss_pred CCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
..++.+.+.++|+.+++.+--+..+++-|+..|+|+|.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~ 51 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKE 51 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEE
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEec
Confidence 37888999999999999999999999999999999887
No 22
>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=87.34 E-value=4.5 Score=32.74 Aligned_cols=55 Identities=18% Similarity=0.302 Sum_probs=34.9
Q ss_pred ccCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 185 SKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 185 ~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
...-+.|+|.+..-....++-...+++.++.|..+-..|++.|..+++++..+..
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 4456889996643333344445566666677777777777777777777666654
No 23
>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=87.27 E-value=1.2 Score=36.71 Aligned_cols=47 Identities=11% Similarity=0.154 Sum_probs=41.0
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
-+.+.++...+++.+.+.++|+.+++.+..++.+++.|+.-|+|+..
T Consensus 12 l~~l~~la~~~~~~~s~~eia~~l~is~~~v~~~l~~L~~~Gli~~~ 58 (130)
T TIGR02944 12 TLVLTTLAQNDSQPYSAAEIAEQTGLNAPTVSKILKQLSLAGIVTSK 58 (130)
T ss_pred HHHHHHHHhCCCCCccHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 34566666667788999999999999999999999999999999864
No 24
>PF13730 HTH_36: Helix-turn-helix domain
Probab=87.03 E-value=0.93 Score=31.85 Aligned_cols=29 Identities=31% Similarity=0.356 Sum_probs=27.9
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhccce
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLI 181 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLI 181 (295)
....+|+.+|+.+|.++-.++.||..|+|
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 69999999999999999999999999986
No 25
>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=86.14 E-value=0.53 Score=36.23 Aligned_cols=29 Identities=41% Similarity=0.486 Sum_probs=23.1
Q ss_pred HHHHHhhh---hhhhhhhhhhHhhhccceecc
Q 022537 156 RTAEVLEV---QKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 156 ~aA~~L~V---qKRRIYDItNVLEgIGLIeK~ 184 (295)
.+|+.+++ ..|||||+++-|+-+|||+-.
T Consensus 27 ~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~ 58 (85)
T PF09079_consen 27 ELCESLGVDPLSYRRFSDYLSELEMLGLIESE 58 (85)
T ss_dssp HHHHHTTS----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEE
Confidence 44555555 789999999999999999866
No 26
>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=85.32 E-value=2.8 Score=29.23 Aligned_cols=47 Identities=23% Similarity=0.359 Sum_probs=38.7
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccC
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
..++.++...+ +...++++.+++.+.-++-+++.|+.-|+|.+....
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 44555555543 899999999999999999999999999999976433
No 27
>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=84.86 E-value=1.4 Score=32.55 Aligned_cols=54 Identities=11% Similarity=0.162 Sum_probs=38.9
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccc-eeccccCceEEecCC
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL-IEKTSKNHIRWKGSD 195 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL-IeK~~KN~i~W~G~~ 195 (295)
+.+.++.+. .+...++|+.|+|+++-++--+..|+.-|+ |...++..+-+.+.+
T Consensus 4 ~il~~L~~~---~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~~~ 58 (69)
T TIGR00122 4 RLLALLADN---PFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTVGKGYRLPPPIP 58 (69)
T ss_pred HHHHHHHcC---CcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCCceEecCccc
Confidence 455665533 456999999999999999999999998888 333344444444444
No 28
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=84.33 E-value=4.2 Score=29.62 Aligned_cols=50 Identities=22% Similarity=0.260 Sum_probs=38.6
Q ss_pred HHHHHHHHh---CCCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceeccccC
Q 022537 138 RKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 138 kkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
..+.+.+.. .++..+ ...++|++++|++.=+.+.++.|+.-|+|++..+.
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 445555543 256688 99999999999999999999999999999987543
No 29
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=83.61 E-value=6.2 Score=36.66 Aligned_cols=55 Identities=11% Similarity=0.225 Sum_probs=44.0
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecC
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~ 194 (295)
..+++|.... ..+.+.++|+.|++.|=.+|.+++-|+..|++++.....-.+.|.
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 3556665443 458899999999999999999999999999999875555455664
No 30
>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=83.58 E-value=1 Score=34.29 Aligned_cols=22 Identities=41% Similarity=0.665 Sum_probs=20.0
Q ss_pred hhhhhhhhhhhHhhhccceecc
Q 022537 163 VQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 163 VqKRRIYDItNVLEgIGLIeK~ 184 (295)
...|||+|++|-||..|||+-.
T Consensus 44 l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 44 LTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred CcHHHHHHHHHHHHHcCCeEEE
Confidence 4789999999999999999865
No 31
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=83.22 E-value=1.8 Score=28.87 Aligned_cols=35 Identities=26% Similarity=0.358 Sum_probs=31.9
Q ss_pred ceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+...++|+.+++.+..++.+++.|+.-|+|++..
T Consensus 8 ~~s~~~la~~l~~s~~tv~~~l~~L~~~g~l~~~~ 42 (48)
T smart00419 8 PLTRQEIAELLGLTRETVSRTLKRLEKEGLISREG 42 (48)
T ss_pred ccCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 35788999999999999999999999999999864
No 32
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=82.57 E-value=2.6 Score=28.95 Aligned_cols=40 Identities=20% Similarity=0.294 Sum_probs=35.2
Q ss_pred CCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceeccccC
Q 022537 148 KDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 148 ~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
++..+ ...++|+.++|.+=-+...++.|+.-|+|++....
T Consensus 16 ~~~~l~s~~~la~~~~vs~~tv~~~l~~L~~~g~i~~~~~~ 56 (60)
T smart00345 16 PGDKLPSERELAAQLGVSRTTVREALSRLEAEGLVQRRPGS 56 (60)
T ss_pred CCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 45567 89999999999999999999999999999876443
No 33
>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=81.55 E-value=3 Score=28.89 Aligned_cols=41 Identities=29% Similarity=0.477 Sum_probs=34.6
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceec
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (295)
.+.++.. +...+.++|+.|++.+=-++==+++|+..|+|+|
T Consensus 7 Il~~L~~---~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 7 ILKLLSE---GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp HHHHHTT---SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred HHHHHHh---CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 3444443 7899999999999999999999999999999986
No 34
>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=81.36 E-value=22 Score=33.98 Aligned_cols=43 Identities=21% Similarity=0.245 Sum_probs=37.2
Q ss_pred CCCceeHHHHHHHhh--hhhhhhhhhhhHhhhccceeccccCceEEe
Q 022537 148 KDGTLDLNRTAEVLE--VQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (295)
.++.-|..++|.+|+ |.--.+=|.+..|+-+|||+|.+-+ .|.
T Consensus 134 ~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g--~y~ 178 (271)
T TIGR02147 134 MPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDG--FYK 178 (271)
T ss_pred CCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCC--cEE
Confidence 567778999999998 8889999999999999999998655 454
No 35
>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=80.37 E-value=3.1 Score=31.82 Aligned_cols=49 Identities=22% Similarity=0.285 Sum_probs=40.9
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecccc
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (295)
.++++.+-.+...=+.-.+++..++...|-++=++++|+..|||.|..-
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 4567777766655566677889999999999999999999999999865
No 36
>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=80.34 E-value=12 Score=30.94 Aligned_cols=53 Identities=19% Similarity=0.270 Sum_probs=34.7
Q ss_pred CceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 187 NHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 187 N~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
.-+.|+|.+..-...+++...-++..++.|...-..|.+.|..+++++..+.+
T Consensus 70 ~v~v~iG~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~ 122 (129)
T cd00584 70 KVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEA 122 (129)
T ss_pred EEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34778887654333445555666777777777777777777777777766654
No 37
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=79.20 E-value=1.8 Score=32.40 Aligned_cols=42 Identities=17% Similarity=0.230 Sum_probs=34.4
Q ss_pred CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCce
Q 022537 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i 189 (295)
..+.+++.++|..|+++..-+=+++.+|+..|.|+|...+.-
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 457899999999999999999999999999999999876543
No 38
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=78.52 E-value=13 Score=33.04 Aligned_cols=54 Identities=9% Similarity=0.071 Sum_probs=42.9
Q ss_pred HHHHHHHHHHh---CCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCce
Q 022537 136 LTRKFINLIQE---AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (295)
Q Consensus 136 LTkkFI~ll~~---a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i 189 (295)
+...+.+.+.. .|+..+.-.++|+.|||+|=-+=+.+..|+..|||+.....-+
T Consensus 16 v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~g~ 72 (221)
T PRK11414 16 VENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQAF 72 (221)
T ss_pred HHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCCce
Confidence 34444555543 3788888999999999999999999999999999997755433
No 39
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=78.19 E-value=17 Score=30.56 Aligned_cols=51 Identities=18% Similarity=0.239 Sum_probs=28.0
Q ss_pred ceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022537 188 HIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 188 ~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lt 238 (295)
-+.|+|.+..-.-.+++.+..|++.++.|...-..|.+.|.++++++..+.
T Consensus 78 V~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~~ 128 (140)
T PRK03947 78 VIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQLA 128 (140)
T ss_pred EEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466788664322234444555555566565555555555555555555443
No 40
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=77.13 E-value=5.6 Score=32.41 Aligned_cols=44 Identities=18% Similarity=0.289 Sum_probs=36.5
Q ss_pred HHHHHhCC-CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 141 INLIQEAK-DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 141 I~ll~~a~-~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
+.++...+ .+.+...++|+.+++.++.+++|+..|+.-|+|...
T Consensus 14 l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 14 LLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred HHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 33333333 448999999999999999999999999999999864
No 41
>PHA02943 hypothetical protein; Provisional
Probab=77.04 E-value=9.3 Score=34.40 Aligned_cols=49 Identities=22% Similarity=0.230 Sum_probs=42.6
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCce
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i 189 (295)
..+++++ ..|.....++|+.||++--....++-|||--|.|.+......
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 4577888 678888999999999999999999999999999999765543
No 42
>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=76.80 E-value=6.3 Score=28.64 Aligned_cols=45 Identities=31% Similarity=0.471 Sum_probs=38.7
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
.+.++++++ .+.+.+.++|+.|+|+..-|.==+|.|+.-|+|.|.
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 346677765 479999999999999998888888999999999987
No 43
>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=76.49 E-value=13 Score=29.12 Aligned_cols=27 Identities=19% Similarity=0.287 Sum_probs=21.8
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
+.+.++|+.+||+.+-|.-. |..|+|.
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 46889999999998877766 5568887
No 44
>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=76.34 E-value=22 Score=29.16 Aligned_cols=54 Identities=19% Similarity=0.235 Sum_probs=37.8
Q ss_pred cCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 186 KNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 186 KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
..-+.|+|.+..-...+++.+.-|+..++.|...-..|.+.|.++++++..+.+
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 344678887654333455666677777888888888888888888887777654
No 45
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=76.11 E-value=4 Score=29.53 Aligned_cols=45 Identities=27% Similarity=0.427 Sum_probs=37.7
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
+.+.++ ..++...+.++|+.|++.+--+|-=+++|+..|||+...
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 356789999999999999999999999999999999763
No 46
>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=75.32 E-value=13 Score=30.08 Aligned_cols=78 Identities=17% Similarity=0.247 Sum_probs=43.9
Q ss_pred HHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCC------chhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 156 RTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSIRE 229 (295)
Q Consensus 156 ~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~ 229 (295)
..-..|..+++...|+.+-|+.+. .+...|+-+|.-.... ..+..++..+..+++.|..+...+...+..
T Consensus 20 ~~~~~l~~~~~E~~~v~~EL~~l~----~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~e 95 (105)
T cd00632 20 VQRQKVEAQLNENKKALEELEKLA----DDAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKE 95 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcCC----CcchHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334456668888888888888776 3344455556432111 123333444555555666666666666666
Q ss_pred HHHHHHHH
Q 022537 230 KQELIRTL 237 (295)
Q Consensus 230 ~~~~L~~L 237 (295)
++..|+++
T Consensus 96 lk~~l~~~ 103 (105)
T cd00632 96 LQEKIQQA 103 (105)
T ss_pred HHHHHHHH
Confidence 66666554
No 47
>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=74.27 E-value=5.1 Score=30.30 Aligned_cols=46 Identities=22% Similarity=0.259 Sum_probs=35.6
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhh-hhhhhhhhhHhhhccceeccc
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQ-KRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIGLIeK~~ 185 (295)
||.-+....+..-.+.++|+.||+. ..-+++-+..||.-|+|++..
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 4444444556677999999999996 999999999999999999874
No 48
>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=73.89 E-value=39 Score=30.02 Aligned_cols=45 Identities=22% Similarity=0.288 Sum_probs=38.3
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
.+.+.++... +.+...++|+.|++.+=-+.-.++.||.-|+|++.
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 34999999999999999999999999999999876
No 49
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=73.78 E-value=19 Score=33.19 Aligned_cols=50 Identities=12% Similarity=0.324 Sum_probs=39.8
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc-cCceE
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS-KNHIR 190 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~-KN~i~ 190 (295)
.++++...+ ..+.+.++|+.|++.|=-+|-+++-|+..|++++.. .+.|.
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 445554443 349999999999999999999999999999999863 34443
No 50
>PRK10870 transcriptional repressor MprA; Provisional
Probab=72.96 E-value=33 Score=30.14 Aligned_cols=41 Identities=17% Similarity=0.263 Sum_probs=36.6
Q ss_pred HhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 145 QEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 145 ~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
...+++.+...++|+.|++.+=-+-=+++-||.-|||+|..
T Consensus 65 ~~~~~~~it~~eLa~~l~l~~~tvsr~v~rLe~kGlV~R~~ 105 (176)
T PRK10870 65 ESQENHSIQPSELSCALGSSRTNATRIADELEKRGWIERRE 105 (176)
T ss_pred hcCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 34567789999999999999999999999999999999973
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=72.51 E-value=8.9 Score=30.54 Aligned_cols=46 Identities=15% Similarity=0.202 Sum_probs=38.0
Q ss_pred CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCC
Q 022537 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD 195 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~ 195 (295)
....+.-.++|+.+|+.|--+.-+++.||-.|+|++..+ ..|.|..
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~GlI~r~~~--~~~~~~n 89 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARRRIIFRQGM--MGIVGVN 89 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeecC--CceeecC
Confidence 345678899999999999999999999999999997753 3455543
No 52
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=72.20 E-value=41 Score=31.67 Aligned_cols=43 Identities=21% Similarity=0.410 Sum_probs=35.4
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceec
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (295)
++.|.++.+-| .-..+++..|||..--|-+=.-.||--|||+-
T Consensus 18 R~Il~lLt~~p---~yvsEiS~~lgvsqkAVl~HL~~LE~AGlveS 60 (217)
T COG1777 18 RRILQLLTRRP---CYVSEISRELGVSQKAVLKHLRILERAGLVES 60 (217)
T ss_pred HHHHHHHhcCc---hHHHHHHhhcCcCHHHHHHHHHHHHHcCCchh
Confidence 45777787777 55678889999999999999999999998875
No 53
>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=72.16 E-value=18 Score=29.56 Aligned_cols=84 Identities=18% Similarity=0.253 Sum_probs=45.6
Q ss_pred HHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCC------chhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSI 227 (295)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~~E~~LD~lI 227 (295)
+..++..+..-.+-+=..-.|++.+.-+. .+...|+-+|.-...- ..+..++..+..+++.|+.++..|...+
T Consensus 19 ~~~l~~q~~~le~~~~E~~~v~~eL~~l~-~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l 97 (110)
T TIGR02338 19 LQAVATQKQQVEAQLKEAEKALEELERLP-DDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQL 97 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCC-CcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444443344445555666665555 3456666677432111 1233344455556666777777777777
Q ss_pred HHHHHHHHHHh
Q 022537 228 REKQELIRTLE 238 (295)
Q Consensus 228 ~~~~~~L~~Lt 238 (295)
.+++++|+.+.
T Consensus 98 ~e~q~~l~~~~ 108 (110)
T TIGR02338 98 KELQEKIQEAL 108 (110)
T ss_pred HHHHHHHHHHh
Confidence 77777776664
No 54
>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=72.02 E-value=13 Score=28.90 Aligned_cols=38 Identities=32% Similarity=0.519 Sum_probs=32.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
-+.+++.|.+|.+.|...|..+...|+.++.++.++..
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 35678999999999999999999999999988887754
No 55
>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=72.01 E-value=7.8 Score=30.74 Aligned_cols=51 Identities=20% Similarity=0.337 Sum_probs=41.2
Q ss_pred cHHHHHHHHHHHHHhC--CCCceeHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 132 SLGLLTRKFINLIQEA--KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 132 SLglLTkkFI~ll~~a--~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
+|..+.++.+++|++. .+.=+.+++++++|++....|.+++.-|..-|+|=
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 6889999999999872 22349999999999999999999999999999884
No 56
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=71.86 E-value=55 Score=27.02 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=32.3
Q ss_pred ceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+...++|+.+++.+--+--+++.||.-|+|+|..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 35689999999999999999999999999999983
No 57
>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=71.69 E-value=19 Score=31.81 Aligned_cols=45 Identities=22% Similarity=0.271 Sum_probs=37.9
Q ss_pred ceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCc------eEEecCC
Q 022537 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNH------IRWKGSD 195 (295)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~------i~W~G~~ 195 (295)
.+...++|+.++++++-++..+..|+--++|.|...+. +-|+|..
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y~iNP~~~~kG~~ 125 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAYMINPNFFFKGDR 125 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeEEECcHHheeCcH
Confidence 45889999999999999999999999999999986543 3566643
No 58
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=71.32 E-value=7.4 Score=39.53 Aligned_cols=75 Identities=21% Similarity=0.362 Sum_probs=49.5
Q ss_pred hhhhhhhhhhhhHhhhcc-ceeccccCceEEe-cCCCCCCchhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHH
Q 022537 162 EVQKRRIYDITNVLEGIG-LIEKTSKNHIRWK-GSDSLGTSKLDDQVARLKAEIE---SLHAEECRIDDSIREKQELIRT 236 (295)
Q Consensus 162 ~VqKRRIYDItNVLEgIG-LIeK~~KN~i~W~-G~~~s~~~~~~~~~~~Lk~El~---~L~~~E~~LD~lI~~~~~~L~~ 236 (295)
.|.|||=|-|=+-.--+| ||-|..-+..+|. |.-. +...+-+.+||++.+ ++....+.|+.-++.+.+++++
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 578888776655444444 7888888889994 3221 233345667766554 5666677788778888877777
Q ss_pred Hhh
Q 022537 237 LEE 239 (295)
Q Consensus 237 Lte 239 (295)
|..
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=70.72 E-value=30 Score=32.13 Aligned_cols=53 Identities=13% Similarity=0.246 Sum_probs=41.3
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEec
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (295)
.+++|.. ....+.+.++|+.+|+.|=.+|=+++-|+..|++++.........|
T Consensus 33 IL~~l~~-~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~~~Y~lG 85 (274)
T PRK11569 33 LLEWIAE-SNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGELGHWAIG 85 (274)
T ss_pred HHHHHHh-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEecC
Confidence 4555544 3456899999999999999999999999999999986444333345
No 60
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=70.48 E-value=6.9 Score=30.03 Aligned_cols=32 Identities=28% Similarity=0.322 Sum_probs=30.1
Q ss_pred HHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
+.++|+.|+|.+=-++.++..|+.-|+|.+..
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~ 33 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEP 33 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcC
Confidence 56899999999999999999999999999985
No 61
>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=70.37 E-value=11 Score=26.23 Aligned_cols=38 Identities=26% Similarity=0.349 Sum_probs=32.8
Q ss_pred CCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 148 KDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 148 ~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
++..+ ...++|+.+++.+=.+...++-|+.-|+|++..
T Consensus 21 ~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 21 PGDRLPSERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 33344 599999999999999999999999999998764
No 62
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=70.35 E-value=32 Score=31.73 Aligned_cols=54 Identities=22% Similarity=0.217 Sum_probs=44.0
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEec
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (295)
++.++++++ .+.+...++|+.|+|+.+.|.--++.|+.-|+|.+....-+.+.+
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 345677763 468999999999999999999999999999999887555555554
No 63
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=70.35 E-value=4.3 Score=40.02 Aligned_cols=29 Identities=34% Similarity=0.608 Sum_probs=27.1
Q ss_pred HHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
+..+++.++++.||+|||+|-|+.+|+|.
T Consensus 304 y~~~~~~~~~~~~~~~~ii~~L~~lgiv~ 332 (366)
T COG1474 304 YESLCERLRTSQRRFSDIISELEGLGIVS 332 (366)
T ss_pred HHHHHhhhCchHHHHHHHHHHHHhcCeEE
Confidence 67788888999999999999999999999
No 64
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=70.33 E-value=50 Score=27.19 Aligned_cols=31 Identities=10% Similarity=0.059 Sum_probs=26.4
Q ss_pred CceeHHHHHHHhhhhhhhhhhhhhHhhhccc
Q 022537 150 GTLDLNRTAEVLEVQKRRIYDITNVLEGIGL 180 (295)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 180 (295)
+-..+.++|.+|||+.--||-+.+-+..-|+
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 65
>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=70.09 E-value=14 Score=27.35 Aligned_cols=42 Identities=24% Similarity=0.331 Sum_probs=36.7
Q ss_pred HHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 143 LIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 143 ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+.+ .++.+...++|+.|+|.+=-..+.++-|+.-|||+...
T Consensus 15 ~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 15 ELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 3344 88999999999999999999999999999999999764
No 66
>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=69.57 E-value=36 Score=29.72 Aligned_cols=41 Identities=20% Similarity=0.288 Sum_probs=37.1
Q ss_pred CCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccC
Q 022537 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
.|+..+.-.++|+.|||+|=-+=+.+..|+.-|||+...+.
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~ 70 (212)
T TIGR03338 30 PPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNR 70 (212)
T ss_pred CCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCC
Confidence 47888999999999999999999999999999999977543
No 67
>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=69.10 E-value=47 Score=27.42 Aligned_cols=38 Identities=16% Similarity=0.175 Sum_probs=27.7
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEecC
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKGS 194 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G~ 194 (295)
.+.++|..+||..|-| --.|.+|||. ....|.|++-+.
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 5789999999988754 3448999997 445667777543
No 68
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=68.24 E-value=89 Score=27.89 Aligned_cols=41 Identities=27% Similarity=0.305 Sum_probs=38.1
Q ss_pred CCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccC
Q 022537 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
.|+..++.+++|+.|||+|--|=+.+..|+.-|||+.....
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 48999999999999999999999999999999999998444
No 69
>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=67.27 E-value=33 Score=27.58 Aligned_cols=38 Identities=21% Similarity=0.305 Sum_probs=25.1
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhcccee-ccccCceEEec
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE-KTSKNHIRWKG 193 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe-K~~KN~i~W~G 193 (295)
+.+.++|+.+||..+-|- -.|-.|||. ....|.+++-.
T Consensus 2 ~~i~eva~~~gvs~~tlR----~ye~~Gll~~~r~~~g~R~Y~ 40 (102)
T cd04789 2 YTISELAEKAGISRSTLL----YYEKLGLITGTRNANGYRLYP 40 (102)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCcCCCCCeeCC
Confidence 568899999999887442 345567775 23346666654
No 70
>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=66.97 E-value=9.1 Score=28.08 Aligned_cols=52 Identities=23% Similarity=0.293 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHhCCC----------CceeHHHHHHHhhhhhhhhhhhhhHhhhccceecccc
Q 022537 135 LLTRKFINLIQEAKD----------GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 135 lLTkkFI~ll~~a~~----------g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (295)
.++.-|+.++...+. ..+...++|+.+|+.++.+--+++-|+.-|+|+...+
T Consensus 2 Rla~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 2 RLARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp HHHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred hHHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 355666666654321 2457899999999999999999999999999997644
No 71
>PF13518 HTH_28: Helix-turn-helix domain
Probab=66.92 E-value=6.6 Score=26.75 Aligned_cols=37 Identities=14% Similarity=0.339 Sum_probs=30.2
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccc
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL 180 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 180 (295)
.|.++. +|. .+.++|..+||.++.||.++.-++.-|+
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 9999999999999999999999988664
No 72
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=66.86 E-value=37 Score=31.04 Aligned_cols=54 Identities=7% Similarity=0.219 Sum_probs=43.1
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecC
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~ 194 (295)
..++++... +.+.+.++|+.||+.|=-+|-+++.|+..|++++...+.-.+.|.
T Consensus 18 ~IL~~l~~~--~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~ 71 (257)
T PRK15090 18 GILQALGEE--REIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLTL 71 (257)
T ss_pred HHHHHhhcC--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEecH
Confidence 355555433 468999999999999999999999999999999976554445564
No 73
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=66.69 E-value=13 Score=27.75 Aligned_cols=44 Identities=23% Similarity=0.342 Sum_probs=37.0
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
..+.++...+ .+...++|+.+++.+.-++-+++-|+.-|+|++.
T Consensus 14 ~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 14 LVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 3445555443 5889999999999999999999999999999976
No 74
>TIGR02716 C20_methyl_CrtF C-20 methyltransferase BchU. Members of this protein family are the S-adenosylmethionine-depenedent C-20 methyltransferase BchU, part of the pathway of bacteriochlorophyll c production in photosynthetic green sulfur bacteria. The position modified by this enzyme represents the difference between bacteriochlorophylls c and d; strains lacking this protein can only produced bacteriochlorophyll d.
Probab=66.54 E-value=5.2 Score=37.35 Aligned_cols=37 Identities=19% Similarity=0.197 Sum_probs=34.3
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
++...+.++|+++++..|.++-++..|.++|++++..
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~ 57 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED 57 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC
Confidence 3678999999999999999999999999999999864
No 75
>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=65.89 E-value=40 Score=27.47 Aligned_cols=37 Identities=30% Similarity=0.403 Sum_probs=27.6
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEec
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKG 193 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G 193 (295)
.+.++|+.+||..|-| --.|-.|||. +...|.|+|-.
T Consensus 2 ~I~eva~~~gvs~~tL----RyYe~~GLl~p~~r~~~gyR~Y~ 40 (123)
T cd04770 2 KIGELAKAAGVSPDTI----RYYERIGLLPPPQRSENGYRLYG 40 (123)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCCCCCCCCccCC
Confidence 5789999999988855 3367889986 44567777754
No 76
>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=65.43 E-value=34 Score=27.45 Aligned_cols=37 Identities=22% Similarity=0.332 Sum_probs=25.3
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhcccee-ccccCceEEe
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE-KTSKNHIRWK 192 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe-K~~KN~i~W~ 192 (295)
+.+.++|+.+||+.+-| -..|-.||+. ....|.++.-
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 46889999999988866 4456678883 3334555543
No 77
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=65.16 E-value=11 Score=29.53 Aligned_cols=47 Identities=19% Similarity=0.310 Sum_probs=40.9
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
+-++.+.++++. +.+...++|+.+|+...-++..++-|+.-|+|.+.
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 46889999999999999999999999999999954
No 78
>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=65.09 E-value=5.3 Score=26.40 Aligned_cols=22 Identities=32% Similarity=0.548 Sum_probs=20.1
Q ss_pred eeHHHHHHHhhhhhhhhhhhhh
Q 022537 152 LDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItN 173 (295)
+++.++|+.|||.++.||..++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999985
No 79
>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=64.97 E-value=18 Score=26.83 Aligned_cols=35 Identities=26% Similarity=0.303 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 206 ~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
...++.|+..|+.+.+.|.+.+..+++++..|..|
T Consensus 19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~~ 53 (80)
T PF04977_consen 19 YYQLNQEIAELQKEIEELKKENEELKEEIERLKND 53 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 45677778888888888888888888888888333
No 80
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=63.98 E-value=1.1e+02 Score=27.21 Aligned_cols=54 Identities=28% Similarity=0.386 Sum_probs=37.8
Q ss_pred CCcCcHHHHHHHHHHHHH-hCCCCce---------------eHHHHHHHhhh-hhhhhhhhhhHhhhccceec
Q 022537 128 RYDSSLGLLTRKFINLIQ-EAKDGTL---------------DLNRTAEVLEV-QKRRIYDITNVLEGIGLIEK 183 (295)
Q Consensus 128 R~d~SLglLTkkFI~ll~-~a~~g~l---------------dLn~aA~~L~V-qKRRIYDItNVLEgIGLIeK 183 (295)
.++-+...|.++|..+.. -+||... .||+|-..|.= .+|..|++ -|.|+.+...
T Consensus 12 ~~~~d~~~L~~~yr~l~~~~HPDk~~~~~~~~~~~a~~~s~~iN~AY~~L~dp~~Ra~Yll--~l~g~~~~~~ 82 (171)
T PRK05014 12 RYDIDTQLLASRYQELQRQFHPDKFANASERERLLAVQQAATINDAYQTLKHPLKRAEYLL--SLHGFDLAHE 82 (171)
T ss_pred CCCCCHHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHHHHHHHHHHHHCChhHHHHHHH--HhcCCccccc
Confidence 456777889999999875 4565422 37777777876 78999985 5567666544
No 81
>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=63.89 E-value=13 Score=29.89 Aligned_cols=46 Identities=17% Similarity=0.351 Sum_probs=40.1
Q ss_pred HHHHHH--hCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 140 FINLIQ--EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 140 FI~ll~--~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
++.++. .++++.+.+.++|+.+++.+=.+-=+++-||--|+|.|..
T Consensus 30 vL~~l~~~~~~~~~~t~~eL~~~l~~~~stvs~~i~~Le~kg~I~r~~ 77 (109)
T TIGR01889 30 ILYYLGKLENNEGKLTLKEIIKEILIKQSALVKIIKKLSKKGYLSKER 77 (109)
T ss_pred HHHHHHhhhccCCcCcHHHHHHHHCCCHHHHHHHHHHHHHCCCEeccC
Confidence 344444 5677899999999999999999999999999999999874
No 82
>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=63.59 E-value=6.9 Score=31.48 Aligned_cols=37 Identities=19% Similarity=0.337 Sum_probs=34.0
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+.+.+.++|+.+++.+--++=+++-||.-|+|++..
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 83
>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=63.30 E-value=12 Score=27.27 Aligned_cols=36 Identities=25% Similarity=0.389 Sum_probs=28.1
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhh
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLE 176 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLE 176 (295)
+.++++-. .+.+.+.++|+.|+++.|-|..-++-|.
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 46677765 6788999999999999999877666665
No 84
>PRK00215 LexA repressor; Validated
Probab=62.89 E-value=12 Score=32.93 Aligned_cols=43 Identities=16% Similarity=0.200 Sum_probs=37.5
Q ss_pred hCCCCceeHHHHHHHhhh-hhhhhhhhhhHhhhccceeccccCc
Q 022537 146 EAKDGTLDLNRTAEVLEV-QKRRIYDITNVLEGIGLIEKTSKNH 188 (295)
Q Consensus 146 ~a~~g~ldLn~aA~~L~V-qKRRIYDItNVLEgIGLIeK~~KN~ 188 (295)
...+....+.++|+.+++ .|=-++.+++-||.-|+|++.....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~~ 61 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGRS 61 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCCc
Confidence 445667899999999999 9999999999999999999886543
No 85
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=62.86 E-value=42 Score=29.74 Aligned_cols=49 Identities=10% Similarity=0.074 Sum_probs=41.5
Q ss_pred CCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCC
Q 022537 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD 195 (295)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~ 195 (295)
.|+..+...++|+.|||+|-=+=+.+..|+.-|||+.....-+.....+
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~~ 74 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASMS 74 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCCC
Confidence 3788899999999999999999999999999999998766555555443
No 86
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=62.80 E-value=20 Score=32.67 Aligned_cols=37 Identities=24% Similarity=0.251 Sum_probs=34.6
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
..++.|.++++.||++|=++-=.+-+|++.||+.|.-
T Consensus 39 ~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~ 75 (177)
T COG1510 39 RKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVF 75 (177)
T ss_pred CCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhh
Confidence 5678999999999999999999999999999999873
No 87
>PRK09954 putative kinase; Provisional
Probab=62.56 E-value=10 Score=36.03 Aligned_cols=47 Identities=15% Similarity=0.290 Sum_probs=40.8
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
.-++.+.++++.+ .+...++|+.|+|.|..++..++-|+.-|+|++.
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 3456888888554 7999999999999999999999999999999755
No 88
>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=62.48 E-value=15 Score=30.66 Aligned_cols=37 Identities=19% Similarity=0.285 Sum_probs=33.6
Q ss_pred CCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceec
Q 022537 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (295)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (295)
..++.+.+.++|+.+++..+-+..|+..|.--|||.-
T Consensus 21 ~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 21 AETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 3445899999999999999999999999999999974
No 89
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=61.38 E-value=16 Score=30.14 Aligned_cols=41 Identities=12% Similarity=0.227 Sum_probs=35.6
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
-.....++++++.......+++.++|+.+|+.+|.+.-+..
T Consensus 7 ~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk 47 (127)
T PRK11511 7 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFK 47 (127)
T ss_pred cHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 34566789999999998999999999999999999887665
No 90
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.01 E-value=9.2 Score=32.19 Aligned_cols=40 Identities=33% Similarity=0.390 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 134 glLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
++||.|=..++.-.=..-+.|.++|+.++|+|-.|||=++
T Consensus 16 sLLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIK 55 (105)
T COG2739 16 SLLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIK 55 (105)
T ss_pred HHHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHH
Confidence 4788887777765555678999999999999999999765
No 91
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=60.89 E-value=17 Score=33.55 Aligned_cols=54 Identities=24% Similarity=0.397 Sum_probs=44.6
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEec
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (295)
..++++...+.+ +.+.++|+++|+.|=-.|=+++.|+-.|++++...+.-.+.|
T Consensus 8 ~iL~~l~~~~~~-l~l~ela~~~glpksT~~RlL~tL~~~G~v~~d~~~g~Y~Lg 61 (246)
T COG1414 8 AILDLLAEGPGG-LSLAELAERLGLPKSTVHRLLQTLVELGYVEQDPEDGRYRLG 61 (246)
T ss_pred HHHHHHHhCCCC-CCHHHHHHHhCcCHHHHHHHHHHHHHCCCEEEcCCCCcEeeh
Confidence 467777775444 899999999999999999999999999999999876333344
No 92
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=60.74 E-value=37 Score=31.55 Aligned_cols=55 Identities=16% Similarity=0.091 Sum_probs=41.8
Q ss_pred HHHHHHH-hCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEec
Q 022537 139 KFINLIQ-EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (295)
Q Consensus 139 kFI~ll~-~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (295)
+-|.++. ......+...++|+.|++.+..+.-++.-||.-|+|+|.....-+|.-
T Consensus 8 k~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v~ 63 (217)
T PRK14165 8 KKLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLIT 63 (217)
T ss_pred HHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEEE
Confidence 3444443 334456889999999999999999999999999999998543334443
No 93
>PRK06474 hypothetical protein; Provisional
Probab=59.42 E-value=1e+02 Score=27.28 Aligned_cols=47 Identities=17% Similarity=0.347 Sum_probs=39.0
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHh-hhhhhhhhhhhhHhhhccceeccc
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+.++++...+.. +...++++.| ++.+=-+|=.+++|+-.|||++..
T Consensus 14 ~~Il~~L~~~~~~-~ta~el~~~l~~is~aTvYrhL~~L~e~GLI~~~~ 61 (178)
T PRK06474 14 MKICQVLMRNKEG-LTPLELVKILKDVPQATLYRHLQTMVDSGILHVVK 61 (178)
T ss_pred HHHHHHHHhCCCC-CCHHHHHHHhcCCCHHHHHHHHHHHHHCCCEEEee
Confidence 3466777665443 9999999999 789999999999999999999754
No 94
>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=59.40 E-value=85 Score=25.35 Aligned_cols=36 Identities=25% Similarity=0.231 Sum_probs=24.0
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEe
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWK 192 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~ 192 (295)
.+.++|+.+||..|-|.-. |..|||. ....|.+++-
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 5789999999988865322 5678883 3344555543
No 95
>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=59.28 E-value=63 Score=29.16 Aligned_cols=33 Identities=24% Similarity=0.236 Sum_probs=29.2
Q ss_pred eHHHHHHHh-hhhhhhhhhhhhHhhhccceeccc
Q 022537 153 DLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 153 dLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.=..+|..+ |+.-|.|.=.+..|...|||.+..
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 346788888 999999999999999999999864
No 96
>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=59.19 E-value=77 Score=24.59 Aligned_cols=80 Identities=13% Similarity=0.311 Sum_probs=35.1
Q ss_pred HHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCC-CCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 156 RTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSL-GTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELI 234 (295)
Q Consensus 156 ~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s-~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L 234 (295)
.+...+.--.+.+..+.-|++-+..+. .+.-.|.+.+.. -....+.-+..|+++++.+..+...|...+..+..+|
T Consensus 16 ~~~~q~~~l~~~~~~~~~~~~eL~~l~---~~~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l 92 (106)
T PF01920_consen 16 QLEQQIQQLERQLRELELTLEELEKLD---DDRKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKL 92 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHTSS---TT-EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhCC---CcchhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333334444444444443 334556444321 1112333344555555555555555555555555555
Q ss_pred HHHh
Q 022537 235 RTLE 238 (295)
Q Consensus 235 ~~Lt 238 (295)
.++.
T Consensus 93 ~~~~ 96 (106)
T PF01920_consen 93 KELK 96 (106)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 5543
No 97
>PRK11050 manganese transport regulator MntR; Provisional
Probab=59.15 E-value=30 Score=29.72 Aligned_cols=42 Identities=19% Similarity=0.148 Sum_probs=36.0
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceE
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (295)
++.+.+.++|+.|+|.+--+..+++-||.-|+|.+.....+.
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 98
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=59.08 E-value=94 Score=29.17 Aligned_cols=52 Identities=13% Similarity=0.175 Sum_probs=40.1
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCc
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNH 188 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~ 188 (295)
.--.+.++++++.+ .+.+.++|+.|+|+.+=|.==+..||.-|++.|.....
T Consensus 17 eR~~~Il~~L~~~~--~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GGa 68 (269)
T PRK09802 17 ERREQIIQRLRQQG--SVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGA 68 (269)
T ss_pred HHHHHHHHHHHHcC--CEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCCE
Confidence 34455777777543 49999999999998877765566789999999886554
No 99
>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=58.88 E-value=29 Score=31.54 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=37.5
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
.++++..+ ...+.+.++|+.+|+.|=.+|-+++-|+..|++++.
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 45555443 456899999999999999999999999999999985
No 100
>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=58.88 E-value=4.9 Score=32.78 Aligned_cols=49 Identities=29% Similarity=0.475 Sum_probs=36.2
Q ss_pred eEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 189 IRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 189 i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
..|.|.+ +.+++..+..|..+++.|..+-..|...+..++.+|..+.+.
T Consensus 13 ~~~rGYd---~~eVD~fl~~l~~~~~~l~~e~~~L~~~~~~l~~~l~~~~~~ 61 (131)
T PF05103_consen 13 KSMRGYD---PDEVDDFLDELAEELERLQRENAELKEEIEELQAQLEELREE 61 (131)
T ss_dssp EEEEEEE---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCT-------
T ss_pred CCCCCcC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhhhhH
Confidence 5788987 468888999999999999998888888888888887777543
No 101
>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=58.75 E-value=75 Score=26.22 Aligned_cols=84 Identities=15% Similarity=0.173 Sum_probs=0.0
Q ss_pred eeHHHHHHHhhhhhh--hhhhhhhHhhhcccee--ccccCceEEe----------------------------cCCCCCC
Q 022537 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLIE--KTSKNHIRWK----------------------------GSDSLGT 199 (295)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIe--K~~KN~i~W~----------------------------G~~~s~~ 199 (295)
+.+.++|..+||+.+ |.| |.+|||. +...|.|++- .......
T Consensus 1 m~IgevA~~~gvs~~tLRyY------e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~ 74 (127)
T cd04784 1 MKIGELAKKTGCSVETIRYY------EKEGLLPAPARSANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDDPE 74 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHH------HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhcCC
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022537 200 SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (295)
Q Consensus 200 ~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~ 241 (295)
.........|+..++.|+++-.+|.++...++..+.....+.
T Consensus 75 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~~~ 116 (127)
T cd04784 75 ASCAEVNALIDEHLAHVRARIAELQALEKQLQALRERCDGAR 116 (127)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCC
No 102
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=58.07 E-value=7.5 Score=32.64 Aligned_cols=33 Identities=27% Similarity=0.473 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
.|...|++.+. ++.+.+|+.|||++.+|-.|+|
T Consensus 13 iL~eeflep~g------lt~~~lA~~lgV~r~~is~lin 45 (104)
T COG3093 13 ILREEFLEPLG------LTQTELAEALGVTRNTISELIN 45 (104)
T ss_pred HHHHHHhcccc------CCHHHHHHHhCCCHHHHHHHHc
Confidence 45577777653 8899999999999999999998
No 103
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=57.70 E-value=17 Score=27.78 Aligned_cols=44 Identities=27% Similarity=0.326 Sum_probs=35.8
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
++..+...++... .++|+.|++.+=-+.-+++-||.-|+|++..
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 4444445554444 9999999999999999999999999999884
No 104
>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=57.66 E-value=22 Score=31.62 Aligned_cols=46 Identities=22% Similarity=0.324 Sum_probs=38.5
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecccc
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (295)
+.+.++.+. +.+.+.++|+.+++.+-.++-.++-|+..|+|++..+
T Consensus 147 ~IL~~l~~~--g~~s~~eia~~l~is~stv~r~L~~Le~~GlI~r~~~ 192 (203)
T TIGR01884 147 KVLEVLKAE--GEKSVKNIAKKLGKSLSTISRHLRELEKKGLVEQKGR 192 (203)
T ss_pred HHHHHHHHc--CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEcC
Confidence 344455433 5689999999999999999999999999999999863
No 105
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=57.20 E-value=22 Score=27.97 Aligned_cols=39 Identities=18% Similarity=0.212 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
.+..+++.++.+.....+++.++|+.+++++|.+.-+..
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~ 43 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFR 43 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 456788999998888899999999999999999887665
No 106
>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=57.01 E-value=1.2e+02 Score=26.51 Aligned_cols=32 Identities=31% Similarity=0.478 Sum_probs=24.9
Q ss_pred cHHHHHHHHHHHHHhCCCCceeHHHHHHHhhh
Q 022537 132 SLGLLTRKFINLIQEAKDGTLDLNRTAEVLEV 163 (295)
Q Consensus 132 SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~V 163 (295)
+|..|+..|.+++.-..++..|-..+++.|.-
T Consensus 2 ~LYel~~~~~~l~~~~e~~~~d~e~~~dtLe~ 33 (162)
T PF05565_consen 2 KLYELTDEYLELLELLEEGDLDEEAIADTLES 33 (162)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHH
Confidence 68889999999998776666887777666654
No 107
>PRK09343 prefoldin subunit beta; Provisional
Probab=54.55 E-value=42 Score=28.15 Aligned_cols=85 Identities=15% Similarity=0.216 Sum_probs=50.9
Q ss_pred HHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCC------chhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSI 227 (295)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~~E~~LD~lI 227 (295)
+..+......-.+.+=..-.|++.+..+.- +-.-|+-.|.=.... ..+..++..+..+++.|+.++..|.+.+
T Consensus 23 l~~~~~q~~~le~q~~e~~~~~~EL~~L~~-d~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ie~~ik~lekq~~~l~~~l 101 (121)
T PRK09343 23 LERLLQQKSQIDLELREINKALEELEKLPD-DTPIYKIVGNLLVKVDKTKVEKELKERKELLELRSRTLEKQEKKLREKL 101 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCC-cchhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333444456667777766652 233344455321111 1344455566777888888899999999
Q ss_pred HHHHHHHHHHhh
Q 022537 228 REKQELIRTLEE 239 (295)
Q Consensus 228 ~~~~~~L~~Lte 239 (295)
.+++.+|+++..
T Consensus 102 ~e~q~~l~~ll~ 113 (121)
T PRK09343 102 KELQAKINEMLS 113 (121)
T ss_pred HHHHHHHHHHHH
Confidence 999999988875
No 108
>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=54.24 E-value=50 Score=25.09 Aligned_cols=38 Identities=11% Similarity=0.330 Sum_probs=28.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
+..+..+.+.+..|+.....++..|..+..+|..+.++
T Consensus 12 e~~l~~~~~~i~~lE~~~~~~e~~i~~~~~~l~~I~~n 49 (71)
T PF10779_consen 12 ETKLDNHEERIDKLEKRDAANEKDIKNLNKQLEKIKSN 49 (71)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455566677788888888888889899999888753
No 109
>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=53.96 E-value=21 Score=31.30 Aligned_cols=49 Identities=18% Similarity=0.291 Sum_probs=39.4
Q ss_pred HHHHHHHH---hCCCCceeHHHHHHHhhhh-hhhhhhhhhHhhhccceecccc
Q 022537 138 RKFINLIQ---EAKDGTLDLNRTAEVLEVQ-KRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 138 kkFI~ll~---~a~~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIGLIeK~~K 186 (295)
++.++++. ...+....+.++|+.|++. +=-++..++.||..|+|++...
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 34555555 3344557899999999998 9999999999999999999753
No 110
>KOG3026 consensus Splicing factor SPF30 [RNA processing and modification]
Probab=53.87 E-value=63 Score=31.09 Aligned_cols=71 Identities=17% Similarity=0.196 Sum_probs=54.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccHhhhhcCC---------CCCCCeEEEEeCCCCCeEEecCCCC
Q 022537 213 IESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDIASLP---------CFQNQTLIAIKAPQASYIEVPDPDE 283 (295)
Q Consensus 213 l~~L~~~E~~LD~lI~~~~~~L~~Lted~~n~~~aYVT~eDI~~i~---------~f~~qTviAIKAP~gT~LEVPdP~e 283 (295)
-++|...|..|+++|.--.+-|+.-.++..+..++||+.+-+++-+ .|.+..+-|++=+.|+.+.++-++.
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 4678889999999998666666666666667789999988777632 2456778888999999999987744
No 111
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=52.98 E-value=20 Score=31.58 Aligned_cols=38 Identities=16% Similarity=0.239 Sum_probs=34.6
Q ss_pred CCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
..++.+.+.++|+.+++.++-+..|++-|.--|||.-.
T Consensus 21 ~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 21 SEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 34568999999999999999999999999999999954
No 112
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=52.74 E-value=23 Score=29.23 Aligned_cols=59 Identities=10% Similarity=0.159 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccH---hhhhcCCCCCCCeEEEEeCCC
Q 022537 207 ARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTE---EDIASLPCFQNQTLIAIKAPQ 272 (295)
Q Consensus 207 ~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~n~~~aYVT~---eDI~~i~~f~~qTviAIKAP~ 272 (295)
..++++++.++++-++|.+....++.++..|.++. .|+.+ +++.= .-.|+++|-|.-|.
T Consensus 30 ~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~-----dyiEe~AR~~Lg~--vk~gEivy~~~~~~ 91 (105)
T PRK00888 30 WRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQ-----EAIEERARNELGM--VKPGETFYRIVPDA 91 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcH-----HHHHHHHHHHcCC--CCCCCEEEEeCCCC
Confidence 34444444444444444444445555555554431 13222 22211 23577777766553
No 113
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=52.73 E-value=1.3e+02 Score=25.82 Aligned_cols=76 Identities=20% Similarity=0.257 Sum_probs=0.0
Q ss_pred eeHHHHHHHhhhhhh--hhhhhhhHhhhccce--eccccCceEEe-----------------cCCCCCCchhHHHHHHH-
Q 022537 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLI--EKTSKNHIRWK-----------------GSDSLGTSKLDDQVARL- 209 (295)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLI--eK~~KN~i~W~-----------------G~~~s~~~~~~~~~~~L- 209 (295)
+.+.++|...||+.| |.|| -+||| .+...|.|++- |+. +.+-..-+
T Consensus 8 ~~IgevAk~~Gvs~~TLRyYE------~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I~~lr~~G~s------L~eI~~ll~ 75 (144)
T PRK13752 8 LTIGVFAKAAGVNVETIRFYQ------RKGLLPEPDKPYGSIRRYGEADVTRVRFVKSAQRLGFS------LDEIAELLR 75 (144)
T ss_pred ccHHHHHHHHCcCHHHHHHHH------HCCCCCCCccCCCCCeecCHHHHHHHHHHHHHHHcCCC------HHHHHHHHh
Q ss_pred -------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 210 -------KAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 210 -------k~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
..-.+-|.++...|++.|.++++....|..
T Consensus 76 ~~~~~~~~~~~~ll~~k~~~l~~~i~~L~~~~~~L~~ 112 (144)
T PRK13752 76 LEDGTHCEEASSLAEHKLKDVREKMADLARMEAVLSE 112 (144)
T ss_pred ccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 114
>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=52.19 E-value=18 Score=28.88 Aligned_cols=41 Identities=17% Similarity=0.473 Sum_probs=33.6
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
|.+-+-++ ++.+.+.++|..|++.+++++++ |...|++-+.
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 66666544 48999999999999999999986 5668888884
No 115
>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=52.16 E-value=17 Score=32.91 Aligned_cols=43 Identities=28% Similarity=0.367 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhh
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEG 177 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEg 177 (295)
.+..+|+.++.+.....+.|.++|+.++++++.+..+..-..|
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G 228 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSA 228 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 4668899999988888999999999999999999988765443
No 116
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=51.77 E-value=21 Score=33.05 Aligned_cols=48 Identities=17% Similarity=0.268 Sum_probs=39.4
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccC
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
++.++++. ..+.+.+.++|+.|+|++.-|+--++.||..|+|.|...+
T Consensus 8 ~~Il~~l~--~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~gg 55 (251)
T PRK13509 8 QILLELLA--QLGFVTVEKVIERLGISPATARRDINKLDESGKLKKVRNG 55 (251)
T ss_pred HHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCC
Confidence 34566666 4689999999999999999888889999999999886433
No 117
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=51.74 E-value=1.8e+02 Score=26.17 Aligned_cols=54 Identities=20% Similarity=0.302 Sum_probs=42.8
Q ss_pred cHH-HHHHHHHHHHHh---CCCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 132 SLG-LLTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 132 SLg-lLTkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
++. .+...+.+.+.. .|+..+ .-.++|+.|||+|=-+-+.+..|+..|||+...
T Consensus 10 ~~~~~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~lgVSRtpVREAL~~L~~eGlv~~~~ 68 (254)
T PRK09464 10 KLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQ 68 (254)
T ss_pred cHHHHHHHHHHHHHHcCCCCCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 444 344556666643 367777 899999999999999999999999999998663
No 118
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=51.52 E-value=1.5e+02 Score=25.08 Aligned_cols=87 Identities=22% Similarity=0.253 Sum_probs=0.0
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEe-----------------cCCC----------CCCchh
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWK-----------------GSDS----------LGTSKL 202 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~-----------------G~~~----------s~~~~~ 202 (295)
+.+.++|..+||..+-|--. |.+|||. +...|.|++- |+.. ......
T Consensus 1 m~Ige~a~~~gvs~~tLRyY----E~~GLl~p~~r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~~~~~~~~ 76 (131)
T cd04786 1 MKIGELAKRSGMAASRIRFY----EAEGLLSSVERSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPADASNWQH 76 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccCCCCH
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENEN 242 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~ 242 (295)
......|+..++.+..+.++|.++...+...+..+..++.
T Consensus 77 ~~~~~~l~~k~~~i~~~i~~L~~~~~~L~~~i~~~~~~~~ 116 (131)
T cd04786 77 DELLAALERKVADIEALEARLAQNKAQLLVLIDLIESKPD 116 (131)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
No 119
>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=51.24 E-value=39 Score=32.77 Aligned_cols=35 Identities=31% Similarity=0.490 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022537 207 ARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (295)
Q Consensus 207 ~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~ 241 (295)
..|.+|++.|+.++.+|++.|..++.++..+.+.+
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 44556677888888888888888888877776543
No 120
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=51.22 E-value=26 Score=29.44 Aligned_cols=41 Identities=17% Similarity=0.265 Sum_probs=35.9
Q ss_pred hCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecccc
Q 022537 146 EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 146 ~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (295)
..++..+...++|+.++|.+.-+-.|+..|+.-|||+....
T Consensus 20 ~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~Glv~s~~G 60 (141)
T PRK11014 20 LPEGRMTSISEVTEVYGVSRNHMVKIINQLSRAGYVTAVRG 60 (141)
T ss_pred CCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhCCEEEEecC
Confidence 34566889999999999999999999999999999986643
No 121
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=51.09 E-value=47 Score=29.93 Aligned_cols=50 Identities=24% Similarity=0.331 Sum_probs=40.8
Q ss_pred HHHHHHHHHh---CCCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceecccc
Q 022537 137 TRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 137 TkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (295)
...+.+.+.. .|+..+ .-.++|+.|||+|==+-+.+..|+..|||+....
T Consensus 13 ~~~i~~~I~~g~l~pG~~LPsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~~ 66 (251)
T PRK09990 13 AERIERLIVDGVLKVGQALPSERRLCEKLGFSRSALREGLTVLRGRGIIETAQG 66 (251)
T ss_pred HHHHHHHHHcCCCCCCCcCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeCC
Confidence 3444444433 478888 8999999999999999999999999999987644
No 122
>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=50.97 E-value=22 Score=29.87 Aligned_cols=36 Identities=8% Similarity=0.314 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhh
Q 022537 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIY 169 (295)
Q Consensus 134 glLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIY 169 (295)
..+..-|++|+.+.+=..+.++++|++-||.|.-+|
T Consensus 6 ~~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY 41 (176)
T TIGR02366 6 KKIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHH
Confidence 356778999999999999999999999999999887
No 123
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=50.76 E-value=20 Score=34.63 Aligned_cols=52 Identities=29% Similarity=0.473 Sum_probs=41.5
Q ss_pred CcHHHHHH-HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 131 SSLGLLTR-KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 131 ~SLglLTk-kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
++|+..++ ..++++. ..+.+++|++|+.||..+--+--=+.|||-.|||+-.
T Consensus 18 kalaS~vRv~Il~lL~--~k~plNvneiAe~lgLpqst~s~~ik~Le~aGlirT~ 70 (308)
T COG4189 18 KALASKVRVAILQLLH--RKGPLNVNEIAEALGLPQSTMSANIKVLEKAGLIRTE 70 (308)
T ss_pred HHHHHHHHHHHHHHHH--HhCCCCHHHHHHHhCCchhhhhhhHHHHHhcCceeee
Confidence 45555553 4556664 4577999999999999999999999999999999854
No 124
>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=50.37 E-value=21 Score=23.24 Aligned_cols=23 Identities=22% Similarity=0.232 Sum_probs=19.9
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhH
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNV 174 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNV 174 (295)
+.+.++|+.|+|.++-||..+.-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 36789999999999999988764
No 125
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=50.09 E-value=54 Score=28.14 Aligned_cols=71 Identities=17% Similarity=0.287 Sum_probs=41.0
Q ss_pred hhhhhHhhhccceeccccCceEEecCCCCCC------chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 169 YDITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 169 YDItNVLEgIGLIeK~~KN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
-+|.-||+-+..+.--. .-|+-.|.=.... .++..+..-|.-++.-|+.+|+.|++.+..++..|+.+..+
T Consensus 37 ~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 37 KEIEKALEELEKLDEDA-PVYKKVGNLLVKVSKEEAVDELEERKETLELRIKTLEKQEEKLQERLEELQSEIQKALGD 113 (119)
T ss_pred HHHHHHHHHHhcCCccc-HHHHHhhhHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 35677777777666442 3344455322111 12333344455556677777777777777777777776654
No 126
>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=50.04 E-value=1.2e+02 Score=25.36 Aligned_cols=37 Identities=22% Similarity=0.251 Sum_probs=26.0
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEec
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKG 193 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G 193 (295)
.+.++|+.+||..+-| -..|.+||+. +...|.|++-.
T Consensus 2 ~I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~ 40 (127)
T TIGR02047 2 KIGELAQKTGVSVETI----RFYEKQGLLPPPARTDNNYRVYT 40 (127)
T ss_pred cHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCCCcCC
Confidence 4788999999987744 2346778884 45567777754
No 127
>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=49.73 E-value=61 Score=24.60 Aligned_cols=57 Identities=23% Similarity=0.315 Sum_probs=47.9
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEe
Q 022537 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (295)
+-.+.+++|....+...---..+..|.+.|+.|==++.=|+.=|.|.|.+-+--.|.
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 456778888877777777778888999999999999999999999999988888884
No 128
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=49.54 E-value=43 Score=25.37 Aligned_cols=52 Identities=21% Similarity=0.408 Sum_probs=37.7
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc--cCc-eEEe
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS--KNH-IRWK 192 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~--KN~-i~W~ 192 (295)
.+++++.. ++.+.-.++|+.+++.+-..-=+++.||.-|.|++.. +.. ..|.
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 45566543 5568899999999999888888999999999999632 222 4684
No 129
>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=49.38 E-value=27 Score=27.19 Aligned_cols=43 Identities=16% Similarity=0.322 Sum_probs=36.2
Q ss_pred HHHhCCCCceeHHHHHHHh-hhhhhhhhhhhhHhhhccceeccc
Q 022537 143 LIQEAKDGTLDLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 143 ll~~a~~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
++..-..|....+++.+.+ +++.+=+.+=+..|+..|||+|..
T Consensus 10 IL~~l~~g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 10 ILRALFQGPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHHHHTTSSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHHhCCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhccc
Confidence 3334444899999999999 999999999999999999999984
No 130
>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=49.12 E-value=34 Score=27.12 Aligned_cols=45 Identities=24% Similarity=0.469 Sum_probs=38.0
Q ss_pred HHHHHHhCCCCceeHHHHHHHh-----hhhhhhhhhhhhHhhhccceeccc
Q 022537 140 FINLIQEAKDGTLDLNRTAEVL-----EVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L-----~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.++++..+ +..++..++.+.| .+.+=-+|=+++.|+..|+|.+..
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 45666655 5778999999998 588999999999999999999874
No 131
>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=48.97 E-value=1.3e+02 Score=24.88 Aligned_cols=37 Identities=22% Similarity=0.255 Sum_probs=27.0
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhccceec--cccCceEEec
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEK--TSKNHIRWKG 193 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~~KN~i~W~G 193 (295)
.+.++|+.+||..+-|. ..|-.|||.. ...|.|++-.
T Consensus 2 ~I~e~a~~~gvs~~tlR----yYe~~GLl~p~~r~~~gyR~Y~ 40 (127)
T TIGR02044 2 NIGQVAKLTGLSSKMIR----YYEEKGLIPPPLRSEGGYRTYT 40 (127)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCCeecC
Confidence 57899999999887553 4567888864 4567777754
No 132
>PRK14127 cell division protein GpsB; Provisional
Probab=48.88 E-value=51 Score=27.74 Aligned_cols=55 Identities=16% Similarity=0.280 Sum_probs=35.6
Q ss_pred ceeccccCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 180 LIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 180 LIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
+..|.=+. .++|.+ ..+++.-+..+-.+.+.|..+-.+|.+.+..++++|.++..
T Consensus 11 I~~KeF~~--~~RGYd---~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 11 ILEKEFKT--SMRGYD---QDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred HhhCccCC--CCCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444333 346876 45677777777777777777777777777777777766654
No 133
>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=48.44 E-value=60 Score=25.30 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=16.3
Q ss_pred eHHHHHHHhhhhhhhhhhhhh
Q 022537 153 DLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItN 173 (295)
.+.++|+.+||..+.|--+.+
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 578899999998877766644
No 134
>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=48.31 E-value=67 Score=28.65 Aligned_cols=28 Identities=29% Similarity=0.431 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 208 RLKAEIESLHAEECRIDDSIREKQELIR 235 (295)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~~~L~ 235 (295)
.++.+|..|..+-..||+.|+.+..+|.
T Consensus 26 ~~~~~I~~L~~e~~~ld~~i~~~~~~L~ 53 (188)
T PF10018_consen 26 ENQARIQQLRAEIEELDEQIRDILKQLK 53 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555555555444443
No 135
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=47.63 E-value=52 Score=29.39 Aligned_cols=39 Identities=18% Similarity=0.244 Sum_probs=33.6
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceE
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (295)
+.-.++|..||+++..+.=+++-|+--|+|+..+.++|.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 345899999999999999999999999999877555554
No 136
>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=47.46 E-value=64 Score=23.80 Aligned_cols=31 Identities=29% Similarity=0.530 Sum_probs=26.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQ 231 (295)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~ 231 (295)
....+++.|+.+++.|..+-+.|.+.|..++
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~ 51 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERLK 51 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4556788899999999999999999999883
No 137
>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=47.38 E-value=52 Score=26.18 Aligned_cols=59 Identities=29% Similarity=0.490 Sum_probs=46.1
Q ss_pred CcHHHHHHHHHHHHHhC-CCCceeHHHHHHHhhhhhhhhhhhhh-HhhhccceeccccCce
Q 022537 131 SSLGLLTRKFINLIQEA-KDGTLDLNRTAEVLEVQKRRIYDITN-VLEGIGLIEKTSKNHI 189 (295)
Q Consensus 131 ~SLglLTkkFI~ll~~a-~~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~~KN~i 189 (295)
.-|..+=++++..+.+. .+|.+-|+.+|..|+..+.-|=|++- -|--.|+|+|+.+.++
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 34556778899988765 88999999999999999999988775 5778999999988764
No 138
>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=47.15 E-value=1.9e+02 Score=25.01 Aligned_cols=55 Identities=18% Similarity=0.266 Sum_probs=32.4
Q ss_pred HHHHHHhCCCCceeHHHHHHHh--hhhhhhhhhhhhHhhhcccee-cc-ccCceEEecCC
Q 022537 140 FINLIQEAKDGTLDLNRTAEVL--EVQKRRIYDITNVLEGIGLIE-KT-SKNHIRWKGSD 195 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L--~VqKRRIYDItNVLEgIGLIe-K~-~KN~i~W~G~~ 195 (295)
.++||. ..+.++..+.+..-| +|.|=-+==++.-|..=|.|. |. +|-.|.|.--+
T Consensus 6 Il~y~~-~qNRPys~~di~~nL~~~~~K~~v~k~Ld~L~~~g~i~~K~~GKqkiY~~~Q~ 64 (169)
T PF07106_consen 6 ILEYMK-EQNRPYSAQDIFDNLHNKVGKTAVQKALDSLVEEGKIVEKEYGKQKIYFANQD 64 (169)
T ss_pred HHHHHH-HcCCCCcHHHHHHHHHhhccHHHHHHHHHHHHhCCCeeeeeecceEEEeeCcc
Confidence 455664 445677888888888 466655444444454445444 33 56677775433
No 139
>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=46.88 E-value=35 Score=31.22 Aligned_cols=47 Identities=23% Similarity=0.376 Sum_probs=34.1
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
+-..||+|++.+ -++.|+++|..+|+.-==+-|-++-|+..|.|+=.
T Consensus 100 lL~~Fi~yIK~~--Kvv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv 146 (188)
T PF09756_consen 100 LLQEFINYIKEH--KVVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGV 146 (188)
T ss_dssp HHHHHHHHHHH---SEE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EE
T ss_pred HHHHHHHHHHHc--ceeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceee
Confidence 778899999966 58999999999999766666777778887766543
No 140
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=46.77 E-value=38 Score=27.97 Aligned_cols=51 Identities=24% Similarity=0.344 Sum_probs=42.9
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
|-.+=.+-+++++. ++...+.++|+++|++...+...+.-||.-|+|.+..
T Consensus 6 lD~~D~~IL~~L~~--d~r~~~~eia~~lglS~~~v~~Ri~~L~~~GiI~~~~ 56 (154)
T COG1522 6 LDDIDRRILRLLQE--DARISNAELAERVGLSPSTVLRRIKRLEEEGVIKGYT 56 (154)
T ss_pred ccHHHHHHHHHHHH--hCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCceeeEE
Confidence 34455678888874 3449999999999999999999999999999999873
No 141
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=46.69 E-value=71 Score=29.48 Aligned_cols=86 Identities=16% Similarity=0.238 Sum_probs=51.7
Q ss_pred CcHHHHHHHHHHHHHhCCCCceeHHH-----------HHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCC
Q 022537 131 SSLGLLTRKFINLIQEAKDGTLDLNR-----------TAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT 199 (295)
Q Consensus 131 ~SLglLTkkFI~ll~~a~~g~ldLn~-----------aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~ 199 (295)
..+....++..+++....+.+..-+. +.-.+.|..-++-+.++-|+++|-+.-..-+ ..
T Consensus 59 ~d~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~g~v~~~~~~-----~~----- 128 (262)
T PF14257_consen 59 KDVEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSELGKVTSRNIS-----SE----- 128 (262)
T ss_pred CCHHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhccCceeeeecc-----cc-----
Confidence 44556667777777766655544433 3456788899999999999999977655322 11
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 200 SKLDDQVARLKAEIESLHAEECRIDDSI 227 (295)
Q Consensus 200 ~~~~~~~~~Lk~El~~L~~~E~~LD~lI 227 (295)
++..+...+++.++.|+.++++|-+++
T Consensus 129 -DvT~~y~D~~arl~~l~~~~~rl~~ll 155 (262)
T PF14257_consen 129 -DVTEQYVDLEARLKNLEAEEERLLELL 155 (262)
T ss_pred -chHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 233333444445555555444444443
No 142
>PHA01750 hypothetical protein
Probab=46.59 E-value=55 Score=25.87 Aligned_cols=31 Identities=23% Similarity=0.409 Sum_probs=19.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 204 DQVARLKAEIESLHAEECRIDDSIREKQELI 234 (295)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L 234 (295)
..+.+|+.|++++....+.|.+++.++...+
T Consensus 42 ~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 42 SELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 3455666677777666666666666655443
No 143
>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=46.19 E-value=84 Score=23.66 Aligned_cols=39 Identities=21% Similarity=0.477 Sum_probs=26.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
+++..+..+...+..++.+-..|-+-|..+.+.++.|..
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 455566666666777777777777777777777776654
No 144
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=45.92 E-value=63 Score=33.01 Aligned_cols=49 Identities=27% Similarity=0.422 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHhCC--CCceeHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 134 GLLTRKFINLIQEAK--DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 134 glLTkkFI~ll~~a~--~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
..|-+.|+.|++... ...+.|.++|+.|++++|-.==|++-|+..|.|+
T Consensus 4 ~~~~~~~~~L~~~~~~~~~~~~l~~la~~l~cs~R~~~~~l~~~~~~gwl~ 54 (552)
T PRK13626 4 ARLQQQFIRLWQCCEGKSQETTLNELAELLNCSRRHMRTLLNTMQQRGWLT 54 (552)
T ss_pred hHHHHHHHHHHHhcCCCcceeeHHHHHHHhcCChhHHHHHHHHHHHCCCee
Confidence 356778999987653 5578999999999999999999999999999876
No 145
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=45.92 E-value=30 Score=26.43 Aligned_cols=42 Identities=19% Similarity=0.199 Sum_probs=32.5
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEE
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W 191 (295)
.+.....+++...++.-.++..+++-|+.-|||++ ..+.|.-
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 67788999999999999999999999999999966 4555544
No 146
>PRK03837 transcriptional regulator NanR; Provisional
Probab=45.90 E-value=52 Score=29.25 Aligned_cols=51 Identities=12% Similarity=0.244 Sum_probs=41.7
Q ss_pred HHHHHHHHHHh---CCCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceecccc
Q 022537 136 LTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 136 LTkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (295)
+-..+.+.+.. .|+..+ ...++|++|||+|-=+=+.+..|+.-|||+...+
T Consensus 18 v~~~l~~~I~~g~l~pG~~Lp~E~~Lae~~gVSRt~VREAL~~L~~eGlv~~~~~ 72 (241)
T PRK03837 18 VEERLEQMIRSGEFGPGDQLPSERELMAFFGVGRPAVREALQALKRKGLVQISHG 72 (241)
T ss_pred HHHHHHHHHHhCCCCCCCCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 44555555543 367778 8999999999999999999999999999997643
No 147
>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=45.73 E-value=41 Score=27.11 Aligned_cols=49 Identities=22% Similarity=0.393 Sum_probs=39.3
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhh-----hhhhhhhhhhhHhhhccceeccccC
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLE-----VQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~-----VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
...++++.+++. .++.+++.+.|. +.+=-||-.++.|+..|+|.|...+
T Consensus 11 ~~Il~~l~~~~~-~~ta~ei~~~l~~~~~~is~~TVYR~L~~L~e~Gli~~~~~~ 64 (120)
T PF01475_consen 11 LAILELLKESPE-HLTAEEIYDKLRKKGPRISLATVYRTLDLLEEAGLIRKIEFG 64 (120)
T ss_dssp HHHHHHHHHHSS-SEEHHHHHHHHHHTTTT--HHHHHHHHHHHHHTTSEEEEEET
T ss_pred HHHHHHHHcCCC-CCCHHHHHHHhhhccCCcCHHHHHHHHHHHHHCCeEEEEEcC
Confidence 347788887777 899999999985 4444699999999999999998644
No 148
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=45.53 E-value=89 Score=26.09 Aligned_cols=38 Identities=16% Similarity=0.202 Sum_probs=33.9
Q ss_pred CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.++.+.+.++|+.|+|.+=-+--+++-|+.-|+|.+..
T Consensus 19 ~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 19 EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec
Confidence 44667899999999999999999999999999999663
No 149
>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=45.39 E-value=19 Score=25.42 Aligned_cols=24 Identities=29% Similarity=0.512 Sum_probs=19.8
Q ss_pred CceeHHHHHHHhhhhhhhhhhhhh
Q 022537 150 GTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
..++++++++.+|+++.-||..++
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 468899999999999999999987
No 150
>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=44.59 E-value=53 Score=26.25 Aligned_cols=46 Identities=24% Similarity=0.307 Sum_probs=37.2
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
+-.|+++.+. +..|-=..+|+.|++.-=-|..+.-.||.+|||++.
T Consensus 11 ~alV~~Y~~~-~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 11 KALVELYIET-GEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHhc-CCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 4455666433 667888888999999888899999999999999975
No 151
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.96 E-value=39 Score=32.88 Aligned_cols=46 Identities=26% Similarity=0.281 Sum_probs=39.2
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccc
Q 022537 199 TSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQ 244 (295)
Q Consensus 199 ~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~n~ 244 (295)
+++-...++.|++||..|+..-..-|++|-+-..+|-+|.-|.+++
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 3445566899999999999999999999999999999999885554
No 152
>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=43.93 E-value=46 Score=30.59 Aligned_cols=56 Identities=23% Similarity=0.431 Sum_probs=40.7
Q ss_pred CcHHHHH------HHHHHHHHhCCCC-ceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCce
Q 022537 131 SSLGLLT------RKFINLIQEAKDG-TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (295)
Q Consensus 131 ~SLglLT------kkFI~ll~~a~~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i 189 (295)
+-||.++ ...++++....+. .++++++++..++.+ -||+..|+.+|++.....+++
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 4567766 3367777766664 899999999999964 699999999999998765544
No 153
>PHA00738 putative HTH transcription regulator
Probab=43.31 E-value=1e+02 Score=26.07 Aligned_cols=72 Identities=19% Similarity=0.266 Sum_probs=49.1
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCchhHHHHHHHHHHHHHH
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESL 216 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L 216 (295)
++.+.+|... +.+...++++.|++.+=.|-==+.||+..|||+........+--.... ....+.|..|++-.
T Consensus 15 r~IL~lL~~~--e~~~V~eLae~l~lSQptVS~HLKvLreAGLV~srK~Gr~vyY~Ln~~-----~~~~~l~~~~~~~~ 86 (108)
T PHA00738 15 RKILELIAEN--YILSASLISHTLLLSYTTVLRHLKILNEQGYIELYKEGRTLYAKIREN-----SKEIQILNSELEGF 86 (108)
T ss_pred HHHHHHHHHc--CCccHHHHHHhhCCCHHHHHHHHHHHHHCCceEEEEECCEEEEEECCC-----ccHHHHHhhHHHHH
Confidence 3466667543 347788999999999999999999999999999765554444333211 12345566666544
No 154
>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=43.26 E-value=59 Score=26.07 Aligned_cols=52 Identities=21% Similarity=0.278 Sum_probs=27.5
Q ss_pred CceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022537 187 NHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 187 N~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lt 238 (295)
.-+.|.|.+..-.-..++.+.-++..++.|+.+.+.|.+.+..++.++..+.
T Consensus 60 ~vlV~lG~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~ 111 (120)
T PF02996_consen 60 KVLVSLGAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQLE 111 (120)
T ss_dssp EEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHH
T ss_pred EEEEEeeCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3567777654322223344444555555555555555555555555555443
No 155
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=43.25 E-value=72 Score=29.62 Aligned_cols=42 Identities=19% Similarity=0.240 Sum_probs=26.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccc
Q 022537 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENH 243 (295)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~n 243 (295)
++.++.++|++|++.|+.+..+++++..+ .++|+++.+-...
T Consensus 73 ~l~~en~~L~~e~~~l~~~~~~~~~l~~e-n~~L~~lL~~~~~ 114 (276)
T PRK13922 73 DLREENEELKKELLELESRLQELEQLEAE-NARLRELLNLKES 114 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHhcCccc
Confidence 34455567777777777777777655554 4667777654443
No 156
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=42.99 E-value=2.6e+02 Score=25.33 Aligned_cols=51 Identities=24% Similarity=0.249 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHh---CCCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 135 LLTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 135 lLTkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+...+.+.+.. .|+..+ .-.++|+.|||+|==+=+.+..|+.-|||+...
T Consensus 13 ~v~~~l~~~I~~g~l~pG~~LpsE~eLa~~~gVSRtpVREAL~~L~~eGlV~~~~ 67 (257)
T PRK10225 13 EVGAMIRDLIIKTPYNPGERLPPEREIAEMLDVTRTVVREALIMLEIKGLVEVRR 67 (257)
T ss_pred HHHHHHHHHHHhCCCCCCCcCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEec
Confidence 344455555543 478888 699999999999999999999999999998664
No 157
>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=42.90 E-value=39 Score=22.96 Aligned_cols=37 Identities=22% Similarity=0.455 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhh
Q 022537 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDI 171 (295)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDI 171 (295)
|..+=+.+|.-.-...+| ++..+|+.||+.++-||.=
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 344445555555444443 4689999999999999863
No 158
>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=42.85 E-value=56 Score=25.42 Aligned_cols=83 Identities=17% Similarity=0.240 Sum_probs=54.3
Q ss_pred HHHHHHhhhhhhhhhhhhhHhhhcc---ceeccccCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 155 NRTAEVLEVQKRRIYDITNVLEGIG---LIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQ 231 (295)
Q Consensus 155 n~aA~~L~VqKRRIYDItNVLEgIG---LIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~ 231 (295)
..--..|.-+++++=+++.-|+.+. -|-+.-.+.|.=...+.. -..+...+..++.+++.|..+...+...+..++
T Consensus 18 ~~q~~~l~~~~~~~~~~~~eL~~l~~~~~~y~~vG~~fv~~~~~~~-~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~ 96 (106)
T PF01920_consen 18 EQQIQQLERQLRELELTLEELEKLDDDRKVYKSVGKMFVKQDKEEA-IEELEERIEKLEKEIKKLEKQLKYLEKKLKELK 96 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHTSSTT-EEEEEETTEEEEEEHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCcchhHHHHhHHHHHhhHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334456666666666666665542 233333343443332211 124667788899999999999999999999999
Q ss_pred HHHHHHh
Q 022537 232 ELIRTLE 238 (295)
Q Consensus 232 ~~L~~Lt 238 (295)
..|..+.
T Consensus 97 ~~l~~~~ 103 (106)
T PF01920_consen 97 KKLYELF 103 (106)
T ss_dssp HHHHCCC
T ss_pred HHHHHHh
Confidence 9998765
No 159
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=42.79 E-value=39 Score=31.97 Aligned_cols=57 Identities=25% Similarity=0.436 Sum_probs=47.7
Q ss_pred CcHHHHHHHHHH-HHHhCCCCceeHHHHHHHhhhhhhhhhhhhh-HhhhccceeccccC
Q 022537 131 SSLGLLTRKFIN-LIQEAKDGTLDLNRTAEVLEVQKRRIYDITN-VLEGIGLIEKTSKN 187 (295)
Q Consensus 131 ~SLglLTkkFI~-ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~~KN 187 (295)
..|...-++++. ++..-.++.+.+..+|..||.....+-|++. .|-..|||++.+..
T Consensus 255 ~~l~~~~~~~l~~~~~~~~~~~~~~~~~a~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 313 (328)
T PRK00080 255 LGLDEMDRKYLRTIIEKFGGGPVGLDTLAAALGEERDTIEDVYEPYLIQQGFIQRTPRG 313 (328)
T ss_pred CCCCHHHHHHHHHHHHHcCCCceeHHHHHHHHCCCcchHHHHhhHHHHHcCCcccCCch
Confidence 456667788887 6666678899999999999999999998888 99999999877544
No 160
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=42.13 E-value=8.1 Score=37.06 Aligned_cols=28 Identities=25% Similarity=0.591 Sum_probs=22.2
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhcc
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIG 179 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIG 179 (295)
+-|..+=-.||..+|=+||.+||+||=-
T Consensus 41 iGLRNLDlimGlE~RiVYd~vdVi~g~~ 68 (272)
T COG2894 41 IGLRNLDLIMGLENRIVYDLVDVIEGEA 68 (272)
T ss_pred cCchhhhhhhcccceeeeeehhhhcCcc
Confidence 3455555668999999999999999854
No 161
>smart00338 BRLZ basic region leucin zipper.
Probab=42.07 E-value=1e+02 Score=22.59 Aligned_cols=34 Identities=24% Similarity=0.430 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 206 ~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
+..|..++..|..+-..|-..+..+..++..|.+
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666777777777777777766666666543
No 162
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=41.61 E-value=37 Score=23.14 Aligned_cols=36 Identities=22% Similarity=0.372 Sum_probs=22.2
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhcc
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIG 179 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIG 179 (295)
.|.++.+ -....++|+.|||.++-+|.|++=.+.-|
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 4455554 46789999999999999999988764333
No 163
>PF12728 HTH_17: Helix-turn-helix domain
Probab=41.26 E-value=22 Score=24.52 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=20.1
Q ss_pred eeHHHHHHHhhhhhhhhhhhhh
Q 022537 152 LDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItN 173 (295)
+++.++|+.|+|.+..||.+++
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999985
No 164
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=41.17 E-value=56 Score=34.92 Aligned_cols=70 Identities=24% Similarity=0.343 Sum_probs=50.5
Q ss_pred hhhhh-hHhhhccceeccccCceEEecCCCCCCc------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 168 IYDIT-NVLEGIGLIEKTSKNHIRWKGSDSLGTS------KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 168 IYDIt-NVLEgIGLIeK~~KN~i~W~G~~~s~~~------~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
.|+.+ +-|..|.=|.+++||++-= .+++-. .++..+..|+.|-+.|..+...+|.-+..+.++|..|..+
T Consensus 478 ~~~lte~QLslIrDIRRRgKNkvAA---QnCRKRKLd~I~nLE~ev~~l~~eKeqLl~Er~~~d~~L~~~kqqls~L~~~ 554 (604)
T KOG3863|consen 478 KYKLTEEQLSLIRDIRRRGKNKVAA---QNCRKRKLDCILNLEDEVEKLQKEKEQLLRERDELDSTLGVMKQQLSELYQE 554 (604)
T ss_pred hcccCHHHHHHhhccccccccchhc---cchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35555 6889999999999998743 222111 3445566777788888888889999999999988777543
No 165
>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=41.13 E-value=2e+02 Score=23.86 Aligned_cols=37 Identities=27% Similarity=0.372 Sum_probs=25.6
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEec
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKG 193 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G 193 (295)
.+.++|+.+||+.+-| --.|-.||+. +...|.|++-.
T Consensus 2 ~I~e~a~~~gvs~~tl----RyYe~~GLl~~~~r~~~g~R~Y~ 40 (127)
T cd01108 2 NIGEAAKLTGLSAKMI----RYYEEIGLIPPPSRSDNGYRVYN 40 (127)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCceecC
Confidence 5788999999987643 2446778885 44567677654
No 166
>PF13551 HTH_29: Winged helix-turn helix
Probab=40.90 E-value=29 Score=26.74 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=25.7
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhcc
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIG 179 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIG 179 (295)
.+.++|..||+.++-+|.+++-++.=|
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 167
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=40.76 E-value=31 Score=30.76 Aligned_cols=39 Identities=13% Similarity=0.205 Sum_probs=35.1
Q ss_pred CCCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 147 AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 147 a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.|+..+ .-.++|++|||+|--+-+.+..|+.-|||+...
T Consensus 26 ~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 367778 799999999999999999999999999999663
No 168
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=40.64 E-value=1.7e+02 Score=24.34 Aligned_cols=47 Identities=21% Similarity=0.291 Sum_probs=40.0
Q ss_pred HHHHHHHHHHhCCCC--ceeHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 136 LTRKFINLIQEAKDG--TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 136 LTkkFI~ll~~a~~g--~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
+...|..|++..++. .+.|.++|+.|.+++|-.==|++-|+..|.|+
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 456788888766644 57999999999999999999999999988875
No 169
>PRK10869 recombination and repair protein; Provisional
Probab=40.60 E-value=54 Score=34.10 Aligned_cols=85 Identities=14% Similarity=0.178 Sum_probs=42.4
Q ss_pred CCcCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCchhHHHHH
Q 022537 128 RYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVA 207 (295)
Q Consensus 128 R~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~ 207 (295)
++|.+|..+...+-+.+-.-.+-.-+|....+.+.+.--|+-.|-+=|.-|.=+.|+ | |.+ ..++-...+
T Consensus 258 ~~d~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~~dp~~l~~ie~Rl~~l~~L~rK----y---g~~---~~~~~~~~~ 327 (553)
T PRK10869 258 GMDSKLSGVLDMLEEALIQIQEASDELRHYLDRLDLDPNRLAELEQRLSKQISLARK----H---HVS---PEELPQHHQ 327 (553)
T ss_pred hhCHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHH----h---CCC---HHHHHHHHH
Confidence 344444444444444443333334444455555555555566665555555555544 1 322 234555566
Q ss_pred HHHHHHHHHHHHHHH
Q 022537 208 RLKAEIESLHAEECR 222 (295)
Q Consensus 208 ~Lk~El~~L~~~E~~ 222 (295)
++++|++.|...+..
T Consensus 328 ~l~~eL~~L~~~e~~ 342 (553)
T PRK10869 328 QLLEEQQQLDDQEDD 342 (553)
T ss_pred HHHHHHHHhhCCHHH
Confidence 677777665544333
No 170
>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=40.53 E-value=22 Score=35.98 Aligned_cols=35 Identities=26% Similarity=0.301 Sum_probs=29.7
Q ss_pred CCCceeHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
.||..+|-++|+++++.-++++|+.+.|...|||+
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 46899999999999999999999999999999985
No 171
>PRK10130 transcriptional regulator EutR; Provisional
Probab=40.52 E-value=32 Score=33.69 Aligned_cols=40 Identities=13% Similarity=0.144 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 134 glLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
..+.+++++++.+..+..+++.++|+.++|++|.|+-...
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 4677888999988888899999999999999999987664
No 172
>PRK01203 prefoldin subunit alpha; Provisional
Probab=40.45 E-value=1.9e+02 Score=25.07 Aligned_cols=37 Identities=19% Similarity=0.313 Sum_probs=22.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lt 238 (295)
+..+++.++++++.|.++-..|...+.+..+.+..|.
T Consensus 5 ~~~~~~~~~~q~e~l~~ql~~L~~a~se~~~~ie~L~ 41 (130)
T PRK01203 5 VEAQLNYIESLISSVDSQIDSLNKTLSEVQQTISFLS 41 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455666667777776666666666666655555543
No 173
>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=39.93 E-value=1.6e+02 Score=23.50 Aligned_cols=28 Identities=18% Similarity=0.392 Sum_probs=20.6
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhccceec
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (295)
+.+.++|+.+||+.+-|--. |..|+|.-
T Consensus 2 ~~i~eva~~~gVs~~tLR~y----e~~Gli~p 29 (98)
T cd01279 2 YPISVAAELLGIHPQTLRVY----DRLGLVSP 29 (98)
T ss_pred cCHHHHHHHHCcCHHHHHHH----HHCCCCCC
Confidence 56889999999988765444 55677763
No 174
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=39.85 E-value=31 Score=28.73 Aligned_cols=37 Identities=16% Similarity=0.187 Sum_probs=34.2
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+.+...++|+.+++.+=-+--+++-||.-|+|+|..
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 4568999999999999999999999999999999973
No 175
>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=39.83 E-value=21 Score=33.62 Aligned_cols=30 Identities=33% Similarity=0.551 Sum_probs=25.1
Q ss_pred HHHHHhh---hhhhhhhhhhhHhhhccceeccc
Q 022537 156 RTAEVLE---VQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 156 ~aA~~L~---VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+|+.++ +..|++||+++-||.+|||+-..
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~ 351 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEE 351 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEE
Confidence 5666666 57899999999999999999764
No 176
>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=38.86 E-value=2e+02 Score=22.82 Aligned_cols=25 Identities=24% Similarity=0.384 Sum_probs=16.4
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhccce
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLI 181 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLI 181 (295)
.+.++|+.+||..+-|--. |..|++
T Consensus 2 ti~eva~~~gvs~~tlR~y----e~~Gll 26 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYY----DEIGLL 26 (103)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCC
Confidence 4678888888877755432 345555
No 177
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=38.84 E-value=64 Score=30.60 Aligned_cols=52 Identities=19% Similarity=0.270 Sum_probs=40.3
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccc-eeccccCceEE
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL-IEKTSKNHIRW 191 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL-IeK~~KN~i~W 191 (295)
.+.+.++.+ +..+...++|+.|+|+|.-++-.+..|+.-|+ |.......|..
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 456677754 46678889999999999999999999999999 54443334554
No 178
>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=38.74 E-value=71 Score=23.16 Aligned_cols=39 Identities=13% Similarity=0.360 Sum_probs=35.2
Q ss_pred CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecccc
Q 022537 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (295)
.++.+++.++=+.||++|+-.--++.-|...|+..+.+-
T Consensus 7 ~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~gd 45 (50)
T PF09107_consen 7 KNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVGD 45 (50)
T ss_dssp TTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETT
T ss_pred cCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeCC
Confidence 378999999999999999999999999999999998864
No 179
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=38.72 E-value=2.2e+02 Score=25.46 Aligned_cols=41 Identities=17% Similarity=0.197 Sum_probs=34.6
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
++..+. ..|.+.-.++|..||++.--+=-+++-|+.-|||.
T Consensus 27 Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~ 67 (178)
T PRK06266 27 VLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLAD 67 (178)
T ss_pred HHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeE
Confidence 444444 34578999999999999999999999999999999
No 180
>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=38.54 E-value=28 Score=28.94 Aligned_cols=40 Identities=28% Similarity=0.397 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhH
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNV 174 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNV 174 (295)
+||.|=-.++.-.=..-+.|.++|+.+||+|=-+||.+.-
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 4676655555555567799999999999999999998764
No 181
>PHA02047 phage lambda Rz1-like protein
Probab=37.87 E-value=29 Score=29.04 Aligned_cols=36 Identities=17% Similarity=0.267 Sum_probs=17.2
Q ss_pred ceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 188 HIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREK 230 (295)
Q Consensus 188 ~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~ 230 (295)
+|+|.|..+ .....|...++.++.+-..+.+....+
T Consensus 25 ~~r~~g~~h-------~~a~~la~qLE~a~~r~~~~Q~~V~~l 60 (101)
T PHA02047 25 SYRALGIAH-------EEAKRQTARLEALEVRYATLQRHVQAV 60 (101)
T ss_pred HHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367877543 233344444444444444444444433
No 182
>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=37.73 E-value=54 Score=27.00 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=22.8
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
++..+.+..|..||-+.|.++.|.++|+.-
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 888888899999999999999999999754
No 183
>KOG0718 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=37.69 E-value=1.5e+02 Score=31.20 Aligned_cols=83 Identities=25% Similarity=0.338 Sum_probs=44.7
Q ss_pred CcCcHHHHHHHHHHHHH-hCCCCce--eHHHHHHHh--------hh----hhhhhhhhhhHhhhccceeccccCceEE-e
Q 022537 129 YDSSLGLLTRKFINLIQ-EAKDGTL--DLNRTAEVL--------EV----QKRRIYDITNVLEGIGLIEKTSKNHIRW-K 192 (295)
Q Consensus 129 ~d~SLglLTkkFI~ll~-~a~~g~l--dLn~aA~~L--------~V----qKRRIYDItNVLEgIGLIeK~~KN~i~W-~ 192 (295)
+|.+=..+-+..-.++. =+||... |...+|+++ +| +||-|||+.-+ ++-+.=-| .
T Consensus 19 kdAt~eeI~~AYrr~~~lfHPDkh~dpd~K~~AE~~F~~i~~AyEVLsDp~kRaIYD~~G~---------qGL~t~gwEl 89 (546)
T KOG0718|consen 19 KDATDEEIKKAYRRLSRLFHPDKHTDPDQKKAAEEKFQRIQRAYEVLSDPQKRAIYDNYGE---------QGLKTEGWEL 89 (546)
T ss_pred cccCHHHHHHHHHHHHHhcCCcccCChhHHHHHHHHHHHHHHHHHHhcChHHHHHHHHhhh---------ccccccCcee
Confidence 34444455554555544 2577665 566666654 33 89999998754 22233346 4
Q ss_pred cCCCCCCchhHHHHHHHHHHHHHHHH--HHHHHHHHH
Q 022537 193 GSDSLGTSKLDDQVARLKAEIESLHA--EECRIDDSI 227 (295)
Q Consensus 193 G~~~s~~~~~~~~~~~Lk~El~~L~~--~E~~LD~lI 227 (295)
|+....+ .++++|.+.|.. +|++|+++.
T Consensus 90 ~~r~~tp-------eEIreE~Erl~r~~de~~l~qr~ 119 (546)
T KOG0718|consen 90 GFRGKTP-------EEIREEYERLQRERDERRLQQRV 119 (546)
T ss_pred ecCCCCH-------HHHHHHHHHHHHHHHHHHHHhhc
Confidence 4443222 346677776653 344444443
No 184
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=37.45 E-value=49 Score=30.66 Aligned_cols=46 Identities=15% Similarity=0.207 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccc
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL 180 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 180 (295)
.+..+.+.++.......++|.++|+.+++++|.|.=+..-.-|+.+
T Consensus 5 ~~i~~~~~~i~~~~~~~~~l~~lA~~~~~S~~~l~r~F~~~~g~s~ 50 (289)
T PRK15121 5 GIIRDLLIWLEGHLDQPLSLDNVAAKAGYSKWHLQRMFKDVTGHAI 50 (289)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 3557789999999999999999999999999888777766555443
No 185
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=37.16 E-value=2.5e+02 Score=23.84 Aligned_cols=81 Identities=17% Similarity=0.239 Sum_probs=0.0
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhccce--eccccCceEEe-----------------cCCCCCCchhHHHHH-----
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLI--EKTSKNHIRWK-----------------GSDSLGTSKLDDQVA----- 207 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLI--eK~~KN~i~W~-----------------G~~~s~~~~~~~~~~----- 207 (295)
+.+.++|+.+||+.+-|--. |-.||| .+...|.|++- |+. -.++..-+.
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Y----e~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~s---L~eI~~~l~~~~~~ 74 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFY----EKQGLMDPEVRTEGGYRLYTEQDLQRLRFIRRAKQLGFT---LEEIRELLSIRLDP 74 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHH----HHCCCCCCcccCCCCCeeeCHHHHHHHHHHHHHHHcCCC---HHHHHHHHHhcccC
Q ss_pred ---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 208 ---RLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 208 ---~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
...+-.+-|..+...|++.|.++++....|..
T Consensus 75 ~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~ 109 (140)
T PRK09514 75 EHHTCQEVKGIVDEKLAEVEAKIAELQHMRRSLQR 109 (140)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 186
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=36.90 E-value=85 Score=25.94 Aligned_cols=11 Identities=18% Similarity=-0.143 Sum_probs=4.8
Q ss_pred HHHHHHHHHHH
Q 022537 135 LLTRKFINLIQ 145 (295)
Q Consensus 135 lLTkkFI~ll~ 145 (295)
.-.-+||..++
T Consensus 42 l~~l~~I~~lr 52 (118)
T cd04776 42 RARLKLILRGK 52 (118)
T ss_pred HHHHHHHHHHH
Confidence 33344444444
No 187
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=36.88 E-value=76 Score=28.87 Aligned_cols=35 Identities=26% Similarity=0.322 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 205 QVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 205 ~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
-+..|++|+..+...+...+..+.++.+..+.|++
T Consensus 28 lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~e 62 (201)
T PF13851_consen 28 LIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSE 62 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 46789999999999999999999988888777765
No 188
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=36.66 E-value=77 Score=32.31 Aligned_cols=58 Identities=17% Similarity=0.338 Sum_probs=46.4
Q ss_pred cHHHHHHH------HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecC
Q 022537 132 SLGLLTRK------FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (295)
Q Consensus 132 SLglLTkk------FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~ 194 (295)
-||+|+-+ .+++|....+..|.|+++|..-++. .-||++.|+.+++|... |. +.|...
T Consensus 304 DLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~---~~DIisTL~~L~m~~y~-k~-~~~~~~ 367 (396)
T KOG2747|consen 304 DLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIR---PDDIISTLQSLNMIKYY-KG-YIISIC 367 (396)
T ss_pred hhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCC---HHHHHHHHHhhCCcccc-CC-eeEEEe
Confidence 47888744 7788877666669999999999984 57999999999999877 33 777653
No 189
>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=36.56 E-value=99 Score=24.50 Aligned_cols=37 Identities=19% Similarity=0.366 Sum_probs=24.7
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhccceec--cccCceEEec
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEK--TSKNHIRWKG 193 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~~KN~i~W~G 193 (295)
.+.++|+.+||..+-|- -.|..|||.- .+.|.|++-.
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 47789999999877553 2367888853 3445565543
No 190
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=36.54 E-value=71 Score=33.26 Aligned_cols=38 Identities=16% Similarity=0.206 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
+.++..|+.|++.|..+...+++.|+.+++.++.|.+-
T Consensus 82 EKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Q 119 (475)
T PRK13729 82 QKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQ 119 (475)
T ss_pred HHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 33344444444444445555666666666666665443
No 191
>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=36.29 E-value=1.4e+02 Score=23.82 Aligned_cols=37 Identities=19% Similarity=0.233 Sum_probs=25.1
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEec
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKG 193 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G 193 (295)
.+.++|+.+||+.+-|- -.|-.|++. +...|.++|-.
T Consensus 2 ~i~e~A~~~gvs~~tlR----~Ye~~Gll~~~~r~~~g~R~Y~ 40 (99)
T cd04772 2 RTVDLARAIGLSPQTVR----NYESLGLIPPAERTANGYRIYT 40 (99)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHcCCCCCCCcCCCCCeecC
Confidence 47789999999776332 226788886 34566677754
No 192
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=36.21 E-value=84 Score=27.09 Aligned_cols=51 Identities=22% Similarity=0.326 Sum_probs=44.9
Q ss_pred CcHHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceec
Q 022537 131 SSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (295)
Q Consensus 131 ~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (295)
..|-.+=++.+.+|+ .++.+...++|+++|++.--++.=++=||.-|+|++
T Consensus 10 ~~lD~~D~~IL~~Lq--~d~R~s~~eiA~~lglS~~tv~~Ri~rL~~~GvI~~ 60 (164)
T PRK11169 10 KDLDRIDRNILNELQ--KDGRISNVELSKRVGLSPTPCLERVRRLERQGFIQG 60 (164)
T ss_pred hhHHHHHHHHHHHhc--cCCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEE
Confidence 446777788999887 667888899999999999999999999999999986
No 193
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=36.15 E-value=1.8e+02 Score=25.63 Aligned_cols=38 Identities=24% Similarity=0.454 Sum_probs=27.8
Q ss_pred eeHHHHHHHhhhhhh--hhhhhhhHhhhcccee--ccccCceEEecCC
Q 022537 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLIE--KTSKNHIRWKGSD 195 (295)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIe--K~~KN~i~W~G~~ 195 (295)
+.+.++|+.+||.++ |.|| .+|||. +...|.|++-+.+
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 468899999999988 5665 567775 3456778886543
No 194
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=36.10 E-value=64 Score=29.24 Aligned_cols=51 Identities=18% Similarity=0.169 Sum_probs=40.5
Q ss_pred HHHHHHHHHHh---CCCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceecccc
Q 022537 136 LTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (295)
Q Consensus 136 LTkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (295)
+...+.+.+.. .|+..+ .-.++|+.|||+|==+=+.+..|+..|||+...+
T Consensus 13 v~~~l~~~I~~g~l~pG~~LpsE~eLae~~gVSRtpVREAL~~L~~eGlV~~~~~ 67 (253)
T PRK11523 13 LAAELKERIEQGVYLVGDKLPAERFIADEKNVSRTVVREAIIMLEVEGYVEVRKG 67 (253)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecC
Confidence 34445555543 367788 4899999999999999999999999999986643
No 195
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=35.94 E-value=45 Score=29.57 Aligned_cols=53 Identities=15% Similarity=0.112 Sum_probs=39.2
Q ss_pred HHHHHHHHHhC---CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceE
Q 022537 137 TRKFINLIQEA---KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (295)
Q Consensus 137 TkkFI~ll~~a---~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (295)
..|+..++... ....+.-.++|+.||++|+-+.=+++-|+--|+|++.. ++|.
T Consensus 152 ~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~-~~i~ 207 (226)
T PRK10402 152 ENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSK-RGYL 207 (226)
T ss_pred HHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeC-CEEE
Confidence 35555555432 11234679999999999999999999999999999874 3443
No 196
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=35.90 E-value=2.5e+02 Score=23.19 Aligned_cols=79 Identities=16% Similarity=0.164 Sum_probs=0.0
Q ss_pred HHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEe-----------------cCCC---------CCCchhHHH
Q 022537 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWK-----------------GSDS---------LGTSKLDDQ 205 (295)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~-----------------G~~~---------s~~~~~~~~ 205 (295)
+.++|..+||..+-|--. |.+|||. +...|.|++- |+.. .........
T Consensus 2 I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~~~~~~~~ 77 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYY----ERKGLLPEPDRPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLVDGTHCREM 77 (124)
T ss_pred HHHHHHHHCcCHHHHHHH----HHCCCCCCCccCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhcccCCCHHHH
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 206 VARLKAEIESLHAEECRIDDSIREKQELIRT 236 (295)
Q Consensus 206 ~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~ 236 (295)
...|+..++.|+++..+|..+...++..+..
T Consensus 78 ~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~ 108 (124)
T TIGR02051 78 YELASRKLKSVQAKMADLLRIERLLEELLEQ 108 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 197
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.79 E-value=60 Score=26.65 Aligned_cols=42 Identities=14% Similarity=0.327 Sum_probs=33.7
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
++.++- ...+..++-++...-|-.||-+-|++..|+|+|+.-
T Consensus 12 Yla~Li-~S~e~~nVP~lm~~TGwPRRT~QDvikAlpglgi~l 53 (95)
T COG4519 12 YLAYLI-DSGETANVPELMAATGWPRRTAQDVIKALPGLGIVL 53 (95)
T ss_pred HHHHHH-hccccCChHHHHHHcCCchhHHHHHHHhCcCCCeEE
Confidence 444554 344567888888999999999999999999999863
No 198
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=35.52 E-value=96 Score=25.52 Aligned_cols=53 Identities=15% Similarity=0.151 Sum_probs=38.5
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccHhhh
Q 022537 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDI 254 (295)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~n~~~aYVT~eDI 254 (295)
.+.+++..+++|++.|+++.+.|.+.|..++... ...|...-..+-||-..+|
T Consensus 31 ~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~-dyiEe~AR~~Lg~vk~gEi 83 (105)
T PRK00888 31 RVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQ-EAIEERARNELGMVKPGET 83 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcH-HHHHHHHHHHcCCCCCCCE
Confidence 5667788999999999999999999999997743 2333323334666666555
No 199
>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=35.49 E-value=1.7e+02 Score=21.48 Aligned_cols=34 Identities=18% Similarity=0.426 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 206 ~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
+..|+.++..|..+-..|-..+..+.+.+..|..
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~ 61 (64)
T PF00170_consen 28 IEELEEKVEELESENEELKKELEQLKKEIQSLKS 61 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5567777777777777777777777777666643
No 200
>TIGR01063 gyrA DNA gyrase, A subunit. This model describes the common type II DNA topoisomerase (DNA gyrase). Two apparently independently arising families, one in the Proteobacteria and one in Gram-positive lineages, are both designated toposisomerase IV.
Probab=35.39 E-value=89 Score=34.19 Aligned_cols=16 Identities=31% Similarity=0.407 Sum_probs=10.1
Q ss_pred CCCCc-eeeeecCCCCC
Q 022537 280 DPDEN-RILVSSKGNIK 295 (295)
Q Consensus 280 dP~e~-~~l~s~~G~I~ 295 (295)
.++|+ .+++|.+|-||
T Consensus 493 i~~e~~~vllS~~GyIK 509 (800)
T TIGR01063 493 IARENVVVTLSHNGYVK 509 (800)
T ss_pred cCcceEEEEEcCCCEEE
Confidence 44554 46778888664
No 201
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=35.39 E-value=3e+02 Score=24.21 Aligned_cols=30 Identities=7% Similarity=0.159 Sum_probs=19.2
Q ss_pred HHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 156 RTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 156 ~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+...++.-...+-++..+++.|.-+...+
T Consensus 24 ~L~~~i~~l~~~~~e~~~~~~tl~~lk~~~ 53 (145)
T COG1730 24 SLQAQIAALNAAISELQTAIETLENLKGAG 53 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 344555666667777777777776666655
No 202
>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=35.26 E-value=1.1e+02 Score=26.94 Aligned_cols=20 Identities=15% Similarity=0.335 Sum_probs=13.2
Q ss_pred eEEEEeCCCCCeEEecCCCC
Q 022537 264 TLIAIKAPQASYIEVPDPDE 283 (295)
Q Consensus 264 TviAIKAP~gT~LEVPdP~e 283 (295)
.+|.|+.-+.|+|++-.-++
T Consensus 58 PFIlV~T~~~a~I~ceiS~D 77 (142)
T PF08781_consen 58 PFILVNTSKKAVIECEISED 77 (142)
T ss_dssp S-EEEEEESS--EEEEE-TT
T ss_pred CEEEEEecCCcEEEEEEcCC
Confidence 47999999999999975543
No 203
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=35.11 E-value=51 Score=27.46 Aligned_cols=32 Identities=28% Similarity=0.454 Sum_probs=25.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQEL 233 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~ 233 (295)
+..+++.+++|++.|.+++..|...|+.+++.
T Consensus 55 l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 55 LQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 44456677888888888888888888888777
No 204
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=35.07 E-value=1.9e+02 Score=25.28 Aligned_cols=35 Identities=14% Similarity=0.172 Sum_probs=32.4
Q ss_pred CCCceeHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
..+.+.-.++|..||++++-+=-+++.|...|||.
T Consensus 25 ~~~~~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~ 59 (158)
T TIGR00373 25 IKGEFTDEEISLELGIKLNEVRKALYALYDAGLAD 59 (158)
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCce
Confidence 35679999999999999999999999999999995
No 205
>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=34.98 E-value=2.7e+02 Score=23.25 Aligned_cols=36 Identities=22% Similarity=0.287 Sum_probs=23.7
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhccceeccc-c-CceEEe
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS-K-NHIRWK 192 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~-K-N~i~W~ 192 (295)
.+.++|..+||..|-| --.|-+|||.-.. . |.|++-
T Consensus 2 ~IgE~A~~~gvs~~TL----RyYE~~GLl~p~r~~~~gyR~Y 39 (133)
T cd04787 2 KVKELANAAGVTPDTV----RFYTRIGLLRPTRDPVNGYRLY 39 (133)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCcCCCCCeeeC
Confidence 5788999999988744 1227888886432 2 555554
No 206
>PRK13503 transcriptional activator RhaS; Provisional
Probab=34.50 E-value=64 Score=28.97 Aligned_cols=39 Identities=5% Similarity=0.115 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
...+++++++.+.....+.|.++|+.++++++.+.-+..
T Consensus 171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 447889999999988999999999999999999887664
No 207
>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=34.41 E-value=1.1e+02 Score=27.23 Aligned_cols=55 Identities=24% Similarity=0.344 Sum_probs=41.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc-------ccccccccHhhhhc
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENEN-------HQKYMFLTEEDIAS 256 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~-------n~~~aYVT~eDI~~ 256 (295)
...++..|++|++.|+.+-+.+=..+..|...|..+.+... ...-.=|+++||.+
T Consensus 27 ~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~~~~~~~~~~~~~~~~~~v~~~eLL~ 88 (188)
T PF10018_consen 27 NQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLPDQADEKLKSIPKAEKRPVDYEELLS 88 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccCCCCHHHHHH
Confidence 45678999999999999999999999999999999872111 11123378888865
No 208
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=34.20 E-value=54 Score=29.70 Aligned_cols=39 Identities=15% Similarity=0.119 Sum_probs=34.9
Q ss_pred CCCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 147 AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 147 a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.|+..+ .-.++|++|||+|==+=+.+..||..|||+...
T Consensus 21 ~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~ 60 (253)
T PRK10421 21 EAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRR 60 (253)
T ss_pred CCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 367778 699999999999999999999999999998553
No 209
>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=33.98 E-value=33 Score=35.71 Aligned_cols=25 Identities=24% Similarity=0.527 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 205 QVARLKAEIESLHAEECRIDDSIRE 229 (295)
Q Consensus 205 ~~~~Lk~El~~L~~~E~~LD~lI~~ 229 (295)
++++|++||++|+++-..|++.|..
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 4555555555555555544444443
No 210
>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=33.93 E-value=36 Score=24.50 Aligned_cols=31 Identities=16% Similarity=0.317 Sum_probs=21.5
Q ss_pred HHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 142 NLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 142 ~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
+.++....|. ...++|..+||.+.-||+|..
T Consensus 14 ~iI~~~e~g~-s~~~ia~~fgv~~sTv~~I~K 44 (53)
T PF04218_consen 14 EIIKRLEEGE-SKRDIAREFGVSRSTVSTILK 44 (53)
T ss_dssp HHHHHHHCTT--HHHHHHHHT--CCHHHHHHH
T ss_pred HHHHHHHcCC-CHHHHHHHhCCCHHHHHHHHH
Confidence 4444444454 899999999999999999985
No 211
>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=33.72 E-value=1.8e+02 Score=29.70 Aligned_cols=37 Identities=16% Similarity=0.213 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
..++.++..++..|..+.++|++.|..++++|..+..
T Consensus 137 ~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~ 173 (525)
T TIGR02231 137 GSEIERLLTEDREAERRIRELEKQLSELQNELNALLT 173 (525)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3445566666677777777777777777777777654
No 212
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=33.26 E-value=77 Score=27.74 Aligned_cols=40 Identities=25% Similarity=0.346 Sum_probs=36.8
Q ss_pred CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccC
Q 022537 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
.++.+-..++|..|+|..--.-..+|=|+..|||+.....
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~ 60 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYG 60 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCC
Confidence 7889999999999999999999999999999999987433
No 213
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=33.08 E-value=49 Score=29.41 Aligned_cols=37 Identities=38% Similarity=0.522 Sum_probs=30.5
Q ss_pred CCceeHHHHHHHhhhhhhh--------------hhhhhhHhhhccceeccc
Q 022537 149 DGTLDLNRTAEVLEVQKRR--------------IYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRR--------------IYDItNVLEgIGLIeK~~ 185 (295)
.+.+-+..++..+|-.||| |=-++.+||.+|||+|..
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 4567788888899996664 788999999999999874
No 214
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=32.95 E-value=1.6e+02 Score=26.46 Aligned_cols=28 Identities=18% Similarity=0.283 Sum_probs=20.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 213 IESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 213 l~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
++-|..+...|++.|.++++.|..+.++
T Consensus 87 ~~lLe~~~~~l~~ri~eLe~~l~~kad~ 114 (175)
T PRK13182 87 FEQLEAQLNTITRRLDELERQLQQKADD 114 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4566777777777777777777777655
No 215
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=32.78 E-value=1.4e+02 Score=26.33 Aligned_cols=38 Identities=39% Similarity=0.510 Sum_probs=24.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022537 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lt 238 (295)
++...++.++++++.|..+-..|...|.+++..+..|.
T Consensus 10 ~l~a~lq~l~~qie~L~~~i~~l~~~~~e~~~~~~tl~ 47 (145)
T COG1730 10 ELAAQLQILQSQIESLQAQIAALNAAISELQTAIETLE 47 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666667777777777777777776666655543
No 216
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=32.42 E-value=80 Score=30.05 Aligned_cols=60 Identities=25% Similarity=0.348 Sum_probs=48.6
Q ss_pred cHHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEe
Q 022537 132 SLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (295)
Q Consensus 132 SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (295)
.|-.-=+.-|+++. ..+|.+.-.++.+.||.+|=-++=|+-=||-.|+|+|..++.=.|.
T Consensus 192 ~L~~~e~~il~~i~-~~GGri~Q~eL~r~lglsktTvsR~L~~LEk~GlIe~~K~G~~n~V 251 (258)
T COG2512 192 DLNEDEKEILDLIR-ERGGRITQAELRRALGLSKTTVSRILRRLEKRGLIEKEKKGRTNIV 251 (258)
T ss_pred CCCHHHHHHHHHHH-HhCCEEeHHHHHHhhCCChHHHHHHHHHHHhCCceEEEEeCCeeEE
Confidence 34444456777775 5678899999999999999999999999999999999877665553
No 217
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=32.34 E-value=1.8e+02 Score=30.05 Aligned_cols=52 Identities=29% Similarity=0.377 Sum_probs=34.6
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhh-hhh---hHhhh--ccceeccccCceEEecCC
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIY-DIT---NVLEG--IGLIEKTSKNHIRWKGSD 195 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIY-DIt---NVLEg--IGLIeK~~KN~i~W~G~~ 195 (295)
+.+.++. ++.+...++|+.|+|+.|-|+ ||. .+|++ ++++.+ + .-|++.+.+
T Consensus 8 ~iL~~L~---~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~-~-~Gy~l~~~~ 65 (584)
T PRK09863 8 KIVDLLE---QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISG-S-AKYHLEILN 65 (584)
T ss_pred HHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheec-C-CceEEEeCC
Confidence 4555553 357899999999999998775 433 34555 444555 2 358887755
No 218
>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=32.16 E-value=1.8e+02 Score=22.01 Aligned_cols=39 Identities=8% Similarity=0.315 Sum_probs=30.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
+.+++..++..+.++....+.|++.......++.++.++
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 456677778888888888888888888888888887765
No 219
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=32.03 E-value=1.7e+02 Score=26.42 Aligned_cols=35 Identities=26% Similarity=0.424 Sum_probs=19.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 206 ~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
...|+.|++.|..+-..|..-+..+.+.+..+.+|
T Consensus 106 ~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eD 140 (161)
T TIGR02894 106 NERLKNQNESLQKRNEELEKELEKLRQRLSTIEED 140 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555555555555555555555554
No 220
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=31.84 E-value=72 Score=29.94 Aligned_cols=41 Identities=7% Similarity=-0.019 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHh
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVL 175 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVL 175 (295)
....++++++.......+++.++|+.+++++|.|+-...-.
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~ 258 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAA 258 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34578999999998999999999999999999998777643
No 221
>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=31.68 E-value=2.9e+02 Score=22.62 Aligned_cols=82 Identities=22% Similarity=0.301 Sum_probs=60.4
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCchhHHHHHHHHHHHHHHH
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLH 217 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~ 217 (295)
--|.-++...--..-++..+.+++.-..+|+-.|=+.|+.+ | ..+++..|+-++..+.
T Consensus 21 ~~~~~~l~~~~a~~~~~~~l~~~~~~~~~Rl~~lE~~l~~L--------------------P--t~~dv~~L~l~l~el~ 78 (106)
T PF10805_consen 21 GIFWLWLRRTYAKREDIEKLEERLDEHDRRLQALETKLEHL--------------------P--TRDDVHDLQLELAELR 78 (106)
T ss_pred HHHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHhC--------------------C--CHHHHHHHHHHHHHHH
Confidence 33444454433335678888888888889988877666532 1 1356788999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhc
Q 022537 218 AEECRIDDSIREKQELIRTLEENE 241 (295)
Q Consensus 218 ~~E~~LD~lI~~~~~~L~~Lted~ 241 (295)
.+-+.+...|+.+..++.-|.|.+
T Consensus 79 G~~~~l~~~l~~v~~~~~lLlE~~ 102 (106)
T PF10805_consen 79 GELKELSARLQGVSHQLDLLLENE 102 (106)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999998888764
No 222
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=31.64 E-value=36 Score=23.45 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=21.8
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
...++|+. .| +.+.++|+.+||+|.-||=+.+
T Consensus 12 ~~i~~l~~---~G-~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 12 EEIKELYA---EG-MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp HHHHHHHH---TT---HHHHHHHTTS-HHHHHHHHC
T ss_pred HHHHHHHH---CC-CCHHHHHHHHCcCHHHHHHHHh
Confidence 34455553 34 8899999999999999997754
No 223
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=31.36 E-value=63 Score=27.79 Aligned_cols=37 Identities=22% Similarity=0.144 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhh
Q 022537 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYD 170 (295)
Q Consensus 134 glLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYD 170 (295)
..|-..+++++.+.+-.-+.++++|++.||.|.-||.
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 4577779999988887889999999999999999994
No 224
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=31.32 E-value=1.6e+02 Score=22.23 Aligned_cols=32 Identities=22% Similarity=0.320 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
.+..+++.++.+.+.+......++.++..|.+
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~ 59 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELSR 59 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 34445555555555555555555555555544
No 225
>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=31.22 E-value=69 Score=29.48 Aligned_cols=55 Identities=27% Similarity=0.468 Sum_probs=42.0
Q ss_pred HHHHHHHHHH-HHHhCCCCceeHHHHHHHhhhhhhhhhhhhh-HhhhccceeccccC
Q 022537 133 LGLLTRKFIN-LIQEAKDGTLDLNRTAEVLEVQKRRIYDITN-VLEGIGLIEKTSKN 187 (295)
Q Consensus 133 LglLTkkFI~-ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~~KN 187 (295)
|...-+.|+. ++..-.++.+.+.++|..||+..+.+..++- .|-..|||++....
T Consensus 236 l~~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g 292 (305)
T TIGR00635 236 LDEIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRG 292 (305)
T ss_pred CCHHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCch
Confidence 3334455666 5555566678899999999999999999888 79999999876544
No 226
>KOG3501 consensus Molecular chaperone Prefoldin, subunit 1 [Posttranslational modification, protein turnover, chaperones]
Probab=31.14 E-value=1.7e+02 Score=25.08 Aligned_cols=40 Identities=18% Similarity=0.406 Sum_probs=34.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
..+..+..+++.++.|+.+...|.....+..+.||+|.+.
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 4555667778889999999999999999999999999865
No 227
>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=30.92 E-value=16 Score=31.15 Aligned_cols=26 Identities=23% Similarity=0.473 Sum_probs=0.0
Q ss_pred hhhhhhhhhhHhhhccceeccccCceEE
Q 022537 164 QKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (295)
Q Consensus 164 qKRRIYDItNVLEgIGLIeK~~KN~i~W 191 (295)
-|+++-+-+..||.+|+|.+. |.|+=
T Consensus 5 lk~~~l~~l~~LE~~G~v~~~--n~yQ~ 30 (142)
T PF03836_consen 5 LKKKILENLKELESLGIVSRS--NNYQD 30 (142)
T ss_dssp ----------------------------
T ss_pred HHHHHHHHHHHHHHCCCCCCc--ccHHH
Confidence 367788889999999999988 66654
No 228
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=30.92 E-value=94 Score=30.88 Aligned_cols=44 Identities=14% Similarity=0.241 Sum_probs=37.9
Q ss_pred CCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceE
Q 022537 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (295)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (295)
..+..+...++++.+++.-+.+-||+.-|+..|+|.+...+.|.
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 229
>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=30.78 E-value=1.4e+02 Score=27.52 Aligned_cols=33 Identities=15% Similarity=0.238 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 207 ARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 207 ~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
..|+.+++.+...+..|.-++..+-+.|..+.+
T Consensus 87 ~~L~~qi~~~~~~~~~l~p~m~~m~~~L~~~v~ 119 (251)
T PF11932_consen 87 ASLEQQIEQIEETRQELVPLMEQMIDELEQFVE 119 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344444444455555555555555555555443
No 230
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=30.72 E-value=81 Score=26.98 Aligned_cols=39 Identities=15% Similarity=0.289 Sum_probs=33.4
Q ss_pred ceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceE
Q 022537 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (295)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (295)
.+.-.++|..||+.++.+.=+.+-|+.-|+|+... ++|.
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~-~~i~ 206 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHG-KTIV 206 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecC-CEEE
Confidence 45679999999999999999999999999998774 3343
No 231
>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=30.41 E-value=2.1e+02 Score=22.31 Aligned_cols=37 Identities=22% Similarity=0.305 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
+.+..||.|++.|..+-..|.+....+.+....|.++
T Consensus 18 eti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e 54 (72)
T PF06005_consen 18 ETIALLQMENEELKEKNNELKEENEELKEENEQLKQE 54 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 4467788888888888777877777777777777654
No 232
>PRK01203 prefoldin subunit alpha; Provisional
Probab=30.32 E-value=1.6e+02 Score=25.58 Aligned_cols=59 Identities=12% Similarity=0.126 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccHhhhhcCCCCCCCeEEEEeCCCCCeEEec
Q 022537 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDIASLPCFQNQTLIAIKAPQASYIEVP 279 (295)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~n~~~aYVT~eDI~~i~~f~~qTviAIKAP~gT~LEVP 279 (295)
.+.+|+.-|+++-+.|.+.|..++..+..+.+ +-+.|..+..-.+..+++ |-|..+-||
T Consensus 4 ~~~~~~~~~~~q~e~l~~ql~~L~~a~se~~~----------~ie~L~~~~~~~~~eiLV---PLg~slYV~ 62 (130)
T PRK01203 4 DVEAQLNYIESLISSVDSQIDSLNKTLSEVQQ----------TISFLSDNELDNSKELLI---SIGSGIFAD 62 (130)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHccccCCCCeEEE---EccCCceEe
Confidence 35566666666666666666666666555533 455666554334444443 777777777
No 233
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=30.20 E-value=78 Score=31.47 Aligned_cols=50 Identities=16% Similarity=0.186 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHh-hhhhhhhhhhhhHhhhccceecc
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
.+.++|+.++....+..++.+.+|..+ ++.++-++.-++.||.+-++-..
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 678899999999999999999999999 79999999999999999999843
No 234
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=29.81 E-value=1.2e+02 Score=26.07 Aligned_cols=33 Identities=18% Similarity=0.231 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 207 ARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 207 ~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
.+|++.++.|+.+.+.|..+.+.++++|.+|..
T Consensus 73 ~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq~ 105 (119)
T COG1382 73 DELEERKETLELRIKTLEKQEEKLQERLEELQS 105 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456666777888888888888888888888764
No 235
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=29.81 E-value=1.8e+02 Score=22.51 Aligned_cols=37 Identities=19% Similarity=0.375 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
...+..+++.+.+|......|-..|....+.|+++.+
T Consensus 13 ~P~l~~~~~~l~el~~sQ~~L~~~i~~~~~~L~~~~~ 49 (92)
T PF14712_consen 13 EPDLDRLDQQLQELRQSQEELLQQIDRLNEKLKELNE 49 (92)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4457788899999999999999999999999999887
No 236
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=29.63 E-value=3.2e+02 Score=22.54 Aligned_cols=86 Identities=15% Similarity=0.154 Sum_probs=0.0
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEe----------------------------cCCCCCCch
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWK----------------------------GSDSLGTSK 201 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~----------------------------G~~~s~~~~ 201 (295)
+.+.++|+.+||+.+-|- -.|..|||. +...|.|+|- .........
T Consensus 1 ~~I~e~a~~~gvs~~tlR----~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~ 76 (126)
T cd04785 1 LSIGELARRTGVNVETIR----YYESIGLLPEPARTAGGYRLYGAAHVERLRFIRRARDLGFSLEEIRALLALSDRPDRS 76 (126)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHhhhhcCCCC
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~ 241 (295)
.....+.|+..++.|+.+-++|......+...+.....+.
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~~~ 116 (126)
T cd04785 77 CAEADAIARAHLADVRARIADLRRLEAELKRMVAACSGGR 116 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCC
No 237
>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=29.58 E-value=3.4e+02 Score=23.70 Aligned_cols=26 Identities=35% Similarity=0.492 Sum_probs=18.6
Q ss_pred eHHHHHHHhhh-hhhhhhhhhhHhhhccc
Q 022537 153 DLNRTAEVLEV-QKRRIYDITNVLEGIGL 180 (295)
Q Consensus 153 dLn~aA~~L~V-qKRRIYDItNVLEgIGL 180 (295)
-+|+|=..|.- .+|..|++. |.|+.+
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 46677777776 679999875 556665
No 238
>PF08222 HTH_CodY: CodY helix-turn-helix domain; InterPro: IPR013198 This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions []. The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk [].; PDB: 2B0L_C.
Probab=29.52 E-value=58 Score=25.05 Aligned_cols=36 Identities=28% Similarity=0.408 Sum_probs=28.5
Q ss_pred CceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 150 GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
|.+--..+|+++|+.|.-|-.-+-=||+.|+|+-.+
T Consensus 3 g~lvas~iAd~~GiTRSvIVNALRKleSaGvIesrS 38 (61)
T PF08222_consen 3 GRLVASKIADRVGITRSVIVNALRKLESAGVIESRS 38 (61)
T ss_dssp EEE-HHHHHHHHT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred ceehHHHHHHHhCccHHHHHHHHHHHHhcCceeecc
Confidence 455567899999999999999999999999999664
No 239
>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=29.37 E-value=3.6e+02 Score=24.11 Aligned_cols=47 Identities=15% Similarity=0.273 Sum_probs=37.4
Q ss_pred HHHHHHHHhCCCCce--eHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 138 RKFINLIQEAKDGTL--DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 138 kkFI~ll~~a~~g~l--dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
+++..++.+.+.-.+ .+..+|..||+.++-|-=++.|+.-+|+|+-.
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 345555556655433 56899999999999999999999999999866
No 240
>TIGR02812 fadR_gamma fatty acid metabolism transcriptional regulator FadR. Members of this family are FadR, a transcriptional regulator of fatty acid metabolism, including both biosynthesis and beta-oxidation. It is found exclusively in a subset of Gammaproteobacteria, with strictly one copy per genome. It has an N-terminal DNA-binding domain and a less well conserved C-terminal long chain acyl-CoA-binding domain. FadR from this family heterologously expressed in Escherichia coli show differences in regulatory response and fatty acid binding profiles. The family is nevertheless designated equivalog, as all member proteins have at least nominally the same function.
Probab=29.37 E-value=3.4e+02 Score=24.09 Aligned_cols=39 Identities=13% Similarity=0.205 Sum_probs=35.8
Q ss_pred CCCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 147 AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 147 a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.|+..+ .-.++|++|||+|==+=+.+..|+.-|||+...
T Consensus 25 ~pG~~LpsE~~La~~lgVSRtpVREAL~~Le~eGlV~~~~ 64 (235)
T TIGR02812 25 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH 64 (235)
T ss_pred CCCCcCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEeC
Confidence 478888 899999999999999999999999999998664
No 241
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=29.36 E-value=1.1e+02 Score=31.83 Aligned_cols=59 Identities=25% Similarity=0.261 Sum_probs=38.8
Q ss_pred hhhhhhhHhhhccceecc-ccCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 167 RIYDITNVLEGIGLIEKT-SKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 167 RIYDItNVLEgIGLIeK~-~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
++-++.|-|+++.=+.|. .+|.-.|+| .|++..+.+...-...|+.|.++++||++|+=
T Consensus 390 k~~k~~kel~~~~E~n~~l~knq~vw~~--------------kl~~~~e~~~~~~~s~d~~I~dLqEQlrDlmf 449 (493)
T KOG0804|consen 390 KLKKCQKELKEEREENKKLIKNQDVWRG--------------KLKELEEREKEALGSKDEKITDLQEQLRDLMF 449 (493)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHhe
Confidence 455666666666533332 244444443 34455566677778899999999999999973
No 242
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=29.35 E-value=1.4e+02 Score=28.16 Aligned_cols=44 Identities=18% Similarity=0.342 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccHhhh
Q 022537 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDI 254 (295)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~n~~~aYVT~eDI 254 (295)
+|+..|+.|..+-.+|-.+|+..+-+|+.+.+. ++-.|+--+++
T Consensus 58 ~l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~r---q~~~y~dld~r 101 (263)
T PRK10803 58 QLQQQLSDNQSDIDSLRGQIQENQYQLNQVVER---QKQIYLQIDSL 101 (263)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH---HHHHHHHHHHH
Confidence 455566666666666666666666666666653 33345444443
No 243
>PF01991 vATP-synt_E: ATP synthase (E/31 kDa) subunit; InterPro: IPR002842 ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (e.g., F-, V- and A-ATPases, which contain rotary motors) and in the type of ions they transport [, ]. The different types include: F-ATPases (F1F0-ATPases), which are found in mitochondria, chloroplasts and bacterial plasma membranes where they are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases), which are primarily found in eukaryotic vacuoles and catalyse ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases), which are found in Archaea and function like F-ATPases (though with respect to their structure and some inhibitor responses, A-ATPases are more closely related to the V-ATPases). P-ATPases (E1E2-ATPases), which are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases, which are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP. The V-ATPases (or V1V0-ATPase) and A-ATPases (or A1A0-ATPase) are each composed of two linked complexes: the V1 or A1 complex contains the catalytic core that hydrolyses/synthesizes ATP, and the V0 or A0 complex that forms the membrane-spanning pore. The V- and A-ATPases both contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis [, , ]. The V- and A-ATPases more closely resemble one another in subunit structure than they do the F-ATPases, although the function of A-ATPases is closer to that of F-ATPases. This entry represents subunit E from the V1 and A1 complexes of V- and A-ATPases, respectively. Subunit E appears to form a tight interaction with subunit G in the F0 complex, which together may act as stators to prevent certain subunits from rotating with the central rotary element, much in the same way as the F0 complex subunit B does in F-ATPases []. In addition to its key role in stator structure, subunit E appears to have a role in mediating interactions with putative regulatory subunits []. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0046961 proton-transporting ATPase activity, rotational mechanism, 0015991 ATP hydrolysis coupled proton transport, 0033178 proton-transporting two-sector ATPase complex, catalytic domain; PDB: 3LG8_A 2KK7_A 4DT0_A 2DM9_A 2DMA_A 3V6I_A 3K5B_A 3J0J_L 2KZ9_A.
Probab=28.93 E-value=1.5e+02 Score=25.49 Aligned_cols=31 Identities=26% Similarity=0.378 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022537 211 AEIESLHAEECRIDDSIREKQELIRTLEENE 241 (295)
Q Consensus 211 ~El~~L~~~E~~LD~lI~~~~~~L~~Lted~ 241 (295)
....-|..++..+++++..+...|..+..++
T Consensus 62 ~r~~~l~~k~~~i~~v~~~~~~~L~~~~~~~ 92 (198)
T PF01991_consen 62 ARRELLEAKQEIIDEVFEEVKEKLKSFSKDP 92 (198)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHCTTCCC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcCH
Confidence 3345677888899999999999999988775
No 244
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=28.92 E-value=1e+02 Score=26.20 Aligned_cols=50 Identities=18% Similarity=0.208 Sum_probs=43.6
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
|-.+=++.+.+|+.. +.....++|+.||++.-.+..=++=|+.-|+|.+.
T Consensus 7 lD~~D~~Il~~Lq~d--~R~s~~eiA~~lglS~~tV~~Ri~rL~~~GvI~~~ 56 (153)
T PRK11179 7 IDNLDRGILEALMEN--ARTPYAELAKQFGVSPGTIHVRVEKMKQAGIITGT 56 (153)
T ss_pred cCHHHHHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeeeE
Confidence 445667889999855 88999999999999999999999999999999865
No 245
>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=28.88 E-value=3e+02 Score=22.00 Aligned_cols=36 Identities=22% Similarity=0.404 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lt 238 (295)
....+.|+.++..|..+-..|...+.+.+..+..+.
T Consensus 5 ~~~~~~l~~~i~~l~~~~~~l~~~~~e~~~~~~~l~ 40 (129)
T cd00890 5 AAQLQQLQQQLEALQQQLQKLEAQLTEYEKAKETLE 40 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344566777777777777777777766665554443
No 246
>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=28.76 E-value=96 Score=24.48 Aligned_cols=29 Identities=14% Similarity=0.267 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 211 AEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 211 ~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
++|..|.+.-+.|++.+..++++|-++..
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 46777777778888888888888877754
No 247
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=28.60 E-value=75 Score=29.02 Aligned_cols=38 Identities=13% Similarity=0.211 Sum_probs=32.9
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
...+++.++.....+.+.+.++|+.++++++++.-+..
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk 221 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFR 221 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46778899988888999999999999999998877654
No 248
>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=28.40 E-value=1.3e+02 Score=24.21 Aligned_cols=34 Identities=15% Similarity=0.366 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (295)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~L 237 (295)
+++..+.+++..|++-=..||+..+.+..+++.|
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 3445555677777777778888888777776653
No 249
>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1
Probab=28.35 E-value=1.9e+02 Score=23.07 Aligned_cols=37 Identities=22% Similarity=0.263 Sum_probs=31.1
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 200 SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRT 236 (295)
Q Consensus 200 ~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~ 236 (295)
..+...+++|-+||+-|+.+-..|.+.+.++..++++
T Consensus 50 ~~lp~~~keLL~EIA~lE~eV~~LE~~v~~L~~~l~~ 86 (88)
T PF14389_consen 50 SSLPKKAKELLEEIALLEAEVAKLEQKVLSLYRQLFQ 86 (88)
T ss_pred ccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4566778889999999999999999999998887753
No 250
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=28.12 E-value=51 Score=30.32 Aligned_cols=56 Identities=20% Similarity=0.215 Sum_probs=42.1
Q ss_pred HHHHHHHHHHHhC---CCCce-eHHHHHHHhhhhhhhhhhhhhHhhhccceeccc-cCceE
Q 022537 135 LLTRKFINLIQEA---KDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS-KNHIR 190 (295)
Q Consensus 135 lLTkkFI~ll~~a---~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~-KN~i~ 190 (295)
.+..++..++.+. ++..+ .=.++|++|||+|-=+=+.+-+|+..|||+-+. ...|.
T Consensus 14 ~v~~~i~~~I~~g~~~~G~~LP~EreLae~fgVSR~~vREAl~~L~a~Glve~r~G~Gt~V 74 (241)
T COG2186 14 EVAEQIGALIVSGELPPGDRLPSERELAERFGVSRTVVREALKRLEAKGLVEIRQGSGTFV 74 (241)
T ss_pred HHHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCcHHHHHHHHHHHHCCCeeecCCCceEe
Confidence 3556666666543 44444 578999999999999999999999999999553 44433
No 251
>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=28.09 E-value=1.2e+02 Score=24.99 Aligned_cols=12 Identities=17% Similarity=0.313 Sum_probs=5.4
Q ss_pred HHHHHHHhhhhh
Q 022537 154 LNRTAEVLEVQK 165 (295)
Q Consensus 154 Ln~aA~~L~VqK 165 (295)
+.++|+.+||+.
T Consensus 3 Igeva~~~gvs~ 14 (118)
T cd04776 3 ISELAREFDVTP 14 (118)
T ss_pred HHHHHHHHCcCH
Confidence 344444444443
No 252
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=27.60 E-value=78 Score=28.94 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=30.4
Q ss_pred HHHHHHHHHHhCCCCc-eeHHHHHHHhhhhhhhhhhhhh
Q 022537 136 LTRKFINLIQEAKDGT-LDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~-ldLn~aA~~L~VqKRRIYDItN 173 (295)
...+.+.++.+.-... +.+.++|..+|+++|.||-+..
T Consensus 198 ~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk 236 (302)
T PRK09685 198 QFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFA 236 (302)
T ss_pred HHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 3457778887665544 9999999999999999998763
No 253
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=27.36 E-value=66 Score=30.67 Aligned_cols=35 Identities=23% Similarity=0.403 Sum_probs=26.8
Q ss_pred CceeHHHHH-------HHhhhh---hhhhhhhhhHhhhccceecc
Q 022537 150 GTLDLNRTA-------EVLEVQ---KRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 150 g~ldLn~aA-------~~L~Vq---KRRIYDItNVLEgIGLIeK~ 184 (295)
+.+...++. +.+++. +|+++|+.+-|+..|||+-.
T Consensus 314 ~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~~~ 358 (394)
T PRK00411 314 DEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINTR 358 (394)
T ss_pred CcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeEEE
Confidence 445555555 557774 59999999999999999854
No 254
>PF05911 DUF869: Plant protein of unknown function (DUF869); InterPro: IPR008587 This family consists of a number of sequences found in plants. The function of this family is unknown.
Probab=27.29 E-value=2.3e+02 Score=31.32 Aligned_cols=102 Identities=18% Similarity=0.217 Sum_probs=54.7
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCC----chhHHHHHH
Q 022537 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT----SKLDDQVAR 208 (295)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~----~~~~~~~~~ 208 (295)
|..+..+|++-|..--.|.-||...++.+.+.-=+|-.--..|..+---.-..+++|.|........ .........
T Consensus 514 fv~~LekeVh~C~DLLsgkadLE~fieE~s~tLdwIls~~~SLqDv~s~~sEIK~~f~~~ss~e~E~~~~dea~~~~~~e 593 (769)
T PF05911_consen 514 FVLVLEKEVHVCQDLLSGKADLERFIEEFSLTLDWILSNCFSLQDVSSMRSEIKKNFDGDSSSEAEINSEDEADTSEKKE 593 (769)
T ss_pred HHHHHHHHHHHHHHHhcchhHHHHHHHHHHHHHHHHHHccchHHHHHHHHHHHHHhhhhcccccccccchHHHHHHHHHH
Confidence 3456678888888777888899999998888555553332233332112233467788844321110 011122334
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 209 LKAEIESLHAEECRIDDSIREKQELI 234 (295)
Q Consensus 209 Lk~El~~L~~~E~~LD~lI~~~~~~L 234 (295)
|+.+++.|..+...|...+..|+++|
T Consensus 594 l~eelE~le~eK~~Le~~L~~~~d~l 619 (769)
T PF05911_consen 594 LEEELEKLESEKEELEMELASCQDQL 619 (769)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55566655555555555444443333
No 255
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=27.28 E-value=85 Score=23.99 Aligned_cols=43 Identities=19% Similarity=0.244 Sum_probs=35.5
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccce
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLI 181 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 181 (295)
++++++.......+.|+++|..+|+.++.+.-...-..|+...
T Consensus 24 ~~~~~i~~~~~~~~~l~~la~~~g~S~~~l~r~f~~~~g~s~~ 66 (127)
T COG2207 24 RALDYIEENLAEPLTLEDLARRLGMSRRTLSRLFKKETGTSPS 66 (127)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHCCCHHHHHHHHHHHHCCCHH
Confidence 7778887767777999999999999999999888866666554
No 256
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=27.20 E-value=5.9e+02 Score=24.76 Aligned_cols=43 Identities=19% Similarity=0.225 Sum_probs=34.1
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEE
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W 191 (295)
...+...++|.+|||.---+-+=+-=|-.=|+|++.+..+|.-
T Consensus 23 qp~v~q~eIA~~lgiT~QaVsehiK~Lv~eG~i~~~gR~~Y~i 65 (260)
T COG1497 23 QPRVKQKEIAKKLGITLQAVSEHIKELVKEGLIEKEGRGEYEI 65 (260)
T ss_pred CCCCCHHHHHHHcCCCHHHHHHHHHHHHhccceeecCCeeEEE
Confidence 3568899999999998777777777778889999976655554
No 257
>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=27.08 E-value=1.2e+02 Score=25.85 Aligned_cols=84 Identities=18% Similarity=0.191 Sum_probs=0.0
Q ss_pred eeHHHHHHHhhhhhh--hhhhhhhHhhhccceeccccCceEEe----------------cCCCCCCchhHHHHHHHHHHH
Q 022537 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLIEKTSKNHIRWK----------------GSDSLGTSKLDDQVARLKAEI 213 (295)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIeK~~KN~i~W~----------------G~~~s~~~~~~~~~~~Lk~El 213 (295)
+.+.++|+.+||+.| |.||=...|. ..+...+.-.+. |+....-.++-.....+..+.
T Consensus 1 y~I~e~a~~~gvs~~TLR~Ye~~GLl~----p~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~~ 76 (134)
T cd04779 1 YRIGQLAHLAGVSKRTIDYYTNLGLLT----PERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQRSDKEQ 76 (134)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC----CccCCCCCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhccccchH
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 214 ESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 214 ~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
+.+..+.+.+..+|..+.+++..|.+
T Consensus 77 ~~~~~~~~~l~~~i~~Le~~l~~L~~ 102 (134)
T cd04779 77 REVAQEVQLVCDQIDGLEHRLKQLKP 102 (134)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
No 258
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=26.89 E-value=1.9e+02 Score=22.86 Aligned_cols=35 Identities=26% Similarity=0.398 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~L 237 (295)
...+..|+++++.|+.+...+...+.-+..++.-|
T Consensus 69 ~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~L 103 (104)
T PF13600_consen 69 SPELKELEEELEALEDELAALQDEIQALEAQIAFL 103 (104)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45677888888888888888888887777766543
No 259
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=26.68 E-value=85 Score=21.47 Aligned_cols=38 Identities=16% Similarity=0.186 Sum_probs=25.7
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
+|.+|..++-..-.....+..+|..+||.--.+..|++
T Consensus 12 ~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 12 ITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 56666666643322337999999999997666666554
No 260
>PRK11642 exoribonuclease R; Provisional
Probab=26.17 E-value=1.1e+02 Score=33.69 Aligned_cols=51 Identities=10% Similarity=0.083 Sum_probs=41.1
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhh----hhhhhhhhhHhhhccceeccccCceE
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQ----KRRIYDITNVLEGIGLIEKTSKNHIR 190 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~Vq----KRRIYDItNVLEgIGLIeK~~KN~i~ 190 (295)
..+++|... +..+.+.+++..|++. +..+..++.-|+..|.|.+..++.|.
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 356666653 4889999999999995 45599999999999999987666653
No 261
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=26.13 E-value=3e+02 Score=23.35 Aligned_cols=24 Identities=17% Similarity=0.313 Sum_probs=17.2
Q ss_pred eeHHHHHHHhhhhhh--hhhhhhhHh
Q 022537 152 LDLNRTAEVLEVQKR--RIYDITNVL 175 (295)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVL 175 (295)
+.+.++|+.+||..+ |.|+=..+|
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~~GLl 27 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQKGLI 27 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCC
Confidence 568899999999776 666544443
No 262
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=26.09 E-value=58 Score=23.05 Aligned_cols=25 Identities=24% Similarity=0.278 Sum_probs=21.6
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhh
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLE 176 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLE 176 (295)
+.|.++|+.+|+..+.|+.+.+-.-
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~ 26 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKET 26 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHh
Confidence 5789999999999999999987543
No 263
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=26.08 E-value=4e+02 Score=22.40 Aligned_cols=51 Identities=18% Similarity=0.249 Sum_probs=39.5
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEE
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W 191 (295)
+.+.++.. .+.+.+.++|+.|++.+=.+-==+.||+..|||+........|
T Consensus 20 ~IL~~L~~--~~~~~v~ela~~l~lsqstvS~HL~~L~~AGLV~~~r~Gr~~~ 70 (117)
T PRK10141 20 GIVLLLRE--SGELCVCDLCTALDQSQPKISRHLALLRESGLLLDRKQGKWVH 70 (117)
T ss_pred HHHHHHHH--cCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCceEEEEEcCEEE
Confidence 35555543 3468899999999999999999999999999998665554444
No 264
>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit, proteobacterial. Operationally, topoisomerase IV is a type II topoisomerase required for the decatenation of chromosome segregation. Not every bacterium has both a topo II and a topo IV. The topo IV families of the Gram-positive bacteria and the Gram-negative bacteria appear not to represent a single clade among the type II topoisomerases, and are represented by separate models for this reason.
Probab=26.06 E-value=1.9e+02 Score=31.68 Aligned_cols=54 Identities=17% Similarity=0.205 Sum_probs=24.1
Q ss_pred CcHHHHHHHHHHHHHhC--CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 131 SSLGLLTRKFINLIQEA--KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 131 ~SLglLTkkFI~ll~~a--~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
.+|..+.+.|+++-.+- ..-..+|..+-++|++-.=.+--..|+=|-|.+|...
T Consensus 337 ~~l~~il~~~~~~R~~~~~rR~~~~l~k~~~rl~il~Gl~ia~~~iDevI~iIR~s 392 (735)
T TIGR01062 337 KNLLEILQEWLVFRRNTVIRRLTYRLNKVLQRLHILEGLRIAFLNIDEVIEIIREE 392 (735)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHcC
Confidence 35555666665554321 1123344445555544443333333444444455433
No 265
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=26.02 E-value=1e+02 Score=28.62 Aligned_cols=48 Identities=19% Similarity=0.212 Sum_probs=38.8
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccC
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (295)
.+.++++++ .+.+.+.++|+.|+|+..-|+==+..||.-|+|.|.-..
T Consensus 8 ~~Il~~l~~--~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~~GG 55 (252)
T PRK10906 8 DAIIELVKQ--QGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRHHGG 55 (252)
T ss_pred HHHHHHHHH--cCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCC
Confidence 456777753 568999999999999888777778999999999887433
No 266
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=26.01 E-value=1.2e+02 Score=26.20 Aligned_cols=43 Identities=16% Similarity=0.181 Sum_probs=35.5
Q ss_pred HHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 142 NLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 142 ~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
-++-..++..+.+.++|+.+++.+.-+.=|+..|.--|||+-.
T Consensus 15 ~~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~ 57 (153)
T PRK11920 15 MYCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETV 57 (153)
T ss_pred HHHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence 3444556677899999999999999999999999999988754
No 267
>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=25.98 E-value=1.2e+02 Score=32.41 Aligned_cols=55 Identities=16% Similarity=0.319 Sum_probs=45.9
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhh----hhhhhhhhhHhhhccceeccccCceEEe
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQ----KRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~Vq----KRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (295)
.+.++++...+...+...+++..|++. |.-++.+++-|+.-|.|.+..++.|...
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 357788888888999999999999984 4559999999999999998777766554
No 268
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=25.88 E-value=1.6e+02 Score=31.75 Aligned_cols=49 Identities=20% Similarity=0.390 Sum_probs=30.9
Q ss_pred cCceEEecCCCCCC--c--h-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 186 KNHIRWKGSDSLGT--S--K-LDDQVARLKAEIESLHAEECRIDDSIREKQELI 234 (295)
Q Consensus 186 KN~i~W~G~~~s~~--~--~-~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L 234 (295)
+.++.|.|...... + + ...+-.+|++|++.|..+-..||..|+.+..++
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 55699998764321 0 1 112334677788888888888888777665543
No 269
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=25.77 E-value=95 Score=29.20 Aligned_cols=39 Identities=21% Similarity=0.300 Sum_probs=33.6
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhH
Q 022537 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNV 174 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNV 174 (295)
..++.+.++.+.....+++.++|+.+++.+|.++-+..-
T Consensus 192 ~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~ 230 (302)
T PRK10371 192 YVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQR 230 (302)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 467788889888888999999999999999988877654
No 270
>COG3888 Predicted transcriptional regulator [Transcription]
Probab=25.67 E-value=1.4e+02 Score=29.47 Aligned_cols=62 Identities=19% Similarity=0.321 Sum_probs=54.3
Q ss_pred HHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc---ccCceEEecCC
Q 022537 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT---SKNHIRWKGSD 195 (295)
Q Consensus 134 glLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~---~KN~i~W~G~~ 195 (295)
..+-.|.+..|+.+...-+|=.++.+.+|++|-++-..+.-||..|+|.++ +|+.=.|....
T Consensus 3 M~~reklir~Lk~a~~~GI~Q~eIeel~GlSKStvSEaLs~LE~~giv~RrkvsGKs~rVwLaey 67 (321)
T COG3888 3 MSLREKLIRELKRAGPEGIDQTEIEELMGLSKSTVSEALSELEKQGIVKRRKVSGKSKRVWLAEY 67 (321)
T ss_pred ccHHHHHHHHHHhcCCCCccHHHHHHHhCcchhHHHHHHHHHHhcCeeeeeeecCcceEEeeccc
Confidence 346678999999888877999999999999999999999999999999987 57888897644
No 271
>PF15358 TSKS: Testis-specific serine kinase substrate
Probab=25.63 E-value=1.3e+02 Score=31.30 Aligned_cols=64 Identities=30% Similarity=0.462 Sum_probs=36.1
Q ss_pred hhhhHhhhc--cceeccccCceEEecCCCCCCchhHHHHHHHHHHHHH----HH---HHHHHHHHHHHHHHHHHHHHh
Q 022537 170 DITNVLEGI--GLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIES----LH---AEECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 170 DItNVLEgI--GLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~----L~---~~E~~LD~lI~~~~~~L~~Lt 238 (295)
||+.+|+++ ||+ +.|++|.=.-.. ...+.++++.||.|..- |+ ++-.+|+..-..+.+..+.++
T Consensus 108 Di~~~l~gvnSGLv--rAKDSItSlKek---t~~vnQHVq~LQseCsvlsEnLErrrQEaeELEgyCsqLk~nCrkVt 180 (558)
T PF15358_consen 108 DITELLEGVNSGLV--RAKDSITSLKEK---TSRVNQHVQTLQSECSVLSENLERRRQEAEELEGYCSQLKENCRKVT 180 (558)
T ss_pred cHHHHHhhhcccce--ecccchhhHHHh---hHHHHHHHHHHHHHhHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 666666665 677 557776543322 23577788888877532 22 333445555555555554444
No 272
>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=25.49 E-value=4.3e+02 Score=22.63 Aligned_cols=38 Identities=21% Similarity=0.227 Sum_probs=23.1
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhccceec-cccCceEEec
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK-TSKNHIRWKG 193 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK-~~KN~i~W~G 193 (295)
+.+.++|+.+||..+-| =-.|.+|||.. ...|.++|-.
T Consensus 2 ~~IgevA~~~Gvs~~tL----RyYE~~GLl~~~r~~~g~R~Y~ 40 (142)
T TIGR01950 2 LTVGELAKRSGVAVSAL----HFYESKGLITSIRNSGNQRRYK 40 (142)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCccCCCCCEEEC
Confidence 56889999999976632 22355666653 2245566643
No 273
>PHA02542 41 41 helicase; Provisional
Probab=25.07 E-value=7.5e+02 Score=25.45 Aligned_cols=113 Identities=15% Similarity=0.184 Sum_probs=55.2
Q ss_pred eHHHHHHHhh--hhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCchhH-HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 153 DLNRTAEVLE--VQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLD-DQVARLKAEIESLHAEECRIDDSIRE 229 (295)
Q Consensus 153 dLn~aA~~L~--VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~-~~~~~Lk~El~~L~~~E~~LD~lI~~ 229 (295)
++...|+.+. ..+|+++++.+ +.+.++....++ .+.......+ ..+..+.+++..+......+.+.+..
T Consensus 86 n~~~ya~~v~~~~~~R~l~~~~~--~~~~~~~~~~~~------~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~ 157 (473)
T PHA02542 86 DLDWLVKETEKWCQDRAMYNALS--KAIEIQDNADKP------LEKRNKKLPDVGAIPDIMQEALAISFDSSVGHDYFED 157 (473)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHH--HHHHHHhccCCC------hhHhhhhccchhhHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 7777777764 48899988877 445444433211 0000000000 01223334444443334444444444
Q ss_pred HHHHHHHHhhhccccccccccHhhhhcCCCCCCCeEEEEeCCCCC
Q 022537 230 KQELIRTLEENENHQKYMFLTEEDIASLPCFQNQTLIAIKAPQAS 274 (295)
Q Consensus 230 ~~~~L~~Lted~~n~~~aYVT~eDI~~i~~f~~qTviAIKAP~gT 274 (295)
+.+...........-...|-.-+++.+ -.|+...+|+|=|+||.
T Consensus 158 ie~~~~~~~~~~~gi~TG~~~LD~~t~-gGl~~G~LiiIaarPgm 201 (473)
T PHA02542 158 YEERYDSYQSKANKIPFKLEILNKITK-GGAERKTLNVLLAGVNV 201 (473)
T ss_pred HHHHHhhccCCCCccCCCcHHHHHhcc-CCCCCCcEEEEEcCCCc
Confidence 333221101111122345555555541 27888999999999984
No 274
>PRK09343 prefoldin subunit beta; Provisional
Probab=24.83 E-value=2.8e+02 Score=23.18 Aligned_cols=32 Identities=19% Similarity=0.295 Sum_probs=20.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
.|...++.++.....|+.....++.++.++..
T Consensus 75 ~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~ 106 (121)
T PRK09343 75 ELKERKELLELRSRTLEKQEKKLREKLKELQA 106 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555566666677777777777777766653
No 275
>PF04102 SlyX: SlyX; InterPro: IPR007236 The SlyX protein has no known function. It is short, less than 80 amino acids, and its gene is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C terminus. The protein may be a coiled-coil structure.; PDB: 3EFG_A.
Probab=24.73 E-value=1.8e+02 Score=22.00 Aligned_cols=38 Identities=21% Similarity=0.371 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
+..+..|.+.+.....+-..|...++.+.++|+++.+.
T Consensus 17 e~~ie~Ln~~v~~Qq~~I~~L~~~l~~L~~rl~~~~~~ 54 (69)
T PF04102_consen 17 EDTIEELNDVVTEQQRQIDRLQRQLRLLRERLRELEDP 54 (69)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHT-------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
No 276
>PF14830 Haemocyan_bet_s: Haemocyanin beta-sandwich; PDB: 1JS8_B 3QJO_A 1LNL_A.
Probab=24.72 E-value=27 Score=29.25 Aligned_cols=14 Identities=50% Similarity=0.821 Sum_probs=10.1
Q ss_pred hhhhhhHhhhccce
Q 022537 168 IYDITNVLEGIGLI 181 (295)
Q Consensus 168 IYDItNVLEgIGLI 181 (295)
=||||.+|+.+||=
T Consensus 57 kydIT~~l~~l~l~ 70 (103)
T PF14830_consen 57 KYDITDALKKLGLH 70 (103)
T ss_dssp EEE-HHHHHHCT--
T ss_pred hhhHHHHHHHcCCC
Confidence 48999999999986
No 277
>TIGR00634 recN DNA repair protein RecN. All proteins in this family for which functions are known are ATP binding proteins involved in the initiation of recombination and recombinational repair.
Probab=24.65 E-value=1.5e+02 Score=30.70 Aligned_cols=57 Identities=21% Similarity=0.381 Sum_probs=26.7
Q ss_pred ceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCchhHHHHHHHHHHHHHHH
Q 022537 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLH 217 (295)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~ 217 (295)
.-+|...++.+.+.--|+.+|-+=|..+.=..|+ .|.+ ..++.....+++.|++.|.
T Consensus 286 ~~~l~~~~~~l~~dp~~L~ele~RL~~l~~LkrK-------yg~s---~e~l~~~~~~l~~eL~~l~ 342 (563)
T TIGR00634 286 TRELQNYLDELEFDPERLNEIEERLAQIKRLKRK-------YGAS---VEEVLEYAEKIKEELDQLD 342 (563)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHH-------hCCC---HHHHHHHHHHHHHHHHHHh
Confidence 3344555555555555566655555544433333 1222 2234444555555555443
No 278
>PTZ00446 vacuolar sorting protein SNF7-like; Provisional
Probab=24.59 E-value=2.9e+02 Score=25.42 Aligned_cols=38 Identities=11% Similarity=0.275 Sum_probs=32.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
....+..|+..++.|...+..|+..|..+.+..+....
T Consensus 25 ~~~AIl~Lk~~~~~L~krq~~Le~kIe~e~~~Ak~~~~ 62 (191)
T PTZ00446 25 IYKAILKNREAIDALEKKQVQVEKKIKQLEIEAKQKVE 62 (191)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55668889999999999999999999988887776553
No 279
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=24.31 E-value=2.3e+02 Score=27.29 Aligned_cols=70 Identities=20% Similarity=0.270 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcc-ccccccccHhhhhcC-------CCCCCCeEEEEeCCCCCeEEec
Q 022537 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEENEN-HQKYMFLTEEDIASL-------PCFQNQTLIAIKAPQASYIEVP 279 (295)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~-n~~~aYVT~eDI~~i-------~~f~~qTviAIKAP~gT~LEVP 279 (295)
.|+.+++.|...-..+...+..+..+|.++....+ ++. +|..||..| ..+.+=.++.+. |+.|++-
T Consensus 234 el~~el~~l~~~i~~~~~~k~~l~~eI~e~~~~~~~~r~---~t~~Ev~~Lk~~~~~Le~~~gw~~~~~~---~~~l~~~ 307 (325)
T PF08317_consen 234 ELQEELEELEEKIEELEEQKQELLAEIAEAEKIREECRG---WTRSEVKRLKAKVDALEKLTGWKIVSIS---GSTLEFR 307 (325)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC---CCHHHHHHHHHHHHHHHHHHCcEEEEEe---CCeEEEE
Confidence 44455555555555666666666666666554332 332 367776654 223344444444 7788876
Q ss_pred CCCC
Q 022537 280 DPDE 283 (295)
Q Consensus 280 dP~e 283 (295)
-.++
T Consensus 308 ~~~~ 311 (325)
T PF08317_consen 308 YKDE 311 (325)
T ss_pred EcCE
Confidence 6555
No 280
>PRK05560 DNA gyrase subunit A; Validated
Probab=24.30 E-value=1.8e+02 Score=31.81 Aligned_cols=16 Identities=31% Similarity=0.553 Sum_probs=9.9
Q ss_pred CCCCc-eeeeecCCCCC
Q 022537 280 DPDEN-RILVSSKGNIK 295 (295)
Q Consensus 280 dP~e~-~~l~s~~G~I~ 295 (295)
.++|+ .+++|.+|-||
T Consensus 495 I~~E~v~vllS~~GyIK 511 (805)
T PRK05560 495 IPEEDVVVTLTHGGYIK 511 (805)
T ss_pred cCCCCEEEEEeCCCEEE
Confidence 44555 46778888654
No 281
>PRK03963 V-type ATP synthase subunit E; Provisional
Probab=24.25 E-value=3.6e+02 Score=23.66 Aligned_cols=31 Identities=19% Similarity=0.278 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 210 KAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 210 k~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
+...+.|..+++-+++++..+.++|.++..+
T Consensus 70 e~r~~~l~ar~el~~~v~~~a~~~l~~~~~~ 100 (198)
T PRK03963 70 EVRRKRLAVQEELISEVLEAVRERLAELPED 100 (198)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 3345667788888999999999999887764
No 282
>PRK09462 fur ferric uptake regulator; Provisional
Probab=24.19 E-value=1.5e+02 Score=25.04 Aligned_cols=46 Identities=15% Similarity=0.403 Sum_probs=38.0
Q ss_pred HHHHHHhCCCCceeHHHHHHHh-----hhhhhhhhhhhhHhhhccceeccc
Q 022537 140 FINLIQEAKDGTLDLNRTAEVL-----EVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L-----~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.+++|.+..++.++..++-+.| .+.+=-+|-+++.|+..|||.+..
T Consensus 22 Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 22 ILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 6677776667788888888888 357788999999999999999864
No 283
>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=24.16 E-value=2.5e+02 Score=24.22 Aligned_cols=8 Identities=13% Similarity=0.297 Sum_probs=4.9
Q ss_pred ccHhhhhc
Q 022537 249 LTEEDIAS 256 (295)
Q Consensus 249 VT~eDI~~ 256 (295)
||.+|+..
T Consensus 142 vs~ee~~~ 149 (169)
T PF07106_consen 142 VSPEEKEK 149 (169)
T ss_pred CCHHHHHH
Confidence 66666654
No 284
>TIGR02787 codY_Gpos GTP-sensing transcriptional pleiotropic repressor CodY. This model represents the full length of CodY, a pleiotropic repressor in Bacillus subtilis and other Firmicutes (low-GC Gram-positive bacteria) that responds to intracellular levels of GTP and branched chain amino acids. The C-terminal helix-turn-helix DNA-binding region is modeled by pfam08222 in Pfam.
Probab=23.92 E-value=1.3e+02 Score=28.93 Aligned_cols=38 Identities=26% Similarity=0.407 Sum_probs=35.7
Q ss_pred CCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
.++.+.-.++|+++||+|=-+-.-+-.||.-|+|+-.+
T Consensus 195 ~egrlse~eLAerlGVSRs~ireAlrkLE~aGvIe~r~ 232 (251)
T TIGR02787 195 NEGLLVASKIADRVGITRSVIVNALRKLESAGVIESRS 232 (251)
T ss_pred ccccccHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 36899999999999999999999999999999999886
No 285
>PF14178 YppF: YppF-like protein
Probab=23.60 E-value=1.4e+02 Score=22.91 Aligned_cols=50 Identities=22% Similarity=0.260 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHh----hhhhhhhhhhhhHhhhcccee
Q 022537 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVL----EVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L----~VqKRRIYDItNVLEgIGLIe 182 (295)
|..|-++|++.-...|...-.|-..|+++ .+.=++.++++-+||..|-+.
T Consensus 3 l~eLk~~F~~~k~y~p~~~NeLLDFar~~Yi~gei~i~eYR~lvreLE~~GA~~ 56 (60)
T PF14178_consen 3 LHELKQKFMQKKKYEPEDMNELLDFARKLYIQGEISINEYRNLVRELEANGAVS 56 (60)
T ss_pred HHHHHHHHHHHhccCcccHHHHHHHHHHHHHhCcccHHHHHHHHHHHHHhCCCC
Confidence 67788999999888888777777778877 457788999999999988654
No 286
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=23.47 E-value=4.4e+02 Score=22.00 Aligned_cols=81 Identities=15% Similarity=0.129 Sum_probs=0.0
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhcccee--ccccCceEEe-----------------------------cCCCCCCc
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWK-----------------------------GSDSLGTS 200 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~-----------------------------G~~~s~~~ 200 (295)
+.+.++|+.+||+.+ -+-..|..|||. +...|.|++- ........
T Consensus 2 ~~I~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~~~~~~~~ 77 (131)
T TIGR02043 2 FQIGELAKLCGVTSD----TLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIKLDATEH 77 (131)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhccCCCC
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRT 236 (295)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~ 236 (295)
........|+..++.|+++.++|..+...+.+-+..
T Consensus 78 ~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~ 113 (131)
T TIGR02043 78 SCAEVKAIVDAKLELVDEKINELTKIRRSLKKLSDA 113 (131)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 287
>PF06717 DUF1202: Protein of unknown function (DUF1202); InterPro: IPR009592 This family consists of several hypothetical bacterial proteins of around 335 residues in length. Members of this family are found exclusively in Escherichia coli and Salmonella species and are often referred to as YggM proteins. The function of this family is unknown.
Probab=23.44 E-value=2.6e+02 Score=27.72 Aligned_cols=52 Identities=13% Similarity=0.218 Sum_probs=34.3
Q ss_pred ccceeccccCceEEecCCCCCCchhHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 178 IGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKA-------EIESLHAEECRIDDSIREKQELIRT 236 (295)
Q Consensus 178 IGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~-------El~~L~~~E~~LD~lI~~~~~~L~~ 236 (295)
|..|.... ..+.|.+.+ ...+++.+++ -+..|+.++.+||..|..++.++..
T Consensus 119 v~~i~tn~-KYLIvn~~~------F~~rf~~Ied~~~~kK~~I~~L~~qisaLdkqi~ai~Kkid~ 177 (308)
T PF06717_consen 119 VPDIKTND-KYLIVNDQD------FNYRFNQIEDEYNRKKNKIPGLNKQISALDKQIVAINKKIDR 177 (308)
T ss_pred CCccccCC-cEEEecchh------HHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34455554 457787754 3344555544 4678888888888888888777765
No 288
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=23.36 E-value=93 Score=21.23 Aligned_cols=30 Identities=20% Similarity=0.257 Sum_probs=25.0
Q ss_pred HHHHHHhCCCCceeHHHHHHHhhhhhhhhh
Q 022537 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIY 169 (295)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIY 169 (295)
-++++.+.+-..+.+.++|+++||.|.-||
T Consensus 5 a~~l~~~~G~~~~s~~~Ia~~~gvs~~~~y 34 (47)
T PF00440_consen 5 ALELFAEKGYEAVSIRDIARRAGVSKGSFY 34 (47)
T ss_dssp HHHHHHHHHTTTSSHHHHHHHHTSCHHHHH
T ss_pred HHHHHHHhCHHhCCHHHHHHHHccchhhHH
Confidence 345666667778999999999999999988
No 289
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=23.35 E-value=85 Score=30.24 Aligned_cols=39 Identities=23% Similarity=0.376 Sum_probs=32.0
Q ss_pred HHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccce
Q 022537 141 INLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLI 181 (295)
Q Consensus 141 I~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 181 (295)
|.++...+. +...++|+.++|++|-||==+|-|..+|+=
T Consensus 14 i~~L~~~~~--vta~~lA~~~~VS~RTi~RDi~~L~~~gvP 52 (311)
T COG2378 14 IQILRAKET--VTAAELADEFEVSVRTIYRDIATLRAAGVP 52 (311)
T ss_pred HHHHHhCcc--chHHHHHHhcCCCHHHHHHHHHHHHHCCCC
Confidence 334444443 999999999999999999999999999984
No 290
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=23.29 E-value=1.2e+02 Score=28.04 Aligned_cols=44 Identities=18% Similarity=0.309 Sum_probs=33.0
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
+.++++++ .+.+.+.++|+.|+|+.--|.==++.||.-|+|.|.
T Consensus 9 ~Il~~L~~--~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 9 AILEYLQK--QGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHHH--cCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 45666653 567999999999999643333226779999999887
No 291
>PRK15185 transcriptional regulator HilD; Provisional
Probab=23.29 E-value=1.1e+02 Score=30.05 Aligned_cols=39 Identities=13% Similarity=0.177 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
.+..+...++.+.+...+++.++|+.+++++|.++-...
T Consensus 206 ~~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK 244 (309)
T PRK15185 206 TLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLA 244 (309)
T ss_pred HHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 366788889989999999999999999999999876643
No 292
>PF05584 Sulfolobus_pRN: Sulfolobus plasmid regulatory protein; InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=23.26 E-value=1.8e+02 Score=22.98 Aligned_cols=46 Identities=20% Similarity=0.305 Sum_probs=40.3
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
++.+++..+... .+.|+++-+..|+.|--+-=.++=|..-|+|++.
T Consensus 6 ~~~~IL~~ls~~---c~TLeeL~ekTgi~k~~LlV~LsrL~k~GiI~Rk 51 (72)
T PF05584_consen 6 VTQKILIILSKR---CCTLEELEEKTGISKNTLLVYLSRLAKRGIIERK 51 (72)
T ss_pred HHHHHHHHHHhc---cCCHHHHHHHHCCCHHHHHHHHHHHHHCCCeeee
Confidence 456777777655 8899999999999999999999999999999987
No 293
>PF07830 PP2C_C: Protein serine/threonine phosphatase 2C, C-terminal domain; InterPro: IPR012911 Protein phosphatase 2C (PP2C) is involved in regulating cellular responses to stress in various eukaryotes. It consists of two domains: an N-terminal catalytic domain and a C-terminal domain characteristic of mammalian PP2Cs. This domain consists of three antiparallel alpha helices, one of which packs against two corresponding alpha-helices of the N-terminal domain. The C-terminal domain does not seem to play a role in catalysis, but it may provide protein substrate specificity due to the cleft that is created between it and the catalytic domain []. ; GO: 0000287 magnesium ion binding, 0004721 phosphoprotein phosphatase activity, 0030145 manganese ion binding; PDB: 2P8E_A 3FXL_A 3FXO_A 1A6Q_A 3FXK_A 3FXM_A 3FXJ_A.
Probab=23.15 E-value=78 Score=25.38 Aligned_cols=42 Identities=24% Similarity=0.443 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhcccccccccc----HhhhhcCC
Q 022537 217 HAEECRIDDSIREKQELIRTLEENENHQKYMFLT----EEDIASLP 258 (295)
Q Consensus 217 ~~~E~~LD~lI~~~~~~L~~Lted~~n~~~aYVT----~eDI~~i~ 258 (295)
.++|++||++|...-..+-+-..+..+..+.||= .+||-+||
T Consensus 18 v~~E~eLd~~l~~rv~ei~~~~~~~~~~~l~~V~~~L~~e~ip~LP 63 (81)
T PF07830_consen 18 VKKEAELDKYLEQRVEEIIEKSSEEENPDLVYVMRTLASEDIPGLP 63 (81)
T ss_dssp HHHHHHHHHHHHHHHHHHT----------HHHHHHHHHHTT-SS--
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCCHHHHHHHHHhccCCCCc
Confidence 4567788888776544443333334444454553 34455544
No 294
>PRK10884 SH3 domain-containing protein; Provisional
Probab=23.09 E-value=1.6e+02 Score=27.18 Aligned_cols=22 Identities=18% Similarity=0.356 Sum_probs=8.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 022537 213 IESLHAEECRIDDSIREKQELI 234 (295)
Q Consensus 213 l~~L~~~E~~LD~lI~~~~~~L 234 (295)
+.+|+.+-++|.+.+..++.++
T Consensus 134 ~~~L~~~n~~L~~~l~~~~~~~ 155 (206)
T PRK10884 134 INGLKEENQKLKNQLIVAQKKV 155 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444443333
No 295
>TIGR03697 NtcA_cyano global nitrogen regulator NtcA, cyanobacterial. Members of this protein family, found in the cyanobacteria, are the global nitrogen regulator NtcA. This DNA-binding transcriptional regulator is required for expressing many different ammonia-repressible genes. The consensus NtcA-binding site is G T A N(8)T A C.
Probab=23.07 E-value=2.1e+02 Score=24.00 Aligned_cols=41 Identities=20% Similarity=0.161 Sum_probs=35.3
Q ss_pred ceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEe
Q 022537 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (295)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (295)
.+.-.++|+.||+.|.-+.-+++-|+.-|+|+... ++|...
T Consensus 143 ~~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~~-~~i~I~ 183 (193)
T TIGR03697 143 RLSHQAIAEAIGSTRVTITRLLGDLRKKKLISIHK-KKITVH 183 (193)
T ss_pred CCCHHHHHHHhCCcHHHHHHHHHHHHHCCCEEecC-CEEEEe
Confidence 35789999999999999999999999999999874 556653
No 296
>PF07889 DUF1664: Protein of unknown function (DUF1664); InterPro: IPR012458 The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=23.06 E-value=2.6e+02 Score=24.12 Aligned_cols=10 Identities=30% Similarity=0.501 Sum_probs=7.0
Q ss_pred ceEEecCCCC
Q 022537 188 HIRWKGSDSL 197 (295)
Q Consensus 188 ~i~W~G~~~s 197 (295)
.+.|+|...+
T Consensus 22 Y~wwKGws~s 31 (126)
T PF07889_consen 22 YMWWKGWSFS 31 (126)
T ss_pred eeeecCCchh
Confidence 4678998653
No 297
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=23.00 E-value=1e+02 Score=22.78 Aligned_cols=47 Identities=6% Similarity=0.018 Sum_probs=32.8
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
.+.+..|.+.-+..-...++|..||+...++++++........+...
T Consensus 7 ~~a~~~L~~~lgr~Pt~eEiA~~lgis~~~v~~~l~~~~~~~Sl~~~ 53 (78)
T PF04539_consen 7 ERARRELEQELGREPTDEEIAEELGISVEEVRELLQASRRPVSLDLP 53 (78)
T ss_dssp HHHHHHHHHHHSS--BHHHHHHHHTS-HHHHHHHHHHHSCCEESSHC
T ss_pred HHHHHHHHHHhCCCCCHHHHHHHHcccHHHHHHHHHhCCCCeEEeee
Confidence 34455555556677899999999999999999999877665555443
No 298
>PF14282 FlxA: FlxA-like protein
Probab=22.91 E-value=1.9e+02 Score=23.75 Aligned_cols=36 Identities=19% Similarity=0.345 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHh
Q 022537 203 DDQVARLKAEIESLHA-----------EECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~-----------~E~~LD~lI~~~~~~L~~Lt 238 (295)
..++..|+++|..|.. +...|...|..++.+|..+.
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 3344555555554433 22344555555555555543
No 299
>COG5625 Predicted transcription regulator containing HTH domain [Transcription]
Probab=22.91 E-value=2.8e+02 Score=23.71 Aligned_cols=46 Identities=17% Similarity=0.278 Sum_probs=35.3
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCC
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD 195 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~ 195 (295)
.+-+.+.+++..|++..|-..|-+-+|--=|++.+.-.. =-|.|.-
T Consensus 34 ~~~mri~ei~rEl~is~rtvr~~v~~l~rrGll~relvq-kgWvGYi 79 (113)
T COG5625 34 GRGMRIREIQRELGISERTVRAAVAVLLRRGLLARELVQ-KGWVGYI 79 (113)
T ss_pred cCCchHHHHHHHHhHHHHHHHHHHHHHHHhhHHHHHHHh-ccceeeE
Confidence 344788999999999999999999999877777654211 2388854
No 300
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=22.87 E-value=2.7e+02 Score=26.64 Aligned_cols=34 Identities=12% Similarity=0.245 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc
Q 022537 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (295)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~ 241 (295)
+|++|+..|.++...+.+.++.=.++|++|.+-.
T Consensus 77 ~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~LL~~~ 110 (283)
T TIGR00219 77 KLRQELLKKNQQLEILTQNLKQENVRLRELLNSP 110 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 4444444442222222222333355566666543
No 301
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=22.79 E-value=1.1e+02 Score=21.48 Aligned_cols=26 Identities=12% Similarity=0.248 Sum_probs=19.4
Q ss_pred CCceeHHHHHHHhhhhhhhhhhhhhH
Q 022537 149 DGTLDLNRTAEVLEVQKRRIYDITNV 174 (295)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNV 174 (295)
.|.+.+..||..+||.+.-|||-++-
T Consensus 14 ~g~~S~r~AA~~ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 14 NGKMSIRKAAKKYGVPRSTLRRRLRG 39 (45)
T ss_dssp TTSS-HHHHHHHHT--HHHHHHHHHH
T ss_pred hCCCCHHHHHHHHCcCHHHHHHHHcC
Confidence 44499999999999999999987764
No 302
>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=22.75 E-value=2.7e+02 Score=22.66 Aligned_cols=35 Identities=29% Similarity=0.373 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~L 237 (295)
....+.|+.+++.|...-..|...|.++...+..|
T Consensus 5 ~~q~~ql~~~i~~l~~~i~~l~~~i~e~~~~~~~L 39 (126)
T TIGR00293 5 AAELQILQQQVESLQAQIAALRALIAELETAIETL 39 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456677777777777777777777776665544
No 303
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.68 E-value=3.9e+02 Score=21.06 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=24.7
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhccceec--cccCceEEec
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEK--TSKNHIRWKG 193 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~~KN~i~W~G 193 (295)
.+.++|+.+||..+-|- -.|..|||.. ...|.|+.-.
T Consensus 2 ~i~eva~~~gvs~~tlR----~ye~~Gll~p~~r~~~gyR~Y~ 40 (96)
T cd04788 2 KIGELARRTGLSVRTLH----HYDHIGLLSPSQRTEGGHRLYD 40 (96)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCccCCCCceeeC
Confidence 57889999999877442 2356888864 3456666544
No 304
>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=22.63 E-value=2.2e+02 Score=22.69 Aligned_cols=35 Identities=17% Similarity=0.408 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~L 237 (295)
..++..|++.++.|..+-..+...|..+.+.|+.+
T Consensus 83 ~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~~ 117 (120)
T PF02996_consen 83 KKRIKELEEQLEKLEKELAELQAQIEQLEQTLQQL 117 (120)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555555555555555555544
No 305
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=22.61 E-value=67 Score=21.98 Aligned_cols=23 Identities=30% Similarity=0.354 Sum_probs=18.6
Q ss_pred ceeHHHHHHHhhhhhhhhhhhhh
Q 022537 151 TLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItN 173 (295)
-+...++|+.+|+.+..|+.+.|
T Consensus 9 gls~~~la~~~gis~~~i~~~~~ 31 (55)
T PF01381_consen 9 GLSQKELAEKLGISRSTISRIEN 31 (55)
T ss_dssp TS-HHHHHHHHTS-HHHHHHHHT
T ss_pred CCCHHHHHHHhCCCcchhHHHhc
Confidence 36779999999999999999876
No 306
>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=22.60 E-value=1.3e+02 Score=24.44 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=16.1
Q ss_pred eHHHHHHHhhhhhhhhhhhhhHhhhcccee
Q 022537 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (295)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (295)
.+.++|+.+||+.+-| --.|.+|||.
T Consensus 2 ~ige~a~~~gvs~~tL----ryYe~~GLi~ 27 (116)
T cd04769 2 YIGELAQQTGVTIKAI----RLYEEKGLLP 27 (116)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCC
Confidence 4667777777776532 3345667775
No 307
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.59 E-value=4e+02 Score=21.19 Aligned_cols=25 Identities=20% Similarity=0.324 Sum_probs=17.5
Q ss_pred eHHHHHHHhhhhhh--hhhhhhhHhhhccceec
Q 022537 153 DLNRTAEVLEVQKR--RIYDITNVLEGIGLIEK 183 (295)
Q Consensus 153 dLn~aA~~L~VqKR--RIYDItNVLEgIGLIeK 183 (295)
.+.++|+..||+.| |.|| .+|||.-
T Consensus 2 ~Ige~a~~~gvs~~tlRyYe------~~GLl~p 28 (107)
T cd04777 2 KIGKFAKKNNITIDTVRHYI------DLGLLIP 28 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHH------HCCCcCC
Confidence 47789999999877 4464 5566544
No 308
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=22.57 E-value=39 Score=31.79 Aligned_cols=29 Identities=34% Similarity=0.495 Sum_probs=25.7
Q ss_pred HHHHHHHhhhhhhhhhhhhhHhhhccceecc
Q 022537 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (295)
|..+|++|+|+.+++-+ |.+++||+|+-.
T Consensus 64 l~~larrlgv~~nt~s~--~a~~~l~~v~d~ 92 (224)
T KOG2255|consen 64 LDMLARRLGVPMNTISS--KALEGLGLVGDV 92 (224)
T ss_pred HHHHHHHhCCcccccCc--ccccceeeecce
Confidence 56678999999999999 999999999854
No 309
>smart00338 BRLZ basic region leucin zipper.
Probab=22.54 E-value=2.6e+02 Score=20.39 Aligned_cols=29 Identities=24% Similarity=0.296 Sum_probs=16.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 211 AEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 211 ~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
..+..|+.+-..|......+..++..|..
T Consensus 26 ~~~~~Le~~~~~L~~en~~L~~~~~~l~~ 54 (65)
T smart00338 26 AEIEELERKVEQLEAENERLKKEIERLRR 54 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666666666666666666555543
No 310
>PRK05638 threonine synthase; Validated
Probab=22.27 E-value=1.3e+02 Score=30.13 Aligned_cols=61 Identities=20% Similarity=0.308 Sum_probs=46.8
Q ss_pred CCCCCCCCCcCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhh--hhhhhhhhhhhHhhhccceecc
Q 022537 121 LNLSNGCRYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLE--VQKRRIYDITNVLEGIGLIEKT 184 (295)
Q Consensus 121 ~tp~~~~R~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIeK~ 184 (295)
.++....|-.-.++.+..+.+.+|.+. .....++++.|+ +.+--||-.+.+||.-|||+..
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 444455565555666666677777754 467889999998 8999999999999999999853
No 311
>COG0497 RecN ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=22.20 E-value=2.4e+02 Score=30.08 Aligned_cols=101 Identities=17% Similarity=0.268 Sum_probs=55.6
Q ss_pred CcCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCchhHHHHHH
Q 022537 129 YDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVAR 208 (295)
Q Consensus 129 ~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~ 208 (295)
+|..|..++..+=+.+-+-.+-.--|+.+++.|.+.-.|+..|-.=|.-+.-+.|+ .|.. ..++.....+
T Consensus 260 ~d~~l~~~~~~l~ea~~~l~ea~~el~~~~~~le~Dp~~L~~ve~Rl~~L~~l~RK-------Y~~~---~~~l~~~~~~ 329 (557)
T COG0497 260 YDGKLSELAELLEEALYELEEASEELRAYLDELEFDPNRLEEVEERLFALKSLARK-------YGVT---IEDLLEYLDK 329 (557)
T ss_pred cChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHH-------hCCC---HHHHHHHHHH
Confidence 34444444444443333333333446666666677777777776666665555554 1322 3356666778
Q ss_pred HHHHHHHHHHHHHHHHHHHH---HHHHHHHHHhh
Q 022537 209 LKAEIESLHAEECRIDDSIR---EKQELIRTLEE 239 (295)
Q Consensus 209 Lk~El~~L~~~E~~LD~lI~---~~~~~L~~Lte 239 (295)
+++|++.|...+..++++-. .+.+++....+
T Consensus 330 ~~~el~~L~~~~~~~~~Le~~~~~l~~~~~~~A~ 363 (557)
T COG0497 330 IKEELAQLDNSEESLEALEKEVKKLKAELLEAAE 363 (557)
T ss_pred HHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHH
Confidence 88888888766665444443 34444444333
No 312
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=22.12 E-value=3.5e+02 Score=28.44 Aligned_cols=59 Identities=12% Similarity=0.200 Sum_probs=0.0
Q ss_pred hhhhHhhhccceeccccCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 170 DITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 170 DItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
++..+|+..|+-+-. ... .+...+.++++++++++++.+.+.+++.++++.+....+..
T Consensus 192 ~~~~~l~~~~f~~~~---------~p~--~~~p~~~l~~l~~~l~~l~~~~~~~~~~l~~~~~~~~~~~~ 250 (646)
T PRK05771 192 EVEEELKKLGFERLE---------LEE--EGTPSELIREIKEELEEIEKERESLLEELKELAKKYLEELL 250 (646)
T ss_pred HHHHHHHHCCCEEec---------CCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 313
>PRK13502 transcriptional activator RhaR; Provisional
Probab=21.91 E-value=1.2e+02 Score=27.44 Aligned_cols=39 Identities=13% Similarity=0.171 Sum_probs=33.3
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhh
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (295)
.+..++++++.+.-...+.++++|..++++.|.+.-+.-
T Consensus 176 ~~~~~~~~~I~~~~~~~~~~~~lA~~~~iS~~~L~r~fk 214 (282)
T PRK13502 176 TLLDKLITALANSLECPFALDAFCQQEQCSERVLRQQFR 214 (282)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 356789999988877789999999999999999887764
No 314
>PRK09039 hypothetical protein; Validated
Probab=21.89 E-value=2.3e+02 Score=27.87 Aligned_cols=30 Identities=10% Similarity=0.142 Sum_probs=16.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022537 209 LKAEIESLHAEECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 209 Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lt 238 (295)
|+++|+.++.++...+..|..+.+.|+...
T Consensus 156 le~~L~~ae~~~~~~~~~i~~L~~~L~~a~ 185 (343)
T PRK09039 156 LEAALDASEKRDRESQAKIADLGRRLNVAL 185 (343)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444455555555666666666666665
No 315
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=21.60 E-value=2.1e+02 Score=25.03 Aligned_cols=41 Identities=12% Similarity=0.075 Sum_probs=33.2
Q ss_pred cCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhh
Q 022537 130 DSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYD 170 (295)
Q Consensus 130 d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYD 170 (295)
+..=..|-..-++++.+..-.-+.++++|+..||.+.-||-
T Consensus 17 ~~~r~~IL~AA~~lf~e~Gy~~~s~~dIA~~aGvs~gtiY~ 57 (212)
T PRK15008 17 SAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLY 57 (212)
T ss_pred HHHHHHHHHHHHHHHHHhCcccCCHHHHHHHhCcCHHHHHH
Confidence 33345566777888887777789999999999999999994
No 316
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is 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: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=21.38 E-value=3e+02 Score=19.57 Aligned_cols=26 Identities=19% Similarity=0.243 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 212 EIESLHAEECRIDDSIREKQELIRTL 237 (295)
Q Consensus 212 El~~L~~~E~~LD~lI~~~~~~L~~L 237 (295)
.+..|..+-..|......+.+++..|
T Consensus 26 ~~~~le~~~~~L~~en~~L~~~i~~L 51 (54)
T PF07716_consen 26 REEELEQEVQELEEENEQLRQEIAQL 51 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444444444
No 317
>PF12761 End3: Actin cytoskeleton-regulatory complex protein END3
Probab=21.34 E-value=2.5e+02 Score=26.03 Aligned_cols=17 Identities=24% Similarity=0.421 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHHh
Q 022537 222 RIDDSIREKQELIRTLE 238 (295)
Q Consensus 222 ~LD~lI~~~~~~L~~Lt 238 (295)
+|.+|+...+++|+++.
T Consensus 136 e~EqLL~YK~~ql~~~~ 152 (195)
T PF12761_consen 136 EFEQLLDYKERQLRELE 152 (195)
T ss_pred HHHHHHHHHHHHHHhhh
Confidence 45566666666666664
No 318
>PRK02793 phi X174 lysis protein; Provisional
Probab=21.28 E-value=3.9e+02 Score=20.60 Aligned_cols=36 Identities=11% Similarity=0.204 Sum_probs=18.2
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~L 237 (295)
++.++..|...+..++.--..|++.+..-+++|..|
T Consensus 6 ~e~Ri~~LE~~lafQe~tIe~Ln~~v~~Qq~~I~~L 41 (72)
T PRK02793 6 LEARLAELESRLAFQEITIEELNVTVTAHEMEMAKL 41 (72)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566666555555544455555444444444433
No 319
>PF11853 DUF3373: Protein of unknown function (DUF3373); InterPro: IPR021803 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=21.25 E-value=90 Score=32.61 Aligned_cols=37 Identities=16% Similarity=0.320 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
..+++.+| +|++|++|-++|.+++.++++++..+...
T Consensus 24 ~~~~~~~q-kie~L~kql~~Lk~q~~~l~~~v~k~e~~ 60 (489)
T PF11853_consen 24 ADDIDLLQ-KIEALKKQLEELKAQQDDLNDRVDKVEKH 60 (489)
T ss_pred hhhhHHHH-HHHHHHHHHHHHHHhhcccccccchhhHh
Confidence 44555666 89999988888888888888877665543
No 320
>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Probab=21.11 E-value=3.1e+02 Score=23.21 Aligned_cols=37 Identities=16% Similarity=0.363 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
.++..++.|+..+...+..|...++.....++...++
T Consensus 80 ~~~~~~ere~~~~~~~~~~l~~~~~~~~~~~k~~kee 116 (151)
T PF11559_consen 80 EQLEELERELASAEEKERQLQKQLKSLEAKLKQEKEE 116 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566666666777777777666666666654
No 321
>PF08181 DegQ: DegQ (SacQ) family; InterPro: IPR012554 This family consists of the DegQ (formerly sacQ) regulatory peptides. The DegQ family of peptides control the rates of synthesis of a class of both secreted and intracellular degradative enzymes in Bacillus subtilis. DegQ is 46 amino acids long and activates the synthesis of degradative enzymes. The expression of this peptide was shown to be subjected both to catabolite repression and DegS-DegU-mediated control. Thus allowing an increase in the rate of synthesis of degQ under conditions of nitrogen starvation [].
Probab=21.10 E-value=2.4e+02 Score=20.34 Aligned_cols=39 Identities=26% Similarity=0.520 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhhc-cccccccc
Q 022537 211 AEIESLHAEECRIDDSIREKQELIRTLEENE-NHQKYMFL 249 (295)
Q Consensus 211 ~El~~L~~~E~~LD~lI~~~~~~L~~Lted~-~n~~~aYV 249 (295)
.+++.|.+---+|+.-|++-..+|+++...- +..+|.|+
T Consensus 4 ~~ieelkqll~rle~eirett~sl~ninksidq~dk~~y~ 43 (46)
T PF08181_consen 4 KKIEELKQLLWRLENEIRETTDSLRNINKSIDQYDKYTYM 43 (46)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHhchhhh
Confidence 3455555555667777777777777765321 22356664
No 322
>PF11972 HTH_13: HTH DNA binding domain; InterPro: IPR021068 The proteins in this entry have not been characterised. They contain a C-terminal helix-turn-helix DNA binding domain.
Probab=20.98 E-value=1.9e+02 Score=21.72 Aligned_cols=47 Identities=21% Similarity=0.321 Sum_probs=36.3
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceE
Q 022537 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (295)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (295)
.+++++-+.| .++...+++.|+|..+---. .++.+|+-|-++..+|+
T Consensus 3 ~Lidll~~~P--~Vsa~mva~~L~vT~~~A~~---li~eLg~rEiTGr~R~R 49 (54)
T PF11972_consen 3 RLIDLLLSRP--LVSAPMVAKELGVTPQAAQR---LIAELGLREITGRGRYR 49 (54)
T ss_pred HHHHHHHhCc--cccHHHHHHHhCCCHHHHHH---HHHHhhceeecCCcccc
Confidence 4778887776 78999999999998876544 45778887777777665
No 323
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=20.98 E-value=1.3e+02 Score=28.91 Aligned_cols=38 Identities=13% Similarity=0.093 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhh
Q 022537 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDIT 172 (295)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDIt 172 (295)
.+..++++++.+.....+.+.++|..+++++|.++-..
T Consensus 142 ~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~F 179 (274)
T PRK09978 142 NMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKL 179 (274)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHH
Confidence 35678999999999999999999999999999887665
No 324
>PF04521 Viral_P18: ssRNA positive strand viral 18kD cysteine rich protein; InterPro: IPR007609 This family represents the 18kDa cysteine-rich protein from ssRNA positive strand viruses.
Probab=20.97 E-value=2.3e+02 Score=24.57 Aligned_cols=31 Identities=23% Similarity=0.335 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 205 QVARLKAEIESLHAEECRIDDSIREKQELIR 235 (295)
Q Consensus 205 ~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~ 235 (295)
++..++.|++.|+.+|..|-..|+.+.+.-+
T Consensus 73 ~l~~~~~~L~~Le~r~e~Lk~~~~~~~~~~~ 103 (120)
T PF04521_consen 73 QLSDLNLELEKLERREEQLKTQIQVLTAAAK 103 (120)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3566788899999888888887777655543
No 325
>PRK01194 V-type ATP synthase subunit E; Provisional
Probab=20.97 E-value=2.6e+02 Score=25.01 Aligned_cols=32 Identities=9% Similarity=0.074 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 208 RLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 208 ~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
.|+.....|..++.-|++.+..+.++|.+|..
T Consensus 67 ~Le~R~~~L~aree~I~~v~~~a~e~L~~l~~ 98 (185)
T PRK01194 67 NIEARSIKREKRREILKDYLDIAYEHLMNITK 98 (185)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHcccC
Confidence 45555678899999999999999999999984
No 326
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=20.95 E-value=1.1e+02 Score=23.84 Aligned_cols=25 Identities=40% Similarity=0.591 Sum_probs=18.7
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHH
Q 022537 199 TSKLDDQVARLKAEIESLHAEECRI 223 (295)
Q Consensus 199 ~~~~~~~~~~Lk~El~~L~~~E~~L 223 (295)
.+++++++..||+|++.|+.+-..-
T Consensus 27 V~El~eRIalLq~EIeRlkAe~~kK 51 (65)
T COG5509 27 VAELEERIALLQAEIERLKAELAKK 51 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4577888888899998887765443
No 327
>KOG4057 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.91 E-value=1.8e+02 Score=26.45 Aligned_cols=38 Identities=26% Similarity=0.346 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhcccccc
Q 022537 209 LKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKY 246 (295)
Q Consensus 209 Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~n~~~ 246 (295)
|.+.|..|..-|+++|.+++...+-|.+|-..+.+.+.
T Consensus 7 ~~dri~Al~~iEkeI~~~mq~Ag~iiqeLgKEK~~~kn 44 (180)
T KOG4057|consen 7 LTDRIQALVTIEKEIDEMMQCAGEIIQELGKEKQIGKN 44 (180)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHhhhhhh
Confidence 34556777888888888888888888888776666554
No 328
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=20.87 E-value=1.4e+02 Score=28.37 Aligned_cols=35 Identities=6% Similarity=0.172 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (295)
Q Consensus 203 ~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~L 237 (295)
..++...+.++..|+..+++|+.+|...++.--+.
T Consensus 35 r~kq~~v~~~l~eLe~~~~el~~~i~~~k~~~~~~ 69 (236)
T PF12269_consen 35 RKKQQKVRNRLQELEKRFKELEAIIARAKQFTVDQ 69 (236)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCc
Confidence 33445567788999999999999999887664443
No 329
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=20.87 E-value=1.1e+02 Score=25.09 Aligned_cols=43 Identities=28% Similarity=0.454 Sum_probs=33.8
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccc
Q 022537 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (295)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (295)
..|..++.+.|+- .|.++|..|+|....|+ ..|.-+|+.-|+.
T Consensus 60 ~~L~~~v~~~pd~--tl~Ela~~l~Vs~~ti~---~~Lkrlg~t~KK~ 102 (119)
T PF01710_consen 60 DELKALVEENPDA--TLRELAERLGVSPSTIW---RALKRLGITRKKK 102 (119)
T ss_pred HHHHHHHHHCCCc--CHHHHHHHcCCCHHHHH---HHHHHcCchhccC
Confidence 5588888877765 45789999999877776 6678889988873
No 330
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=20.86 E-value=6.1e+02 Score=22.64 Aligned_cols=51 Identities=20% Similarity=0.233 Sum_probs=35.7
Q ss_pred CCcCcHHHHHHHHHHHHH-hCCCCc---------------eeHHHHHHHhhh-hhhhhhhhhhHhhhccc
Q 022537 128 RYDSSLGLLTRKFINLIQ-EAKDGT---------------LDLNRTAEVLEV-QKRRIYDITNVLEGIGL 180 (295)
Q Consensus 128 R~d~SLglLTkkFI~ll~-~a~~g~---------------ldLn~aA~~L~V-qKRRIYDItNVLEgIGL 180 (295)
.++-+...|.++|..+-. -+||.. -.||.|=..|.- .+|..|++ .|.|+.+
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 456677889999998875 355532 356777777766 57889988 5557655
No 331
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.85 E-value=2.8e+02 Score=22.21 Aligned_cols=34 Identities=24% Similarity=0.390 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022537 205 QVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 205 ~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lt 238 (295)
.++-||-|++.|+.+-..|.+-.+.++.+...|.
T Consensus 19 TI~LLQmEieELKEknn~l~~e~q~~q~~reaL~ 52 (79)
T COG3074 19 TITLLQMEIEELKEKNNSLSQEVQNAQHQREALE 52 (79)
T ss_pred HHHHHHHHHHHHHHHhhHhHHHHHHHHHHHHHHH
Confidence 3556777777777777766666666665555543
No 332
>COG5124 Protein predicted to be involved in meiotic recombination [Cell division and chromosome partitioning / General function prediction only]
Probab=20.80 E-value=2.5e+02 Score=26.24 Aligned_cols=63 Identities=24% Similarity=0.366 Sum_probs=39.3
Q ss_pred hhhhhhhHhhhccce--eccccCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 167 RIYDITNVLEGIGLI--EKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREK 230 (295)
Q Consensus 167 RIYDItNVLEgIGLI--eK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~ 230 (295)
-+-||+..|-.=|+| +|.+-.+|.|- +..-.-.........|+++++++.+.-..+++-|..-
T Consensus 44 tVKd~lQqlVDDgvV~~EK~GtsN~YWs-F~s~~~qk~~~~~~~l~~~~~~~kqdi~t~~e~i~~e 108 (209)
T COG5124 44 TVKDLLQQLVDDGVVSVEKCGTSNIYWS-FKSQTLQKLYDSSELLKKKIQEVKQDIATYKEEIDKE 108 (209)
T ss_pred HHHHHHHHHhhcCceeeeeeccceeEEe-cchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHH
Confidence 455777777666665 68899999995 3211111222334567777777777777777777643
No 333
>PRK04406 hypothetical protein; Provisional
Probab=20.78 E-value=3.8e+02 Score=20.92 Aligned_cols=37 Identities=16% Similarity=0.388 Sum_probs=19.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lt 238 (295)
+..++..|...+..++..-..|++.+..-+++|..|.
T Consensus 9 le~Ri~~LE~~lAfQE~tIe~LN~~v~~Qq~~I~~L~ 45 (75)
T PRK04406 9 LEERINDLECQLAFQEQTIEELNDALSQQQLLITKMQ 45 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455666665555555555555555555554444443
No 334
>PRK13979 DNA topoisomerase IV subunit A; Provisional
Probab=20.67 E-value=1.9e+02 Score=32.53 Aligned_cols=16 Identities=38% Similarity=0.310 Sum_probs=8.7
Q ss_pred CCCCce-eeeecCCCCC
Q 022537 280 DPDENR-ILVSSKGNIK 295 (295)
Q Consensus 280 dP~e~~-~l~s~~G~I~ 295 (295)
.|+|++ +++|..|=||
T Consensus 513 I~~E~v~v~lS~~GyIK 529 (957)
T PRK13979 513 IVVEDVVITLSNEGFIK 529 (957)
T ss_pred CCCcceEEEEecCCEEE
Confidence 345554 5666666543
No 335
>PRK04325 hypothetical protein; Provisional
Probab=20.65 E-value=4e+02 Score=20.61 Aligned_cols=36 Identities=11% Similarity=0.276 Sum_probs=18.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~L 237 (295)
+..++..|+..+..++.--..|++.|..-+++|..|
T Consensus 7 ~e~Ri~~LE~klAfQE~tIe~LN~vv~~Qq~~I~~L 42 (74)
T PRK04325 7 MEDRITELEIQLAFQEDLIDGLNATVARQQQTLDLL 42 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445566665555555544455555444444444433
No 336
>PF07061 Swi5: Swi5; InterPro: IPR010760 This entry represents Swi5 and is involved in meiotic DNA repair synthesis and meiotic joint molecule formation []. It is known to interact with Swi2, Rhp51 and Swi6 [].
Probab=20.59 E-value=1.6e+02 Score=23.54 Aligned_cols=27 Identities=26% Similarity=0.364 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 207 ARLKAEIESLHAEECRIDDSIREKQEL 233 (295)
Q Consensus 207 ~~Lk~El~~L~~~E~~LD~lI~~~~~~ 233 (295)
..|+++++.|.++...++..|......
T Consensus 3 ~~l~~~~~~L~~~~~~l~~~i~~~~~~ 29 (83)
T PF07061_consen 3 ESLEAEIQELKEQIEQLEKEISELEAE 29 (83)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 456666777777666666666665554
No 337
>PRK00846 hypothetical protein; Provisional
Probab=20.56 E-value=3.5e+02 Score=21.55 Aligned_cols=24 Identities=8% Similarity=0.256 Sum_probs=9.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Q 022537 202 LDDQVARLKAEIESLHAEECRIDD 225 (295)
Q Consensus 202 ~~~~~~~Lk~El~~L~~~E~~LD~ 225 (295)
+..++..|+..+...+.--..|++
T Consensus 11 le~Ri~~LE~rlAfQe~tIe~LN~ 34 (77)
T PRK00846 11 LEARLVELETRLSFQEQALTELSE 34 (77)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455554444333333333333
No 338
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=20.52 E-value=3.1e+02 Score=25.91 Aligned_cols=48 Identities=17% Similarity=0.106 Sum_probs=39.2
Q ss_pred hCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEec
Q 022537 146 EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (295)
Q Consensus 146 ~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (295)
...+-.+++.++|.+|+++.-+-+-++--||--|+|+|.--..=+|+-
T Consensus 14 a~~~~~~t~~ela~~l~~S~qta~R~l~~le~~~~I~R~~~~~Gq~i~ 61 (214)
T COG1339 14 AVRGVKVTSSELAKRLGVSSQTAARKLKELEDEGYITRTISKRGQLIT 61 (214)
T ss_pred hhcCccccHHHHHHHhCcCcHHHHHHHHhhccCCcEEEEecCCCcEEE
Confidence 334466899999999999999999999999999999998544445543
No 339
>PRK00118 putative DNA-binding protein; Validated
Probab=20.50 E-value=69 Score=26.60 Aligned_cols=34 Identities=29% Similarity=0.391 Sum_probs=28.0
Q ss_pred ceeHHHHHHHhhhhhhhhhhhhh--------Hhhhccceecc
Q 022537 151 TLDLNRTAEVLEVQKRRIYDITN--------VLEGIGLIEKT 184 (295)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItN--------VLEgIGLIeK~ 184 (295)
-....++|+.+|+++..+|..+. .++.+|++++.
T Consensus 33 g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~~~~~~~~ 74 (104)
T PRK00118 33 DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEKLHLYEKF 74 (104)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHChHHHH
Confidence 57889999999999988888754 77777887765
No 340
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=20.50 E-value=80 Score=22.37 Aligned_cols=23 Identities=30% Similarity=0.348 Sum_probs=17.8
Q ss_pred ceeHHHHHHHhhhhhhhhhhhhh
Q 022537 151 TLDLNRTAEVLEVQKRRIYDITN 173 (295)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItN 173 (295)
-+...++|+.+++.+..||.|.|
T Consensus 12 ~lt~~~~a~~~~i~~~~i~~~e~ 34 (64)
T PF12844_consen 12 GLTQKDLAEKLGISRSTISKIEN 34 (64)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHC
Confidence 36789999999999999998875
No 341
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=20.40 E-value=2.2e+02 Score=24.97 Aligned_cols=37 Identities=11% Similarity=0.057 Sum_probs=30.6
Q ss_pred HHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEe
Q 022537 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (295)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (295)
-.++|..||+.++.+.-+++-|+.-|++ . ..++|.+.
T Consensus 176 ~~~iA~~lG~tretvsR~l~~L~~~gl~-~-~~~~i~I~ 212 (236)
T PRK09392 176 KRVLASYLGMTPENLSRAFAALASHGVH-V-DGSAVTIT 212 (236)
T ss_pred HHHHHHHhCCChhHHHHHHHHHHhCCeE-e-eCCEEEEc
Confidence 3679999999999999999999999973 3 34567664
No 342
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=20.34 E-value=3.3e+02 Score=23.11 Aligned_cols=40 Identities=13% Similarity=0.143 Sum_probs=34.7
Q ss_pred eeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEe
Q 022537 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (295)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (295)
+.-.++|+.||+.+--+-=+++-|+.-|+|+.. +++|...
T Consensus 150 ~t~~~iA~~lG~tretvsR~l~~l~~~g~I~~~-~~~i~I~ 189 (202)
T PRK13918 150 ATHDELAAAVGSVRETVTKVIGELSREGYIRSG-YGKIQLL 189 (202)
T ss_pred CCHHHHHHHhCccHHHHHHHHHHHHHCCCEEcC-CCEEEEE
Confidence 467899999999999999999999999999854 5667664
No 343
>TIGR01242 26Sp45 26S proteasome subunit P45 family. Many proteins may score above the trusted cutoff because an internal
Probab=20.34 E-value=2.3e+02 Score=27.33 Aligned_cols=36 Identities=22% Similarity=0.370 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 022537 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (295)
Q Consensus 204 ~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lte 239 (295)
.+..+|++++..+..+...+.+.+..++++|..+..
T Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 41 (364)
T TIGR01242 6 VRIRKLEDEKRSLEKEKIRLERELERLRSEIERLRS 41 (364)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 456778888888888888888888888888877654
No 344
>PF06320 GCN5L1: GCN5-like protein 1 (GCN5L1); InterPro: IPR009395 This family consists of several eukaryotic GCN5-like protein 1 (GCN5L1) sequences. The function of this family is unknown [,].
Probab=20.18 E-value=1.7e+02 Score=24.68 Aligned_cols=54 Identities=9% Similarity=0.243 Sum_probs=42.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccHhhhhcC
Q 022537 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDIASL 257 (295)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~~E~~LD~lI~~~~~~L~~Lted~~n~~~aYVT~eDI~~i 257 (295)
.++.+...|+.....|.++-..+-.++..+...|+++= | -+.|+=+.+.|++.|
T Consensus 51 ~ie~e~k~L~~~~~~l~kqt~qw~~~~~~~~~~LKEiG-D--veNWa~~iE~Dl~~i 104 (121)
T PF06320_consen 51 KIEKEAKQLQRNTAKLAKQTDQWLKLVDSFNDALKEIG-D--VENWAEMIERDLRVI 104 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc-c--HHHHHHHHHHHHHHH
Confidence 45556667777788888888888888889999999883 2 455888889998765
No 345
>KOG4098 consensus Molecular chaperone Prefoldin, subunit 2 [Posttranslational modification, protein turnover, chaperones]
Probab=20.14 E-value=3.7e+02 Score=23.83 Aligned_cols=100 Identities=11% Similarity=0.172 Sum_probs=63.7
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhhhhhhhhhhhhhHhhhccceeccccCceEEecCCCCCCchhHHHHHHHHHHHHH
Q 022537 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIES 215 (295)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~ 215 (295)
.++.|+.-|+.-.+..=+|-.-...|+.++|-.-=|+++|+.+.=-.| +|+.+|.-.. ...+..-+-.|+...+.
T Consensus 16 ~q~~v~a~yn~~r~el~~ia~ki~~LE~d~~EH~lVi~tlk~~dp~RK----CfRmIgGvLV-ErTVkeVlP~L~~nke~ 90 (140)
T KOG4098|consen 16 SQQAVVAKYNALRSELQQIASKITDLEMDLREHKLVIETLKDLDPTRK----CFRMIGGVLV-ERTVKEVLPILQTNKEN 90 (140)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHhcChhhH----HHHHhccchh-hhhHHHHhHHHHhhHHH
Confidence 466788877766666666666677788888888888888888765444 4888885432 11233334456666666
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh
Q 022537 216 LHAEECRIDDSIREKQELIRTLEEN 240 (295)
Q Consensus 216 L~~~E~~LD~lI~~~~~~L~~Lted 240 (295)
+..--+.|-+.+......|..+..|
T Consensus 91 i~~~i~~l~~qL~~k~kElnkfk~~ 115 (140)
T KOG4098|consen 91 IEKVIKKLTDQLVQKGKELNKFKKD 115 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 6655555555555555555555544
Done!