Query 023564
Match_columns 280
No_of_seqs 187 out of 463
Neff 4.0
Searched_HMMs 46136
Date Fri Mar 29 05:00:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023564.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023564hhsearch_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 2.4E-53 5.1E-58 403.1 16.5 156 121-276 61-235 (354)
2 PF02319 E2F_TDP: E2F/DP famil 99.9 1.5E-23 3.2E-28 158.8 5.5 66 128-193 1-71 (71)
3 KOG2578 Transcription factor E 99.8 3.5E-20 7.6E-25 174.8 5.3 87 121-212 14-100 (388)
4 KOG2578 Transcription factor E 99.0 2.9E-10 6.4E-15 108.2 4.8 74 123-196 151-240 (388)
5 KOG2829 E2F-like protein [Tran 99.0 4.2E-09 9E-14 99.6 10.5 51 146-197 57-129 (326)
6 PF01978 TrmB: Sugar-specific 95.2 0.027 5.8E-07 41.3 3.8 45 148-192 19-63 (68)
7 PF08279 HTH_11: HTH domain; 94.0 0.096 2.1E-06 36.6 4.0 41 138-179 3-43 (55)
8 COG1378 Predicted transcriptio 93.5 0.42 9.2E-06 44.3 8.5 46 150-195 29-74 (247)
9 smart00420 HTH_DEOR helix_turn 93.0 0.15 3.3E-06 34.1 3.6 45 139-185 4-48 (53)
10 cd00092 HTH_CRP helix_turn_hel 92.7 0.25 5.3E-06 35.1 4.6 54 136-189 5-63 (67)
11 smart00346 HTH_ICLR helix_turn 92.0 0.3 6.4E-06 36.8 4.6 48 138-186 8-55 (91)
12 PF09339 HTH_IclR: IclR helix- 91.8 0.19 4E-06 35.3 2.9 45 139-184 7-51 (52)
13 smart00550 Zalpha Z-DNA-bindin 91.5 0.33 7.2E-06 36.3 4.2 56 137-192 8-63 (68)
14 PF12802 MarR_2: MarR family; 90.1 0.5 1.1E-05 33.2 3.9 46 139-184 9-54 (62)
15 PF13412 HTH_24: Winged helix- 89.8 0.47 1E-05 32.4 3.5 43 138-182 6-48 (48)
16 smart00418 HTH_ARSR helix_turn 87.4 0.71 1.5E-05 31.3 3.1 38 149-186 8-45 (66)
17 COG3355 Predicted transcriptio 86.8 4.5 9.8E-05 34.6 8.2 87 140-239 33-120 (126)
18 PF14394 DUF4423: Domain of un 86.2 9.8 0.00021 33.4 10.3 99 146-244 34-158 (171)
19 PF02082 Rrf2: Transcriptional 85.9 1.3 2.8E-05 33.8 4.1 49 136-184 9-58 (83)
20 TIGR02944 suf_reg_Xantho FeS a 85.7 1.1 2.4E-05 36.6 3.8 47 138-184 12-58 (130)
21 cd00890 Prefoldin Prefoldin is 85.6 3.9 8.5E-05 32.8 7.0 55 185-239 68-122 (129)
22 PF01047 MarR: MarR family; I 85.5 0.99 2.1E-05 31.6 3.0 44 140-185 8-51 (59)
23 PF13730 HTH_36: Helix-turn-he 85.3 0.74 1.6E-05 32.1 2.3 29 153-181 27-55 (55)
24 cd00090 HTH_ARSR Arsenical Res 83.6 2.5 5.4E-05 29.2 4.4 47 138-187 10-56 (78)
25 PF09079 Cdc6_C: CDC6, C termi 82.9 0.54 1.2E-05 35.9 0.8 29 156-184 27-58 (85)
26 PF13463 HTH_27: Winged helix 82.8 1.9 4.1E-05 30.7 3.6 39 147-185 14-52 (68)
27 TIGR00122 birA_repr_reg BirA b 81.5 1.5 3.2E-05 32.2 2.7 54 139-195 4-58 (69)
28 PF00392 GntR: Bacterial regul 81.3 4.3 9.2E-05 29.4 5.0 50 138-187 7-60 (64)
29 smart00419 HTH_CRP helix_turn_ 80.9 1.5 3.3E-05 29.0 2.4 35 151-185 8-42 (48)
30 cd08768 Cdc6_C Winged-helix do 80.7 0.96 2.1E-05 34.1 1.5 44 130-184 22-65 (87)
31 smart00345 HTH_GNTR helix_turn 80.1 2.3 5E-05 29.0 3.1 40 148-187 16-56 (60)
32 PF01022 HTH_5: Bacterial regu 79.3 2.3 5E-05 29.3 2.9 34 150-183 14-47 (47)
33 TIGR02147 Fsuc_second hypothet 78.0 24 0.00052 33.4 10.2 96 147-244 133-256 (271)
34 cd00584 Prefoldin_alpha Prefol 77.3 10 0.00022 31.0 6.7 54 186-239 69-122 (129)
35 PF08220 HTH_DeoR: DeoR-like h 77.2 3.9 8.4E-05 29.5 3.7 44 139-184 4-47 (57)
36 PF04182 B-block_TFIIIC: B-blo 76.5 3.5 7.7E-05 31.3 3.5 49 138-186 5-53 (75)
37 PRK11414 colanic acid/biofilm 75.7 7.3 0.00016 34.2 5.8 52 136-187 16-70 (221)
38 PRK03947 prefoldin subunit alp 75.5 13 0.00028 30.9 7.0 52 186-237 76-127 (140)
39 cd04766 HTH_HspR Helix-Turn-He 74.3 12 0.00025 29.1 5.9 27 152-182 2-28 (91)
40 TIGR00738 rrf2_super rrf2 fami 72.8 5.7 0.00012 32.1 4.0 37 148-184 22-58 (132)
41 PF09012 FeoC: FeoC like trans 72.5 2.1 4.7E-05 31.7 1.4 43 148-190 11-53 (69)
42 PF12840 HTH_20: Helix-turn-he 72.4 3.3 7.1E-05 29.8 2.3 45 139-185 14-58 (61)
43 TIGR02702 SufR_cyano iron-sulf 70.9 35 0.00076 30.1 8.9 45 138-184 4-48 (203)
44 TIGR00293 prefoldin, archaeal 70.6 14 0.0003 30.1 5.8 54 186-239 68-121 (126)
45 PF05732 RepL: Firmicute plasm 70.1 16 0.00034 32.1 6.4 39 151-189 75-113 (165)
46 PRK09834 DNA-binding transcrip 69.8 7 0.00015 35.7 4.4 51 140-191 16-67 (263)
47 smart00529 HTH_DTXR Helix-turn 69.4 4.7 0.0001 30.7 2.7 33 154-186 2-34 (96)
48 COG1510 Predicted transcriptio 69.0 13 0.00028 33.7 5.7 38 148-185 38-75 (177)
49 TIGR01610 phage_O_Nterm phage 68.9 8.1 0.00018 30.5 4.1 46 148-195 44-89 (95)
50 PRK10163 DNA-binding transcrip 68.6 8 0.00017 35.6 4.5 57 138-195 28-84 (271)
51 PF12329 TMF_DNA_bd: TATA elem 68.2 16 0.00035 28.1 5.5 38 202-239 10-47 (74)
52 PRK10870 transcriptional repre 67.4 38 0.00083 29.4 8.3 41 145-185 65-105 (176)
53 PRK03573 transcriptional regul 67.2 63 0.0014 26.4 9.2 35 151-185 46-80 (144)
54 PHA02943 hypothetical protein; 66.0 16 0.00035 32.8 5.6 48 138-188 14-61 (165)
55 PF01726 LexA_DNA_bind: LexA D 66.0 6 0.00013 29.7 2.6 46 140-185 14-60 (65)
56 PF04977 DivIC: Septum formati 65.9 16 0.00034 26.9 4.9 32 206-237 19-50 (80)
57 PF08784 RPA_C: Replication pr 65.7 8.2 0.00018 30.3 3.5 50 132-181 44-95 (102)
58 COG1474 CDC6 Cdc6-related prot 65.7 4.3 9.4E-05 39.6 2.3 30 153-182 303-332 (366)
59 cd04789 HTH_Cfa Helix-Turn-Hel 65.6 29 0.00062 27.7 6.6 38 152-193 2-40 (102)
60 TIGR03338 phnR_burk phosphonat 65.4 19 0.00042 31.1 6.1 41 147-187 30-70 (212)
61 smart00344 HTH_ASNC helix_turn 65.3 7.6 0.00017 30.2 3.2 47 136-184 4-50 (108)
62 cd07377 WHTH_GntR Winged helix 65.0 11 0.00023 26.1 3.7 34 152-185 26-59 (66)
63 PRK06474 hypothetical protein; 64.6 48 0.001 29.1 8.4 47 138-185 14-61 (178)
64 COG1414 IclR Transcriptional r 64.5 9.2 0.0002 35.0 4.1 54 139-193 8-61 (246)
65 PRK09413 IS2 repressor TnpA; R 64.0 59 0.0013 26.5 8.4 31 150-180 28-58 (121)
66 PRK10411 DNA-binding transcrip 63.7 36 0.00079 31.1 7.8 54 138-193 7-60 (240)
67 TIGR02337 HpaR homoprotocatech 63.5 5.4 0.00012 31.8 2.1 37 149-185 40-76 (118)
68 COG1802 GntR Transcriptional r 63.5 68 0.0015 28.4 9.3 41 147-187 35-75 (230)
69 TIGR01764 excise DNA binding d 63.1 4.3 9.3E-05 26.6 1.2 22 152-173 2-23 (49)
70 PF13518 HTH_28: Helix-turn-he 63.1 6.3 0.00014 26.6 2.1 37 140-180 5-41 (52)
71 cd04783 HTH_MerR1 Helix-Turn-H 62.9 65 0.0014 26.4 8.4 37 153-193 2-40 (126)
72 TIGR02716 C20_methyl_CrtF C-20 62.8 4.8 0.0001 37.2 1.9 37 149-185 21-57 (306)
73 cd04770 HTH_HMRTR Helix-Turn-H 62.6 40 0.00087 27.3 7.1 37 153-193 2-40 (123)
74 smart00347 HTH_MARR helix_turn 61.9 14 0.0003 27.3 4.0 45 138-184 13-57 (101)
75 cd04775 HTH_Cfa-like Helix-Tur 61.6 33 0.00072 27.3 6.3 37 152-192 2-39 (102)
76 PRK11511 DNA-binding transcrip 61.6 12 0.00025 30.8 3.8 42 133-174 7-48 (127)
77 TIGR01889 Staph_reg_Sar staphy 61.6 10 0.00022 30.2 3.4 46 140-185 30-77 (109)
78 PF08280 HTH_Mga: M protein tr 61.4 8.4 0.00018 27.9 2.6 36 139-176 9-44 (59)
79 PF01325 Fe_dep_repress: Iron 61.2 16 0.00034 26.9 4.1 44 141-185 13-56 (60)
80 PRK05014 hscB co-chaperone Hsc 61.2 1.1E+02 0.0025 26.8 10.1 97 128-236 12-128 (171)
81 PF13545 HTH_Crp_2: Crp-like h 60.6 8.6 0.00019 27.9 2.6 51 136-186 3-63 (76)
82 COG1777 Predicted transcriptio 60.4 71 0.0015 29.9 9.0 43 138-183 18-60 (217)
83 PRK09954 putative kinase; Prov 59.1 10 0.00022 35.8 3.4 46 137-184 5-50 (362)
84 PRK00215 LexA repressor; Valid 58.9 11 0.00025 32.8 3.5 42 146-187 18-60 (205)
85 PRK10225 DNA-binding transcrip 58.8 62 0.0013 29.1 8.3 51 135-185 13-67 (257)
86 PF05103 DivIVA: DivIVA protei 58.2 5.1 0.00011 32.4 1.1 49 189-240 13-61 (131)
87 KOG1318 Helix loop helix trans 57.9 12 0.00027 37.7 3.9 76 162-239 239-318 (411)
88 PRK10219 DNA-binding transcrip 57.8 16 0.00034 28.5 3.8 40 135-174 5-44 (107)
89 TIGR02338 gimC_beta prefoldin, 57.3 33 0.00072 27.7 5.7 82 156-238 21-108 (110)
90 TIGR02010 IscR iron-sulfur clu 56.6 15 0.00033 30.4 3.7 38 146-183 20-57 (135)
91 cd01109 HTH_YyaN Helix-Turn-He 55.9 38 0.00082 27.2 5.8 35 153-191 2-38 (113)
92 TIGR02431 pcaR_pcaU beta-ketoa 55.6 25 0.00054 31.6 5.2 44 140-184 14-57 (248)
93 PRK14165 winged helix-turn-hel 55.2 36 0.00078 31.4 6.2 54 139-192 8-62 (217)
94 PRK09802 DNA-binding transcrip 55.2 85 0.0018 29.2 8.7 52 135-188 17-68 (269)
95 PRK09464 pdhR transcriptional 55.1 62 0.0013 29.0 7.6 54 132-185 10-68 (254)
96 PF10779 XhlA: Haemolysin XhlA 54.8 45 0.00099 25.1 5.7 38 203-240 12-49 (71)
97 PF05565 Sipho_Gp157: Siphovir 54.8 1.1E+02 0.0025 26.5 9.0 88 132-239 2-89 (162)
98 COG2739 Uncharacterized protei 54.5 10 0.00022 31.8 2.3 40 134-173 16-55 (105)
99 COG1846 MarR Transcriptional r 54.4 15 0.00032 27.9 3.1 44 140-185 27-70 (126)
100 PF07106 TBPIP: Tat binding pr 54.3 1.3E+02 0.0028 25.8 9.2 55 140-195 6-64 (169)
101 COG3093 VapI Plasmid maintenan 54.3 7 0.00015 32.6 1.3 33 135-173 13-45 (104)
102 PRK11534 DNA-binding transcrip 53.8 50 0.0011 29.0 6.7 48 147-194 26-73 (224)
103 PF04111 APG6: Autophagy prote 53.8 32 0.0007 33.0 5.9 37 206-242 59-95 (314)
104 cd00632 Prefoldin_beta Prefold 53.7 38 0.00082 27.1 5.4 76 158-237 22-103 (105)
105 PRK09343 prefoldin subunit bet 53.6 41 0.00088 28.0 5.8 74 166-240 35-114 (121)
106 TIGR02366 DHAK_reg probable di 53.2 15 0.00033 30.5 3.3 35 135-169 7-41 (176)
107 PF01920 Prefoldin_2: Prefoldi 52.7 59 0.0013 25.1 6.3 67 168-237 28-102 (106)
108 cd00632 Prefoldin_beta Prefold 52.7 45 0.00098 26.6 5.7 34 206-239 65-98 (105)
109 PRK11050 manganese transport r 52.6 30 0.00064 29.5 4.9 43 149-191 49-91 (152)
110 COG1382 GimC Prefoldin, chaper 52.3 47 0.001 28.3 6.0 71 170-241 38-114 (119)
111 PRK15090 DNA-binding transcrip 52.0 20 0.00044 32.5 4.0 55 138-194 17-71 (257)
112 TIGR01884 cas_HTH CRISPR locus 51.7 22 0.00048 31.3 4.1 46 139-186 147-192 (203)
113 TIGR02297 HpaA 4-hydroxyphenyl 51.2 16 0.00034 32.8 3.1 43 135-177 186-228 (287)
114 PRK13509 transcriptional repre 51.2 15 0.00032 33.7 3.1 46 138-185 8-53 (251)
115 cd07153 Fur_like Ferric uptake 50.2 23 0.0005 27.9 3.6 45 140-185 6-55 (116)
116 PRK11569 transcriptional repre 49.5 82 0.0018 29.0 7.6 54 139-193 32-85 (274)
117 TIGR00498 lexA SOS regulatory 49.0 21 0.00045 31.1 3.5 48 138-185 9-60 (199)
118 COG2894 MinD Septum formation 48.9 6.9 0.00015 37.3 0.5 28 152-179 41-68 (272)
119 PRK09990 DNA-binding transcrip 48.5 41 0.00088 30.1 5.4 50 137-186 13-66 (251)
120 cd04762 HTH_MerR-trunc Helix-T 48.2 17 0.00036 23.5 2.2 23 152-174 1-23 (49)
121 cd04784 HTH_CadR-PbrR Helix-Tu 48.0 1.2E+02 0.0026 24.8 7.7 84 152-241 1-116 (127)
122 PF03428 RP-C: Replication pro 47.7 1.2E+02 0.0025 27.3 8.0 33 153-185 72-105 (177)
123 TIGR02047 CadR-PbrR Cd(II)/Pb( 47.4 57 0.0012 27.0 5.7 84 152-239 1-107 (127)
124 TIGR02338 gimC_beta prefoldin, 47.3 54 0.0012 26.5 5.4 34 206-239 69-102 (110)
125 PRK10857 DNA-binding transcrip 47.2 19 0.00041 31.5 2.9 39 146-184 20-58 (164)
126 PRK11014 transcriptional repre 47.0 22 0.00048 29.6 3.2 41 146-186 20-60 (141)
127 PF05377 FlaC_arch: Flagella a 46.5 77 0.0017 23.7 5.6 38 201-238 4-41 (55)
128 PF04977 DivIC: Septum formati 46.4 64 0.0014 23.6 5.3 30 201-230 21-50 (80)
129 PRK00888 ftsB cell division pr 46.4 25 0.00054 28.8 3.3 31 202-232 32-62 (105)
130 smart00338 BRLZ basic region l 46.3 77 0.0017 23.1 5.7 35 205-239 27-61 (65)
131 PRK09391 fixK transcriptional 46.0 40 0.00086 29.8 4.9 39 152-190 180-218 (230)
132 PF03374 ANT: Phage antirepres 45.6 20 0.00043 28.4 2.7 41 140-184 14-54 (111)
133 PF01920 Prefoldin_2: Prefoldi 45.0 58 0.0013 25.1 5.1 30 209-238 67-96 (106)
134 PHA01750 hypothetical protein 44.9 59 0.0013 25.6 5.0 31 204-234 42-72 (75)
135 PRK14127 cell division protein 44.9 60 0.0013 27.1 5.4 55 179-238 10-64 (109)
136 COG4189 Predicted transcriptio 44.8 22 0.00049 34.2 3.2 52 131-184 18-70 (308)
137 PF05930 Phage_AlpA: Prophage 44.7 14 0.0003 26.0 1.4 24 150-173 2-25 (51)
138 PF02996 Prefoldin: Prefoldin 43.3 58 0.0013 25.9 5.0 70 167-237 41-110 (120)
139 PRK13626 transcriptional regul 43.2 59 0.0013 32.9 6.2 48 135-182 5-54 (552)
140 PF01475 FUR: Ferric uptake re 42.9 30 0.00065 27.7 3.3 49 138-187 11-64 (120)
141 KOG3990 Uncharacterized conser 42.7 41 0.00089 32.5 4.6 46 199-244 220-265 (305)
142 PRK10130 transcriptional regul 42.6 24 0.00053 34.2 3.2 40 134-173 239-278 (350)
143 cd00592 HTH_MerR-like Helix-Tu 41.9 63 0.0014 25.0 4.9 21 153-173 2-22 (100)
144 PF04703 FaeA: FaeA-like prote 41.9 39 0.00085 25.4 3.6 52 140-192 5-59 (62)
145 PF02954 HTH_8: Bacterial regu 41.8 29 0.00064 23.4 2.7 37 133-171 2-38 (42)
146 PF02796 HTH_7: Helix-turn-hel 41.7 13 0.00029 25.4 0.9 32 138-173 12-43 (45)
147 PF03444 HrcA_DNA-bdg: Winged 41.6 48 0.001 26.3 4.2 47 137-184 10-56 (78)
148 PF10018 Med4: Vitamin-D-recep 41.6 1.1E+02 0.0023 27.2 6.8 33 206-238 24-56 (188)
149 COG1522 Lrp Transcriptional re 41.2 36 0.00079 27.8 3.6 51 133-185 6-56 (154)
150 PRK00080 ruvB Holliday junctio 41.1 41 0.00089 31.5 4.4 57 131-187 255-313 (328)
151 PRK03837 transcriptional regul 41.0 20 0.00043 31.6 2.2 51 136-186 18-72 (241)
152 PF05491 RuvB_C: Holliday junc 40.6 49 0.0011 26.2 4.1 59 131-189 4-64 (76)
153 TIGR02044 CueR Cu(I)-responsiv 40.4 2.1E+02 0.0045 23.5 8.0 37 153-193 2-40 (127)
154 PRK09863 putative frv operon r 40.0 79 0.0017 32.3 6.5 52 139-195 8-65 (584)
155 PF12728 HTH_17: Helix-turn-he 40.0 17 0.00036 24.9 1.2 22 152-173 2-23 (51)
156 TIGR02043 ZntR Zn(II)-responsi 39.9 1.4E+02 0.0029 24.9 6.9 81 152-239 2-102 (131)
157 PF13384 HTH_23: Homeodomain-l 39.6 28 0.0006 23.5 2.3 34 140-177 10-43 (50)
158 PF01638 HxlR: HxlR-like helix 39.3 29 0.00064 26.8 2.7 42 144-185 11-53 (90)
159 PF13551 HTH_29: Winged helix- 39.3 23 0.00051 27.0 2.1 27 153-179 14-40 (112)
160 PRK15121 right oriC-binding tr 39.2 34 0.00074 31.4 3.5 46 135-180 5-50 (289)
161 PRK13922 rod shape-determining 37.9 75 0.0016 29.2 5.5 40 202-242 74-113 (276)
162 PRK11512 DNA-binding transcrip 37.8 25 0.00054 29.1 2.1 37 149-185 52-88 (144)
163 PF01853 MOZ_SAS: MOZ/SAS fami 37.7 51 0.0011 30.1 4.3 56 131-189 123-185 (188)
164 COG4519 Uncharacterized protei 37.6 44 0.00095 27.3 3.4 42 140-182 12-53 (95)
165 PF12793 SgrR_N: Sugar transpo 37.4 1.4E+02 0.0031 24.7 6.6 47 136-182 2-50 (115)
166 cd01106 HTH_TipAL-Mta Helix-Tu 37.4 1.7E+02 0.0038 22.9 6.8 17 153-169 2-18 (103)
167 PF09756 DDRGK: DDRGK domain; 37.3 42 0.00092 30.4 3.7 47 136-184 100-146 (188)
168 PRK00888 ftsB cell division pr 37.3 79 0.0017 25.8 5.0 36 205-240 28-63 (105)
169 PF04218 CENP-B_N: CENP-B N-te 36.4 28 0.00061 24.9 2.0 31 142-173 14-44 (53)
170 PF09904 HTH_43: Winged helix- 36.0 42 0.00091 27.4 3.1 30 153-182 23-52 (90)
171 cd04776 HTH_GnyR Helix-Turn-He 36.0 90 0.002 25.6 5.2 12 134-145 41-52 (118)
172 PF10018 Med4: Vitamin-D-recep 35.8 1E+02 0.0023 27.2 5.9 38 201-238 26-63 (188)
173 PF00170 bZIP_1: bZIP transcri 35.7 1.5E+02 0.0033 21.5 5.9 34 205-238 27-60 (64)
174 cd01279 HTH_HspR-like Helix-Tu 35.6 1.6E+02 0.0035 23.2 6.4 28 152-183 2-29 (98)
175 PRK04984 fatty acid metabolism 35.5 29 0.00064 30.6 2.4 39 147-185 26-65 (239)
176 PF14947 HTH_45: Winged helix- 34.9 34 0.00074 25.9 2.4 42 149-191 17-58 (77)
177 PF02295 z-alpha: Adenosine de 34.9 91 0.002 23.5 4.6 57 136-192 5-61 (66)
178 PRK13503 transcriptional activ 34.8 45 0.00097 29.7 3.4 39 135-173 171-209 (278)
179 PF13851 GAS: Growth-arrest sp 34.7 83 0.0018 28.4 5.2 36 204-239 27-62 (201)
180 PHA00738 putative HTH transcri 34.6 1.2E+02 0.0026 25.5 5.7 72 138-216 15-86 (108)
181 KOG0804 Cytoplasmic Zn-finger 34.6 78 0.0017 32.8 5.4 86 167-273 390-478 (493)
182 cd01108 HTH_CueR Helix-Turn-He 34.5 2.6E+02 0.0056 23.0 7.7 89 152-244 1-119 (127)
183 PF09940 DUF2172: Domain of un 34.5 21 0.00045 35.9 1.3 45 134-182 342-386 (386)
184 COG1373 Predicted ATPase (AAA+ 34.4 46 0.001 32.8 3.7 50 135-184 220-270 (398)
185 PRK10869 recombination and rep 34.3 61 0.0013 33.4 4.7 79 129-217 259-337 (553)
186 PRK13729 conjugal transfer pil 33.9 80 0.0017 32.7 5.4 37 202-238 81-117 (475)
187 PRK11886 bifunctional biotin-- 33.6 62 0.0013 30.4 4.3 52 138-191 7-59 (319)
188 PRK11753 DNA-binding transcrip 33.3 63 0.0014 27.4 4.0 36 151-186 168-203 (211)
189 PRK13182 racA polar chromosome 33.3 1.2E+02 0.0027 27.0 5.9 27 214-240 88-114 (175)
190 PRK10402 DNA-binding transcrip 33.3 52 0.0011 28.9 3.5 50 137-186 152-204 (226)
191 PRK01203 prefoldin subunit alp 33.1 1.3E+02 0.0028 25.9 5.8 39 201-239 4-42 (130)
192 PRK03902 manganese transport t 33.0 1.2E+02 0.0027 25.0 5.6 38 148-185 19-56 (142)
193 cd04777 HTH_MerR-like_sg1 Heli 32.7 2E+02 0.0044 22.7 6.6 25 153-183 2-28 (107)
194 TIGR02928 orc1/cdc6 family rep 32.7 22 0.00047 33.1 1.1 30 156-185 319-351 (365)
195 PRK09393 ftrA transcriptional 32.5 53 0.0011 30.5 3.6 42 135-176 218-259 (322)
196 PRK10803 tol-pal system protei 32.5 1.1E+02 0.0023 28.6 5.7 36 202-237 59-94 (263)
197 PRK09514 zntR zinc-responsive 32.4 2.3E+02 0.0051 23.8 7.2 81 152-239 2-109 (140)
198 PF04297 UPF0122: Putative hel 32.3 29 0.00062 28.7 1.7 40 135-174 17-56 (101)
199 PRK09333 30S ribosomal protein 32.3 48 0.001 29.3 3.1 37 149-185 65-115 (150)
200 PF09107 SelB-wing_3: Elongati 32.1 62 0.0013 23.3 3.2 41 148-188 7-47 (50)
201 COG1730 GIM5 Predicted prefold 31.5 2.4E+02 0.0052 24.7 7.3 28 158-185 26-53 (145)
202 COG2378 Predicted transcriptio 31.3 38 0.00082 32.3 2.5 30 152-181 23-52 (311)
203 PF14817 HAUS5: HAUS augmin-li 31.0 95 0.0021 33.1 5.6 50 186-235 56-110 (632)
204 COG1382 GimC Prefoldin, chaper 30.9 94 0.002 26.5 4.5 34 206-239 72-105 (119)
205 KOG0718 Molecular chaperone (D 30.5 74 0.0016 33.2 4.5 11 164-174 69-79 (546)
206 PRK10421 DNA-binding transcrip 30.4 37 0.00079 30.5 2.2 39 147-185 21-60 (253)
207 TIGR00635 ruvB Holliday juncti 30.4 68 0.0015 29.2 3.9 54 135-188 238-293 (305)
208 PF14257 DUF4349: Domain of un 30.3 84 0.0018 28.7 4.5 54 131-184 59-123 (262)
209 KOG2747 Histone acetyltransfer 29.8 1.1E+02 0.0023 31.1 5.4 57 132-193 304-366 (396)
210 cd04772 HTH_TioE_rpt1 First He 29.8 1.4E+02 0.0031 23.6 5.3 37 153-193 2-40 (99)
211 PRK10572 DNA-binding transcrip 29.7 60 0.0013 29.4 3.4 38 136-173 184-221 (290)
212 cd04788 HTH_NolA-AlbR Helix-Tu 29.4 2.4E+02 0.0053 22.0 6.5 37 153-193 2-40 (96)
213 PRK11169 leucine-responsive tr 29.2 88 0.0019 26.7 4.2 51 131-183 10-60 (164)
214 TIGR02051 MerR Hg(II)-responsi 29.1 3.2E+02 0.007 22.4 8.6 92 154-249 2-121 (124)
215 PF06005 DUF904: Protein of un 29.1 2.1E+02 0.0046 22.1 5.9 37 204-240 18-54 (72)
216 PRK09685 DNA-binding transcrip 29.0 55 0.0012 29.6 3.1 38 136-173 198-236 (302)
217 PF07889 DUF1664: Protein of u 28.8 1.7E+02 0.0036 25.1 5.7 10 188-197 22-31 (126)
218 COG2512 Predicted membrane-ass 28.7 77 0.0017 29.9 4.0 60 132-192 192-251 (258)
219 PRK09975 DNA-binding transcrip 28.5 61 0.0013 27.6 3.1 37 134-170 14-50 (213)
220 PF10779 XhlA: Haemolysin XhlA 28.4 2.1E+02 0.0046 21.5 5.7 39 202-240 4-42 (71)
221 COG1730 GIM5 Predicted prefold 28.4 1.7E+02 0.0038 25.6 5.9 40 201-240 10-49 (145)
222 cd04790 HTH_Cfa-like_unk Helix 28.3 2.4E+02 0.0051 24.7 6.8 37 152-194 2-42 (172)
223 PF11932 DUF3450: Protein of u 28.1 1.6E+02 0.0034 26.9 5.9 17 220-236 100-116 (251)
224 cd04782 HTH_BltR Helix-Turn-He 28.0 1.3E+02 0.0028 23.6 4.7 36 153-192 2-39 (97)
225 PF11853 DUF3373: Protein of u 27.9 48 0.001 34.3 2.7 26 212-237 32-57 (489)
226 PRK10371 DNA-binding transcrip 27.7 62 0.0013 30.2 3.2 40 136-175 192-231 (302)
227 cd04787 HTH_HMRTR_unk Helix-Tu 27.7 3.5E+02 0.0076 22.3 8.8 89 152-244 1-119 (133)
228 PRK00411 cdc6 cell division co 27.3 37 0.00079 32.1 1.7 35 150-184 314-358 (394)
229 PF13600 DUF4140: N-terminal d 27.1 1.9E+02 0.004 22.7 5.4 35 203-237 69-103 (104)
230 PF14712 Snapin_Pallidin: Snap 27.1 2.1E+02 0.0045 22.0 5.6 37 203-239 13-49 (92)
231 cd00890 Prefoldin Prefoldin is 27.0 2E+02 0.0043 22.9 5.7 37 201-237 91-127 (129)
232 PF13542 HTH_Tnp_ISL3: Helix-t 26.9 59 0.0013 22.1 2.3 38 136-173 12-49 (52)
233 COG1321 TroR Mn-dependent tran 26.9 86 0.0019 27.2 3.8 43 148-190 21-63 (154)
234 PRK10906 DNA-binding transcrip 26.8 57 0.0012 30.1 2.8 45 138-184 8-52 (252)
235 COG2919 Septum formation initi 26.7 66 0.0014 26.6 2.9 32 202-233 55-86 (117)
236 COG2207 AraC AraC-type DNA-bin 26.7 75 0.0016 24.1 3.0 43 139-181 24-66 (127)
237 PRK11523 DNA-binding transcrip 26.4 51 0.0011 29.6 2.4 51 136-186 13-67 (253)
238 KOG1062 Vesicle coat complex A 26.4 1.8E+02 0.0039 32.3 6.6 126 129-256 379-516 (866)
239 PF09340 NuA4: Histone acetylt 26.4 1.1E+02 0.0024 24.0 3.9 28 211-238 2-29 (80)
240 PF03836 RasGAP_C: RasGAP C-te 26.4 22 0.00047 30.1 0.0 27 164-192 5-31 (142)
241 PF10805 DUF2730: Protein of u 26.1 3.6E+02 0.0078 21.9 8.5 81 139-241 22-102 (106)
242 TIGR02812 fadR_gamma fatty aci 26.0 2.9E+02 0.0063 24.3 7.1 39 147-185 25-64 (235)
243 TIGR02209 ftsL_broad cell divi 25.8 2E+02 0.0044 21.5 5.3 30 209-238 29-58 (85)
244 PF14389 Lzipper-MIP1: Leucine 25.4 2.4E+02 0.0052 22.3 5.8 38 199-236 49-86 (88)
245 KOG2255 Peptidyl-tRNA hydrolas 25.0 37 0.0008 31.8 1.2 29 154-184 64-92 (224)
246 PRK05638 threonine synthase; V 24.9 97 0.0021 30.7 4.2 61 121-184 357-419 (442)
247 PRK06266 transcription initiat 24.8 3.4E+02 0.0073 24.1 7.2 52 139-192 26-84 (178)
248 PF10141 ssDNA-exonuc_C: Singl 24.6 3.4E+02 0.0074 24.0 7.2 47 138-184 101-149 (195)
249 TIGR00373 conserved hypothetic 24.6 3.3E+02 0.007 23.6 6.9 35 148-182 25-59 (158)
250 TIGR00714 hscB Fe-S protein as 24.5 3.7E+02 0.0081 23.2 7.3 26 153-180 41-67 (157)
251 PF07106 TBPIP: Tat binding pr 24.3 2.2E+02 0.0047 24.4 5.8 31 222-257 120-150 (169)
252 KOG3501 Molecular chaperone Pr 24.3 2.5E+02 0.0054 23.9 5.8 41 201-241 71-111 (114)
253 PRK15185 transcriptional regul 24.2 82 0.0018 30.7 3.4 39 135-173 206-244 (309)
254 PF14830 Haemocyan_bet_s: Haem 24.1 29 0.00063 28.9 0.3 15 167-181 56-70 (103)
255 PF08222 HTH_CodY: CodY helix- 23.9 49 0.0011 25.3 1.5 36 150-185 3-38 (61)
256 PF05225 HTH_psq: helix-turn-h 23.9 65 0.0014 22.4 2.0 26 149-174 14-39 (45)
257 PRK04214 rbn ribonuclease BN/u 23.9 1.1E+02 0.0024 30.2 4.3 44 147-190 306-349 (412)
258 PF14282 FlxA: FlxA-like prote 23.8 1.7E+02 0.0037 23.8 4.8 15 204-218 26-40 (106)
259 PRK11179 DNA-binding transcrip 23.7 1E+02 0.0022 26.0 3.5 50 133-184 7-56 (153)
260 smart00342 HTH_ARAC helix_turn 23.6 50 0.0011 23.2 1.4 26 152-177 2-27 (84)
261 PRK10434 srlR DNA-bindng trans 23.0 89 0.0019 28.8 3.3 44 139-184 9-52 (256)
262 PRK09462 fur ferric uptake reg 23.0 1.2E+02 0.0025 25.5 3.7 47 139-185 21-72 (148)
263 PF03962 Mnd1: Mnd1 family; I 22.7 4.4E+02 0.0096 23.5 7.6 32 161-192 25-58 (188)
264 PF07061 Swi5: Swi5; InterPro 22.7 1.3E+02 0.0029 23.8 3.8 28 207-234 3-30 (83)
265 PF07716 bZIP_2: Basic region 22.6 2.8E+02 0.006 19.6 5.1 26 212-237 26-51 (54)
266 PF08657 DASH_Spc34: DASH comp 22.4 2.5E+02 0.0053 26.7 6.1 40 201-240 177-216 (259)
267 COG2186 FadR Transcriptional r 22.4 57 0.0012 29.7 1.9 56 135-190 14-74 (241)
268 PRK09978 DNA-binding transcrip 22.4 89 0.0019 29.7 3.2 39 135-173 142-180 (274)
269 TIGR03697 NtcA_cyano global ni 22.4 1.5E+02 0.0032 24.6 4.3 41 151-192 143-183 (193)
270 COG5509 Uncharacterized small 22.3 94 0.002 24.0 2.7 24 199-222 27-50 (65)
271 PF10046 BLOC1_2: Biogenesis o 22.1 2.2E+02 0.0047 22.8 5.0 35 203-237 65-99 (99)
272 cd04785 HTH_CadR-PbrR-like Hel 22.0 4.4E+02 0.0096 21.5 7.5 86 152-241 1-116 (126)
273 PRK10141 DNA-binding transcrip 22.0 4.1E+02 0.0089 22.1 6.8 51 139-191 20-70 (117)
274 PRK00118 putative DNA-binding 21.9 49 0.0011 27.3 1.2 34 151-184 33-74 (104)
275 PRK11920 rirA iron-responsive 21.8 1.1E+02 0.0023 26.2 3.4 42 143-184 16-57 (153)
276 PF15358 TSKS: Testis-specific 21.7 1.6E+02 0.0035 30.5 5.0 65 170-239 108-181 (558)
277 cd04773 HTH_TioE_rpt2 Second H 21.7 4.2E+02 0.0092 21.2 7.7 27 153-183 2-28 (108)
278 TIGR02231 conserved hypothetic 21.6 1.9E+02 0.0042 29.2 5.6 39 202-240 136-174 (525)
279 PF04111 APG6: Autophagy prote 21.5 2.1E+02 0.0046 27.5 5.6 29 206-234 45-73 (314)
280 COG1349 GlpR Transcriptional r 21.5 1.1E+02 0.0024 28.2 3.6 45 138-184 8-52 (253)
281 PF11853 DUF3373: Protein of u 21.4 86 0.0019 32.5 3.1 31 203-233 30-60 (489)
282 cd01110 HTH_SoxR Helix-Turn-He 21.1 3.3E+02 0.007 23.0 6.1 81 152-239 2-108 (139)
283 PF05911 DUF869: Plant protein 20.9 2.6E+02 0.0057 30.6 6.7 103 133-235 514-620 (769)
284 PHA02047 phage lambda Rz1-like 20.8 85 0.0018 26.2 2.4 8 188-195 25-32 (101)
285 PRK05771 V-type ATP synthase s 20.7 3.3E+02 0.0071 28.4 7.2 57 170-237 192-248 (646)
286 PRK03578 hscB co-chaperone Hsc 20.7 6E+02 0.013 22.5 9.6 51 128-180 17-84 (176)
287 PRK09343 prefoldin subunit bet 20.3 2.2E+02 0.0047 23.7 4.8 33 207-239 74-106 (121)
288 cd04769 HTH_MerR2 Helix-Turn-H 20.2 1.6E+02 0.0034 23.8 3.9 26 153-182 2-27 (116)
289 PF08614 ATG16: Autophagy prot 20.2 3.1E+02 0.0066 24.2 6.0 37 203-239 115-151 (194)
290 PF01381 HTH_3: Helix-turn-hel 20.2 55 0.0012 22.2 1.0 23 151-173 9-31 (55)
291 PF02996 Prefoldin: Prefoldin 20.1 2.8E+02 0.006 21.9 5.2 68 164-238 51-118 (120)
No 1
>KOG2577 consensus Transcription factor E2F/dimerization partner (TDP) [Transcription]
Probab=100.00 E-value=2.4e-53 Score=403.12 Aligned_cols=156 Identities=51% Similarity=0.741 Sum_probs=150.3
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCCCCCCc
Q 023564 121 LNLSNGCRYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTS 200 (280)
Q Consensus 121 ~tp~~~~R~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~ 200 (280)
.+|...+|+++|||+||+|||.|++++|||++|||+||++|+|+|||||||||||||||||+|++||+|+|+|.+.+..+
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 45678899999999999999999999999999999999999999999999999999999999999999999999987667
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCcccccChHhhcCCCCCccchh---------------
Q 023564 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFLTEEDIASLPCFQVIAV--------------- 265 (280)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~~n~~~~YVT~eDI~~l~~fq~qTv--------------- 265 (280)
+..++.+.|++|++.|.++|+.||++|++|+++|+.|++|.+|++|+||||+||++|+.|++|||
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 78888999999999999999999999999999999999999999999999999999999999999
Q ss_pred ----eeeeeehhhhh
Q 023564 266 ----NLRIYLKSIFS 276 (280)
Q Consensus 266 ----~lqI~LkS~~~ 276 (280)
.+||+|||++.
T Consensus 221 ~~~~~~~i~L~s~~G 235 (354)
T KOG2577|consen 221 PDEDRYQIRLKSNQG 235 (354)
T ss_pred CCCCceEEEeccCCC
Confidence 79999999985
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=1.5e-23 Score=158.79 Aligned_cols=66 Identities=53% Similarity=0.882 Sum_probs=62.9
Q ss_pred CCCCcHHHHHHHHHHHHHhCCCCceeHHHHHHHh---cc--cceehhhhhhhhhhccccccccCCceEEec
Q 023564 128 RYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVL---EV--QKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (280)
Q Consensus 128 R~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L---~V--qKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (280)
|.++||+.||++||++|...+++.++|+++|+.| ++ +|||||||+||||++|||+|.+|+.|+|+|
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=99.80 E-value=3.5e-20 Score=174.85 Aligned_cols=87 Identities=37% Similarity=0.611 Sum_probs=78.9
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCCCCCCc
Q 023564 121 LNLSNGCRYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTS 200 (280)
Q Consensus 121 ~tp~~~~R~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~ 200 (280)
..+.-++|+++|||+||.+|+.++....-..+-|+.||.+|||.|||||||+||||+||++.|.+||.|.|+|++
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 455678999999999999999999877777899999999999999999999999999999999999999999987
Q ss_pred hhHHHHHHHHHH
Q 023564 201 KLDDQVARLKAE 212 (280)
Q Consensus 201 ~~~~~~~~Lk~E 212 (280)
.+...+.+||+|
T Consensus 89 aiPral~eLqeE 100 (388)
T KOG2578|consen 89 AIPRALFELQEE 100 (388)
T ss_pred hhhHHHHHHHHH
Confidence 456667777776
No 4
>KOG2578 consensus Transcription factor E2F/dimerization partner (TDP)-like proteins [Transcription]
Probab=99.00 E-value=2.9e-10 Score=108.23 Aligned_cols=74 Identities=39% Similarity=0.610 Sum_probs=65.3
Q ss_pred CCCCCCCCCcHHHHHHHHHHHHHhCCCC-ceeHHHHHHHhc----------ccceehhhhhhhhhhccccccc-----cC
Q 023564 123 LSNGCRYDSSLGLLTRKFINLIQEAKDG-TLDLNRTAEVLE----------VQKRRIYDITNVLEGIGLIEKT-----SK 186 (280)
Q Consensus 123 p~~~~R~d~SLglLTkkFI~ll~~a~~g-~ldLn~aA~~L~----------VqKRRIYDItNVLEgIGLIeK~-----~K 186 (280)
+....|+++||++||++||.++-++++. .|.|+.||..|- ..-||+|||.|||-+++||+|+ .|
T Consensus 151 ~k~DnrkekSL~lL~qnFvklflcs~~~~lvslD~Aak~Ll~ds~~~~~mRtkvRRLYDIANVlssm~LIeKtH~l~trk 230 (388)
T KOG2578|consen 151 SKRDNRKEKSLWLLAQNFVKLFLCSDDDILVSLDSAAKALLKDSEDEPPMRTKVRRLYDIANVLSSMNLIEKTHYLFTRK 230 (388)
T ss_pred CcccchhhhHHHHHHHHHHHheeccccceEEeecHHHHHHhcCCCCCccHHHHHHHHHHHHHHHHHhhhhhhhccccccc
Confidence 3456789999999999999999999888 889999998874 3569999999999999999997 48
Q ss_pred CceEEecCCC
Q 023564 187 NHIRWKGSDS 196 (280)
Q Consensus 187 N~i~W~G~~~ 196 (280)
..|+|.|...
T Consensus 231 PafrwlG~~~ 240 (388)
T KOG2578|consen 231 PAFRWLGSKP 240 (388)
T ss_pred chhheeCCCc
Confidence 9999999664
No 5
>KOG2829 consensus E2F-like protein [Transcription]
Probab=98.96 E-value=4.2e-09 Score=99.62 Aligned_cols=51 Identities=37% Similarity=0.600 Sum_probs=43.2
Q ss_pred hCCCCceeHHHHHHHhc----------------------ccceehhhhhhhhhhccccccccCCceEEecCCCC
Q 023564 146 EAKDGTLDLNRTAEVLE----------------------VQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSL 197 (280)
Q Consensus 146 ~a~~g~ldLn~aA~~L~----------------------VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s 197 (280)
....|....+++|+.|- -.|||+||.+|||.++.+|.|. |..|+|+|+...
T Consensus 57 ve~Kg~TtYneVADelVaef~~~n~~~~i~~n~~~yd~KNIRRRVYDALNVlmAmnIIsKd-KKEIrW~GLP~~ 129 (326)
T KOG2829|consen 57 VERKGTTTYNEVADELVAEFAGANNYSHICPNEQEYDQKNIRRRVYDALNVLMAMNIISKD-KKEIRWIGLPAT 129 (326)
T ss_pred HHhcCCccHHHHHHHHHHHHhccccccccCccccccchHHHHHHHHHHHHHHHHHHHHhcc-cceeeeeccCcc
Confidence 34677888888888873 3699999999999999999999 667999999854
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=95.20 E-value=0.027 Score=41.29 Aligned_cols=45 Identities=24% Similarity=0.425 Sum_probs=41.0
Q ss_pred CCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEe
Q 023564 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (280)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (280)
..+.....++|+.+++.+..+|++++-|+.-|+|++...+.+.|.
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 567899999999999999999999999999999999987776664
No 7
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=93.97 E-value=0.096 Score=36.64 Aligned_cols=41 Identities=27% Similarity=0.387 Sum_probs=35.3
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIG 179 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIG 179 (280)
.+.+.++..+.+. +...++|+.|+|++|-|+.-++.|+..|
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 4567778666666 9999999999999999999999999998
No 8
>COG1378 Predicted transcriptional regulators [Transcription]
Probab=93.46 E-value=0.42 Score=44.30 Aligned_cols=46 Identities=22% Similarity=0.399 Sum_probs=38.7
Q ss_pred CceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCC
Q 023564 150 GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD 195 (280)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~ 195 (280)
|...-.++|+..||.+=|+|||++.||+=|+|+.....--.+.-.+
T Consensus 29 g~~tA~eis~~sgvP~~kvY~vl~sLe~kG~v~~~~g~P~~y~av~ 74 (247)
T COG1378 29 GEATAKEISEASGVPRPKVYDVLRSLEKKGLVEVIEGRPKKYRAVP 74 (247)
T ss_pred CCccHHHHHHHcCCCchhHHHHHHHHHHCCCEEeeCCCCceEEeCC
Confidence 5667789999999999999999999999999999866555555444
No 9
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=92.97 E-value=0.15 Score=34.06 Aligned_cols=45 Identities=27% Similarity=0.435 Sum_probs=38.6
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.++.++.+. +.+.+.++|+.|++.++.+|.++.-|+..|+|++..
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 459999999999999999999999999999998764
No 10
>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=92.71 E-value=0.25 Score=35.06 Aligned_cols=54 Identities=20% Similarity=0.250 Sum_probs=42.6
Q ss_pred HHHHHHHHHHhC-----CCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCce
Q 023564 136 LTRKFINLIQEA-----KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (280)
Q Consensus 136 LTkkFI~ll~~a-----~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i 189 (280)
+..-|+.+.... ..+.+...++|+.+++.+..++.+++.|+.-|+|++.....|
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 444555555433 446789999999999999999999999999999998763433
No 11
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=92.05 E-value=0.3 Score=36.80 Aligned_cols=48 Identities=25% Similarity=0.388 Sum_probs=40.3
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
...++++.+.+ +.+.+.++|+.+++.+..+|-+++.|+..|+|++...
T Consensus 8 ~~Il~~l~~~~-~~~t~~~ia~~l~i~~~tv~r~l~~L~~~g~l~~~~~ 55 (91)
T smart00346 8 LAVLRALAEEP-GGLTLAELAERLGLSKSTAHRLLNTLQELGYVEQDGQ 55 (91)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHhCCCHHHHHHHHHHHHHCCCeeecCC
Confidence 44566665543 4699999999999999999999999999999998643
No 12
>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=91.75 E-value=0.19 Score=35.34 Aligned_cols=45 Identities=20% Similarity=0.353 Sum_probs=37.1
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
..++++..++.+ +.+.++|+.+|+.|=-+|-+++.|+..|++++.
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 345556555555 799999999999999999999999999999874
No 13
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=91.50 E-value=0.33 Score=36.32 Aligned_cols=56 Identities=21% Similarity=0.315 Sum_probs=46.9
Q ss_pred HHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEe
Q 023564 137 TRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (280)
Q Consensus 137 TkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (280)
-.+.+.++...++..+.+.++|+.||+.++-+.-++.-|+.-|+|++.+-+-=.|.
T Consensus 8 ~~~IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~G~V~~~~~~~~~W~ 63 (68)
T smart00550 8 EEKILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKKGKVCKQGGTPPLWK 63 (68)
T ss_pred HHHHHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecCCCCCceE
Confidence 35778888877654599999999999999999999999999999999865434673
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=90.09 E-value=0.5 Score=33.21 Aligned_cols=46 Identities=24% Similarity=0.340 Sum_probs=40.7
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
..+.++...++..+.+.++|+.|++.|=.+--+++-||.-|+|++.
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 4566677788888999999999999999999999999999999987
No 15
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=89.80 E-value=0.47 Score=32.44 Aligned_cols=43 Identities=30% Similarity=0.450 Sum_probs=35.8
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
.+.+.++.+.| .+...++|+.+++.+..++.+++-|+.-|+|+
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 56777887644 49999999999999999999999999999985
No 16
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=87.43 E-value=0.71 Score=31.25 Aligned_cols=38 Identities=24% Similarity=0.376 Sum_probs=34.4
Q ss_pred CCceeHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
.+.+.++++++.|++.+..++++++.|+.-|+|+...+
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 17
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=86.79 E-value=4.5 Score=34.63 Aligned_cols=87 Identities=23% Similarity=0.383 Sum_probs=57.7
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCCC-CCCchhHHHHHHHHHHHHHHHH
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDS-LGTSKLDDQVARLKAEIESLHA 218 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~-s~~~~~~~~~~~Lk~El~~L~~ 218 (280)
|..|++ +.+.++.+++|+.|+..|=.+|-.++=|.-.|||+|.--+. .|..- ---..++. .+++..
T Consensus 33 ~~~LL~--~~~~~tvdelae~lnr~rStv~rsl~~L~~~GlV~Rek~~~---~~Ggy~yiY~~i~~--ee~k~~------ 99 (126)
T COG3355 33 YKALLE--ENGPLTVDELAEILNRSRSTVYRSLQNLLEAGLVEREKVNL---KGGGYYYLYKPIDP--EEIKKK------ 99 (126)
T ss_pred HHHHHh--hcCCcCHHHHHHHHCccHHHHHHHHHHHHHcCCeeeeeecc---CCCceeEEEecCCH--HHHHHH------
Confidence 555554 78889999999999999999999999999999999885442 22220 00001111 122222
Q ss_pred HHHHHHHHHHHHHHHHHHhhh
Q 023564 219 EECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 219 eE~~LD~~I~~~~~~L~~Lte 239 (280)
.++.||++-..+.+-|+++..
T Consensus 100 i~~~l~~w~~~~~~~i~~~~~ 120 (126)
T COG3355 100 ILKDLDEWYDKMKQLIEEFEK 120 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHhc
Confidence 345677777777777776654
No 18
>PF14394 DUF4423: Domain of unknown function (DUF4423)
Probab=86.17 E-value=9.8 Score=33.43 Aligned_cols=99 Identities=19% Similarity=0.248 Sum_probs=62.2
Q ss_pred hCCCCceeHHHHHHHh--cccceehhhhhhhhhhccccccccCCceEEecCCCCCCchh-HHHHHHHHHHHHH-----HH
Q 023564 146 EAKDGTLDLNRTAEVL--EVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKL-DDQVARLKAEIES-----LH 217 (280)
Q Consensus 146 ~a~~g~ldLn~aA~~L--~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~-~~~~~~Lk~El~~-----L~ 217 (280)
.-.++.-|...+|++| +|.--.+=+.++.|+-+|||+|...+.|.=.-...+.+.++ ...+..++.+.-+ |+
T Consensus 34 ~l~~~~~d~~~iak~l~p~is~~ev~~sL~~L~~~gli~k~~~g~y~~t~~~l~~~~~~~~~avr~~h~q~~~lA~~al~ 113 (171)
T PF14394_consen 34 PLMPFAPDPEWIAKRLRPKISAEEVRDSLEFLEKLGLIKKDGDGKYVQTDKSLTTSSEIPSEAVRSYHKQMLELAQEALD 113 (171)
T ss_pred hcCCCCCCHHHHHHHhcCCCCHHHHHHHHHHHHHCCCeEECCCCcEEEecceeeCCCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 3456666999999999 99999999999999999999999775444322112222222 2223333333222 11
Q ss_pred ------------------HHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 023564 218 ------------------AEECRIDDSIREKQELIRTLEENENHQ 244 (280)
Q Consensus 218 ------------------~eE~~LD~~I~~~~~~L~~Lted~~n~ 244 (280)
..=.++-+.|+.++.++..+.+...+.
T Consensus 114 ~~p~~~R~~s~~T~~vs~~~~~ki~~~i~~fRk~i~~i~~~~~~~ 158 (171)
T PF14394_consen 114 RVPPEERDFSGLTMSVSREDYEKIKKEIREFRKKIIAIAEEDKEP 158 (171)
T ss_pred hCCccccceeeeEEEeCHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 122345566777777777776654443
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=85.92 E-value=1.3 Score=33.80 Aligned_cols=49 Identities=22% Similarity=0.341 Sum_probs=39.9
Q ss_pred HHHHHHHHHHhCCCC-ceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 136 LTRKFINLIQEAKDG-TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 136 LTkkFI~ll~~a~~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
.+-+++.++...+++ .+.+.++|+.+++..+.+..|++-|+--|+|+..
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~ 58 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKAGLIESS 58 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEec
Confidence 445667777655554 4999999999999999999999999999999864
No 20
>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=85.65 E-value=1.1 Score=36.61 Aligned_cols=47 Identities=11% Similarity=0.154 Sum_probs=41.0
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
-+.+.++...+++.+++.++|+.+++.+..++.++..|+.-|+|+..
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 21
>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=85.63 E-value=3.9 Score=32.79 Aligned_cols=55 Identities=18% Similarity=0.302 Sum_probs=34.0
Q ss_pred cCCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 185 SKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 185 ~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
...-+.|+|.+..-....++.+..++..++.|..+-..|++.|..+++++..+..
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 4557889997654333344445566666666666666666666666666666543
No 22
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=85.46 E-value=0.99 Score=31.64 Aligned_cols=44 Identities=25% Similarity=0.400 Sum_probs=36.2
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
++.++.+.++ +.+.++|+.+++.+-.+-.+++-||.-|+|+|..
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 3444454444 9999999999999999999999999999999873
No 23
>PF13730 HTH_36: Helix-turn-helix domain
Probab=85.33 E-value=0.74 Score=32.08 Aligned_cols=29 Identities=31% Similarity=0.356 Sum_probs=27.9
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhcccc
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLI 181 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLI 181 (280)
....+|+.+|+.+|.++..++.||-.|+|
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~~G~I 55 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEEKGLI 55 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHCcCC
Confidence 79999999999999999999999999986
No 24
>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=83.59 E-value=2.5 Score=29.17 Aligned_cols=47 Identities=23% Similarity=0.359 Sum_probs=38.7
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCC
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (280)
..++.++...+ +...++|+.+++.+..++-+++.|+.-|+|.+....
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 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=82.86 E-value=0.54 Score=35.90 Aligned_cols=29 Identities=41% Similarity=0.486 Sum_probs=22.9
Q ss_pred HHHHHhcc---cceehhhhhhhhhhccccccc
Q 023564 156 RTAEVLEV---QKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 156 ~aA~~L~V---qKRRIYDItNVLEgIGLIeK~ 184 (280)
.+|+.+++ ..|||+|+++-|+-+|||+-.
T Consensus 27 ~lc~~~~~~pls~~r~~~~l~eL~~~gli~~~ 58 (85)
T PF09079_consen 27 ELCESLGVDPLSYRRFSDYLSELEMLGLIESE 58 (85)
T ss_dssp HHHHHTTS----HHHHHHHHHHHHHTTSEEEE
T ss_pred HHHHHcCCCCCCHHHHHHHHHHHHhCCCeEEE
Confidence 34555554 789999999999999999866
No 26
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=82.81 E-value=1.9 Score=30.73 Aligned_cols=39 Identities=33% Similarity=0.452 Sum_probs=32.2
Q ss_pred CCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
..++.+.+.++|+.+++.+--+..+++-|+..|+|+|..
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~glv~~~~ 52 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEKGLVEKER 52 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHTTSEEEEE
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEecC
Confidence 378889999999999999999999999999999998873
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=81.51 E-value=1.5 Score=32.20 Aligned_cols=54 Identities=11% Similarity=0.167 Sum_probs=38.4
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccc-cccccCCceEEecCC
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL-IEKTSKNHIRWKGSD 195 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL-IeK~~KN~i~W~G~~ 195 (280)
+.+.++.+ +.+...++|+.++|+++-++.-+..|+.-|+ |....+..+-+.+.+
T Consensus 4 ~il~~L~~---~~~~~~eLa~~l~vS~~tv~~~l~~L~~~g~~i~~~~~g~~l~~~~~ 58 (69)
T TIGR00122 4 RLLALLAD---NPFSGEKLGEALGMSRTAVNKHIQTLREWGVDVLTVGKGYRLPPPIP 58 (69)
T ss_pred HHHHHHHc---CCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEecCCceEecCccc
Confidence 45555553 3466999999999999999999999988888 333344444444443
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=81.30 E-value=4.3 Score=29.37 Aligned_cols=50 Identities=22% Similarity=0.260 Sum_probs=38.5
Q ss_pred HHHHHHHHh---CCCCce-eHHHHHHHhcccceehhhhhhhhhhccccccccCC
Q 023564 138 RKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (280)
Q Consensus 138 kkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (280)
..+.+.+.. .++..+ ...++|++++|++.-+.+.++.|+.-|+|++..+.
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 444455543 356678 99999999999999999999999999999987543
No 29
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=80.95 E-value=1.5 Score=28.99 Aligned_cols=35 Identities=26% Similarity=0.358 Sum_probs=32.0
Q ss_pred ceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.+...++|+.+++.+..++.+++.|+.-|+|++..
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 36788999999999999999999999999999764
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=80.66 E-value=0.96 Score=34.07 Aligned_cols=44 Identities=27% Similarity=0.430 Sum_probs=30.2
Q ss_pred CCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 130 DSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 130 d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
+.+++.+-+.+..+|+...-. -...|||+||+|-||..|||+-.
T Consensus 22 ~~~~~~vy~~Y~~~c~~~~~~-----------~l~~~~~~~~l~~L~~~gli~~~ 65 (87)
T cd08768 22 EATTGEVYEVYEELCEEIGVD-----------PLTQRRISDLLSELEMLGLLETE 65 (87)
T ss_pred CccHHHHHHHHHHHHHHcCCC-----------CCcHHHHHHHHHHHHHcCCeEEE
Confidence 345566666666666432100 14789999999999999999865
No 31
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=80.06 E-value=2.3 Score=28.99 Aligned_cols=40 Identities=20% Similarity=0.294 Sum_probs=35.1
Q ss_pred CCCce-eHHHHHHHhcccceehhhhhhhhhhccccccccCC
Q 023564 148 KDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (280)
Q Consensus 148 ~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (280)
++..+ ...++|+.++|++=-+...++.|+.-|+|++....
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 45566 89999999999999999999999999999876443
No 32
>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=79.26 E-value=2.3 Score=29.26 Aligned_cols=34 Identities=29% Similarity=0.427 Sum_probs=31.6
Q ss_pred CceeHHHHHHHhcccceehhhhhhhhhhcccccc
Q 023564 150 GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (280)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (280)
+...+.++|+.|++.+=-++-=+++|+..|+|+|
T Consensus 14 ~~~~~~el~~~l~~s~~~vs~hL~~L~~~glV~~ 47 (47)
T PF01022_consen 14 GPLTVSELAEELGLSQSTVSHHLKKLREAGLVEK 47 (47)
T ss_dssp SSEEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred CCCchhhHHHhccccchHHHHHHHHHHHCcCeeC
Confidence 7899999999999999999999999999999986
No 33
>TIGR02147 Fsuc_second hypothetical protein, TIGR02147. This family consists of the 40 members of a paralogous protein family in the rumen anaerobe Fibrobacter succinogenes S85. Member proteins are about 270 residues long and appear to lack signal sequences and transmembrane helices. The only perfectly conserved residue is a glycine in an otherwise poorly conserved region, suggesting members are not enzymes. The family is not characterized.
Probab=78.05 E-value=24 Score=33.45 Aligned_cols=96 Identities=16% Similarity=0.192 Sum_probs=60.6
Q ss_pred CCCCceeHHHHHHHhc--ccceehhhhhhhhhhccccccccCCceEEecCC--CCCCchh-HHHHHHHHHHHHHH-----
Q 023564 147 AKDGTLDLNRTAEVLE--VQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD--SLGTSKL-DDQVARLKAEIESL----- 216 (280)
Q Consensus 147 a~~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~--~s~~~~~-~~~~~~Lk~El~~L----- 216 (280)
-.++.-|..++|++++ |.--.+=|.+..|+-+|||+|..-+ .|.=.+ .+.+.++ ...+...+.+.-.|
T Consensus 133 ~~~~~~~~~~ia~~l~p~is~~ev~~sL~~L~~~glikk~~~g--~y~~t~~~l~~~~~~~~~avr~~h~q~l~lA~~al 210 (271)
T TIGR02147 133 VMPFADDPEELAKRCFPKISAEQVKESLDLLERLGLIKKNEDG--FYKQTDKAVSTGDEVIPLAVRQYQKQMIDLAKEAL 210 (271)
T ss_pred cCCCCCCHHHHHHHhCCCCCHHHHHHHHHHHHHCCCeeECCCC--cEEeecceeecCCccchHHHHHHHHHHHHHHHHHH
Confidence 3667778999999999 8888999999999999999998755 453222 2222222 22233443332222
Q ss_pred ------------------HHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 023564 217 ------------------HAEECRIDDSIREKQELIRTLEENENHQ 244 (280)
Q Consensus 217 ------------------~~eE~~LD~~I~~~~~~L~~Lted~~n~ 244 (280)
...=.++-+.|+.++.++..+.++..+.
T Consensus 211 ~~~p~~eR~~S~lT~~i~~~~~~~i~~~i~~fRk~i~~i~~~~~~~ 256 (271)
T TIGR02147 211 DALPPSERDVSTVTFGISEEAYKEIVKKIQEFRKEVLAIATKDKEE 256 (271)
T ss_pred HhCCccccccceeeEecCHHHHHHHHHHHHHHHHHHHHHHhcCCCc
Confidence 1112345566777777777776655443
No 34
>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=77.25 E-value=10 Score=30.96 Aligned_cols=54 Identities=19% Similarity=0.268 Sum_probs=35.3
Q ss_pred CCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 186 KNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 186 KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
..-+.|+|.+..-...+++.+.-++..++.|...-..|.+.|..+++++..+.+
T Consensus 69 ~~v~v~iG~g~~vE~~~~eA~~~l~~r~~~l~~~~~~l~~~l~~l~~~~~~~~~ 122 (129)
T cd00584 69 DKVLVDLGTGYYVEKDLEEAIEFLDKKIEELTKQIEKLQKELAKLKDQINTLEA 122 (129)
T ss_pred CEEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345778887754333445556667777777777777777777777777766543
No 35
>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=77.23 E-value=3.9 Score=29.51 Aligned_cols=44 Identities=32% Similarity=0.471 Sum_probs=38.6
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
+.++++++ .+.+.+.++|+.|+|+..-|.-=+|.|+.-|+|.|.
T Consensus 4 ~Il~~l~~--~~~~s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~ 47 (57)
T PF08220_consen 4 QILELLKE--KGKVSVKELAEEFGVSEMTIRRDLNKLEKQGLIKRT 47 (57)
T ss_pred HHHHHHHH--cCCEEHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEE
Confidence 45677764 589999999999999999999889999999999887
No 36
>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=76.47 E-value=3.5 Score=31.25 Aligned_cols=49 Identities=22% Similarity=0.285 Sum_probs=40.2
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
.++++.+-.+...=+.-.+++..+++..|-++=++++||..|||.|+.-
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 4567777666555556667889999999999999999999999999865
No 37
>PRK11414 colanic acid/biofilm transcriptional regulator; Provisional
Probab=75.68 E-value=7.3 Score=34.22 Aligned_cols=52 Identities=10% Similarity=0.073 Sum_probs=42.0
Q ss_pred HHHHHHHHHHh---CCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCC
Q 023564 136 LTRKFINLIQE---AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (280)
Q Consensus 136 LTkkFI~ll~~---a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (280)
+...+.+.+.. .|+..+.-.++|+.|||+|=-+=+.+..|+..|||+.....
T Consensus 16 v~~~l~~~I~~g~l~pG~~L~e~~La~~lgVSRtpVREAL~~L~~eGLV~~~~~~ 70 (221)
T PRK11414 16 VENDLKHQLSIGALKPGARLITKNLAEQLGMSITPVREALLRLVSVNALSVAPAQ 70 (221)
T ss_pred HHHHHHHHHHhCCCCCCCccCHHHHHHHHCCCchhHHHHHHHHHHCCCEEecCCC
Confidence 34444454433 47888889999999999999999999999999999977554
No 38
>PRK03947 prefoldin subunit alpha; Reviewed
Probab=75.54 E-value=13 Score=30.92 Aligned_cols=52 Identities=17% Similarity=0.243 Sum_probs=29.4
Q ss_pred CCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 186 KNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 186 KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
..-+.|.|.+..--..+++.+..|+..++.|...-..|.+.|.+.++++..+
T Consensus 76 ~kV~v~lG~g~~vE~~~~eA~~~l~~~~~~l~~~~~~l~~~l~~~~~~~~~~ 127 (140)
T PRK03947 76 DKVIVSLGAGYSAEKDLDEAIEILDKRKEELEKALEKLEEALQKLASRIAQL 127 (140)
T ss_pred CeEEEEcCCCEEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456788876543233455555666666666555555555555555555544
No 39
>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=74.25 E-value=12 Score=29.10 Aligned_cols=27 Identities=19% Similarity=0.287 Sum_probs=21.9
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
+.+.++|+.+||+.+-|.-. |..|+|.
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 46789999999999887766 5568886
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=72.77 E-value=5.7 Score=32.09 Aligned_cols=37 Identities=22% Similarity=0.396 Sum_probs=33.8
Q ss_pred CCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
..+.+...++|+.+++.+..+++|+..|+.-|+|...
T Consensus 22 ~~~~~s~~eia~~~~i~~~~v~~il~~L~~~gli~~~ 58 (132)
T TIGR00738 22 DEGPVSVKEIAERQGISRSYLEKILRTLRRAGLVESV 58 (132)
T ss_pred CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCcEEec
Confidence 3458999999999999999999999999999999864
No 41
>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=72.45 E-value=2.1 Score=31.68 Aligned_cols=43 Identities=16% Similarity=0.208 Sum_probs=34.9
Q ss_pred CCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceE
Q 023564 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (280)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (280)
..+.+++.++|..|+++..-+=+++.+|+..|.|+|...+.-.
T Consensus 11 ~~~~~S~~eLa~~~~~s~~~ve~mL~~l~~kG~I~~~~~~~~~ 53 (69)
T PF09012_consen 11 ERGRVSLAELAREFGISPEAVEAMLEQLIRKGYIRKVDMSSCC 53 (69)
T ss_dssp HS-SEEHHHHHHHTT--HHHHHHHHHHHHCCTSCEEEEEE--S
T ss_pred HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCcEEEecCCCCC
Confidence 4688999999999999999999999999999999998765443
No 42
>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=72.40 E-value=3.3 Score=29.77 Aligned_cols=45 Identities=27% Similarity=0.427 Sum_probs=37.7
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
+.+.++ ..++.+.+.++|+.|++.+-.+|-=+++|+..|||+...
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 467789999999999999999999999999999998763
No 43
>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=70.93 E-value=35 Score=30.05 Aligned_cols=45 Identities=22% Similarity=0.288 Sum_probs=38.3
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
.+.+.++... +.+...++|+.|++.+=-+.-.+..||.-|+|++.
T Consensus 4 ~~IL~~L~~~--~~~t~~eLA~~lgis~~tV~~~L~~Le~~GlV~r~ 48 (203)
T TIGR02702 4 EDILSYLLKQ--GQATAAALAEALAISPQAVRRHLKDLETEGLIEYE 48 (203)
T ss_pred HHHHHHHHHc--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeEEe
Confidence 4566667654 34999999999999999999999999999999876
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=70.55 E-value=14 Score=30.11 Aligned_cols=54 Identities=19% Similarity=0.235 Sum_probs=41.1
Q ss_pred CCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 186 KNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 186 KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
..-+.|+|.+..--..+++.+.-|+..++.|...-..|.+.|.++++++..+.+
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 566789998754334456667788888888888888888888888888877654
No 45
>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=70.06 E-value=16 Score=32.14 Aligned_cols=39 Identities=21% Similarity=0.210 Sum_probs=34.8
Q ss_pred ceeHHHHHHHhcccceehhhhhhhhhhccccccccCCce
Q 023564 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (280)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i 189 (280)
.++..++|+.++++++-++..+..|+--++|.|...+.|
T Consensus 75 ~~t~~~ia~~l~iS~~Tv~r~ik~L~e~~iI~k~~~G~Y 113 (165)
T PF05732_consen 75 VATQKEIAEKLGISKPTVSRAIKELEEKNIIKKIRNGAY 113 (165)
T ss_pred EeeHHHHHHHhCCCHHHHHHHHHHHHhCCcEEEccCCeE
Confidence 568899999999999999999999999999999865533
No 46
>PRK09834 DNA-binding transcriptional activator MhpR; Provisional
Probab=69.82 E-value=7 Score=35.68 Aligned_cols=51 Identities=12% Similarity=0.313 Sum_probs=40.3
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc-CCceEE
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS-KNHIRW 191 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~-KN~i~W 191 (280)
.++++...+ +.+.+.++|+.|++.|=-+|-+++-|+..|++++.. ...|..
T Consensus 16 iL~~l~~~~-~~ls~~eia~~lgl~kstv~RlL~tL~~~g~v~~~~~~~~Y~L 67 (263)
T PRK09834 16 VLRALNRLD-GGATVGLLAELTGLHRTTVRRLLETLQEEGYVRRSASDDSFRL 67 (263)
T ss_pred HHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCCCcEEE
Confidence 445554443 349999999999999999999999999999999863 344443
No 47
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=69.42 E-value=4.7 Score=30.66 Aligned_cols=33 Identities=27% Similarity=0.292 Sum_probs=30.5
Q ss_pred HHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
+.++|+.|+|.+=.++.++..|+.-|+|.+...
T Consensus 2 ~~ela~~l~is~stvs~~l~~L~~~glI~r~~~ 34 (96)
T smart00529 2 TSEIAERLNVSPPTVTQMLKKLEKDGLVEYEPY 34 (96)
T ss_pred HHHHHHHhCCChHHHHHHHHHHHHCCCEEEcCC
Confidence 568999999999999999999999999999863
No 48
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=69.03 E-value=13 Score=33.73 Aligned_cols=38 Identities=24% Similarity=0.246 Sum_probs=35.2
Q ss_pred CCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
...++.|.++++.||++|=++-=.+-+|++.||++|+-
T Consensus 38 s~~Pmtl~Ei~E~lg~Sks~vS~~lkkL~~~~lV~~~~ 75 (177)
T COG1510 38 SRKPLTLDEIAEALGMSKSNVSMGLKKLQDWNLVKKVF 75 (177)
T ss_pred cCCCccHHHHHHHHCCCcchHHHHHHHHHhcchHHhhh
Confidence 36778999999999999999999999999999999874
No 49
>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=68.92 E-value=8.1 Score=30.51 Aligned_cols=46 Identities=15% Similarity=0.202 Sum_probs=38.0
Q ss_pred CCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCC
Q 023564 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD 195 (280)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~ 195 (280)
....+.-.++|+.+|+.|.-+..+++.||--|+|++..+ ..|.|..
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 455788899999999999999999999999999997653 3454543
No 50
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=68.57 E-value=8 Score=35.61 Aligned_cols=57 Identities=11% Similarity=0.204 Sum_probs=44.2
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCC
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSD 195 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~ 195 (280)
-..++++...+ ..+.+.++|+.|++.|=.+|.+++.|+..|++++.....-.+.|..
T Consensus 28 l~IL~~~~~~~-~~~tl~eIa~~lglpkStv~RlL~tL~~~G~l~~~~~~~~Y~lG~~ 84 (271)
T PRK10163 28 IAILQYLEKSG-GSSSVSDISLNLDLPLSTTFRLLKVLQAADFVYQDSQLGWWHIGLG 84 (271)
T ss_pred HHHHHHHHhCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEEecHH
Confidence 34556665443 4588999999999999999999999999999998755544445543
No 51
>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=68.24 E-value=16 Score=28.12 Aligned_cols=38 Identities=32% Similarity=0.519 Sum_probs=31.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
-+.+|..|..|.+.|...|..+...|+.++..+.++..
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 35778999999999999999999999988888877643
No 52
>PRK10870 transcriptional repressor MprA; Provisional
Probab=67.41 E-value=38 Score=29.43 Aligned_cols=41 Identities=17% Similarity=0.263 Sum_probs=36.6
Q ss_pred HhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 145 QEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 145 ~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
...+++.+...++|+.+++.+=.+--+++-||.-|+|+|..
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 34567789999999999999999999999999999999974
No 53
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=67.16 E-value=63 Score=26.44 Aligned_cols=35 Identities=17% Similarity=0.282 Sum_probs=32.4
Q ss_pred ceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.+...++|+.+++.+--+--+++.||.-|+|+|..
T Consensus 46 ~~t~~eLa~~l~~~~~tvt~~v~~Le~~GlV~r~~ 80 (144)
T PRK03573 46 EQSQIQLAKAIGIEQPSLVRTLDQLEEKGLISRQT 80 (144)
T ss_pred CCCHHHHHHHhCCChhhHHHHHHHHHHCCCEeeec
Confidence 35689999999999999999999999999999984
No 54
>PHA02943 hypothetical protein; Provisional
Probab=66.04 E-value=16 Score=32.76 Aligned_cols=48 Identities=23% Similarity=0.241 Sum_probs=41.9
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNH 188 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~ 188 (280)
..+++++ ..|.....++|+.||++--....++=|||--|.|++.....
T Consensus 14 ~eILE~L---k~G~~TtseIAkaLGlS~~qa~~~LyvLErEG~VkrV~~G~ 61 (165)
T PHA02943 14 IKTLRLL---ADGCKTTSRIANKLGVSHSMARNALYQLAKEGMVLKVEIGR 61 (165)
T ss_pred HHHHHHH---hcCCccHHHHHHHHCCCHHHHHHHHHHHHHcCceEEEeecc
Confidence 4577787 67888899999999999999999999999999999976553
No 55
>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=65.97 E-value=6 Score=29.69 Aligned_cols=46 Identities=22% Similarity=0.259 Sum_probs=35.5
Q ss_pred HHHHHHhCCCCceeHHHHHHHhccc-ceehhhhhhhhhhcccccccc
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQ-KRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIGLIeK~~ 185 (280)
||.-+....+-.-.+.++|+.||+. ..-+++.+..||.-|+|++..
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 4444444556677999999999995 999999999999999999874
No 56
>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=65.88 E-value=16 Score=26.89 Aligned_cols=32 Identities=28% Similarity=0.286 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 206 VARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 206 ~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
...++.|+..|+.+-+.+.+.+..+++++..|
T Consensus 19 ~~~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 19 YYQLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45666777777777777777777777777777
No 57
>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=65.70 E-value=8.2 Score=30.35 Aligned_cols=50 Identities=20% Similarity=0.362 Sum_probs=40.2
Q ss_pred cHHHHHHHHHHHHHhC--CCCceeHHHHHHHhcccceehhhhhhhhhhcccc
Q 023564 132 SLGLLTRKFINLIQEA--KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLI 181 (280)
Q Consensus 132 SLglLTkkFI~ll~~a--~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 181 (280)
+|..+.++.+++|++. .+.=+.++++++.|++....|.+++.-|..-|+|
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~eG~I 95 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNEGHI 95 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHTTSE
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhCCeE
Confidence 6889999999999872 2234999999999999999999999999998887
No 58
>COG1474 CDC6 Cdc6-related protein, AAA superfamily ATPase [DNA replication, recombination, and repair / Posttranslational modification, protein turnover, chaperones]
Probab=65.69 E-value=4.3 Score=39.65 Aligned_cols=30 Identities=33% Similarity=0.556 Sum_probs=27.1
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
-+..+++.++++.||+|||+|-|+++|+|.
T Consensus 303 ~y~~~~~~~~~~~~~~~~ii~~L~~lgiv~ 332 (366)
T COG1474 303 VYESLCERLRTSQRRFSDIISELEGLGIVS 332 (366)
T ss_pred HHHHHHhhhCchHHHHHHHHHHHHhcCeEE
Confidence 456778888889999999999999999998
No 59
>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=65.58 E-value=29 Score=27.67 Aligned_cols=38 Identities=21% Similarity=0.305 Sum_probs=24.9
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhccccc-cccCCceEEec
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE-KTSKNHIRWKG 193 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe-K~~KN~i~W~G 193 (280)
+.+.++|+.+||..+-|- -.|-.|||. ....|.+++-.
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 568899999999887443 345567775 23346666643
No 60
>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=65.40 E-value=19 Score=31.12 Aligned_cols=41 Identities=20% Similarity=0.288 Sum_probs=37.1
Q ss_pred CCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCC
Q 023564 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (280)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (280)
.|+..+.-.++|+.|||+|=-+=+.+..|+.-|||+...+.
T Consensus 30 ~pG~~L~e~~La~~lgVSRtpVReAL~~L~~eGlv~~~~~~ 70 (212)
T TIGR03338 30 PPGAKLNESDIAARLGVSRGPVREAFRALEEAGLVRNEKNR 70 (212)
T ss_pred CCCCEecHHHHHHHhCCChHHHHHHHHHHHHCCCEEEecCC
Confidence 47888999999999999999999999999999999976543
No 61
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=65.31 E-value=7.6 Score=30.23 Aligned_cols=47 Identities=19% Similarity=0.310 Sum_probs=40.9
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
+-++.+.++++. +.+...++|+.+++...-++..++-|+.-|+|.+.
T Consensus 4 ~D~~il~~L~~~--~~~~~~~la~~l~~s~~tv~~~l~~L~~~g~i~~~ 50 (108)
T smart00344 4 IDRKILEELQKD--ARISLAELAKKVGLSPSTVHNRVKRLEEEGVIKGY 50 (108)
T ss_pred HHHHHHHHHHHh--CCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCeece
Confidence 346788888764 56899999999999999999999999999999954
No 62
>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=65.03 E-value=11 Score=26.10 Aligned_cols=34 Identities=26% Similarity=0.334 Sum_probs=31.2
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
....++|+.+++.+=.+...++-|+.-|+|++..
T Consensus 26 ~~~~~la~~~~is~~~v~~~l~~L~~~G~i~~~~ 59 (66)
T cd07377 26 PSERELAEELGVSRTTVREALRELEAEGLVERRP 59 (66)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecC
Confidence 4599999999999999999999999999998764
No 63
>PRK06474 hypothetical protein; Provisional
Probab=64.64 E-value=48 Score=29.15 Aligned_cols=47 Identities=17% Similarity=0.347 Sum_probs=39.0
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHh-cccceehhhhhhhhhhcccccccc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.+.++++...+.. +...++++.| ++.+=-+|-.+++|+-.|||++..
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 64
>COG1414 IclR Transcriptional regulator [Transcription]
Probab=64.50 E-value=9.2 Score=35.03 Aligned_cols=54 Identities=24% Similarity=0.397 Sum_probs=44.3
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEec
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (280)
..++++...+.+ +.+.++|+.+|+.|=..|-+++.|+-.|++++...+.-.+.|
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 467777764444 899999999999999999999999999999999876333344
No 65
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=64.01 E-value=59 Score=26.54 Aligned_cols=31 Identities=10% Similarity=0.059 Sum_probs=26.4
Q ss_pred CceeHHHHHHHhcccceehhhhhhhhhhccc
Q 023564 150 GTLDLNRTAEVLEVQKRRIYDITNVLEGIGL 180 (280)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 180 (280)
+-..+.++|..+||+.--||-+.+-+..-|.
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 66
>PRK10411 DNA-binding transcriptional activator FucR; Provisional
Probab=63.69 E-value=36 Score=31.09 Aligned_cols=54 Identities=22% Similarity=0.216 Sum_probs=43.8
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEec
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (280)
.+.+++++ ..+.+...++|+.|+|+.+.|..-++.|+.-|+|.+....-+.+.+
T Consensus 7 ~~Il~~l~--~~~~~~~~eLa~~l~VS~~TiRRdL~~L~~~~~l~r~~Gga~~~~~ 60 (240)
T PRK10411 7 QAIVDLLL--NHTSLTTEALAEQLNVSKETIRRDLNELQTQGKILRNHGRAKYIHR 60 (240)
T ss_pred HHHHHHHH--HcCCCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEecCeEEEecC
Confidence 34566776 3568999999999999999999999999999999887555555554
No 67
>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=63.53 E-value=5.4 Score=31.82 Aligned_cols=37 Identities=19% Similarity=0.337 Sum_probs=34.1
Q ss_pred CCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.+.+.+.++|+.+++.+--+.-+++-||.-|+|++..
T Consensus 40 ~~~~t~~ela~~~~~~~~tvs~~l~~Le~~GlI~r~~ 76 (118)
T TIGR02337 40 QGSMEFTQLANQACILRPSLTGILARLERDGLVTRLK 76 (118)
T ss_pred cCCcCHHHHHHHhCCCchhHHHHHHHHHHCCCEEecc
Confidence 4568899999999999999999999999999999974
No 68
>COG1802 GntR Transcriptional regulators [Transcription]
Probab=63.51 E-value=68 Score=28.36 Aligned_cols=41 Identities=27% Similarity=0.305 Sum_probs=38.2
Q ss_pred CCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCC
Q 023564 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKN 187 (280)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN 187 (280)
.|+..++.+++|+.|||+|--|=+.+..|++-|||+....-
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 48999999999999999999999999999999999998544
No 69
>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=63.08 E-value=4.3 Score=26.61 Aligned_cols=22 Identities=32% Similarity=0.548 Sum_probs=20.1
Q ss_pred eeHHHHHHHhcccceehhhhhh
Q 023564 152 LDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItN 173 (280)
+++.++|+.|||.++.||..++
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHH
Confidence 5789999999999999999985
No 70
>PF13518 HTH_28: Helix-turn-helix domain
Probab=63.06 E-value=6.3 Score=26.62 Aligned_cols=37 Identities=14% Similarity=0.339 Sum_probs=30.2
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccc
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL 180 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 180 (280)
.|.++. +|. .+.++|..+||.+..||.++.-.+.-|+
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 71
>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=62.91 E-value=65 Score=26.38 Aligned_cols=37 Identities=16% Similarity=0.178 Sum_probs=27.0
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhccccc--cccCCceEEec
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKG 193 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G 193 (280)
.+.++|..+||+.+-| =-.|-+|||. ....|.|++-+
T Consensus 2 ~I~e~a~~~gvs~~tl----R~Ye~~GLl~~~~r~~~gyR~Y~ 40 (126)
T cd04783 2 TIGELAKAAGVNVETI----RYYQRRGLLPEPPRPEGGYRRYP 40 (126)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCCCCCcCCCCCeecC
Confidence 5788999999988755 3348899997 34466777754
No 72
>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=62.77 E-value=4.8 Score=37.19 Aligned_cols=37 Identities=19% Similarity=0.197 Sum_probs=34.4
Q ss_pred CCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
++...+.++|+++++..|.++-+...|.++|++++..
T Consensus 21 ~gp~t~~eLA~~~~~~~~~~~~lL~~L~~lgll~~~~ 57 (306)
T TIGR02716 21 EGPKDLATLAADTGSVPPRLEMLLETLRQMRVINLED 57 (306)
T ss_pred cCCCCHHHHHHHcCCChHHHHHHHHHHHhCCCeEecC
Confidence 3688999999999999999999999999999999864
No 73
>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=62.63 E-value=40 Score=27.26 Aligned_cols=37 Identities=30% Similarity=0.384 Sum_probs=27.2
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhccccc--cccCCceEEec
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKG 193 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G 193 (280)
.+.++|+.+||..+-|- -.|-.|||. +...|.|+|-.
T Consensus 2 ~I~eva~~~gvs~~tLR----yYe~~GLl~p~~r~~~gyR~Y~ 40 (123)
T cd04770 2 KIGELAKAAGVSPDTIR----YYERIGLLPPPQRSENGYRLYG 40 (123)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCCCCCCCCccCC
Confidence 57899999999887553 367888886 34567777753
No 74
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=61.91 E-value=14 Score=27.34 Aligned_cols=45 Identities=22% Similarity=0.311 Sum_probs=37.3
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
...+.++...+ .+...++|+.+++.+..++.+++-|+.-|+|++.
T Consensus 13 ~~il~~l~~~~--~~~~~~la~~~~~s~~~i~~~l~~L~~~g~v~~~ 57 (101)
T smart00347 13 FLVLRILYEEG--PLSVSELAKRLGVSPSTVTRVLDRLEKKGLIRRL 57 (101)
T ss_pred HHHHHHHHHcC--CcCHHHHHHHHCCCchhHHHHHHHHHHCCCeEec
Confidence 34445555443 5889999999999999999999999999999976
No 75
>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=61.57 E-value=33 Score=27.25 Aligned_cols=37 Identities=22% Similarity=0.332 Sum_probs=24.9
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhccccc-cccCCceEEe
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE-KTSKNHIRWK 192 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe-K~~KN~i~W~ 192 (280)
+.+.++|+.+||+.+-| -..|-.|||. ....|.++.-
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 46889999999998876 3456678883 3334555443
No 76
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=61.57 E-value=12 Score=30.78 Aligned_cols=42 Identities=12% Similarity=0.208 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhh
Q 023564 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNV 174 (280)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNV 174 (280)
-.....++++++.......+++.++|+.+|+.+|.+.-+..-
T Consensus 7 ~~~~i~~~~~~I~~~~~~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 7 DAITIHSILDWIEDNLESPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred cHHHHHHHHHHHHHhcCCCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 355668999999999999999999999999999998877653
No 77
>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=61.56 E-value=10 Score=30.19 Aligned_cols=46 Identities=17% Similarity=0.351 Sum_probs=40.2
Q ss_pred HHHHHH--hCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 140 FINLIQ--EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 140 FI~ll~--~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
++.++. .++++.+.+.++|+.+++.+=.+-=+++-||--|+|+|..
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 78
>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=61.43 E-value=8.4 Score=27.87 Aligned_cols=36 Identities=25% Similarity=0.389 Sum_probs=28.4
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhh
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLE 176 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLE 176 (280)
+.++++-. .+.+.+.++|+.|+++.|-|..-++-|.
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 6778999999999999999877777665
No 79
>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=61.24 E-value=16 Score=26.86 Aligned_cols=44 Identities=25% Similarity=0.336 Sum_probs=37.4
Q ss_pred HHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 141 INLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 141 I~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
|-.+.+ .++.+...++|+.|+|.+=-..+.++-|+.-|||+...
T Consensus 13 Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~GlV~~~~ 56 (60)
T PF01325_consen 13 IYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEKGLVEYEP 56 (60)
T ss_dssp HHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEET
T ss_pred HHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHCCCEEecC
Confidence 333344 88899999999999999999999999999999998764
No 80
>PRK05014 hscB co-chaperone HscB; Provisional
Probab=61.16 E-value=1.1e+02 Score=26.78 Aligned_cols=97 Identities=22% Similarity=0.340 Sum_probs=55.3
Q ss_pred CCCCcHHHHHHHHHHHHH-hCCCCce---------------eHHHHHHHhcc-cceehhhhhhhhhhccccccccCCceE
Q 023564 128 RYDSSLGLLTRKFINLIQ-EAKDGTL---------------DLNRTAEVLEV-QKRRIYDITNVLEGIGLIEKTSKNHIR 190 (280)
Q Consensus 128 R~d~SLglLTkkFI~ll~-~a~~g~l---------------dLn~aA~~L~V-qKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (280)
.++-+...|.++|..+.. -.||... .||+|-+.|.= .+|..|++ -|.|+.+......
T Consensus 12 ~~~~d~~~L~~~yr~l~~~~HPDk~~~~~~~~~~~a~~~s~~iN~AY~~L~dp~~Ra~Yll--~l~g~~~~~~~~~---- 85 (171)
T PRK05014 12 RYDIDTQLLASRYQELQRQFHPDKFANASERERLLAVQQAATINDAYQTLKHPLKRAEYLL--SLHGFDLAHEQHT---- 85 (171)
T ss_pred CCCCCHHHHHHHHHHHHHHhCcCCCCCCcHHHHHHHHHHHHHHHHHHHHHCChhHHHHHHH--HhcCCccccccCC----
Confidence 456677889999998875 4565422 37777777876 68999985 5567766544311
Q ss_pred EecCCCCCCchhHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHH
Q 023564 191 WKGSDSLGTSKLDDQVARLKAEIESLHA---EECRIDDSIREKQELIRT 236 (280)
Q Consensus 191 W~G~~~s~~~~~~~~~~~Lk~El~~L~~---eE~~LD~~I~~~~~~L~~ 236 (280)
.. +.+.-.++-+++++++.+.. .+..|+++..++++.+..
T Consensus 86 -----~~-d~efLme~me~rE~le~~~~~~d~~~~l~~l~~~~~~~~~~ 128 (171)
T PRK05014 86 -----VR-DTAFLMEQMELREELEDIEQSKDPEAALESFIKRVKKMFKT 128 (171)
T ss_pred -----cC-CHHHHHHHHHHHHHHHhhccccCHHHHHHHHHHHHHHHHHH
Confidence 11 22333444566666665431 133344444444444333
No 81
>PF13545 HTH_Crp_2: Crp-like helix-turn-helix domain; PDB: 3LA2_A 3LA3_B 3LA7_A 3B02_A 3E97_A 2H6C_B 1OMI_A 2BGC_H 2BEO_A 2GAU_A ....
Probab=60.59 E-value=8.6 Score=27.94 Aligned_cols=51 Identities=24% Similarity=0.313 Sum_probs=40.2
Q ss_pred HHHHHHHHHHhCCC----------CceeHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 136 LTRKFINLIQEAKD----------GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 136 LTkkFI~ll~~a~~----------g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
++.-|+.++...+. ..+...++|+.+|+.++.+--+++-|+.-|+|+...+
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~g~I~~~~~ 63 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDEGIIEVKRG 63 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHTTSEEEETT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEcCC
Confidence 55666666654321 2357899999999999999999999999999997644
No 82
>COG1777 Predicted transcriptional regulators [Transcription]
Probab=60.37 E-value=71 Score=29.92 Aligned_cols=43 Identities=21% Similarity=0.410 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (280)
++.|.++.+.| .-..+++..|||..--|-+=.-.||--|||+-
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 55777877777 55678888899988888888888888888875
No 83
>PRK09954 putative kinase; Provisional
Probab=59.11 E-value=10 Score=35.80 Aligned_cols=46 Identities=15% Similarity=0.312 Sum_probs=40.3
Q ss_pred HHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 137 TRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 137 TkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
-++.++++++.+ .+...++|+.|+|.|..++..++=|+.-|+|++.
T Consensus 5 ~~~il~~l~~~~--~~s~~~la~~l~~s~~~v~~~i~~L~~~g~i~~~ 50 (362)
T PRK09954 5 EKEILAILRRNP--LIQQNEIADILQISRSRVAAHIMDLMRKGRIKGK 50 (362)
T ss_pred HHHHHHHHHHCC--CCCHHHHHHHHCCCHHHHHHHHHHHHHCCCcCCc
Confidence 456788887554 8999999999999999999999999999999755
No 84
>PRK00215 LexA repressor; Validated
Probab=58.88 E-value=11 Score=32.83 Aligned_cols=42 Identities=17% Similarity=0.207 Sum_probs=37.1
Q ss_pred hCCCCceeHHHHHHHhcc-cceehhhhhhhhhhccccccccCC
Q 023564 146 EAKDGTLDLNRTAEVLEV-QKRRIYDITNVLEGIGLIEKTSKN 187 (280)
Q Consensus 146 ~a~~g~ldLn~aA~~L~V-qKRRIYDItNVLEgIGLIeK~~KN 187 (280)
...+....+.++|+.+++ .|=.++.+++-||.-|+|++....
T Consensus 18 ~~~~~~~s~~ela~~~~~~~~~tv~~~l~~L~~~g~i~~~~~~ 60 (205)
T PRK00215 18 EETGYPPSRREIADALGLRSPSAVHEHLKALERKGFIRRDPGR 60 (205)
T ss_pred HHhCCCCCHHHHHHHhCCCChHHHHHHHHHHHHCCCEEeCCCC
Confidence 445667899999999999 999999999999999999988654
No 85
>PRK10225 DNA-binding transcriptional repressor UxuR; Provisional
Probab=58.78 E-value=62 Score=29.06 Aligned_cols=51 Identities=24% Similarity=0.249 Sum_probs=41.0
Q ss_pred HHHHHHHHHHHh---CCCCce-eHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 135 LLTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 135 lLTkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.+...+.+.+.. .|+..+ .-.++|+.|||+|==+=+.+..|+.-|||+...
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 344445555533 478888 699999999999999999999999999998664
No 86
>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=58.17 E-value=5.1 Score=32.37 Aligned_cols=49 Identities=29% Similarity=0.475 Sum_probs=36.0
Q ss_pred eEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023564 189 IRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (280)
Q Consensus 189 i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted 240 (280)
..|.|.+ +.+++..+..+..+++.|..+-..|...+..++.+|..+.+.
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 5678887 568889999999999999988888888888888887777543
No 87
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=57.91 E-value=12 Score=37.70 Aligned_cols=76 Identities=18% Similarity=0.328 Sum_probs=48.6
Q ss_pred cccceehhhhhhhhhhc-cccccccCCceEEecCCCCCCchhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHh
Q 023564 162 EVQKRRIYDITNVLEGI-GLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIE---SLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 162 ~VqKRRIYDItNVLEgI-GLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~---~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
.|.|||=|-|=+-.--+ .||-|..-+..+|. .... -+...+-+++|+++.+ ++....+.|+.-++.+.+++++|
T Consensus 239 eVERRRR~nIN~~IkeLg~liP~~~~~~~~~n-KgtI-Lk~s~dYIr~Lqq~~q~~~E~~~rqk~le~~n~~L~~rieeL 316 (411)
T KOG1318|consen 239 EVERRRRENINDRIKELGQLIPKCNSEDMKSN-KGTI-LKASCDYIRELQQTLQRARELENRQKKLESTNQELALRIEEL 316 (411)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCcchhhcc-cchh-hHHHHHHHHHHHHHHHHHHHHHhhhhHHHhHHHHHHHHHHHH
Confidence 37888877665544444 37888888889995 2221 1233445677776654 45566677777777777777777
Q ss_pred hh
Q 023564 238 EE 239 (280)
Q Consensus 238 te 239 (280)
..
T Consensus 317 k~ 318 (411)
T KOG1318|consen 317 KS 318 (411)
T ss_pred HH
Confidence 54
No 88
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=57.82 E-value=16 Score=28.55 Aligned_cols=40 Identities=18% Similarity=0.207 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhh
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNV 174 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNV 174 (280)
.+..+++.++.+.....+++.++|+.+++++|.+.-+..=
T Consensus 5 ~~~~~~~~~i~~~~~~~~~~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQPLNIDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4567889999988888999999999999999998877653
No 89
>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=57.32 E-value=33 Score=27.73 Aligned_cols=82 Identities=17% Similarity=0.240 Sum_probs=43.7
Q ss_pred HHHHHhcccceehhhhhhhhhhccccccccCCceEEecCCCCCC------chhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 156 RTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSIRE 229 (280)
Q Consensus 156 ~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~ 229 (280)
.++..+..-.+-+=....|++.+.-+. .+...|+-.|.=.... ..+...+..+...+..|..++..|...+.+
T Consensus 21 ~l~~q~~~le~~~~E~~~v~~eL~~l~-~d~~vyk~VG~vlv~~~~~e~~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e 99 (110)
T TIGR02338 21 AVATQKQQVEAQLKEAEKALEELERLP-DDTPVYKSVGNLLVKTDKEEAIQELKEKKETLELRVKTLQRQEERLREQLKE 99 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHcCC-CcchhHHHhchhhheecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333334455555555554 3445555555321110 123344555666677777777777777777
Q ss_pred HHHHHHHhh
Q 023564 230 KQELIRTLE 238 (280)
Q Consensus 230 ~~~~L~~Lt 238 (280)
++.+|+.+.
T Consensus 100 ~q~~l~~~~ 108 (110)
T TIGR02338 100 LQEKIQEAL 108 (110)
T ss_pred HHHHHHHHh
Confidence 777777653
No 90
>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=56.63 E-value=15 Score=30.41 Aligned_cols=38 Identities=18% Similarity=0.286 Sum_probs=34.0
Q ss_pred hCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccc
Q 023564 146 EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (280)
Q Consensus 146 ~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (280)
+..++.+.+.++|+.+++..+-+..|+..|.--|||.-
T Consensus 20 ~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~glv~s 57 (135)
T TIGR02010 20 NAETGPVTLADISERQGISLSYLEQLFAKLRKAGLVKS 57 (135)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCceEE
Confidence 33455899999999999999999999999999999974
No 91
>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=55.91 E-value=38 Score=27.18 Aligned_cols=35 Identities=26% Similarity=0.269 Sum_probs=23.6
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhccccc--cccCCceEE
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRW 191 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W 191 (280)
.+.++|+.+||..|.|--. |..|||. ....|.+++
T Consensus 2 ~i~e~a~~~gvs~~tlr~y----e~~gll~~~~r~~~gyR~ 38 (113)
T cd01109 2 TIKEVAEKTGLSADTLRYY----EKEGLLPPVKRDENGIRD 38 (113)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCcc
Confidence 5789999999998866433 5678883 233455554
No 92
>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=55.57 E-value=25 Score=31.64 Aligned_cols=44 Identities=16% Similarity=0.190 Sum_probs=37.3
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
.++++..+ ...+.+.++|+.+|+.|=.+|.+++-|+..|++++.
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 44555433 456899999999999999999999999999999985
No 93
>PRK14165 winged helix-turn-helix domain-containing protein/riboflavin kinase; Provisional
Probab=55.23 E-value=36 Score=31.35 Aligned_cols=54 Identities=17% Similarity=0.099 Sum_probs=41.4
Q ss_pred HHHHHHH-hCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEe
Q 023564 139 KFINLIQ-EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (280)
Q Consensus 139 kFI~ll~-~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (280)
+-|.++. ......+...++|+.|++.+..+.-++.-||--|+|+|.....-+|.
T Consensus 8 k~iallg~l~~~~~IS~~eLA~~L~iS~~Tvsr~Lk~LEe~GlI~R~~~~r~~~v 62 (217)
T PRK14165 8 KKLALLGAVNNTVKISSSEFANHTGTSSKTAARILKQLEDEGYITRTIVPRGQLI 62 (217)
T ss_pred HHHHHHhccCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEEEcCCceEE
Confidence 3344443 33455688999999999999999999999999999999854333443
No 94
>PRK09802 DNA-binding transcriptional regulator AgaR; Provisional
Probab=55.18 E-value=85 Score=29.21 Aligned_cols=52 Identities=15% Similarity=0.224 Sum_probs=41.3
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCc
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNH 188 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~ 188 (280)
.--.+.++++++. +.+.+.++|+.|+|+.+-|.-=+..||.-|++.|.-...
T Consensus 17 eR~~~Il~~L~~~--~~vtv~eLa~~l~VS~~TIRRDL~~Le~~G~l~r~~GGa 68 (269)
T PRK09802 17 ERREQIIQRLRQQ--GSVQVNDLSALYGVSTVTIRNDLAFLEKQGIAVRAYGGA 68 (269)
T ss_pred HHHHHHHHHHHHc--CCEeHHHHHHHHCCCHHHHHHHHHHHHhCCCeEEEeCCE
Confidence 3445677777754 449999999999999888877778899999999876444
No 95
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=55.08 E-value=62 Score=28.95 Aligned_cols=54 Identities=20% Similarity=0.302 Sum_probs=42.7
Q ss_pred cHH-HHHHHHHHHHHh---CCCCce-eHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 132 SLG-LLTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 132 SLg-lLTkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
++. .+...+.+.+.. .|+..+ .-.++|+.|||+|=-+-+.+..|+..|||+...
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 899999999999999999999999999998653
No 96
>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=54.77 E-value=45 Score=25.13 Aligned_cols=38 Identities=11% Similarity=0.330 Sum_probs=29.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023564 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (280)
Q Consensus 203 ~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted 240 (280)
+..+.++.+.+..|+.....++..|..+.++|..+.++
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 34455666777888888888889999999999988753
No 97
>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=54.76 E-value=1.1e+02 Score=26.46 Aligned_cols=88 Identities=25% Similarity=0.350 Sum_probs=49.9
Q ss_pred cHHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCCCCCCchhHHHHHHHHH
Q 023564 132 SLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKA 211 (280)
Q Consensus 132 SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~ 211 (280)
+|..|+..|.+++.-..++..|-..+++.|.--.=.|. +=. -|-..|+ ......+..+++
T Consensus 2 ~LYel~~~~~~l~~~~e~~~~d~e~~~dtLe~i~~~~~---~K~----------~~~~~~I-------k~~ea~~e~~k~ 61 (162)
T PF05565_consen 2 KLYELTDEYLELLELLEEGDLDEEAIADTLESIEDEIE---EKA----------DNIAKVI-------KNLEADIEAIKA 61 (162)
T ss_pred CHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHH---HHH----------HHHHHHH-------HHhHHHHHHHHH
Confidence 58889999999998776666888877776654111111 111 1112221 012333445566
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 212 EIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 212 El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
|+..|...-+.++..+.++++.|...++
T Consensus 62 E~krL~~rkk~~e~~~~~Lk~yL~~~m~ 89 (162)
T PF05565_consen 62 EIKRLQERKKSIENRIDRLKEYLLDAME 89 (162)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6666666666666666666666665543
No 98
>COG2739 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.54 E-value=10 Score=31.78 Aligned_cols=40 Identities=33% Similarity=0.390 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 134 glLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
.+||.|=..++.--=..-++|.++|+.++|+|-.|||=++
T Consensus 16 sLLT~KQ~~Y~~lyy~dDlSl~EIAee~~VSRqAIyDnIK 55 (105)
T COG2739 16 SLLTKKQKNYLELYYLDDLSLSEIAEEFNVSRQAIYDNIK 55 (105)
T ss_pred HHHhHHHHHHHHHHHHhhccHHHHHHHhCccHHHHHHHHH
Confidence 4678776666655455668999999999999999999765
No 99
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=54.37 E-value=15 Score=27.85 Aligned_cols=44 Identities=27% Similarity=0.326 Sum_probs=35.9
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
++..+...++... .++|+.|++.+=.+--+++-||.-|+|++..
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 4444455554444 9999999999999999999999999999884
No 100
>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=54.32 E-value=1.3e+02 Score=25.84 Aligned_cols=55 Identities=18% Similarity=0.262 Sum_probs=30.2
Q ss_pred HHHHHHhCCCCceeHHHHHHHhc--ccceehhhhhhhhhhccccc-cc-cCCceEEecCC
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLE--VQKRRIYDITNVLEGIGLIE-KT-SKNHIRWKGSD 195 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIe-K~-~KN~i~W~G~~ 195 (280)
.++||. ..+.++..+.+.+-|+ |.|=-+==+..-|..=|.|. |. +|-.|.|.-.+
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 345554 4456777777777774 55544333344443344433 33 56777775433
No 101
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=54.29 E-value=7 Score=32.62 Aligned_cols=33 Identities=27% Similarity=0.473 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
.|...|++.+. ++.+.+|+.|||++.+|-.|+|
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 35567776653 8899999999999999999998
No 102
>PRK11534 DNA-binding transcriptional regulator CsiR; Provisional
Probab=53.79 E-value=50 Score=28.97 Aligned_cols=48 Identities=10% Similarity=0.072 Sum_probs=40.6
Q ss_pred CCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecC
Q 023564 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (280)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~ 194 (280)
.|+..+...++|+.|||+|-=+=+.+..|+.-|||+.....-+.....
T Consensus 26 ~pG~~L~e~eLae~lgVSRtpVREAL~~L~~eGlv~~~~~~G~~V~~~ 73 (224)
T PRK11534 26 QPDEKLRMSLLTSRYALGVGPLREALSQLVAERLVTVVNQKGYRVASM 73 (224)
T ss_pred CCCCcCCHHHHHHHHCCChHHHHHHHHHHHHCCCEEEeCCCceEeCCC
Confidence 478889999999999999999999999999999999776554544443
No 103
>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=53.77 E-value=32 Score=33.05 Aligned_cols=37 Identities=30% Similarity=0.455 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 023564 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEENEN 242 (280)
Q Consensus 206 ~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~~ 242 (280)
...|.+|++.|+.++.+|++.|..++.++..+.+.+.
T Consensus 59 e~~l~~eL~~LE~e~~~l~~el~~le~e~~~l~~eE~ 95 (314)
T PF04111_consen 59 EEELLQELEELEKEREELDQELEELEEELEELDEEEE 95 (314)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456677888888888999999998888888866544
No 104
>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=53.69 E-value=38 Score=27.08 Aligned_cols=76 Identities=17% Similarity=0.261 Sum_probs=43.3
Q ss_pred HHHhcccceehhhhhhhhhhccccccccCCceEEecCCCCC-C-----chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 158 AEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLG-T-----SKLDDQVARLKAEIESLHAEECRIDDSIREKQ 231 (280)
Q Consensus 158 A~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~-~-----~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~ 231 (280)
-..|..+.+...|+.+-|+.+. .+...|+=+|.-... + ..+...+..+..++..|..+...+...+.+++
T Consensus 22 ~~~l~~~~~E~~~v~~EL~~l~----~d~~vy~~VG~vfv~~~~~ea~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk 97 (105)
T cd00632 22 RQKVEAQLNENKKALEELEKLA----DDAEVYKLVGNVLVKQEKEEARTELKERLETIELRIKRLERQEEDLQEKLKELQ 97 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHcCC----CcchHHHHhhhHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445567788888888877775 333444445532111 0 12334445556666666666666666666666
Q ss_pred HHHHHh
Q 023564 232 ELIRTL 237 (280)
Q Consensus 232 ~~L~~L 237 (280)
.+|+++
T Consensus 98 ~~l~~~ 103 (105)
T cd00632 98 EKIQQA 103 (105)
T ss_pred HHHHHH
Confidence 666654
No 105
>PRK09343 prefoldin subunit beta; Provisional
Probab=53.57 E-value=41 Score=28.00 Aligned_cols=74 Identities=15% Similarity=0.240 Sum_probs=45.7
Q ss_pred eehhhhhhhhhhccccccccCCceEEecCCCCC-C-----chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 166 RRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLG-T-----SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 166 RRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~-~-----~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
+.+=+.-.|++-+..+.- +-.-|+=.|.=... + .++...+..+..++..|+.++..|.+.+.+++.+|+.+..
T Consensus 35 ~q~~e~~~~~~EL~~L~~-d~~VYk~VG~vlv~qd~~e~~~~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~~l~~ll~ 113 (121)
T PRK09343 35 LELREINKALEELEKLPD-DTPIYKIVGNLLVKVDKTKVEKELKERKELLELRSRTLEKQEKKLREKLKELQAKINEMLS 113 (121)
T ss_pred HHHHHHHHHHHHHHcCCC-cchhHHHhhHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455666666666652 12333334421111 1 2344556667778888999999999999999999998764
Q ss_pred h
Q 023564 240 N 240 (280)
Q Consensus 240 d 240 (280)
.
T Consensus 114 ~ 114 (121)
T PRK09343 114 K 114 (121)
T ss_pred h
Confidence 3
No 106
>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=53.22 E-value=15 Score=30.46 Aligned_cols=35 Identities=9% Similarity=0.334 Sum_probs=32.4
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehh
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIY 169 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIY 169 (280)
.+..-|++|+.+.+=..+.++++|++-||.|.-+|
T Consensus 7 ~I~~a~~~Ll~~k~~~~ITV~~I~~~AgvsR~TFY 41 (176)
T TIGR02366 7 KIAKAFKDLMEVQAFSKISVSDIMSTAQIRRQTFY 41 (176)
T ss_pred HHHHHHHHHHHHCCCccCCHHHHHHHhCCCHHHHH
Confidence 46678999999999999999999999999999887
No 107
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=52.75 E-value=59 Score=25.06 Aligned_cols=67 Identities=13% Similarity=0.307 Sum_probs=29.9
Q ss_pred hhhhhhhhhhccccccccCCceEEecCCCCC-CchhH-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 168 IYDITNVLEGIGLIEKTSKNHIRWKGSDSLG-TSKLD-------DQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 168 IYDItNVLEgIGLIeK~~KN~i~W~G~~~s~-~~~~~-------~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
+-.+.-|++-+..+. -+...|.+.+..- ....+ ..+..++.++..|..+...+...+..++..|..+
T Consensus 28 ~~~~~~~~~eL~~l~---~~~~~y~~vG~~fv~~~~~~~~~~L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~~~l~~~ 102 (106)
T PF01920_consen 28 LRELELTLEELEKLD---DDRKVYKSVGKMFVKQDKEEAIEELEERIEKLEKEIKKLEKQLKYLEKKLKELKKKLYEL 102 (106)
T ss_dssp HHHHHHHHHHHHTSS---TT-EEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_pred HHHHHHHHHHHHhCC---CcchhHHHHhHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444443 3356676554321 11222 3334444555555555555555555555555443
No 108
>cd00632 Prefoldin_beta Prefoldin beta; Prefoldin is a hexameric molecular chaperone complex, composed of two evolutionarily related subunits (alpha and beta), which are found in both eukaryotes and archaea. Prefoldin binds and stabilizes newly synthesized polypeptides allowing them to fold correctly. The hexameric structure consists of a double beta barrel assembly with six protruding coiled-coils. The alpha prefoldin subunits have two beta hairpin structures while the beta prefoldin subunits (this CD) have only one hairpin that is most similar to the second hairpin of the alpha subunit. The prefoldin hexamer consists of two alpha and four beta subunits and is assembled from the beta hairpins of all six subunits. The alpha subunits initially dimerize providing a structural nucleus for the assembly of the beta subunits. In archaea, there is usually only one gene for each subunit while in eukaryotes there two or more paralogous genes encoding each subunit adding heterogeneity to the st
Probab=52.67 E-value=45 Score=26.63 Aligned_cols=34 Identities=24% Similarity=0.381 Sum_probs=24.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 206 ~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
+..|.+.++.|...-..|+..+..+..++.++..
T Consensus 65 ~~~Le~~~e~le~~i~~l~~~~~~l~~~~~elk~ 98 (105)
T cd00632 65 RTELKERLETIELRIKRLERQEEDLQEKLKELQE 98 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666777777777777777777777777654
No 109
>PRK11050 manganese transport regulator MntR; Provisional
Probab=52.58 E-value=30 Score=29.49 Aligned_cols=43 Identities=19% Similarity=0.139 Sum_probs=36.5
Q ss_pred CCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEE
Q 023564 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (280)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W 191 (280)
++.+.+.++|+.|+|.+--+..++.-||.-|+|.+.....+.+
T Consensus 49 ~~~~t~~eLA~~l~is~stVsr~l~~Le~~GlI~r~~~~~v~L 91 (152)
T PRK11050 49 VGEARQVDIAARLGVSQPTVAKMLKRLARDGLVEMRPYRGVFL 91 (152)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEecCCceEE
Confidence 4568899999999999999999999999999999865443433
No 110
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=52.25 E-value=47 Score=28.30 Aligned_cols=71 Identities=17% Similarity=0.296 Sum_probs=42.2
Q ss_pred hhhhhhhhccccccccCCceEEecCCCCCC------chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 023564 170 DITNVLEGIGLIEKTSKNHIRWKGSDSLGT------SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (280)
Q Consensus 170 DItNVLEgIGLIeK~~KN~i~W~G~~~s~~------~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~ 241 (280)
+|.-||+-++.|.--. .-|+-.|.=.... .++..+..-|.-++.-|+.+|+.|++.+++++..|+.+..+.
T Consensus 38 E~~~al~Ele~l~eD~-~vYk~VG~llvk~~k~~~~~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq~~i~~~l~~~ 114 (119)
T COG1382 38 EIEKALEELEKLDEDA-PVYKKVGNLLVKVSKEEAVDELEERKETLELRIKTLEKQEEKLQERLEELQSEIQKALGDA 114 (119)
T ss_pred HHHHHHHHHhcCCccc-HHHHHhhhHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4666777776665432 3344444221111 123344445556677788888888888888888888776543
No 111
>PRK15090 DNA-binding transcriptional regulator KdgR; Provisional
Probab=52.02 E-value=20 Score=32.48 Aligned_cols=55 Identities=7% Similarity=0.212 Sum_probs=42.9
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecC
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGS 194 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~ 194 (280)
-..++++.. .+.+.+.++|+.+++.|=.+|-+++.|+..|++++...+.-...|.
T Consensus 17 l~IL~~l~~--~~~l~l~eia~~lgl~kstv~Rll~tL~~~G~l~~~~~~~~Y~lG~ 71 (257)
T PRK15090 17 FGILQALGE--EREIGITELSQRVMMSKSTVYRFLQTMKTLGYVAQEGESEKYSLTL 71 (257)
T ss_pred HHHHHHhhc--CCCCCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCcEEecH
Confidence 345555543 3468999999999999999999999999999999975544444553
No 112
>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=51.68 E-value=22 Score=31.32 Aligned_cols=46 Identities=22% Similarity=0.324 Sum_probs=38.4
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
+.+.++.+. +.+.+.++|+.+++.+-.++-.++-||..|+|++..+
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 113
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=51.19 E-value=16 Score=32.84 Aligned_cols=43 Identities=28% Similarity=0.367 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhh
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEG 177 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEg 177 (280)
.+..+|+.++.+.....++|.++|+.++++++.+..+..-..|
T Consensus 186 ~~~~~~~~~I~~~~~~~~sl~~lA~~~~~S~~~l~r~Fk~~~G 228 (287)
T TIGR02297 186 YLFNRFNFLIEENYKQHLRLPEYADRLGISESRLNDICRRFSA 228 (287)
T ss_pred HHHHHHHHHHHHhhccCCCHHHHHHHHCCCHHHHHHHHHHHhC
Confidence 4568899999999888999999999999999999988765443
No 114
>PRK13509 transcriptional repressor UlaR; Provisional
Probab=51.17 E-value=15 Score=33.70 Aligned_cols=46 Identities=17% Similarity=0.270 Sum_probs=38.9
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.+-++++. ..+.+.+.++|+.|+|++.-|+--++.||..|+|.|..
T Consensus 8 ~~Il~~l~--~~~~~~~~ela~~l~vS~~TirRdL~~Le~~g~i~r~~ 53 (251)
T PRK13509 8 QILLELLA--QLGFVTVEKVIERLGISPATARRDINKLDESGKLKKVR 53 (251)
T ss_pred HHHHHHHH--HcCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEec
Confidence 34556665 56899999999999999999988899999999998853
No 115
>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=50.16 E-value=23 Score=27.88 Aligned_cols=45 Identities=24% Similarity=0.469 Sum_probs=37.9
Q ss_pred HHHHHHhCCCCceeHHHHHHHh-----cccceehhhhhhhhhhcccccccc
Q 023564 140 FINLIQEAKDGTLDLNRTAEVL-----EVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L-----~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.++++..+ ++.++..++.+.| .+.+=-+|-+++.|+..|+|.+..
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 116
>PRK11569 transcriptional repressor IclR; Provisional
Probab=49.47 E-value=82 Score=29.00 Aligned_cols=54 Identities=15% Similarity=0.262 Sum_probs=41.4
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEec
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (280)
..++++.. ....+.+.++|+.+|+.|=.+|-+++-|+..|++++.........|
T Consensus 32 ~IL~~l~~-~~~~~~lseia~~lglpksTv~RlL~tL~~~G~l~~~~~~~~Y~lG 85 (274)
T PRK11569 32 KLLEWIAE-SNGSVALTELAQQAGLPNSTTHRLLTTMQQQGFVRQVGELGHWAIG 85 (274)
T ss_pred HHHHHHHh-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHCCCEEEcCCCCeEecC
Confidence 34555544 3456899999999999999999999999999999986443333344
No 117
>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=49.02 E-value=21 Score=31.07 Aligned_cols=48 Identities=19% Similarity=0.304 Sum_probs=38.9
Q ss_pred HHHHHHHH---hCCCCceeHHHHHHHhccc-ceehhhhhhhhhhcccccccc
Q 023564 138 RKFINLIQ---EAKDGTLDLNRTAEVLEVQ-KRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 138 kkFI~ll~---~a~~g~ldLn~aA~~L~Vq-KRRIYDItNVLEgIGLIeK~~ 185 (280)
.+.++++. ...+....+.++|+.|++. +=-++..+..||..|+|++..
T Consensus 9 ~~iL~~l~~~~~~~~~~~~~~ela~~~~~~s~~tv~~~l~~L~~~g~i~~~~ 60 (199)
T TIGR00498 9 QEVLDLIRAHIESTGYPPSIREIARAVGLRSPSAAEEHLKALERKGYIERDP 60 (199)
T ss_pred HHHHHHHHHHHHhcCCCCcHHHHHHHhCCCChHHHHHHHHHHHHCCCEecCC
Confidence 34555554 3344557899999999998 999999999999999999975
No 118
>COG2894 MinD Septum formation inhibitor-activating ATPase [Cell division and chromosome partitioning]
Probab=48.91 E-value=6.9 Score=37.30 Aligned_cols=28 Identities=25% Similarity=0.591 Sum_probs=22.3
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhcc
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIG 179 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIG 179 (280)
+-|..+=-.||..+|=+||.+||+||=-
T Consensus 41 iGLRNLDlimGlE~RiVYd~vdVi~g~~ 68 (272)
T COG2894 41 IGLRNLDLIMGLENRIVYDLVDVIEGEA 68 (272)
T ss_pred cCchhhhhhhcccceeeeeehhhhcCcc
Confidence 3445555569999999999999999854
No 119
>PRK09990 DNA-binding transcriptional regulator GlcC; Provisional
Probab=48.48 E-value=41 Score=30.06 Aligned_cols=50 Identities=24% Similarity=0.331 Sum_probs=40.7
Q ss_pred HHHHHHHHHh---CCCCce-eHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 137 TRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 137 TkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
.....+.+.. .|+..+ .-.++|+.|||+|==+-+.+..|+..|||+....
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 3444444432 478888 8999999999999999999999999999987644
No 120
>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=48.21 E-value=17 Score=23.48 Aligned_cols=23 Identities=22% Similarity=0.232 Sum_probs=19.8
Q ss_pred eeHHHHHHHhcccceehhhhhhh
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNV 174 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNV 174 (280)
+.+.++|+.|+|.++-||..+.-
T Consensus 1 ~s~~e~a~~lgvs~~tl~~~~~~ 23 (49)
T cd04762 1 LTTKEAAELLGVSPSTLRRWVKE 23 (49)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHc
Confidence 36789999999999999988764
No 121
>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=47.96 E-value=1.2e+02 Score=24.80 Aligned_cols=84 Identities=15% Similarity=0.173 Sum_probs=0.0
Q ss_pred eeHHHHHHHhcccce--ehhhhhhhhhhccccc--cccCCceEEe----------------------------cCCCCCC
Q 023564 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLIE--KTSKNHIRWK----------------------------GSDSLGT 199 (280)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIe--K~~KN~i~W~----------------------------G~~~s~~ 199 (280)
+.+.++|+.+||+.+ |.| |-+|||. +...|.|++- .......
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 023564 200 SKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (280)
Q Consensus 200 ~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~ 241 (280)
.........|+..++.|+++-.+|.++.+.++..+.....+.
T Consensus 75 ~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~~~ 116 (127)
T cd04784 75 ASCAEVNALIDEHLAHVRARIAELQALEKQLQALRERCDGAR 116 (127)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCC
No 122
>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=47.75 E-value=1.2e+02 Score=27.28 Aligned_cols=33 Identities=24% Similarity=0.236 Sum_probs=29.4
Q ss_pred eHHHHHHHh-cccceehhhhhhhhhhcccccccc
Q 023564 153 DLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 153 dLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.=..+|..+ |+.-|.|--.+..|...|||.+..
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 446788899 999999999999999999999864
No 123
>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=47.39 E-value=57 Score=27.00 Aligned_cols=84 Identities=18% Similarity=0.155 Sum_probs=0.0
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhccccc--cccCCceEEecCCCC----------CCchhHHHHHHH----------
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKGSDSL----------GTSKLDDQVARL---------- 209 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G~~~s----------~~~~~~~~~~~L---------- 209 (280)
+.+.++|+.+||+.+-|.-. |.+||+. +...|.|++-+.+.. ..|..-..+..+
T Consensus 1 m~I~e~a~~~gvs~~tlR~Y----e~~GLl~~~~r~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~~~~~~~ 76 (127)
T TIGR02047 1 MKIGELAQKTGVSVETIRFY----EKQGLLPPPARTDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQDKPEKS 76 (127)
T ss_pred CcHHHHHHHHCcCHHHHHHH----HHCCCCCCCCcCCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhCCCCC
Q ss_pred -HHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 210 -KAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 210 -k~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
.+-.+-|..+...|++.|.++++....|.+
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~ 107 (127)
T TIGR02047 77 CSDVNALLDEHISHVRARIIKLQALIEQLVD 107 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 124
>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=47.35 E-value=54 Score=26.52 Aligned_cols=34 Identities=21% Similarity=0.307 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 206 ~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
+..|+..++.++..-..|++.+..++.++.++-.
T Consensus 69 ~~~l~~r~e~ie~~i~~lek~~~~l~~~l~e~q~ 102 (110)
T TIGR02338 69 IQELKEKKETLELRVKTLQRQEERLREQLKELQE 102 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566677777777777777778777777777643
No 125
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=47.17 E-value=19 Score=31.48 Aligned_cols=39 Identities=15% Similarity=0.241 Sum_probs=34.9
Q ss_pred hCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 146 EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 146 ~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
...++.+.+.++|+.+++.++-+..|++-|.--|||.-.
T Consensus 20 ~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~aGLv~s~ 58 (164)
T PRK10857 20 NSEAGPVPLADISERQGISLSYLEQLFSRLRKNGLVSSV 58 (164)
T ss_pred CCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEeC
Confidence 344568999999999999999999999999999999953
No 126
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=46.95 E-value=22 Score=29.56 Aligned_cols=41 Identities=17% Similarity=0.265 Sum_probs=35.8
Q ss_pred hCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 146 EAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 146 ~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
..++..+...++|+.++|++.-+-.|+..|+.-|||+....
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 127
>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=46.51 E-value=77 Score=23.74 Aligned_cols=38 Identities=21% Similarity=0.488 Sum_probs=26.3
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
+++..+..+...+..++.+-+.|-+.|+.+.+.++.|.
T Consensus 4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ll 41 (55)
T PF05377_consen 4 ELENELPRIESSINTVKKENEEISESVEKIEENVKDLL 41 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45556666677777777777777777777777777664
No 128
>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=46.38 E-value=64 Score=23.59 Aligned_cols=30 Identities=30% Similarity=0.531 Sum_probs=25.4
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 201 KLDDQVARLKAEIESLHAEECRIDDSIREK 230 (280)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~ 230 (280)
....++..|+.+++.|..+-+.|.+.|+.+
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356678889999999999999999999888
No 129
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=46.37 E-value=25 Score=28.78 Aligned_cols=31 Identities=23% Similarity=0.252 Sum_probs=19.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQE 232 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~ 232 (280)
...++..+++|++.|+++.+.|...|..++.
T Consensus 32 l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 32 VNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 4455566666666666666666666666654
No 130
>smart00338 BRLZ basic region leucin zipper.
Probab=46.35 E-value=77 Score=23.10 Aligned_cols=35 Identities=23% Similarity=0.433 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 205 QVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 205 ~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
.+..|+.+++.|..+-..|-..+..+..++..|.+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~ 61 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKS 61 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35667777777777777777777777777776654
No 131
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=45.97 E-value=40 Score=29.84 Aligned_cols=39 Identities=18% Similarity=0.244 Sum_probs=33.6
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhccccccccCCceE
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (280)
+.-.++|..||+++..+.-+++-|+--|+|+..+.++|.
T Consensus 180 lt~~~IA~~lGisretlsR~L~~L~~~GlI~~~~~~~i~ 218 (230)
T PRK09391 180 MSRRDIADYLGLTIETVSRALSQLQDRGLIGLSGARQIE 218 (230)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCcEEecCCceEE
Confidence 355899999999999999999999999999877555554
No 132
>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=45.61 E-value=20 Score=28.36 Aligned_cols=41 Identities=17% Similarity=0.465 Sum_probs=32.8
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
|.+-+-+ .++.+.+.++|..|++..++++++ |...|++-+.
T Consensus 14 ~~d~~~~-~~~~~ti~~~AK~L~i~~~~l~~~---Lr~~g~l~~~ 54 (111)
T PF03374_consen 14 FYDAFVD-SDGLYTIREAAKLLGIGRNKLFQW---LREKGWLYRR 54 (111)
T ss_pred HHHHHHc-CCCCccHHHHHHHhCCCHHHHHHH---HHhCCceEEC
Confidence 5555543 459999999999999999999886 5668888884
No 133
>PF01920 Prefoldin_2: Prefoldin subunit; InterPro: IPR002777 Prefoldin (PFD) is a chaperone that interacts exclusively with type II chaperonins, hetero-oligomers lacking an obligate co-chaperonin that are found only in eukaryotes (chaperonin-containing T-complex polypeptide-1 (CCT)) and archaea. Eukaryotic PFD is a multi-subunit complex containing six polypeptides in the molecular mass range of 14-23 kDa. In archaea, on the other hand, PFD is composed of two types of subunits, two alpha and four beta. The six subunits associate to form two back-to-back up-and-down eight-stranded barrels, from which hang six coiled coils. Each subunit contributes one (beta subunits) or two (alpha subunits) beta hairpin turns to the barrels. The coiled coils are formed by the N and C termini of an individual subunit. Overall, this unique arrangement resembles a jellyfish. The eukaryotic PFD hexamer is composed of six different subunits; however, these can be grouped into two alpha-like (PFD3 and -5) and four beta-like (PFD1, -2, -4, and -6) subunits based on amino acid sequence similarity with their archaeal counterparts. Eukaryotic PFD has a six-legged structure similar to that seen in the archaeal homologue [, ]. This family contains the archaeal beta subunit, eukaryotic prefoldin subunits 1, 2, 4 and 6. Eukaryotic PFD has been shown to bind both actin and tubulin co-translationally. The chaperone then delivers the target protein to CCT, interacting with the chaperonin through the tips of the coiled coils. No authentic target proteins of any archaeal PFD have been identified, to date.; GO: 0051082 unfolded protein binding, 0006457 protein folding, 0016272 prefoldin complex; PDB: 2ZDI_B 3AEI_B 2ZQM_A 1FXK_A.
Probab=45.02 E-value=58 Score=25.07 Aligned_cols=30 Identities=20% Similarity=0.406 Sum_probs=17.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 209 LKAEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 209 Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
|+++++.+..+-..|...+..+..++.++.
T Consensus 67 L~~~~~~~~~~i~~l~~~~~~l~~~l~~~~ 96 (106)
T PF01920_consen 67 LEERIEKLEKEIKKLEKQLKYLEKKLKELK 96 (106)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555555666666666666665554
No 134
>PHA01750 hypothetical protein
Probab=44.94 E-value=59 Score=25.56 Aligned_cols=31 Identities=23% Similarity=0.409 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 204 DQVARLKAEIESLHAEECRIDDSIREKQELI 234 (280)
Q Consensus 204 ~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L 234 (280)
..+.+|+.|++++....++|.+++.++...+
T Consensus 42 ~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 42 SELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 3455667777777666666666666665544
No 135
>PRK14127 cell division protein GpsB; Provisional
Probab=44.86 E-value=60 Score=27.15 Aligned_cols=55 Identities=16% Similarity=0.273 Sum_probs=30.9
Q ss_pred cccccccCCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 179 GLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 179 GLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
.+..|.=+.. ++|.+ +.+++.-+..+-.+.+.|..+-..|.+.+..+.++|.++.
T Consensus 10 DI~~KeF~~~--~RGYd---~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~ 64 (109)
T PRK14127 10 DILEKEFKTS--MRGYD---QDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELT 64 (109)
T ss_pred HHhhCccCCC--CCCCC---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444433 45776 4466666666665555555555555555555555555554
No 136
>COG4189 Predicted transcriptional regulator [Transcription]
Probab=44.78 E-value=22 Score=34.15 Aligned_cols=52 Identities=29% Similarity=0.473 Sum_probs=41.9
Q ss_pred CcHHHHHH-HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 131 SSLGLLTR-KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 131 ~SLglLTk-kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
++|+..++ ..++++. ..+.+++|++|+.||...--+--=+-|||-.|||+-.
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 45666553 4666665 4577999999999999999999999999999999844
No 137
>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=44.74 E-value=14 Score=25.96 Aligned_cols=24 Identities=29% Similarity=0.512 Sum_probs=19.8
Q ss_pred CceeHHHHHHHhcccceehhhhhh
Q 023564 150 GTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
..+++.++++.+|+++..||..++
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 468999999999999999999987
No 138
>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=43.32 E-value=58 Score=25.85 Aligned_cols=70 Identities=19% Similarity=0.197 Sum_probs=36.2
Q ss_pred ehhhhhhhhhhccccccccCCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 167 RIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 167 RIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
-+-+|...+-.=|-|... ..-+.|.|.+..--...++.+.-++..+..|+..-..+.+.+..++.++..+
T Consensus 41 ~lvplg~~~~v~g~i~~~-~~vlV~lG~~~~vE~s~~eA~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~ 110 (120)
T PF02996_consen 41 ILVPLGSGVFVPGKIPDT-DKVLVSLGAGYYVEMSLEEAIEFLKKRIKELEEQLEKLEKELAELQAQIEQL 110 (120)
T ss_dssp EEEEECTTEEEEEE-SST-TEEEEEEETTEEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCH
T ss_pred eeecCCCCeEEEEEeCCC-CEEEEEeeCCeEEEecHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444333 3467788866432222344455555566666666666666666666555544
No 139
>PRK13626 transcriptional regulator SgrR; Provisional
Probab=43.22 E-value=59 Score=32.91 Aligned_cols=48 Identities=27% Similarity=0.427 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHhCC--CCceeHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 135 LLTRKFINLIQEAK--DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 135 lLTkkFI~ll~~a~--~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
.|-+.|+.|++... +..+.|.++|+.|.+++|-.==|++-|+.-|.|+
T Consensus 5 ~~~~~~~~L~~~~~~~~~~~~l~~la~~l~cs~R~~~~~l~~~~~~gwl~ 54 (552)
T PRK13626 5 RLQQQFIRLWQCCEGKSQETTLNELAELLNCSRRHMRTLLNTMQQRGWLT 54 (552)
T ss_pred HHHHHHHHHHHhcCCCcceeeHHHHHHHhcCChhHHHHHHHHHHHCCCee
Confidence 56778999987653 5578999999999999999999999999988765
No 140
>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=42.88 E-value=30 Score=27.68 Aligned_cols=49 Identities=22% Similarity=0.393 Sum_probs=39.3
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhc-----ccceehhhhhhhhhhccccccccCC
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLE-----VQKRRIYDITNVLEGIGLIEKTSKN 187 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~-----VqKRRIYDItNVLEgIGLIeK~~KN 187 (280)
...++++.+.+. .++.+++.+.|. +.+=-||-.++.|+..|+|.|...+
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 4555699999999999999998643
No 141
>KOG3990 consensus Uncharacterized conserved protein [Function unknown]
Probab=42.71 E-value=41 Score=32.51 Aligned_cols=46 Identities=26% Similarity=0.281 Sum_probs=39.7
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 023564 199 TSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQ 244 (280)
Q Consensus 199 ~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~~n~ 244 (280)
+++....++.|++||..|+..-..-|++|-+-..+|-+|..|.+++
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 4555567899999999999999999999999999999999885555
No 142
>PRK10130 transcriptional regulator EutR; Provisional
Probab=42.55 E-value=24 Score=34.19 Aligned_cols=40 Identities=13% Similarity=0.144 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 134 glLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
..+.+++++++.+..+..+++.++|+.++|++|.++-...
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 4677889999998888899999999999999999987764
No 143
>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=41.93 E-value=63 Score=24.96 Aligned_cols=21 Identities=19% Similarity=0.270 Sum_probs=16.0
Q ss_pred eHHHHHHHhcccceehhhhhh
Q 023564 153 DLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItN 173 (280)
.+.++|+.+||..+.|-.+..
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 567889999998877766644
No 144
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=41.92 E-value=39 Score=25.42 Aligned_cols=52 Identities=21% Similarity=0.408 Sum_probs=37.7
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc--CCc-eEEe
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS--KNH-IRWK 192 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~--KN~-i~W~ 192 (280)
.+++++.. .+.+.-.++|+.+++.+-..-=+.+.||.-|.|++.. +.. ..|.
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 45556543 5568999999999999888888999999999999632 222 4685
No 145
>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=41.82 E-value=29 Score=23.43 Aligned_cols=37 Identities=22% Similarity=0.455 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhh
Q 023564 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDI 171 (280)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDI 171 (280)
|..+=+.+|.-.-...+| ++..+|+.||+.++-||.=
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 344445555555444444 3689999999999999853
No 146
>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=41.67 E-value=13 Score=25.44 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
...++|+. .| +.+.++|+.++|+|.-||-|.+
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 44455553 34 8899999999999999998764
No 147
>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=41.65 E-value=48 Score=26.34 Aligned_cols=47 Identities=23% Similarity=0.287 Sum_probs=37.6
Q ss_pred HHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 137 TRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 137 TkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
-+-.|+++.. .+..|-=..+|+.|++.-=-|-.+.-.||.+|||+++
T Consensus 10 L~alV~~Y~~-~~~PVgSk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ 56 (78)
T PF03444_consen 10 LKALVELYIE-TGEPVGSKTIAEELGRSPATIRNEMADLEELGLVESQ 56 (78)
T ss_pred HHHHHHHHHh-cCCCcCHHHHHHHHCCChHHHHHHHHHHHHCCCccCC
Confidence 3445555543 3677888888999999888899999999999999975
No 148
>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=41.58 E-value=1.1e+02 Score=27.15 Aligned_cols=33 Identities=24% Similarity=0.335 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 206 ~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
.+.++.+|..|..+-..||+.|+.+..+|...-
T Consensus 24 hq~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~ 56 (188)
T PF10018_consen 24 HQENQARIQQLRAEIEELDEQIRDILKQLKEAR 56 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566777777777777777777766666543
No 149
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=41.21 E-value=36 Score=27.82 Aligned_cols=51 Identities=24% Similarity=0.344 Sum_probs=42.8
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
|-.+=.+-+++++. ++.+.+.++|+++|++...+...+.-||.-|+|.+..
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 34455677888864 4449999999999999999999999999999999874
No 150
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=41.13 E-value=41 Score=31.54 Aligned_cols=57 Identities=25% Similarity=0.436 Sum_probs=47.3
Q ss_pred CcHHHHHHHHHH-HHHhCCCCceeHHHHHHHhcccceehhhhhh-hhhhccccccccCC
Q 023564 131 SSLGLLTRKFIN-LIQEAKDGTLDLNRTAEVLEVQKRRIYDITN-VLEGIGLIEKTSKN 187 (280)
Q Consensus 131 ~SLglLTkkFI~-ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~~KN 187 (280)
..|...-++++. ++..-.++.+.+..+|..||.....+-|++- .|=..|||++....
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 6667678899999999999999998888888 88899999877554
No 151
>PRK03837 transcriptional regulator NanR; Provisional
Probab=40.98 E-value=20 Score=31.61 Aligned_cols=51 Identities=12% Similarity=0.244 Sum_probs=41.7
Q ss_pred HHHHHHHHHHh---CCCCce-eHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 136 LTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 136 LTkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
+...+.+.+.. .|+..+ ...++|+.|||+|--+=+.+..||.-|||+....
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 152
>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=40.58 E-value=49 Score=26.16 Aligned_cols=59 Identities=29% Similarity=0.490 Sum_probs=45.5
Q ss_pred CcHHHHHHHHHHHHHhC-CCCceeHHHHHHHhcccceehhhhhh-hhhhccccccccCCce
Q 023564 131 SSLGLLTRKFINLIQEA-KDGTLDLNRTAEVLEVQKRRIYDITN-VLEGIGLIEKTSKNHI 189 (280)
Q Consensus 131 ~SLglLTkkFI~ll~~a-~~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~~KN~i 189 (280)
.-|..+=++++..+.+. .+|.+-|+.+|..|+..+.-|=|++- -|--.|+|+|+.+.++
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 88999999999999999999888765 5778999999988764
No 153
>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=40.42 E-value=2.1e+02 Score=23.50 Aligned_cols=37 Identities=22% Similarity=0.255 Sum_probs=26.4
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhcccccc--ccCCceEEec
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEK--TSKNHIRWKG 193 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~~KN~i~W~G 193 (280)
.+.++|+.+||+.+-|. ..|-.|||.. ...|.|++-+
T Consensus 2 ~I~e~a~~~gvs~~tlR----yYe~~GLl~p~~r~~~gyR~Y~ 40 (127)
T TIGR02044 2 NIGQVAKLTGLSSKMIR----YYEEKGLIPPPLRSEGGYRTYT 40 (127)
T ss_pred CHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCCeecC
Confidence 57889999999887553 4567888864 4467777753
No 154
>PRK09863 putative frv operon regulatory protein; Provisional
Probab=40.04 E-value=79 Score=32.25 Aligned_cols=52 Identities=23% Similarity=0.292 Sum_probs=34.9
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh----hhhh--ccccccccCCceEEecCC
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN----VLEG--IGLIEKTSKNHIRWKGSD 195 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN----VLEg--IGLIeK~~KN~i~W~G~~ 195 (280)
+.+.++. ++.+...++|+.|+|+.|-|+-=++ +|++ +++|.+ +.-|++.+.+
T Consensus 8 ~iL~~L~---~~~~t~~~LA~~l~VS~RTIr~dI~~in~~l~~~~~~~i~~--~~Gy~l~~~~ 65 (584)
T PRK09863 8 KIVDLLE---QQDRSGGELAQQLGVSRRTIVRDIAYINFTLNGKAIGSISG--SAKYHLEILN 65 (584)
T ss_pred HHHHHHH---cCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHhcchhheec--CCceEEEeCC
Confidence 4455553 3578999999999999998864444 3455 444555 2358887654
No 155
>PF12728 HTH_17: Helix-turn-helix domain
Probab=39.99 E-value=17 Score=24.92 Aligned_cols=22 Identities=23% Similarity=0.496 Sum_probs=20.2
Q ss_pred eeHHHHHHHhcccceehhhhhh
Q 023564 152 LDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItN 173 (280)
+++.++|+.|+|.+..||.+++
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 156
>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=39.94 E-value=1.4e+02 Score=24.87 Aligned_cols=81 Identities=20% Similarity=0.234 Sum_probs=0.0
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhccccc--cccCCceEEecCCCCCCchhHHHHHHHH------HHHHHHHHHH---
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKGSDSLGTSKLDDQVARLK------AEIESLHAEE--- 220 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G~~~s~~~~~~~~~~~Lk------~El~~L~~eE--- 220 (280)
+.+.++|+.+||+.+ -+-.-|..|||. +...|.|++-+.+ .-..-..+..|+ +|+..+-...
T Consensus 2 ~~I~e~a~~~gvs~~----tlR~Ye~~GLl~p~~r~~~gyR~Y~~~---~l~~l~~I~~lr~~G~sl~eI~~~l~~~~~~ 74 (131)
T TIGR02043 2 FQIGELAKLCGVTSD----TLRFYEKNGLIKPAGRTDSGYRLYTDE---DQKRLRFILKAKELGFTLDEIKELLSIKLDA 74 (131)
T ss_pred CCHHHHHHHHCcCHH----HHHHHHHCCCCCCCCcCCCCceecCHH---HHHHHHHHHHHHHcCCCHHHHHHHHHhhccC
Q ss_pred ---------HHHHHHHHHHHHHHHHhhh
Q 023564 221 ---------CRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 221 ---------~~LD~~I~~~~~~L~~Lte 239 (280)
.-|++.+..+++++.+|..
T Consensus 75 ~~~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (131)
T TIGR02043 75 TEHSCAEVKAIVDAKLELVDEKINELTK 102 (131)
T ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHHH
No 157
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=39.57 E-value=28 Score=23.54 Aligned_cols=34 Identities=21% Similarity=0.355 Sum_probs=21.9
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhh
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEG 177 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEg 177 (280)
.|.++.+ -....++|+.|||+++-+|.|++=.+-
T Consensus 10 ii~l~~~----G~s~~~ia~~lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 10 IIRLLRE----GWSIREIAKRLGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp HHHHHHH----T--HHHHHHHHTS-HHHHHHHHT----
T ss_pred HHHHHHC----CCCHHHHHHHHCcCHHHHHHHHHHccc
Confidence 4444444 467899999999999999999886543
No 158
>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=39.31 E-value=29 Score=26.76 Aligned_cols=42 Identities=17% Similarity=0.307 Sum_probs=35.8
Q ss_pred HHhCCCCceeHHHHHHHh-cccceehhhhhhhhhhcccccccc
Q 023564 144 IQEAKDGTLDLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 144 l~~a~~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
+..-..|....+++.+.+ +++.+-+.+=...|+..|||+|..
T Consensus 11 L~~l~~g~~rf~el~~~l~~is~~~L~~~L~~L~~~GLv~r~~ 53 (90)
T PF01638_consen 11 LRALFQGPMRFSELQRRLPGISPKVLSQRLKELEEAGLVERRV 53 (90)
T ss_dssp HHHHTTSSEEHHHHHHHSTTS-HHHHHHHHHHHHHTTSEEEEE
T ss_pred HHHHHhCCCcHHHHHHhcchhHHHHHHHHHHHHHHcchhhccc
Confidence 333444899999999999 899999999999999999999974
No 159
>PF13551 HTH_29: Winged helix-turn helix
Probab=39.27 E-value=23 Score=27.04 Aligned_cols=27 Identities=19% Similarity=0.308 Sum_probs=25.6
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhcc
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIG 179 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIG 179 (280)
.+.++|..||+.++-+|.+++-.+.=|
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 160
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=39.19 E-value=34 Score=31.39 Aligned_cols=46 Identities=15% Similarity=0.207 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccc
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL 180 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL 180 (280)
....+.+.++.......++|.++|+.+++++|.|.-+..-.-|+.+
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 3567889999999999999999999999999888877776555443
No 161
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=37.95 E-value=75 Score=29.23 Aligned_cols=40 Identities=18% Similarity=0.229 Sum_probs=24.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcC
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENEN 242 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~~ 242 (280)
+.++-..|++|+..|+.+..+++++.+ -.++|+.+.+-..
T Consensus 74 l~~en~~L~~e~~~l~~~~~~~~~l~~-en~~L~~lL~~~~ 113 (276)
T PRK13922 74 LREENEELKKELLELESRLQELEQLEA-ENARLRELLNLKE 113 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHhcCcc
Confidence 444556777777777777777765544 3466666654433
No 162
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=37.81 E-value=25 Score=29.06 Aligned_cols=37 Identities=16% Similarity=0.187 Sum_probs=34.3
Q ss_pred CCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.+.+...++|+.+++.+=-+--+++-||.-|+|+|..
T Consensus 52 ~~~~t~~eLa~~l~i~~~tvsr~l~~Le~~GlI~R~~ 88 (144)
T PRK11512 52 AACITPVELKKVLSVDLGALTRMLDRLVCKGWVERLP 88 (144)
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEecc
Confidence 4568999999999999999999999999999999974
No 163
>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=37.68 E-value=51 Score=30.07 Aligned_cols=56 Identities=23% Similarity=0.431 Sum_probs=40.4
Q ss_pred CcHHHHH------HHHHHHHHhCCCC-ceeHHHHHHHhcccceehhhhhhhhhhccccccccCCce
Q 023564 131 SSLGLLT------RKFINLIQEAKDG-TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHI 189 (280)
Q Consensus 131 ~SLglLT------kkFI~ll~~a~~g-~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i 189 (280)
+-||.++ ...++++....+. .++++++++..++.+ -||+..|+.+|+|.....+.+
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 4467766 3367777666664 899999999999965 699999999999987755443
No 164
>COG4519 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.64 E-value=44 Score=27.30 Aligned_cols=42 Identities=14% Similarity=0.327 Sum_probs=33.5
Q ss_pred HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 140 FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 140 FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
++.++- ...+..++-++...-|-.||-+-|++-.|+|+|+.-
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 344443 344567888888999999999999999999999863
No 165
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=37.44 E-value=1.4e+02 Score=24.68 Aligned_cols=47 Identities=21% Similarity=0.291 Sum_probs=39.1
Q ss_pred HHHHHHHHHHhCCCC--ceeHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 136 LTRKFINLIQEAKDG--TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 136 LTkkFI~ll~~a~~g--~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
+...|..|++.-+++ .+.|.++|+.|.+++|-.==|++-|+..|.|+
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 456778888766644 57999999999999999999999999888765
No 166
>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=37.40 E-value=1.7e+02 Score=22.94 Aligned_cols=17 Identities=18% Similarity=0.255 Sum_probs=12.2
Q ss_pred eHHHHHHHhcccceehh
Q 023564 153 DLNRTAEVLEVQKRRIY 169 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIY 169 (280)
.+.++|+.+||..+-|-
T Consensus 2 ti~eva~~~gvs~~tlR 18 (103)
T cd01106 2 TVGEVAKLTGVSVRTLH 18 (103)
T ss_pred CHHHHHHHHCcCHHHHH
Confidence 46778888888776554
No 167
>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=37.27 E-value=42 Score=30.43 Aligned_cols=47 Identities=23% Similarity=0.376 Sum_probs=34.3
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
+-..||+|++.+ -++.|+++|..+++.-==+-|-++-|+..|.|+=.
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 788999999855 68999999999999766666777778887766543
No 168
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=37.27 E-value=79 Score=25.84 Aligned_cols=36 Identities=8% Similarity=0.140 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023564 205 QVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (280)
Q Consensus 205 ~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted 240 (280)
....++++++.++++-.+|.+....++.++..|.++
T Consensus 28 ~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~ 63 (105)
T PRK00888 28 DYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGG 63 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc
Confidence 456889999999999999999999999999999875
No 169
>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=36.43 E-value=28 Score=24.93 Aligned_cols=31 Identities=16% Similarity=0.317 Sum_probs=21.3
Q ss_pred HHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 142 NLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 142 ~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
+.++....|. ...++|..+||.+.-|++|..
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 3343344454 899999999999999999985
No 170
>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=36.03 E-value=42 Score=27.45 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=22.7
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
++..+.+..|..||-+.|.++.|.++|+.-
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 888888889999999999999999999753
No 171
>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=35.99 E-value=90 Score=25.58 Aligned_cols=12 Identities=17% Similarity=-0.128 Sum_probs=5.5
Q ss_pred HHHHHHHHHHHH
Q 023564 134 GLLTRKFINLIQ 145 (280)
Q Consensus 134 glLTkkFI~ll~ 145 (280)
..-.-+||..++
T Consensus 41 ~l~~l~~I~~lr 52 (118)
T cd04776 41 DRARLKLILRGK 52 (118)
T ss_pred HHHHHHHHHHHH
Confidence 334444555554
No 172
>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=35.83 E-value=1e+02 Score=27.18 Aligned_cols=38 Identities=29% Similarity=0.430 Sum_probs=32.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
....+|..|++|++.|..+-+.+=..+..|...|..+.
T Consensus 26 ~~~~~I~~L~~e~~~ld~~i~~~~~~L~~~~~~L~~~~ 63 (188)
T PF10018_consen 26 ENQARIQQLRAEIEELDEQIRDILKQLKEARKELRTLP 63 (188)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567889999999999998888888999999998886
No 173
>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=35.71 E-value=1.5e+02 Score=21.49 Aligned_cols=34 Identities=18% Similarity=0.407 Sum_probs=24.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 205 QVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 205 ~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
.+..|+.++..|..+-..|-..+..+.+.+..|.
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~ 60 (64)
T PF00170_consen 27 YIEELEEKVEELESENEELKKELEQLKKEIQSLK 60 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566777777777777777777777777777664
No 174
>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=35.56 E-value=1.6e+02 Score=23.23 Aligned_cols=28 Identities=18% Similarity=0.392 Sum_probs=20.6
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhcccccc
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (280)
+.+.++|+.+||+.+.|--+ |-.|+|.-
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 56889999999988765544 45667653
No 175
>PRK04984 fatty acid metabolism regulator; Provisional
Probab=35.46 E-value=29 Score=30.65 Aligned_cols=39 Identities=13% Similarity=0.205 Sum_probs=35.1
Q ss_pred CCCCce-eHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 147 AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 147 a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.|+..+ .-.++|+.|||+|=-+-+-+..|+.-|||+...
T Consensus 26 ~pG~~LPsE~eLae~~gVSRt~VReAL~~L~~eGlv~~~~ 65 (239)
T PRK04984 26 PPGSILPAERELSELIGVTRTTLREVLQRLARDGWLTIQH 65 (239)
T ss_pred CCCCcCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 367778 799999999999999999999999999999653
No 176
>PF14947 HTH_45: Winged helix-turn-helix; PDB: 1XSX_B 1R7J_A.
Probab=34.93 E-value=34 Score=25.92 Aligned_cols=42 Identities=19% Similarity=0.199 Sum_probs=32.5
Q ss_pred CCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEE
Q 023564 149 DGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (280)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W 191 (280)
.+.....+++...++.-.++..+++-|+.-|||++ ..+.|.-
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 67788899999999999999999999999999965 4555544
No 177
>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=34.91 E-value=91 Score=23.49 Aligned_cols=57 Identities=23% Similarity=0.315 Sum_probs=47.7
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEe
Q 023564 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (280)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (280)
+-.+.++++....+...-.-..+..|.+.|+.|==+..=||.=|.|.|.+-+--.|.
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 456778888877777777888888899999999999999999999999988888884
No 178
>PRK13503 transcriptional activator RhaS; Provisional
Probab=34.81 E-value=45 Score=29.67 Aligned_cols=39 Identities=5% Similarity=0.115 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
...+++++++.+.....++|.++|+.++++++.+..+..
T Consensus 171 ~~i~~~~~~I~~~~~~~~tl~~lA~~~~lS~~~l~r~Fk 209 (278)
T PRK13503 171 ARLNQLLAWLEDHFAEEVNWEALADQFSLSLRTLHRQLK 209 (278)
T ss_pred HHHHHHHHHHHHhhcCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 457889999999999999999999999999999887664
No 179
>PF13851 GAS: Growth-arrest specific micro-tubule binding
Probab=34.74 E-value=83 Score=28.38 Aligned_cols=36 Identities=25% Similarity=0.338 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 204 ~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
.-|..|++|+..+...|...+..+.+++++.+.|++
T Consensus 27 ~lIksLKeei~emkk~e~~~~k~m~ei~~eN~~L~e 62 (201)
T PF13851_consen 27 ELIKSLKEEIAEMKKKEERNEKLMAEISQENKRLSE 62 (201)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 447889999999999999999999988888777765
No 180
>PHA00738 putative HTH transcription regulator
Probab=34.65 E-value=1.2e+02 Score=25.53 Aligned_cols=72 Identities=19% Similarity=0.266 Sum_probs=48.8
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCCCCCCchhHHHHHHHHHHHHHH
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESL 216 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L 216 (280)
++.+.++... +.+...++++.|++.+=.|-==+.||+..|||+........+--.... ....+.|..|++-.
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 3466666543 347888999999999999999999999999999765554444333311 12345566665544
No 181
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=34.56 E-value=78 Score=32.77 Aligned_cols=86 Identities=21% Similarity=0.172 Sum_probs=50.0
Q ss_pred ehhhhhhhhhhccccccc-cCCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCc
Q 023564 167 RIYDITNVLEGIGLIEKT-SKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQK 245 (280)
Q Consensus 167 RIYDItNVLEgIGLIeK~-~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~~n~~ 245 (280)
++-++.|-|+++.=+.|. -+|.-.|+| .|++..+.+...-...|+.|.++++||++|+---+
T Consensus 390 k~~k~~kel~~~~E~n~~l~knq~vw~~--------------kl~~~~e~~~~~~~s~d~~I~dLqEQlrDlmf~le--- 452 (493)
T KOG0804|consen 390 KLKKCQKELKEEREENKKLIKNQDVWRG--------------KLKELEEREKEALGSKDEKITDLQEQLRDLMFFLE--- 452 (493)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHH--------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHhHheehh---
Confidence 455566666665533332 244444443 34455566667778899999999999999863322
Q ss_pred ccccChHhhc-CCCCCccchh-eeeeeehh
Q 023564 246 YMFLTEEDIA-SLPCFQVIAV-NLRIYLKS 273 (280)
Q Consensus 246 ~~YVT~eDI~-~l~~fq~qTv-~lqI~LkS 273 (280)
+.+.|+ .-...|+.|| .-+|..++
T Consensus 453 ----~qqklk~dt~eIqegtI~~~~~s~~~ 478 (493)
T KOG0804|consen 453 ----AQQKLKSDTDEIQEGTILITQISPSS 478 (493)
T ss_pred ----hhhhhhcchhhhcCceeeccCCCCCc
Confidence 333442 3335566666 33454443
No 182
>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=34.49 E-value=2.6e+02 Score=22.97 Aligned_cols=89 Identities=19% Similarity=0.180 Sum_probs=0.0
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhcccc--ccccCCceEEe----------------------------cCCCCCCch
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLI--EKTSKNHIRWK----------------------------GSDSLGTSK 201 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLI--eK~~KN~i~W~----------------------------G~~~s~~~~ 201 (280)
+.+.++|+.+||+.+-|- -.|-.||+ .+...|.|++- .........
T Consensus 1 m~I~e~a~~~gvs~~tlR----yYe~~GLl~~~~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~ 76 (127)
T cd01108 1 MNIGEAAKLTGLSAKMIR----YYEEIGLIPPPSRSDNGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRDPSRA 76 (127)
T ss_pred CCHHHHHHHHCcCHHHHH----HHHHCCCCCCCCcCCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCCCC
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQ 244 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~~n~ 244 (280)
.......|+..++.+..+-..|..+...+...+.....+....
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~L~~~~~~l~~~~~~~~~~~~~~ 119 (127)
T cd01108 77 SADVKALALEHIAELERKIAELQAMRRTLQQLADSCHGDDRPD 119 (127)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCC
No 183
>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=34.48 E-value=21 Score=35.94 Aligned_cols=45 Identities=22% Similarity=0.242 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 134 glLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
..+-..|+.+ .||..+|-++|+++++.-++++|+.+.|...|||+
T Consensus 342 ~~~~l~~L~~----~DG~~slldIA~~~~~~~~~~~~~~~~l~~~~Llk 386 (386)
T PF09940_consen 342 QMAMLWVLNY----SDGKNSLLDIAERIGLPFDELADAARKLLEAGLLK 386 (386)
T ss_dssp HHHHHHHHHH-----EEEEEHHHHHHHHT--HHHHHHHHHHHHHTT-EE
T ss_pred HHHHHHHHHh----ccCCCcHHHHHHHHCcCHHHHHHHHHHHHHcCCCC
Confidence 3444555555 47899999999999999999999999999999985
No 184
>COG1373 Predicted ATPase (AAA+ superfamily) [General function prediction only]
Probab=34.36 E-value=46 Score=32.76 Aligned_cols=50 Identities=16% Similarity=0.186 Sum_probs=46.5
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHh-cccceehhhhhhhhhhccccccc
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVL-EVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L-~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
.+.++++.++-...+..++.+.+|..+ ++.++-++.-++.||..-++-..
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 89999999999999999999833
No 185
>PRK10869 recombination and repair protein; Provisional
Probab=34.33 E-value=61 Score=33.45 Aligned_cols=79 Identities=14% Similarity=0.201 Sum_probs=37.0
Q ss_pred CCCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCCCCCCchhHHHHHH
Q 023564 129 YDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVAR 208 (280)
Q Consensus 129 ~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~ 208 (280)
+|.+|..+...+-..+..-.+-.-+|....+.+.+.-.|+-.|-+-|.-|.=+.|+ .|.+ ..++-...++
T Consensus 259 ~d~~~~~~~~~l~~~~~~l~~~~~~l~~~~~~~~~dp~~l~~ie~Rl~~l~~L~rK-------yg~~---~~~~~~~~~~ 328 (553)
T PRK10869 259 MDSKLSGVLDMLEEALIQIQEASDELRHYLDRLDLDPNRLAELEQRLSKQISLARK-------HHVS---PEELPQHHQQ 328 (553)
T ss_pred hCHhHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCHHHHHHHHHHHHHHHHHHHH-------hCCC---HHHHHHHHHH
Confidence 34444444444444433333334444444455555555555555555555545544 1322 2344444555
Q ss_pred HHHHHHHHH
Q 023564 209 LKAEIESLH 217 (280)
Q Consensus 209 Lk~El~~L~ 217 (280)
+++|++.|.
T Consensus 329 l~~eL~~L~ 337 (553)
T PRK10869 329 LLEEQQQLD 337 (553)
T ss_pred HHHHHHHhh
Confidence 555555543
No 186
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=33.86 E-value=80 Score=32.69 Aligned_cols=37 Identities=14% Similarity=0.198 Sum_probs=18.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
++.++..|+.|++.|..+...+++.|+++++.+..|.
T Consensus 81 LEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk 117 (475)
T PRK13729 81 MQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALA 117 (475)
T ss_pred HHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHH
Confidence 3344444555544343444555555555555555553
No 187
>PRK11886 bifunctional biotin--[acetyl-CoA-carboxylase] synthetase/biotin operon repressor; Provisional
Probab=33.59 E-value=62 Score=30.41 Aligned_cols=52 Identities=19% Similarity=0.270 Sum_probs=40.2
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccc-cccccCCceEE
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGL-IEKTSKNHIRW 191 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGL-IeK~~KN~i~W 191 (280)
.+.+.++.+ +..+...++|+.|+|+|.-++-.+..|+.-|+ |.......|..
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 456667753 56788889999999999999999999999999 54433234554
No 188
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=33.33 E-value=63 Score=27.39 Aligned_cols=36 Identities=17% Similarity=0.319 Sum_probs=32.3
Q ss_pred ceeHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
.+.-.++|..||+.++.+.-+.+-|+.-|+|+...+
T Consensus 168 ~~t~~~lA~~lG~tr~tvsR~l~~l~~~gii~~~~~ 203 (211)
T PRK11753 168 KITRQEIGRIVGCSREMVGRVLKMLEDQGLISAHGK 203 (211)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEecCC
Confidence 466799999999999999999999999999987743
No 189
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=33.30 E-value=1.2e+02 Score=27.01 Aligned_cols=27 Identities=19% Similarity=0.281 Sum_probs=16.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023564 214 ESLHAEECRIDDSIREKQELIRTLEEN 240 (280)
Q Consensus 214 ~~L~~eE~~LD~~I~~~~~~L~~Lted 240 (280)
+-|..+...+++.|.++++.+..+.++
T Consensus 88 ~lLe~~~~~l~~ri~eLe~~l~~kad~ 114 (175)
T PRK13182 88 EQLEAQLNTITRRLDELERQLQQKADD 114 (175)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 445556666666666666666665544
No 190
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=33.28 E-value=52 Score=28.90 Aligned_cols=50 Identities=16% Similarity=0.163 Sum_probs=38.1
Q ss_pred HHHHHHHHHhC---CCCceeHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 137 TRKFINLIQEA---KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 137 TkkFI~ll~~a---~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
..|+..++... ....+.-.++|+.||++|+.+.-+++-|+--|+|++..+
T Consensus 152 ~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~G~I~~~~~ 204 (226)
T PRK10402 152 ENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQDGYLKKSKR 204 (226)
T ss_pred HHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHCCCEEeeCC
Confidence 45555555422 122356799999999999999999999999999998743
No 191
>PRK01203 prefoldin subunit alpha; Provisional
Probab=33.05 E-value=1.3e+02 Score=25.93 Aligned_cols=39 Identities=18% Similarity=0.325 Sum_probs=32.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
++..+++.++++++.|.++-..|...+.+..+.+..|..
T Consensus 4 ~~~~~~~~~~~q~e~l~~ql~~L~~a~se~~~~ie~L~~ 42 (130)
T PRK01203 4 DVEAQLNYIESLISSVDSQIDSLNKTLSEVQQTISFLSD 42 (130)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 456778888999999998888888888888888888755
No 192
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=33.04 E-value=1.2e+02 Score=24.98 Aligned_cols=38 Identities=16% Similarity=0.202 Sum_probs=33.9
Q ss_pred CCCceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
..+.+.+.++|+.|+|.+=-+-.+++-|+.-|+|.+..
T Consensus 19 ~~~~~~~~ela~~l~vs~~svs~~l~~L~~~Gli~~~~ 56 (142)
T PRK03902 19 EKGYARVSDIAEALSVHPSSVTKMVQKLDKDEYLIYEK 56 (142)
T ss_pred cCCCcCHHHHHHHhCCChhHHHHHHHHHHHCCCEEEec
Confidence 45667899999999999999999999999999999663
No 193
>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=32.67 E-value=2e+02 Score=22.70 Aligned_cols=25 Identities=16% Similarity=0.259 Sum_probs=17.0
Q ss_pred eHHHHHHHhccccee--hhhhhhhhhhcccccc
Q 023564 153 DLNRTAEVLEVQKRR--IYDITNVLEGIGLIEK 183 (280)
Q Consensus 153 dLn~aA~~L~VqKRR--IYDItNVLEgIGLIeK 183 (280)
.+.++|+..||+.|- .|| -+|||..
T Consensus 2 ~Ige~a~~~gvs~~tlRyYe------~~GLl~p 28 (107)
T cd04777 2 KIGKFAKKNNITIDTVRHYI------DLGLLIP 28 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHH------HCCCcCC
Confidence 467888999987773 454 5566543
No 194
>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=32.65 E-value=22 Score=33.14 Aligned_cols=30 Identities=33% Similarity=0.551 Sum_probs=25.2
Q ss_pred HHHHHhc---ccceehhhhhhhhhhcccccccc
Q 023564 156 RTAEVLE---VQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 156 ~aA~~L~---VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.+|+.++ +..|++||+++-||.+|||+-..
T Consensus 319 ~~~~~~~~~~~~~~~~~~~l~~l~~~gli~~~~ 351 (365)
T TIGR02928 319 EVCEDIGVDPLTQRRISDLLNELDMLGLVEAEE 351 (365)
T ss_pred HHHHhcCCCCCcHHHHHHHHHHHHhcCCeEEEE
Confidence 5666666 57799999999999999999764
No 195
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=32.54 E-value=53 Score=30.53 Aligned_cols=42 Identities=7% Similarity=-0.019 Sum_probs=36.1
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhh
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLE 176 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLE 176 (280)
....++++++.......+++.++|+.++++.|.|.-...-.-
T Consensus 218 ~~~~~~~~~i~~~~~~~~sl~~lA~~~~~S~~~l~r~fk~~~ 259 (322)
T PRK09393 218 DRLGPLIDWMRAHLAEPHTVASLAARAAMSPRTFLRRFEAAT 259 (322)
T ss_pred HHHHHHHHHHHhccCCCCCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 455789999999999999999999999999999988776443
No 196
>PRK10803 tol-pal system protein YbgF; Provisional
Probab=32.49 E-value=1.1e+02 Score=28.63 Aligned_cols=36 Identities=17% Similarity=0.247 Sum_probs=17.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
+..++..|+.||..|+-+-+++.-.|+.++++-+++
T Consensus 59 l~~ql~~lq~ev~~LrG~~E~~~~~l~~~~~rq~~~ 94 (263)
T PRK10803 59 LQQQLSDNQSDIDSLRGQIQENQYQLNQVVERQKQI 94 (263)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 334455555555555544444444444444444443
No 197
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=32.39 E-value=2.3e+02 Score=23.83 Aligned_cols=81 Identities=17% Similarity=0.239 Sum_probs=0.0
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhcccc--ccccCCceEEe-----------------cCCCCCCchhHHHHH-----
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLI--EKTSKNHIRWK-----------------GSDSLGTSKLDDQVA----- 207 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLI--eK~~KN~i~W~-----------------G~~~s~~~~~~~~~~----- 207 (280)
+.+.++|+.+||+.+-|--. |-.||| .+...|.|++- |+. -.++..-+.
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 023564 208 ---RLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 208 ---~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
...+-.+-|..+...|++.|.++++....|..
T Consensus 75 ~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~ 109 (140)
T PRK09514 75 EHHTCQEVKGIVDEKLAEVEAKIAELQHMRRSLQR 109 (140)
T ss_pred CcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 198
>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=32.34 E-value=29 Score=28.68 Aligned_cols=40 Identities=28% Similarity=0.397 Sum_probs=26.4
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhh
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNV 174 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNV 174 (280)
+||.+=-.++.--=..-++|.++|+.++|+|=-+||.+.-
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 4665544444444567799999999999999999998764
No 199
>PRK09333 30S ribosomal protein S19e; Provisional
Probab=32.33 E-value=48 Score=29.32 Aligned_cols=37 Identities=38% Similarity=0.522 Sum_probs=30.7
Q ss_pred CCceeHHHHHHHhccccee--------------hhhhhhhhhhcccccccc
Q 023564 149 DGTLDLNRTAEVLEVQKRR--------------IYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRR--------------IYDItNVLEgIGLIeK~~ 185 (280)
.+.+-+..++..+|..||| |=-|+.+||.+|||+|..
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 778999999999999874
No 200
>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=32.14 E-value=62 Score=23.32 Aligned_cols=41 Identities=12% Similarity=0.354 Sum_probs=35.9
Q ss_pred CCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCc
Q 023564 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNH 188 (280)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~ 188 (280)
.++.+++.++=+.|+++|+-.--|..-|...|+..+.+--+
T Consensus 7 ~~~~itv~~~rd~lg~sRK~ai~lLE~lD~~g~T~R~gd~R 47 (50)
T PF09107_consen 7 KNGEITVAEFRDLLGLSRKYAIPLLEYLDREGITRRVGDKR 47 (50)
T ss_dssp TTSSBEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTEE
T ss_pred cCCcCcHHHHHHHHCccHHHHHHHHHHHhccCCEEEeCCEE
Confidence 48899999999999999999999999999999999886433
No 201
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=31.52 E-value=2.4e+02 Score=24.68 Aligned_cols=28 Identities=7% Similarity=0.188 Sum_probs=16.2
Q ss_pred HHHhcccceehhhhhhhhhhcccccccc
Q 023564 158 AEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 158 A~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
...++.-...+-++..+++.|.-+...+
T Consensus 26 ~~~i~~l~~~~~e~~~~~~tl~~lk~~~ 53 (145)
T COG1730 26 QAQIAALNAAISELQTAIETLENLKGAG 53 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3344445556666666666666665554
No 202
>COG2378 Predicted transcriptional regulator [Transcription]
Probab=31.29 E-value=38 Score=32.34 Aligned_cols=30 Identities=27% Similarity=0.349 Sum_probs=28.7
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhcccc
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLI 181 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 181 (280)
+...++|+.++|++|-||-=+|-|+..|+=
T Consensus 23 vta~~lA~~~~VS~RTi~RDi~~L~~~gvP 52 (311)
T COG2378 23 VTAAELADEFEVSVRTIYRDIATLRAAGVP 52 (311)
T ss_pred chHHHHHHhcCCCHHHHHHHHHHHHHCCCC
Confidence 999999999999999999999999999985
No 203
>PF14817 HAUS5: HAUS augmin-like complex subunit 5
Probab=30.96 E-value=95 Score=33.10 Aligned_cols=50 Identities=20% Similarity=0.381 Sum_probs=33.5
Q ss_pred CCceEEecCCCCCC--c--h-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 186 KNHIRWKGSDSLGT--S--K-LDDQVARLKAEIESLHAEECRIDDSIREKQELIR 235 (280)
Q Consensus 186 KN~i~W~G~~~s~~--~--~-~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~ 235 (280)
+.++.|.|...... + + ....-.+|++||+.|..+-..||..|+.+..++.
T Consensus 56 RgNl~~~~~~~~~~~~~~~e~~~~~r~~L~~everLraei~~l~~~I~~~e~e~~ 110 (632)
T PF14817_consen 56 RGNLLWYGHQQSKERKKSRENEARRRRELEKEVERLRAEIQELDKEIESREREVS 110 (632)
T ss_pred HcceeeccccccccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 55689999765421 1 1 1123457788888888888888888887766654
No 204
>COG1382 GimC Prefoldin, chaperonin cofactor [Posttranslational modification, protein turnover, chaperones]
Probab=30.89 E-value=94 Score=26.53 Aligned_cols=34 Identities=21% Similarity=0.258 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 206 ~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
+.+|++.++.|+..-..|+.+.+.+++++.+|..
T Consensus 72 ~~eL~er~E~Le~ri~tLekQe~~l~e~l~eLq~ 105 (119)
T COG1382 72 VDELEERKETLELRIKTLEKQEEKLQERLEELQS 105 (119)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567777888899999999999999999988864
No 205
>KOG0718 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=30.49 E-value=74 Score=33.23 Aligned_cols=11 Identities=55% Similarity=0.616 Sum_probs=9.4
Q ss_pred cceehhhhhhh
Q 023564 164 QKRRIYDITNV 174 (280)
Q Consensus 164 qKRRIYDItNV 174 (280)
+||-|||+.-+
T Consensus 69 ~kRaIYD~~G~ 79 (546)
T KOG0718|consen 69 QKRAIYDNYGE 79 (546)
T ss_pred HHHHHHHHhhh
Confidence 89999998754
No 206
>PRK10421 DNA-binding transcriptional repressor LldR; Provisional
Probab=30.40 E-value=37 Score=30.51 Aligned_cols=39 Identities=15% Similarity=0.119 Sum_probs=34.9
Q ss_pred CCCCce-eHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 147 AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 147 a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.|+..+ .-.++|+.|||+|=-+=+.+..||..|||+...
T Consensus 21 ~pG~~LpsE~eLae~~gVSRtpVREAL~~Le~~GlV~~~~ 60 (253)
T PRK10421 21 EAGMKLPAERQLAMQLGVSRNSLREALAKLVSEGVLLSRR 60 (253)
T ss_pred CCCCcCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEeC
Confidence 467778 699999999999999999999999999998553
No 207
>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=30.37 E-value=68 Score=29.20 Aligned_cols=54 Identities=26% Similarity=0.455 Sum_probs=41.1
Q ss_pred HHHHHHHH-HHHhCCCCceeHHHHHHHhcccceehhhhhh-hhhhccccccccCCc
Q 023564 135 LLTRKFIN-LIQEAKDGTLDLNRTAEVLEVQKRRIYDITN-VLEGIGLIEKTSKNH 188 (280)
Q Consensus 135 lLTkkFI~-ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN-VLEgIGLIeK~~KN~ 188 (280)
..-+.++. ++..-.++.+.+.++|..||+..+.+..++- .|=-.|||++.....
T Consensus 238 ~~~~~~L~al~~~~~~~~~~~~~ia~~lg~~~~~~~~~~e~~Li~~~li~~~~~g~ 293 (305)
T TIGR00635 238 EIDRKLLSVLIEQFQGGPVGLKTLAAALGEDADTIEDVYEPYLLQIGFLQRTPRGR 293 (305)
T ss_pred HHHHHHHHHHHHHhCCCcccHHHHHHHhCCCcchHHHhhhHHHHHcCCcccCCchh
Confidence 34455666 5555556678899999999999999999777 788899998775543
No 208
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=30.31 E-value=84 Score=28.74 Aligned_cols=54 Identities=11% Similarity=0.147 Sum_probs=38.3
Q ss_pred CcHHHHHHHHHHHHHhCCCCceeHHH-----------HHHHhcccceehhhhhhhhhhccccccc
Q 023564 131 SSLGLLTRKFINLIQEAKDGTLDLNR-----------TAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 131 ~SLglLTkkFI~ll~~a~~g~ldLn~-----------aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
..+....++..+++....+.+..-+. +.-.+.|..-++-+.++-|+++|-+.-.
T Consensus 59 ~d~~~a~~~i~~~~~~~gG~i~~~~~~~~~~~~~~~~~~ltiRVP~~~~~~~l~~l~~~g~v~~~ 123 (262)
T PF14257_consen 59 KDVEKAVKKIENLVESYGGYIESSSSSSSGGSDDERSASLTIRVPADKFDSFLDELSELGKVTSR 123 (262)
T ss_pred CCHHHHHHHHHHHHHHcCCEEEEEeeecccCCCCcceEEEEEEECHHHHHHHHHHHhccCceeee
Confidence 45666677777777776655544443 2345668889999999999999977655
No 209
>KOG2747 consensus Histone acetyltransferase (MYST family) [Chromatin structure and dynamics]
Probab=29.81 E-value=1.1e+02 Score=31.12 Aligned_cols=57 Identities=16% Similarity=0.325 Sum_probs=45.3
Q ss_pred cHHHHHHH------HHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEec
Q 023564 132 SLGLLTRK------FINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKG 193 (280)
Q Consensus 132 SLglLTkk------FI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G 193 (280)
-||+|+-+ .++++....+..|.|+++|+.-++. .-||++.|+.+++|.... . +.|..
T Consensus 304 DLGllsYrsYW~~~ll~~L~~~~~~~isI~~iS~~Tgi~---~~DIisTL~~L~m~~y~k-~-~~~~~ 366 (396)
T KOG2747|consen 304 DLGLLSYRSYWRCVLLELLRKHRGEHISIKEISKETGIR---PDDIISTLQSLNMIKYYK-G-YIISI 366 (396)
T ss_pred hhhHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHhhCCC---HHHHHHHHHhhCCccccC-C-eeEEE
Confidence 47888744 7777877666669999999999984 579999999999998763 3 77764
No 210
>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=29.78 E-value=1.4e+02 Score=23.56 Aligned_cols=37 Identities=19% Similarity=0.233 Sum_probs=24.6
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhccccc--cccCCceEEec
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWKG 193 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~G 193 (280)
.+.++|+.+||+.+-|- -.|-.|++. +...|.++|-.
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 46789999999776432 126788886 34566677643
No 211
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=29.68 E-value=60 Score=29.36 Aligned_cols=38 Identities=13% Similarity=0.211 Sum_probs=33.0
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
...+++.++.....+.+.+.++|+.++++++++.-+..
T Consensus 184 ~i~~~~~~i~~~~~~~isl~~lA~~~~lS~~~l~r~Fk 221 (290)
T PRK10572 184 RVREACQYISDHLASEFDIESVAQHVCLSPSRLAHLFR 221 (290)
T ss_pred HHHHHHHHHHhcccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 46778889988889999999999999999998877664
No 212
>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=29.42 E-value=2.4e+02 Score=22.03 Aligned_cols=37 Identities=16% Similarity=0.223 Sum_probs=24.5
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhcccccc--ccCCceEEec
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEK--TSKNHIRWKG 193 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~~KN~i~W~G 193 (280)
.+.++|+.+||+.+-|- -.|..|||.. ...|.|+.-.
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 57889999999877443 2356888864 3346666543
No 213
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=29.20 E-value=88 Score=26.71 Aligned_cols=51 Identities=22% Similarity=0.326 Sum_probs=44.9
Q ss_pred CcHHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccccc
Q 023564 131 SSLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (280)
Q Consensus 131 ~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (280)
..|-.+=++.+.+|+ .++.+...++|+.+|++.--++.=++=||.-|+|++
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 446777788999886 678889999999999999999999999999999986
No 214
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=29.11 E-value=3.2e+02 Score=22.35 Aligned_cols=92 Identities=15% Similarity=0.161 Sum_probs=0.0
Q ss_pred HHHHHHHhcccceehhhhhhhhhhccccc--cccCCceEEe-----------------cCCC---------CCCchhHHH
Q 023564 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWK-----------------GSDS---------LGTSKLDDQ 205 (280)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~-----------------G~~~---------s~~~~~~~~ 205 (280)
+.++|+.+||+.+-|--. |-+|||. +...|.|++- |+.. .........
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 HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCccccc
Q 023564 206 VARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQKYMFL 249 (280)
Q Consensus 206 ~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~~n~~~~YV 249 (280)
...|+..++.|+++-.+|..+...++..+....+.........+
T Consensus 78 ~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~~~~~~~c~~~ 121 (124)
T TIGR02051 78 YELASRKLKSVQAKMADLLRIERLLEELLEQCPANKGNTSCPII 121 (124)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCCCCCCCccc
No 215
>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=29.06 E-value=2.1e+02 Score=22.11 Aligned_cols=37 Identities=22% Similarity=0.305 Sum_probs=27.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023564 204 DQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (280)
Q Consensus 204 ~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted 240 (280)
+.+..|+.|++.|..+-..|.+....+.+....|.++
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 4567788888888888777777777777776666544
No 216
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=29.04 E-value=55 Score=29.64 Aligned_cols=38 Identities=21% Similarity=0.292 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhCCCCc-eeHHHHHHHhcccceehhhhhh
Q 023564 136 LTRKFINLIQEAKDGT-LDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 136 LTkkFI~ll~~a~~g~-ldLn~aA~~L~VqKRRIYDItN 173 (280)
...+.+.++.+.-... +++.++|..+||++|.||-+.-
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 3457788887765554 9999999999999999998764
No 217
>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=28.80 E-value=1.7e+02 Score=25.13 Aligned_cols=10 Identities=30% Similarity=0.501 Sum_probs=7.2
Q ss_pred ceEEecCCCC
Q 023564 188 HIRWKGSDSL 197 (280)
Q Consensus 188 ~i~W~G~~~s 197 (280)
.+.|+|...+
T Consensus 22 Y~wwKGws~s 31 (126)
T PF07889_consen 22 YMWWKGWSFS 31 (126)
T ss_pred eeeecCCchh
Confidence 4678998754
No 218
>COG2512 Predicted membrane-associated trancriptional regulator [Transcription]
Probab=28.66 E-value=77 Score=29.94 Aligned_cols=60 Identities=25% Similarity=0.348 Sum_probs=49.0
Q ss_pred cHHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEe
Q 023564 132 SLGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (280)
Q Consensus 132 SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (280)
.|-.-=+.-|+++. ..+|.+.-.++.+.||.+|=-++-|+-=||-.|+|+|..++.=.|.
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 34444466777775 5678899999999999999999999999999999999877665553
No 219
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=28.54 E-value=61 Score=27.60 Aligned_cols=37 Identities=22% Similarity=0.144 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhh
Q 023564 134 GLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYD 170 (280)
Q Consensus 134 glLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYD 170 (280)
..|-..+++++.+.+-.-+.++++|+..||.|..||.
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 4567778899988877889999999999999999995
No 220
>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=28.44 E-value=2.1e+02 Score=21.45 Aligned_cols=39 Identities=8% Similarity=0.315 Sum_probs=30.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted 240 (280)
+.+.+..++..+.++....+.|+........++.++.++
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 456677788888888888888888888888887777654
No 221
>COG1730 GIM5 Predicted prefoldin, molecular chaperone implicated in de novo protein folding [Posttranslational modification, protein turnover, chaperones]
Probab=28.40 E-value=1.7e+02 Score=25.56 Aligned_cols=40 Identities=38% Similarity=0.468 Sum_probs=32.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023564 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (280)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted 240 (280)
++...++.++++++.|..+-..|...|.+++..+..|...
T Consensus 10 ~l~a~lq~l~~qie~L~~~i~~l~~~~~e~~~~~~tl~~l 49 (145)
T COG1730 10 ELAAQLQILQSQIESLQAQIAALNAAISELQTAIETLENL 49 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566678888999999999999999999888887776543
No 222
>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=28.28 E-value=2.4e+02 Score=24.68 Aligned_cols=37 Identities=24% Similarity=0.469 Sum_probs=27.0
Q ss_pred eeHHHHHHHhcccce--ehhhhhhhhhhccccc--cccCCceEEecC
Q 023564 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLIE--KTSKNHIRWKGS 194 (280)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIe--K~~KN~i~W~G~ 194 (280)
+.+.++|+.+||+++ |.|| -+|||. +...|.|++-+.
T Consensus 2 ~~I~evA~~~gvs~~tLRyYe------~~GLl~p~~r~~~gyR~Y~~ 42 (172)
T cd04790 2 LTISQLARQFGLSRSTLLYYE------RIGLLSPSARSESNYRLYGE 42 (172)
T ss_pred CCHHHHHHHHCcCHHHHHHHH------HCCCCCCCccCCCCCccCCH
Confidence 468899999999988 5564 567775 345677887653
No 223
>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=28.10 E-value=1.6e+02 Score=26.94 Aligned_cols=17 Identities=0% Similarity=0.001 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHHHHHH
Q 023564 220 ECRIDDSIREKQELIRT 236 (280)
Q Consensus 220 E~~LD~~I~~~~~~L~~ 236 (280)
++.|.-++..|-+.|..
T Consensus 100 ~~~l~p~m~~m~~~L~~ 116 (251)
T PF11932_consen 100 RQELVPLMEQMIDELEQ 116 (251)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33333333333333333
No 224
>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=27.97 E-value=1.3e+02 Score=23.65 Aligned_cols=36 Identities=19% Similarity=0.409 Sum_probs=23.9
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhcccccc--ccCCceEEe
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEK--TSKNHIRWK 192 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK--~~KN~i~W~ 192 (280)
.+.++|+.+||+.+.|-- .|..|||.- .+.|.|++-
T Consensus 2 ~i~eva~~~gvs~~tlR~----ye~~Gll~p~~~~~~gyR~Y 39 (97)
T cd04782 2 TTGEFAKLCGISKQTLFH----YDKIGLFKPEIVKENGYRYY 39 (97)
T ss_pred CHHHHHHHHCcCHHHHHH----HHHCCCCCCCccCCCCCccC
Confidence 477899999998776533 366788853 334555554
No 225
>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=27.87 E-value=48 Score=34.30 Aligned_cols=26 Identities=12% Similarity=0.231 Sum_probs=12.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 212 EIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 212 El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
+|++|++|-++|.+++.++++++..+
T Consensus 32 kie~L~kql~~Lk~q~~~l~~~v~k~ 57 (489)
T PF11853_consen 32 KIEALKKQLEELKAQQDDLNDRVDKV 57 (489)
T ss_pred HHHHHHHHHHHHHHhhcccccccchh
Confidence 45555544444444444444444333
No 226
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=27.75 E-value=62 Score=30.18 Aligned_cols=40 Identities=20% Similarity=0.307 Sum_probs=34.4
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhh
Q 023564 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVL 175 (280)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVL 175 (280)
..++.+.++.+.....+++.++|+.+++++|.++-+..--
T Consensus 192 ~i~~~~~~i~~~~~~~~tl~~lA~~~~~S~~~l~r~Fk~~ 231 (302)
T PRK10371 192 YVSQMLGFIAENYDQALTINDVAEHVKLNANYAMGIFQRV 231 (302)
T ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 5678888998888889999999999999999888877543
No 227
>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=27.72 E-value=3.5e+02 Score=22.35 Aligned_cols=89 Identities=12% Similarity=0.119 Sum_probs=0.0
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhccccccccC--CceEEe----------------------------cCCCCCCch
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK--NHIRWK----------------------------GSDSLGTSK 201 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K--N~i~W~----------------------------G~~~s~~~~ 201 (280)
+.+.++|..+||+.|.| =-.|-+|||.-... |.|++- .........
T Consensus 1 m~IgE~A~~~gvs~~TL----RyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~~~~ 76 (133)
T cd04787 1 MKVKELANAAGVTPDTV----RFYTRIGLLRPTRDPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQGESP 76 (133)
T ss_pred CCHHHHHHHHCcCHHHH----HHHHHCCCCCCCcCCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhccCCCc
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENENHQ 244 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~~n~ 244 (280)
.......|++.++.|+.+-.+|..++..+...+..........
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~l~~~~~~l~~~~~~~~~~~~~~ 119 (133)
T cd04787 77 CPMVRRLIEQRLAETERRIKELLKLRDRMQQAVSQWQQMPDGA 119 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCC
No 228
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=27.28 E-value=37 Score=32.09 Aligned_cols=35 Identities=23% Similarity=0.387 Sum_probs=26.9
Q ss_pred CceeHHHHH-------HHhcc---cceehhhhhhhhhhccccccc
Q 023564 150 GTLDLNRTA-------EVLEV---QKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 150 g~ldLn~aA-------~~L~V---qKRRIYDItNVLEgIGLIeK~ 184 (280)
+.+...++. +.+++ .+|+++|+.+-|+..|||+-.
T Consensus 314 ~~~~~~~i~~~y~~l~~~~~~~~~~~~~~~~~l~~L~~~glI~~~ 358 (394)
T PRK00411 314 DEVTTGEVYEEYKELCEELGYEPRTHTRFYEYINKLDMLGIINTR 358 (394)
T ss_pred CcccHHHHHHHHHHHHHHcCCCcCcHHHHHHHHHHHHhcCCeEEE
Confidence 445555555 45777 459999999999999999854
No 229
>PF13600 DUF4140: N-terminal domain of unknown function (DUF4140)
Probab=27.15 E-value=1.9e+02 Score=22.70 Aligned_cols=35 Identities=26% Similarity=0.398 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 203 ~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
...+..|+++++.|+.+-..+...+.-+..++.-|
T Consensus 69 ~~~~~~l~~~l~~l~~~~~~~~~~~~~~~~~~~~L 103 (104)
T PF13600_consen 69 SPELKELEEELEALEDELAALQDEIQALEAQIAFL 103 (104)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45677888888888888888888888777776644
No 230
>PF14712 Snapin_Pallidin: Snapin/Pallidin
Probab=27.12 E-value=2.1e+02 Score=21.99 Aligned_cols=37 Identities=19% Similarity=0.375 Sum_probs=32.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 203 ~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
...+..+.+.+.+|......|-..|....+.|+++.+
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 3457788999999999999999999999999999887
No 231
>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=26.98 E-value=2e+02 Score=22.89 Aligned_cols=37 Identities=30% Similarity=0.427 Sum_probs=27.0
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
.+...+..|+.+++.|..+-..+.+.+..+...|+.+
T Consensus 91 ~l~~r~~~l~~~~~~l~~~~~~~~~~~~~l~~~l~~~ 127 (129)
T cd00890 91 FLKKRLETLEKQIEKLEKQLEKLQDQITELQEELQQL 127 (129)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3556667777777777777777777777777777664
No 232
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=26.95 E-value=59 Score=22.08 Aligned_cols=38 Identities=16% Similarity=0.186 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 136 LTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 136 LTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
+|.+|..++-..-.....+..+|..+||.--.+..|++
T Consensus 12 ~T~~~~~~i~~~~~~~~s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 12 ITKRLEQYILKLLRESRSFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHHHhhcCCHHHHHHHHCCCHHHHHHHHH
Confidence 56677766644333338999999999997666666554
No 233
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=26.92 E-value=86 Score=27.22 Aligned_cols=43 Identities=23% Similarity=0.334 Sum_probs=38.2
Q ss_pred CCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceE
Q 023564 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (280)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (280)
.++.+-..++|..|+|..--.-..+|=|+..|||+......|.
T Consensus 21 ~~~~~~~~diA~~L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~ 63 (154)
T COG1321 21 EKGFARTKDIAERLKVSPPSVTEMLKRLERLGLVEYEPYGGVT 63 (154)
T ss_pred ccCcccHHHHHHHhCCCcHHHHHHHHHHHHCCCeEEecCCCeE
Confidence 7899999999999999999999999999999999997444333
No 234
>PRK10906 DNA-binding transcriptional repressor GlpR; Provisional
Probab=26.79 E-value=57 Score=30.07 Aligned_cols=45 Identities=20% Similarity=0.231 Sum_probs=38.3
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
.+.+++++ ..+.+.+.++|+.|+|+..-|+--+..||--|+|.|.
T Consensus 8 ~~Il~~l~--~~~~~~~~ela~~l~vS~~TiRRdL~~Le~~g~l~r~ 52 (252)
T PRK10906 8 DAIIELVK--QQGYVSTEELVEHFSVSPQTIRRDLNDLAEQNKILRH 52 (252)
T ss_pred HHHHHHHH--HcCCEeHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEe
Confidence 44567775 4568999999999999998888889999999999886
No 235
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=26.69 E-value=66 Score=26.60 Aligned_cols=32 Identities=28% Similarity=0.454 Sum_probs=26.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQEL 233 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~ 233 (280)
+..++..+++|++.|.+++..|...|+.+++.
T Consensus 55 l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 55 LQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34556678888999999999999999888887
No 236
>COG2207 AraC AraC-type DNA-binding domain-containing proteins [Transcription]
Probab=26.69 E-value=75 Score=24.07 Aligned_cols=43 Identities=19% Similarity=0.244 Sum_probs=35.9
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhcccc
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLI 181 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLI 181 (280)
+++.++.......++++++|..+|+.++.+.-...-..|+...
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 7777777777777999999999999999999888877766554
No 237
>PRK11523 DNA-binding transcriptional repressor ExuR; Provisional
Probab=26.45 E-value=51 Score=29.60 Aligned_cols=51 Identities=18% Similarity=0.169 Sum_probs=40.2
Q ss_pred HHHHHHHHHHh---CCCCce-eHHHHHHHhcccceehhhhhhhhhhccccccccC
Q 023564 136 LTRKFINLIQE---AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSK 186 (280)
Q Consensus 136 LTkkFI~ll~~---a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~K 186 (280)
+...+.+.+.. .|+..+ .-.++|+.|||+|==+=+-+..||..|||+....
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 33444555432 377788 5899999999999999999999999999986644
No 238
>KOG1062 consensus Vesicle coat complex AP-1, gamma subunit [Intracellular trafficking, secretion, and vesicular transport]
Probab=26.44 E-value=1.8e+02 Score=32.28 Aligned_cols=126 Identities=16% Similarity=0.177 Sum_probs=81.6
Q ss_pred CCCcHHHHHHHHHHHHHhCCCC-----ceeHHHHHHHhcccceehhhhh-hhhhhcccccccc--CCceEEecCCCCCCc
Q 023564 129 YDSSLGLLTRKFINLIQEAKDG-----TLDLNRTAEVLEVQKRRIYDIT-NVLEGIGLIEKTS--KNHIRWKGSDSLGTS 200 (280)
Q Consensus 129 ~d~SLglLTkkFI~ll~~a~~g-----~ldLn~aA~~L~VqKRRIYDIt-NVLEgIGLIeK~~--KN~i~W~G~~~s~~~ 200 (280)
.+..+..++++.++|+...++. .--+.++|+++.=.|||..|++ +||+..|=.-+.. .|-++-++... ..
T Consensus 379 n~~Nv~~mv~eLl~fL~~~d~~~k~~~as~I~~laEkfaP~k~W~idtml~Vl~~aG~~V~~dv~~nll~LIa~~~--~e 456 (866)
T KOG1062|consen 379 NESNVRVMVKELLEFLESSDEDFKADIASKIAELAEKFAPDKRWHIDTMLKVLKTAGDFVNDDVVNNLLRLIANAF--QE 456 (866)
T ss_pred ccccHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHhcCCcchhHHHHHHHHHHhcccccchhhHHHHHHHHhcCC--cc
Confidence 4566778999999999876433 2367889999999999999986 5888888655543 24444443221 11
Q ss_pred hhHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHhhhhcCCC-cccccChHhhcC
Q 023564 201 KLDDQVARLKAEIE---SLHAEECRIDDSIREKQELIRTLEENENHQ-KYMFLTEEDIAS 256 (280)
Q Consensus 201 ~~~~~~~~Lk~El~---~L~~eE~~LD~~I~~~~~~L~~Lted~~n~-~~~YVT~eDI~~ 256 (280)
..+..+.+|-.-+. .+.-.+..|-+.+.||=-+--+|.-|..+. ...-||++||..
T Consensus 457 ~~~y~~~rLy~a~~~~~~~~is~e~l~qVa~W~IGEYGdlll~~~~~~~p~~vtesdivd 516 (866)
T KOG1062|consen 457 LHEYAVLRLYLALSEDTLLDISQEPLLQVASWCIGEYGDLLLDGANEEEPIKVTESDIVD 516 (866)
T ss_pred hhhHHHHHHHHHHhhhhhhhhhhhhHHHHHHHHhhhhhHHhhcCccccCCCcCCHHHHHH
Confidence 12222333332222 235567778888999988888776665444 355689998864
No 239
>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=26.43 E-value=1.1e+02 Score=23.97 Aligned_cols=28 Identities=14% Similarity=0.278 Sum_probs=19.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 211 AEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 211 ~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
++|..|.+.-+.||+.+..++++|-++-
T Consensus 2 ~~L~~l~~~k~~Le~~L~~lE~qIy~~E 29 (80)
T PF09340_consen 2 KELKELLQKKKKLEKDLAALEKQIYDKE 29 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4666677777777777777777777663
No 240
>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=26.40 E-value=22 Score=30.13 Aligned_cols=27 Identities=22% Similarity=0.430 Sum_probs=0.0
Q ss_pred cceehhhhhhhhhhccccccccCCceEEe
Q 023564 164 QKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (280)
Q Consensus 164 qKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (280)
-|+++-+-+..||.+|+|.+. |.|+=+
T Consensus 5 lk~~~l~~l~~LE~~G~v~~~--n~yQ~l 31 (142)
T PF03836_consen 5 LKKKILENLKELESLGIVSRS--NNYQDL 31 (142)
T ss_dssp -----------------------------
T ss_pred HHHHHHHHHHHHHHCCCCCCc--ccHHHH
Confidence 467888889999999999988 666653
No 241
>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=26.13 E-value=3.6e+02 Score=21.90 Aligned_cols=81 Identities=22% Similarity=0.309 Sum_probs=58.2
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCCCCCCchhHHHHHHHHHHHHHHHH
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHA 218 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~ 218 (280)
-|.-++...--..-++..+.+++.-..+|+-.|=+.|+.+ | ....+..|+-++..+.-
T Consensus 22 ~~~~~l~~~~a~~~~~~~l~~~~~~~~~Rl~~lE~~l~~L--------------------P--t~~dv~~L~l~l~el~G 79 (106)
T PF10805_consen 22 IFWLWLRRTYAKREDIEKLEERLDEHDRRLQALETKLEHL--------------------P--TRDDVHDLQLELAELRG 79 (106)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHHHHHHHHHHHHHHhC--------------------C--CHHHHHHHHHHHHHHHh
Confidence 3444444333334577888888888888887776665532 1 23567889999999999
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhc
Q 023564 219 EECRIDDSIREKQELIRTLEENE 241 (280)
Q Consensus 219 eE~~LD~~I~~~~~~L~~Lted~ 241 (280)
+=+.+...|+-+..++.-|.|.+
T Consensus 80 ~~~~l~~~l~~v~~~~~lLlE~~ 102 (106)
T PF10805_consen 80 ELKELSARLQGVSHQLDLLLENE 102 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999988887764
No 242
>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=26.02 E-value=2.9e+02 Score=24.31 Aligned_cols=39 Identities=13% Similarity=0.205 Sum_probs=35.8
Q ss_pred CCCCce-eHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 147 AKDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 147 a~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
.|+..+ .-.++|+.|||+|==+=+.+-.||.-|||+...
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 243
>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=25.83 E-value=2e+02 Score=21.50 Aligned_cols=30 Identities=23% Similarity=0.320 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 209 LKAEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 209 Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
+..+++++..+.+.+......++.++..|.
T Consensus 29 ~~~~~~~~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 29 LNNELQKLQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 334444444444444444444444444443
No 244
>PF14389 Lzipper-MIP1: Leucine-zipper of ternary complex factor MIP1
Probab=25.39 E-value=2.4e+02 Score=22.33 Aligned_cols=38 Identities=21% Similarity=0.257 Sum_probs=31.4
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 199 TSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRT 236 (280)
Q Consensus 199 ~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~ 236 (280)
+..++..++.|=+||.-|+.+-..|++.+.++..++++
T Consensus 49 ~~~lp~~~keLL~EIA~lE~eV~~LE~~v~~L~~~l~~ 86 (88)
T PF14389_consen 49 PSSLPKKAKELLEEIALLEAEVAKLEQKVLSLYRQLFQ 86 (88)
T ss_pred cccCChHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34567778889999999999999999999988887763
No 245
>KOG2255 consensus Peptidyl-tRNA hydrolase [Translation, ribosomal structure and biogenesis]
Probab=24.99 E-value=37 Score=31.76 Aligned_cols=29 Identities=34% Similarity=0.495 Sum_probs=26.1
Q ss_pred HHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 154 LNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 154 Ln~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
|+.+|++|+|+.+++-+ |.+++||+|+-.
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 56789999999999999 999999999854
No 246
>PRK05638 threonine synthase; Validated
Probab=24.90 E-value=97 Score=30.71 Aligned_cols=61 Identities=20% Similarity=0.308 Sum_probs=47.5
Q ss_pred CCCCCCCCCCCcHHHHHHHHHHHHHhCCCCceeHHHHHHHhc--ccceehhhhhhhhhhccccccc
Q 023564 121 LNLSNGCRYDSSLGLLTRKFINLIQEAKDGTLDLNRTAEVLE--VQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 121 ~tp~~~~R~d~SLglLTkkFI~ll~~a~~g~ldLn~aA~~L~--VqKRRIYDItNVLEgIGLIeK~ 184 (280)
..+....|-.-.++.+..+.+.+|.+. .+...++++.|+ +.+--||-.+.+||.-|||+..
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 444556665555666666777777644 477889999998 8999999999999999999853
No 247
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=24.85 E-value=3.4e+02 Score=24.13 Aligned_cols=52 Identities=19% Similarity=0.275 Sum_probs=40.0
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccc--c-----ccCCceEEe
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE--K-----TSKNHIRWK 192 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K-----~~KN~i~W~ 192 (280)
+++..+. ..|.+.-.++|..||++.--+=-+.+-|+.-|||. + .+...|.|.
T Consensus 26 ~Vl~~L~--~~g~~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~ 84 (178)
T PRK06266 26 EVLKALI--KKGEVTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWK 84 (178)
T ss_pred HHHHHHH--HcCCcCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEE
Confidence 3444443 34578999999999999999999999999999999 2 123467776
No 248
>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=24.59 E-value=3.4e+02 Score=24.01 Aligned_cols=47 Identities=15% Similarity=0.273 Sum_probs=37.7
Q ss_pred HHHHHHHHhCCCCce--eHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 138 RKFINLIQEAKDGTL--DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 138 kkFI~ll~~a~~g~l--dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
+++..++.+.+.-.+ .+..+|..|++.++-|-=++.|+.-+|+|+-.
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 445556666655433 57899999999999999999999999999866
No 249
>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=24.58 E-value=3.3e+02 Score=23.63 Aligned_cols=35 Identities=14% Similarity=0.172 Sum_probs=32.4
Q ss_pred CCCceeHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 148 KDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 148 ~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
..+.+.-+++|..||++++-+=-+.+.|...|||+
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 250
>TIGR00714 hscB Fe-S protein assembly co-chaperone HscB. This model describes the small subunit, Hsc20 (20K heat shock cognate protein) of a pair of proteins Hsc66-Hsc20, related to the DnaK-DnaJ heat shock proteins, which also serve as molecular chaperones. Hsc20, unlike DnaJ, appears not to have chaperone activity on its own, but to act solely as a regulatory subunit for Hsc66 (i.e., to be a co-chaperone). The gene for Hsc20 in E. coli, hscB, is not induced by heat shock.
Probab=24.52 E-value=3.7e+02 Score=23.22 Aligned_cols=26 Identities=35% Similarity=0.492 Sum_probs=18.5
Q ss_pred eHHHHHHHhcc-cceehhhhhhhhhhccc
Q 023564 153 DLNRTAEVLEV-QKRRIYDITNVLEGIGL 180 (280)
Q Consensus 153 dLn~aA~~L~V-qKRRIYDItNVLEgIGL 180 (280)
-+|+|=..|.- .+|..|++. |.|+.+
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 251
>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=24.33 E-value=2.2e+02 Score=24.43 Aligned_cols=31 Identities=19% Similarity=0.326 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHhhhhcCCCcccccChHhhcCC
Q 023564 222 RIDDSIREKQELIRTLEENENHQKYMFLTEEDIASL 257 (280)
Q Consensus 222 ~LD~~I~~~~~~L~~Lted~~n~~~~YVT~eDI~~l 257 (280)
.|.+.|..+...|..|... ..-||.+|+..+
T Consensus 120 ~l~~e~~~l~~kL~~l~~~-----~~~vs~ee~~~~ 150 (169)
T PF07106_consen 120 ELEEEIEELEEKLEKLRSG-----SKPVSPEEKEKL 150 (169)
T ss_pred HHHHHHHHHHHHHHHHHhC-----CCCCCHHHHHHH
Confidence 3333444444444444432 122777777643
No 252
>KOG3501 consensus Molecular chaperone Prefoldin, subunit 1 [Posttranslational modification, protein turnover, chaperones]
Probab=24.25 E-value=2.5e+02 Score=23.90 Aligned_cols=41 Identities=17% Similarity=0.400 Sum_probs=34.6
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 023564 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (280)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~ 241 (280)
..+..+..+++.|+.|+....-|+....+..+.|++|.+..
T Consensus 71 ~leak~k~see~IeaLqkkK~YlEk~v~eaE~nLrellqs~ 111 (114)
T KOG3501|consen 71 HLEAKMKSSEEKIEALQKKKTYLEKTVSEAEQNLRELLQSR 111 (114)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45566677888899999999999999999999999987653
No 253
>PRK15185 transcriptional regulator HilD; Provisional
Probab=24.19 E-value=82 Score=30.70 Aligned_cols=39 Identities=13% Similarity=0.177 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
.+..+...++.+.+...+++.++|+.+++++|.++-...
T Consensus 206 ~~~erV~~~I~~n~~~~~SledLA~~lgmS~~tL~R~FK 244 (309)
T PRK15185 206 TLKERVYNIISSSPSRQWKLTDVADHIFMSTSTLKRKLA 244 (309)
T ss_pred HHHHHHHHHHHhCccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 366788899999999999999999999999999877654
No 254
>PF14830 Haemocyan_bet_s: Haemocyanin beta-sandwich; PDB: 1JS8_B 3QJO_A 1LNL_A.
Probab=24.09 E-value=29 Score=28.88 Aligned_cols=15 Identities=47% Similarity=0.727 Sum_probs=10.5
Q ss_pred ehhhhhhhhhhcccc
Q 023564 167 RIYDITNVLEGIGLI 181 (280)
Q Consensus 167 RIYDItNVLEgIGLI 181 (280)
==||||.+|+.+||=
T Consensus 56 ykydIT~~l~~l~l~ 70 (103)
T PF14830_consen 56 YKYDITDALKKLGLH 70 (103)
T ss_dssp EEEE-HHHHHHCT--
T ss_pred chhhHHHHHHHcCCC
Confidence 348999999999986
No 255
>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=23.92 E-value=49 Score=25.33 Aligned_cols=36 Identities=28% Similarity=0.408 Sum_probs=28.4
Q ss_pred CceeHHHHHHHhcccceehhhhhhhhhhcccccccc
Q 023564 150 GTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 150 g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
|.+--..+|++.|+.|.-|-.-+-=||..|+|+-.+
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 455667899999999999988888999999999664
No 256
>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=23.88 E-value=65 Score=22.40 Aligned_cols=26 Identities=12% Similarity=0.248 Sum_probs=19.4
Q ss_pred CCceeHHHHHHHhcccceehhhhhhh
Q 023564 149 DGTLDLNRTAEVLEVQKRRIYDITNV 174 (280)
Q Consensus 149 ~g~ldLn~aA~~L~VqKRRIYDItNV 174 (280)
.|.+.+..||..+||.+.-|+|.++-
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 34499999999999999999987764
No 257
>PRK04214 rbn ribonuclease BN/unknown domain fusion protein; Reviewed
Probab=23.86 E-value=1.1e+02 Score=30.16 Aligned_cols=44 Identities=14% Similarity=0.241 Sum_probs=38.1
Q ss_pred CCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceE
Q 023564 147 AKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIR 190 (280)
Q Consensus 147 a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~ 190 (280)
..+..+...++++.+++.-+.+-||..-|+..|+|.+...+.|.
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 35568899999999999999999999999999999987666443
No 258
>PF14282 FlxA: FlxA-like protein
Probab=23.77 E-value=1.7e+02 Score=23.77 Aligned_cols=15 Identities=20% Similarity=0.510 Sum_probs=7.0
Q ss_pred HHHHHHHHHHHHHHH
Q 023564 204 DQVARLKAEIESLHA 218 (280)
Q Consensus 204 ~~~~~Lk~El~~L~~ 218 (280)
.++..|+++|..|..
T Consensus 26 ~Qi~~Lq~ql~~l~~ 40 (106)
T PF14282_consen 26 KQIKQLQEQLQELSQ 40 (106)
T ss_pred HHHHHHHHHHHHHHc
Confidence 334455555544433
No 259
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=23.74 E-value=1e+02 Score=26.02 Aligned_cols=50 Identities=18% Similarity=0.208 Sum_probs=43.3
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
|-.+=++.+++++.. +.....++|+.||++.-.+..=++=|+.-|+|.+.
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 445667888999754 88999999999999999999999999999999865
No 260
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=23.64 E-value=50 Score=23.18 Aligned_cols=26 Identities=27% Similarity=0.351 Sum_probs=21.9
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhh
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEG 177 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEg 177 (280)
+.|.++|+.+++..+.|+.+..-.-|
T Consensus 2 ~~~~~la~~~~~s~~~l~~~f~~~~~ 27 (84)
T smart00342 2 LTLEDLAEALGMSPRHLQRLFKKETG 27 (84)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHhC
Confidence 57899999999999999998875533
No 261
>PRK10434 srlR DNA-bindng transcriptional repressor SrlR; Provisional
Probab=23.00 E-value=89 Score=28.76 Aligned_cols=44 Identities=20% Similarity=0.324 Sum_probs=34.1
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
+.+++++ ..+.+.+.++|+.|+|+.--|.-=++.||.-|+|.|.
T Consensus 9 ~Il~~L~--~~~~v~v~eLa~~l~VS~~TIRRDL~~Le~~g~l~r~ 52 (256)
T PRK10434 9 AILEYLQ--KQGKTSVEELAQYFDTTGTTIRKDLVILEHAGTVIRT 52 (256)
T ss_pred HHHHHHH--HcCCEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEE
Confidence 4555665 3577999999999999765554447789999999887
No 262
>PRK09462 fur ferric uptake regulator; Provisional
Probab=22.96 E-value=1.2e+02 Score=25.48 Aligned_cols=47 Identities=15% Similarity=0.373 Sum_probs=38.2
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhc-----ccceehhhhhhhhhhcccccccc
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLE-----VQKRRIYDITNVLEGIGLIEKTS 185 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~-----VqKRRIYDItNVLEgIGLIeK~~ 185 (280)
..++++.+.+++.++..++-+.|. +.+=-+|-+++.|+..|||.+..
T Consensus 21 ~Il~~l~~~~~~h~sa~eI~~~l~~~~~~i~~aTVYR~L~~L~e~Gli~~~~ 72 (148)
T PRK09462 21 KILEVLQEPDNHHVSAEDLYKRLIDMGEEIGLATVYRVLNQFDDAGIVTRHN 72 (148)
T ss_pred HHHHHHHhCCCCCCCHHHHHHHHHhhCCCCCHHHHHHHHHHHHHCCCEEEEE
Confidence 356677666667888888888884 57788999999999999999864
No 263
>PF03962 Mnd1: Mnd1 family; InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae (Baker's yeast). The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair [].
Probab=22.71 E-value=4.4e+02 Score=23.53 Aligned_cols=32 Identities=22% Similarity=0.385 Sum_probs=21.0
Q ss_pred hcccceehhhhhhhhhhcccc--ccccCCceEEe
Q 023564 161 LEVQKRRIYDITNVLEGIGLI--EKTSKNHIRWK 192 (280)
Q Consensus 161 L~VqKRRIYDItNVLEgIGLI--eK~~KN~i~W~ 192 (280)
=||.-=-+=||+.-|-.=||| +|.+-..|.|-
T Consensus 25 ~gI~~~~VKdvlq~LvDDglV~~EKiGssn~YWs 58 (188)
T PF03962_consen 25 KGIVSMSVKDVLQSLVDDGLVHVEKIGSSNYYWS 58 (188)
T ss_pred cCCchhhHHHHHHHHhccccchhhhccCeeEEEe
Confidence 344444455666666555554 69999999995
No 264
>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=22.66 E-value=1.3e+02 Score=23.76 Aligned_cols=28 Identities=25% Similarity=0.385 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 207 ARLKAEIESLHAEECRIDDSIREKQELI 234 (280)
Q Consensus 207 ~~Lk~El~~L~~eE~~LD~~I~~~~~~L 234 (280)
..|.++++.|.++...++..|......+
T Consensus 3 ~~l~~~~~~L~~~~~~l~~~i~~~~~~l 30 (83)
T PF07061_consen 3 ESLEAEIQELKEQIEQLEKEISELEAEL 30 (83)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4566777777777777777777666553
No 265
>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=22.65 E-value=2.8e+02 Score=19.62 Aligned_cols=26 Identities=19% Similarity=0.243 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 212 EIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 212 El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
.+..|..+-..|......+.+++..|
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 34444444444444444444444443
No 266
>PF08657 DASH_Spc34: DASH complex subunit Spc34 ; InterPro: IPR013966 The DASH complex is a ~10 subunit microtubule-binding complex that is transferred to the kinetochore prior to mitosis []. In Saccharomyces cerevisiae (Baker's yeast) DASH forms both rings and spiral structures on microtubules in vitro [, ]. Components of the DASH complex, including Dam1, Duo1, Spc34, Dad1 and Ask1, are essential and connect the centromere to the plus end of spindle microtubules [].
Probab=22.45 E-value=2.5e+02 Score=26.69 Aligned_cols=40 Identities=10% Similarity=0.290 Sum_probs=33.9
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023564 201 KLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (280)
Q Consensus 201 ~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted 240 (280)
+..+++..|+.+-..|...-..|...|.+.+.+|..+...
T Consensus 177 ga~eki~~Lr~~y~~l~~~i~~lE~~VaeQ~~qL~~~n~~ 216 (259)
T PF08657_consen 177 GAREKIAALRQRYNQLSNSIAYLEAEVAEQEAQLERMNRS 216 (259)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3567788999999999999999999999999999988543
No 267
>COG2186 FadR Transcriptional regulators [Transcription]
Probab=22.43 E-value=57 Score=29.74 Aligned_cols=56 Identities=20% Similarity=0.216 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHhC---CCCce-eHHHHHHHhcccceehhhhhhhhhhccccccc-cCCceE
Q 023564 135 LLTRKFINLIQEA---KDGTL-DLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT-SKNHIR 190 (280)
Q Consensus 135 lLTkkFI~ll~~a---~~g~l-dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~-~KN~i~ 190 (280)
.+..++..++... ++..+ .=.++|++|||+|--+=+.+-+||..|||+-. +...|.
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 3445566666433 44444 57899999999999999999999999999955 344443
No 268
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=22.43 E-value=89 Score=29.75 Aligned_cols=39 Identities=13% Similarity=0.094 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhh
Q 023564 135 LLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 135 lLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItN 173 (280)
.+..++++++.+.....+++.++|..+++++|.++-+..
T Consensus 142 ~~~~~v~~yI~~~~~~~lsl~~lA~~~g~S~~~L~R~Fk 180 (274)
T PRK09978 142 NMRTRVCTVINNNIAHEWTLARIASELLMSPSLLKKKLR 180 (274)
T ss_pred HHHHHHHHHHHhcccCCCCHHHHHHHHCcCHHHHHHHHH
Confidence 356789999999999999999999999999998877664
No 269
>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=22.40 E-value=1.5e+02 Score=24.64 Aligned_cols=41 Identities=20% Similarity=0.161 Sum_probs=35.3
Q ss_pred ceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEe
Q 023564 151 TLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWK 192 (280)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~ 192 (280)
.+.-.++|+.||+.|.-+.-+++-|+.-|+|+... ++|...
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 35789999999999999999999999999998874 456554
No 270
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=22.30 E-value=94 Score=24.01 Aligned_cols=24 Identities=42% Similarity=0.645 Sum_probs=18.8
Q ss_pred CchhHHHHHHHHHHHHHHHHHHHH
Q 023564 199 TSKLDDQVARLKAEIESLHAEECR 222 (280)
Q Consensus 199 ~~~~~~~~~~Lk~El~~L~~eE~~ 222 (280)
.+++++.+..||+||+.|+.+-..
T Consensus 27 V~El~eRIalLq~EIeRlkAe~~k 50 (65)
T COG5509 27 VAELEERIALLQAEIERLKAELAK 50 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 457788899999999998776544
No 271
>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=22.10 E-value=2.2e+02 Score=22.79 Aligned_cols=35 Identities=14% Similarity=0.318 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 203 ~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
-.++..+.++|..|+.-=..||+..+.+..+++.|
T Consensus 65 l~~Id~Ie~~V~~LE~~v~~LD~ysk~LE~k~k~l 99 (99)
T PF10046_consen 65 LQQIDQIEEQVTELEQTVYELDEYSKELESKFKKL 99 (99)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 34455566677777777777888877777776643
No 272
>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=22.04 E-value=4.4e+02 Score=21.53 Aligned_cols=86 Identities=15% Similarity=0.154 Sum_probs=0.0
Q ss_pred eeHHHHHHHhcccceehhhhhhhhhhccccc--cccCCceEEe----------------------------cCCCCCCch
Q 023564 152 LDLNRTAEVLEVQKRRIYDITNVLEGIGLIE--KTSKNHIRWK----------------------------GSDSLGTSK 201 (280)
Q Consensus 152 ldLn~aA~~L~VqKRRIYDItNVLEgIGLIe--K~~KN~i~W~----------------------------G~~~s~~~~ 201 (280)
+.+.++|+.+||+.+-|- -.|..|||. +...|.|+|- .........
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 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEENE 241 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted~ 241 (280)
.....+.|+..++.|+.+-++|......+...+.....+.
T Consensus 77 ~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~~~ 116 (126)
T cd04785 77 CAEADAIARAHLADVRARIADLRRLEAELKRMVAACSGGR 116 (126)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCCC
No 273
>PRK10141 DNA-binding transcriptional repressor ArsR; Provisional
Probab=21.98 E-value=4.1e+02 Score=22.14 Aligned_cols=51 Identities=18% Similarity=0.249 Sum_probs=39.6
Q ss_pred HHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEE
Q 023564 139 KFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRW 191 (280)
Q Consensus 139 kFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W 191 (280)
+.+.++.. .+.+.+.++|+.|++.+=.+-==+.||+..|||+........|
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 34555543 3458899999999999999999999999999998666554444
No 274
>PRK00118 putative DNA-binding protein; Validated
Probab=21.91 E-value=49 Score=27.31 Aligned_cols=34 Identities=29% Similarity=0.391 Sum_probs=28.1
Q ss_pred ceeHHHHHHHhcccceehhhhhh--------hhhhccccccc
Q 023564 151 TLDLNRTAEVLEVQKRRIYDITN--------VLEGIGLIEKT 184 (280)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItN--------VLEgIGLIeK~ 184 (280)
-....++|+.+|+++..+|..+. .++.+|++++.
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 77778887765
No 275
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=21.80 E-value=1.1e+02 Score=26.24 Aligned_cols=42 Identities=17% Similarity=0.203 Sum_probs=31.0
Q ss_pred HHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 143 LIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 143 ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
++-..++..+.+.++|+.+++.+.-+.=|+..|.--|||+-.
T Consensus 16 ~LA~~~~~~~s~~eIA~~~~is~~~L~kIl~~L~~aGlv~S~ 57 (153)
T PRK11920 16 YCAANDGKLSRIPEIARAYGVSELFLFKILQPLVEAGLVETV 57 (153)
T ss_pred HHHhCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHCCCEEee
Confidence 444456667888999999988887777777777777777643
No 276
>PF15358 TSKS: Testis-specific serine kinase substrate
Probab=21.73 E-value=1.6e+02 Score=30.51 Aligned_cols=65 Identities=29% Similarity=0.458 Sum_probs=39.1
Q ss_pred hhhhhhhhc--cccccccCCceEEecCCCCCCchhHHHHHHHHHHHHH----H---HHHHHHHHHHHHHHHHHHHHhhh
Q 023564 170 DITNVLEGI--GLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIES----L---HAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 170 DItNVLEgI--GLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~----L---~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
||+.+|+|+ ||+ ..|++|.=.-.. ...+.++++.||.|..- | .++-.+|+..-..+.+..+.+++
T Consensus 108 Di~~~l~gvnSGLv--rAKDSItSlKek---t~~vnQHVq~LQseCsvlsEnLErrrQEaeELEgyCsqLk~nCrkVt~ 181 (558)
T PF15358_consen 108 DITELLEGVNSGLV--RAKDSITSLKEK---TSRVNQHVQTLQSECSVLSENLERRRQEAEELEGYCSQLKENCRKVTR 181 (558)
T ss_pred cHHHHHhhhcccce--ecccchhhHHHh---hHHHHHHHHHHHHHhHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhh
Confidence 677777776 677 557766543211 23577888888887533 2 34445566666666666665554
No 277
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=21.68 E-value=4.2e+02 Score=21.16 Aligned_cols=27 Identities=22% Similarity=0.306 Sum_probs=20.2
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhcccccc
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIEK 183 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIeK 183 (280)
.+.++|+.+||+.+-|.-. |-.|+|..
T Consensus 2 ~i~eva~~~gvs~~tlR~y----e~~Gll~p 28 (108)
T cd04773 2 TIGELAHLLGVPPSTLRHW----EKEGLLSP 28 (108)
T ss_pred CHHHHHHHHCcCHHHHHHH----HHCCCCCC
Confidence 5788999999988866544 56677754
No 278
>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=21.60 E-value=1.9e+02 Score=29.17 Aligned_cols=39 Identities=15% Similarity=0.180 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 023564 202 LDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEEN 240 (280)
Q Consensus 202 ~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lted 240 (280)
+..++..+..++.+|..+.++|++.|..++++|..+...
T Consensus 136 ~~~~~~~~~~~~~~~~~~~~~~~~~l~~l~~~l~~l~~~ 174 (525)
T TIGR02231 136 NGSEIERLLTEDREAERRIRELEKQLSELQNELNALLTG 174 (525)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccC
Confidence 345566777788888888888888888888888888753
No 279
>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=21.49 E-value=2.1e+02 Score=27.50 Aligned_cols=29 Identities=24% Similarity=0.345 Sum_probs=14.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 206 VARLKAEIESLHAEECRIDDSIREKQELI 234 (280)
Q Consensus 206 ~~~Lk~El~~L~~eE~~LD~~I~~~~~~L 234 (280)
+..+++|++.|+.+|.+|-+.+..+.++-
T Consensus 45 ~~~~~~el~~le~Ee~~l~~eL~~LE~e~ 73 (314)
T PF04111_consen 45 IEELEEELEKLEQEEEELLQELEELEKER 73 (314)
T ss_dssp -HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555555555555555555444433
No 280
>COG1349 GlpR Transcriptional regulators of sugar metabolism [Transcription / Carbohydrate transport and metabolism]
Probab=21.46 E-value=1.1e+02 Score=28.21 Aligned_cols=45 Identities=27% Similarity=0.438 Sum_probs=38.2
Q ss_pred HHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccc
Q 023564 138 RKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKT 184 (280)
Q Consensus 138 kkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~ 184 (280)
++-+++++ ..|.+.+.++|+.|+|+.=-|.-=+|.||.=|++.|.
T Consensus 8 ~~Il~~l~--~~g~v~v~eLa~~~~VS~~TIRRDL~~Le~~g~l~R~ 52 (253)
T COG1349 8 QKILELLK--EKGKVSVEELAELFGVSEMTIRRDLNELEEQGLLLRV 52 (253)
T ss_pred HHHHHHHH--HcCcEEHHHHHHHhCCCHHHHHHhHHHHHHCCcEEEE
Confidence 45677776 4799999999999999877777678999999999997
No 281
>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=21.38 E-value=86 Score=32.54 Aligned_cols=31 Identities=19% Similarity=0.385 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 203 DDQVARLKAEIESLHAEECRIDDSIREKQEL 233 (280)
Q Consensus 203 ~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~ 233 (280)
.+++++|++||++|+++-.+|++.|....++
T Consensus 30 ~qkie~L~kql~~Lk~q~~~l~~~v~k~e~~ 60 (489)
T PF11853_consen 30 LQKIEALKKQLEELKAQQDDLNDRVDKVEKH 60 (489)
T ss_pred HHHHHHHHHHHHHHHHhhcccccccchhhHh
Confidence 3478899999999998888888888765553
No 282
>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=21.06 E-value=3.3e+02 Score=22.98 Aligned_cols=81 Identities=21% Similarity=0.301 Sum_probs=0.0
Q ss_pred eeHHHHHHHhcccce--ehhhhhhhhhhccccccccCCceEE----------------ecCCCCCCchhHHHHHHHHHH-
Q 023564 152 LDLNRTAEVLEVQKR--RIYDITNVLEGIGLIEKTSKNHIRW----------------KGSDSLGTSKLDDQVARLKAE- 212 (280)
Q Consensus 152 ldLn~aA~~L~VqKR--RIYDItNVLEgIGLIeK~~KN~i~W----------------~G~~~s~~~~~~~~~~~Lk~E- 212 (280)
+.+.++|+.+||..+ |.|+=..+|.. .+...|.-.| .|+. -.++..-+..+..+
T Consensus 2 ~~I~EvA~~~Gvs~~tLRyYE~~GLl~p----~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~s---l~eI~~~l~~~~~~~ 74 (139)
T cd01110 2 LSVGEVAKRSGVAVSALHFYEQKGLIAS----WRNAGNQRRYPRDVLRRIAFIKVAQRLGLS---LAEIAEALATLPEDR 74 (139)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCC----CcCCCCCeEECHHHHHHHHHHHHHHHcCCC---HHHHHHHHHHhccCC
Q ss_pred -------HHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 213 -------IESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 213 -------l~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
.+-+......|++.|.++++.+..|.+
T Consensus 75 ~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~ 108 (139)
T cd01110 75 TPTKADWERLSRAWRDRLDERIAELQQLRDQLDG 108 (139)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 283
>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=20.86 E-value=2.6e+02 Score=30.62 Aligned_cols=103 Identities=17% Similarity=0.216 Sum_probs=55.4
Q ss_pred HHHHHHHHHHHHHhCCCCceeHHHHHHHhcccceehhhhhhhhhhccccccccCCceEEecCCCCCC----chhHHHHHH
Q 023564 133 LGLLTRKFINLIQEAKDGTLDLNRTAEVLEVQKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGT----SKLDDQVAR 208 (280)
Q Consensus 133 LglLTkkFI~ll~~a~~g~ldLn~aA~~L~VqKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~----~~~~~~~~~ 208 (280)
|.....+|++-|+.--.|.-||...++.+.+.==+|-.--..|..+---.-.-+..+.|........ .........
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 4456678888888878888999999988887544442222222221112223366788843221110 111222345
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 023564 209 LKAEIESLHAEECRIDDSIREKQELIR 235 (280)
Q Consensus 209 Lk~El~~L~~eE~~LD~~I~~~~~~L~ 235 (280)
|+.+++.|..+...|+..+..|+++|+
T Consensus 594 l~eelE~le~eK~~Le~~L~~~~d~lE 620 (769)
T PF05911_consen 594 LEEELEKLESEKEELEMELASCQDQLE 620 (769)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566666666555555554444444443
No 284
>PHA02047 phage lambda Rz1-like protein
Probab=20.84 E-value=85 Score=26.21 Aligned_cols=8 Identities=25% Similarity=0.111 Sum_probs=4.8
Q ss_pred ceEEecCC
Q 023564 188 HIRWKGSD 195 (280)
Q Consensus 188 ~i~W~G~~ 195 (280)
.|+|.|..
T Consensus 25 ~~r~~g~~ 32 (101)
T PHA02047 25 SYRALGIA 32 (101)
T ss_pred HHHHHHHH
Confidence 36777744
No 285
>PRK05771 V-type ATP synthase subunit I; Validated
Probab=20.70 E-value=3.3e+02 Score=28.43 Aligned_cols=57 Identities=12% Similarity=0.240 Sum_probs=0.0
Q ss_pred hhhhhhhhccccccccCCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 023564 170 DITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTL 237 (280)
Q Consensus 170 DItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~L 237 (280)
++..+|+..|+-+-. ... .+...+.++++++++++++.+.+++++.++++.+....+
T Consensus 192 ~~~~~l~~~~f~~~~---------~p~--~~~p~~~l~~l~~~l~~l~~~~~~~~~~l~~~~~~~~~~ 248 (646)
T PRK05771 192 EVEEELKKLGFERLE---------LEE--EGTPSELIREIKEELEEIEKERESLLEELKELAKKYLEE 248 (646)
T ss_pred HHHHHHHHCCCEEec---------CCC--CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 286
>PRK03578 hscB co-chaperone HscB; Provisional
Probab=20.65 E-value=6e+02 Score=22.50 Aligned_cols=51 Identities=20% Similarity=0.233 Sum_probs=35.4
Q ss_pred CCCCcHHHHHHHHHHHHH-hCCCCc---------------eeHHHHHHHhcc-cceehhhhhhhhhhccc
Q 023564 128 RYDSSLGLLTRKFINLIQ-EAKDGT---------------LDLNRTAEVLEV-QKRRIYDITNVLEGIGL 180 (280)
Q Consensus 128 R~d~SLglLTkkFI~ll~-~a~~g~---------------ldLn~aA~~L~V-qKRRIYDItNVLEgIGL 180 (280)
.++-+...|.++|..+.. -.||.. -.||.|=.+|.- .+|..|++ .|.|+.+
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 456677889999998874 345532 356777777776 57889987 5557665
No 287
>PRK09343 prefoldin subunit beta; Provisional
Probab=20.35 E-value=2.2e+02 Score=23.66 Aligned_cols=33 Identities=18% Similarity=0.282 Sum_probs=22.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 207 ARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 207 ~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
..|...++.++..-..|+.....++.++.++-.
T Consensus 74 ~~l~~r~E~ie~~ik~lekq~~~l~~~l~e~q~ 106 (121)
T PRK09343 74 KELKERKELLELRSRTLEKQEKKLREKLKELQA 106 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455566666777777777777777777776643
No 288
>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=20.25 E-value=1.6e+02 Score=23.78 Aligned_cols=26 Identities=23% Similarity=0.298 Sum_probs=15.1
Q ss_pred eHHHHHHHhcccceehhhhhhhhhhccccc
Q 023564 153 DLNRTAEVLEVQKRRIYDITNVLEGIGLIE 182 (280)
Q Consensus 153 dLn~aA~~L~VqKRRIYDItNVLEgIGLIe 182 (280)
.+.++|+.+||+.+-| --.|.+|||.
T Consensus 2 ~ige~a~~~gvs~~tL----ryYe~~GLi~ 27 (116)
T cd04769 2 YIGELAQQTGVTIKAI----RLYEEKGLLP 27 (116)
T ss_pred CHHHHHHHHCcCHHHH----HHHHHCCCCC
Confidence 4566777777766532 2335566664
No 289
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 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 []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.
Probab=20.20 E-value=3.1e+02 Score=24.21 Aligned_cols=37 Identities=22% Similarity=0.445 Sum_probs=25.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 023564 203 DDQVARLKAEIESLHAEECRIDDSIREKQELIRTLEE 239 (280)
Q Consensus 203 ~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lte 239 (280)
...+..|+.++..|..+-..|++.|+.....+..|.+
T Consensus 115 ~~~l~~l~~~~~~L~~~~~~l~~~l~ek~k~~e~l~D 151 (194)
T PF08614_consen 115 ERRLAELEAELAQLEEKIKDLEEELKEKNKANEILQD 151 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456677777777777777777777777666666654
No 290
>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=20.16 E-value=55 Score=22.24 Aligned_cols=23 Identities=30% Similarity=0.354 Sum_probs=18.5
Q ss_pred ceeHHHHHHHhcccceehhhhhh
Q 023564 151 TLDLNRTAEVLEVQKRRIYDITN 173 (280)
Q Consensus 151 ~ldLn~aA~~L~VqKRRIYDItN 173 (280)
-++..++|+.+||.+..|+.|.|
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 291
>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=20.05 E-value=2.8e+02 Score=21.92 Aligned_cols=68 Identities=18% Similarity=0.249 Sum_probs=41.9
Q ss_pred cceehhhhhhhhhhccccccccCCceEEecCCCCCCchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 023564 164 QKRRIYDITNVLEGIGLIEKTSKNHIRWKGSDSLGTSKLDDQVARLKAEIESLHAEECRIDDSIREKQELIRTLE 238 (280)
Q Consensus 164 qKRRIYDItNVLEgIGLIeK~~KN~i~W~G~~~s~~~~~~~~~~~Lk~El~~L~~eE~~LD~~I~~~~~~L~~Lt 238 (280)
-+=+|.|.-.||=.|| -|.|-+...+.. -..+..++..|++.++.|..+-..+...|..+.+.|..+.
T Consensus 51 v~g~i~~~~~vlV~lG------~~~~vE~s~~eA-~~~l~~r~~~l~~~~~~l~~~~~~~~~~~~~~~~~l~~~~ 118 (120)
T PF02996_consen 51 VPGKIPDTDKVLVSLG------AGYYVEMSLEEA-IEFLKKRIKELEEQLEKLEKELAELQAQIEQLEQTLQQLY 118 (120)
T ss_dssp EEEE-SSTTEEEEEEE------TTEEEEEEHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH
T ss_pred EEEEeCCCCEEEEEee------CCeEEEecHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4555666666666666 455666544311 1234556677777777777777777777777777776653
Done!