Query 046691
Match_columns 222
No_of_seqs 32 out of 34
Neff 3.0
Searched_HMMs 46136
Date Fri Mar 29 03:30:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/046691.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/046691hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF00627 UBA: UBA/TS-N domain; 98.6 6.8E-08 1.5E-12 62.3 3.4 34 184-217 4-37 (37)
2 cd00194 UBA Ubiquitin Associat 98.5 1.2E-07 2.5E-12 60.4 3.9 35 185-219 4-38 (38)
3 smart00165 UBA Ubiquitin assoc 98.5 1.7E-07 3.6E-12 59.5 3.7 34 185-218 4-37 (37)
4 KOG0011 Nucleotide excision re 97.6 0.00017 3.7E-09 67.5 7.2 42 144-185 131-172 (340)
5 PF00627 UBA: UBA/TS-N domain; 97.6 0.00014 3.1E-09 46.8 4.5 35 149-183 3-37 (37)
6 cd00194 UBA Ubiquitin Associat 97.5 0.00022 4.9E-09 45.2 4.6 36 149-184 2-37 (38)
7 COG5207 UBP14 Isopeptidase T [ 97.5 0.00011 2.4E-09 73.0 4.4 70 150-219 560-658 (749)
8 KOG0944 Ubiquitin-specific pro 97.3 0.00037 8E-09 70.5 6.3 72 149-220 572-673 (763)
9 smart00165 UBA Ubiquitin assoc 97.3 0.00045 9.8E-09 43.7 4.5 35 149-183 2-36 (37)
10 KOG2561 Adaptor protein NUB1, 97.0 0.0032 7E-08 61.9 9.0 73 148-220 374-467 (568)
11 KOG2561 Adaptor protein NUB1, 97.0 0.0017 3.7E-08 63.7 7.0 71 148-218 303-411 (568)
12 TIGR00601 rad23 UV excision re 96.8 0.0014 3E-08 61.6 4.1 44 147-197 155-198 (378)
13 smart00546 CUE Domain that may 96.7 0.0032 6.9E-08 41.5 4.0 37 184-221 4-43 (43)
14 TIGR00601 rad23 UV excision re 95.9 0.01 2.3E-07 55.9 4.5 40 181-220 155-194 (378)
15 PF02845 CUE: CUE domain; Int 95.6 0.01 2.2E-07 39.1 2.5 35 186-220 5-41 (42)
16 PRK00117 recX recombination re 94.2 0.26 5.7E-06 39.6 7.5 70 149-218 29-114 (157)
17 PF09288 UBA_3: Fungal ubiquit 91.1 0.23 5E-06 36.2 2.8 25 150-174 11-35 (55)
18 PF08938 HBS1_N: HBS1 N-termin 90.9 0.15 3.3E-06 37.9 1.9 27 195-221 45-71 (79)
19 PF09288 UBA_3: Fungal ubiquit 90.0 0.33 7.1E-06 35.4 2.9 32 187-218 14-54 (55)
20 KOG0418 Ubiquitin-protein liga 86.6 0.73 1.6E-05 41.0 3.4 40 181-220 161-200 (200)
21 COG5207 UBP14 Isopeptidase T [ 86.1 0.79 1.7E-05 46.5 3.7 36 183-218 559-595 (749)
22 PRK14136 recX recombination re 84.7 3.8 8.2E-05 38.5 7.3 68 148-215 179-262 (309)
23 KOG0011 Nucleotide excision re 84.5 1.1 2.4E-05 42.7 3.7 39 182-220 135-173 (340)
24 PF14555 UBA_4: UBA-like domai 83.1 2.6 5.6E-05 27.9 4.1 38 177-220 2-39 (43)
25 PF02631 RecX: RecX family; I 83.0 4.4 9.5E-05 31.3 5.9 50 155-204 1-67 (121)
26 cd04777 HTH_MerR-like_sg1 Heli 82.9 2.6 5.7E-05 32.1 4.6 55 150-207 15-69 (107)
27 PF07223 DUF1421: Protein of u 82.2 1.1 2.5E-05 42.5 2.8 25 146-170 319-343 (358)
28 KOG0010 Ubiquitin-like protein 82.1 1.9 4E-05 42.9 4.4 44 177-220 449-493 (493)
29 PF06972 DUF1296: Protein of u 82.1 3.1 6.8E-05 30.9 4.5 38 182-220 8-45 (60)
30 PF09278 MerR-DNA-bind: MerR, 81.7 2.4 5.3E-05 29.1 3.7 34 181-215 2-35 (65)
31 cd04783 HTH_MerR1 Helix-Turn-H 81.6 2.8 6.1E-05 32.9 4.4 58 150-208 15-72 (126)
32 PRK14135 recX recombination re 81.5 6.6 0.00014 34.1 7.1 60 149-208 75-151 (263)
33 cd04784 HTH_CadR-PbrR Helix-Tu 80.3 3.7 8E-05 32.2 4.7 58 150-208 15-72 (127)
34 TIGR02051 MerR Hg(II)-responsi 80.2 3.7 8E-05 32.4 4.7 66 150-216 14-80 (124)
35 cd04785 HTH_CadR-PbrR-like Hel 80.0 3.7 8.1E-05 32.4 4.7 56 150-208 15-72 (126)
36 cd04765 HTH_MlrA-like_sg2 Heli 79.3 4.3 9.4E-05 31.2 4.7 68 148-217 13-85 (99)
37 cd04773 HTH_TioE_rpt2 Second H 79.3 4.2 9.2E-05 31.4 4.7 65 149-214 14-80 (108)
38 PF03474 DMA: DMRTA motif; In 79.1 1.9 4.2E-05 29.5 2.4 23 196-218 17-39 (39)
39 cd04769 HTH_MerR2 Helix-Turn-H 78.1 4.9 0.00011 31.2 4.7 59 149-209 14-72 (116)
40 PF08784 RPA_C: Replication pr 77.6 0.64 1.4E-05 35.0 -0.3 48 172-220 45-92 (102)
41 PRK13752 putative transcriptio 77.1 4.5 9.9E-05 33.2 4.5 59 150-209 22-80 (144)
42 PF12244 DUF3606: Protein of u 76.4 6.8 0.00015 27.9 4.7 39 146-184 16-56 (57)
43 cd01111 HTH_MerD Helix-Turn-He 76.3 4.1 8.9E-05 31.7 3.9 60 150-210 15-74 (107)
44 cd04788 HTH_NolA-AlbR Helix-Tu 75.4 5.9 0.00013 29.9 4.4 57 150-209 15-73 (96)
45 PRK13749 transcriptional regul 75.0 4.3 9.4E-05 32.9 3.8 59 150-209 18-76 (121)
46 PRK14134 recX recombination re 75.0 14 0.0003 33.5 7.4 62 148-209 78-154 (283)
47 cd04776 HTH_GnyR Helix-Turn-He 74.7 6.3 0.00014 31.1 4.6 57 150-209 15-71 (118)
48 PF08587 UBA_2: Ubiquitin asso 74.3 0.64 1.4E-05 32.8 -1.0 43 148-191 2-45 (46)
49 COG2137 OraA Uncharacterized p 74.0 12 0.00027 32.1 6.5 71 148-218 37-125 (174)
50 PLN03196 MOC1-like protein; Pr 73.6 8.2 0.00018 37.5 5.9 24 149-172 233-256 (487)
51 KOG2689 Predicted ubiquitin re 73.2 4.2 9E-05 38.1 3.7 33 152-184 4-37 (290)
52 PRK14137 recX recombination re 73.2 17 0.00037 31.5 7.3 70 148-217 57-141 (195)
53 cd01109 HTH_YyaN Helix-Turn-He 73.1 7 0.00015 30.1 4.4 58 149-207 14-71 (113)
54 PRK10227 DNA-binding transcrip 73.1 7.5 0.00016 31.5 4.8 58 150-208 15-72 (135)
55 cd04770 HTH_HMRTR Helix-Turn-H 72.8 8 0.00017 30.0 4.7 58 150-208 15-72 (123)
56 cd04787 HTH_HMRTR_unk Helix-Tu 72.7 6.7 0.00015 31.2 4.3 58 151-209 16-73 (133)
57 cd04768 HTH_BmrR-like Helix-Tu 71.8 6.5 0.00014 29.7 3.9 57 150-207 15-71 (96)
58 PRK00117 recX recombination re 71.8 19 0.0004 29.0 6.7 61 148-208 78-155 (157)
59 TIGR01950 SoxR redox-sensitive 71.8 8.4 0.00018 31.6 4.8 57 149-207 15-71 (142)
60 PF02536 mTERF: mTERF; InterP 71.6 10 0.00022 33.4 5.6 61 147-207 174-268 (345)
61 PF11626 Rap1_C: TRF2-interact 70.8 4 8.6E-05 30.7 2.5 31 189-219 4-34 (87)
62 PRK14135 recX recombination re 69.9 26 0.00057 30.4 7.7 60 148-207 125-203 (263)
63 cd01105 HTH_GlnR-like Helix-Tu 69.3 12 0.00026 27.9 4.8 68 149-220 15-84 (88)
64 PF02536 mTERF: mTERF; InterP 68.7 2.2 4.9E-05 37.5 0.9 55 149-206 140-199 (345)
65 cd01282 HTH_MerR-like_sg3 Heli 68.5 10 0.00022 29.5 4.4 57 150-208 15-71 (112)
66 TIGR02044 CueR Cu(I)-responsiv 68.3 12 0.00025 29.6 4.8 58 149-207 14-71 (127)
67 cd04786 HTH_MerR-like_sg7 Heli 68.1 11 0.00024 30.4 4.7 56 150-206 15-70 (131)
68 PRK14136 recX recombination re 67.7 15 0.00033 34.6 6.1 62 149-210 229-306 (309)
69 COG0789 SoxR Predicted transcr 67.5 11 0.00023 28.6 4.3 34 178-211 42-75 (124)
70 cd01107 HTH_BmrR Helix-Turn-He 66.2 11 0.00023 29.1 4.1 57 151-208 16-73 (108)
71 TIGR02047 CadR-PbrR Cd(II)/Pb( 66.2 11 0.00024 29.9 4.3 58 150-208 15-72 (127)
72 TIGR02054 MerD mercuric resist 65.1 12 0.00026 30.1 4.4 59 150-209 18-76 (120)
73 PRK15002 redox-sensitivie tran 64.8 14 0.0003 30.9 4.8 56 149-206 25-80 (154)
74 KOG0944 Ubiquitin-specific pro 64.6 7.3 0.00016 40.5 3.7 67 148-218 539-608 (763)
75 PRK09514 zntR zinc-responsive 63.5 16 0.00035 29.6 4.8 56 150-206 16-71 (140)
76 cd04782 HTH_BltR Helix-Turn-He 63.2 17 0.00036 27.6 4.6 65 149-216 14-78 (97)
77 TIGR02043 ZntR Zn(II)-responsi 63.1 16 0.00035 29.1 4.8 56 150-206 16-71 (131)
78 cd01106 HTH_TipAL-Mta Helix-Tu 63.1 15 0.00033 27.7 4.4 57 150-207 15-71 (103)
79 PF15187 Augurin: Oesophageal 62.1 7.8 0.00017 32.0 2.7 29 175-203 24-71 (114)
80 cd04778 HTH_MerR-like_sg2 Heli 60.0 14 0.0003 32.5 4.1 64 150-215 16-81 (219)
81 smart00422 HTH_MERR helix_turn 59.8 20 0.00043 24.4 4.2 54 149-204 14-68 (70)
82 cd04781 HTH_MerR-like_sg6 Heli 59.1 19 0.0004 28.1 4.4 55 150-206 15-69 (120)
83 cd01108 HTH_CueR Helix-Turn-He 58.8 21 0.00045 28.2 4.6 58 150-208 15-72 (127)
84 smart00299 CLH Clathrin heavy 56.5 88 0.0019 23.9 7.8 10 175-184 55-64 (140)
85 cd01392 HTH_LacI Helix-turn-he 56.3 36 0.00079 22.0 4.8 45 157-203 6-50 (52)
86 cd04790 HTH_Cfa-like_unk Helix 55.2 21 0.00045 30.0 4.3 58 150-208 16-73 (172)
87 COG4598 HisP ABC-type histidin 53.8 6 0.00013 36.2 0.9 50 162-211 160-231 (256)
88 PF02631 RecX: RecX family; I 53.5 23 0.00049 27.3 4.0 55 150-205 47-118 (121)
89 PLN03196 MOC1-like protein; Pr 52.9 43 0.00094 32.6 6.6 56 147-204 123-182 (487)
90 PRK06369 nac nascent polypepti 52.6 13 0.00027 30.6 2.5 43 157-219 72-114 (115)
91 TIGR00264 alpha-NAC-related pr 51.6 13 0.00029 30.6 2.5 39 159-217 76-114 (116)
92 PRK00116 ruvA Holliday junctio 50.1 55 0.0012 27.9 6.1 137 73-219 22-189 (192)
93 PRK10014 DNA-binding transcrip 50.1 31 0.00068 29.5 4.7 47 157-205 15-61 (342)
94 cd04775 HTH_Cfa-like Helix-Tur 49.7 32 0.00069 26.2 4.2 54 149-206 15-70 (102)
95 cd04764 HTH_MlrA-like_sg1 Heli 48.4 23 0.0005 24.4 3.0 50 148-203 13-66 (67)
96 PRK09492 treR trehalose repres 48.4 33 0.00072 29.0 4.5 47 157-205 13-59 (315)
97 COG0751 GlyS Glycyl-tRNA synth 47.3 84 0.0018 32.8 7.9 91 113-212 450-560 (691)
98 PRK10703 DNA-binding transcrip 47.1 41 0.00089 28.9 4.9 47 157-205 10-56 (341)
99 cd01110 HTH_SoxR Helix-Turn-He 46.9 21 0.00045 29.0 3.0 55 150-206 16-70 (139)
100 cd04780 HTH_MerR-like_sg5 Heli 45.7 53 0.0011 25.0 4.9 66 151-217 16-83 (95)
101 PF05402 PqqD: Coenzyme PQQ sy 45.6 86 0.0019 21.5 5.5 44 151-194 21-66 (68)
102 TIGR02405 trehalos_R_Ecol treh 44.9 43 0.00094 28.6 4.7 47 157-205 10-56 (311)
103 KOG1267 Mitochondrial transcri 44.6 32 0.00069 32.1 4.1 53 152-207 236-291 (413)
104 PF07499 RuvA_C: RuvA, C-termi 44.4 42 0.00091 22.6 3.7 21 151-171 6-26 (47)
105 smart00354 HTH_LACI helix_turn 43.8 67 0.0014 22.8 4.8 45 157-204 9-54 (70)
106 cd04750 Commd2 COMM_Domain con 43.3 1.5E+02 0.0032 24.9 7.6 61 152-212 6-84 (166)
107 cd08317 Death_ank Death domain 43.0 28 0.0006 25.7 2.9 30 189-218 22-52 (84)
108 cd08315 Death_TRAILR_DR4_DR5 D 42.8 32 0.00069 26.6 3.3 31 188-218 25-55 (96)
109 COG2137 OraA Uncharacterized p 42.5 58 0.0013 28.1 5.1 64 149-212 88-170 (174)
110 PF07499 RuvA_C: RuvA, C-termi 42.5 49 0.0011 22.3 3.8 33 186-218 7-43 (47)
111 cd04789 HTH_Cfa Helix-Turn-Hel 42.1 51 0.0011 25.2 4.3 50 150-203 16-67 (102)
112 PF13411 MerR_1: MerR HTH fami 41.3 26 0.00056 23.9 2.3 53 148-204 13-67 (69)
113 cd04767 HTH_HspR-like_MBC Heli 40.3 25 0.00055 28.6 2.5 60 149-214 15-78 (120)
114 KOG4000 Uncharacterized conser 39.9 46 0.001 31.2 4.4 63 56-118 208-279 (291)
115 PRK01233 glyS glycyl-tRNA synt 38.7 1.1E+02 0.0023 31.7 7.1 89 113-210 446-549 (682)
116 cd04779 HTH_MerR-like_sg4 Heli 38.4 70 0.0015 26.1 4.8 58 149-208 14-71 (134)
117 PF10440 WIYLD: Ubiquitin-bind 38.4 30 0.00065 25.9 2.4 29 182-210 11-43 (65)
118 cd04774 HTH_YfmP Helix-Turn-He 38.2 73 0.0016 24.3 4.6 58 148-207 13-71 (96)
119 KOG1071 Mitochondrial translat 38.1 29 0.00063 33.3 2.9 32 186-217 50-82 (340)
120 PRK14134 recX recombination re 37.2 1.3E+02 0.0027 27.4 6.7 58 149-206 128-206 (283)
121 smart00299 CLH Clathrin heavy 37.0 52 0.0011 25.2 3.6 34 150-184 87-120 (140)
122 cd08306 Death_FADD Fas-associa 36.6 1.6E+02 0.0035 22.1 6.2 52 157-208 22-74 (86)
123 PF13249 Prenyltrans_2: Prenyl 36.6 45 0.00098 24.1 3.1 55 164-219 28-103 (113)
124 PF14490 HHH_4: Helix-hairpin- 36.4 8.7 0.00019 29.0 -0.7 64 149-212 9-75 (94)
125 TIGR01926 peroxid_rel uncharac 36.4 1.1E+02 0.0024 24.5 5.6 50 156-206 90-157 (177)
126 cd00592 HTH_MerR-like Helix-Tu 36.3 88 0.0019 23.0 4.7 58 149-209 14-72 (100)
127 PRK09526 lacI lac repressor; R 36.3 71 0.0015 27.4 4.7 47 157-205 14-60 (342)
128 KOG0743 AAA+-type ATPase [Post 35.6 26 0.00056 34.8 2.2 70 147-219 350-429 (457)
129 PHA02591 hypothetical protein; 35.3 74 0.0016 25.2 4.2 31 151-184 51-81 (83)
130 cd01279 HTH_HspR-like Helix-Tu 34.7 49 0.0011 25.2 3.2 54 148-206 14-71 (98)
131 PLN02688 pyrroline-5-carboxyla 34.6 96 0.0021 26.4 5.2 54 164-217 182-240 (266)
132 PRK10727 DNA-binding transcrip 34.1 75 0.0016 27.5 4.6 47 157-205 10-56 (343)
133 PRK10423 transcriptional repre 33.9 88 0.0019 26.5 4.9 46 158-205 8-53 (327)
134 COG5270 PUA domain (predicted 33.4 32 0.00069 31.0 2.2 32 82-121 36-67 (202)
135 TIGR01481 ccpA catabolite cont 32.7 89 0.0019 26.6 4.7 47 157-205 10-56 (329)
136 PRK10401 DNA-binding transcrip 32.2 93 0.002 26.9 4.8 47 157-205 10-56 (346)
137 cd01104 HTH_MlrA-CarA Helix-Tu 32.2 53 0.0011 22.3 2.7 29 175-204 40-68 (68)
138 PRK14603 ruvA Holliday junctio 32.0 72 0.0016 27.7 4.1 52 72-123 21-78 (197)
139 PF10152 DUF2360: Predicted co 31.7 61 0.0013 26.8 3.5 31 147-177 111-144 (148)
140 PF02092 tRNA_synt_2f: Glycyl- 31.5 1.3E+02 0.0029 30.2 6.4 85 111-204 442-547 (548)
141 KOG1924 RhoA GTPase effector D 31.2 1.8E+02 0.004 31.6 7.5 16 195-210 714-729 (1102)
142 KOG0418 Ubiquitin-protein liga 31.1 63 0.0014 29.1 3.6 34 148-181 162-195 (200)
143 COG0023 SUI1 Translation initi 30.6 32 0.00069 27.9 1.6 26 169-200 77-102 (104)
144 PF08671 SinI: Anti-repressor 29.6 58 0.0013 21.0 2.4 25 180-204 3-27 (30)
145 PRK14604 ruvA Holliday junctio 29.4 85 0.0019 27.2 4.1 144 72-218 21-189 (195)
146 COG0325 Predicted enzyme with 29.1 1.1E+02 0.0025 27.8 5.0 56 157-213 34-105 (228)
147 PF03765 CRAL_TRIO_N: CRAL/TRI 28.6 1.3E+02 0.0027 20.2 4.1 43 177-219 2-54 (55)
148 PRK14987 gluconate operon tran 28.4 1E+02 0.0022 26.4 4.4 47 157-205 14-60 (331)
149 PRK15043 transcriptional regul 28.4 1E+02 0.0022 28.1 4.5 34 177-210 44-77 (243)
150 PRK14137 recX recombination re 28.3 2E+02 0.0044 25.0 6.3 56 150-205 106-178 (195)
151 PF12554 MOZART1: Mitotic-spin 28.2 1.6E+02 0.0035 20.8 4.6 33 152-184 11-45 (48)
152 PF14748 P5CR_dimer: Pyrroline 28.2 2.2E+02 0.0048 22.0 5.9 22 149-170 25-46 (107)
153 PRK12491 pyrroline-5-carboxyla 27.8 1.6E+02 0.0035 26.1 5.7 21 149-169 184-204 (272)
154 cd08319 Death_RAIDD Death doma 27.8 2.6E+02 0.0056 21.3 6.0 57 156-212 21-78 (83)
155 cd01105 HTH_GlnR-like Helix-Tu 27.2 1.4E+02 0.003 22.2 4.4 35 151-185 50-84 (88)
156 PRK00939 translation initiatio 27.2 40 0.00087 26.6 1.6 25 169-199 74-98 (99)
157 PF02954 HTH_8: Bacterial regu 26.9 32 0.00069 22.5 0.9 22 196-217 7-28 (42)
158 KOG4329 DNA-binding protein [G 26.8 39 0.00085 33.3 1.8 42 176-217 213-266 (445)
159 COG0632 RuvA Holliday junction 26.7 1.6E+02 0.0034 26.1 5.3 24 150-173 158-181 (201)
160 PRK05441 murQ N-acetylmuramic 26.7 1.7E+02 0.0037 26.6 5.8 28 190-217 271-298 (299)
161 cd08327 CARD_RAIDD Caspase act 26.0 2.2E+02 0.0048 22.2 5.5 59 147-209 22-92 (94)
162 TIGR00211 glyS glycyl-tRNA syn 25.9 3E+02 0.0064 28.7 7.8 99 112-219 450-574 (691)
163 PRK11303 DNA-binding transcrip 25.8 1.5E+02 0.0033 25.2 5.0 46 158-205 10-58 (328)
164 cd04772 HTH_TioE_rpt1 First He 25.7 1.5E+02 0.0032 22.6 4.4 67 148-218 13-82 (99)
165 PF14872 GHL5: Hypothetical gl 25.6 1.1E+02 0.0025 32.3 4.8 32 186-217 598-637 (811)
166 PRK07634 pyrroline-5-carboxyla 25.5 2E+02 0.0043 24.0 5.6 28 171-198 173-201 (245)
167 COG1308 EGD2 Transcription fac 25.1 62 0.0013 27.0 2.4 26 193-218 96-121 (122)
168 PRK14908 glycyl-tRNA synthetas 25.0 2.9E+02 0.0064 30.2 7.8 88 113-209 764-873 (1000)
169 PF00356 LacI: Bacterial regul 24.9 1.5E+02 0.0032 20.3 3.9 39 157-197 8-46 (46)
170 smart00733 Mterf Mitochondrial 24.9 83 0.0018 17.3 2.3 19 174-195 13-31 (31)
171 PRK14606 ruvA Holliday junctio 24.8 1.5E+02 0.0033 25.5 4.8 145 73-218 23-182 (188)
172 PF02662 FlpD: Methyl-viologen 24.8 34 0.00073 27.4 0.8 38 155-193 86-124 (124)
173 KOG1924 RhoA GTPase effector D 24.6 2.8E+02 0.006 30.4 7.4 10 160-169 713-722 (1102)
174 cd00474 SUI1_eIF1 The SUI1/eIF 24.5 44 0.00095 25.1 1.3 27 167-199 48-74 (77)
175 cd08306 Death_FADD Fas-associa 24.4 1E+02 0.0023 23.1 3.3 30 189-218 20-50 (86)
176 PRK14602 ruvA Holliday junctio 24.0 1.1E+02 0.0023 26.7 3.8 50 73-122 23-79 (203)
177 PRK07993 DNA polymerase III su 23.9 5.2E+02 0.011 23.9 8.4 40 146-185 166-207 (334)
178 TIGR01089 fucI L-fucose isomer 23.8 1.6E+02 0.0034 30.4 5.3 20 151-170 210-229 (587)
179 cd04763 HTH_MlrA-like Helix-Tu 23.8 1E+02 0.0022 21.3 3.0 53 148-203 13-67 (68)
180 cd08318 Death_NMPP84 Death dom 23.4 74 0.0016 23.9 2.3 30 189-218 25-54 (86)
181 PF04533 Herpes_U44: Herpes vi 23.2 91 0.002 28.2 3.2 12 151-162 36-47 (210)
182 PRK03980 flap endonuclease-1; 22.8 67 0.0015 29.4 2.4 28 175-207 250-277 (292)
183 PF05182 Fip1: Fip1 motif; In 22.8 77 0.0017 22.3 2.2 21 171-191 25-45 (45)
184 cd08317 Death_ank Death domain 22.8 2.6E+02 0.0056 20.6 5.1 51 157-207 24-75 (84)
185 PRK15081 glutathione ABC trans 22.6 2.8E+02 0.0061 25.2 6.3 57 146-203 30-91 (306)
186 PF13977 TetR_C_6: Bacterial t 22.5 2.3E+02 0.005 20.1 4.8 57 162-218 2-58 (115)
187 PF14490 HHH_4: Helix-hairpin- 22.5 1.1E+02 0.0024 23.0 3.2 38 178-215 4-41 (94)
188 PF00749 tRNA-synt_1c: tRNA sy 22.4 1.3E+02 0.0028 27.6 4.2 57 148-206 249-307 (314)
189 KOG1194 Predicted DNA-binding 22.3 1.2E+02 0.0026 30.8 4.2 43 175-219 140-182 (534)
190 PHA02591 hypothetical protein; 22.1 80 0.0017 25.0 2.4 22 183-204 49-70 (83)
191 TIGR00084 ruvA Holliday juncti 22.1 1.1E+02 0.0024 26.3 3.5 132 73-208 22-173 (191)
192 cd04766 HTH_HspR Helix-Turn-He 21.7 1.1E+02 0.0024 22.6 3.0 56 150-207 16-72 (91)
193 cd08316 Death_FAS_TNFRSF6 Deat 21.7 1E+02 0.0022 24.3 2.9 29 189-217 27-56 (97)
194 COG4154 FucU Fucose dissimilat 21.5 75 0.0016 27.3 2.3 34 185-218 13-58 (144)
195 PHA03364 hypothetical protein; 21.5 1.6E+02 0.0035 27.4 4.5 67 151-217 45-123 (264)
196 PF11239 DUF3040: Protein of u 21.5 66 0.0014 23.9 1.8 15 110-124 5-19 (82)
197 cd04785 HTH_CadR-PbrR-like Hel 21.4 2.4E+02 0.0052 22.2 5.0 59 151-209 49-115 (126)
198 COG3769 Predicted hydrolase (H 21.1 65 0.0014 30.1 2.0 67 148-219 126-201 (274)
199 cd08777 Death_RIP1 Death Domai 21.1 1.3E+02 0.0028 22.8 3.3 12 190-201 21-32 (86)
200 KOG4577 Transcription factor L 21.0 1.6E+02 0.0035 28.5 4.6 41 3-46 292-334 (383)
201 PF11219 DUF3014: Protein of u 20.9 1.2E+02 0.0025 26.2 3.3 28 186-220 78-105 (158)
202 PF11626 Rap1_C: TRF2-interact 20.9 1.5E+02 0.0033 22.1 3.6 35 152-186 1-35 (87)
203 cd08784 Death_DRs Death Domain 20.8 1.3E+02 0.0028 22.2 3.2 31 188-218 17-47 (79)
204 cd08316 Death_FAS_TNFRSF6 Deat 20.7 3.5E+02 0.0075 21.3 5.7 56 152-207 23-80 (97)
205 cd08804 Death_ank2 Death domai 20.2 1.2E+02 0.0025 22.9 2.9 29 189-217 22-51 (84)
206 PF15652 Tox-SHH: HNH/Endo VII 20.2 99 0.0022 25.1 2.6 31 175-205 64-94 (100)
207 PRK13342 recombination factor 20.1 2.5E+02 0.0053 26.2 5.5 51 152-202 253-309 (413)
No 1
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=98.55 E-value=6.8e-08 Score=62.26 Aligned_cols=34 Identities=29% Similarity=0.431 Sum_probs=30.4
Q ss_pred HHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHH
Q 046691 184 NGYTILREMGFSSNNVAEVLIMYENDTDKALAHL 217 (222)
Q Consensus 184 ~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~L 217 (222)
..+.+|++|||+.+.+.+||..|+||.|+|++.|
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 4578999999999999999999999999999976
No 2
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=98.52 E-value=1.2e-07 Score=60.41 Aligned_cols=35 Identities=31% Similarity=0.446 Sum_probs=32.5
Q ss_pred HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691 185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG 219 (222)
Q Consensus 185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs 219 (222)
.+++|.+|||+.+.+..||..|+||.++|++.|++
T Consensus 4 ~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~~ 38 (38)
T cd00194 4 KLEQLLEMGFSREEARKALRATNNNVERAVEWLLE 38 (38)
T ss_pred HHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHhC
Confidence 46899999999999999999999999999999874
No 3
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=98.47 E-value=1.7e-07 Score=59.51 Aligned_cols=34 Identities=29% Similarity=0.376 Sum_probs=31.8
Q ss_pred HHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691 185 GYTILREMGFSSNNVAEVLIMYENDTDKALAHLL 218 (222)
Q Consensus 185 ~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LL 218 (222)
.+++|.+|||+.+.+..||.+|+||.++|++.|+
T Consensus 4 ~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L~ 37 (37)
T smart00165 4 KIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37 (37)
T ss_pred HHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHC
Confidence 4689999999999999999999999999999885
No 4
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=97.60 E-value=0.00017 Score=67.52 Aligned_cols=42 Identities=29% Similarity=0.440 Sum_probs=37.0
Q ss_pred CCCCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691 144 VGSGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG 185 (222)
Q Consensus 144 ~~~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~ 185 (222)
.+...+-.|.++++||+.||.|.+|++.==.||+.++|||..
T Consensus 131 ~G~~~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl~ 172 (340)
T KOG0011|consen 131 VGSEYEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYLLN 172 (340)
T ss_pred ccchhHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHhc
Confidence 556678899999999999999999999766799999999754
No 5
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=97.58 E-value=0.00014 Score=46.77 Aligned_cols=35 Identities=17% Similarity=0.359 Sum_probs=31.9
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFA 183 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl 183 (222)
+..|.+|++|||+++.+..||..-+.|.+++.+||
T Consensus 3 ~~~v~~L~~mGf~~~~~~~AL~~~~~nve~A~~~L 37 (37)
T PF00627_consen 3 EEKVQQLMEMGFSREQAREALRACNGNVERAVDWL 37 (37)
T ss_dssp HHHHHHHHHHTS-HHHHHHHHHHTTTSHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHcCCCHHHHHHhC
Confidence 46799999999999999999999999999999986
No 6
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=97.49 E-value=0.00022 Score=45.22 Aligned_cols=36 Identities=17% Similarity=0.332 Sum_probs=33.1
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN 184 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~ 184 (222)
+..|.+|++|||++++|..||...+.|.+|+.+|+.
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~~~d~~~A~~~L~ 37 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRATNNNVERAVEWLL 37 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHHh
Confidence 357899999999999999999999999999999974
No 7
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=97.48 E-value=0.00011 Score=73.04 Aligned_cols=70 Identities=14% Similarity=0.269 Sum_probs=62.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHHH----------------------------HHHHHhcCCCCchHH
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGD-NPTKVREFANG----------------------------YTILREMGFSSNNVA 200 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~~----------------------------~~~L~EMGFp~~~Va 200 (222)
-+|++|++|||+.++.++||-+.|. |.+-++.+|-. .+-|-||||..+...
T Consensus 560 s~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLFqHMdDPdlndP~~~~~~vPKkDkeVdE~~~~Slle~Gln~n~~R 639 (749)
T COG5207 560 SLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLFQHMDDPDLNDPFVPPPNVPKKDKEVDESKARSLLENGLNPNLCR 639 (749)
T ss_pred HHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHHhhccCcccCCCCCCCCCCCcccccccHHHHHHHHHcCCCHHHHH
Confidence 3899999999999999999999998 77777777633 678899999999999
Q ss_pred HHHHhccCCHHHHHHHHhc
Q 046691 201 EVLIMYENDTDKALAHLLG 219 (222)
Q Consensus 201 eAL~~~dND~DKAL~~LLs 219 (222)
+||+..+||.+++.+-+|+
T Consensus 640 kal~~~n~d~~r~V~w~~N 658 (749)
T COG5207 640 KALMDMNTDSKRRVVWCIN 658 (749)
T ss_pred HHHHHccCCchheEEEEEe
Confidence 9999999999999887765
No 8
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=97.34 E-value=0.00037 Score=70.46 Aligned_cols=72 Identities=21% Similarity=0.375 Sum_probs=61.5
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhH-HHHHHHH-----------------------------HHHHHhcCCCCch
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTK-VREFANG-----------------------------YTILREMGFSSNN 198 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~K-V~EFl~~-----------------------------~~~L~EMGFp~~~ 198 (222)
.-+|.+|++|||+.+|..+||-..|.+..+ +.-++.. ...+-+|||..+-
T Consensus 572 ~s~i~qL~~MGFp~eac~rAly~tgN~~aEaA~NWl~~HMdDpd~~~p~vvp~~~~~a~~~~~~e~~v~si~smGf~~~q 651 (763)
T KOG0944|consen 572 RSVISQLVEMGFPEEACRRALYYTGNSGAEAASNWLMEHMDDPDIDDPFVVPGNSPKADAREVDEESVASIVSMGFSRNQ 651 (763)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhhhcCccHHHHHHHHHHhccCcccCCceecCCCCCccccCCCChhHheeeeeecCcHHH
Confidence 348999999999999999999999885444 4444433 7788999999999
Q ss_pred HHHHHHhccCCHHHHHHHHhcc
Q 046691 199 VAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 199 VaeAL~~~dND~DKAL~~LLs~ 220 (222)
...||...||+.++|.|-+++.
T Consensus 652 a~~aL~~~n~nveravDWif~h 673 (763)
T KOG0944|consen 652 AIKALKATNNNVERAVDWIFSH 673 (763)
T ss_pred HHHHHHhcCccHHHHHHHHHhc
Confidence 9999999999999999988764
No 9
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=97.34 E-value=0.00045 Score=43.69 Aligned_cols=35 Identities=17% Similarity=0.366 Sum_probs=32.5
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFA 183 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl 183 (222)
+..|.++++|||+++.+..||..-+.|.+++.+|+
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~~~d~~~A~~~L 36 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAANGNVERAAEYL 36 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 35789999999999999999999999999999987
No 10
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.03 E-value=0.0032 Score=61.87 Aligned_cols=73 Identities=23% Similarity=0.323 Sum_probs=62.1
Q ss_pred CcH-HHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH--------------------HHHHHhcCCCCchHHHHHHhc
Q 046691 148 SDP-VVSRYIALGLNREAVHIAVANYGDNPTKVREFANG--------------------YTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 148 ~DP-~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~--------------------~~~L~EMGFp~~~VaeAL~~~ 206 (222)
-|| -+..|++|||.+++|+.||+.--.|..|..+-++- +.+|--|||.....-.||-..
T Consensus 374 vn~rs~~rL~~mGyer~la~eaL~r~~Ndi~~aldllq~esdel~~n~~~~p~~vd~~~la~Lv~mGF~e~~A~~ALe~~ 453 (568)
T KOG2561|consen 374 VNPRSLERLVSMGYERELAAEALRRNENDIQKALDLLQDESDELESNKPKRPEQVDGISLAELVSMGFEEGKARSALEAG 453 (568)
T ss_pred cCHHHHHHHHhcchHhHHHHHHHHhccCcHHHHHHhcCCcchhhhccCCCCCcccchhhHHHHHHhccccchHHHHHHhc
Confidence 355 67789999999999999999765566666655432 899999999999999999999
Q ss_pred cCCHHHHHHHHhcc
Q 046691 207 ENDTDKALAHLLGS 220 (222)
Q Consensus 207 dND~DKAL~~LLs~ 220 (222)
.|..|+|+..|+.+
T Consensus 454 gnn~~~a~~~L~~s 467 (568)
T KOG2561|consen 454 GNNEDTAQRLLSAS 467 (568)
T ss_pred CCcHHHHHHHHHHh
Confidence 99999999999864
No 11
>KOG2561 consensus Adaptor protein NUB1, contains UBA domain [Posttranslational modification, protein turnover, chaperones; Signal transduction mechanisms]
Probab=97.01 E-value=0.0017 Score=63.70 Aligned_cols=71 Identities=25% Similarity=0.351 Sum_probs=60.1
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH--------------------------------------HHHH
Q 046691 148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG--------------------------------------YTIL 189 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~--------------------------------------~~~L 189 (222)
-|....-+++|||-..-+.+||..--.+-+.++.|+.. ++.|
T Consensus 303 ~d~~lsllv~mGfeesdaRlaLRsc~g~Vd~AvqfI~erre~laq~R~k~~a~Ere~~~r~k~~n~~~~~wvn~rs~~rL 382 (568)
T KOG2561|consen 303 NDETLSLLVGMGFEESDARLALRSCNGDVDSAVQFIIERREKLAQKREKDLAREREILERKKYGNTPMKKWVNPRSLERL 382 (568)
T ss_pred cchHHHHHHHcCCCchHHHHHHHhccccHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHhcCCCcccccCHHHHHHH
Confidence 46777888999999999999998555566666666543 7799
Q ss_pred HhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691 190 REMGFSSNNVAEVLIMYENDTDKALAHLL 218 (222)
Q Consensus 190 ~EMGFp~~~VaeAL~~~dND~DKAL~~LL 218 (222)
.+|||....+++||...+||.++||+.|=
T Consensus 383 ~~mGyer~la~eaL~r~~Ndi~~aldllq 411 (568)
T KOG2561|consen 383 VSMGYERELAAEALRRNENDIQKALDLLQ 411 (568)
T ss_pred HhcchHhHHHHHHHHhccCcHHHHHHhcC
Confidence 99999999999999999999999999874
No 12
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=96.77 E-value=0.0014 Score=61.62 Aligned_cols=44 Identities=20% Similarity=0.394 Sum_probs=38.1
Q ss_pred CCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCc
Q 046691 147 GSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSN 197 (222)
Q Consensus 147 ~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~ 197 (222)
..+-+|..+++|||+|+.|.+||+.==.|+++++|||. +|.|.+
T Consensus 155 ~~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~-------tGIP~~ 198 (378)
T TIGR00601 155 ERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLL-------TGIPED 198 (378)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHH-------hCCCcc
Confidence 34779999999999999999999977779999999986 578854
No 13
>smart00546 CUE Domain that may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two protein of the IL-1 signal transduction pathway, tollip and TAB2. Ponting (Biochem. J.) "Proteins of the Endoplasmic reticulum" (in press)
Probab=96.65 E-value=0.0032 Score=41.51 Aligned_cols=37 Identities=22% Similarity=0.390 Sum_probs=31.6
Q ss_pred HHHHHHHhcCCCC---chHHHHHHhccCCHHHHHHHHhccC
Q 046691 184 NGYTILREMGFSS---NNVAEVLIMYENDTDKALAHLLGSS 221 (222)
Q Consensus 184 ~~~~~L~EMGFp~---~~VaeAL~~~dND~DKAL~~LLs~s 221 (222)
....+|++| ||. ..|..+|..|+||.|.|++.||..+
T Consensus 4 ~~v~~L~~m-FP~l~~~~I~~~L~~~~g~ve~~i~~LL~~~ 43 (43)
T smart00546 4 EALHDLKDM-FPNLDEEVIKAVLEANNGNVEATINNLLEGS 43 (43)
T ss_pred HHHHHHHHH-CCCCCHHHHHHHHHHcCCCHHHHHHHHHcCC
Confidence 457889999 886 5778889999999999999999764
No 14
>TIGR00601 rad23 UV excision repair protein Rad23. All proteins in this family for which functions are known are components of a multiprotein complex used for targeting nucleotide excision repair to specific parts of the genome. In humans, Rad23 complexes with the XPC protein. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=95.87 E-value=0.01 Score=55.86 Aligned_cols=40 Identities=28% Similarity=0.337 Sum_probs=37.6
Q ss_pred HHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691 181 EFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 181 EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
||....++|.||||+.+.|..||-..-|+.|+|+|.||++
T Consensus 155 ~~e~~I~~i~eMGf~R~qV~~ALRAafNNPdRAVEYL~tG 194 (378)
T TIGR00601 155 ERETTIEEIMEMGYEREEVERALRAAFNNPDRAVEYLLTG 194 (378)
T ss_pred HHHHHHHHHHHhCCCHHHHHHHHHHHhCCHHHHHHHHHhC
Confidence 6777788999999999999999999999999999999986
No 15
>PF02845 CUE: CUE domain; InterPro: IPR003892 This domain may be involved in binding ubiquitin-conjugating enzymes (UBCs). CUE domains also occur in two proteins of the IL-1 signal transduction pathway, tollip and TAB2.; GO: 0005515 protein binding; PDB: 2EKF_A 1OTR_A 1P3Q_Q 1MN3_A 1WGL_A 2EJS_A 2DAE_A 2DHY_A 2DI0_A.
Probab=95.64 E-value=0.01 Score=39.08 Aligned_cols=35 Identities=26% Similarity=0.346 Sum_probs=29.2
Q ss_pred HHHHHhc--CCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691 186 YTILREM--GFSSNNVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 186 ~~~L~EM--GFp~~~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
..+|++| .++.+.|..+|..|+||.|.|++.||..
T Consensus 5 v~~L~~mFP~~~~~~I~~~L~~~~~~ve~ai~~LL~~ 41 (42)
T PF02845_consen 5 VQQLQEMFPDLDREVIEAVLQANNGDVEAAIDALLEM 41 (42)
T ss_dssp HHHHHHHSSSS-HHHHHHHHHHTTTTHHHHHHHHHHH
T ss_pred HHHHHHHCCCCCHHHHHHHHHHcCCCHHHHHHHHHcC
Confidence 4567777 5667889999999999999999999975
No 16
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=94.22 E-value=0.26 Score=39.63 Aligned_cols=70 Identities=19% Similarity=0.287 Sum_probs=53.2
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHc---C--CChhHHHHHHHH-----------HHHHHhcCCCCchHHHHHHhccCCHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANY---G--DNPTKVREFANG-----------YTILREMGFSSNNVAEVLIMYENDTDK 212 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~y---G--dd~~KV~EFl~~-----------~~~L~EMGFp~~~VaeAL~~~dND~DK 212 (222)
-.+..||..+|++.+.+..+|+.+ | +|..-+..|+.. -..|+.-||+.+.|.+||..++-|.+.
T Consensus 29 ~el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~g~~~I~~~L~~kGi~~~~I~~~l~~~~~d~~e 108 (157)
T PRK00117 29 AELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRARKGYGPRRIRQELRQKGVDREIIEEALAELDIDWEE 108 (157)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCchHHHHHHHHHHcCCCHHHHHHHHHHcCccHHH
Confidence 457889999999999999999833 3 365666666544 467899999999999999988755555
Q ss_pred HHHHHh
Q 046691 213 ALAHLL 218 (222)
Q Consensus 213 AL~~LL 218 (222)
++..++
T Consensus 109 ~a~~~~ 114 (157)
T PRK00117 109 LARELA 114 (157)
T ss_pred HHHHHH
Confidence 544443
No 17
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=91.06 E-value=0.23 Score=36.17 Aligned_cols=25 Identities=20% Similarity=0.414 Sum_probs=14.6
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGD 174 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGd 174 (222)
.+|.++++|||++++|-.|++..|-
T Consensus 11 ~lVd~F~~mGF~~dkVvevlrrlgi 35 (55)
T PF09288_consen 11 DLVDQFENMGFERDKVVEVLRRLGI 35 (55)
T ss_dssp HHHHHHHHHT--HHHHHHHHHHS--
T ss_pred HHHHHHHHcCCcHHHHHHHHHHhCC
Confidence 4667777777777777777776654
No 18
>PF08938 HBS1_N: HBS1 N-terminus; InterPro: IPR015033 This domain is found in various eukaryotic HBS1-like proteins. ; PDB: 1UFZ_A 3IZQ_1.
Probab=90.94 E-value=0.15 Score=37.94 Aligned_cols=27 Identities=33% Similarity=0.393 Sum_probs=23.3
Q ss_pred CCchHHHHHHhccCCHHHHHHHHhccC
Q 046691 195 SSNNVAEVLIMYENDTDKALAHLLGSS 221 (222)
Q Consensus 195 p~~~VaeAL~~~dND~DKAL~~LLs~s 221 (222)
+...|.+||..|+.|++|||+.||+..
T Consensus 45 ~e~~i~eal~~~~fDvekAl~~Ll~~~ 71 (79)
T PF08938_consen 45 PEEQIKEALWHYYFDVEKALDYLLSKF 71 (79)
T ss_dssp -CCHHHHHHHHTTT-CCHHHHHHHHCC
T ss_pred CHHHHHHHHHHHcCCHHHHHHHHHHhc
Confidence 889999999999999999999999763
No 19
>PF09288 UBA_3: Fungal ubiquitin-associated domain ; InterPro: IPR015368 This C-terminal domain is found in ubiquitin binding proteins, it adopts a structure consisting of a three alpha-helix bundle. This domain is predominantly found in fungi []. ; PDB: 1TTE_A.
Probab=90.03 E-value=0.33 Score=35.37 Aligned_cols=32 Identities=34% Similarity=0.485 Sum_probs=20.1
Q ss_pred HHHHhcCCCCchHHHHHHhccCC---------HHHHHHHHh
Q 046691 187 TILREMGFSSNNVAEVLIMYEND---------TDKALAHLL 218 (222)
Q Consensus 187 ~~L~EMGFp~~~VaeAL~~~dND---------~DKAL~~LL 218 (222)
.+|..|||+.++|-+||-.-+-+ .++.|+.||
T Consensus 14 d~F~~mGF~~dkVvevlrrlgik~~n~~dn~t~~~ilEELL 54 (55)
T PF09288_consen 14 DQFENMGFERDKVVEVLRRLGIKSMNGVDNETENKILEELL 54 (55)
T ss_dssp HHHHHHT--HHHHHHHHHHS--SS--SS--HHHHHHHHHHT
T ss_pred HHHHHcCCcHHHHHHHHHHhCCCCCCCccchhHHHHHHHHh
Confidence 46778999999999999754322 345666665
No 20
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=86.62 E-value=0.73 Score=41.03 Aligned_cols=40 Identities=28% Similarity=0.160 Sum_probs=34.5
Q ss_pred HHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691 181 EFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 181 EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
.+-+....|.+|||..+.+-.+|-..+-+..+|++.||++
T Consensus 161 ~~~~~v~~l~~mGf~~~~~i~~L~~~~w~~~~a~~~~~s~ 200 (200)
T KOG0418|consen 161 WDKKKVDSLIEMGFSELEAILVLSGSDWNLADATEQLLSG 200 (200)
T ss_pred hhHHHHHHHHHhcccHHHHHHHhhccccchhhhhHhhccC
Confidence 3444457789999999999999999999999999999874
No 21
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=86.08 E-value=0.79 Score=46.53 Aligned_cols=36 Identities=28% Similarity=0.410 Sum_probs=30.4
Q ss_pred HHHHHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHh
Q 046691 183 ANGYTILREMGFSSNNVAEVLIMYEN-DTDKALAHLL 218 (222)
Q Consensus 183 l~~~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LL 218 (222)
-.+..||.+||||+...+.||....| |.|-|..-|.
T Consensus 559 qs~I~qL~~mGfp~~~~~rAL~~tgNqDaEsAMNWLF 595 (749)
T COG5207 559 QSLIRQLVDMGFPEEDAARALGITGNQDAESAMNWLF 595 (749)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhhccCcchHHHHHHHH
Confidence 45689999999999999999999988 7777766554
No 22
>PRK14136 recX recombination regulator RecX; Provisional
Probab=84.69 E-value=3.8 Score=38.55 Aligned_cols=68 Identities=9% Similarity=0.102 Sum_probs=51.0
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHH-----HcCCChhHHHHHHHH----------HHHHHhcCCCCchHHHHHHhccCCH-H
Q 046691 148 SDPVVSRYIALGLNREAVHIAVA-----NYGDNPTKVREFANG----------YTILREMGFSSNNVAEVLIMYENDT-D 211 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~-----~yGdd~~KV~EFl~~----------~~~L~EMGFp~~~VaeAL~~~dND~-D 211 (222)
.-.+..||..+||+.+.|..+|+ +|-+|..=+..|+.. -..|+.-|...+.|.+||...+.|. +
T Consensus 179 e~ELr~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~R~~kkGp~rIrqELrQKGId~eLIEqALeeieEDE~E 258 (309)
T PRK14136 179 RAELARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVHRRASRVGSARIVSELKRHAVGDALVESVGAQLRETEFE 258 (309)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhchhHHHHHHHHHHcCCCHHHHHHHHHhccHhHHH
Confidence 34588899999999999999987 445566666666544 5678899999999999999776444 4
Q ss_pred HHHH
Q 046691 212 KALA 215 (222)
Q Consensus 212 KAL~ 215 (222)
.|++
T Consensus 259 ~A~~ 262 (309)
T PRK14136 259 RAQA 262 (309)
T ss_pred HHHH
Confidence 4433
No 23
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=84.47 E-value=1.1 Score=42.65 Aligned_cols=39 Identities=23% Similarity=0.390 Sum_probs=34.9
Q ss_pred HHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691 182 FANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 182 Fl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
+=....++.+||+..+.|--||-..=|+.|+|++.||++
T Consensus 135 ~e~~V~~Im~MGy~re~V~~AlRAafNNPeRAVEYLl~G 173 (340)
T KOG0011|consen 135 YEQTVQQIMEMGYDREEVERALRAAFNNPERAVEYLLNG 173 (340)
T ss_pred hHHHHHHHHHhCccHHHHHHHHHHhhCChhhhHHHHhcC
Confidence 334567899999999999999999999999999999986
No 24
>PF14555 UBA_4: UBA-like domain; PDB: 2DAL_A 3BQ3_A 2L4E_A 2L4F_A 2DZL_A 2L2D_A 2DAM_A 1V92_A 3E21_A.
Probab=83.08 E-value=2.6 Score=27.88 Aligned_cols=38 Identities=16% Similarity=0.264 Sum_probs=27.9
Q ss_pred hHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691 177 TKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 177 ~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
+||.+|+. +. |-..+.....|-+||+|.++||+.++..
T Consensus 2 e~i~~F~~----iT--g~~~~~A~~~L~~~~wdle~Av~~y~~~ 39 (43)
T PF14555_consen 2 EKIAQFMS----IT--GADEDVAIQYLEANNWDLEAAVNAYFDD 39 (43)
T ss_dssp HHHHHHHH----HH---SSHHHHHHHHHHTTT-HHHHHHHHHHS
T ss_pred HHHHHHHH----HH--CcCHHHHHHHHHHcCCCHHHHHHHHHhC
Confidence 46666653 33 5677888888999999999999998764
No 25
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=83.00 E-value=4.4 Score=31.32 Aligned_cols=50 Identities=16% Similarity=0.286 Sum_probs=35.0
Q ss_pred HHHcCCCHHHHHHHHH---HcCC--ChhHHHHHHHH------------HHHHHhcCCCCchHHHHHH
Q 046691 155 YIALGLNREAVHIAVA---NYGD--NPTKVREFANG------------YTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 155 y~amG~~reaV~~Av~---~yGd--d~~KV~EFl~~------------~~~L~EMGFp~~~VaeAL~ 204 (222)
|..+||+.+.|..+|+ .+|- |..=+..|+.. -..|+.-|.+.+.|.+||.
T Consensus 1 L~~kg~~~e~I~~vi~~l~~~gyidD~~ya~~~v~~~~~~~~~G~~~I~~~L~~kGi~~~~i~~~l~ 67 (121)
T PF02631_consen 1 LKRKGFSEEAIEEVIDRLKELGYIDDERYAESYVRSRLRRKGKGPRRIRQKLKQKGIDREIIEEALE 67 (121)
T ss_dssp HHHTT--HHHHHHHHHHHHHTTSS-HHHHHHHHHHHHHHHTT--HHHHHHHHHHTT--HHHHHHHHT
T ss_pred CcccCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHhcccccccHHHHHHHHHHHCCChHHHHHHHH
Confidence 4578999998888887 3343 66666667665 4579999999999999998
No 26
>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=82.94 E-value=2.6 Score=32.14 Aligned_cols=55 Identities=20% Similarity=0.156 Sum_probs=39.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
.+++.|-..|+=.-+- ..+|=.=.++.++.+.....|+++||+.++|++.|...+
T Consensus 15 ~tlRyYe~~GLl~p~~---~~g~r~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~ 69 (107)
T cd04777 15 DTVRHYIDLGLLIPEK---KGGQYFFDEKCQDDLEFILELKGLGFSLIEIQKIFSYKR 69 (107)
T ss_pred HHHHHHHHCCCcCCcc---CCCccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhcc
Confidence 4889999999832221 112112233555999999999999999999999886643
No 27
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=82.20 E-value=1.1 Score=42.52 Aligned_cols=25 Identities=24% Similarity=0.464 Sum_probs=21.2
Q ss_pred CCCcHHHHHHHHcCCCHHHHHHHHH
Q 046691 146 SGSDPVVSRYIALGLNREAVHIAVA 170 (222)
Q Consensus 146 ~~~DP~V~ky~amG~~reaV~~Av~ 170 (222)
.+-|.+|+|++.|||.||.|.--|+
T Consensus 319 ~p~ddvidKv~~MGf~rDqV~a~v~ 343 (358)
T PF07223_consen 319 HPYDDVIDKVASMGFRRDQVRATVR 343 (358)
T ss_pred CcHHHHHHHHHHcCCcHHHHHHHHH
Confidence 3469999999999999999965555
No 28
>KOG0010 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones; General function prediction only]
Probab=82.14 E-value=1.9 Score=42.87 Aligned_cols=44 Identities=25% Similarity=0.369 Sum_probs=37.2
Q ss_pred hHHHHHHHHHHHHHhcCCCCc-hHHHHHHhccCCHHHHHHHHhcc
Q 046691 177 TKVREFANGYTILREMGFSSN-NVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 177 ~KV~EFl~~~~~L~EMGFp~~-~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
.-=.+|-..|+||.+|||--. .--+||+.-..|..+|++.||..
T Consensus 449 ~pe~r~q~QLeQL~~MGF~nre~nlqAL~atgGdi~aAverll~s 493 (493)
T KOG0010|consen 449 PPEERYQTQLEQLNDMGFLDREANLQALRATGGDINAAVERLLGS 493 (493)
T ss_pred CchHHHHHHHHHHHhcCCccHHHHHHHHHHhcCcHHHHHHHHhcC
Confidence 344689999999999999754 45689999999999999999863
No 29
>PF06972 DUF1296: Protein of unknown function (DUF1296); InterPro: IPR009719 This family represents a conserved region approximately 60 residues long within a number of plant proteins of unknown function.
Probab=82.13 E-value=3.1 Score=30.95 Aligned_cols=38 Identities=16% Similarity=0.185 Sum_probs=30.4
Q ss_pred HHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691 182 FANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 182 Fl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
-++.+.....- ++..+|-.+|..|+.|.+.|.+-||+-
T Consensus 8 ~VQ~iKEiv~~-hse~eIya~L~ecnMDpnea~qrLL~q 45 (60)
T PF06972_consen 8 TVQSIKEIVGC-HSEEEIYAMLKECNMDPNEAVQRLLSQ 45 (60)
T ss_pred HHHHHHHHhcC-CCHHHHHHHHHHhCCCHHHHHHHHHhc
Confidence 34444444444 789999999999999999999999973
No 30
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=81.73 E-value=2.4 Score=29.13 Aligned_cols=34 Identities=35% Similarity=0.485 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHH
Q 046691 181 EFANGYTILREMGFSSNNVAEVLIMYENDTDKALA 215 (222)
Q Consensus 181 EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~ 215 (222)
+=+.....+++.||+.++|++.|...++ .+...+
T Consensus 2 ~rL~~I~~~r~lGfsL~eI~~~l~l~~~-~~~~~~ 35 (65)
T PF09278_consen 2 ERLQFIRRLRELGFSLEEIRELLELYDQ-GDPPCA 35 (65)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHCCS-HCHHHH
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHhccCC-CCCCHH
Confidence 3456677889999999999999987776 444433
No 31
>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=81.55 E-value=2.8 Score=32.94 Aligned_cols=58 Identities=21% Similarity=0.271 Sum_probs=39.6
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
.+++.|-..|+=.... +--.+|-.=.....+.+.....|+++||+.+.|++.|-.+++
T Consensus 15 ~tlR~Ye~~GLl~~~~-r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~ 72 (126)
T cd04783 15 ETIRYYQRRGLLPEPP-RPEGGYRRYPEETVTRLRFIKRAQELGFTLDEIAELLELDDG 72 (126)
T ss_pred HHHHHHHHCCCCCCCC-cCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccC
Confidence 3677888888743111 111122224556677788888999999999999999887765
No 32
>PRK14135 recX recombination regulator RecX; Provisional
Probab=81.52 E-value=6.6 Score=34.07 Aligned_cols=60 Identities=12% Similarity=0.133 Sum_probs=46.9
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHH---cCC--ChhHHHHHHHH------------HHHHHhcCCCCchHHHHHHhccC
Q 046691 149 DPVVSRYIALGLNREAVHIAVAN---YGD--NPTKVREFANG------------YTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~---yGd--d~~KV~EFl~~------------~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
-.+..||...|++.+.+..+|+. +|- |..-+..|+.. -..|+..||+.+.|.+||..++.
T Consensus 75 ~el~~kL~~kg~~~~~Ie~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~~g~~~I~~kL~~kGi~~~~Ie~~l~~l~~ 151 (263)
T PRK14135 75 KEVRDYLKKHEISEEIISEVIDKLKEEKYIDDKEYAESYVRTNINTGDKGPRVIKQKLLQKGIEDEIIEEALSEYTE 151 (263)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhccccchHHHHHHHHHcCCCHHHHHHHHHhCCh
Confidence 56888999999999999999983 343 55555555543 45688999999999999998754
No 33
>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=80.30 E-value=3.7 Score=32.25 Aligned_cols=58 Identities=16% Similarity=0.138 Sum_probs=40.4
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
.+++.|-++|+=....- .--.|-.=..+..+.+.....|+++||+.+.|++.|-.+++
T Consensus 15 ~tLRyYe~~GLl~p~~r-~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~ 72 (127)
T cd04784 15 ETIRYYEKEGLLPAPAR-SANNYRLYDEEHLERLLFIRRCRSLDMSLDEIRTLLQLQDD 72 (127)
T ss_pred HHHHHHHHCCCCCCCCc-CCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhc
Confidence 46788888887432111 11123335567788888899999999999999998876543
No 34
>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=80.25 E-value=3.7 Score=32.43 Aligned_cols=66 Identities=17% Similarity=0.192 Sum_probs=42.2
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC-CHHHHHHH
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN-DTDKALAH 216 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~ 216 (222)
.+++.|-.+|+=.... +.--.|-.=..+..+.+.....|+++||+.+.|++.|-..+. +.+..++.
T Consensus 14 ~tlR~Ye~~GLl~~~~-r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~~~~~~~~~~~ 80 (124)
T TIGR02051 14 ETIRYYERKGLLPEPD-RPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLVDGTHCREMYEL 80 (124)
T ss_pred HHHHHHHHCCCCCCCc-cCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhcccCCCHHHHHHH
Confidence 3677888888743221 111122223456777788889999999999999998876654 23444443
No 35
>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=79.97 E-value=3.7 Score=32.40 Aligned_cols=56 Identities=18% Similarity=0.185 Sum_probs=37.9
Q ss_pred HHHHHHHHcCCCHHH--HHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 150 PVVSRYIALGLNREA--VHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 150 P~V~ky~amG~~rea--V~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
.+++.|-+.|+=... -.-+... =..+..+-+.....|+++||+.+.|++.|..+++
T Consensus 15 ~tlR~Ye~~Gll~~~~r~~~g~R~---Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~ 72 (126)
T cd04785 15 ETIRYYESIGLLPEPARTAGGYRL---YGAAHVERLRFIRRARDLGFSLEEIRALLALSDR 72 (126)
T ss_pred HHHHHHHHCCCCCCCCcCCCCccc---cCHHHHHHHHHHHHHHHCCCCHHHHHHHHhhhhc
Confidence 467778888875421 1112222 3345667777888899999999999999876654
No 36
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=79.33 E-value=4.3 Score=31.21 Aligned_cols=68 Identities=13% Similarity=0.067 Sum_probs=41.6
Q ss_pred CcHHHHHHHHc-CCCHHHHHHHHHHcCC-ChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC---HHHHHHHH
Q 046691 148 SDPVVSRYIAL-GLNREAVHIAVANYGD-NPTKVREFANGYTILREMGFSSNNVAEVLIMYEND---TDKALAHL 217 (222)
Q Consensus 148 ~DP~V~ky~am-G~~reaV~~Av~~yGd-d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND---~DKAL~~L 217 (222)
...+++.|... |+..- .+.-.+|-. +.+-|..+..-...|+++||+.+.|++.|..+++. ++.|+++|
T Consensus 13 s~~tLR~ye~~~gli~p--~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~~~~~~~~~~~~~ 85 (99)
T cd04765 13 PPHVLRYWETEFPQLKP--VKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGAAAIREEEAEERL 85 (99)
T ss_pred CHHHHHHHHHHcCCCCC--cCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccccccchhhHHHHH
Confidence 34567777665 65421 111011111 55555554444445799999999999999987775 66666665
No 37
>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=79.26 E-value=4.2 Score=31.44 Aligned_cols=65 Identities=15% Similarity=0.112 Sum_probs=40.9
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc--CCHHHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE--NDTDKAL 214 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d--ND~DKAL 214 (222)
-.++..|.++|+=.-..... -+|=.=.....+.+.....|+++||+...|++.|...+ ++.+...
T Consensus 14 ~~tlR~ye~~Gll~p~~~~~-~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~~~~~~~ 80 (108)
T cd04773 14 PSTLRHWEKEGLLSPDREPE-TGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQLRHAGGTEALA 80 (108)
T ss_pred HHHHHHHHHCCCCCCCcCCC-CCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHhhcCCCHHHHH
Confidence 45788888888843211000 01111234556677788999999999999999998653 4444433
No 38
>PF03474 DMA: DMRTA motif; InterPro: IPR005173 This region is found to the C terminus of the DM DNA-binding domain IPR001275 from INTERPRO []. DM-domain proteins with this motif are known as DMRTA proteins. The function of this region is unknown.
Probab=79.09 E-value=1.9 Score=29.51 Aligned_cols=23 Identities=17% Similarity=0.255 Sum_probs=19.6
Q ss_pred CchHHHHHHhccCCHHHHHHHHh
Q 046691 196 SNNVAEVLIMYENDTDKALAHLL 218 (222)
Q Consensus 196 ~~~VaeAL~~~dND~DKAL~~LL 218 (222)
.+.+.-+|--|++|.-+|||++|
T Consensus 17 r~~Le~iL~~C~GDvv~AIE~~l 39 (39)
T PF03474_consen 17 RSVLELILQRCNGDVVQAIEQFL 39 (39)
T ss_pred hHHHHHHHHHcCCcHHHHHHHhC
Confidence 35577788999999999999986
No 39
>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=78.13 E-value=4.9 Score=31.25 Aligned_cols=59 Identities=17% Similarity=0.152 Sum_probs=41.7
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
-.+++.|-++|+=.-...-+ +|-.=.....+.+.....|+++||+.++|++.|..++.+
T Consensus 14 ~~tLryYe~~GLi~p~~~~~--~yR~Y~~~d~~~l~~I~~lr~~G~sl~eI~~~l~~~~~~ 72 (116)
T cd04769 14 IKAIRLYEEKGLLPSPKRSG--NYRVYDAQHVECLRFIKEARQLGFTLAELKAIFAGHEGR 72 (116)
T ss_pred HHHHHHHHHCCCCCCCCCCC--CceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccccC
Confidence 45788888888743211111 232234566777888899999999999999999888754
No 40
>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=77.55 E-value=0.64 Score=35.04 Aligned_cols=48 Identities=29% Similarity=0.288 Sum_probs=36.8
Q ss_pred cCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691 172 YGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 172 yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
...-.+||.+||+. ..-.+-|-+-+.|++-|-+-.++..+||+.|+..
T Consensus 45 ~~~~~~~Vl~~i~~-~~~~~~Gv~v~~I~~~l~~~~~~v~~al~~L~~e 92 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQ-QPNSEEGVHVDEIAQQLGMSENEVRKALDFLSNE 92 (102)
T ss_dssp S-HHHHHHHHHHHC-----TTTEEHHHHHHHSTS-HHHHHHHHHHHHHT
T ss_pred CCHHHHHHHHHHHh-cCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHhC
Confidence 33457899999999 7777889999999999988899999999999864
No 41
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=77.12 E-value=4.5 Score=33.19 Aligned_cols=59 Identities=17% Similarity=0.134 Sum_probs=39.9
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
.+++.|-..|+=.... +.--+|-.=.++..+.+.....|+++||+.+.|++.|-.+++.
T Consensus 22 ~TLRyYE~~GLl~p~~-r~~~gyR~Y~~~~l~rl~~I~~lr~~G~sL~eI~~ll~~~~~~ 80 (144)
T PRK13752 22 ETIRFYQRKGLLPEPD-KPYGSIRRYGEADVTRVRFVKSAQRLGFSLDEIAELLRLEDGT 80 (144)
T ss_pred HHHHHHHHCCCCCCCc-cCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhccCCC
Confidence 4677777778754211 1111233345677888999999999999999999887665543
No 42
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=76.36 E-value=6.8 Score=27.90 Aligned_cols=39 Identities=28% Similarity=0.465 Sum_probs=31.6
Q ss_pred CCCcHHHHHHH--HcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691 146 SGSDPVVSRYI--ALGLNREAVHIAVANYGDNPTKVREFAN 184 (222)
Q Consensus 146 ~~~DP~V~ky~--amG~~reaV~~Av~~yGdd~~KV~EFl~ 184 (222)
...|+..-+|- .-|.+.+++..||+..|.+.++|.+||.
T Consensus 16 ~~~e~~ev~ywa~~~gvt~~~L~~AV~~vG~~~~~V~~~L~ 56 (57)
T PF12244_consen 16 DLSEPYEVRYWAKRFGVTEEQLREAVRAVGNSRAAVRAYLG 56 (57)
T ss_pred CCCCHHHHHHHHHHHCcCHHHHHHHHHHHCcCHHHHHHHHc
Confidence 34455444444 7799999999999999999999999985
No 43
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=76.30 E-value=4.1 Score=31.75 Aligned_cols=60 Identities=15% Similarity=0.139 Sum_probs=39.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCH
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDT 210 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~ 210 (222)
.+++.|-+.|+=+..-.-. -+|=.=.....+.+.....|+++||+...|++.|...+++.
T Consensus 15 ~tlR~ye~~GLl~p~~r~~-~g~R~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~~~~ 74 (107)
T cd01111 15 HIVRDYLLRGLLHPVARTE-GGYGLFDDCALQRLRFVRAAFEAGIGLDELARLCRALDAGD 74 (107)
T ss_pred HHHHHHHHCCCCCCCCcCC-CCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhCCC
Confidence 4667777777643311000 11222344566777888889999999999999998876553
No 44
>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=75.38 E-value=5.9 Score=29.94 Aligned_cols=57 Identities=18% Similarity=0.116 Sum_probs=38.1
Q ss_pred HHHHHHHHcCCCHHHH--HHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC
Q 046691 150 PVVSRYIALGLNREAV--HIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 150 P~V~ky~amG~~reaV--~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
.++..|-++|+=.... .-+-.. =.....+-+.....|+++||+.++|++.|...+.+
T Consensus 15 ~tlR~ye~~Gll~p~~r~~~gyR~---Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~~~~ 73 (96)
T cd04788 15 RTLHHYDHIGLLSPSQRTEGGHRL---YDRADIRRLHQIIALRRLGFSLREIGRALDGPDFD 73 (96)
T ss_pred HHHHHHHHCCCCCCCccCCCCcee---eCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCCChh
Confidence 4677777888754321 111112 23356677888888999999999999988765543
No 45
>PRK13749 transcriptional regulator MerD; Provisional
Probab=75.04 E-value=4.3 Score=32.90 Aligned_cols=59 Identities=17% Similarity=0.155 Sum_probs=42.2
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
.+++-|-+.|+=.... +.--+|-.=..+..+-+.....++++||+.++|++.|...+.+
T Consensus 18 ~tiR~YE~~GLl~p~~-r~~~gyR~Y~~~~l~rL~~I~~~r~~G~sL~eI~~ll~l~~~~ 76 (121)
T PRK13749 18 HIVRDYLLRGLLRPVA-CTTGGYGLFDDAALQRLCFVRAAFEAGIGLDALARLCRALDAA 76 (121)
T ss_pred HHHHHHHHCCCCCCCC-cCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhcCC
Confidence 4677777777643211 1112333345677888999999999999999999999998774
No 46
>PRK14134 recX recombination regulator RecX; Provisional
Probab=74.98 E-value=14 Score=33.49 Aligned_cols=62 Identities=13% Similarity=0.194 Sum_probs=49.9
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHH-----HcCCChhHHHHHHHH----------HHHHHhcCCCCchHHHHHHhccCC
Q 046691 148 SDPVVSRYIALGLNREAVHIAVA-----NYGDNPTKVREFANG----------YTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~-----~yGdd~~KV~EFl~~----------~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
+-.+..||...||+.+.|..+|+ +|=||..=+..|+.. -..|+.-|.+.+.|.+||...+-+
T Consensus 78 e~Elr~KL~~k~~~~~~Ie~vI~~L~e~~yldD~ryA~~yv~~~~~~~G~~~I~~eL~qKGI~~~iIe~al~~~~~e 154 (283)
T PRK14134 78 EKQIKEKLYLKEYDEDAVNRVIRFLKEYNFIDDDKYCDMYIREKINSYGRNKIKYTLLNKGIKENIIIEKINNIDEE 154 (283)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhhHHHHHHHHHHCCCCHHHHHHHHHhCChh
Confidence 56788999999999999999998 344466666666653 577999999999999999976544
No 47
>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=74.68 E-value=6.3 Score=31.07 Aligned_cols=57 Identities=18% Similarity=0.168 Sum_probs=41.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
.+++-|-.+|+=.-. ..+ +|=.=.....+.+.....|+++||+.+.|++.|..++.+
T Consensus 15 ~tlRyYe~~GLl~p~-r~~--gyR~Y~~~~l~~l~~I~~lr~~G~~L~~I~~~l~~~~~~ 71 (118)
T cd04776 15 RTLRFYEDKGLLSPE-RRG--QTRVYSRRDRARLKLILRGKRLGFSLEEIRELLDLYDPP 71 (118)
T ss_pred HHHHHHHHCCCCCCc-CCC--CccccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhccC
Confidence 477888888875431 122 332234566778888888999999999999999887653
No 48
>PF08587 UBA_2: Ubiquitin associated domain (UBA) ; InterPro: IPR013896 This is a UBA (ubiquitin associated) protein []. Ubiquitin is involved in intracellular proteolysis. ; GO: 0004674 protein serine/threonine kinase activity; PDB: 3H4J_B.
Probab=74.34 E-value=0.64 Score=32.85 Aligned_cols=43 Identities=19% Similarity=0.482 Sum_probs=24.0
Q ss_pred CcHHHHHHH-HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHh
Q 046691 148 SDPVVSRYI-ALGLNREAVHIAVANYGDNPTKVREFANGYTILRE 191 (222)
Q Consensus 148 ~DP~V~ky~-amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~E 191 (222)
.|.+|.+|. .||+.|+.+..||+. ........|-..+|..++|
T Consensus 2 de~vv~~Ls~tMGY~kdeI~eaL~~-~~~~~~~neIkDAY~L~kE 45 (46)
T PF08587_consen 2 DEDVVSKLSKTMGYDKDEIYEALES-SEPSPQSNEIKDAYLLMKE 45 (46)
T ss_dssp -HCCHHHHHCTT---HHHHHHHCCS-SS------SSCCHHHHHHH
T ss_pred cHHHHHHHHHHhCCCHHHHHHHHHc-CCCcchHHHHHHHHHHHhc
Confidence 356889998 899999999999986 2222334444455555554
No 49
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=73.95 E-value=12 Score=32.15 Aligned_cols=71 Identities=13% Similarity=0.249 Sum_probs=55.5
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHH-----HcCCChhHHHHHHHH-----------HHHHHhcCCCCchHHHHHHhcc--CC
Q 046691 148 SDPVVSRYIALGLNREAVHIAVA-----NYGDNPTKVREFANG-----------YTILREMGFSSNNVAEVLIMYE--ND 209 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~-----~yGdd~~KV~EFl~~-----------~~~L~EMGFp~~~VaeAL~~~d--ND 209 (222)
+..+-.||...||+.+.|..+|. +|-||..-+..|+.. ...|..+|-..+.|.+||...+ +.
T Consensus 37 e~ELr~kL~k~~~~~~~Ie~Vi~~l~~~~~ldD~~fAe~~i~~r~~~g~G~~rl~qeL~qkGi~~~~Ie~aL~~~~~~~~ 116 (174)
T COG2137 37 EKELRRKLAKKEFSEEIIEEVIDRLAEEGYLDDTRFAEAYIRSRSRKGKGPARLKQELKQKGIDDEIIEEALELIDEEDE 116 (174)
T ss_pred HHHHHHHHHhccCCHHHHHHHHHHHHHcCcccHHHHHHHHHHHHHhcccChHHHHHHHHHcCCCHHHHHHHHhccchHHH
Confidence 45677889999999999999987 677788888888765 6789999999999999998332 34
Q ss_pred HHHHHHHHh
Q 046691 210 TDKALAHLL 218 (222)
Q Consensus 210 ~DKAL~~LL 218 (222)
.+.|.+.+.
T Consensus 117 ~~~a~~~~~ 125 (174)
T COG2137 117 QERARKVLR 125 (174)
T ss_pred HHHHHHHHH
Confidence 555655554
No 50
>PLN03196 MOC1-like protein; Provisional
Probab=73.55 E-value=8.2 Score=37.51 Aligned_cols=24 Identities=33% Similarity=0.350 Sum_probs=14.9
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHc
Q 046691 149 DPVVSRYIALGLNREAVHIAVANY 172 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~y 172 (222)
-|.+.-|.++|++++.|..+|..+
T Consensus 233 ~P~v~fL~~lGv~~~~I~~il~~~ 256 (487)
T PLN03196 233 KPKVDYLESLGLPRLAVARILEKR 256 (487)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhC
Confidence 466666666666666666666544
No 51
>KOG2689 consensus Predicted ubiquitin regulatory protein [Posttranslational modification, protein turnover, chaperones]
Probab=73.25 E-value=4.2 Score=38.11 Aligned_cols=33 Identities=15% Similarity=0.294 Sum_probs=25.7
Q ss_pred HHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHH
Q 046691 152 VSRYIALGLNREAVHIAVANYGD-NPTKVREFAN 184 (222)
Q Consensus 152 V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~ 184 (222)
+..|++|||++..+..||+-||. +-+-|.+++.
T Consensus 4 ~~~l~~mgfps~k~e~al~~~~n~~~e~al~wl~ 37 (290)
T KOG2689|consen 4 AQSLEEMGFPSGKAEKALAVYGNRGIEQALDWLE 37 (290)
T ss_pred HHHHHHhcCchhhhhhHhhhhccccHHHHHHHHH
Confidence 36788888888888888888866 7777777763
No 52
>PRK14137 recX recombination regulator RecX; Provisional
Probab=73.17 E-value=17 Score=31.53 Aligned_cols=70 Identities=14% Similarity=0.142 Sum_probs=48.8
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHH---cCC-ChhH-HHHHHH--------HHHHHHhcCCCCchHHHHHHhccCC--HHH
Q 046691 148 SDPVVSRYIALGLNREAVHIAVAN---YGD-NPTK-VREFAN--------GYTILREMGFSSNNVAEVLIMYEND--TDK 212 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~---yGd-d~~K-V~EFl~--------~~~~L~EMGFp~~~VaeAL~~~dND--~DK 212 (222)
.-.+-.||...|++.+.|..+|+. +|- |... +..|.. --..|+.-|.+.+.|.+||..++.| .|.
T Consensus 57 ~~ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~~~k~~Gp~rI~~eL~qKGI~~~lI~~al~~~d~ede~e~ 136 (195)
T PRK14137 57 AAELRAKLERRSEDEALVTEVLERVQELGYQDDAQVARAENSRRGVGALRVRQTLRRRGVEETLIEETLAARDPQEEQQE 136 (195)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhcCchHHHHHHHHHHcCCCHHHHHHHHHhcCchhHHHH
Confidence 345788899999999999999883 333 4443 333321 1467889999999999999988643 355
Q ss_pred HHHHH
Q 046691 213 ALAHL 217 (222)
Q Consensus 213 AL~~L 217 (222)
|++.+
T Consensus 137 a~~l~ 141 (195)
T PRK14137 137 ARNLL 141 (195)
T ss_pred HHHHH
Confidence 55544
No 53
>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=73.11 E-value=7 Score=30.07 Aligned_cols=58 Identities=17% Similarity=0.118 Sum_probs=37.9
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
-.+++.|...|+-.... +--.+|=.=..+..+-+.....|+++||+.+.|++.|...+
T Consensus 14 ~~tlr~ye~~gll~~~~-r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (113)
T cd01109 14 ADTLRYYEKEGLLPPVK-RDENGIRDFTEEDLEWLEFIKCLRNTGMSIKDIKEYAELRR 71 (113)
T ss_pred HHHHHHHHHCCCCCCCC-cCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHc
Confidence 35778888888764221 10011112233456677888899999999999999887654
No 54
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=73.09 E-value=7.5 Score=31.53 Aligned_cols=58 Identities=14% Similarity=0.216 Sum_probs=38.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
.+++-|-..|+=...- +.=.+|=.=..+..+.+.....|+++||+.++|++.|..+++
T Consensus 15 ~tlRyYE~~GLl~p~~-r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~~~~ 72 (135)
T PRK10227 15 KAIRFYEEKGLVTPPM-RSENGYRTYTQQHLNELTLLRQARQVGFNLEESGELVNLFND 72 (135)
T ss_pred HHHHHHHHCCCCCCcc-cCCCCcccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhcc
Confidence 4677777777743221 000122223456778888899999999999999999876553
No 55
>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=72.78 E-value=8 Score=29.95 Aligned_cols=58 Identities=16% Similarity=0.161 Sum_probs=36.6
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
.+++.|-+.|+=....- .-.+|=.=..+..+-+.....|+++||+.+.|++.|-.++.
T Consensus 15 ~tLRyYe~~GLl~p~~r-~~~gyR~Y~~~~i~~l~~I~~lr~~G~sl~eI~~~l~~~~~ 72 (123)
T cd04770 15 DTIRYYERIGLLPPPQR-SENGYRLYGEADLARLRFIRRAQALGFSLAEIRELLSLRDD 72 (123)
T ss_pred HHHHHHHHCCCCCCCCC-CCCCCccCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhhc
Confidence 35667777776431100 00122223345667778888899999999999998876654
No 56
>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=72.66 E-value=6.7 Score=31.23 Aligned_cols=58 Identities=24% Similarity=0.249 Sum_probs=38.1
Q ss_pred HHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC
Q 046691 151 VVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 151 ~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
+++.|-+.|+=.... ..=.+|=.=.+...+.+.....|+++||+.+.|++.|-.++.+
T Consensus 16 TLRyYE~~GLl~p~r-~~~~gyR~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~~ 73 (133)
T cd04787 16 TVRFYTRIGLLRPTR-DPVNGYRLYSEKDLSRLRFILSARQLGFSLKDIKEILSHADQG 73 (133)
T ss_pred HHHHHHHCCCCCCCc-CCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhhhccC
Confidence 567777777644311 0001111234567778888999999999999999988766543
No 57
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=71.85 E-value=6.5 Score=29.71 Aligned_cols=57 Identities=23% Similarity=0.182 Sum_probs=36.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
.+++.|-.+|+=...... -.+|=.=..+..+-+.....|+++||+.+.|++.|...+
T Consensus 15 ~tLRyye~~Gll~p~~~~-~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 15 RTLRHYDDIGLFKPAKIA-ENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHHHCCCCCCCccC-CCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCc
Confidence 466777777765332110 001112334556677778889999999999999887644
No 58
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=71.81 E-value=19 Score=28.98 Aligned_cols=61 Identities=23% Similarity=0.235 Sum_probs=41.5
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHHcCCCh-hHHHHH----------------HHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 148 SDPVVSRYIALGLNREAVHIAVANYGDNP-TKVREF----------------ANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~-~KV~EF----------------l~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
...+..+|..+|++.+.+..+++.+..++ +.+.+. -+.+..|.--||+.+.|..||-...+
T Consensus 78 ~~~I~~~L~~kGi~~~~I~~~l~~~~~d~~e~a~~~~~k~~~~~~~~~~~~k~Ki~~~L~rkGF~~~~I~~~l~~~~~ 155 (157)
T PRK00117 78 PRRIRQELRQKGVDREIIEEALAELDIDWEELARELARKKFRRPLPDDAKEKAKLVRFLARRGFSMDVIQRVLRNALD 155 (157)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHcCccHHHHHHHHHHHHcCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHhhhc
Confidence 45688999999999999999999875333 222222 23355566667777777777755443
No 59
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR. SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulfur cluster activates SoxR. The physiological role in E. coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In E. coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.
Probab=71.79 E-value=8.4 Score=31.55 Aligned_cols=57 Identities=14% Similarity=0.121 Sum_probs=39.7
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
-.+++.|-..|+=.. + +-=.+|=.=..+..+.+.....|+++||+.+.|++.|...+
T Consensus 15 ~~tLRyYE~~GLl~~-~-r~~~g~R~Y~~~di~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (142)
T TIGR01950 15 VSALHFYESKGLITS-I-RNSGNQRRYKRDVLRRVAVIKAAQRVGIPLATIGEALAVLP 71 (142)
T ss_pred HHHHHHHHHCCCCCC-c-cCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHhcc
Confidence 357778888887543 1 11011211236788899999999999999999999997543
No 60
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=71.65 E-value=10 Score=33.39 Aligned_cols=61 Identities=18% Similarity=0.335 Sum_probs=42.0
Q ss_pred CCcHHHHHHHHcCCCHHHHHHHHHHcCC----ChhHHH------------------------------HHHHHHHHHHhc
Q 046691 147 GSDPVVSRYIALGLNREAVHIAVANYGD----NPTKVR------------------------------EFANGYTILREM 192 (222)
Q Consensus 147 ~~DP~V~ky~amG~~reaV~~Av~~yGd----d~~KV~------------------------------EFl~~~~~L~EM 192 (222)
.-.|.|+-|-+.|++.+.+...+..+-. +.+++. .....+.-|+++
T Consensus 174 ~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~l 253 (345)
T PF02536_consen 174 ELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQSL 253 (345)
T ss_dssp CCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHHHHHHHHh
Confidence 3578888899999999999998886433 554421 123347778889
Q ss_pred CCCCchHHHHHHhcc
Q 046691 193 GFSSNNVAEVLIMYE 207 (222)
Q Consensus 193 GFp~~~VaeAL~~~d 207 (222)
||+.+.|+..+..|=
T Consensus 254 G~s~~ei~~mv~~~P 268 (345)
T PF02536_consen 254 GFSEEEIAKMVRRFP 268 (345)
T ss_dssp T--HHHHHHHHHHSG
T ss_pred cCcHHHHHHHHHhCc
Confidence 999999999887763
No 61
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=70.78 E-value=4 Score=30.72 Aligned_cols=31 Identities=26% Similarity=0.380 Sum_probs=19.2
Q ss_pred HHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691 189 LREMGFSSNNVAEVLIMYENDTDKALAHLLG 219 (222)
Q Consensus 189 L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs 219 (222)
+.+.||....|..||..|..|.+.|...+|.
T Consensus 4 ~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~ 34 (87)
T PF11626_consen 4 YEELGYSREFVTHALYATSGDPELARRFVLN 34 (87)
T ss_dssp HHHHTB-HHHHHHHHHHTTTBHHHHHHHHHH
T ss_pred HHHhCCCHHHHHHHHHHhCCCHHHHHHHHHH
Confidence 5566666666666666666666666665543
No 62
>PRK14135 recX recombination regulator RecX; Provisional
Probab=69.94 E-value=26 Score=30.39 Aligned_cols=60 Identities=18% Similarity=0.278 Sum_probs=44.7
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHHcCC-C----hhHHHHHH--------------HHHHHHHhcCCCCchHHHHHHhcc
Q 046691 148 SDPVVSRYIALGLNREAVHIAVANYGD-N----PTKVREFA--------------NGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~yGd-d----~~KV~EFl--------------~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
.-.+..+|..+|++.+.+..||+.+-. + ..++.+.. +....|.--||+.+.|..||-..+
T Consensus 125 ~~~I~~kL~~kGi~~~~Ie~~l~~l~~~~~~d~a~~~~~k~~~~~~~~~~~~~k~Ki~~~L~rkGf~~~~I~~~l~~~~ 203 (263)
T PRK14135 125 PRVIKQKLLQKGIEDEIIEEALSEYTEEDQIEVAQKLAEKLLKKYQKLPFKALKQKIIQSLLTKGFSYEVIKAALEELD 203 (263)
T ss_pred hHHHHHHHHHcCCCHHHHHHHHHhCChhhHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHhCCCCHHHHHHHHHHcc
Confidence 346889999999999999999997733 2 12232221 124668889999999999999875
No 63
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=69.31 E-value=12 Score=27.89 Aligned_cols=68 Identities=13% Similarity=0.049 Sum_probs=44.3
Q ss_pred cHHHHHHHHcCCCHHHHHH--HHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691 149 DPVVSRYIALGLNREAVHI--AVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~--Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
-.++..|-+.|+-.-.-.. +-..| + ..-++-+.....|+++||+...|++.|.. +++.+..+..||.-
T Consensus 15 ~~tLR~ye~~Gll~p~r~~~~g~R~Y--s-~~dv~~l~~I~~Lr~~G~sl~~i~~~l~~-~~~~~~~~~~~~~~ 84 (88)
T cd01105 15 PRQLRYWEEKGLIKSIRSDGGGQRKY--S-LADVDRLLVIKELLDEGFTLAAAVEKLRR-RRVQAEVRRRLMKD 84 (88)
T ss_pred HHHHHHHHHCCCCCCCccCCCCceec--C-HHHHHHHHHHHHHHHCCCCHHHHHHHHHH-ccCHHHHHHHHHHH
Confidence 4567777777774311000 11111 3 34455677788889999999999998874 45788888887753
No 64
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=68.71 E-value=2.2 Score=37.46 Aligned_cols=55 Identities=22% Similarity=0.385 Sum_probs=34.3
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHc-----CCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 149 DPVVSRYIALGLNREAVHIAVANY-----GDNPTKVREFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~y-----Gdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
++.|+.+.++|++.+.+.+.++.. .+.++.+..- ++-|+++||+.++|..++..|
T Consensus 140 ~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~~~~~~~~~~---v~~L~~~G~~~~~i~~~l~~~ 199 (345)
T PF02536_consen 140 KERVEFLKELGFDPEKIGRVIAKNPRLLLSDSESELKPK---VEFLRSLGFSKEDIGKLLRKC 199 (345)
T ss_dssp HCHHHHHCCCTSSHHHHCCCHHHHHHHHCGSCCCCCHHH---HHHHHHCTT-GHHHHHHHHHT
T ss_pred HHHHHHHHHhCCCchhhcccccccchhhccccHHHHHHH---HHHHHhhcccchhhhHHhhcc
Confidence 556777778888887776666533 3344333333 233567888888888887764
No 65
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=68.51 E-value=10 Score=29.47 Aligned_cols=57 Identities=16% Similarity=0.159 Sum_probs=39.4
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
.+++.|-..|+=.. .+---+|=.=.....+.+.....|+++||+.+.|++.|...++
T Consensus 15 ~tlR~Ye~~GLl~p--~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~~~~~ 71 (112)
T cd01282 15 RSLRYYEEQGLLVP--ERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLPCLRG 71 (112)
T ss_pred HHHHHHHHCCCCCC--CcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHhhC
Confidence 46778888887543 1211111113456677888899999999999999998876654
No 66
>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=68.35 E-value=12 Score=29.56 Aligned_cols=58 Identities=17% Similarity=0.265 Sum_probs=38.7
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
-.+++.|-.+|+=..... --..|-.=.++..+.+.....|+++||+.+.|++.|...+
T Consensus 14 ~~tlRyYe~~GLl~p~~r-~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~ 71 (127)
T TIGR02044 14 SKMIRYYEEKGLIPPPLR-SEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLNLWN 71 (127)
T ss_pred HHHHHHHHHCCCCCCCCc-CCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhc
Confidence 346777888887543211 0012333345677788888889999999999999886543
No 67
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=68.08 E-value=11 Score=30.40 Aligned_cols=56 Identities=20% Similarity=0.219 Sum_probs=36.2
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
.+++.|-.+|+=.... +.--.|=.=..+..+.+.....|+++||+.+.|++.|...
T Consensus 15 ~tLRyYE~~GLl~p~~-r~~~gyR~Y~~~~v~~l~~I~~lr~~GfsL~eI~~ll~~~ 70 (131)
T cd04786 15 SRIRFYEAEGLLSSVE-RSANGYRDYPPETVWVLEIISSAQQAGFSLDEIRQLLPAD 70 (131)
T ss_pred HHHHHHHHCCCCCCCC-cCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 4677777888743211 1101111133556777888888999999999999988654
No 68
>PRK14136 recX recombination regulator RecX; Provisional
Probab=67.71 E-value=15 Score=34.62 Aligned_cols=62 Identities=21% Similarity=0.223 Sum_probs=46.2
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCCh---------hH-------HHHHHHHHHHHHhcCCCCchHHHHHHhccCCH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNP---------TK-------VREFANGYTILREMGFSSNNVAEVLIMYENDT 210 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~---------~K-------V~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~ 210 (222)
-.+..+|..+|++.+.+..||+.+..++ +| -.+..+.+.-|.--||..+.|..+|-.++++.
T Consensus 229 ~rIrqELrQKGId~eLIEqALeeieEDE~E~A~~L~eKK~~~~~~d~kek~K~iRfL~rRGFS~D~I~~vLk~~~de~ 306 (309)
T PRK14136 229 ARIVSELKRHAVGDALVESVGAQLRETEFERAQAVWRKKFGALPQTPAERAKQARFLAARGFSSATIVKLLKVGDDEF 306 (309)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhccHhHHHHHHHHHHHHhcccCcCHHHHHHHHHHHHHCCCCHHHHHHHHHhchhcc
Confidence 3478889999999999999888663222 11 12345557778889999999999998887754
No 69
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=67.49 E-value=11 Score=28.62 Aligned_cols=34 Identities=26% Similarity=0.358 Sum_probs=27.4
Q ss_pred HHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHH
Q 046691 178 KVREFANGYTILREMGFSSNNVAEVLIMYENDTD 211 (222)
Q Consensus 178 KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~D 211 (222)
+..+.+.....|++.||+.+.|++.|-.++-+..
T Consensus 42 ~dl~~l~~I~~~r~~G~~L~~I~~~l~~~~~~~~ 75 (124)
T COG0789 42 EDLELLQIIKTLRELGFSLAEIKELLDLLSAGES 75 (124)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHhcccccch
Confidence 3377788888888999999999999988876543
No 70
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=66.24 E-value=11 Score=29.10 Aligned_cols=57 Identities=23% Similarity=0.306 Sum_probs=36.7
Q ss_pred HHHHHHHcCCCHH-HHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 151 VVSRYIALGLNRE-AVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 151 ~V~ky~amG~~re-aV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
+++.|.+.|+=.- ++.. =-+|=.=.++..+.+.....|+.+||+.+.|...|-.+++
T Consensus 16 tlR~ye~~GLi~p~~~~~-~ngyR~Y~~~~i~~l~~I~~lr~~G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 16 ALRYYDKIGLLKPAYVDP-DTGYRYYSAEQLERLNRIKYLRDLGFPLEEIKEILDADND 73 (108)
T ss_pred HHHHHHHcCCCCCCcCCC-CCCccccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCH
Confidence 5666777776532 1110 0011123456677788899999999999999987776654
No 71
>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=66.18 E-value=11 Score=29.90 Aligned_cols=58 Identities=16% Similarity=0.092 Sum_probs=40.8
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
.+++.|-..|+=..... .-.+|-.=.....+.+.....|+++||+.+.|++.|-.++.
T Consensus 15 ~tlR~Ye~~GLl~~~~r-~~~gyR~Y~~~~l~~l~~I~~lr~lG~sL~eI~~~l~~~~~ 72 (127)
T TIGR02047 15 ETIRFYEKQGLLPPPAR-TDNNYRVYTVGHVERLAFIRNCRTLDMSLAEIRQLLRYQDK 72 (127)
T ss_pred HHHHHHHHCCCCCCCCc-CCCCCCcCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhhC
Confidence 47888888888542211 11234444566778888888999999999999998876544
No 72
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=65.11 E-value=12 Score=30.13 Aligned_cols=59 Identities=17% Similarity=0.134 Sum_probs=40.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
.+++-|-..|+=.-..--. -+|-.=.+...+-+.....|++.||+.++|++.|...+.+
T Consensus 18 ~tlR~Ye~~GLL~p~~r~~-~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll~~~~~~ 76 (120)
T TIGR02054 18 HVVRDYLLRGLLHPVRRTT-SGYGIFDDASLQRLRFVRAAFEAGIGLGELARLCRALDAA 76 (120)
T ss_pred HHHHHHHHCCCCCCCccCC-CCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhhccC
Confidence 4677777777754221100 1233334567788889999999999999999998776664
No 73
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=64.84 E-value=14 Score=30.90 Aligned_cols=56 Identities=14% Similarity=0.169 Sum_probs=40.5
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
=.+++.|-.+|+=.. + +--.+|-.=.++..+.+.....|+++||+.+.|++.|..+
T Consensus 25 ~~TlRyYE~~GLi~~-~-r~~~g~R~Y~~~~i~~L~~I~~lr~lG~sL~eIk~ll~~~ 80 (154)
T PRK15002 25 VSALHFYESKGLITS-I-RNSGNQRRYKRDVLRYVAIIKIAQRIGIPLATIGEAFGVL 80 (154)
T ss_pred HHHHHHHHHCCCCCC-c-cCCCCCEEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 357888889998543 1 1111222233477899999999999999999999998764
No 74
>KOG0944 consensus Ubiquitin-specific protease UBP14 [Posttranslational modification, protein turnover, chaperones]
Probab=64.61 E-value=7.3 Score=40.54 Aligned_cols=67 Identities=21% Similarity=0.256 Sum_probs=40.6
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHHcCCChhH--HHHHHHHHHHHHhcCCCCchHHHHHHhccC-CHHHHHHHHh
Q 046691 148 SDPVVSRYIALGLNREAVHIAVANYGDNPTK--VREFANGYTILREMGFSSNNVAEVLIMYEN-DTDKALAHLL 218 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~K--V~EFl~~~~~L~EMGFp~~~VaeAL~~~dN-D~DKAL~~LL 218 (222)
++=-+..|..+|+.... ++|-.---+..| ..|+ ...||.|||||++.-..||.-..| |.|.|--.|+
T Consensus 539 e~ldls~~rs~g~~p~e--e~lpde~~~~~~~~~d~s--~i~qL~~MGFp~eac~rAly~tgN~~aEaA~NWl~ 608 (763)
T KOG0944|consen 539 EELDLSSYRSKGLQPGE--EALPDEAPETSEFAADRS--VISQLVEMGFPEEACRRALYYTGNSGAEAASNWLM 608 (763)
T ss_pred hhhchhhhhhcCCCCcc--cccCCcCcccCccchhHH--HHHHHHHcCCCHHHHHHHHhhhcCccHHHHHHHHH
Confidence 34456777788843321 111111113333 3333 378999999999999999999955 5566655544
No 75
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=63.47 E-value=16 Score=29.61 Aligned_cols=56 Identities=16% Similarity=0.166 Sum_probs=36.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
.+++.|-.+|+=.... +-=-.|-.=..+..+.+.....|+++||+.+.|++.|...
T Consensus 16 ~tlR~Ye~~GLl~p~~-r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~ 71 (140)
T PRK09514 16 DTLRFYEKQGLMDPEV-RTEGGYRLYTEQDLQRLRFIRRAKQLGFTLEEIRELLSIR 71 (140)
T ss_pred HHHHHHHHCCCCCCcc-cCCCCCeeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 4778888888743211 1000122233456677777888999999999999988654
No 76
>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=63.23 E-value=17 Score=27.55 Aligned_cols=65 Identities=17% Similarity=0.218 Sum_probs=40.0
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAH 216 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~ 216 (222)
-.+++.|.++|+=.....-. -+|=.=..+..+.+.....|+++||+.+.|++.|... +.+...+.
T Consensus 14 ~~tlR~ye~~Gll~p~~~~~-~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~~--~~~~~~~~ 78 (97)
T cd04782 14 KQTLFHYDKIGLFKPEIVKE-NGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNR--NPDELIEL 78 (97)
T ss_pred HHHHHHHHHCCCCCCCccCC-CCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC--CHHHHHHH
Confidence 35778888888832211000 1122234456677777888999999999999987644 44444433
No 77
>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=63.14 E-value=16 Score=29.10 Aligned_cols=56 Identities=18% Similarity=0.193 Sum_probs=37.1
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
.+++.|-..|+=..... --..|=.=.....+-+.....|+++||+.+.|++.|...
T Consensus 16 ~tlR~Ye~~GLl~p~~r-~~~gyR~Y~~~~l~~l~~I~~lr~~G~sl~eI~~~l~~~ 71 (131)
T TIGR02043 16 DTLRFYEKNGLIKPAGR-TDSGYRLYTDEDQKRLRFILKAKELGFTLDEIKELLSIK 71 (131)
T ss_pred HHHHHHHHCCCCCCCCc-CCCCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHhh
Confidence 46777888887543221 001111123556777888888999999999999988765
No 78
>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=63.11 E-value=15 Score=27.74 Aligned_cols=57 Identities=21% Similarity=0.245 Sum_probs=33.8
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
.++..|...|+=... .+.-.+|-.=.....+-+..+..|+++||+.+.|++.|-..+
T Consensus 15 ~tlR~ye~~Gll~~~-~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 15 RTLHYYDEIGLLKPS-RRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHHHCCCCCCC-ccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcCc
Confidence 467777777763221 000001111123334445566779999999999999987766
No 79
>PF15187 Augurin: Oesophageal cancer-related gene 4
Probab=62.09 E-value=7.8 Score=31.96 Aligned_cols=29 Identities=28% Similarity=0.479 Sum_probs=21.7
Q ss_pred ChhHHHHHHHH-------------------HHHHHhcCCCCchHHHHH
Q 046691 175 NPTKVREFANG-------------------YTILREMGFSSNNVAEVL 203 (222)
Q Consensus 175 d~~KV~EFl~~-------------------~~~L~EMGFp~~~VaeAL 203 (222)
.+.|++|||.. |.||.=|||.+.....-|
T Consensus 24 ~~skAkeFL~~l~R~kR~lWDRsrPdVQQW~qQFlYmGFDEak~E~Dl 71 (114)
T PF15187_consen 24 PESKAKEFLASLKRQKRQLWDRSRPDVQQWYQQFLYMGFDEAKFEDDL 71 (114)
T ss_pred CHHHHHHHHHHhhhHHHhhhccCCHHHHHHHHHHHHhcchHHHhhhhH
Confidence 46777777766 789999999887665443
No 80
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=60.01 E-value=14 Score=32.50 Aligned_cols=64 Identities=20% Similarity=0.164 Sum_probs=44.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC--CHHHHHH
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN--DTDKALA 215 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN--D~DKAL~ 215 (222)
.+++-|-+.|+=...-.. .+|+.=.+.-.+-+..+..|+++||+.+.|++.|-..+. |.+.+|+
T Consensus 16 ~tIR~Ye~~GLL~p~r~~--~~~r~Y~~~~v~rL~~I~~l~~~G~~L~~I~~~l~~~~~g~~l~~~l~ 81 (219)
T cd04778 16 RNVRAYQDRGLLPPPRRR--GRVAIYNDSHLARLRLINQLLERGYTLAHIAELLAAWEQGRDLGDVLG 81 (219)
T ss_pred HHHHHHHHCCCCCCcccC--CCCcccCHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhhcCCCHHHHHh
Confidence 367788888876432221 245554455567888899999999999999998887665 5555544
No 81
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=59.85 E-value=20 Score=24.42 Aligned_cols=54 Identities=20% Similarity=0.268 Sum_probs=31.4
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHHHHHHHHhcCCCCchHHHHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFANGYTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~ 204 (222)
..++.+|.+.|+-...+.. -.++-. +.+-|. -+..+..|+++||+.+.|+.+|-
T Consensus 14 ~~tlr~~~~~gli~~~~~~-~~g~r~y~~~dl~-~l~~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 14 VRTLRYYERIGLLPPPIRT-EGGYRLYSDEDLE-RLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHHHHCCCCCCCccC-CCCCEecCHHHHH-HHHHHHHHHHcCCCHHHHHHHHh
Confidence 4467777777774321000 001111 444443 34556777999999999999875
No 82
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, an
Probab=59.11 E-value=19 Score=28.15 Aligned_cols=55 Identities=16% Similarity=0.094 Sum_probs=38.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
.+++-|-..|+=...- .. .+|-.=.++..+.+.....|+++||+.+.|++.|...
T Consensus 15 ~tlRyYe~~GLl~p~~-~~-~gyR~Y~~~~l~~l~~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 15 STLRYYEEKGLIASIG-RR-GLRRQYDPQVLDRLALIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred HHHHHHHHCCCCCCCc-CC-CCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcc
Confidence 4677788888754311 11 1333345677788888999999999999999877554
No 83
>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=58.80 E-value=21 Score=28.22 Aligned_cols=58 Identities=19% Similarity=0.281 Sum_probs=37.5
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
.+++.|-..|+=....... .+|=.=..+..+.+.....|+++||+.+.|++.|-.+++
T Consensus 15 ~tlRyYe~~GLl~~~~r~~-~g~R~Y~~~~~~~l~~I~~lr~~G~sL~eI~~~l~~~~~ 72 (127)
T cd01108 15 KMIRYYEEIGLIPPPSRSD-NGYRVYNQRDIEELRFIRRARDLGFSLEEIRELLALWRD 72 (127)
T ss_pred HHHHHHHHCCCCCCCCcCC-CCceecCHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHhC
Confidence 4677777888754221110 112123345666788888899999999999998876554
No 84
>smart00299 CLH Clathrin heavy chain repeat homology.
Probab=56.52 E-value=88 Score=23.89 Aligned_cols=10 Identities=30% Similarity=0.338 Sum_probs=6.2
Q ss_pred ChhHHHHHHH
Q 046691 175 NPTKVREFAN 184 (222)
Q Consensus 175 d~~KV~EFl~ 184 (222)
+++|+.+|+.
T Consensus 55 ~~~~ll~~l~ 64 (140)
T smart00299 55 DPQKEIERLD 64 (140)
T ss_pred CHHHHHHHHH
Confidence 5566666666
No 85
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=56.30 E-value=36 Score=21.98 Aligned_cols=45 Identities=20% Similarity=0.267 Sum_probs=30.7
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHH
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVL 203 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL 203 (222)
.+|+++..|.+.+. |...-+..-.......+++|||..+.++..|
T Consensus 6 ~~gvs~~tvs~~l~--g~~~vs~~~~~~i~~~~~~l~~~~~~~~~~~ 50 (52)
T cd01392 6 AAGVSVATVSRVLN--GKPRVSEETRERVLAAAEELGYRPNAAARSL 50 (52)
T ss_pred HHCcCHHHHHHHHc--CCCCCCHHHHHHHHHHHHHhCCCCCHHHHHh
Confidence 46999999999887 3321122223344667889999999887765
No 86
>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=55.15 E-value=21 Score=29.97 Aligned_cols=58 Identities=17% Similarity=0.162 Sum_probs=37.0
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
.++..|-..|+=.-.. +.-..|=.-.++.++-+.....|+++||+.+.|+..|-..+.
T Consensus 16 ~tLRyYe~~GLl~p~~-r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~ 73 (172)
T cd04790 16 STLLYYERIGLLSPSA-RSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGD 73 (172)
T ss_pred HHHHHHHHCCCCCCCc-cCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCh
Confidence 4677788888743211 100122223345566667888899999999999998765543
No 87
>COG4598 HisP ABC-type histidine transport system, ATPase component [Amino acid transport and metabolism]
Probab=53.76 E-value=6 Score=36.17 Aligned_cols=50 Identities=26% Similarity=0.361 Sum_probs=40.4
Q ss_pred HHHHHHHHHHcCC-----------ChhHHHHHHHHHHHH-----------HhcCCCCchHHHHHHhccCCHH
Q 046691 162 REAVHIAVANYGD-----------NPTKVREFANGYTIL-----------REMGFSSNNVAEVLIMYENDTD 211 (222)
Q Consensus 162 reaV~~Av~~yGd-----------d~~KV~EFl~~~~~L-----------~EMGFp~~~VaeAL~~~dND~D 211 (222)
|.++++||+|-=+ ||+-|.|-|+-+..| +||||..+.-..++..|++-.|
T Consensus 160 R~aIARaLameP~vmLFDEPTSALDPElVgEVLkv~~~LAeEgrTMv~VTHEM~FAR~Vss~v~fLh~G~iE 231 (256)
T COG4598 160 RVAIARALAMEPEVMLFDEPTSALDPELVGEVLKVMQDLAEEGRTMVVVTHEMGFARDVSSHVIFLHQGKIE 231 (256)
T ss_pred HHHHHHHHhcCCceEeecCCcccCCHHHHHHHHHHHHHHHHhCCeEEEEeeehhHHHhhhhheEEeecceec
Confidence 5677888886432 899999999999988 5799999999998888876443
No 88
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=53.54 E-value=23 Score=27.34 Aligned_cols=55 Identities=22% Similarity=0.351 Sum_probs=34.2
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHH-----------------HHHHHHHHhcCCCCchHHHHHHh
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREF-----------------ANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EF-----------------l~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
-+..+|..+|++.+.+..+|+.+ +..+.+.++ -+.+..|.--||+.+.|..+|-.
T Consensus 47 ~I~~~L~~kGi~~~~i~~~l~~~-~~~e~a~~~~~kk~~~~~~~~~~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 47 RIRQKLKQKGIDREIIEEALEEY-DEEEEALELAEKKYRRYRKPSDRKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp HHHHHHHHTT--HHHHHHHHTCS--HHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred HHHHHHHHHCCChHHHHHHHHHh-hHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 46788888999988888888721 112223333 23377788899999999988765
No 89
>PLN03196 MOC1-like protein; Provisional
Probab=52.88 E-value=43 Score=32.63 Aligned_cols=56 Identities=18% Similarity=0.271 Sum_probs=35.7
Q ss_pred CCcHHHHHHHHcCCCHHHHHHHHHHcCC----ChhHHHHHHHHHHHHHhcCCCCchHHHHHH
Q 046691 147 GSDPVVSRYIALGLNREAVHIAVANYGD----NPTKVREFANGYTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 147 ~~DP~V~ky~amG~~reaV~~Av~~yGd----d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~ 204 (222)
.-.|+++-|.+.||+...+...|..|=. +.+ .+....+.-|+++||..+.|..+|.
T Consensus 123 ~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve--~~L~P~v~fL~~lGvs~~~i~~~l~ 182 (487)
T PLN03196 123 NMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVV--VDLAPVVKYLQGLDVKRQDIPRVLE 182 (487)
T ss_pred hhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHH--HHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3467888888999999999988887643 322 2233334444556666666655553
No 90
>PRK06369 nac nascent polypeptide-associated complex protein; Reviewed
Probab=52.56 E-value=13 Score=30.59 Aligned_cols=43 Identities=14% Similarity=0.215 Sum_probs=32.4
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG 219 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs 219 (222)
+-|++.+-|.+-++.-|.+.+| +.+||-.||||.-.||-.|-+
T Consensus 72 ~~~i~~edI~lv~~q~gvs~~~--------------------A~~AL~~~~gDl~~AI~~L~~ 114 (115)
T PRK06369 72 EVEIPEEDIELVAEQTGVSEEE--------------------ARKALEEANGDLAEAILKLSS 114 (115)
T ss_pred cCCCCHHHHHHHHHHHCcCHHH--------------------HHHHHHHcCCcHHHHHHHHhc
Confidence 3477777777776666665555 567999999999999987743
No 91
>TIGR00264 alpha-NAC-related protein. This hypothetical protein is found so far only in the Archaea. Its C-terminal domain of about 40 amino acids is homologous to the C-termini of the nascent polypeptide-associated complex alpha chain (alpha-NAC) and its yeast ortholog Egd2p and to the huntingtin-interacting protein HYPK. It shows weaker similarity, possibly through shared structural constraints rather than through homology, with the amino-terminal domain of elongation factor Ts. Alpha-NAC plays a role in preventing nascent polypeptides from binding inappropriately to membrane-targeting apparatus during translation, but is also active as a transcription regulator.
Probab=51.56 E-value=13 Score=30.63 Aligned_cols=39 Identities=10% Similarity=0.205 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHH
Q 046691 159 GLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHL 217 (222)
Q Consensus 159 G~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~L 217 (222)
+++.+-|.+-.+.-|.+.+| +.+||-.||||.-.||-.|
T Consensus 76 ~i~~eDI~lV~eq~gvs~e~--------------------A~~AL~~~~gDl~~AI~~L 114 (116)
T TIGR00264 76 EITEDDIELVMKQCNVSKEE--------------------ARRALEECGGDLAEAIMKL 114 (116)
T ss_pred CCCHHHHHHHHHHhCcCHHH--------------------HHHHHHHcCCCHHHHHHHh
Confidence 46777777666655555554 5679999999999999766
No 92
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=50.13 E-value=55 Score=27.85 Aligned_cols=137 Identities=15% Similarity=0.166 Sum_probs=74.8
Q ss_pred CCceeEEeecCCcccCCC-----CCC--CCccc-cCCCCCcccchhHHHHHHHHHhhhcCCc--------CccccCCCCC
Q 046691 73 SGLGIRVALKPEYRITPP-----PTL--SPQVG-DIPRSNFHFDFDFERRVLAEAEKENQNW--------SRLGMENIPS 136 (222)
Q Consensus 73 sg~girV~ikpeyRitPP-----p~l--~p~~~-ei~rS~fqfDf~lERkiLAEaek~~~nw--------sk~g~~n~~~ 136 (222)
.|+|.+|.+.+.....=| ..| --.+. |.+| .|-|.-..||++..+-..-..=+ +.|+.+....
T Consensus 22 ~gvGY~v~~~~~~~~~l~~~~~~~~l~~~~~~rd~~~~-l~gF~~~~ek~~f~~L~~i~GIGpk~A~~il~~fg~~~l~~ 100 (192)
T PRK00116 22 NGVGYEVQVPMRTLYELPEVGEEVKLYTHLVVREDAIL-LYGFLTKEERELFRLLISVSGVGPKLALAILSGLSPEELVQ 100 (192)
T ss_pred CCEEEEEEeCHHHHHhccCCCCeEEEEEEEEEechhHH-HcCcCCHHHHHHHHHHhcCCCCCHHHHHHHHHhCCHHHHHH
Confidence 588888888876655432 000 11122 2355 48888666776644433321111 2222211100
Q ss_pred CCCCCCCCCCCCcHHHHHHHH-cCCCHHHHHHHHHHcCCChhHHH-----------HHHHHHHHHHhcCCCCchHHHHHH
Q 046691 137 KNEPTSSVGSGSDPVVSRYIA-LGLNREAVHIAVANYGDNPTKVR-----------EFANGYTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 137 ~~~~tss~~~~~DP~V~ky~a-mG~~reaV~~Av~~yGdd~~KV~-----------EFl~~~~~L~EMGFp~~~VaeAL~ 204 (222)
. ..-+| +..|.. .|++...+.+-+..|-++-.+.. ..-..+..|..+||..+.+..|+.
T Consensus 101 ~-------i~~~d--~~~L~~v~Gig~k~A~~I~~~l~~~~~~~~~~~~~~~~~~~~~~ev~~aL~~LG~~~~~a~~~~~ 171 (192)
T PRK00116 101 A-------IANGD--VKALTKVPGIGKKTAERIVLELKDKLAAAASAAAAAAAASSALEEAVSALVALGYKPKEASKAVA 171 (192)
T ss_pred H-------HHhCC--HHHHHhCCCCCHHHHHHHHHHHHHHhhcccccccccccccchHHHHHHHHHHcCCCHHHHHHHHH
Confidence 0 00012 223443 38888887777766654332110 133567888999999999999998
Q ss_pred hcc---CCHHHHHHHHhc
Q 046691 205 MYE---NDTDKALAHLLG 219 (222)
Q Consensus 205 ~~d---ND~DKAL~~LLs 219 (222)
... +|.+..|...|.
T Consensus 172 ~~~~~~~~~~~~i~~aL~ 189 (192)
T PRK00116 172 KILKEAASVEELIREALK 189 (192)
T ss_pred HHhccCCCHHHHHHHHHH
Confidence 874 478887776654
No 93
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=50.08 E-value=31 Score=29.52 Aligned_cols=47 Identities=28% Similarity=0.360 Sum_probs=36.9
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
.-|.++.-|.+||.+-+.=-+|.+|-+. ...+||||.++..+.+|..
T Consensus 15 ~agVS~~TVSr~Ln~~~~vs~~tr~~V~--~~a~elgY~p~~~a~~l~~ 61 (342)
T PRK10014 15 AAGVSVSTVSLVLSGKGRISTATGERVN--QAIEELGFVRNRQASALRG 61 (342)
T ss_pred HhCCCHHHHHHHHCCCCCCCHHHHHHHH--HHHHHhCCCcCHHHHhhcc
Confidence 4599999999999876664455556554 6688999999999988853
No 94
>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=49.75 E-value=32 Score=26.23 Aligned_cols=54 Identities=15% Similarity=0.090 Sum_probs=37.2
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCC--ChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGD--NPTKVREFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGd--d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
-.++..|-.+|+=... + -.+ |. =.++..+.+.....|+++||+.+.|++.|...
T Consensus 15 ~~tLR~ye~~Gll~~~--r-~~~-g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~~~ 70 (102)
T cd04775 15 RSTLLYYESIGLIPSA--R-SEA-NYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQP 70 (102)
T ss_pred HHHHHHHHHCCCCCCC--C-CCC-CCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHcCC
Confidence 3577888888887321 1 111 32 34556677888888999999999999877543
No 95
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=48.38 E-value=23 Score=24.44 Aligned_cols=50 Identities=20% Similarity=0.254 Sum_probs=31.7
Q ss_pred CcHHHHHHHHc-CCCHHHHHHHHHHcCC---ChhHHHHHHHHHHHHHhcCCCCchHHHHH
Q 046691 148 SDPVVSRYIAL-GLNREAVHIAVANYGD---NPTKVREFANGYTILREMGFSSNNVAEVL 203 (222)
Q Consensus 148 ~DP~V~ky~am-G~~reaV~~Av~~yGd---d~~KV~EFl~~~~~L~EMGFp~~~VaeAL 203 (222)
...++..|.+. |+.. .+ ..-|. +.+.| +-+.....|+++||+.+.|++.|
T Consensus 13 s~~tlR~~~~~g~l~~---~~--~~~g~R~y~~~~l-~~l~~i~~l~~~g~~l~~i~~~l 66 (67)
T cd04764 13 KPHTLRYYEKEFNLYI---PR--TENGRRYYTDEDI-ELLKKIKTLLEKGLSIKEIKEIL 66 (67)
T ss_pred CHHHHHHHHHhcCCCC---CC--CCCCceeeCHHHH-HHHHHHHHHHHCCCCHHHHHHHh
Confidence 34577888765 5441 11 11222 44444 45566888888999999999876
No 96
>PRK09492 treR trehalose repressor; Provisional
Probab=48.37 E-value=33 Score=29.00 Aligned_cols=47 Identities=19% Similarity=0.276 Sum_probs=35.1
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
.-|.++.-|.++|.+-+.=-++.+|-+ +...+||||.++.++.+|..
T Consensus 13 ~agVS~~TVSrvLn~~~~vs~~tr~rV--~~~a~elgY~pn~~a~~l~~ 59 (315)
T PRK09492 13 LSGVGKSTVSRVLNNESGVSEETRERV--EAVINQHGFSPSKSARAMRG 59 (315)
T ss_pred HhCCCHHHHhHHhCCCCCCCHHHHHHH--HHHHHHHCCCcCHHHHHhhc
Confidence 459999999999987665333445543 35688999999999988753
No 97
>COG0751 GlyS Glycyl-tRNA synthetase, beta subunit [Translation, ribosomal structure and biogenesis]
Probab=47.25 E-value=84 Score=32.84 Aligned_cols=91 Identities=23% Similarity=0.339 Sum_probs=67.9
Q ss_pred HHHHHHHhhhcCCcCccccCCCCCCCCCCCCCCCCCcH---------HHHHHHHcCCCHH---HHHHHHHHcCC------
Q 046691 113 RRVLAEAEKENQNWSRLGMENIPSKNEPTSSVGSGSDP---------VVSRYIALGLNRE---AVHIAVANYGD------ 174 (222)
Q Consensus 113 RkiLAEaek~~~nwsk~g~~n~~~~~~~tss~~~~~DP---------~V~ky~amG~~re---aV~~Av~~yGd------ 174 (222)
=.|||=|.|=..=-+=|+.+..|+-+ .|| +++-+++++++.+ .+..++..|+.
T Consensus 450 g~~valADKLDTLvg~F~iG~iPtGS---------kDPyALRRaAlGiirIi~~~~l~l~l~~ll~~~~~~~~~~~~~~~ 520 (691)
T COG0751 450 GAVVALADKLDTLVGFFGIGLIPTGS---------KDPYALRRAALGILRIILEKNLDLDLEELLDKAVASFKSKLTNAK 520 (691)
T ss_pred HHHHHHHHHHHHHHHHHhccCCcCCC---------CCcHHHHHHHhHHHHHHHHhCCCCCHHHHHHHHHHHhhhhccccc
Confidence 36777777765555668888887764 677 6677778877643 44556767765
Q ss_pred ChhHHHHHHHH--HHHHHhcCCCCchHHHHHHhccCCHHH
Q 046691 175 NPTKVREFANG--YTILREMGFSSNNVAEVLIMYENDTDK 212 (222)
Q Consensus 175 d~~KV~EFl~~--~~~L~EMGFp~~~VaeAL~~~dND~DK 212 (222)
..+++.+|+.. ..-|.++||+-+.|.-+|.....|...
T Consensus 521 ~~~~l~~F~~~Rl~~~l~d~g~~~dii~AVL~~~~~~l~~ 560 (691)
T COG0751 521 VLEELLDFFLGRLRTYLQDEGYRKDIIDAVLALNPTDLLD 560 (691)
T ss_pred hHHHHHHHHHHHHHHHHHccCCCHHHHHHHHcCCCCCHHH
Confidence 67789999776 778899999999999999888766543
No 98
>PRK10703 DNA-binding transcriptional repressor PurR; Provisional
Probab=47.09 E-value=41 Score=28.90 Aligned_cols=47 Identities=17% Similarity=0.279 Sum_probs=34.4
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
.-|+++.-|.++|.+.+.=.++.+|-+ +...+||||.++.++..|..
T Consensus 10 ~agVS~~TVSrvLn~~~~vs~~tr~~V--~~~a~elgY~pn~~a~~l~~ 56 (341)
T PRK10703 10 RAGVSTTTVSHVINKTRFVAEETRNAV--WAAIKELHYSPSAVARSLKV 56 (341)
T ss_pred HhCCCHHHHHHHHcCCCCCCHHHHHHH--HHHHHHHCCCcCHHHHHHhh
Confidence 349999999999987666333334433 34578999999999998853
No 99
>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=46.90 E-value=21 Score=28.98 Aligned_cols=55 Identities=20% Similarity=0.189 Sum_probs=36.9
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
.+++.|-..|+=.- + +-=.+|-.=..+..+.+.....|+++||+.+.|++.|..+
T Consensus 16 ~tLRyYE~~GLl~p-~-r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~~~ 70 (139)
T cd01110 16 SALHFYEQKGLIAS-W-RNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALATL 70 (139)
T ss_pred HHHHHHHHCCCCCC-C-cCCCCCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 46777888887432 1 1111222234567788888889999999999999988643
No 100
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=45.74 E-value=53 Score=25.04 Aligned_cols=66 Identities=21% Similarity=0.223 Sum_probs=39.7
Q ss_pred HHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHh-cCCCCchHHHHHHh-ccCCHHHHHHHH
Q 046691 151 VVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILRE-MGFSSNNVAEVLIM-YENDTDKALAHL 217 (222)
Q Consensus 151 ~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~E-MGFp~~~VaeAL~~-~dND~DKAL~~L 217 (222)
+++.|...|+=....... .+|-.=....++.+.....|+. +||+...|++.|-. .+....+=++.|
T Consensus 16 tlR~Ye~~GLl~p~~r~~-~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~~~~~~~~~~~~~~ 83 (95)
T cd04780 16 TIKYYLREGLLPEGRRLA-PNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDAIADASLPSTLLAL 83 (95)
T ss_pred HHHHHHHCCCCCCCcCCC-CCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhcCcccHHHHHHHH
Confidence 677777777733211000 0111124556777888888885 99999999999877 333334444433
No 101
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=45.58 E-value=86 Score=21.47 Aligned_cols=44 Identities=23% Similarity=0.230 Sum_probs=25.9
Q ss_pred HHHHHHHcCCCHHHHHHHHH-HcCCChhHHHHH-HHHHHHHHhcCC
Q 046691 151 VVSRYIALGLNREAVHIAVA-NYGDNPTKVREF-ANGYTILREMGF 194 (222)
Q Consensus 151 ~V~ky~amG~~reaV~~Av~-~yGdd~~KV~EF-l~~~~~L~EMGF 194 (222)
.+-++++.+.+.+.+..+|+ .|+.+++.+.+= ...+.+|++.|+
T Consensus 21 ~Iw~~~~g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~L~~~gl 66 (68)
T PF05402_consen 21 FIWELLDGPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQLREKGL 66 (68)
T ss_dssp HHHHH--SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTT-
T ss_pred HHHHHccCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHCcC
Confidence 45566677788888777776 887777655443 444677888775
No 102
>TIGR02405 trehalos_R_Ecol trehalose operon repressor, proteobacterial. This family consists of repressors of the LacI family typically associated with trehalose utilization operons. Trehalose is imported as trehalose-6-phosphate and then hydrolyzed by alpha,alpha-phosphotrehalase to glucose and glucose-6-P. This family includes repressors mostly from Gammaproteobacteria and does not include the GntR family TreR of Bacillus subtilis
Probab=44.89 E-value=43 Score=28.60 Aligned_cols=47 Identities=17% Similarity=0.249 Sum_probs=35.0
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
.-|.++.-|.+||.+.+.=-++.+|=+ +...+|+||..+..+..|..
T Consensus 10 ~agVS~sTVSr~Ln~~~~vs~~tr~rV--~~~a~~lgY~pn~~a~~l~~ 56 (311)
T TIGR02405 10 LAGVGKSTVSRVLNNEPKVSIETRERV--EQVIQQSGFVPSKSARAMRG 56 (311)
T ss_pred HhCCCHHHHHHHhCCCCCCCHHHHHHH--HHHHHHHCCCcCHHHHHhhc
Confidence 469999999999986655223334443 66788999999999888753
No 103
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=44.62 E-value=32 Score=32.10 Aligned_cols=53 Identities=17% Similarity=0.193 Sum_probs=39.3
Q ss_pred HHHHHHcC---CCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 152 VSRYIALG---LNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 152 V~ky~amG---~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
+.+++.|| ..+.-|..++..++..++++.|=+..|..+ ||+.++|...+.+|=
T Consensus 236 ~~~i~~~g~~p~~~~~v~~~~~~~~~~~~~i~~kv~~l~~~---Gf~~~di~~~~~k~P 291 (413)
T KOG1267|consen 236 LPFLLTLGFDPKTREFVKAPILLSYSSEKTLEPKVEVLKSL---GFSREEIWKMVKKCP 291 (413)
T ss_pred hhhHHHhccCCchhHHHhhhhhhcccccccHHHHHHHHHHc---CCCHHHHHHHHHhCc
Confidence 45566788 445556666777777888888877776666 999999999987763
No 104
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=44.43 E-value=42 Score=22.60 Aligned_cols=21 Identities=24% Similarity=0.441 Sum_probs=9.5
Q ss_pred HHHHHHHcCCCHHHHHHHHHH
Q 046691 151 VVSRYIALGLNREAVHIAVAN 171 (222)
Q Consensus 151 ~V~ky~amG~~reaV~~Av~~ 171 (222)
++.-|+..||.+..+..||..
T Consensus 6 ~~~AL~~LGy~~~e~~~av~~ 26 (47)
T PF07499_consen 6 ALEALISLGYSKAEAQKAVSK 26 (47)
T ss_dssp HHHHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHHH
Confidence 444444455555444444443
No 105
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=43.78 E-value=67 Score=22.79 Aligned_cols=45 Identities=20% Similarity=0.323 Sum_probs=31.1
Q ss_pred HcCCCHHHHHHHHHHcCC-ChhHHHHHHHHHHHHHhcCCCCchHHHHHH
Q 046691 157 ALGLNREAVHIAVANYGD-NPTKVREFANGYTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 157 amG~~reaV~~Av~~yGd-d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~ 204 (222)
..|+++..|.+++..=.. .++ . -...+..++||||..+..+..|.
T Consensus 9 ~~gvS~~TVSr~ln~~~~v~~~-t--~~~i~~~~~~~gy~~~~~~~~~~ 54 (70)
T smart00354 9 LAGVSKATVSRVLNGNGRVSEE-T--REKVLAAMEELGYIPNRVARSLK 54 (70)
T ss_pred HHCCCHHHHHHHHCCCCCCCHH-H--HHHHHHHHHHhCCCCCHHHHHHh
Confidence 459999999999863222 211 1 22345678999999998888765
No 106
>cd04750 Commd2 COMM_Domain containing protein 2. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=43.28 E-value=1.5e+02 Score=24.90 Aligned_cols=61 Identities=16% Similarity=0.243 Sum_probs=44.0
Q ss_pred HHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH------------------HHHHHhcCCCCchHHHHHHhccCCHHH
Q 046691 152 VSRYIALGLNREAVHIAVANYGDNPTKVREFANG------------------YTILREMGFSSNNVAEVLIMYENDTDK 212 (222)
Q Consensus 152 V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~------------------~~~L~EMGFp~~~VaeAL~~~dND~DK 212 (222)
.-.|+..|-|......|-+.+|-+++.|+.-+.+ -..|.++||+.+.+.-..-.+.+.+..
T Consensus 6 a~~~l~~g~n~~~~~~~A~~l~i~~~~vk~~v~aL~~ll~~a~K~~l~~~~~~~~L~~l~~~~e~~~~l~~~y~~~~~~ 84 (166)
T cd04750 6 AIEFLFKGINQKKYEGAARKLEVEVETVQHGVEALVYLLIESTKLKLSERDFQDSIEFLGFSDDLNEILLQLYESNRKE 84 (166)
T ss_pred HHHHHHcCCChHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 4468889999999999999999888887776555 345889999986655544444444433
No 107
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=42.96 E-value=28 Score=25.74 Aligned_cols=30 Identities=27% Similarity=0.304 Sum_probs=22.9
Q ss_pred HHhcCCCCchHHHHHHhccCCH-HHHHHHHh
Q 046691 189 LREMGFSSNNVAEVLIMYENDT-DKALAHLL 218 (222)
Q Consensus 189 L~EMGFp~~~VaeAL~~~dND~-DKAL~~LL 218 (222)
-++|||+.+.|...-..|.||. ++|.+.|.
T Consensus 22 Ar~Lg~~~~dI~~i~~~~~~~~~eq~~~mL~ 52 (84)
T cd08317 22 ARELGVSETDIDLIKAENPNSLAQQAQAMLK 52 (84)
T ss_pred HHHcCCCHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 4678999999988888887775 77777663
No 108
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=42.75 E-value=32 Score=26.64 Aligned_cols=31 Identities=19% Similarity=0.337 Sum_probs=27.2
Q ss_pred HHHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691 188 ILREMGFSSNNVAEVLIMYENDTDKALAHLL 218 (222)
Q Consensus 188 ~L~EMGFp~~~VaeAL~~~dND~DKAL~~LL 218 (222)
..|.+||+.+.|..+-..|-+|.|+..+.|.
T Consensus 25 laR~LGLse~~I~~i~~~~~~~~eq~~qmL~ 55 (96)
T cd08315 25 LMRQLGLSENEIDVAKANERVTREQLYQMLL 55 (96)
T ss_pred HHHHcCCCHHHHHHHHHHCCCCHHHHHHHHH
Confidence 4589999999999999999999888888875
No 109
>COG2137 OraA Uncharacterized protein conserved in bacteria [General function prediction only]
Probab=42.52 E-value=58 Score=28.06 Aligned_cols=64 Identities=22% Similarity=0.295 Sum_probs=45.2
Q ss_pred cHHHHHHHHcCCCHHHHHHHHH-----------------HcCCC--hhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC
Q 046691 149 DPVVSRYIALGLNREAVHIAVA-----------------NYGDN--PTKVREFANGYTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~-----------------~yGdd--~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
.-+-.+|..+|++.+.+..|+. .|+.. +.+-.+-.+....|.--||..+.|.+||..-+-+
T Consensus 88 ~rl~qeL~qkGi~~~~Ie~aL~~~~~~~~~~~a~~~~~kk~~~~~~~~~~~~k~Ki~r~L~~rGFs~~~i~~~l~~~~~~ 167 (174)
T COG2137 88 ARLKQELKQKGIDDEIIEEALELIDEEDEQERARKVLRKKFKRENKPPDKKEKAKIQRFLLRRGFSYEVIKEALNEAEEE 167 (174)
T ss_pred HHHHHHHHHcCCCHHHHHHHHhccchHHHHHHHHHHHHHHhCccccCcchhHHHHHHHHHHHcCCCHHHHHHHHHHhhhc
Confidence 3466788899999888888877 22332 1333334555677778999999999999887666
Q ss_pred HHH
Q 046691 210 TDK 212 (222)
Q Consensus 210 ~DK 212 (222)
.|.
T Consensus 168 ~~e 170 (174)
T COG2137 168 EDE 170 (174)
T ss_pred ccc
Confidence 554
No 110
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=42.46 E-value=49 Score=22.27 Aligned_cols=33 Identities=15% Similarity=0.293 Sum_probs=15.3
Q ss_pred HHHHHhcCCCCchHHHHHHhc----cCCHHHHHHHHh
Q 046691 186 YTILREMGFSSNNVAEVLIMY----ENDTDKALAHLL 218 (222)
Q Consensus 186 ~~~L~EMGFp~~~VaeAL~~~----dND~DKAL~~LL 218 (222)
...|..+||....|..|+... +.|.+..|...|
T Consensus 7 ~~AL~~LGy~~~e~~~av~~~~~~~~~~~e~~ik~aL 43 (47)
T PF07499_consen 7 LEALISLGYSKAEAQKAVSKLLEKPGMDVEELIKQAL 43 (47)
T ss_dssp HHHHHHTTS-HHHHHHHHHHHHHSTTS-HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHHHhhcCCCCCHHHHHHHHH
Confidence 344555566655555555444 224444444443
No 111
>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=42.10 E-value=51 Score=25.19 Aligned_cols=50 Identities=22% Similarity=0.133 Sum_probs=34.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCC--ChhHHHHHHHHHHHHHhcCCCCchHHHHH
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGD--NPTKVREFANGYTILREMGFSSNNVAEVL 203 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGd--d~~KV~EFl~~~~~L~EMGFp~~~VaeAL 203 (222)
.+++.|-+.|+=.. + +- . -|. =.++.++.+.....|+++||+.+.|.+.|
T Consensus 16 ~tlR~ye~~Gll~~-~-r~-~-~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l 67 (102)
T cd04789 16 STLLYYEKLGLITG-T-RN-A-NGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACL 67 (102)
T ss_pred HHHHHHHHCCCCCC-C-cC-C-CCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHH
Confidence 46778888887653 1 11 1 222 34455667778889999999999998865
No 112
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=41.31 E-value=26 Score=23.94 Aligned_cols=53 Identities=21% Similarity=0.194 Sum_probs=33.2
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHHcCC--ChhHHHHHHHHHHHHHhcCCCCchHHHHHH
Q 046691 148 SDPVVSRYIALGLNREAVHIAVANYGD--NPTKVREFANGYTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~yGd--d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~ 204 (222)
...+++.|...|+ ..... ..-|. =.....+-+..+..|+++||+.+.|++.|-
T Consensus 13 s~~tlr~y~~~gl-l~~~~---~~~g~r~y~~~dv~~l~~i~~l~~~G~sl~~I~~~l~ 67 (69)
T PF13411_consen 13 SPSTLRYYEREGL-LPPPR---DENGYRYYSEEDVERLREIKELRKQGMSLEEIKKLLK 67 (69)
T ss_dssp THHHHHHHHHTTS-STTBE---STTSSEEE-HHHHHHHHHHHHHHHTTTHHHHHHHHH-
T ss_pred CHHHHHHHHHhcC-ccccc---ccCceeeccHHHHHHHHHHHHHHHCcCCHHHHHHHHc
Confidence 3456777777776 11111 11121 234456667788889999999999999874
No 113
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=40.28 E-value=25 Score=28.60 Aligned_cols=60 Identities=17% Similarity=0.151 Sum_probs=40.4
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCC---ChhHHHHHHHHHHHHHh-cCCCCchHHHHHHhccCCHHHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGD---NPTKVREFANGYTILRE-MGFSSNNVAEVLIMYENDTDKAL 214 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGd---d~~KV~EFl~~~~~L~E-MGFp~~~VaeAL~~~dND~DKAL 214 (222)
-.+++.|...|+=.-.. . -|. +++.| +-+.....|++ +||+.+.|.+.|.++..+..|+.
T Consensus 15 ~~TLR~wE~~GLl~p~r----~-~G~R~Ys~~dv-~rL~~I~~L~~e~G~~l~eI~~~L~l~~~~~~~~~ 78 (120)
T cd04767 15 PETLRIWERHGLIKPAR----R-NGQRLYSNNDL-KRLRFIKKLINEKGLNIAGVKQILSMYPCWSIRDC 78 (120)
T ss_pred HHHHHHHHHCCCCCCcC----C-CCcEEECHHHH-HHHHHHHHHHHHcCCCHHHHHHHHHhCcccccccc
Confidence 34677788888765421 1 233 44444 45666777776 99999999999988776665543
No 114
>KOG4000 consensus Uncharacterized conserved protein [Function unknown]
Probab=39.94 E-value=46 Score=31.24 Aligned_cols=63 Identities=16% Similarity=0.299 Sum_probs=42.2
Q ss_pred CCCCCCCCCCCCC-CCCCCCceeEEeecCCcccCCCCCCCCccccCCCC--------CcccchhHHHHHHHH
Q 046691 56 VSRTSSYNASPSP-SSSSSGLGIRVALKPEYRITPPPTLSPQVGDIPRS--------NFHFDFDFERRVLAE 118 (222)
Q Consensus 56 ~~r~~~~~~~~~~-~s~ssg~girV~ikpeyRitPPp~l~p~~~ei~rS--------~fqfDf~lERkiLAE 118 (222)
..|+++|....+. .--+-=.|+-.+|.+.|=..+=-|-+-++-+|+.- ...|+|-.||+||+-
T Consensus 208 s~r~~~~~~~~~g~y~~~a~dG~~f~~~~~Fv~~~~s~~~~~l~di~~~~~l~~l~k~y~Ysf~tE~~il~~ 279 (291)
T KOG4000|consen 208 SQRPAPPRPAGVGTYGGTATDGTYFELEVPFVMDVRSQRNQALNDIPTLPELSTLLKSYDYSFQTERQILCT 279 (291)
T ss_pred CCCCCCCccccCCCcceeeccCcceEeecceeecccccCcccccCCccchhHHHHHHhccchhHhHHHHHhh
Confidence 4566666554332 11223346777777888777766777777777654 578999999999975
No 115
>PRK01233 glyS glycyl-tRNA synthetase subunit beta; Validated
Probab=38.74 E-value=1.1e+02 Score=31.75 Aligned_cols=89 Identities=24% Similarity=0.379 Sum_probs=62.2
Q ss_pred HHHHHHHhhhcCCcCccccCCCCCCCCCCCCCCCCCcH---------HHHHHHHcCCCHH---HHHHHHHHcCCCh-hHH
Q 046691 113 RRVLAEAEKENQNWSRLGMENIPSKNEPTSSVGSGSDP---------VVSRYIALGLNRE---AVHIAVANYGDNP-TKV 179 (222)
Q Consensus 113 RkiLAEaek~~~nwsk~g~~n~~~~~~~tss~~~~~DP---------~V~ky~amG~~re---aV~~Av~~yGdd~-~KV 179 (222)
=.||+=|.|--.=-+=|+.+..|+-+ .|| +++-+++.+++.+ .+..|+..|..+. +++
T Consensus 446 g~ilaiADKlDtL~g~F~ig~~PTGS---------~DPfaLRR~A~GIirIi~~~~~~l~L~~li~~a~~~~~~~~~~~l 516 (682)
T PRK01233 446 GAAVALADKLDTLVGIFGIGEIPTGS---------KDPFALRRAALGILRIILEKGLDLDLDELIEKAVSLYNANVLDDV 516 (682)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCcCCC---------CCCHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhhHHHHH
Confidence 45677776654444556666666654 788 5666778887754 5677777775533 578
Q ss_pred HHHHHH--HHHHHhcCCCCchHHHHHHhccCCH
Q 046691 180 REFANG--YTILREMGFSSNNVAEVLIMYENDT 210 (222)
Q Consensus 180 ~EFl~~--~~~L~EMGFp~~~VaeAL~~~dND~ 210 (222)
.+|+.. ...|.+-||..+.|.-+|.....|.
T Consensus 517 ~~F~~~Rl~~~l~~~g~~~dvi~AVl~~~~~~~ 549 (682)
T PRK01233 517 LDFFLDRLKALLQDEGIRYDVIDAVLALRPDDL 549 (682)
T ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHccCCCCH
Confidence 999776 6678899999999999887555454
No 116
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=38.41 E-value=70 Score=26.15 Aligned_cols=58 Identities=16% Similarity=0.131 Sum_probs=38.1
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
-.++..|-+.|+=.- .+.-..|-.=.....+.+.....|+++||+.+.|.+.|..++.
T Consensus 14 ~~TLR~Ye~~GLl~p--~r~~~g~R~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~~~~~ 71 (134)
T cd04779 14 KRTIDYYTNLGLLTP--ERSDSNYRYYDETALDRLQLIEHLKGQRLSLAEIKDQLEEVQR 71 (134)
T ss_pred HHHHHHHHHCCCCCC--ccCCCCCeeECHHHHHHHHHHHHHHHCCCCHHHHHHHHHhhcc
Confidence 347788888887541 1110112112345667778888889999999999998876654
No 117
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=38.35 E-value=30 Score=25.93 Aligned_cols=29 Identities=24% Similarity=0.567 Sum_probs=19.9
Q ss_pred HHHHHHHHHhcCCCCchHH----HHHHhccCCH
Q 046691 182 FANGYTILREMGFSSNNVA----EVLIMYENDT 210 (222)
Q Consensus 182 Fl~~~~~L~EMGFp~~~Va----eAL~~~dND~ 210 (222)
+-.++..++.|||+...|. ..|-++|+|.
T Consensus 11 ~daA~dam~~lG~~~~~v~~vl~~LL~lY~~nW 43 (65)
T PF10440_consen 11 IDAALDAMRQLGFSKKQVRPVLKNLLKLYDGNW 43 (65)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCCc
Confidence 4566778888888877665 4456677663
No 118
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=38.22 E-value=73 Score=24.26 Aligned_cols=58 Identities=21% Similarity=0.194 Sum_probs=38.2
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHh-cCCCCchHHHHHHhcc
Q 046691 148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILRE-MGFSSNNVAEVLIMYE 207 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~E-MGFp~~~VaeAL~~~d 207 (222)
.-.+++.|...|+=.- .+--..|-.=.....+.+.....|++ +||+.+.|++.|-.+.
T Consensus 13 s~~tLR~ye~~Gll~p--~r~~~g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~ 71 (96)
T cd04774 13 TKRTLKYYEEIGLVSP--ERSEGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLERPL 71 (96)
T ss_pred CHHHHHHHHHCCCCCC--CcCCCCCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhccc
Confidence 3457788888887641 11101111123455677888899998 9999999998887655
No 119
>KOG1071 consensus Mitochondrial translation elongation factor EF-Tsmt, catalyzes nucleotide exchange on EF-Tumt [Translation, ribosomal structure and biogenesis]
Probab=38.06 E-value=29 Score=33.31 Aligned_cols=32 Identities=28% Similarity=0.153 Sum_probs=26.0
Q ss_pred HHHHH-hcCCCCchHHHHHHhccCCHHHHHHHH
Q 046691 186 YTILR-EMGFSSNNVAEVLIMYENDTDKALAHL 217 (222)
Q Consensus 186 ~~~L~-EMGFp~~~VaeAL~~~dND~DKAL~~L 217 (222)
+.+|| +-|.+-.+++.||..|+||.++|-+.|
T Consensus 50 lk~LR~kTgas~~ncKkALee~~gDl~~A~~~L 82 (340)
T KOG1071|consen 50 LKKLREKTGASMVNCKKALEECGGDLVLAEEWL 82 (340)
T ss_pred HHHHHHHcCCcHHHHHHHHHHhCCcHHHHHHHH
Confidence 33444 569999999999999999999987765
No 120
>PRK14134 recX recombination regulator RecX; Provisional
Probab=37.20 E-value=1.3e+02 Score=27.41 Aligned_cols=58 Identities=14% Similarity=0.169 Sum_probs=41.5
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCCh--hHH-------------------HHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNP--TKV-------------------REFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~--~KV-------------------~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
--+..+|..+|++.+.+..||+.+-.+. +.+ .+.-+...-|.--||..+.|..||-..
T Consensus 128 ~~I~~eL~qKGI~~~iIe~al~~~~~e~e~e~a~~l~~Kk~~~~~~~~~~~~k~k~Kl~~~L~rrGFs~~~I~~vl~~~ 206 (283)
T PRK14134 128 NKIKYTLLNKGIKENIIIEKINNIDEEKEKKVAYKLAEKKYKILILSEKNKFKIYKKLGPYLISRGYSSNIAEWILNEL 206 (283)
T ss_pred HHHHHHHHHCCCCHHHHHHHHHhCChhhHHHHHHHHHHHhhcccccccccHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
Confidence 3477889999999999999999765422 111 122334566788899999999888555
No 121
>smart00299 CLH Clathrin heavy chain repeat homology.
Probab=36.96 E-value=52 Score=25.17 Aligned_cols=34 Identities=24% Similarity=0.261 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFAN 184 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~ 184 (222)
.+|--|..+|...+||..++.+.+ |.+++.+|+.
T Consensus 87 ~~~~l~~k~~~~~~Al~~~l~~~~-d~~~a~~~~~ 120 (140)
T smart00299 87 EAVELYKKDGNFKDAIVTLIEHLG-NYEKAIEYFV 120 (140)
T ss_pred HHHHHHHhhcCHHHHHHHHHHccc-CHHHHHHHHH
Confidence 344455556666666666665542 3555555555
No 122
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=36.63 E-value=1.6e+02 Score=22.11 Aligned_cols=52 Identities=13% Similarity=0.153 Sum_probs=41.9
Q ss_pred HcCCCHHHHHHHHHHcCCC-hhHHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 157 ALGLNREAVHIAVANYGDN-PTKVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd-~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
..||+...+...-.++.+| .+++.+-|....+-...+...+.+.+||-.|+-
T Consensus 22 ~LGlse~~Id~i~~~~~~~~~eq~~~mL~~W~~~~g~~At~~~L~~aL~~~~l 74 (86)
T cd08306 22 KLGLSETKIESIEEAHPRNLREQVRQSLREWKKIKKKEAKVADLIKALRDCQL 74 (86)
T ss_pred HcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhHCcchHHHHHHHHHHHcCc
Confidence 5688888888888888665 478888888888877888888888888888775
No 123
>PF13249 Prenyltrans_2: Prenyltransferase-like; PDB: 1O6R_B 1O6Q_B 1H35_C 1H3A_C 1SQC_A 1UMP_A 1O6H_C 1O79_B 1GSZ_C 1H37_C ....
Probab=36.58 E-value=45 Score=24.12 Aligned_cols=55 Identities=22% Similarity=0.278 Sum_probs=32.4
Q ss_pred HHHHHHHHcCC--ChhHH--HHHHHHHHHHHhcCCCCch------------HHHHHHhccCC-----HHHHHHHHhc
Q 046691 164 AVHIAVANYGD--NPTKV--REFANGYTILREMGFSSNN------------VAEVLIMYEND-----TDKALAHLLG 219 (222)
Q Consensus 164 aV~~Av~~yGd--d~~KV--~EFl~~~~~L~EMGFp~~~------------VaeAL~~~dND-----~DKAL~~LLs 219 (222)
.|.+||..+|. +.+|+ .+||..... .+=||.... +.-+|..++++ .+||++-||+
T Consensus 28 ~al~aL~~~g~~~~~~~~~~~~~L~~~q~-~dGg~~~~~~~~~~~~~~t~~~l~~l~~~~~~~~~~~~~~a~~~l~~ 103 (113)
T PF13249_consen 28 FALLALAALGEEPDRDRAAAVEWLLSQQN-PDGGWGSNPDGGPPDVYTTYVALAALELLGRPDDEEAVRKAVDWLLS 103 (113)
T ss_dssp HHHHHHHHHTSHHCHHHHHHHHHHHHHB--TTSGBBSSTTTT-BSHHHHHHHHHHHHHHT-GGCHTTHCCHHHHHHH
T ss_pred HHHHHHHHhCCcccHHHHHHHHHHHHhCC-CCCCccCCCCCCCccHHHHHHHHHHHHHcCCCcccHHHHHHHHHHHH
Confidence 35567777777 66778 899888444 566665442 12233333333 4677777775
No 124
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=36.44 E-value=8.7 Score=28.99 Aligned_cols=64 Identities=17% Similarity=0.300 Sum_probs=33.4
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCCChhH-HHHHHHHHHH-HHhcCCCC-chHHHHHHhccCCHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGDNPTK-VREFANGYTI-LREMGFSS-NNVAEVLIMYENDTDK 212 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGdd~~K-V~EFl~~~~~-L~EMGFp~-~~VaeAL~~~dND~DK 212 (222)
..++..|...|++...+....+.||++.-+ +.|=-..+.. +..+||.. |.+|..|=.--+|..+
T Consensus 9 ~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~~nPY~L~~~i~gi~F~~aD~iA~~~g~~~~d~~R 75 (94)
T PF14490_consen 9 RELMAFLQEYGLSPKLAMKLYKKYGDDAIEILKENPYRLIEDIDGIGFKTADKIALKLGIEPDDPRR 75 (94)
T ss_dssp HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHHH-STCCCB-SSSSBHHHHHHHHHTTT--TT-HHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHHChHHHHHHccCCCHHHHHHHHHHcCCCCCCHHH
Confidence 457888999999999999999999984332 2221111222 33555542 3444444334444443
No 125
>TIGR01926 peroxid_rel uncharacterized peroxidase-related enzyme. This protein family with length of about 200 amino acids. One member, from Myxococcus xanthus, is a selenoprotein, with an otherwise conserved Cys replaced by Sec. This family is drawn narrowly enough to suggest that These proteins contain a domain described by TIGR00778, with a CxxCxxxHxxxxxxxG motif. Some members of that family are known to act as peroxidases or correlate with resistance to oxidative stress.
Probab=36.35 E-value=1.1e+02 Score=24.53 Aligned_cols=50 Identities=22% Similarity=0.269 Sum_probs=31.8
Q ss_pred HHcCCCHHHHHHHHHHcCC------ChhHHHHHHHH------------HHHHHhcCCCCchHHHHHHhc
Q 046691 156 IALGLNREAVHIAVANYGD------NPTKVREFANG------------YTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 156 ~amG~~reaV~~Av~~yGd------d~~KV~EFl~~------------~~~L~EMGFp~~~VaeAL~~~ 206 (222)
.++|...+.+. +|..+.+ .+.-+.+|+.. +.+|++.||....|-|+++.+
T Consensus 90 ~~~g~~~~~~~-ai~~~~~~~~~~~~e~a~l~~a~~~~~~~~~v~~~~~~~l~~~g~s~~eivel~~~i 157 (177)
T TIGR01926 90 RQLSGDPDLAD-AVAVNFRDADLSPRERAMLDFAVKLTATPAKVNEADFAALRAAGFSDLDILDLIHSV 157 (177)
T ss_pred HHhcCCHHHHH-HHHhCcccCCCCHHHHHHHHHHHHHhhCcccCCHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 34566655443 4443321 34556677655 667889999999998887654
No 126
>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=36.28 E-value=88 Score=23.05 Aligned_cols=58 Identities=21% Similarity=0.184 Sum_probs=35.5
Q ss_pred cHHHHHHHHcCCCHHHHHHHHHHcCC-ChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCC
Q 046691 149 DPVVSRYIALGLNREAVHIAVANYGD-NPTKVREFANGYTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~~yGd-d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
..++..|...|+=. .+ +--.++-. +.+- ++-+..+..|+.+||+...|+.+|...+.+
T Consensus 14 ~~tlr~~~~~Gll~-~~-~~~~g~r~y~~~d-v~~l~~i~~l~~~g~~~~~i~~~l~~~~~~ 72 (100)
T cd00592 14 VRTLRYYEEKGLLP-PE-RSENGYRLYSEED-LERLRLIRRLRELGLSLKEIRELLDARDEE 72 (100)
T ss_pred HHHHHHHHHCCCcC-CC-cCCCCCcccCHHH-HHHHHHHHHHHHcCCCHHHHHHHHhccccc
Confidence 45777888888732 11 10001111 3333 344555667777999999999999887776
No 127
>PRK09526 lacI lac repressor; Reviewed
Probab=36.27 E-value=71 Score=27.38 Aligned_cols=47 Identities=21% Similarity=0.254 Sum_probs=34.3
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
..|.++.-|.++|-+.+.=-++.+|=+ +...+||||.++.++.+|..
T Consensus 14 ~aGVS~~TVSrvLn~~~~vs~~tr~rV--~~~a~elgY~pn~~a~~l~~ 60 (342)
T PRK09526 14 YAGVSYQTVSRVLNQASHVSAKTREKV--EAAMAELNYVPNRVAQQLAG 60 (342)
T ss_pred HhCCCHHHHHHHhcCCCCCCHHHHHHH--HHHHHHHCCCcCHHHHHhhc
Confidence 459999999999987665333344433 45678899999999988753
No 128
>KOG0743 consensus AAA+-type ATPase [Posttranslational modification, protein turnover, chaperones]
Probab=35.65 E-value=26 Score=34.80 Aligned_cols=70 Identities=30% Similarity=0.391 Sum_probs=46.8
Q ss_pred CCcHHHHH------HHHcCCCHH-HHHHHHHHc-CC--ChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHH
Q 046691 147 GSDPVVSR------YIALGLNRE-AVHIAVANY-GD--NPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAH 216 (222)
Q Consensus 147 ~~DP~V~k------y~amG~~re-aV~~Av~~y-Gd--d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~ 216 (222)
.-||+... =+-||+=.. ++..=..|| |- +.....||.. .+.+-=-++..|+|.|.+++||.|+||..
T Consensus 350 kLDPALlRpGRmDmhI~mgyCtf~~fK~La~nYL~~~~~h~L~~eie~---l~~~~~~tPA~V~e~lm~~~~dad~~lk~ 426 (457)
T KOG0743|consen 350 KLDPALLRPGRMDMHIYMGYCTFEAFKTLASNYLGIEEDHRLFDEIER---LIEETEVTPAQVAEELMKNKNDADVALKG 426 (457)
T ss_pred hcCHhhcCCCcceeEEEcCCCCHHHHHHHHHHhcCCCCCcchhHHHHH---HhhcCccCHHHHHHHHhhccccHHHHHHH
Confidence 45775433 345676444 443333455 43 3555666655 44555568999999999999999999999
Q ss_pred Hhc
Q 046691 217 LLG 219 (222)
Q Consensus 217 LLs 219 (222)
|+.
T Consensus 427 Lv~ 429 (457)
T KOG0743|consen 427 LVE 429 (457)
T ss_pred HHH
Confidence 985
No 129
>PHA02591 hypothetical protein; Provisional
Probab=35.27 E-value=74 Score=25.17 Aligned_cols=31 Identities=23% Similarity=0.311 Sum_probs=26.1
Q ss_pred HHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHH
Q 046691 151 VVSRYIALGLNREAVHIAVANYGDNPTKVREFAN 184 (222)
Q Consensus 151 ~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~ 184 (222)
+++.|.+.||+.++++.. +|-+.++|..|+.
T Consensus 51 vA~eL~eqGlSqeqIA~~---LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASL---LGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHH---hCCCHHHHHHHHh
Confidence 678899999999998876 5788999988875
No 130
>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=34.71 E-value=49 Score=25.15 Aligned_cols=54 Identities=19% Similarity=0.293 Sum_probs=34.5
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHHc-CC--ChhHHHHHHHHHHHHHh-cCCCCchHHHHHHhc
Q 046691 148 SDPVVSRYIALGLNREAVHIAVANY-GD--NPTKVREFANGYTILRE-MGFSSNNVAEVLIMY 206 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~y-Gd--d~~KV~EFl~~~~~L~E-MGFp~~~VaeAL~~~ 206 (222)
...++..|...|+-.- ...- |. =..+..+.+.....|++ +||+.+.|+..|...
T Consensus 14 s~~tLR~ye~~Gli~p-----~r~~~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~l~ 71 (98)
T cd01279 14 HPQTLRVYDRLGLVSP-----ARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIELY 71 (98)
T ss_pred CHHHHHHHHHCCCCCC-----CcCCCCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhh
Confidence 4457777777776532 1111 22 22344556667777777 999999999988775
No 131
>PLN02688 pyrroline-5-carboxylate reductase
Probab=34.56 E-value=96 Score=26.40 Aligned_cols=54 Identities=13% Similarity=0.057 Sum_probs=32.1
Q ss_pred HHHHHHHHcCCChhHHHHHHHHH-----HHHHhcCCCCchHHHHHHhccCCHHHHHHHH
Q 046691 164 AVHIAVANYGDNPTKVREFANGY-----TILREMGFSSNNVAEVLIMYENDTDKALAHL 217 (222)
Q Consensus 164 aV~~Av~~yGdd~~KV~EFl~~~-----~~L~EMGFp~~~VaeAL~~~dND~DKAL~~L 217 (222)
++.+|-...|=+++++.+++... ..+.+-|.....+.+.+....+-++++|+.|
T Consensus 182 a~~ea~~~~Gl~~~~a~~~~~~~~~gs~~l~~~~~~~~~~l~~~v~spgG~t~~~l~~l 240 (266)
T PLN02688 182 ALADGGVAAGLPRDVALSLAAQTVLGAAKMVLETGKHPGQLKDMVTSPGGTTIAGVHEL 240 (266)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHhCCCCchHHHHHHHHH
Confidence 44444445666777777775442 2244567777777666666666666666555
No 132
>PRK10727 DNA-binding transcriptional regulator GalR; Provisional
Probab=34.10 E-value=75 Score=27.49 Aligned_cols=47 Identities=15% Similarity=0.180 Sum_probs=33.5
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
..|.+..-|.++|-+-+.=-+|.+|=+ +...+||||.++.++..|..
T Consensus 10 ~aGVS~~TVSrvLn~~~~Vs~~tr~rV--~~~a~elgY~pn~~ar~l~~ 56 (343)
T PRK10727 10 LAGVSVATVSRVINNSPKASEASRLAV--HSAMESLSYHPNANARALAQ 56 (343)
T ss_pred HhCCCHHHHHHHhCCCCCCCHHHHHHH--HHHHHHHCCCCCHHHHhhhh
Confidence 359999999999987665222333322 45678999999999988854
No 133
>PRK10423 transcriptional repressor RbsR; Provisional
Probab=33.94 E-value=88 Score=26.53 Aligned_cols=46 Identities=11% Similarity=0.200 Sum_probs=33.1
Q ss_pred cCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 158 LGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 158 mG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
-|.+..-|.++|-+-+.=-++.+|=+ +...+||||.++.++.+|..
T Consensus 8 agVS~~TVSrvLn~~~~vs~~tr~rV--~~~a~~lgY~pn~~a~~l~~ 53 (327)
T PRK10423 8 AGVSTSTVSHVINKDRFVSEAITAKV--EAAIKELNYAPSALARSLKL 53 (327)
T ss_pred hCCcHHHHHHHhCCCCCCCHHHHHHH--HHHHHHHCCCccHHHHHHhh
Confidence 49999999999976665223333322 34577999999999998864
No 134
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=33.38 E-value=32 Score=30.96 Aligned_cols=32 Identities=38% Similarity=0.665 Sum_probs=26.8
Q ss_pred cCCcccCCCCCCCCccccCCCCCcccchhHHHHHHHHHhh
Q 046691 82 KPEYRITPPPTLSPQVGDIPRSNFHFDFDFERRVLAEAEK 121 (222)
Q Consensus 82 kpeyRitPPp~l~p~~~ei~rS~fqfDf~lERkiLAEaek 121 (222)
-.+.|+|||.-+.| -|++|.++=|++|-|+=-
T Consensus 36 ~~~l~LTpPaD~R~--------~fp~die~Irevl~ee~G 67 (202)
T COG5270 36 VEELRLTPPADVRP--------AFPYDIEVIREVLVEEFG 67 (202)
T ss_pred ceEEEeCCCCCccc--------cCchHHHHHHHHHHHhcC
Confidence 35789999998877 799999999999988744
No 135
>TIGR01481 ccpA catabolite control protein A. Catabolite control protein A is a LacI family global transcriptional regulator found in Gram-positive bacteria. CcpA is involved in repressing carbohydrate utilization genes [ex: alpha-amylase (amyE), acetyl-coenzyme A synthase (acsA)] and in activating genes involved in transporting excess carbon from the cell [ex: acetate kinase (ackA), alpha-acetolactate synthase (alsS)]. Additionally, disruption of CcpA in Bacillus megaterium, Staphylococcus xylosus, Lactobacillus casei and Lactocacillus pentosus also decreases growth rate, which suggests CcpA is involved in the regulation of other metabolic pathways.
Probab=32.66 E-value=89 Score=26.62 Aligned_cols=47 Identities=17% Similarity=0.253 Sum_probs=34.6
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
.-|.+..-|.++|-+-+.=-+|.+|-+ +...+||||.++.++.+|..
T Consensus 10 ~agvS~~TVSrvLn~~~~vs~~tr~rV--~~~a~~lgY~pn~~a~~l~~ 56 (329)
T TIGR01481 10 EAGVSMATVSRVVNGNPNVKPATRKKV--LEVIKRLDYRPNAVARGLAS 56 (329)
T ss_pred HhCCCHHHHHHHhCCCCCCCHHHHHHH--HHHHHHHCCCCCHHHHHHhh
Confidence 359999999999987665333344433 45778999999999988864
No 136
>PRK10401 DNA-binding transcriptional regulator GalS; Provisional
Probab=32.20 E-value=93 Score=26.94 Aligned_cols=47 Identities=21% Similarity=0.284 Sum_probs=34.0
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
.-|.++.-|.++|.+.+.=-++.+|=+ +...+||||.++.++.+|..
T Consensus 10 ~aGVS~~TVSrvLn~~~~Vs~~tr~kV--~~~a~elgY~pn~~a~~l~~ 56 (346)
T PRK10401 10 QAGVSVATVSRVLNNSALVSADTREAV--MKAVSELGYRPNANAQALAT 56 (346)
T ss_pred HhCCCHHHHHHHHCCCCCCCHHHHHHH--HHHHHHHCCCCCHHHHHhhc
Confidence 359999999999986655223333322 45678999999999998864
No 137
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=32.15 E-value=53 Score=22.31 Aligned_cols=29 Identities=14% Similarity=0.079 Sum_probs=20.5
Q ss_pred ChhHHHHHHHHHHHHHhcCCCCchHHHHHH
Q 046691 175 NPTKVREFANGYTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 175 d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~ 204 (222)
+++.|. -+..+..|++.||+.++|++.|+
T Consensus 40 t~~~v~-~l~~i~~l~~~g~~l~~i~~~~~ 68 (68)
T cd01104 40 SEADVA-RLRLIRRLTSEGVRISQAAALAL 68 (68)
T ss_pred CHHHHH-HHHHHHHHHHCCCCHHHHHHHhC
Confidence 344444 35556777789999999998763
No 138
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=32.01 E-value=72 Score=27.66 Aligned_cols=52 Identities=15% Similarity=0.150 Sum_probs=33.2
Q ss_pred CCCceeEEeecCC--cccCC--CCCCCC--ccccCCCCCcccchhHHHHHHHHHhhhc
Q 046691 72 SSGLGIRVALKPE--YRITP--PPTLSP--QVGDIPRSNFHFDFDFERRVLAEAEKEN 123 (222)
Q Consensus 72 ssg~girV~ikpe--yRitP--Pp~l~p--~~~ei~rS~fqfDf~lERkiLAEaek~~ 123 (222)
..|+|.+|.+... +++.. .+.|-- .+.|-....|-|.-..||++..---+.|
T Consensus 21 ~~GvGY~V~vs~~~~~~l~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~L~~V~ 78 (197)
T PRK14603 21 AGGVGLEVQCPAPTLARLVEGQEAELHTRLVVREDALSLYGFPDEDSLELFELLLGVS 78 (197)
T ss_pred ECCEEEEEEcCHHHHHHcCCCCeEEEEEEEEEccCCceeeCcCCHHHHHHHHHHhCcC
Confidence 3688888888765 34410 111111 1244467889999999999987776653
No 139
>PF10152 DUF2360: Predicted coiled-coil domain-containing protein (DUF2360); InterPro: IPR019309 This entry represents a component of the WASH complex. The WASH complex is present at the surface of endosomes and recruits and activates the Arp2/3 complex to induce actin polymerisation. The WASH complex plays a key role in the fission of tubules that serve as transport intermediates during endosome sorting []. The WASH complex's subunit structure: F-actin-capping protein subunit alpha (CAPZA1, CAPZA2 or CAPZA3), F-actin-capping protein subunit beta (CAPZB), WASH (WASH1, WASH2P, WASH3P, WASH4P, WASH5P or WASH6P), FAM21 (FAM21A, FAM21B or FAM21C), KIAA1033, KIAA0196 (strumpellin) and CCDC53.
Probab=31.69 E-value=61 Score=26.83 Aligned_cols=31 Identities=32% Similarity=0.601 Sum_probs=26.8
Q ss_pred CCcHHHHHHH---HcCCCHHHHHHHHHHcCCChh
Q 046691 147 GSDPVVSRYI---ALGLNREAVHIAVANYGDNPT 177 (222)
Q Consensus 147 ~~DP~V~ky~---amG~~reaV~~Av~~yGdd~~ 177 (222)
..||.-+||- .||+++++|..-+++=|-|+.
T Consensus 111 ~~dP~y~kYfKMl~~GvP~~aVk~KM~~eGlDp~ 144 (148)
T PF10152_consen 111 KDDPRYAKYFKMLKMGVPREAVKQKMQAEGLDPS 144 (148)
T ss_pred cCCccHHHHHHHHHcCCCHHHHHHHHHHcCCCHH
Confidence 4799888875 789999999999999888875
No 140
>PF02092 tRNA_synt_2f: Glycyl-tRNA synthetase beta subunit; InterPro: IPR015944 The aminoacyl-tRNA synthetases (6.1.1 from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold and are mostly monomeric, while class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet formation, flanked by alpha-helices [], and are mostly dimeric or multimeric. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic aci, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. The 10 class I synthetases are considered to have in common the catalytic domain structure based on the Rossmann fold, which is totally different from the class II catalytic domain structure. The class I synthetases are further divided into three subclasses, a, b and c, according to sequence homology. No conserved structural features for tRNA recognition by class I synthetases have been established. Class-II tRNA synthetases do not share a high degree of similarity, however at least three conserved regions are present [, , ]. In most eubacteria, glycyl-tRNA synthetase (6.1.1.14 from EC) is an alpha2/beta2 tetramer composed of 2 different subunits [, , ] while in archaea, eukaryota and some eubacteria, glycyl-tRNA synthetase is an alpha2 dimer (see IPR002315 from INTERPRO). This entry represents the beta subunit of the tetrameric enzyme. What is most interesting is the lack of similarity between the two types: divergence at the sequence level is so great that it is impossible to infer descent from common genes. The alpha (see IPR002310 from INTERPRO) and beta subunits also lack significant sequence similarity. However, they are translated from a single mRNA [], and a single chain glycyl-tRNA synthetase from Chlamydia trachomatis has been found to have significant similarity with both domains, suggesting divergence from a single polypeptide chain []. This entry represents the beta subunit of glycyl-tRNA synthetase.; GO: 0000166 nucleotide binding, 0004820 glycine-tRNA ligase activity, 0005524 ATP binding, 0006426 glycyl-tRNA aminoacylation, 0005737 cytoplasm
Probab=31.54 E-value=1.3e+02 Score=30.25 Aligned_cols=85 Identities=25% Similarity=0.327 Sum_probs=61.1
Q ss_pred HHHHHHHHHhhhcCCcCccccCCCCCCCCCCCCCCCCCcH---------HHHHHHHcCCCH---HHHHHHHHHcCCC---
Q 046691 111 FERRVLAEAEKENQNWSRLGMENIPSKNEPTSSVGSGSDP---------VVSRYIALGLNR---EAVHIAVANYGDN--- 175 (222)
Q Consensus 111 lERkiLAEaek~~~nwsk~g~~n~~~~~~~tss~~~~~DP---------~V~ky~amG~~r---eaV~~Av~~yGdd--- 175 (222)
..=.||+=|+|-..=-+=|+.+..|+-+ .|| +++-+++.+++. +.+..|+..|+.+
T Consensus 442 ~~g~ilsiADKlDtl~g~F~ig~~PtGs---------kDPfaLRRaa~GIirIi~e~~~~l~L~~li~~a~~~~~~~~~~ 512 (548)
T PF02092_consen 442 PIGAILSIADKLDTLVGFFGIGEIPTGS---------KDPFALRRAALGIIRIIIEKKLDLDLKELIEKALELYPKQGKD 512 (548)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCCCC---------CCcHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhhhhccC
Confidence 3457777777765544557777777664 898 566677888774 5678899989842
Q ss_pred ----hhHHHHHHHH--HHHHHhcCCCCchHHHHHH
Q 046691 176 ----PTKVREFANG--YTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 176 ----~~KV~EFl~~--~~~L~EMGFp~~~VaeAL~ 204 (222)
.+.|.+|+.. ...|.+.||+.+.|.-+|.
T Consensus 513 ~~~~~~~v~~F~~~Rl~~~l~~~g~~~d~i~aVl~ 547 (548)
T PF02092_consen 513 KEEILEEVLEFFLERLKNYLKEEGYRYDVIEAVLA 547 (548)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHhhc
Confidence 3456667654 6778899999999988774
No 141
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=31.19 E-value=1.8e+02 Score=31.63 Aligned_cols=16 Identities=13% Similarity=0.341 Sum_probs=10.8
Q ss_pred CCchHHHHHHhccCCH
Q 046691 195 SSNNVAEVLIMYENDT 210 (222)
Q Consensus 195 p~~~VaeAL~~~dND~ 210 (222)
+-..|+-+++.||-|.
T Consensus 714 pyeeik~~ILevne~v 729 (1102)
T KOG1924|consen 714 PYEEIKNVILEVNEDV 729 (1102)
T ss_pred CHHHHHHHHhhccHHH
Confidence 4456777787777653
No 142
>KOG0418 consensus Ubiquitin-protein ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.12 E-value=63 Score=29.10 Aligned_cols=34 Identities=15% Similarity=0.193 Sum_probs=24.4
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHH
Q 046691 148 SDPVVSRYIALGLNREAVHIAVANYGDNPTKVRE 181 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~E 181 (222)
.+..|.+|++|||+++.+-++|..-+-|-.+.-|
T Consensus 162 ~~~~v~~l~~mGf~~~~~i~~L~~~~w~~~~a~~ 195 (200)
T KOG0418|consen 162 DKKKVDSLIEMGFSELEAILVLSGSDWNLADATE 195 (200)
T ss_pred hHHHHHHHHHhcccHHHHHHHhhccccchhhhhH
Confidence 4569999999999998887777644444444444
No 143
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=30.61 E-value=32 Score=27.87 Aligned_cols=26 Identities=31% Similarity=0.507 Sum_probs=20.7
Q ss_pred HHHcCCChhHHHHHHHHHHHHHhcCCCCchHH
Q 046691 169 VANYGDNPTKVREFANGYTILREMGFSSNNVA 200 (222)
Q Consensus 169 v~~yGdd~~KV~EFl~~~~~L~EMGFp~~~Va 200 (222)
|+-.||...||.|||.. |||+.+++.
T Consensus 77 IeiQGdhr~~v~~~L~~------~G~k~k~i~ 102 (104)
T COG0023 77 IEIQGDHRDKVKELLIK------KGFKVKNIG 102 (104)
T ss_pred EEEeChHHHHHHHHHHH------cCCchhhcc
Confidence 45679999999999754 999988763
No 144
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=29.65 E-value=58 Score=21.05 Aligned_cols=25 Identities=24% Similarity=0.332 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHhcCCCCchHHHHHH
Q 046691 180 REFANGYTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 180 ~EFl~~~~~L~EMGFp~~~VaeAL~ 204 (222)
.|++..+...++||.+.+.|.+=|-
T Consensus 3 ~EW~~Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 3 EEWVELIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 5788888888999998888887664
No 145
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=29.36 E-value=85 Score=27.23 Aligned_cols=144 Identities=14% Similarity=0.121 Sum_probs=70.8
Q ss_pred CCCceeEEeecCCcccC-C----CCCCCC--ccccCCCCCcccchhHHHHHHHHHhhhcCCcCccccCCCCCCCCCCCCC
Q 046691 72 SSGLGIRVALKPEYRIT-P----PPTLSP--QVGDIPRSNFHFDFDFERRVLAEAEKENQNWSRLGMENIPSKNEPTSSV 144 (222)
Q Consensus 72 ssg~girV~ikpeyRit-P----Pp~l~p--~~~ei~rS~fqfDf~lERkiLAEaek~~~nwsk~g~~n~~~~~~~tss~ 144 (222)
..|+|.+|.+.....-. | ..+|-- .+.|-....|-|--..||++-..--+.|.=.-|....=...-. +..-.
T Consensus 21 ~~GvGY~v~vs~~~~~~l~~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~Al~iLs~~~-~~el~ 99 (195)
T PRK14604 21 TGGVGLLIYAPRSVLAAIGAIGDEVFLYTHLIVREDALTLYGFSTPAQRQLFELLIGVSGVGPKAALNLLSSGT-PDELQ 99 (195)
T ss_pred ECCEEEEEEeCHHHHHHhccCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhCcCCcCHHHHHHHHcCCC-HHHHH
Confidence 35888888887554432 1 122211 1245577889999999999988876664332221110000000 00000
Q ss_pred CCCCcHHHHHHH-HcCCCHHHHHHHHHHcCCC-------------hhHHHHHHHHHHHHHhcCCCCchHHHHHHhc----
Q 046691 145 GSGSDPVVSRYI-ALGLNREAVHIAVANYGDN-------------PTKVREFANGYTILREMGFSSNNVAEVLIMY---- 206 (222)
Q Consensus 145 ~~~~DP~V~ky~-amG~~reaV~~Av~~yGdd-------------~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~---- 206 (222)
......-+..|+ -.|...--+++=+..+.|. .+. .+-.....|..+||....+..|+...
T Consensus 100 ~aI~~~D~~~L~kvpGIGkKtAerIilELk~K~~~~~~~~~~~~~~~~--~~~e~~~aL~~LGy~~~ea~~ai~~i~~~~ 177 (195)
T PRK14604 100 LAIAGGDVARLARVPGIGKKTAERIVLELKGKIDVRQLSGSTSPAVSA--LDRELSEILISLGYSAAEAAAAIAALPSDA 177 (195)
T ss_pred HHHHhCCHHHHhhCCCCCHHHHHHHHHHHHHHhccccccccccccccc--cHHHHHHHHHHcCCCHHHHHHHHHHHhhcC
Confidence 000000011111 1333333333222222221 111 12346788999999999999999776
Q ss_pred cCCHHHHHHHHh
Q 046691 207 ENDTDKALAHLL 218 (222)
Q Consensus 207 dND~DKAL~~LL 218 (222)
+.|.+..|...|
T Consensus 178 ~~~~~~~ir~aL 189 (195)
T PRK14604 178 PPDLEERLRLAL 189 (195)
T ss_pred CCCHHHHHHHHH
Confidence 447776665554
No 146
>COG0325 Predicted enzyme with a TIM-barrel fold [General function prediction only]
Probab=29.14 E-value=1.1e+02 Score=27.76 Aligned_cols=56 Identities=21% Similarity=0.216 Sum_probs=41.5
Q ss_pred HcCCCHHHHHHHHHHcCC---ChhHHHHHHHHHHHHHhcC---------CCCchHHHHHH----hccCCHHHH
Q 046691 157 ALGLNREAVHIAVANYGD---NPTKVREFANGYTILREMG---------FSSNNVAEVLI----MYENDTDKA 213 (222)
Q Consensus 157 amG~~reaV~~Av~~yGd---d~~KV~EFl~~~~~L~EMG---------Fp~~~VaeAL~----~~dND~DKA 213 (222)
.+-++.+++..|++ .|. .+++|+||+..+..|+++. -.+++|+.+.- .|.-|+.|=
T Consensus 34 SK~~~~~~I~~~~~-aG~r~fGENrvQe~~~K~~~l~~~~~i~WHfIG~LQsNK~k~v~~~~~~ihSlDr~kl 105 (228)
T COG0325 34 SKTVPAEDIREAYE-AGQRHFGENRVQEALDKIEALKDLPDIEWHFIGPLQSNKVKLVAENFDWIHSLDRLKL 105 (228)
T ss_pred eCCCCHHHHHHHHH-cCChhhcchHHHHHHHHHHhcCcCCCeEEEEechhhhhHHHHHHhhcceeeecCHHHH
Confidence 34567788887777 455 8999999999999999985 46677776654 455666653
No 147
>PF03765 CRAL_TRIO_N: CRAL/TRIO, N-terminal domain; InterPro: IPR008273 This entry defines the N-terminal of various retinaldehyde/retinal-binding proteins that may be functional components of the visual cycle. Cellular retinaldehyde-binding protein (CRALBP) carries 11-cis-retinol or 11-cis-retinaldehyde as endogenous ligands and may function as a substrate carrier protein that modulates interaction of these retinoids with visual cycle enzymes []. The multidomain protein Trio binds the LAR transmembrane tyrosine phosphatase, contains a protein kinase domain, and has separate rac-specific and rho-specific guanine nucleotide exchange factor domains []. Trio is a multifunctional protein that integrates and amplifies signals involved in coordinating actin remodeling, which is necessary for cell migration and growth. Other members of the family are transfer proteins that include, guanine nucleotide exchange factor that may function as an effector of RAC1, phosphatidylinositol/phosphatidylcholine transfer protein that is required for the transport of secretory proteins from the golgi complex and alpha-tocopherol transfer protein that enhances the transfer of the ligand between separate membranes.; PDB: 1OIZ_A 1R5L_A 1OIP_A 3HX3_A 3HY5_A 1AUA_A 3Q8G_A 3B7Q_B 3B7Z_A 3B7N_A ....
Probab=28.59 E-value=1.3e+02 Score=20.22 Aligned_cols=43 Identities=19% Similarity=0.210 Sum_probs=26.2
Q ss_pred hHHHHHHHHHHHH----------HhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691 177 TKVREFANGYTIL----------REMGFSSNNVAEVLIMYENDTDKALAHLLG 219 (222)
Q Consensus 177 ~KV~EFl~~~~~L----------~EMGFp~~~VaeAL~~~dND~DKAL~~LLs 219 (222)
+|+.+|...+..+ ....++-..+-.=|-..+.|+++|.+.|..
T Consensus 2 ~~l~~l~~~l~~~~~~~~~~~~~~~~~~~d~~llRFLRARkf~v~~A~~mL~~ 54 (55)
T PF03765_consen 2 QKLKQLREHLSELDEKAPGLWDDEKEDHDDNFLLRFLRARKFDVEKAFKMLKK 54 (55)
T ss_dssp HHHHHHHHHHHH--GGGTHHHTTHTSS-SHHHHHHHHHHTTT-HHHHHHHHHH
T ss_pred HHHHHHHHHHHHhccchhcccccccCCCCHHHHHHHHHHccCCHHHHHHHHHh
Confidence 4556665555543 233333345566677889999999998864
No 148
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=28.45 E-value=1e+02 Score=26.44 Aligned_cols=47 Identities=19% Similarity=0.282 Sum_probs=33.5
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
.-|.++.-|.++|-+.+.=-++.+|=+ +...+||||.++..+..|..
T Consensus 14 ~agVS~~TVSrvLn~~~~vs~~tr~rV--~~~a~elgY~pn~~a~~l~~ 60 (331)
T PRK14987 14 RVGVTKMTVSRFLRNPEQVSVALRGKI--AAALDELGYIPNRAPDILSN 60 (331)
T ss_pred HhCCCHHHhhhhhCCCCCCCHHHHHHH--HHHHHHhCCCccHHHHHHhh
Confidence 359999999999976655222333322 45678999999999988854
No 149
>PRK15043 transcriptional regulator MirA; Provisional
Probab=28.40 E-value=1e+02 Score=28.05 Aligned_cols=34 Identities=12% Similarity=-0.017 Sum_probs=23.7
Q ss_pred hHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCH
Q 046691 177 TKVREFANGYTILREMGFSSNNVAEVLIMYENDT 210 (222)
Q Consensus 177 ~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~ 210 (222)
++..+-+.....|+++||+.+.|++.|...+.+.
T Consensus 44 ~~dv~rL~~I~~l~~~G~~i~eIk~ll~~~~~~~ 77 (243)
T PRK15043 44 DADIDRIREIKRWIDNGVQVSKVKMLLSNENVDV 77 (243)
T ss_pred HHHHHHHHHHHHHHHcCCCHHHHHHHHhccchhh
Confidence 3445566677777888888888888777554443
No 150
>PRK14137 recX recombination regulator RecX; Provisional
Probab=28.33 E-value=2e+02 Score=24.97 Aligned_cols=56 Identities=18% Similarity=0.253 Sum_probs=36.9
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCCh--hHHHHH---------------HHHHHHHHhcCCCCchHHHHHHh
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNP--TKVREF---------------ANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~--~KV~EF---------------l~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
-+..+|..+|++.+-+..||+.+-.+. +.+.+. -+.+.-|.--||..+.|..||-.
T Consensus 106 rI~~eL~qKGI~~~lI~~al~~~d~ede~e~a~~l~~KK~~~~~~~~~~k~K~~~~L~rRGFs~~~I~~al~~ 178 (195)
T PRK14137 106 RVRQTLRRRGVEETLIEETLAARDPQEEQQEARNLLERRWSSFARKRDPRASAYAFLARRGFSGAVIWPAIRE 178 (195)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhcCchhHHHHHHHHHHHhccccCcchhHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 377888899999999999998773211 111111 23356666778888777776643
No 151
>PF12554 MOZART1: Mitotic-spindle organizing gamma-tubulin ring associated; InterPro: IPR022214 This family of proteins is found in eukaryotes. Proteins in this family are typically between 71 and 105 amino acids in length. There is a single completely conserved residue L that may be functionally important.
Probab=28.24 E-value=1.6e+02 Score=20.83 Aligned_cols=33 Identities=27% Similarity=0.531 Sum_probs=23.2
Q ss_pred HHHHHHcCCCHHHHHHHHH--HcCCChhHHHHHHH
Q 046691 152 VSRYIALGLNREAVHIAVA--NYGDNPTKVREFAN 184 (222)
Q Consensus 152 V~ky~amG~~reaV~~Av~--~yGdd~~KV~EFl~ 184 (222)
+.++..-|++++...+.|+ ..|-||+...+-++
T Consensus 11 iS~lLntgLd~etL~ici~L~e~GVnPeaLA~vI~ 45 (48)
T PF12554_consen 11 ISDLLNTGLDRETLSICIELCENGVNPEALAAVIK 45 (48)
T ss_pred HHHHHcCCCCHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 4567788888888887777 55667776655443
No 152
>PF14748 P5CR_dimer: Pyrroline-5-carboxylate reductase dimerisation; PDB: 2RCY_D 3TRI_A 2IZZ_B 2GR9_B 2GRA_B 2GER_C 1YQG_A 2AG8_A 3GT0_A 2AMF_E ....
Probab=28.22 E-value=2.2e+02 Score=22.00 Aligned_cols=22 Identities=32% Similarity=0.421 Sum_probs=13.3
Q ss_pred cHHHHHHHHcCCCHHHHHHHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAVA 170 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av~ 170 (222)
|-++.--+.+|++++.+...+.
T Consensus 25 eal~~a~v~~Gl~~~~A~~lv~ 46 (107)
T PF14748_consen 25 EALADAAVAQGLPREEARKLVA 46 (107)
T ss_dssp HHHHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHHHcCCCHHHHHHHHH
Confidence 3456666778888887766554
No 153
>PRK12491 pyrroline-5-carboxylate reductase; Reviewed
Probab=27.79 E-value=1.6e+02 Score=26.11 Aligned_cols=21 Identities=10% Similarity=0.124 Sum_probs=13.1
Q ss_pred cHHHHHHHHcCCCHHHHHHHH
Q 046691 149 DPVVSRYIALGLNREAVHIAV 169 (222)
Q Consensus 149 DP~V~ky~amG~~reaV~~Av 169 (222)
|-++.--+++||+++.+..-+
T Consensus 184 eal~~a~v~~Gl~~~~A~~l~ 204 (272)
T PRK12491 184 EAMADAAVLGGMPRKQAYKFA 204 (272)
T ss_pred HHHHHHHHHcCCCHHHHHHHH
Confidence 455566667777777665443
No 154
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=27.78 E-value=2.6e+02 Score=21.32 Aligned_cols=57 Identities=16% Similarity=0.117 Sum_probs=44.6
Q ss_pred HHcCCCHHHHHHHHHHcCCCh-hHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHH
Q 046691 156 IALGLNREAVHIAVANYGDNP-TKVREFANGYTILREMGFSSNNVAEVLIMYENDTDK 212 (222)
Q Consensus 156 ~amG~~reaV~~Av~~yGdd~-~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DK 212 (222)
...||+...+...-.++-+|- ++|.+-+....+=..-+.+...+.+||-.|+-|.++
T Consensus 21 r~Lgls~~~I~~i~~~~p~~l~eQv~~mL~~W~~r~G~~ATv~~L~~aL~~~~~~~~~ 78 (83)
T cd08319 21 LDLGLSQTDIYRCKENHPHNVQSQIVEALVKWRQRFGKKATVQSLIQSLKAVEVDPSV 78 (83)
T ss_pred HHcCCCHHHHHHHHHhCCCCHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHcCCCHHH
Confidence 367888888887777776653 677777777777777788888999999999988775
No 155
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.19 E-value=1.4e+02 Score=22.21 Aligned_cols=35 Identities=11% Similarity=0.110 Sum_probs=29.1
Q ss_pred HHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691 151 VVSRYIALGLNREAVHIAVANYGDNPTKVREFANG 185 (222)
Q Consensus 151 ~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~ 185 (222)
.+.+|.+.|++.+.+..-+....+..+++.-|.+.
T Consensus 50 ~I~~Lr~~G~sl~~i~~~l~~~~~~~~~~~~~~~~ 84 (88)
T cd01105 50 VIKELLDEGFTLAAAVEKLRRRRVQAEVRRRLMKD 84 (88)
T ss_pred HHHHHHHCCCCHHHHHHHHHHccCHHHHHHHHHHH
Confidence 57888999999999999999888777777766554
No 156
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=27.19 E-value=40 Score=26.61 Aligned_cols=25 Identities=36% Similarity=0.662 Sum_probs=20.2
Q ss_pred HHHcCCChhHHHHHHHHHHHHHhcCCCCchH
Q 046691 169 VANYGDNPTKVREFANGYTILREMGFSSNNV 199 (222)
Q Consensus 169 v~~yGdd~~KV~EFl~~~~~L~EMGFp~~~V 199 (222)
|+-.||..++|.+||. ++||+..+|
T Consensus 74 I~iQGD~r~~v~~~L~------~~G~~~~~i 98 (99)
T PRK00939 74 IELQGDHRERVKELLI------KMGFSEENI 98 (99)
T ss_pred EEEeCcHHHHHHHHHH------HcCCChhhc
Confidence 5567999999998876 489998775
No 157
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=26.87 E-value=32 Score=22.46 Aligned_cols=22 Identities=18% Similarity=0.145 Sum_probs=13.8
Q ss_pred CchHHHHHHhccCCHHHHHHHH
Q 046691 196 SNNVAEVLIMYENDTDKALAHL 217 (222)
Q Consensus 196 ~~~VaeAL~~~dND~DKAL~~L 217 (222)
...|..||-.|+++..+|-+.|
T Consensus 7 ~~~i~~aL~~~~gn~~~aA~~L 28 (42)
T PF02954_consen 7 KQLIRQALERCGGNVSKAARLL 28 (42)
T ss_dssp HHHHHHHHHHTTT-HHHHHHHH
T ss_pred HHHHHHHHHHhCCCHHHHHHHH
Confidence 3456777777777777665543
No 158
>KOG4329 consensus DNA-binding protein [General function prediction only]
Probab=26.82 E-value=39 Score=33.34 Aligned_cols=42 Identities=24% Similarity=0.223 Sum_probs=27.6
Q ss_pred hhHHHHHHHH--HHHHHhcCCCCc----------hHHHHHHhccCCHHHHHHHH
Q 046691 176 PTKVREFANG--YTILREMGFSSN----------NVAEVLIMYENDTDKALAHL 217 (222)
Q Consensus 176 ~~KV~EFl~~--~~~L~EMGFp~~----------~VaeAL~~~dND~DKAL~~L 217 (222)
+.+|-||+.. -.+-++|+=|.- .+-=+|++||.|+++||..|
T Consensus 213 edEVie~l~k~v~~~~~~~~~p~~P~gt~vkDnEqAL~~LvkcnfDteeAlrr~ 266 (445)
T KOG4329|consen 213 EDEVIEFLLKAVVRLRKEHDQPCPPEGTEVKDNEQALYELVKCNFDTEEALRRL 266 (445)
T ss_pred hHHHHHHHHHHHHhhhcccCCCCCCccccccccHHHHHHHHHcCCcHHHHHHhc
Confidence 4677777654 223445655432 23347999999999999876
No 159
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=26.73 E-value=1.6e+02 Score=26.11 Aligned_cols=24 Identities=25% Similarity=0.326 Sum_probs=17.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcC
Q 046691 150 PVVSRYIALGLNREAVHIAVANYG 173 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yG 173 (222)
..|.-|.++||.+..+..||...-
T Consensus 158 ~~v~AL~~LGy~~~e~~~av~~v~ 181 (201)
T COG0632 158 EAVEALVALGYKEKEIKKAVKKVL 181 (201)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHH
Confidence 337778888888888888777443
No 160
>PRK05441 murQ N-acetylmuramic acid-6-phosphate etherase; Reviewed
Probab=26.69 E-value=1.7e+02 Score=26.60 Aligned_cols=28 Identities=25% Similarity=0.189 Sum_probs=19.4
Q ss_pred HhcCCCCchHHHHHHhccCCHHHHHHHH
Q 046691 190 REMGFSSNNVAEVLIMYENDTDKALAHL 217 (222)
Q Consensus 190 ~EMGFp~~~VaeAL~~~dND~DKAL~~L 217 (222)
...|+......+.|..+++...+||+.+
T Consensus 271 ~~~~~~~~~a~~~l~~~~g~~~~~~~~~ 298 (299)
T PRK05441 271 ILTGLDAAEAKALLARHGGFLRKALAEL 298 (299)
T ss_pred HHhCCCHHHHHHHHHHcCCCHHHHHhhc
Confidence 3446777777777777777777777643
No 161
>cd08327 CARD_RAIDD Caspase activation and recruitment domain of RIP-associated ICH-1 homologous protein with a death domain. Caspase activation and recruitment domain (CARD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal CARD, which interacts with the caspase-2 CARD, and a C-terminal Death domain (DD), which interacts with the DD of PIDD. In general, CARDs are DDs associated with caspases. They are known to be important in the signaling pathways for apoptosis, inflammation and host-defense mechanisms. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodime
Probab=25.98 E-value=2.2e+02 Score=22.20 Aligned_cols=59 Identities=15% Similarity=0.140 Sum_probs=41.6
Q ss_pred CCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHH------------HHHHHhcCCCCchHHHHHHhccCC
Q 046691 147 GSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANG------------YTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 147 ~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~------------~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
+.|++...|...|.=-+.-..-|+..+...+|+..++.. ++.|+| | ..+++-|++-+++
T Consensus 22 ~~~~v~~~L~~~gIlT~~~~e~I~a~~T~~~k~~~LLdiLp~RG~~AF~~F~~aL~e--~--~~l~~~l~~~~~~ 92 (94)
T cd08327 22 VDGLVIQYLYQEGILTESHVEEIESQTTSRRKTMKLLDILPSRGPKAFHAFLDSLEE--F--PWVRDKLLKLREE 92 (94)
T ss_pred chHHHHHHHHhCCCCCHHHHHHHHccCChHHHHHHHHHHHHhhChhHHHHHHHHHHH--H--HHHHHHHHHHHhc
Confidence 345666767888876666777777788888888777654 556666 5 6788888776554
No 162
>TIGR00211 glyS glycyl-tRNA synthetase, tetrameric type, beta subunit. The glycyl-tRNA synthetases differ even among the eubacteria in oligomeric structure. In Escherichia coli and most others, it is a heterodimer of two alpha chains and two beta chains, encoded by tandem genes. The genes are similar, but fused, in Chlamydia trachomatis. By contrast, the glycyl-tRNA synthetases of Thermus thermophilus and of archaea and eukaryotes differ considerably; they are homodimeric, mutually similar, and not detected by this model.
Probab=25.93 E-value=3e+02 Score=28.66 Aligned_cols=99 Identities=27% Similarity=0.354 Sum_probs=65.5
Q ss_pred HHHHHHHHhhhcCCcCccccCCCCCCCCCCCCCCCCCcH---------HHHHHHHcCCCH---HHHHHHHHHcCC---C-
Q 046691 112 ERRVLAEAEKENQNWSRLGMENIPSKNEPTSSVGSGSDP---------VVSRYIALGLNR---EAVHIAVANYGD---N- 175 (222)
Q Consensus 112 ERkiLAEaek~~~nwsk~g~~n~~~~~~~tss~~~~~DP---------~V~ky~amG~~r---eaV~~Av~~yGd---d- 175 (222)
.=.||+=|.|--.=-+=|+.+..|+-+ .|| +++-+++.+++. +.+..|+..|+. +
T Consensus 450 ~g~ivsiADKlDtL~g~F~iG~~PTGS---------~DPfaLRR~A~GIirIi~~~~~~l~L~~li~~a~~~~~~~~~~~ 520 (691)
T TIGR00211 450 VGSVVAMADKLDTLASIFGIGQIPTGS---------KDPFALRRAALGVLRIIVEKNLEIDLEELLTNFVLLQGDKLTNS 520 (691)
T ss_pred HHHHHHHHHHHHHHHHHHhCCCCcCCC---------CCCHHHHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhhhhcccch
Confidence 346777777764444556776666654 788 566677777774 456778888854 1
Q ss_pred --hhHHHHHHHH--HHHHHhcCCCCchHHHHHHhccCC------HHHHHHHHhc
Q 046691 176 --PTKVREFANG--YTILREMGFSSNNVAEVLIMYEND------TDKALAHLLG 219 (222)
Q Consensus 176 --~~KV~EFl~~--~~~L~EMGFp~~~VaeAL~~~dND------~DKAL~~LLs 219 (222)
-+++.+|+.. ...|++.||+.+.|.-+|..-..| +-+||..+..
T Consensus 521 ~~~~~l~~F~~~Rl~~~l~~~g~~~dvi~AVl~~~~~~~~~~~~r~~aL~~~~~ 574 (691)
T TIGR00211 521 NVLEDLEDFFLQRFRALLQDEGIDVDVIQAVLARRETDPADFDARAQALSHFRD 574 (691)
T ss_pred hHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHHccCCCCHHHHHHHHHHHHHHHc
Confidence 1247788766 566789999999999888743322 3356665554
No 163
>PRK11303 DNA-binding transcriptional regulator FruR; Provisional
Probab=25.77 E-value=1.5e+02 Score=25.20 Aligned_cols=46 Identities=22% Similarity=0.281 Sum_probs=32.7
Q ss_pred cCCCHHHHHHHHHHcC---CChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 158 LGLNREAVHIAVANYG---DNPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 158 mG~~reaV~~Av~~yG---dd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
-|.++.-|.++|-+-+ .=.++.+|=+ +...+||||.++.++.+|..
T Consensus 10 aGVS~~TVSrvLn~~~~~~~Vs~~tr~rV--~~~a~elgY~pn~~a~~l~~ 58 (328)
T PRK11303 10 AGVSRTTASYVINGKAKQYRVSDKTVEKV--MAVVREHNYHPNAVAAGLRA 58 (328)
T ss_pred hCCCHHHHHHHHcCCCCCCCcCHHHHHHH--HHHHHHhCCCCCHHHHHhhc
Confidence 4999999999997654 2112233322 55788999999999988864
No 164
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=25.66 E-value=1.5e+02 Score=22.62 Aligned_cols=67 Identities=22% Similarity=0.188 Sum_probs=39.2
Q ss_pred CcHHHHHHHHcCCCHHH--HHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc-cCCHHHHHHHHh
Q 046691 148 SDPVVSRYIALGLNREA--VHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMY-ENDTDKALAHLL 218 (222)
Q Consensus 148 ~DP~V~ky~amG~~rea--V~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~-dND~DKAL~~LL 218 (222)
.-.++..|-..|+=... -.-+-..| ++ ..++.+.....|+ .||..+.+.+.+... ++|.+++++.|-
T Consensus 13 s~~tlR~Ye~~Gll~~~~r~~~g~R~Y--~~-~~v~~l~~I~~l~-~g~~l~~i~~~~~~~~~~~~~~~~~ll~ 82 (99)
T cd04772 13 SPQTVRNYESLGLIPPAERTANGYRIY--TD-KHIAALRAYRALL-PGYGYRVAQRIMRAVHAGIVASALALVD 82 (99)
T ss_pred CHHHHHHHHHcCCCCCCCcCCCCCeec--CH-HHHHHHHHHHHHh-hCCCHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 34577888888875421 11122222 33 3345566666666 688888887755543 467777777654
No 165
>PF14872 GHL5: Hypothetical glycoside hydrolase 5
Probab=25.58 E-value=1.1e+02 Score=32.33 Aligned_cols=32 Identities=13% Similarity=0.333 Sum_probs=25.2
Q ss_pred HHHHHhcCCCC--------chHHHHHHhccCCHHHHHHHH
Q 046691 186 YTILREMGFSS--------NNVAEVLIMYENDTDKALAHL 217 (222)
Q Consensus 186 ~~~L~EMGFp~--------~~VaeAL~~~dND~DKAL~~L 217 (222)
|.+|++|||.. ..+..|+..-|=|.+++-+.|
T Consensus 598 F~~lK~lGF~~le~Lr~F~~aL~~am~~tdYdL~~vA~~c 637 (811)
T PF14872_consen 598 FPRLKQLGFTDLEELRQFMKALQAAMEETDYDLETVADAC 637 (811)
T ss_pred HHHHHHcCCccHHHHHHHHHHHHHHHHhhcCCHHHHHHHH
Confidence 99999999986 456778888888888755444
No 166
>PRK07634 pyrroline-5-carboxylate reductase; Reviewed
Probab=25.55 E-value=2e+02 Score=24.02 Aligned_cols=28 Identities=18% Similarity=0.290 Sum_probs=12.0
Q ss_pred HcCCChhHHHHHHHH-HHHHHhcCCCCch
Q 046691 171 NYGDNPTKVREFANG-YTILREMGFSSNN 198 (222)
Q Consensus 171 ~yGdd~~KV~EFl~~-~~~L~EMGFp~~~ 198 (222)
--|+++.=+..|+.. .+.+.++||+.+.
T Consensus 173 ~~gs~pa~~~~~~~a~~~~~~~~Gl~~~~ 201 (245)
T PRK07634 173 VTGSAPAFLYYFAESLIEATKSYGVDEET 201 (245)
T ss_pred hhcchHHHHHHHHHHHHHHHHHcCCCHHH
Confidence 334444444444443 2233444555444
No 167
>COG1308 EGD2 Transcription factor homologous to NACalpha-BTF3 [Transcription]
Probab=25.13 E-value=62 Score=27.05 Aligned_cols=26 Identities=23% Similarity=0.257 Sum_probs=21.1
Q ss_pred CCCCchHHHHHHhccCCHHHHHHHHh
Q 046691 193 GFSSNNVAEVLIMYENDTDKALAHLL 218 (222)
Q Consensus 193 GFp~~~VaeAL~~~dND~DKAL~~LL 218 (222)
|-+.+.+-+||-.|++|.-.||-+|.
T Consensus 96 ~VsreeA~kAL~e~~GDlaeAIm~L~ 121 (122)
T COG1308 96 GVSREEAIKALEEAGGDLAEAIMKLT 121 (122)
T ss_pred CCCHHHHHHHHHHcCCcHHHHHHHhc
Confidence 45566677899999999999998874
No 168
>PRK14908 glycyl-tRNA synthetase; Provisional
Probab=24.96 E-value=2.9e+02 Score=30.16 Aligned_cols=88 Identities=22% Similarity=0.288 Sum_probs=59.8
Q ss_pred HHHHHHHhhhcCCcCccccCCCCCCCCCCCCCCCCCcH---------HHHHHHHcCCCH---HHHHHHHHHcC-C----C
Q 046691 113 RRVLAEAEKENQNWSRLGMENIPSKNEPTSSVGSGSDP---------VVSRYIALGLNR---EAVHIAVANYG-D----N 175 (222)
Q Consensus 113 RkiLAEaek~~~nwsk~g~~n~~~~~~~tss~~~~~DP---------~V~ky~amG~~r---eaV~~Av~~yG-d----d 175 (222)
=.|||=|.|=-.=-+=|+.+..|+-+ .|| +++-+++.+++. +.+..|+..|+ . +
T Consensus 764 G~ilalADKlDTLvG~FaiG~~PTGS---------kDPfALRRaAlGIirIl~e~~l~l~L~~ll~~a~~~~~~~~~~~~ 834 (1000)
T PRK14908 764 GALLSLADRLDNLLGCFALGLKPTSS---------SDPYALRRQALGVLTLLRATPASLDLEDLLARLARHFPSTTVWVK 834 (1000)
T ss_pred HHHHHHHHHHHHHHHHHhCCCCcCCC---------CCCHHHHHHHHHHHHHHHhcCCCCcHHHHHHHHHHhhcccccccc
Confidence 45666666654444456666666654 788 567777888774 56778888885 1 2
Q ss_pred h---hHHHHHHHH--HHHHHhcCCCCchHHHHHHhccCC
Q 046691 176 P---TKVREFANG--YTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 176 ~---~KV~EFl~~--~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
. ++|.+|+.. ...|.+.||..+.|.-+|.....|
T Consensus 835 ~~~~~~l~~Fi~~Rl~~~l~d~G~~~dvI~AVl~~~~~~ 873 (1000)
T PRK14908 835 EAVLDEVLEFVWGRLKTQLLDLGFDKDEIAAVLPDACKN 873 (1000)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCHHHHHHHHccCCCC
Confidence 1 247788765 566789999999999999754334
No 169
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=24.94 E-value=1.5e+02 Score=20.28 Aligned_cols=39 Identities=18% Similarity=0.287 Sum_probs=25.7
Q ss_pred HcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCc
Q 046691 157 ALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSN 197 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~ 197 (222)
..|++..-|.++|.+-+.=-.+..|-+ +...++|||.+|
T Consensus 8 ~agvS~~TVSr~ln~~~~vs~~tr~rI--~~~a~~lgY~pN 46 (46)
T PF00356_consen 8 EAGVSKSTVSRVLNGPPRVSEETRERI--LEAAEELGYRPN 46 (46)
T ss_dssp HHTSSHHHHHHHHTTCSSSTHHHHHHH--HHHHHHHTB-SS
T ss_pred HHCcCHHHHHHHHhCCCCCCHHHHHHH--HHHHHHHCCCCC
Confidence 569999999999998766222233322 345678888764
No 170
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=24.87 E-value=83 Score=17.34 Aligned_cols=19 Identities=32% Similarity=0.571 Sum_probs=10.9
Q ss_pred CChhHHHHHHHHHHHHHhcCCC
Q 046691 174 DNPTKVREFANGYTILREMGFS 195 (222)
Q Consensus 174 dd~~KV~EFl~~~~~L~EMGFp 195 (222)
.+.+++.+ .+.-|++|||+
T Consensus 13 ~~~~~l~~---~~~~l~~~g~~ 31 (31)
T smart00733 13 YSEKKLKP---KVEFLKELGFS 31 (31)
T ss_pred ccHHHhhH---HHHHHHHcCCC
Confidence 34555554 45556688874
No 171
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.83 E-value=1.5e+02 Score=25.55 Aligned_cols=145 Identities=12% Similarity=0.140 Sum_probs=73.4
Q ss_pred CCceeEEeecCCcccC----CCCCCC--CccccCCCCCcccchhHHHHHHHHHhhhcCCcCccccCCCCCCCCCCCCCCC
Q 046691 73 SGLGIRVALKPEYRIT----PPPTLS--PQVGDIPRSNFHFDFDFERRVLAEAEKENQNWSRLGMENIPSKNEPTSSVGS 146 (222)
Q Consensus 73 sg~girV~ikpeyRit----PPp~l~--p~~~ei~rS~fqfDf~lERkiLAEaek~~~nwsk~g~~n~~~~~~~tss~~~ 146 (222)
.|+|.+|.+++...-. =...|- -++.|-....|-|--..||++...--+.|.=.-|....=...-. +..-...
T Consensus 23 ~GvGY~v~~~~~~~~~l~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li~V~GIGpK~AL~iLs~~~-~~el~~a 101 (188)
T PRK14606 23 SGVVFEIVCDVQTSEEVEEGGECFLHTFLSVSQDGITLYGFSNERKKELFLSLTKVSRLGPKTALKIISNED-AETLVTM 101 (188)
T ss_pred CcEEEEEEeCHHHHHHcCCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhccCCccHHHHHHHHcCCC-HHHHHHH
Confidence 5888888887542221 111111 12355577889999999999988877663322221110000000 0000000
Q ss_pred CCcHHHHHHH-HcCCCHHHHHHHHHHcCCChhH-----HHHHHHHHHHHHhcCCCCchHHHHHHhc---cCCHHHHHHHH
Q 046691 147 GSDPVVSRYI-ALGLNREAVHIAVANYGDNPTK-----VREFANGYTILREMGFSSNNVAEVLIMY---ENDTDKALAHL 217 (222)
Q Consensus 147 ~~DP~V~ky~-amG~~reaV~~Av~~yGdd~~K-----V~EFl~~~~~L~EMGFp~~~VaeAL~~~---dND~DKAL~~L 217 (222)
-...-+..|+ --|..+--+++=+..+-|.-++ ...+-..+..|..+||....+..|+... +.|.|..|...
T Consensus 102 I~~~D~~~L~~vpGIGkKtAerIilELkdK~~~~~~~~~~~~~e~~~AL~~LGy~~~ea~~av~~~~~~~~~~e~lik~A 181 (188)
T PRK14606 102 IASQDVEGLSKLPGISKKTAERIVMELKDEFESAGIKDMRIYHESLEALVSLGYPEKQAREAVKHVYREGMKTSELIKEA 181 (188)
T ss_pred HHhCCHHHHhhCCCCCHHHHHHHHHHHHHhhccccCCCcccHHHHHHHHHHcCCCHHHHHHHHHHHhhCCCCHHHHHHHH
Confidence 0001122232 2455555554444433332111 1123446788999999999999998777 33666555554
Q ss_pred h
Q 046691 218 L 218 (222)
Q Consensus 218 L 218 (222)
|
T Consensus 182 L 182 (188)
T PRK14606 182 L 182 (188)
T ss_pred H
Confidence 4
No 172
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=24.79 E-value=34 Score=27.45 Aligned_cols=38 Identities=21% Similarity=0.319 Sum_probs=22.0
Q ss_pred HHHcCCCHHHHHHHHHHcCCChhHHHHHHHH-HHHHHhcC
Q 046691 155 YIALGLNREAVHIAVANYGDNPTKVREFANG-YTILREMG 193 (222)
Q Consensus 155 y~amG~~reaV~~Av~~yGdd~~KV~EFl~~-~~~L~EMG 193 (222)
|-.+|+++++|.+.-. ...+.++..+.++. ..++++||
T Consensus 86 L~~~Gi~~eRv~~~~~-~~~~~~~fa~~~~~f~~~i~~lG 124 (124)
T PF02662_consen 86 LEELGIEPERVRLYWI-SAPEGKRFAEIVNEFTERIKELG 124 (124)
T ss_pred HHHcCCChhHeEEEEe-CcccHHHHHHHHHHHHHHHHHcC
Confidence 3478888888876433 33355555555444 34566666
No 173
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=24.63 E-value=2.8e+02 Score=30.36 Aligned_cols=10 Identities=10% Similarity=0.262 Sum_probs=4.2
Q ss_pred CCHHHHHHHH
Q 046691 160 LNREAVHIAV 169 (222)
Q Consensus 160 ~~reaV~~Av 169 (222)
++-+.+-.++
T Consensus 713 mpyeeik~~I 722 (1102)
T KOG1924|consen 713 MPYEEIKNVI 722 (1102)
T ss_pred CCHHHHHHHH
Confidence 3444444443
No 174
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=24.52 E-value=44 Score=25.12 Aligned_cols=27 Identities=33% Similarity=0.647 Sum_probs=19.4
Q ss_pred HHHHHcCCChhHHHHHHHHHHHHHhcCCCCchH
Q 046691 167 IAVANYGDNPTKVREFANGYTILREMGFSSNNV 199 (222)
Q Consensus 167 ~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~V 199 (222)
..|+-.||..++|.+|| .++||..++|
T Consensus 48 ~~I~lQGD~r~~v~~~L------~~~g~~~~~i 74 (77)
T cd00474 48 EVIELQGDQRKKIKEFL------IKMGFAKDNI 74 (77)
T ss_pred CEEEEeCcHHHHHHHHH------HHcCCCHHHe
Confidence 34455688888888875 5689988655
No 175
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=24.36 E-value=1e+02 Score=23.13 Aligned_cols=30 Identities=13% Similarity=0.246 Sum_probs=24.4
Q ss_pred HHhcCCCCchHHHHHHhccCCH-HHHHHHHh
Q 046691 189 LREMGFSSNNVAEVLIMYENDT-DKALAHLL 218 (222)
Q Consensus 189 L~EMGFp~~~VaeAL~~~dND~-DKAL~~LL 218 (222)
.+++||+...|...-..|-+|. |++.+.|.
T Consensus 20 aR~LGlse~~Id~i~~~~~~~~~eq~~~mL~ 50 (86)
T cd08306 20 ARKLGLSETKIESIEEAHPRNLREQVRQSLR 50 (86)
T ss_pred HHHcCCCHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 5788999999999998887776 77777664
No 176
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=23.96 E-value=1.1e+02 Score=26.67 Aligned_cols=50 Identities=20% Similarity=0.155 Sum_probs=31.0
Q ss_pred CCceeEEeecCC--cccCC---CCCCCCc--cccCCCCCcccchhHHHHHHHHHhhh
Q 046691 73 SGLGIRVALKPE--YRITP---PPTLSPQ--VGDIPRSNFHFDFDFERRVLAEAEKE 122 (222)
Q Consensus 73 sg~girV~ikpe--yRitP---Pp~l~p~--~~ei~rS~fqfDf~lERkiLAEaek~ 122 (222)
.|+|.+|.|... .++.. .+.|--. +.|-.-..|=|--..||++..---+.
T Consensus 23 ~GvGY~v~i~~~~~~~l~~~g~~v~l~t~~~vrEd~~~LyGF~~~~Er~lF~~Li~V 79 (203)
T PRK14602 23 GGVGYEVFLPAHTLARLPEKGGQVSFFVHTVVREDALELFGFATWDERQTFIVLISI 79 (203)
T ss_pred CCEEEEEEcCHHHHHHhccCCCeEEEEEEEEEecCcceeeCCCCHHHHHHHHHHhCC
Confidence 688888888755 23311 1111111 24446788999999999988776555
No 177
>PRK07993 DNA polymerase III subunit delta'; Validated
Probab=23.88 E-value=5.2e+02 Score=23.90 Aligned_cols=40 Identities=8% Similarity=0.111 Sum_probs=29.5
Q ss_pred CCCcHHHHHHH-Hc-CCCHHHHHHHHHHcCCChhHHHHHHHH
Q 046691 146 SGSDPVVSRYI-AL-GLNREAVHIAVANYGDNPTKVREFANG 185 (222)
Q Consensus 146 ~~~DP~V~ky~-am-G~~reaV~~Av~~yGdd~~KV~EFl~~ 185 (222)
.+.+..+..+. +. |.+.+.+..++...+.++.++.+++..
T Consensus 166 ~~~~~~~~~~L~~~~~~~~~~a~~~~~la~G~~~~Al~l~~~ 207 (334)
T PRK07993 166 PPPEQYALTWLSREVTMSQDALLAALRLSAGAPGAALALLQP 207 (334)
T ss_pred CCCHHHHHHHHHHccCCCHHHHHHHHHHcCCCHHHHHHHhcC
Confidence 44556666544 54 899888888888888899999888643
No 178
>TIGR01089 fucI L-fucose isomerase. This enzyme catalyzes the first step in fucose metabolism, and has been characterized in Escherichia coli and Bacteroides thetaiotaomicron.
Probab=23.81 E-value=1.6e+02 Score=30.43 Aligned_cols=20 Identities=20% Similarity=0.199 Sum_probs=15.3
Q ss_pred HHHHHHHcCCCHHHHHHHHH
Q 046691 151 VVSRYIALGLNREAVHIAVA 170 (222)
Q Consensus 151 ~V~ky~amG~~reaV~~Av~ 170 (222)
+|++.-..-++.+.+.+|++
T Consensus 210 ivrR~~~~iyd~eE~e~Al~ 229 (587)
T TIGR01089 210 IRRRIDQKIYDEEELEMALA 229 (587)
T ss_pred HHHHHhccCCCHHHHHHHHH
Confidence 55555557799999999987
No 179
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=23.75 E-value=1e+02 Score=21.29 Aligned_cols=53 Identities=13% Similarity=0.071 Sum_probs=31.3
Q ss_pred CcHHHHHHHHc-CCCHHHHHHHHHHcCC-ChhHHHHHHHHHHHHHhcCCCCchHHHHH
Q 046691 148 SDPVVSRYIAL-GLNREAVHIAVANYGD-NPTKVREFANGYTILREMGFSSNNVAEVL 203 (222)
Q Consensus 148 ~DP~V~ky~am-G~~reaV~~Av~~yGd-d~~KV~EFl~~~~~L~EMGFp~~~VaeAL 203 (222)
...++..|.+. |+.... +--.++-. +.+.+. -+.....|++.||+.++|++.|
T Consensus 13 s~~tlr~ye~~~gl~~~~--r~~~g~R~yt~~di~-~l~~i~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 13 KPHVLRAWEREFGLLKPQ--RSDGGHRLFNDADID-RILEIKRWIDNGVQVSKVKKLL 67 (68)
T ss_pred CHHHHHHHHHhcCCCCCC--cCCCCCcccCHHHHH-HHHHHHHHHHcCCCHHHHHHHh
Confidence 34567777764 766321 11111212 444444 4455777788999999999876
No 180
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=23.36 E-value=74 Score=23.89 Aligned_cols=30 Identities=10% Similarity=0.057 Sum_probs=21.1
Q ss_pred HHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691 189 LREMGFSSNNVAEVLIMYENDTDKALAHLL 218 (222)
Q Consensus 189 L~EMGFp~~~VaeAL~~~dND~DKAL~~LL 218 (222)
.+++||+.+.|...=..|.+..+++.+.|.
T Consensus 25 ar~LGls~~dI~~i~~~~~~~~eq~~~mL~ 54 (86)
T cd08318 25 APHLEMKDKEIRAIESDSEDIKMQAKQLLV 54 (86)
T ss_pred HHHcCCCHHHHHHHHhcCCCHHHHHHHHHH
Confidence 468899888887766566555677776663
No 181
>PF04533 Herpes_U44: Herpes virus U44 protein; InterPro: IPR007619 This entry represents proteins from dsDNA beta-herpesvirinae and gamma-herpesvirinae viruses. The function is not known, and the proteins are named variously as U44, BSRF1, UL71, and M71. The entry also includes BSRF1.
Probab=23.19 E-value=91 Score=28.22 Aligned_cols=12 Identities=17% Similarity=0.288 Sum_probs=5.9
Q ss_pred HHHHHHHcCCCH
Q 046691 151 VVSRYIALGLNR 162 (222)
Q Consensus 151 ~V~ky~amG~~r 162 (222)
-+...++|||+.
T Consensus 36 ~l~~ei~~~~pp 47 (210)
T PF04533_consen 36 RLQAEIEMGFPP 47 (210)
T ss_pred HHHHHHHccCCC
Confidence 344445555555
No 182
>PRK03980 flap endonuclease-1; Provisional
Probab=22.80 E-value=67 Score=29.38 Aligned_cols=28 Identities=29% Similarity=0.349 Sum_probs=19.5
Q ss_pred ChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 175 NPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 175 d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
|.+++.+||. .|.||+.+.|..+|-.-.
T Consensus 250 d~~~l~~fl~-----~e~~f~~~rv~~~~~~l~ 277 (292)
T PRK03980 250 DKEGIIEFLV-----EEHDFSEERVKKALERLE 277 (292)
T ss_pred CHHHHHHHHh-----ccCCCCHHHHHHHHHHHH
Confidence 4455555543 589999999998886653
No 183
>PF05182 Fip1: Fip1 motif; InterPro: IPR007854 This short motif is about 40 amino acids in length and is found in the Fip1 protein that is a component of a Saccharomyces cerevisiae pre-mRNA polyadenylation factor that directly interacts with poly(A) polymerase []. This region of Fip1 is needed for the interaction with the Yth1 subunit of the complex and for specific polyadenylation of the cleaved mRNA precursor [].
Probab=22.76 E-value=77 Score=22.29 Aligned_cols=21 Identities=38% Similarity=0.542 Sum_probs=18.9
Q ss_pred HcCCChhHHHHHHHHHHHHHh
Q 046691 171 NYGDNPTKVREFANGYTILRE 191 (222)
Q Consensus 171 ~yGdd~~KV~EFl~~~~~L~E 191 (222)
|||=|++.-.+||....+||.
T Consensus 25 NYGf~E~tW~~Y~~kq~~~R~ 45 (45)
T PF05182_consen 25 NYGFNEETWREYCKKQRQLRK 45 (45)
T ss_pred CCCCCHHHHHHHHHHHHHhhC
Confidence 799999999999999998873
No 184
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=22.75 E-value=2.6e+02 Score=20.58 Aligned_cols=51 Identities=10% Similarity=0.146 Sum_probs=38.6
Q ss_pred HcCCCHHHHHHHHHHcCCC-hhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 157 ALGLNREAVHIAVANYGDN-PTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 157 amG~~reaV~~Av~~yGdd-~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
.+||+..-+..--.++.++ .+++.+.|....+-.........+.+||..++
T Consensus 24 ~Lg~~~~dI~~i~~~~~~~~~eq~~~mL~~W~~r~g~~at~~~L~~AL~~i~ 75 (84)
T cd08317 24 ELGVSETDIDLIKAENPNSLAQQAQAMLKLWLEREGKKATGNSLEKALKKIG 75 (84)
T ss_pred HcCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHhcCCcchHHHHHHHHHHcC
Confidence 6788888888777777654 47788888877766655588888888888765
No 185
>PRK15081 glutathione ABC transporter permease GsiC; Provisional
Probab=22.60 E-value=2.8e+02 Score=25.22 Aligned_cols=57 Identities=16% Similarity=0.130 Sum_probs=41.0
Q ss_pred CCCcHHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHH--hcCCCC---chHHHHH
Q 046691 146 SGSDPVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILR--EMGFSS---NNVAEVL 203 (222)
Q Consensus 146 ~~~DP~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~--EMGFp~---~~VaeAL 203 (222)
.|+||+.. +.....+.|+++..-+.||=|.-=.+.|.+-+..+- |+|.+- ..|.+.+
T Consensus 30 ~Pgdp~~~-~~~~~~~~e~~~~~~~~~Gld~p~~~qy~~~l~~~~~gd~G~S~~~~~~V~~~i 91 (306)
T PRK15081 30 LPGDPARL-AAGPEADAQVVALVRQQLGLDQPLPHQFWHYISNALQGDFGTSMVSRRPVSEEI 91 (306)
T ss_pred CCCCHHHH-hcCCCCCHHHHHHHHHHhCCCCCHHHHHHHHHHHHhccCCccCCCCCCCHHHHH
Confidence 47899653 544457889999888899998888888877665554 788773 3455544
No 186
>PF13977 TetR_C_6: Bacterial transcriptional repressor; PDB: 2NX4_C 3CRJ_C 3E7Q_B 2NP5_A 3QBM_B 2G3B_B 2GFN_A.
Probab=22.51 E-value=2.3e+02 Score=20.11 Aligned_cols=57 Identities=12% Similarity=-0.029 Sum_probs=32.2
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691 162 REAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLL 218 (222)
Q Consensus 162 reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LL 218 (222)
++++...|..+=....+-.+++..+-.|.........+++.+........+.|..+|
T Consensus 2 ~e~l~~~~~~~~~~~~~~~~~~~l~~~~~~~a~~~p~l~~~~~~~~~~~~~~l~~~l 58 (115)
T PF13977_consen 2 RERLRAILDALLPASEEDPREWRLWLEFWAEARRDPELRALLREAYARWRSRLAELL 58 (115)
T ss_dssp HHHHHHHHHHHSTCSHHHHHHHHHHHHHHHHCTT-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHccCHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555555555444444455555666666666666666666666655555555544
No 187
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=22.46 E-value=1.1e+02 Score=22.99 Aligned_cols=38 Identities=21% Similarity=0.297 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHH
Q 046691 178 KVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALA 215 (222)
Q Consensus 178 KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~ 215 (222)
+-.++-..+..|.++||+...+....-.+..+.-+.|+
T Consensus 4 ~~~~~~~~~~~L~~~gl~~~~a~kl~~~yg~~ai~~l~ 41 (94)
T PF14490_consen 4 ENRGLRELMAFLQEYGLSPKLAMKLYKKYGDDAIEILK 41 (94)
T ss_dssp -----HHHHHHHHHTT--HHHHHHHHHHH-TTHHHHHH
T ss_pred HHHHHHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHH
Confidence 44566777889999999999999988888875554443
No 188
>PF00749 tRNA-synt_1c: tRNA synthetases class I (E and Q), catalytic domain; InterPro: IPR020058 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Glutamyl-tRNA synthetase (6.1.1.17 from EC) is a class Ic synthetase and shows several similarities with glutaminyl-tRNA synthetase concerning structure and catalytic properties. It is an alpha2 dimer. To date one crystal structure of a glutamyl-tRNA synthetase (Thermus thermophilus) has been solved. The molecule has the form of a bent cylinder and consists of four domains. The N-terminal half (domains 1 and 2) contains the 'Rossman fold' typical for class I synthetases and resembles the corresponding part of Escherichia coli GlnRS, whereas the C-terminal half exhibits a GluRS-specific structure []. ; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016876 ligase activity, forming aminoacyl-tRNA and related compounds, 0043039 tRNA aminoacylation, 0005737 cytoplasm; PDB: 2HZ7_A 2CFO_A 4A91_A 1NZJ_A 1N78_A 1G59_C 2CV2_A 2CV1_A 2CV0_B 1GLN_A ....
Probab=22.42 E-value=1.3e+02 Score=27.57 Aligned_cols=57 Identities=19% Similarity=0.316 Sum_probs=40.1
Q ss_pred CcHH--HHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhc
Q 046691 148 SDPV--VSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILREMGFSSNNVAEVLIMY 206 (222)
Q Consensus 148 ~DP~--V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~ 206 (222)
.+.. +..|.+.|++++++...|+..|-.+....||++.....+. |..+.+...++.+
T Consensus 249 ~~~~i~~~~~r~~g~~~~~~l~~L~~lG~~~~~~~e~~~~~~~~~~--f~~~~~~~~~~~f 307 (314)
T PF00749_consen 249 GAKSIELGDYREWGDPPEATLNYLARLGWSPEAIREFFSLDELIKQ--FDLSKISKSPAVF 307 (314)
T ss_dssp SHHBHHHHHHHHTT-THHHHHHHHHHTTB-HCTHHCHHHHHHHHHH--C-GGGBHSSHEEH
T ss_pred ccccccccccccCCCCHHHHHHHHHHhcCCcchhhhhcCHHHHHHH--hhHhhccCchHHh
Confidence 4556 7899999999999999999999998889999877544443 3444444444433
No 189
>KOG1194 consensus Predicted DNA-binding protein, contains Myb-like, SANT and ELM2 domains [Transcription]
Probab=22.29 E-value=1.2e+02 Score=30.76 Aligned_cols=43 Identities=21% Similarity=0.207 Sum_probs=32.9
Q ss_pred ChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhc
Q 046691 175 NPTKVREFANGYTILREMGFSSNNVAEVLIMYENDTDKALAHLLG 219 (222)
Q Consensus 175 d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs 219 (222)
+..|+.||+.--..+ -|.+.+.+-.-|..|++|+|+|+..|..
T Consensus 140 ~D~kL~EYI~~A~~r--Y~i~ieqAL~iL~~h~~d~d~A~~~l~r 182 (534)
T KOG1194|consen 140 QDDKLEEYISEAKER--YGIPIEQALFILFWHKHDFDLAHADLAR 182 (534)
T ss_pred cHHHHHHHHHHHHHh--cCCcHHHHHHHHHhhcccchHHHHHHhh
Confidence 566888887543332 4777777888899999999999998864
No 190
>PHA02591 hypothetical protein; Provisional
Probab=22.15 E-value=80 Score=24.98 Aligned_cols=22 Identities=23% Similarity=0.261 Sum_probs=18.4
Q ss_pred HHHHHHHHhcCCCCchHHHHHH
Q 046691 183 ANGYTILREMGFSSNNVAEVLI 204 (222)
Q Consensus 183 l~~~~~L~EMGFp~~~VaeAL~ 204 (222)
++.-.+|.++||....||+.|=
T Consensus 49 ~~vA~eL~eqGlSqeqIA~~LG 70 (83)
T PHA02591 49 ISVTHELARKGFTVEKIASLLG 70 (83)
T ss_pred HHHHHHHHHcCCCHHHHHHHhC
Confidence 3456789999999999999984
No 191
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA 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=22.13 E-value=1.1e+02 Score=26.26 Aligned_cols=132 Identities=12% Similarity=0.145 Sum_probs=66.0
Q ss_pred CCceeEEeecCCcccCCCC----CCCC--ccccCCCCCcccchhHHHHHHHHHhhhcCCcCccccCCCCCCCCCCCCC--
Q 046691 73 SGLGIRVALKPEYRITPPP----TLSP--QVGDIPRSNFHFDFDFERRVLAEAEKENQNWSRLGMENIPSKNEPTSSV-- 144 (222)
Q Consensus 73 sg~girV~ikpeyRitPPp----~l~p--~~~ei~rS~fqfDf~lERkiLAEaek~~~nwsk~g~~n~~~~~~~tss~-- 144 (222)
.|+|.+|.+.+...-.=+. .|-- ++.|-.-..|=|--..||++..+--+-+.=+-|....=...-. ....
T Consensus 22 ~GvGY~v~v~~~~~~~l~~g~~v~l~t~~~vred~~~LyGF~~~~Er~lF~~L~~V~GIGpK~Al~iL~~~~--~~el~~ 99 (191)
T TIGR00084 22 NGVGYELQVPMTCAYELNLEQKAQVFTHLVVREDAELLFGFNTLEERELFKELIKVNGVGPKLALAILSNMS--PEEFVY 99 (191)
T ss_pred CCEEEEEEecHHHHHhcCCCCeEEEEEEEEEecCCceeeCCCCHHHHHHHHHHhCCCCCCHHHHHHHHhcCC--HHHHHH
Confidence 5888888888655543111 1111 1244467889999999999998877664444331111000000 0000
Q ss_pred -CCCCcHHHHHHH-HcCCCHHHHHHHHHHcCCChh----------HHHHHHHHHHHHHhcCCCCchHHHHHHhccC
Q 046691 145 -GSGSDPVVSRYI-ALGLNREAVHIAVANYGDNPT----------KVREFANGYTILREMGFSSNNVAEVLIMYEN 208 (222)
Q Consensus 145 -~~~~DP~V~ky~-amG~~reaV~~Av~~yGdd~~----------KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dN 208 (222)
...+|+ ..+. -.|+..--+++=+..+-+.-+ .....-.....|..+||....|..|+....+
T Consensus 100 aI~~~d~--~~L~~ipGiGkKtAerIileLk~k~~~~~~~~~~~~~~~~~~e~~~aL~~LGy~~~e~~~ai~~~~~ 173 (191)
T TIGR00084 100 AIETEEV--KALVKIPGVGKKTAERLLLELKGKLKGNKNLEMFTPTEAARDELFEALVSLGYKPQEIQQALKKIKN 173 (191)
T ss_pred HHHhCCH--HHHHhCCCCCHHHHHHHHHHHHhhhcccccccccccccchHHHHHHHHHHcCCCHHHHHHHHHHHhh
Confidence 000111 1111 234444444333322111000 0011234567888999999999999987643
No 192
>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=21.72 E-value=1.1e+02 Score=22.62 Aligned_cols=56 Identities=18% Similarity=0.156 Sum_probs=32.3
Q ss_pred HHHHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHHHHHHh-cCCCCchHHHHHHhcc
Q 046691 150 PVVSRYIALGLNREAVHIAVANYGDNPTKVREFANGYTILRE-MGFSSNNVAEVLIMYE 207 (222)
Q Consensus 150 P~V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~~~L~E-MGFp~~~VaeAL~~~d 207 (222)
.++..|.+.|+=.-. +--.+|-.=..+..+-+.....|++ +||+.+.|+..|-+.+
T Consensus 16 ~tLr~ye~~Gli~p~--r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~ 72 (91)
T cd04766 16 QTLRLYERLGLLSPS--RTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEE 72 (91)
T ss_pred HHHHHHHHCCCcCCC--cCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 467777777765420 1000111113334455566667776 9999999999886543
No 193
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=21.70 E-value=1e+02 Score=24.26 Aligned_cols=29 Identities=24% Similarity=0.437 Sum_probs=23.5
Q ss_pred HHhcCCCCchHHHHHHhccCCH-HHHHHHH
Q 046691 189 LREMGFSSNNVAEVLIMYENDT-DKALAHL 217 (222)
Q Consensus 189 L~EMGFp~~~VaeAL~~~dND~-DKAL~~L 217 (222)
.|.+||+...|.++-..|.+|. |+..+.|
T Consensus 27 aR~lglse~~Id~I~~~~~~d~~Eq~~qmL 56 (97)
T cd08316 27 VRKSGLSEPKIDEIKLDNPQDTAEQKVQLL 56 (97)
T ss_pred HHHcCCCHHHHHHHHHcCCCChHHHHHHHH
Confidence 4889999999999999997775 6666655
No 194
>COG4154 FucU Fucose dissimilation pathway protein FucU [Carbohydrate transport and metabolism]
Probab=21.52 E-value=75 Score=27.33 Aligned_cols=34 Identities=32% Similarity=0.471 Sum_probs=24.5
Q ss_pred HHHHHHhcC-----------CCCchHHHHHHhccC-CHHHHHHHHh
Q 046691 185 GYTILREMG-----------FSSNNVAEVLIMYEN-DTDKALAHLL 218 (222)
Q Consensus 185 ~~~~L~EMG-----------Fp~~~VaeAL~~~dN-D~DKAL~~LL 218 (222)
.+..|++|| ||.+.++.=|+-+|| ....+|+..|
T Consensus 13 lL~tLr~MGHGDeivl~DanfPa~s~a~~lir~Dg~s~~~~l~AIl 58 (144)
T COG4154 13 LLKTLREMGHGDEIVLSDANFPAHSVARRVIRADGVSAADLLDAIL 58 (144)
T ss_pred HHHHHHHhCCCCeEEEecCCCChhHhhhheEecCCcchHHHHHHHH
Confidence 356677777 899999999999985 4455555544
No 195
>PHA03364 hypothetical protein; Provisional
Probab=21.50 E-value=1.6e+02 Score=27.45 Aligned_cols=67 Identities=30% Similarity=0.278 Sum_probs=51.1
Q ss_pred HHHHHHHcCCCHHHHHHHHHHcCCChhHH------HHHH-HHHHHHHhcCCCCch-----HHHHHHhccCCHHHHHHHH
Q 046691 151 VVSRYIALGLNREAVHIAVANYGDNPTKV------REFA-NGYTILREMGFSSNN-----VAEVLIMYENDTDKALAHL 217 (222)
Q Consensus 151 ~V~ky~amG~~reaV~~Av~~yGdd~~KV------~EFl-~~~~~L~EMGFp~~~-----VaeAL~~~dND~DKAL~~L 217 (222)
+.-|+-..|++-=...+|+.|-|...++| .||- ..|+.+++||++.+. -+++|-+|=|+..+.+..+
T Consensus 45 v~~~my~~gln~~LlREal~N~Gv~Dn~VL~RKVP~eyW~~lYd~l~~~~~~~~~l~~e~~aa~L~~~Ln~~~~~~~~l 123 (264)
T PHA03364 45 VCCKMYNRGLNILLLRETLANTGVRDNVVLGRKVPVEYWKLLYDALKEMGVSEEMLFSESRAAQLWLHLNSRPALLGGL 123 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCccceeecCCCCHHHHHHHHHHHHHhCCcHHhhcChhhHHHHHHHHhcChhHHHHH
Confidence 34566688999999999999999955544 6774 459999999999764 4778888877777666543
No 196
>PF11239 DUF3040: Protein of unknown function (DUF3040); InterPro: IPR021401 Some members in this family of proteins with unknown function are annotated as membrane proteins however this cannot be confirmed.
Probab=21.47 E-value=66 Score=23.87 Aligned_cols=15 Identities=33% Similarity=0.527 Sum_probs=12.8
Q ss_pred hHHHHHHHHHhhhcC
Q 046691 110 DFERRVLAEAEKENQ 124 (222)
Q Consensus 110 ~lERkiLAEaek~~~ 124 (222)
+.|||+|+|-|+.-.
T Consensus 5 e~E~r~L~eiEr~L~ 19 (82)
T PF11239_consen 5 EHEQRRLEEIERQLR 19 (82)
T ss_pred HHHHHHHHHHHHHHH
Confidence 689999999998843
No 197
>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=21.40 E-value=2.4e+02 Score=22.17 Aligned_cols=59 Identities=10% Similarity=0.141 Sum_probs=36.5
Q ss_pred HHHHHHHcCCCHHHHHHHHHHcCC---ChhHHHHHHHH-----HHHHHhcCCCCchHHHHHHhccCC
Q 046691 151 VVSRYIALGLNREAVHIAVANYGD---NPTKVREFANG-----YTILREMGFSSNNVAEVLIMYEND 209 (222)
Q Consensus 151 ~V~ky~amG~~reaV~~Av~~yGd---d~~KV~EFl~~-----~~~L~EMGFp~~~VaeAL~~~dND 209 (222)
.|..+-++||+.+.+..-+..+.. +..++.+++.. -.++.++---.+.+...+..|.++
T Consensus 49 ~I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~l~~~~~~l~~~i~~L~~~~~~L~~~~~~~~~~ 115 (126)
T cd04785 49 FIRRARDLGFSLEEIRALLALSDRPDRSCAEADAIARAHLADVRARIADLRRLEAELKRMVAACSGG 115 (126)
T ss_pred HHHHHHHCCCCHHHHHHHHhhhhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence 677888999999999987775433 34566666554 233334333344555555555554
No 198
>COG3769 Predicted hydrolase (HAD superfamily) [General function prediction only]
Probab=21.12 E-value=65 Score=30.12 Aligned_cols=67 Identities=21% Similarity=0.347 Sum_probs=42.6
Q ss_pred CcHHHHHHHHcCCCHHHHHHHHHH-------cCCChhHHHHHHHHHHHHHhcCCCCchHHHHHHhccCCH--HHHHHHHh
Q 046691 148 SDPVVSRYIALGLNREAVHIAVAN-------YGDNPTKVREFANGYTILREMGFSSNNVAEVLIMYENDT--DKALAHLL 218 (222)
Q Consensus 148 ~DP~V~ky~amG~~reaV~~Av~~-------yGdd~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~dND~--DKAL~~LL 218 (222)
.|..+++++ |+||++|++|.+. +=+.+.....| -+.|+|.||.--.=+---..|+|.. ++|..-||
T Consensus 126 d~~ei~e~T--Glpre~aaLa~~rEyseti~~rs~d~~~~~~---~~~L~e~glt~v~garf~~v~~as~gKg~Aa~~ll 200 (274)
T COG3769 126 DDEEIAEWT--GLPREQAALAMLREYSETIIWRSSDERMAQF---TARLNERGLTFVHGARFWHVLDASAGKGQAANWLL 200 (274)
T ss_pred CHHHHHHHh--CCChHHhHHHHHHHhhhheeecccchHHHHH---HHHHHhcCceEEeccceEEEeccccCccHHHHHHH
Confidence 566666664 9999999999872 12233334334 4678899998655444444555554 66776666
Q ss_pred c
Q 046691 219 G 219 (222)
Q Consensus 219 s 219 (222)
.
T Consensus 201 ~ 201 (274)
T COG3769 201 E 201 (274)
T ss_pred H
Confidence 3
No 199
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=21.06 E-value=1.3e+02 Score=22.82 Aligned_cols=12 Identities=33% Similarity=0.902 Sum_probs=5.8
Q ss_pred HhcCCCCchHHH
Q 046691 190 REMGFSSNNVAE 201 (222)
Q Consensus 190 ~EMGFp~~~Vae 201 (222)
++|||+...|..
T Consensus 21 r~LG~s~~eI~~ 32 (86)
T cd08777 21 RKLGFTESEIEE 32 (86)
T ss_pred HHcCCCHHHHHH
Confidence 444555544444
No 200
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=21.00 E-value=1.6e+02 Score=28.52 Aligned_cols=41 Identities=29% Similarity=0.581 Sum_probs=25.1
Q ss_pred cccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCc--ccCCC
Q 046691 3 YDFRNRANSSYSLYGPPPSASSGGSAPSHHPMYGSSLYP--RIGQQ 46 (222)
Q Consensus 3 yd~r~r~~~~~~~y~~~~~~~~~~~~~~~~p~~~~~~yp--~vgq~ 46 (222)
|-|-+|.|+++..|.++. +..+-+++||+.....|+ .+|++
T Consensus 292 y~~~~r~gsP~~~p~sp~---sp~s~p~~~~l~s~~~~~dtnl~~~ 334 (383)
T KOG4577|consen 292 YSFHSREGSPYGYPPSPE---SPSSLPPPMPLLSPLVYTDTNLGTP 334 (383)
T ss_pred eeccCCCCCCCCCCCCCC---CCCCCCCCcccCCcccccccccccc
Confidence 555667776655554433 234456678887777777 56666
No 201
>PF11219 DUF3014: Protein of unknown function (DUF3014); InterPro: IPR021382 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=20.94 E-value=1.2e+02 Score=26.18 Aligned_cols=28 Identities=25% Similarity=0.503 Sum_probs=23.8
Q ss_pred HHHHHhcCCCCchHHHHHHhccCCHHHHHHHHhcc
Q 046691 186 YTILREMGFSSNNVAEVLIMYENDTDKALAHLLGS 220 (222)
Q Consensus 186 ~~~L~EMGFp~~~VaeAL~~~dND~DKAL~~LLs~ 220 (222)
-+.+.|+|||-...-..|+ +||++||++
T Consensus 78 qqAy~ElGyp~~~F~d~l~-------~aid~lL~a 105 (158)
T PF11219_consen 78 QQAYAELGYPDRYFNDRLL-------AAIDHLLAA 105 (158)
T ss_pred HHHHHHhCCCcccHHHHHH-------HHHHHHHcC
Confidence 4568999999998888887 699999986
No 202
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=20.85 E-value=1.5e+02 Score=22.15 Aligned_cols=35 Identities=29% Similarity=0.477 Sum_probs=28.7
Q ss_pred HHHHHHcCCCHHHHHHHHHHcCCChhHHHHHHHHH
Q 046691 152 VSRYIALGLNREAVHIAVANYGDNPTKVREFANGY 186 (222)
Q Consensus 152 V~ky~amG~~reaV~~Av~~yGdd~~KV~EFl~~~ 186 (222)
+.+|.+.|++++.|..||..--.+...+..|+..+
T Consensus 1 i~~~~~~g~~~~~v~~aL~~tSgd~~~a~~~vl~~ 35 (87)
T PF11626_consen 1 IKHYEELGYSREFVTHALYATSGDPELARRFVLNF 35 (87)
T ss_dssp -HHHHHHTB-HHHHHHHHHHTTTBHHHHHHHHHHC
T ss_pred CchHHHhCCCHHHHHHHHHHhCCCHHHHHHHHHHH
Confidence 35688999999999999998888999999976554
No 203
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=20.80 E-value=1.3e+02 Score=22.21 Aligned_cols=31 Identities=19% Similarity=0.345 Sum_probs=23.3
Q ss_pred HHHhcCCCCchHHHHHHhccCCHHHHHHHHh
Q 046691 188 ILREMGFSSNNVAEVLIMYENDTDKALAHLL 218 (222)
Q Consensus 188 ~L~EMGFp~~~VaeAL~~~dND~DKAL~~LL 218 (222)
..|.|||..+.|...-..|-+..|++.+.|.
T Consensus 17 laR~LGls~~~I~~ie~~~~~~~eq~~~mL~ 47 (79)
T cd08784 17 FFRKLGLSDNEIKVAELDNPQHRDRVYELLR 47 (79)
T ss_pred HHHHcCCCHHHHHHHHHcCCchHHHHHHHHH
Confidence 4568899988888877776556777777774
No 204
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=20.65 E-value=3.5e+02 Score=21.25 Aligned_cols=56 Identities=7% Similarity=0.083 Sum_probs=43.5
Q ss_pred HHHHH-HcCCCHHHHHHHHHHcCC-ChhHHHHHHHHHHHHHhcCCCCchHHHHHHhcc
Q 046691 152 VSRYI-ALGLNREAVHIAVANYGD-NPTKVREFANGYTILREMGFSSNNVAEVLIMYE 207 (222)
Q Consensus 152 V~ky~-amG~~reaV~~Av~~yGd-d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~~d 207 (222)
+.+|. ..||+-..+.....++.. -.+++.+-|....+.+.+....+.+-+||-.|+
T Consensus 23 wK~faR~lglse~~Id~I~~~~~~d~~Eq~~qmL~~W~~~~G~~a~~~~Li~aLr~~~ 80 (97)
T cd08316 23 VKKFVRKSGLSEPKIDEIKLDNPQDTAEQKVQLLRAWYQSHGKTGAYRTLIKTLRKAK 80 (97)
T ss_pred HHHHHHHcCCCHHHHHHHHHcCCCChHHHHHHHHHHHHHHhCCCchHHHHHHHHHHcc
Confidence 45554 788998888888888865 568888888888888777777777777877765
No 205
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other
Probab=20.21 E-value=1.2e+02 Score=22.87 Aligned_cols=29 Identities=28% Similarity=0.440 Sum_probs=20.9
Q ss_pred HHhcCCCCchHHHHHHhccCCH-HHHHHHH
Q 046691 189 LREMGFSSNNVAEVLIMYENDT-DKALAHL 217 (222)
Q Consensus 189 L~EMGFp~~~VaeAL~~~dND~-DKAL~~L 217 (222)
.++|||+..+|...=..|-||. +.+.+.|
T Consensus 22 Ar~Lg~se~dI~~i~~~~~~~~~eq~~~mL 51 (84)
T cd08804 22 ARELDFTEEQIHQIRIENPNSLQDQSHALL 51 (84)
T ss_pred HHHcCCCHHHHHHHHHHCcccHHHHHHHHH
Confidence 3899999999998888875664 4444443
No 206
>PF15652 Tox-SHH: HNH/Endo VII superfamily toxin with a SHH signature
Probab=20.17 E-value=99 Score=25.11 Aligned_cols=31 Identities=26% Similarity=0.319 Sum_probs=27.6
Q ss_pred ChhHHHHHHHHHHHHHhcCCCCchHHHHHHh
Q 046691 175 NPTKVREFANGYTILREMGFSSNNVAEVLIM 205 (222)
Q Consensus 175 d~~KV~EFl~~~~~L~EMGFp~~~VaeAL~~ 205 (222)
+.+--.||-..+.+|.+-||+.+...++|-.
T Consensus 64 ~t~~~~Ef~~~~~eM~dAGV~~~~~~~~l~~ 94 (100)
T PF15652_consen 64 STTLQEEFNNSYREMFDAGVSKECRKKALKA 94 (100)
T ss_pred cchHHHHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6667789999999999999999999999864
No 207
>PRK13342 recombination factor protein RarA; Reviewed
Probab=20.08 E-value=2.5e+02 Score=26.24 Aligned_cols=51 Identities=16% Similarity=0.292 Sum_probs=38.2
Q ss_pred HHHHHHcCCCHHHHH-----HHHHHcCC-ChhHHHHHHHHHHHHHhcCCCCchHHHH
Q 046691 152 VSRYIALGLNREAVH-----IAVANYGD-NPTKVREFANGYTILREMGFSSNNVAEV 202 (222)
Q Consensus 152 V~ky~amG~~reaV~-----~Av~~yGd-d~~KV~EFl~~~~~L~EMGFp~~~VaeA 202 (222)
+.++++.|.+...+. .|.+..|- |+.+..==+.+++..+.+|||+..+.=|
T Consensus 253 l~~~l~~G~d~~~i~rrl~~~a~edig~a~~~~~~~~~~~~~~~~~~g~pe~~~~l~ 309 (413)
T PRK13342 253 LARMLEAGEDPLFIARRLVIIASEDIGLADPNALQVAVAAADAVERIGMPEGRIALA 309 (413)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHhhcccCHHHHHHHHHHHHHHHHhCCcHHHHHHH
Confidence 456677896666554 45567776 7788777788899999999999887543
Done!