Query 036073
Match_columns 241
No_of_seqs 171 out of 1121
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 09:09:23 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036073.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036073hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0077 PheA Prephenate dehydr 100.0 2.8E-82 6E-87 562.2 25.2 228 13-240 2-232 (279)
2 PRK11899 prephenate dehydratas 100.0 1.7E-80 3.7E-85 555.2 26.5 229 11-239 2-231 (279)
3 PLN02317 arogenate dehydratase 100.0 2.1E-79 4.6E-84 565.0 26.0 236 4-239 85-320 (382)
4 PRK10622 pheA bifunctional cho 100.0 1.1E-74 2.3E-79 538.6 25.4 229 11-239 101-334 (386)
5 PRK11898 prephenate dehydratas 100.0 6.4E-74 1.4E-78 514.5 26.6 226 13-239 1-234 (283)
6 KOG2797 Prephenate dehydratase 100.0 4.3E-68 9.3E-73 469.2 19.2 236 4-239 81-318 (377)
7 PF00800 PDT: Prephenate dehyd 100.0 8.8E-60 1.9E-64 397.9 16.6 177 16-192 1-181 (181)
8 PRK06034 hypothetical protein; 99.4 7.5E-14 1.6E-18 124.8 4.6 83 4-90 85-170 (279)
9 cd04904 ACT_AAAH ACT domain of 99.4 4.8E-13 1E-17 97.2 4.4 38 203-240 1-38 (74)
10 cd04931 ACT_PAH ACT domain of 99.4 8.2E-13 1.8E-17 99.8 5.5 41 199-239 11-51 (90)
11 cd04930 ACT_TH ACT domain of t 99.3 2.3E-12 4.9E-17 101.6 5.0 39 201-239 40-78 (115)
12 cd04929 ACT_TPH ACT domain of 99.3 5.6E-12 1.2E-16 91.9 4.5 37 203-239 1-37 (74)
13 cd04880 ACT_AAAH-PDT-like ACT 99.0 3.1E-10 6.6E-15 82.0 4.2 36 204-239 1-36 (75)
14 cd04905 ACT_CM-PDT C-terminal 98.9 3.4E-09 7.5E-14 77.5 4.9 38 202-239 1-38 (80)
15 TIGR01270 Trp_5_monoox tryptop 98.8 3.3E-09 7.1E-14 100.6 5.6 41 199-239 28-68 (464)
16 PRK08818 prephenate dehydrogen 97.8 2.3E-05 5.1E-10 73.3 4.2 36 201-236 294-330 (370)
17 PF01842 ACT: ACT domain; Int 97.8 5.1E-05 1.1E-09 52.2 4.8 37 203-239 1-37 (66)
18 TIGR01269 Tyr_3_monoox tyrosin 97.3 0.00034 7.3E-09 66.4 4.9 38 202-239 37-75 (457)
19 cd04886 ACT_ThrD-II-like C-ter 97.1 0.00057 1.2E-08 47.2 3.7 33 206-238 2-34 (73)
20 cd04908 ACT_Bt0572_1 N-termina 97.0 0.00096 2.1E-08 46.7 4.3 34 204-237 3-36 (66)
21 cd04882 ACT_Bt0572_2 C-termina 96.9 0.0011 2.3E-08 45.4 3.5 34 205-238 2-35 (65)
22 KOG3820 Aromatic amino acid hy 96.7 0.0018 4E-08 60.5 4.5 39 201-239 35-73 (461)
23 PRK06737 acetolactate synthase 96.7 0.0027 5.7E-08 46.5 4.3 36 203-238 3-38 (76)
24 PRK11152 ilvM acetolactate syn 96.6 0.0035 7.5E-08 45.9 4.4 37 202-238 3-39 (76)
25 cd04884 ACT_CBS C-terminal ACT 96.5 0.0037 7.9E-08 44.3 4.1 33 205-237 2-34 (72)
26 cd04909 ACT_PDH-BS C-terminal 96.3 0.0062 1.3E-07 42.5 4.3 34 204-237 3-36 (69)
27 cd04883 ACT_AcuB C-terminal AC 96.2 0.0086 1.9E-07 41.9 4.4 35 203-237 2-36 (72)
28 cd04889 ACT_PDH-BS-like C-term 96.0 0.01 2.2E-07 39.8 3.8 33 206-238 2-34 (56)
29 cd04903 ACT_LSD C-terminal ACT 95.9 0.012 2.6E-07 40.3 3.8 33 205-237 2-34 (71)
30 cd04879 ACT_3PGDH-like ACT_3PG 95.7 0.015 3.3E-07 39.6 3.8 34 205-238 2-35 (71)
31 cd04878 ACT_AHAS N-terminal AC 95.7 0.02 4.4E-07 39.1 4.5 35 204-238 2-36 (72)
32 PRK13562 acetolactate synthase 95.7 0.017 3.7E-07 43.1 4.1 37 202-238 2-38 (84)
33 cd04885 ACT_ThrD-I Tandem C-te 95.6 0.012 2.6E-07 41.5 3.1 30 206-236 2-31 (68)
34 cd02116 ACT ACT domains are co 95.5 0.021 4.6E-07 35.8 3.6 33 206-238 2-34 (60)
35 PF13291 ACT_4: ACT domain; PD 95.5 0.023 5E-07 40.9 4.2 39 200-238 4-42 (80)
36 cd04874 ACT_Af1403 N-terminal 95.4 0.029 6.2E-07 38.5 4.4 34 204-237 2-35 (72)
37 cd04902 ACT_3PGDH-xct C-termin 95.4 0.019 4.2E-07 40.0 3.4 33 205-237 2-34 (73)
38 PRK08178 acetolactate synthase 95.3 0.033 7.1E-07 42.6 4.6 36 202-237 8-43 (96)
39 cd04887 ACT_MalLac-Enz ACT_Mal 95.2 0.033 7.1E-07 39.2 4.0 33 205-237 2-34 (74)
40 PF13710 ACT_5: ACT domain; PD 95.1 0.025 5.3E-07 39.7 3.2 27 211-237 1-27 (63)
41 cd04926 ACT_ACR_4 C-terminal 95.0 0.056 1.2E-06 38.5 4.9 35 203-237 2-36 (72)
42 cd04899 ACT_ACR-UUR-like_2 C-t 94.8 0.061 1.3E-06 37.3 4.7 36 203-238 1-36 (70)
43 cd04895 ACT_ACR_1 ACT domain-c 94.6 0.067 1.5E-06 38.7 4.4 30 203-232 2-31 (72)
44 cd04888 ACT_PheB-BS C-terminal 94.4 0.073 1.6E-06 37.4 4.3 33 204-236 2-34 (76)
45 cd04881 ACT_HSDH-Hom ACT_HSDH_ 94.4 0.069 1.5E-06 37.1 4.2 34 205-238 3-36 (79)
46 cd04873 ACT_UUR-ACR-like ACT d 94.4 0.084 1.8E-06 36.2 4.5 34 204-237 2-35 (70)
47 cd04906 ACT_ThrD-I_1 First of 94.3 0.038 8.3E-07 40.7 2.7 26 204-229 3-28 (85)
48 COG4747 ACT domain-containing 94.3 0.058 1.3E-06 42.9 3.7 34 202-235 69-102 (142)
49 cd04901 ACT_3PGDH C-terminal A 94.2 0.034 7.5E-07 38.4 2.2 33 205-237 2-34 (69)
50 cd04896 ACT_ACR-like_3 ACT dom 94.1 0.077 1.7E-06 38.7 3.9 28 204-231 2-29 (75)
51 PRK00194 hypothetical protein; 93.4 0.12 2.7E-06 38.0 4.1 35 202-236 3-37 (90)
52 cd04877 ACT_TyrR N-terminal AC 93.3 0.15 3.3E-06 36.2 4.3 33 205-237 3-35 (74)
53 cd04875 ACT_F4HF-DF N-terminal 93.2 0.16 3.4E-06 36.0 4.2 32 205-236 2-33 (74)
54 PRK04435 hypothetical protein; 93.1 0.16 3.5E-06 41.5 4.7 35 201-235 68-102 (147)
55 cd04872 ACT_1ZPV ACT domain pr 92.9 0.16 3.4E-06 37.4 3.9 34 203-236 2-35 (88)
56 PRK08198 threonine dehydratase 92.8 0.49 1.1E-05 44.5 8.0 36 201-236 326-361 (404)
57 cd04876 ACT_RelA-SpoT ACT dom 92.3 0.19 4.2E-06 33.0 3.4 32 206-237 2-33 (71)
58 PRK06382 threonine dehydratase 91.9 0.21 4.5E-06 47.3 4.4 35 201-235 329-363 (406)
59 cd04870 ACT_PSP_1 CT domains f 91.9 0.26 5.7E-06 35.1 4.0 30 207-236 4-33 (75)
60 TIGR01127 ilvA_1Cterm threonin 91.8 0.24 5.3E-06 46.1 4.7 35 202-236 305-339 (380)
61 cd04900 ACT_UUR-like_1 ACT dom 91.6 0.33 7.2E-06 34.4 4.2 29 204-232 3-31 (73)
62 PRK08577 hypothetical protein; 91.5 0.41 8.9E-06 38.3 5.1 37 202-238 56-92 (136)
63 cd04897 ACT_ACR_3 ACT domain-c 91.1 0.43 9.3E-06 34.8 4.4 29 203-231 2-30 (75)
64 PRK08526 threonine dehydratase 91.0 0.82 1.8E-05 43.4 7.4 177 47-235 161-359 (403)
65 PRK06545 prephenate dehydrogen 90.5 0.27 5.8E-06 45.7 3.6 34 202-235 290-323 (359)
66 PF13740 ACT_6: ACT domain; PD 90.5 0.42 9.2E-06 34.2 3.9 31 205-235 3-35 (76)
67 COG4492 PheB ACT domain-contai 90.3 0.42 9.2E-06 38.7 4.0 34 201-234 71-104 (150)
68 PF12974 Phosphonate-bd: ABC t 90.3 0.32 6.9E-06 42.0 3.6 84 12-104 104-202 (243)
69 PRK08639 threonine dehydratase 90.1 0.94 2E-05 43.0 7.0 35 201-236 335-370 (420)
70 cd04869 ACT_GcvR_2 ACT domains 90.1 0.55 1.2E-05 33.4 4.2 32 205-236 2-33 (81)
71 PRK11151 DNA-binding transcrip 89.4 9.9 0.00022 33.5 12.7 144 11-164 90-246 (305)
72 PF00497 SBP_bac_3: Bacterial 89.0 3.4 7.4E-05 33.7 8.8 50 12-63 109-159 (225)
73 TIGR00363 lipoprotein, YaeC fa 88.9 16 0.00036 32.4 13.8 148 12-170 18-200 (258)
74 smart00079 PBPe Eukaryotic hom 87.9 1.5 3.2E-05 33.9 5.6 80 14-103 14-104 (134)
75 PRK15007 putative ABC transpor 87.7 1.9 4E-05 36.7 6.6 49 13-63 126-174 (243)
76 smart00062 PBPb Bacterial peri 87.3 3.5 7.5E-05 32.6 7.7 51 13-65 106-156 (219)
77 TIGR01096 3A0103s03R lysine-ar 87.3 1.6 3.5E-05 37.1 5.9 50 12-63 130-180 (250)
78 TIGR01728 SsuA_fam ABC transpo 87.2 4.4 9.6E-05 34.9 8.8 138 14-161 1-157 (288)
79 PRK11589 gcvR glycine cleavage 87.1 0.71 1.5E-05 39.4 3.6 32 205-236 98-129 (190)
80 COG2716 GcvR Glycine cleavage 87.0 1.7 3.7E-05 36.6 5.6 31 207-237 97-127 (176)
81 cd08411 PBP2_OxyR The C-termin 86.9 13 0.00029 29.2 13.1 123 33-165 26-157 (200)
82 cd04891 ACT_AK-LysC-DapG-like_ 86.7 1.4 3.1E-05 28.7 4.3 29 207-235 6-34 (61)
83 cd08417 PBP2_Nitroaromatics_li 86.7 14 0.0003 29.0 11.6 121 34-165 26-155 (200)
84 cd04925 ACT_ACR_2 ACT domain-c 86.6 1.1 2.4E-05 31.9 3.9 30 204-233 2-31 (74)
85 cd04913 ACT_AKii-LysC-BS-like_ 85.9 1.3 2.7E-05 30.3 3.8 28 207-234 7-34 (75)
86 cd08445 PBP2_BenM_CatM_CatR Th 85.8 16 0.00035 29.0 13.3 120 34-163 27-158 (203)
87 PRK09959 hybrid sensory histid 85.6 1.8 4E-05 45.9 6.5 49 13-63 164-212 (1197)
88 cd04927 ACT_ACR-like_2 Second 85.5 1.4 3.1E-05 31.6 4.0 27 206-232 4-30 (76)
89 cd00134 PBPb Bacterial peripla 85.4 2.6 5.5E-05 33.6 5.9 50 12-63 104-153 (218)
90 PRK07334 threonine dehydratase 85.3 1.4 3E-05 41.6 4.9 38 200-237 324-361 (403)
91 PRK09959 hybrid sensory histid 84.9 1.5 3.2E-05 46.6 5.4 49 13-63 407-455 (1197)
92 cd08452 PBP2_AlsR The C-termin 84.7 18 0.00039 28.7 13.4 122 33-164 25-157 (197)
93 PRK11260 cystine transporter s 84.6 2.7 6E-05 36.5 6.2 49 13-63 149-197 (266)
94 TIGR01124 ilvA_2Cterm threonin 84.2 3.9 8.4E-05 40.0 7.5 176 46-236 157-357 (499)
95 cd04907 ACT_ThrD-I_2 Second of 83.8 2.1 4.5E-05 31.4 4.3 32 204-236 3-34 (81)
96 PRK09495 glnH glutamine ABC tr 83.6 2.8 6.1E-05 35.9 5.7 49 13-63 131-179 (247)
97 cd08453 PBP2_IlvR The C-termin 83.3 20 0.00044 28.2 12.7 121 34-164 26-160 (200)
98 PF13379 NMT1_2: NMT1-like fam 82.5 13 0.00028 32.2 9.5 144 11-161 5-180 (252)
99 cd04932 ACT_AKiii-LysC-EC_1 AC 82.1 2.4 5.3E-05 30.4 4.0 27 209-235 11-37 (75)
100 PRK11553 alkanesulfonate trans 81.7 7.9 0.00017 34.5 8.1 54 8-62 23-83 (314)
101 PRK09508 leuO leucine transcri 81.3 10 0.00023 33.7 8.7 122 33-165 137-266 (314)
102 COG3830 ACT domain-containing 80.5 2.3 4.9E-05 32.2 3.4 25 210-234 11-35 (90)
103 cd08412 PBP2_PAO1_like The C-t 80.5 25 0.00054 27.4 12.1 122 33-164 25-154 (198)
104 cd08462 PBP2_NodD The C-termin 80.5 26 0.00056 27.8 10.1 32 33-64 25-56 (200)
105 cd04914 ACT_AKi-DapG-BS_1 ACT 80.5 2.6 5.7E-05 29.4 3.6 27 209-236 9-35 (67)
106 cd04893 ACT_GcvR_1 ACT domains 80.4 3.5 7.5E-05 29.5 4.3 31 205-235 4-34 (77)
107 PF12727 PBP_like: PBP superfa 80.2 13 0.00027 31.6 8.4 124 45-172 20-165 (193)
108 PRK11917 bifunctional adhesin/ 80.1 5.2 0.00011 35.0 6.2 96 12-129 147-246 (259)
109 TIGR02079 THD1 threonine dehyd 79.5 2.9 6.2E-05 39.7 4.6 36 201-236 324-359 (409)
110 cd04935 ACT_AKiii-DAPDC_1 ACT 78.2 2.9 6.2E-05 30.0 3.3 27 209-235 11-37 (75)
111 PF03401 TctC: Tripartite tric 77.1 5.5 0.00012 35.5 5.5 135 9-148 102-260 (274)
112 cd08435 PBP2_GbpR The C-termin 76.9 33 0.00071 26.7 12.5 122 33-164 25-158 (201)
113 cd04933 ACT_AK1-AT_1 ACT domai 75.6 3.7 8E-05 29.9 3.3 27 209-235 11-37 (78)
114 PRK12483 threonine dehydratase 75.6 8 0.00017 38.1 6.6 179 46-236 177-377 (521)
115 PRK10341 DNA-binding transcrip 75.5 47 0.001 29.5 11.1 33 34-66 123-156 (312)
116 PRK11242 DNA-binding transcrip 75.5 54 0.0012 28.4 12.8 121 34-164 117-247 (296)
117 PRK09224 threonine dehydratase 74.9 9.6 0.00021 37.2 7.0 34 201-236 327-360 (504)
118 cd04912 ACT_AKiii-LysC-EC-like 74.3 5.5 0.00012 28.2 3.9 30 208-237 10-39 (75)
119 TIGR02995 ectoine_ehuB ectoine 74.3 7.3 0.00016 34.1 5.5 49 13-63 144-193 (275)
120 cd08450 PBP2_HcaR The C-termin 74.2 39 0.00085 26.2 11.9 32 33-64 25-57 (196)
121 cd04928 ACT_TyrKc Uncharacteri 73.4 5.1 0.00011 28.6 3.5 28 205-232 4-31 (68)
122 TIGR01693 UTase_glnD [Protein- 73.3 6.4 0.00014 40.8 5.6 37 200-236 777-813 (850)
123 PF00497 SBP_bac_3: Bacterial 73.1 18 0.00039 29.3 7.3 123 27-165 30-165 (225)
124 cd08461 PBP2_DntR_like_3 The C 73.1 40 0.00087 26.3 9.2 123 33-166 25-157 (198)
125 smart00062 PBPb Bacterial peri 73.1 43 0.00092 26.2 10.1 109 37-161 41-156 (219)
126 PRK10859 membrane-bound lytic 73.0 18 0.00039 34.9 8.3 49 13-63 149-202 (482)
127 PF00585 Thr_dehydrat_C: C-ter 72.9 1.9 4.1E-05 32.3 1.2 35 201-236 9-43 (91)
128 PLN02550 threonine dehydratase 72.7 9.7 0.00021 38.1 6.4 178 47-236 250-449 (591)
129 cd08459 PBP2_DntR_NahR_LinR_li 72.2 45 0.00098 26.1 10.5 121 34-165 26-155 (201)
130 cd08446 PBP2_Chlorocatechol Th 71.7 46 0.00099 26.0 13.5 122 33-164 26-158 (198)
131 cd08440 PBP2_LTTR_like_4 TThe 71.7 44 0.00094 25.7 13.3 121 34-164 26-155 (197)
132 PRK12679 cbl transcriptional r 71.2 75 0.0016 28.2 11.9 144 11-163 92-248 (316)
133 cd08426 PBP2_LTTR_like_5 The C 70.6 48 0.001 25.8 13.0 121 34-164 26-155 (199)
134 PRK12684 transcriptional regul 70.4 78 0.0017 28.1 11.9 143 11-164 92-249 (313)
135 cd04936 ACT_AKii-LysC-BS-like_ 70.3 5.9 0.00013 26.1 3.1 30 209-238 10-39 (63)
136 PRK12683 transcriptional regul 69.2 83 0.0018 27.9 12.9 120 34-163 119-248 (309)
137 TIGR02424 TF_pcaQ pca operon t 68.8 79 0.0017 27.5 12.9 122 33-164 118-251 (300)
138 cd08413 PBP2_CysB_like The C-t 68.4 57 0.0012 25.7 11.8 122 33-164 25-156 (198)
139 PF13840 ACT_7: ACT domain ; P 67.9 14 0.00031 25.5 4.8 25 211-235 19-43 (65)
140 cd08421 PBP2_LTTR_like_1 The C 67.9 55 0.0012 25.4 12.7 122 33-164 25-155 (198)
141 PRK11092 bifunctional (p)ppGpp 67.8 14 0.00031 37.7 6.5 38 200-237 624-661 (702)
142 COG0725 ModA ABC-type molybdat 67.8 10 0.00022 33.8 5.0 47 19-65 145-195 (258)
143 cd04934 ACT_AK-Hom3_1 CT domai 67.6 7.2 0.00016 27.8 3.2 26 210-235 12-37 (73)
144 cd08485 PBP2_ClcR The C-termin 67.6 60 0.0013 25.7 12.7 141 14-164 3-158 (198)
145 COG0317 SpoT Guanosine polypho 67.4 15 0.00032 37.6 6.4 39 200-238 625-663 (701)
146 TIGR01098 3A0109s03R phosphate 67.3 12 0.00026 31.9 5.2 89 12-103 140-238 (254)
147 PRK11063 metQ DL-methionine tr 67.2 93 0.002 27.7 13.7 108 12-129 31-152 (271)
148 cd08460 PBP2_DntR_like_1 The C 66.7 19 0.00042 28.5 6.0 121 33-164 25-153 (200)
149 PRK06349 homoserine dehydrogen 66.6 7.2 0.00016 37.2 4.0 33 205-237 351-383 (426)
150 cd04868 ACT_AK-like ACT domain 66.2 8.7 0.00019 24.4 3.2 26 211-236 12-37 (60)
151 PRK05007 PII uridylyl-transfer 66.1 8.8 0.00019 40.2 4.8 33 200-232 806-838 (884)
152 cd04923 ACT_AK-LysC-DapG-like_ 66.1 7.1 0.00015 25.7 2.8 29 209-237 10-38 (63)
153 cd08486 PBP2_CbnR The C-termin 66.1 65 0.0014 25.5 13.7 140 14-163 3-157 (198)
154 PRK12680 transcriptional regul 65.9 1E+02 0.0022 27.8 12.8 145 11-164 92-250 (327)
155 TIGR03339 phn_lysR aminoethylp 65.9 84 0.0018 26.8 12.9 138 12-161 87-236 (279)
156 cd04922 ACT_AKi-HSDH-ThrA_2 AC 65.8 8 0.00017 25.9 3.1 26 209-234 11-36 (66)
157 PRK11482 putative DNA-binding 65.1 1E+02 0.0022 27.5 12.8 122 32-165 141-270 (317)
158 cd04937 ACT_AKi-DapG-BS_2 ACT 65.1 7 0.00015 26.7 2.7 28 209-236 11-38 (64)
159 cd04924 ACT_AK-Arch_2 ACT doma 65.0 8.6 0.00019 25.7 3.1 26 209-234 11-36 (66)
160 KOG2663 Acetolactate synthase, 64.9 7.8 0.00017 34.8 3.5 33 201-233 76-108 (309)
161 TIGR00691 spoT_relA (p)ppGpp s 64.7 17 0.00037 36.9 6.4 37 200-236 608-644 (683)
162 cd04890 ACT_AK-like_1 ACT doma 63.9 9.8 0.00021 25.5 3.2 26 210-235 11-36 (62)
163 PRK10872 relA (p)ppGpp synthet 63.7 20 0.00043 36.9 6.6 52 183-237 650-701 (743)
164 cd04919 ACT_AK-Hom3_2 ACT doma 63.6 9.3 0.0002 25.7 3.1 26 209-234 11-36 (66)
165 PRK01759 glnD PII uridylyl-tra 63.5 11 0.00025 39.2 5.0 33 200-232 781-813 (854)
166 cd08466 PBP2_LeuO The C-termin 62.4 72 0.0016 24.8 10.6 123 33-166 25-156 (200)
167 PF03466 LysR_substrate: LysR 62.1 76 0.0016 24.9 13.3 123 33-165 31-162 (209)
168 COG2107 Predicted periplasmic 61.9 19 0.00041 32.5 5.4 51 13-65 95-145 (272)
169 cd08451 PBP2_BudR The C-termin 61.7 73 0.0016 24.6 14.1 33 32-64 25-58 (199)
170 TIGR03871 ABC_peri_MoxJ_2 quin 60.7 21 0.00046 29.8 5.4 50 12-63 103-161 (232)
171 PRK05092 PII uridylyl-transfer 60.6 14 0.00029 39.0 5.0 35 201-235 842-876 (931)
172 COG0834 HisJ ABC-type amino ac 60.6 16 0.00034 31.2 4.7 49 13-63 146-196 (275)
173 PRK11716 DNA-binding transcrip 60.3 1E+02 0.0023 25.9 12.8 123 33-164 92-223 (269)
174 cd08438 PBP2_CidR The C-termin 59.6 79 0.0017 24.3 13.3 30 34-63 26-56 (197)
175 PRK09906 DNA-binding transcrip 59.0 1.2E+02 0.0026 26.3 13.3 122 33-164 115-247 (296)
176 cd08437 PBP2_MleR The substrat 58.9 85 0.0018 24.5 12.2 122 33-163 25-156 (198)
177 cd04916 ACT_AKiii-YclM-BS_2 AC 58.9 13 0.00028 24.8 3.1 26 209-234 11-36 (66)
178 TIGR00719 sda_beta L-serine de 58.8 15 0.00032 31.6 4.1 33 202-234 148-180 (208)
179 PRK15010 ABC transporter lysin 58.6 30 0.00064 29.8 6.1 50 12-63 132-183 (260)
180 PF12916 DUF3834: Protein of u 58.3 20 0.00044 30.9 4.8 72 12-88 67-143 (201)
181 cd08468 PBP2_Pa0477 The C-term 57.8 92 0.002 24.5 10.6 32 33-64 25-57 (202)
182 PF09084 NMT1: NMT1/THI5 like; 57.6 1.1E+02 0.0023 25.2 14.0 105 37-149 23-139 (216)
183 PRK10859 membrane-bound lytic 57.5 49 0.0011 31.9 8.0 50 13-62 44-107 (482)
184 PRK10797 glutamate and asparta 57.5 19 0.0004 32.4 4.8 50 12-63 152-205 (302)
185 cd04921 ACT_AKi-HSDH-ThrA-like 57.3 21 0.00046 24.9 4.2 27 208-234 10-36 (80)
186 PRK03601 transcriptional regul 56.1 1.4E+02 0.0029 25.9 11.4 114 33-164 114-231 (275)
187 cd08444 PBP2_Cbl The C-termina 55.8 99 0.0022 24.3 12.9 122 33-164 25-156 (198)
188 cd08425 PBP2_CynR The C-termin 55.4 96 0.0021 24.0 11.2 121 34-164 27-157 (197)
189 PF12974 Phosphonate-bd: ABC t 54.9 67 0.0014 27.3 7.7 113 37-159 31-165 (243)
190 PRK03381 PII uridylyl-transfer 54.7 20 0.00044 36.9 5.0 33 202-234 707-739 (774)
191 cd08443 PBP2_CysB The C-termin 53.8 1.1E+02 0.0024 24.1 12.9 123 33-164 25-156 (198)
192 PRK11139 DNA-binding transcrip 53.8 1.5E+02 0.0033 25.8 10.4 118 34-165 120-246 (297)
193 cd08414 PBP2_LTTR_aromatics_li 53.6 1E+02 0.0022 23.7 13.0 31 34-64 26-57 (197)
194 cd04892 ACT_AK-like_2 ACT doma 53.5 18 0.00039 23.3 3.1 26 209-234 10-35 (65)
195 PRK03059 PII uridylyl-transfer 53.2 22 0.00048 37.1 5.0 32 201-232 785-816 (856)
196 cd08420 PBP2_CysL_like C-termi 52.6 1E+02 0.0023 23.6 12.9 121 34-164 26-158 (201)
197 cd08436 PBP2_LTTR_like_3 The C 52.5 1E+02 0.0022 23.6 12.3 33 33-65 25-58 (194)
198 cd08465 PBP2_ToxR The C-termin 52.3 1.2E+02 0.0025 24.0 9.2 32 34-65 26-58 (200)
199 TIGR03427 ABC_peri_uca ABC tra 51.3 18 0.00038 33.3 3.6 52 9-63 102-160 (328)
200 PRK09224 threonine dehydratase 51.2 18 0.0004 35.3 3.9 35 201-236 422-456 (504)
201 COG3181 Uncharacterized protei 51.1 12 0.00026 34.6 2.5 93 21-113 157-266 (319)
202 cd08433 PBP2_Nac The C-teminal 51.0 1.1E+02 0.0025 23.6 13.0 122 33-164 25-155 (198)
203 cd08418 PBP2_TdcA The C-termin 50.8 1.1E+02 0.0025 23.5 12.0 120 34-165 26-156 (201)
204 PRK15437 histidine ABC transpo 50.8 48 0.001 28.5 6.2 50 12-63 132-183 (259)
205 TIGR00656 asp_kin_monofn aspar 50.5 81 0.0018 29.4 8.0 96 131-235 190-296 (401)
206 PRK04374 PII uridylyl-transfer 50.4 26 0.00056 36.8 5.0 32 201-232 795-826 (869)
207 PRK10216 DNA-binding transcrip 50.2 1.4E+02 0.0031 26.4 9.3 125 33-164 122-262 (319)
208 cd08464 PBP2_DntR_like_2 The C 50.1 1.2E+02 0.0026 23.5 9.6 122 33-165 25-155 (200)
209 COG2150 Predicted regulator of 49.8 27 0.00059 29.2 4.1 33 204-236 97-129 (167)
210 cd08416 PBP2_MdcR The C-termin 49.0 1.2E+02 0.0027 23.4 13.1 122 33-164 25-157 (199)
211 cd08419 PBP2_CbbR_RubisCO_like 47.7 1.3E+02 0.0027 23.1 14.0 121 34-164 25-154 (197)
212 cd08449 PBP2_XapR The C-termin 47.7 1.3E+02 0.0028 23.2 12.6 31 34-64 26-57 (197)
213 cd08456 PBP2_LysR The C-termin 47.2 1.3E+02 0.0028 23.2 12.9 122 33-164 25-155 (196)
214 TIGR01096 3A0103s03R lysine-ar 47.1 1.7E+02 0.0037 24.5 9.4 114 36-165 64-186 (250)
215 cd08423 PBP2_LTTR_like_6 The C 46.7 1.3E+02 0.0029 23.1 12.1 31 34-64 26-57 (200)
216 TIGR01729 taurine_ABC_bnd taur 46.1 2.1E+02 0.0045 25.1 11.6 136 15-160 2-156 (300)
217 PRK12682 transcriptional regul 45.9 2.1E+02 0.0045 25.1 13.6 53 11-63 92-149 (309)
218 cd08483 PBP2_HvrB The C-termin 45.8 64 0.0014 24.9 5.7 116 34-164 26-149 (190)
219 CHL00180 rbcR LysR transcripti 45.7 2.1E+02 0.0045 25.1 14.4 53 11-63 94-151 (305)
220 cd08457 PBP2_OccR The C-termin 45.6 1.4E+02 0.0031 23.1 12.7 120 33-162 25-153 (196)
221 PRK00275 glnD PII uridylyl-tra 45.1 35 0.00076 35.9 5.0 32 201-232 813-844 (895)
222 PRK09986 DNA-binding transcrip 44.1 2.1E+02 0.0045 24.6 14.4 144 11-164 96-255 (294)
223 PRK11480 tauA taurine transpor 43.9 31 0.00067 31.1 4.0 142 10-161 21-179 (320)
224 TIGR03427 ABC_peri_uca ABC tra 43.9 2.6E+02 0.0056 25.6 12.8 130 36-173 36-178 (328)
225 cd00134 PBPb Bacterial peripla 43.7 1E+02 0.0022 24.1 6.7 113 36-164 39-158 (218)
226 cd08441 PBP2_MetR The C-termin 43.6 1.5E+02 0.0033 22.9 12.3 142 14-165 2-156 (198)
227 KOG4028 Uncharacterized conser 43.1 22 0.00048 28.9 2.5 34 14-47 108-142 (175)
228 PRK11480 tauA taurine transpor 42.9 32 0.0007 31.0 3.9 51 10-63 119-176 (320)
229 cd08415 PBP2_LysR_opines_like 42.7 1.5E+02 0.0033 22.7 12.0 123 32-164 24-155 (196)
230 PF09084 NMT1: NMT1/THI5 like; 42.4 72 0.0016 26.3 5.8 55 9-66 89-150 (216)
231 cd08467 PBP2_SyrM The C-termin 42.1 1.7E+02 0.0037 23.0 9.8 122 33-165 25-155 (200)
232 TIGR01693 UTase_glnD [Protein- 41.9 34 0.00074 35.5 4.4 32 201-232 667-698 (850)
233 cd08442 PBP2_YofA_SoxR_like Th 41.8 1.6E+02 0.0034 22.5 13.1 122 33-165 25-152 (193)
234 TIGR02122 TRAP_TAXI TRAP trans 40.9 81 0.0017 27.7 6.2 56 9-64 27-90 (320)
235 cd08427 PBP2_LTTR_like_2 The C 40.6 1.7E+02 0.0036 22.5 14.4 31 33-63 25-56 (195)
236 TIGR01098 3A0109s03R phosphate 40.5 2.2E+02 0.0048 23.9 13.5 54 11-64 31-93 (254)
237 cd08448 PBP2_LTTR_aromatics_li 40.4 1.7E+02 0.0036 22.4 14.2 31 33-63 25-56 (197)
238 TIGR00787 dctP tripartite ATP- 40.3 2.4E+02 0.0053 24.3 9.4 150 18-175 3-197 (257)
239 cd08481 PBP2_GcdR_like The C-t 39.7 1.3E+02 0.0029 23.0 6.7 119 34-166 26-153 (194)
240 TIGR01729 taurine_ABC_bnd taur 39.2 53 0.0011 29.0 4.7 50 11-63 98-154 (300)
241 TIGR02122 TRAP_TAXI TRAP trans 39.1 47 0.001 29.3 4.3 50 13-63 141-197 (320)
242 PRK11553 alkanesulfonate trans 38.8 54 0.0012 29.1 4.7 51 10-63 126-183 (314)
243 PRK06635 aspartate kinase; Rev 38.7 52 0.0011 30.8 4.7 29 208-236 349-377 (404)
244 cd04918 ACT_AK1-AT_2 ACT domai 38.6 61 0.0013 22.0 4.0 26 209-234 10-35 (65)
245 PRK10837 putative DNA-binding 37.9 2.6E+02 0.0056 24.0 12.5 53 11-63 88-145 (290)
246 PRK11790 D-3-phosphoglycerate 37.6 30 0.00066 32.8 3.0 34 202-235 338-371 (409)
247 PRK13581 D-3-phosphoglycerate 36.9 34 0.00074 33.5 3.3 75 160-234 388-484 (526)
248 cd04920 ACT_AKiii-DAPDC_2 ACT 36.6 35 0.00076 23.2 2.5 30 209-238 10-39 (63)
249 TIGR03870 ABC_MoxJ methanol ox 35.9 1.1E+02 0.0023 26.2 6.0 47 15-63 108-170 (246)
250 COG2844 GlnD UTP:GlnB (protein 35.5 46 0.001 34.6 4.0 33 200-232 789-821 (867)
251 PRK09084 aspartate kinase III; 34.7 2.9E+02 0.0062 26.6 9.2 99 131-235 235-342 (448)
252 PRK15421 DNA-binding transcrip 33.9 3.4E+02 0.0074 24.1 12.4 143 12-164 89-243 (317)
253 PF13379 NMT1_2: NMT1-like fam 33.7 1.2E+02 0.0025 26.1 5.9 50 12-63 120-177 (252)
254 PRK08961 bifunctional aspartat 33.6 2.6E+02 0.0056 29.3 9.3 100 131-237 251-360 (861)
255 PRK06291 aspartate kinase; Pro 33.6 4.4E+02 0.0096 25.3 10.5 97 131-234 249-356 (465)
256 PRK15437 histidine ABC transpo 33.5 3E+02 0.0066 23.4 9.7 28 36-64 66-93 (259)
257 KOG1250 Threonine/serine dehyd 33.5 65 0.0014 31.0 4.4 110 119-233 284-404 (457)
258 PRK01759 glnD PII uridylyl-tra 33.3 56 0.0012 34.2 4.3 32 201-232 676-707 (854)
259 cd04915 ACT_AK-Ectoine_2 ACT d 32.6 51 0.0011 22.6 2.8 24 212-235 14-37 (66)
260 PRK05007 PII uridylyl-transfer 32.6 59 0.0013 34.1 4.4 32 201-232 700-731 (884)
261 PRK09861 cytoplasmic membrane 32.5 3.6E+02 0.0079 24.0 12.1 50 12-61 32-86 (272)
262 TIGR00656 asp_kin_monofn aspar 32.3 44 0.00096 31.2 3.2 29 208-236 346-374 (401)
263 cd08430 PBP2_IlvY The C-termin 32.1 2.3E+02 0.005 21.7 14.2 124 33-165 25-157 (199)
264 PF00072 Response_reg: Respons 31.6 56 0.0012 23.5 3.1 78 112-193 4-82 (112)
265 COG3482 Uncharacterized conser 31.6 65 0.0014 28.5 3.8 46 14-62 2-47 (237)
266 PF14503 YhfZ_C: YhfZ C-termin 31.0 3.2E+02 0.007 24.1 8.1 112 38-161 45-166 (232)
267 PRK09034 aspartate kinase; Rev 30.6 4.7E+02 0.01 25.1 10.0 98 130-234 234-343 (454)
268 cd08432 PBP2_GcdR_TrpI_HvrB_Am 29.7 2.1E+02 0.0046 21.8 6.3 119 34-165 26-152 (194)
269 PF03180 Lipoprotein_9: NLPA l 29.3 1E+02 0.0022 27.1 4.7 105 14-130 1-120 (237)
270 TIGR00657 asp_kinases aspartat 28.1 98 0.0021 29.4 4.8 29 208-236 387-415 (441)
271 PLN02550 threonine dehydratase 26.6 67 0.0015 32.3 3.4 57 173-236 485-543 (591)
272 TIGR03431 PhnD phosphonate ABC 26.5 1.6E+02 0.0035 25.7 5.6 52 12-63 134-195 (288)
273 PRK06635 aspartate kinase; Rev 26.5 71 0.0015 29.9 3.5 27 209-235 270-296 (404)
274 PRK08210 aspartate kinase I; R 26.5 75 0.0016 29.8 3.6 95 132-234 195-304 (403)
275 TIGR03431 PhnD phosphonate ABC 25.7 2E+02 0.0043 25.1 6.0 52 12-63 27-87 (288)
276 cd00404 Aconitase_swivel Aconi 25.7 52 0.0011 24.7 1.9 49 14-65 16-68 (88)
277 PRK11062 nhaR transcriptional 25.7 4.5E+02 0.0097 22.9 11.7 145 34-192 119-275 (296)
278 cd08447 PBP2_LTTR_aromatics_li 25.6 3.1E+02 0.0067 21.0 13.7 30 34-63 26-56 (198)
279 cd04911 ACT_AKiii-YclM-BS_1 AC 25.6 71 0.0015 23.2 2.6 24 210-233 12-35 (76)
280 PRK12483 threonine dehydratase 25.2 63 0.0014 31.9 2.9 29 202-230 440-469 (521)
281 cd01580 AcnA_IRP_Swivel Aconit 25.0 63 0.0014 27.2 2.5 59 16-78 99-161 (171)
282 cd08469 PBP2_PnbR The C-termin 24.9 3.5E+02 0.0076 21.4 9.5 31 34-64 26-57 (221)
283 PRK15010 ABC transporter lysin 24.9 4.3E+02 0.0094 22.4 10.6 112 37-164 67-188 (260)
284 PRK07377 hypothetical protein; 24.5 1.1E+02 0.0024 26.1 3.9 31 33-63 106-136 (184)
285 cd08439 PBP2_LrhA_like The C-t 23.6 1.1E+02 0.0024 23.6 3.7 31 33-63 25-56 (185)
286 PRK03381 PII uridylyl-transfer 23.5 96 0.0021 32.1 4.0 31 202-232 599-629 (774)
287 PRK13584 hisG ATP phosphoribos 23.5 3.3E+02 0.0071 23.6 6.7 149 14-187 2-178 (204)
288 cd08431 PBP2_HupR The C-termin 23.3 1E+02 0.0023 23.8 3.5 32 32-63 24-56 (195)
289 TIGR01327 PGDH D-3-phosphoglyc 23.2 58 0.0012 32.0 2.3 75 160-234 387-483 (525)
290 PRK05092 PII uridylyl-transfer 22.9 1.3E+02 0.0028 31.8 4.9 32 201-232 731-762 (931)
291 PRK01686 hisG ATP phosphoribos 22.9 5.1E+02 0.011 22.5 8.1 140 13-173 3-178 (215)
292 TIGR01728 SsuA_fam ABC transpo 22.5 1.6E+02 0.0034 25.1 4.7 48 13-63 101-155 (288)
293 COG0040 HisG ATP phosphoribosy 22.0 5.1E+02 0.011 23.7 7.9 88 12-103 93-192 (290)
294 PF08212 Lipocalin_2: Lipocali 22.0 1.3E+02 0.0028 23.7 3.8 26 212-237 117-142 (143)
295 cd04871 ACT_PSP_2 ACT domains 21.7 74 0.0016 23.1 2.1 27 210-236 7-34 (84)
296 smart00094 TR_FER Transferrin. 21.2 1.1E+02 0.0023 28.5 3.5 28 35-62 27-54 (332)
297 cd04917 ACT_AKiii-LysC-EC_2 AC 21.0 1.1E+02 0.0023 20.5 2.7 28 210-237 12-39 (64)
298 KOG1349 Gpi-anchor transamidas 20.2 85 0.0019 28.4 2.5 60 105-164 155-214 (309)
No 1
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=2.8e-82 Score=562.22 Aligned_cols=228 Identities=43% Similarity=0.634 Sum_probs=215.4
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCC-CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEE
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPN-CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQ 91 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~-~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~ 91 (241)
.++|+||||+|||||+||+++|++ .+..||+||+|||++|++|++||||||||||++|+|++|+|+|.+.+|.|+||+.
T Consensus 2 ~~~iayLGP~Gtfs~~Aa~~~f~~~~~~~p~~ti~evf~ave~g~aD~gVVPIENS~eG~V~~tlDlL~~~~l~IvgE~~ 81 (279)
T COG0077 2 TMKIAYLGPEGTFSEQAARKLFGSGAELLPCSTIEDVFKAVENGEADYGVVPIENSIEGSVNETLDLLAETDLQIVGEIV 81 (279)
T ss_pred CceeEEeCCCccHHHHHHHHhccccceeccCCCHHHHHHHHHcCCCceEEEEeeecCCcchHHHHHhhccCCcEEEEEEE
Confidence 589999999999999999999998 7999999999999999999999999999999999999999999999999999999
Q ss_pred EeeeeeeecCCCCCcCCeeEEEecHHHHHHHHHHHHhc--CCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCc
Q 036073 92 FVANFCLLALPGIREEKLKCVLSHPQALASSDIVQTQL--GVARENIDDTASAAQYVASNGLRDAGVVASARAAEIYGLN 169 (241)
Q Consensus 92 l~I~~~L~~~~g~~~~~i~~V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~ 169 (241)
+||+|||++++|.++++|++|||||||++||++||+++ ++++++++|||+||+++++.+++..|||||+.||++|||+
T Consensus 82 lpI~h~L~~~~~~~l~~Ik~vySHpqalaQc~~~L~~~~p~~~~~~~~STa~Aak~v~~~~~~~~AAIas~~aA~~YgL~ 161 (279)
T COG0077 82 LPIHHCLLVKGGVDLEEIKTVYSHPQALAQCRKFLRAHLPGVEIEYTSSTAEAAKLVAEGPDETVAAIASELAAELYGLD 161 (279)
T ss_pred EEEEEEEEecCCCChhhCeEEEeCcHHHHHHHHHHHHcCCCceEEEcCCHHHHHHHHHhCCCcCeeEEcCHHHHHHcCcH
Confidence 99999999998889999999999999999999999997 6999999999999999999877899999999999999999
Q ss_pred eeecccCCCCCCceeEEEEeeCCCCCCCCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccCC
Q 036073 170 ILADRIQDDPDNITRFLVLARDPIMPRTDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVYF 240 (241)
Q Consensus 170 il~~~I~d~~~N~TRF~vl~~~~~~~~~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~~ 240 (241)
+|+++|||.++|+|||+||+|+......+...||||+|.++|+||+|+++|++|++||||||||||||++.
T Consensus 162 il~~~I~D~~~N~TRF~vl~r~~~~~~~~~~~kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~ 232 (279)
T COG0077 162 ILAENIEDEPNNRTRFLVLSRRKPPSVSDGPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKT 232 (279)
T ss_pred hHhhcccCCCCCeEEEEEEeccCCCCcCCCCceEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCC
Confidence 99999999999999999999862211122457999999999999999999999999999999999999873
No 2
>PRK11899 prephenate dehydratase; Provisional
Probab=100.00 E-value=1.7e-80 Score=555.16 Aligned_cols=229 Identities=41% Similarity=0.582 Sum_probs=216.9
Q ss_pred CCccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEE
Q 036073 11 GTKVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEV 90 (241)
Q Consensus 11 ~~~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~ 90 (241)
..++|||||||+|||||+||+++|++.+++||.||++||++|++|++||||||||||++|+|.+|+|+|.+++++|+||+
T Consensus 2 ~~~~kvaylGp~GsfS~~Aa~~~~~~~~~v~~~s~~~vf~av~~g~~d~gVvPiENS~~G~V~~~~Dll~~~~l~Iv~E~ 81 (279)
T PRK11899 2 SKTNRIAFQGEPGANSHLACRDAFPDMEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVADIHHLLPESGLHIVGEY 81 (279)
T ss_pred CCCCEEEEECCCCCHHHHHHHHhcCcCceeecCCHHHHHHHHHCCCCCEEEEEeeccCCccHHHHHHHHhcCCCEEEEEE
Confidence 35688999999999999999999998899999999999999999999999999999999999999999999999999999
Q ss_pred EEeeeeeeecCCCCCcCCeeEEEecHHHHHHHHHHHHhcCCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCce
Q 036073 91 QFVANFCLLALPGIREEKLKCVLSHPQALASSDIVQTQLGVARENIDDTASAAQYVASNGLRDAGVVASARAAEIYGLNI 170 (241)
Q Consensus 91 ~l~I~~~L~~~~g~~~~~i~~V~SHpqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~i 170 (241)
.+||+|||++++|.++++|++||||||||+||++||++++++.+++.|||+||+++++.++++.|||+|+.||++|||++
T Consensus 82 ~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAIas~~aa~~YgL~i 161 (279)
T PRK11899 82 FLPIRHQLMALPGATLEEIKTVHSHPHALGQCRKIIRALGLKPVVAADTAGAARLVAERGDPSMAALASRLAAELYGLDI 161 (279)
T ss_pred EEEeeEEEecCCCCCHHHCeEEEEeHHHHHHHHHHHHHcCCeEEEcCChHHHHHHHHhcCCCCeeEeCCHHHHHHcCCcc
Confidence 99999999999999999999999999999999999999999999999999999999987777899999999999999999
Q ss_pred eecccCCCCCCceeEEEEeeCCCC-CCCCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 171 LADRIQDDPDNITRFLVLARDPIM-PRTDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 171 l~~~I~d~~~N~TRF~vl~~~~~~-~~~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
|+++|||.++|+|||+||+|++.. +...+.+||||+|.++|+||+|+++|++|+++|||||||||||++
T Consensus 162 l~~~IqD~~~N~TRF~vi~~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~ 231 (279)
T PRK11899 162 LAENIEDADHNTTRFVVLSREADWAARGDGPIVTTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVG 231 (279)
T ss_pred hhhcccCCcccceeEEEEecCCCCCCCCCCCceEEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecC
Confidence 999999999999999999998642 222345699999999999999999999999999999999999986
No 3
>PLN02317 arogenate dehydratase
Probab=100.00 E-value=2.1e-79 Score=565.02 Aligned_cols=236 Identities=67% Similarity=1.108 Sum_probs=223.4
Q ss_pred ccCCCCCCCccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCC
Q 036073 4 ISVTPNDGTKVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHR 83 (241)
Q Consensus 4 ~~~~~~~~~~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~ 83 (241)
++.+...+..+|||||||+|||||+||+++|++.+++||+||++||++|++|++||||||||||++|+|.+|||+|.+++
T Consensus 85 ~~~~~~~~~~~rVaylGp~GtfSe~AA~~~f~~~e~vp~~sf~~vf~AVe~g~ad~gVvPIENS~~GsV~~t~DlL~~~~ 164 (382)
T PLN02317 85 LSPSPMHGSKLRVAYQGVPGAYSEAAARKAYPNCEAVPCEQFEAAFQAVELWLADRAVLPIENSLGGSIHRNYDLLLRHR 164 (382)
T ss_pred hcccccCCCCcEEEEECCCcCHHHHHHHHhhCcCceeecCCHHHHHHHHHCCCCCEEEEEEeccCccchHHHHHHHhcCC
Confidence 34455666678999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEEEEeeeeeeecCCCCCcCCeeEEEecHHHHHHHHHHHHhcCCceEeccCHHHHHHHHHhcCCCCeEEecCHhhH
Q 036073 84 LHIVGEVQFVANFCLLALPGIREEKLKCVLSHPQALASSDIVQTQLGVARENIDDTASAAQYVASNGLRDAGVVASARAA 163 (241)
Q Consensus 84 l~I~~E~~l~I~~~L~~~~g~~~~~i~~V~SHpqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 163 (241)
++|+||+++||+|||++++|.++++|++||||||||+||++||++++++++++.|||+||++|++.+.++.|||||+.||
T Consensus 165 l~IvgEv~l~I~h~Ll~~~g~~l~~Ik~VySHPQALaQC~~~L~~~~~~~~~~~sTA~AA~~Va~~~~~~~AAIaS~~aA 244 (382)
T PLN02317 165 LHIVGEVQLPVHHCLLALPGVRKEELKRVISHPQALAQCENTLTKLGVVREAVDDTAGAAKMVAANGLRDTAAIASARAA 244 (382)
T ss_pred CEEEEEEEEEeeeEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHcCCeEEEcCCHHHHHHHHHhcCCCCceeecCHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999998777789999999999
Q ss_pred HhcCCceeecccCCCCCCceeEEEEeeCCCCCCCCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 164 EIYGLNILADRIQDDPDNITRFLVLARDPIMPRTDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 164 ~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~~~~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
++|||++|+++|||+++|+|||++|+|++..+..+..+||||+|.++|+||+|+++|++|+.+|||||||||||.+
T Consensus 245 ~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KTSivfsl~~~pG~L~k~L~~Fa~~~INLtkIESRP~~ 320 (382)
T PLN02317 245 ELYGLDILAEGIQDDSDNVTRFLMLAREPIIPRTDRPFKTSIVFSLEEGPGVLFKALAVFALRDINLTKIESRPQR 320 (382)
T ss_pred HHcCCcchhhhhcCCCCCeeeEEEEecCCcCCCCCCCccEEEEEEcCCCCchHHHHHHHHHHCCCCEEEEEeeecC
Confidence 9999999999999999999999999998764544456799999999999999999999999999999999999986
No 4
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=100.00 E-value=1.1e-74 Score=538.56 Aligned_cols=229 Identities=31% Similarity=0.457 Sum_probs=213.2
Q ss_pred CCccEEEEeCCCCcHHHHHHHhhCCC----CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEE
Q 036073 11 GTKVRISFKGSPGSFTEDAALKAYPN----CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHI 86 (241)
Q Consensus 11 ~~~~~ia~LGp~GtfS~~Aa~~~~~~----~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I 86 (241)
...++||||||+|||||+||+++|+. ...++|+||++||++|++|++||||||||||++|+|.+|||+|.+++++|
T Consensus 101 ~~~~~va~lGp~GtfSh~Aa~~~~~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~DlL~~~~l~I 180 (386)
T PRK10622 101 PHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVLPIENTSSGAINDVYDLLQHTSLSI 180 (386)
T ss_pred cccceEEEECCCCcHHHHHHHHhhccccccccccCCCCHHHHHHHHHCCCCCEEEEEEecCCceehHHHHHHHhcCCCEE
Confidence 44578999999999999999998753 23458999999999999999999999999999999999999999999999
Q ss_pred EEEEEEeeeeeeecCCCCCcCCeeEEEecHHHHHHHHHHHHhc-CCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 87 VGEVQFVANFCLLALPGIREEKLKCVLSHPQALASSDIVQTQL-GVARENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 87 ~~E~~l~I~~~L~~~~g~~~~~i~~V~SHpqal~Qc~~fl~~~-~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
+||+.+||+|||++.+|.++++|++||||||||+||++||+++ +++.++++||++||+++++.++++.|||+|+.||++
T Consensus 181 ~~E~~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~aa~~ 260 (386)
T PRK10622 181 VGEMTLPIDHCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRYPHWKIEYTESTAAAMEKVAQANSPHVAALGSEAGGAL 260 (386)
T ss_pred EEEEEEEEEEEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHCCCceEEEcCChHHHHHHHHhcCCCCEEEECCHHHHHH
Confidence 9999999999999999999999999999999999999999996 789999999999999999877778899999999999
Q ss_pred cCCceeecccCCCCCCceeEEEEeeCCCCCCCCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 166 YGLNILADRIQDDPDNITRFLVLARDPIMPRTDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 166 ygL~il~~~I~d~~~N~TRF~vl~~~~~~~~~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
|||++|+++|||.++|+|||++|++++..+.....+||||+|.++|+||+|+++|++|+.+|||||||||||++
T Consensus 261 ygL~vl~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~~L~~Fa~~giNLtkIeSRP~~ 334 (386)
T PRK10622 261 YGLQVLERNLANQQQNITRFIVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTKLESRPIH 334 (386)
T ss_pred cCCcChhhcCcCCccccceEEEEecCCCCCCCCCCCcEEEEEEcCCCCcHHHHHHHHHHHcCCCeeEEEeeecC
Confidence 99999999999999999999999998743333334699999999999999999999999999999999999986
No 5
>PRK11898 prephenate dehydratase; Provisional
Probab=100.00 E-value=6.4e-74 Score=514.49 Aligned_cols=226 Identities=42% Similarity=0.561 Sum_probs=210.9
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCC---CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccC-CeEEEE
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPN---CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRH-RLHIVG 88 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~---~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~-~l~I~~ 88 (241)
|+|||||||+|||||+||+++|++ .++++|+||++||++|++|++||||||||||++|+|.+|+|+|.++ +++|+|
T Consensus 1 ~~~va~lGp~Gs~s~~Aa~~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~v~~~~d~L~~~~~~~iv~ 80 (283)
T PRK11898 1 MMKIAYLGPEGTFTEAAALKFFPADGEAELVPYDSIPDVLDAVEAGEVDYAVVPIENSIEGSVNPTLDYLAHGSPLQIVA 80 (283)
T ss_pred CcEEEEECCCCCHHHHHHHHhhccccccceEecCCHHHHHHHHHcCCCCEEEEEecccCceecHHHHHHhccCCCcEEEE
Confidence 578999999999999999999965 7899999999999999999999999999999999999999999764 899999
Q ss_pred EEEEeeeeeeecCCCCCcCCeeEEEecHHHHHHHHHHHHhc--CCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhc
Q 036073 89 EVQFVANFCLLALPGIREEKLKCVLSHPQALASSDIVQTQL--GVARENIDDTASAAQYVASNGLRDAGVVASARAAEIY 166 (241)
Q Consensus 89 E~~l~I~~~L~~~~g~~~~~i~~V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y 166 (241)
|+.+||+|||++++|.. ++|++||||||||+||++||+++ +++.+++.|||+||+++++++..+.|||+|+.||++|
T Consensus 81 E~~l~I~~~L~~~~~~~-~~i~~V~SHpqal~QC~~~l~~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y 159 (283)
T PRK11898 81 EIVLPIAQHLLVHPGHA-AKIRTVYSHPQALAQCRKWLAEHLPGAELEPANSTAAAAQYVAEHPDEPIAAIASELAAELY 159 (283)
T ss_pred EEEeeeeEEEeCCCCCh-hcCeEEEEeHHHHHHHHHHHHhcCCCCEEEEcCchHHHHHHHhcCCCCCeEEECCHHHHHHc
Confidence 99999999999999866 99999999999999999999996 8999999999999999998766678999999999999
Q ss_pred CCceeecccCCCCCCceeEEEEeeCCC-CCCCCCCceEEEEEecCC-CchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 167 GLNILADRIQDDPDNITRFLVLARDPI-MPRTDKPFKTSIVFTLDE-GPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 167 gL~il~~~I~d~~~N~TRF~vl~~~~~-~~~~~~~~ktsi~~~~~~-~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
||++|+++|||.++|+|||++|+|++. .+...+.+||||+|+++| +||+|+++|++|+.+|||||+|||||++
T Consensus 160 gL~il~~~I~d~~~N~TRF~vi~~~~~~~~~~~~~~ktslif~l~~~~pGsL~~~L~~F~~~~INLt~IeSRP~~ 234 (283)
T PRK11898 160 GLEILAEDIQDYPNNRTRFWLLGRKKPPPPLRTGGDKTSLVLTLPNNLPGALYKALSEFAWRGINLTRIESRPTK 234 (283)
T ss_pred CCcEehhcCCCCCccceEEEEEEcCcccCCCCCCCCeEEEEEEeCCCCccHHHHHHHHHHHCCCCeeeEecccCC
Confidence 999999999999999999999999864 222345679999999976 5999999999999999999999999986
No 6
>KOG2797 consensus Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=4.3e-68 Score=469.21 Aligned_cols=236 Identities=59% Similarity=0.992 Sum_probs=225.4
Q ss_pred ccCCCCCCCccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCC
Q 036073 4 ISVTPNDGTKVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHR 83 (241)
Q Consensus 4 ~~~~~~~~~~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~ 83 (241)
++-++-.+...||+|||++|+|||.||.+.|++++-+||+.|+.+|++|+...+||+|+|||||+.|+|..+||+|.++.
T Consensus 81 l~psp~~~s~lRva~qg~pgaysesaa~ka~pn~~avpc~~f~~afqave~w~vD~AVLPiENS~gGsIhrnYDLLlrh~ 160 (377)
T KOG2797|consen 81 LSPSPMHGSTLRVAYQGVPGAYSESAALKAYPNCEAVPCDQFEAAFQAVELWIVDYAVLPIENSTGGSIHRNYDLLLRHR 160 (377)
T ss_pred cccCCCCCceEEEEeecCCchhhhhhhhhhcCCcccccHhHHHHHHHHHHHhhccceeeeeeccCCceeeechHHHhhcc
Confidence 44556667778999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEEEEeeeeeeecCCCCCcCCeeEEEecHHHHHHHHHHHHhcC--CceEeccCHHHHHHHHHhcCCCCeEEecCHh
Q 036073 84 LHIVGEVQFVANFCLLALPGIREEKLKCVLSHPQALASSDIVQTQLG--VARENIDDTASAAQYVASNGLRDAGVVASAR 161 (241)
Q Consensus 84 l~I~~E~~l~I~~~L~~~~g~~~~~i~~V~SHpqal~Qc~~fl~~~~--~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~ 161 (241)
+.|+||+.+||+|||++.+|+..+++++|.||||||+||..||++++ +.++.++|||+||+.++.....+++||+|++
T Consensus 161 lhiVgEv~vPvhHCLi~~~gv~~e~~~~VlSHPQal~Qce~~L~~l~~~~~r~a~~dTa~Aa~~~s~~~~~d~~AIASe~ 240 (377)
T KOG2797|consen 161 LHIVGEVQVPVHHCLIALPGVRKEEVVRVLSHPQALGQCECSLTKLGPNAAREAVSDTAGAAEQISASNTADTAAIASER 240 (377)
T ss_pred hheeeEEecceeeeEecCCCCChhheeeeecCcHHHHHHHHHHHhcccceeeeeccchHHHHHHHHhcccccHHHHHHHH
Confidence 99999999999999999999999999999999999999999999974 8899999999999999988888899999999
Q ss_pred hHHhcCCceeecccCCCCCCceeEEEEeeCCCCCCCCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 162 AAEIYGLNILADRIQDDPDNITRFLVLARDPIMPRTDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 162 aa~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~~~~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
||++|||.||+++|||+.+|+|||++|.|++..|..+...||||+|...+.||.|.++|++|+.|+||||+|||||-+
T Consensus 241 aA~ly~l~Il~~~IqDd~~NvTRFLmLar~p~ip~t~rl~ktsivf~~~~gp~vLfkvl~vfa~r~inltkIesRP~h 318 (377)
T KOG2797|consen 241 AAELYGLNILEKNIQDDLGNVTRFLMLAREPIIPDTDRLFKTSIVFFREKGPGVLFKVLSVFAFRSINLTKIESRPFH 318 (377)
T ss_pred HHHHhcchhhhhhcccccCCeeEEEEEeccCCCCCCCccceeeEEEEeecCCchHHHHHHHHHhhhceeeeeeccccc
Confidence 999999999999999999999999999999998887778899999998889999999999999999999999999954
No 7
>PF00800 PDT: Prephenate dehydratase Caution this is only a partial structure.; InterPro: IPR001086 Prephenate dehydratase (4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate to phenylpyruvate. In microorganisms it is part of the terminal pathway of phenylalanine biosynthesis. In some bacteria such as Escherichia coli PDT is part of a bifunctional enzyme (P-protein) that also catalyses the transformation of chorismate into prephenate (chorismate mutase, IPR002701 from INTERPRO, 5.4.99.5 from EC) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional PDT aligns well with the C-terminal part of P-proteins [].; GO: 0004664 prephenate dehydratase activity, 0009094 L-phenylalanine biosynthetic process; PDB: 3MWB_B 2QMX_A 2QMW_A 3LUY_A.
Probab=100.00 E-value=8.8e-60 Score=397.86 Aligned_cols=177 Identities=44% Similarity=0.698 Sum_probs=164.3
Q ss_pred EEEeCCCCcHHHHHHHhhC--CCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEe
Q 036073 16 ISFKGSPGSFTEDAALKAY--PNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFV 93 (241)
Q Consensus 16 ia~LGp~GtfS~~Aa~~~~--~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~ 93 (241)
||||||+|||||+||++|| ++.++++|+||++||++|++|++||||||||||++|.|.+|+|+|.+.++.|+||+.+|
T Consensus 1 Ia~LGP~GT~S~~Aa~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~~vvPiENs~~G~V~~t~d~L~~~~l~i~~e~~l~ 80 (181)
T PF00800_consen 1 IAYLGPEGTFSHEAAQQYFGGPDAEIVPCDSFEEVFDAVEEGEADYGVVPIENSLEGSVSETLDLLIDSDLYIVGEIVLP 80 (181)
T ss_dssp EEEESSTTSHHHHHHCCCCTTTCSEEEEESSHHHHHHHHHCTSSSEEEEEEECTTTCECHHHHHHHHTSSCEEEEEEEEE
T ss_pred CEEeCCCCCHHHHHHHHHHHhhccceEecCCHHHHHHHHHcCCCceEEEeEeeecCCEeHHHHHHHhcCCceEEEEEEec
Confidence 7999999999999999999 56899999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeecCCCCCcCCeeEEEecHHHHHHHHHHHHhc--CCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCcee
Q 036073 94 ANFCLLALPGIREEKLKCVLSHPQALASSDIVQTQL--GVARENIDDTASAAQYVASNGLRDAGVVASARAAEIYGLNIL 171 (241)
Q Consensus 94 I~~~L~~~~g~~~~~i~~V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il 171 (241)
|+|||+++++.++++|++|||||||++||++||+++ +++++.+.||++||++++..+.++.|||+|+.||++|||++|
T Consensus 81 i~~~L~~~~~~~l~~i~~V~SHp~al~Qc~~~l~~~~p~~~~~~~~Sta~Aa~~v~~~~~~~~aAI~s~~aa~~y~L~il 160 (181)
T PF00800_consen 81 IHHCLLAKPGTSLSDIKTVYSHPQALAQCREFLEKHLPGAEIVEASSTAEAAEKVAASEGPGDAAIASEEAAELYGLEIL 160 (181)
T ss_dssp --EEEEECTT--GGG-SEEEEEHHHHHHTHHHHHHT-TTSEEEEESSHHHHHHHCCCCTBTTEEEEEECCHHHHTTEEEE
T ss_pred cccEEeccCCCchhcceEEEEchHHHHHHHHHHHhcCCceEEEeCCCHHHHHHHHHhccCCCeEEECCHHHHHHcCccCh
Confidence 999999999999999999999999999999999997 799999999999999987777788999999999999999999
Q ss_pred ecccCCCCCCceeEEEEeeCC
Q 036073 172 ADRIQDDPDNITRFLVLARDP 192 (241)
Q Consensus 172 ~~~I~d~~~N~TRF~vl~~~~ 192 (241)
+++|||.++|+|||+||+|++
T Consensus 161 ~~~I~d~~~N~TRF~vi~~~~ 181 (181)
T PF00800_consen 161 ARNIQDNPNNYTRFLVIGKEP 181 (181)
T ss_dssp ECS-SSSTT-EEEEEEEECCT
T ss_pred hhcCCCCCCCeEeEEEEecCC
Confidence 999999999999999999874
No 8
>PRK06034 hypothetical protein; Provisional
Probab=99.44 E-value=7.5e-14 Score=124.75 Aligned_cols=83 Identities=11% Similarity=0.051 Sum_probs=67.1
Q ss_pred ccCCCCCCCccEE-EEeCCCCcHHHHHHHhhCCC-CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccc-
Q 036073 4 ISVTPNDGTKVRI-SFKGSPGSFTEDAALKAYPN-CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLL- 80 (241)
Q Consensus 4 ~~~~~~~~~~~~i-a~LGp~GtfS~~Aa~~~~~~-~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~- 80 (241)
|+.|+..+...+| +||||+|||||+||++||+. .+.++|.||++||++|++|++|||||||+++ .+... -.|.
T Consensus 85 is~Sr~lQ~~~~V~a~lG~~gs~s~~AA~~~FG~s~~~~~~~s~~dVf~AV~~g~adyGVVPI~~~-~~~WW---~~L~~ 160 (279)
T PRK06034 85 IATFTYVQAPFSVHADGSGGEAAMRDSARFHFGFTVPYVPHFSAQAVVEAVARSKGDLGLVSLTSS-DTPWW---GRLEA 160 (279)
T ss_pred HHHHHHhcCCceEEEEeCCccHHHHHHHHHHhccccCCccCCCHHHHHHHHHcCCCCEEEEECCCC-CCcHH---HHhcc
Confidence 5667777888999 99999999999999999985 6888999999999999999999999999544 34443 3333
Q ss_pred cCCeEEEEEE
Q 036073 81 RHRLHIVGEV 90 (241)
Q Consensus 81 ~~~l~I~~E~ 90 (241)
....+|++-.
T Consensus 161 ~~~~~iiarl 170 (279)
T PRK06034 161 EGAPKIIARL 170 (279)
T ss_pred CCCCeEEEeC
Confidence 3447776543
No 9
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=99.37 E-value=4.8e-13 Score=97.19 Aligned_cols=38 Identities=34% Similarity=0.451 Sum_probs=36.1
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccCC
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVYF 240 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~~ 240 (241)
||++|+++|+||+|+++|+.|+.+|||||+|||||.+-
T Consensus 1 tsl~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~ 38 (74)
T cd04904 1 TSLIFSLKEEVGALARALKLFEEFGVNLTHIESRPSRR 38 (74)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCC
Confidence 68999999999999999999999999999999999863
No 10
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.37 E-value=8.2e-13 Score=99.80 Aligned_cols=41 Identities=34% Similarity=0.449 Sum_probs=38.7
Q ss_pred CCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 199 KPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 199 ~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
..+||+|+|.++|+||+|+++|++|+.+||||++|||||.+
T Consensus 11 ~~~ktslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~ 51 (90)
T cd04931 11 KNGVISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSR 51 (90)
T ss_pred CCCcEEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCC
Confidence 44689999999999999999999999999999999999986
No 11
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.30 E-value=2.3e-12 Score=101.60 Aligned_cols=39 Identities=26% Similarity=0.363 Sum_probs=37.6
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
+||||+|.++|+||+|+++|++|+.+||||++|||||++
T Consensus 40 ~ktSlifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~ 78 (115)
T cd04930 40 QKATLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSR 78 (115)
T ss_pred ccEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCC
Confidence 599999999999999999999999999999999999985
No 12
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.26 E-value=5.6e-12 Score=91.87 Aligned_cols=37 Identities=32% Similarity=0.447 Sum_probs=35.5
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
|+++|.++|+||+|+++|++|+++||||++|||||.+
T Consensus 1 tsl~~~l~~~~g~L~~iL~~f~~~~inl~~IeSRP~~ 37 (74)
T cd04929 1 TSVIFSLKNEVGGLAKALKLFQELGINVVHIESRKSK 37 (74)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCC
Confidence 5899999999999999999999999999999999975
No 13
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=99.01 E-value=3.1e-10 Score=82.01 Aligned_cols=36 Identities=53% Similarity=0.691 Sum_probs=34.2
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
+++|.++|+||+|+++|+.|+.+|+||++|||||.+
T Consensus 1 sl~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~ 36 (75)
T cd04880 1 SLVFSLKNKPGALAKALKVFAERGINLTKIESRPSR 36 (75)
T ss_pred CEEEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecC
Confidence 578999999999999999999999999999999986
No 14
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=98.86 E-value=3.4e-09 Score=77.55 Aligned_cols=38 Identities=55% Similarity=0.653 Sum_probs=36.2
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
|+++.|.++|+||+|+++|+.|+++||||++|+|||.+
T Consensus 1 ~~sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~ 38 (80)
T cd04905 1 KTSIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSK 38 (80)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcC
Confidence 58999999999999999999999999999999999974
No 15
>TIGR01270 Trp_5_monoox tryptophan 5-monooxygenase, tetrameric. This model describes tryptophan 5-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tyrosine 3-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=98.84 E-value=3.3e-09 Score=100.60 Aligned_cols=41 Identities=32% Similarity=0.390 Sum_probs=39.0
Q ss_pred CCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 199 KPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 199 ~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
+.+||||+|+++|+||+|+++|+.|+.+||||++|||||++
T Consensus 28 ~~~ktSLIFsL~d~pGaL~~vL~vFa~~gINLThIESRPsk 68 (464)
T TIGR01270 28 GVQRLSIIFSLSNVVGDLSKAIAIFQDRHINILHLESRDSK 68 (464)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHCCCCEEEEECCcCC
Confidence 45799999999999999999999999999999999999986
No 16
>PRK08818 prephenate dehydrogenase; Provisional
Probab=97.77 E-value=2.3e-05 Score=73.30 Aligned_cols=36 Identities=25% Similarity=0.409 Sum_probs=33.5
Q ss_pred ceEEEEEecC-CCchHHHHHHHHHHHCCceeeeeeee
Q 036073 201 FKTSIVFTLD-EGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 201 ~ktsi~~~~~-~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.-++|.|.++ |+||+|+++|++|+++||||++|||-
T Consensus 294 ~~~~l~~~v~~d~pG~L~~vl~~la~~~INit~Ies~ 330 (370)
T PRK08818 294 EPLTLSVYLPEDRPGSLRTLLHVFEQHGVNLSSIHSS 330 (370)
T ss_pred cceEEEEECCCCCCChHHHHHHHHHHcCcccceEEEe
Confidence 4688999997 99999999999999999999999993
No 17
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=97.75 E-value=5.1e-05 Score=52.19 Aligned_cols=37 Identities=16% Similarity=0.283 Sum_probs=33.1
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
+.+.+..+|+||.|.++++.|+++|||+..+++++..
T Consensus 1 ~~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~ 37 (66)
T PF01842_consen 1 YRVRVIVPDRPGILADVTEILADHGINIDSISQSSDK 37 (66)
T ss_dssp EEEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEES
T ss_pred CEEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecC
Confidence 3577788999999999999999999999999998753
No 18
>TIGR01269 Tyr_3_monoox tyrosine 3-monooxygenase, tetrameric. This model describes tyrosine 3-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tryptophan 5-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=97.27 E-value=0.00034 Score=66.42 Aligned_cols=38 Identities=13% Similarity=0.075 Sum_probs=33.9
Q ss_pred eEEEEEecCCC-chHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 202 KTSIVFTLDEG-PGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 202 ktsi~~~~~~~-pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
.++++|.++++ +|+|.++|..|..++|||+.|||||.+
T Consensus 37 ~~~~~~~~~~~~~g~L~~~l~~f~~~~inl~hiEsr~~~ 75 (457)
T TIGR01269 37 MQNNQFYIRTKEISSLHRILKYIETFKLNLVHFETRPTR 75 (457)
T ss_pred ceeEEEEeccCcchhHHHHHHHHHHcCCcEEEeecCCcc
Confidence 56778888754 999999999999999999999999975
No 19
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.12 E-value=0.00057 Score=47.25 Aligned_cols=33 Identities=36% Similarity=0.413 Sum_probs=30.2
Q ss_pred EEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 206 VFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 206 ~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
.+.++|+||.|.++++.++..|+|+++|.+++.
T Consensus 2 ~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~ 34 (73)
T cd04886 2 RVELPDRPGQLAKLLAVIAEAGANIIEVSHDRA 34 (73)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEEEEEEEec
Confidence 467899999999999999999999999998874
No 20
>cd04908 ACT_Bt0572_1 N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains. Included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem ACT domains as seen in the uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related ACT domains. These tandem ACT domain proteins belong to the superfamily of ACT regulatory domains.
Probab=97.04 E-value=0.00096 Score=46.66 Aligned_cols=34 Identities=21% Similarity=0.372 Sum_probs=29.8
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
-|.+.++|+||.|.++++.|+++|+|+..+..-+
T Consensus 3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~ 36 (66)
T cd04908 3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIAD 36 (66)
T ss_pred EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEe
Confidence 3566889999999999999999999999887644
No 21
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.91 E-value=0.0011 Score=45.43 Aligned_cols=34 Identities=18% Similarity=0.358 Sum_probs=29.4
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
+.+.++|+||.|.++++.|+++|+|+.++...|.
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~ 35 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVE 35 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEcc
Confidence 4567899999999999999999999998875443
No 22
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=96.72 E-value=0.0018 Score=60.49 Aligned_cols=39 Identities=26% Similarity=0.367 Sum_probs=36.7
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeeccC
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARVY 239 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~~ 239 (241)
..++++|.+.+++|+|.++|+.|...++|+..|||||.+
T Consensus 35 ~~~~~if~~r~~~~~l~~~Lk~f~~~~vnl~HiEsR~s~ 73 (461)
T KOG3820|consen 35 ARISLIFSLRNKVGALARALKAFEEFHVNLLHIESRPSE 73 (461)
T ss_pred ceEEEEEEecccchHHHHHHHHhhhcCceEEEeeccccc
Confidence 478899999999999999999999999999999999975
No 23
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=96.70 E-value=0.0027 Score=46.53 Aligned_cols=36 Identities=17% Similarity=0.343 Sum_probs=31.9
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
-+|.+-+.|+||.|.++++.|++||+|+.+|..-|.
T Consensus 3 ~tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~t 38 (76)
T PRK06737 3 HTFSLVIHNDPSVLLRISGIFARRGYYISSLNLNER 38 (76)
T ss_pred EEEEEEEecCCCHHHHHHHHHhccCcceEEEEeccc
Confidence 467777899999999999999999999999987664
No 24
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=96.61 E-value=0.0035 Score=45.91 Aligned_cols=37 Identities=16% Similarity=0.247 Sum_probs=32.4
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
|-+|.+.+.|+||.|.++++.|+.||.|+.+|.--|+
T Consensus 3 ~~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t 39 (76)
T PRK11152 3 QHQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQN 39 (76)
T ss_pred eEEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeec
Confidence 4577788899999999999999999999999876653
No 25
>cd04884 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.54 E-value=0.0037 Score=44.33 Aligned_cols=33 Identities=18% Similarity=0.372 Sum_probs=28.7
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
+.+.++|+||+|.++++.++++|+|+.++...+
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~ 34 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAF 34 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEecc
Confidence 456889999999999999999999998885433
No 26
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.34 E-value=0.0062 Score=42.50 Aligned_cols=34 Identities=12% Similarity=0.358 Sum_probs=29.6
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
.+.+.++|+||.|.++++.|+.+|+|+..+...+
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~ 36 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILE 36 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEE
Confidence 3566789999999999999999999999887544
No 27
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.21 E-value=0.0086 Score=41.94 Aligned_cols=35 Identities=29% Similarity=0.475 Sum_probs=30.3
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
+.+.+.++|+||.|.++++.|+++|+|+.++..-+
T Consensus 2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~ 36 (72)
T cd04883 2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYP 36 (72)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEec
Confidence 35677889999999999999999999999886433
No 28
>cd04889 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate. Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Also included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem A
Probab=96.01 E-value=0.01 Score=39.82 Aligned_cols=33 Identities=21% Similarity=0.383 Sum_probs=28.8
Q ss_pred EEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 206 VFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 206 ~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
.+.++|+||.|.++++.|.++|+|+..+...+.
T Consensus 2 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~ 34 (56)
T cd04889 2 SVFVENKPGRLAEVTEILAEAGINIKAISIAET 34 (56)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEc
Confidence 457799999999999999999999988876553
No 29
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.87 E-value=0.012 Score=40.31 Aligned_cols=33 Identities=30% Similarity=0.511 Sum_probs=29.6
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
|.+..+|+||.|.++++.|+++|+|+.++..++
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~ 34 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSR 34 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEe
Confidence 566778999999999999999999999987665
No 30
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=95.71 E-value=0.015 Score=39.61 Aligned_cols=34 Identities=24% Similarity=0.410 Sum_probs=30.6
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
+.+..+|+||.|.++++.|+++|+|+.++++++-
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~ 35 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRK 35 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEecc
Confidence 5667899999999999999999999999988764
No 31
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=95.71 E-value=0.02 Score=39.14 Aligned_cols=35 Identities=26% Similarity=0.498 Sum_probs=31.2
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
+|.+..+|+||.|.+++..|+++++|+.++..++.
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~ 36 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPT 36 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeec
Confidence 56778899999999999999999999999987653
No 32
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=95.67 E-value=0.017 Score=43.06 Aligned_cols=37 Identities=11% Similarity=0.227 Sum_probs=31.5
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
|-.|.+-+.|+||.|.++-+.|++||+|+.+|.--|.
T Consensus 2 k~~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~T 38 (84)
T PRK13562 2 TRILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHS 38 (84)
T ss_pred cEEEEEEEECCCCHHHHHHHHHhccCcCeeeEEeccc
Confidence 3467777899999999999999999999999875543
No 33
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.64 E-value=0.012 Score=41.46 Aligned_cols=30 Identities=30% Similarity=0.419 Sum_probs=26.7
Q ss_pred EEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 206 VFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 206 ~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+.+|++||+|.++++.++. +-|++.++=|
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~ 31 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYR 31 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEE
Confidence 46789999999999999999 9999987654
No 34
>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-p
Probab=95.48 E-value=0.021 Score=35.78 Aligned_cols=33 Identities=30% Similarity=0.404 Sum_probs=29.1
Q ss_pred EEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 206 VFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 206 ~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
.+..+++||.|.++++.|+.+++|+.++.+++.
T Consensus 2 ~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~ 34 (60)
T cd02116 2 TVSGPDRPGLLAKVLSVLAEAGINITSIEQRTS 34 (60)
T ss_pred EEEecCCCchHHHHHHHHHHCCCcEEEEEeEEc
Confidence 456788999999999999999999999987653
No 35
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=95.46 E-value=0.023 Score=40.92 Aligned_cols=39 Identities=15% Similarity=0.348 Sum_probs=32.5
Q ss_pred CceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 200 PFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 200 ~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
.+.+.|.+...|+||.|.++++.++..|+|+..+..+..
T Consensus 4 ~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~ 42 (80)
T PF13291_consen 4 SFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTN 42 (80)
T ss_dssp -EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE-
T ss_pred EEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEe
Confidence 457888888999999999999999999999999998764
No 36
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.43 E-value=0.029 Score=38.54 Aligned_cols=34 Identities=24% Similarity=0.235 Sum_probs=29.8
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
.|.+..+|+||.|.++++.|+++++|+.++...+
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~ 35 (72)
T cd04874 2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFI 35 (72)
T ss_pred eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEec
Confidence 4567779999999999999999999999887654
No 37
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=95.38 E-value=0.019 Score=39.98 Aligned_cols=33 Identities=27% Similarity=0.432 Sum_probs=29.0
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
+++..+|+||.|.++++.|+++|+|+..+.+.+
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~ 34 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGR 34 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeec
Confidence 456789999999999999999999998887654
No 38
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=95.30 E-value=0.033 Score=42.57 Aligned_cols=36 Identities=22% Similarity=0.456 Sum_probs=31.3
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
+-.|.+-+.|+||.|.++-+.|++||.|+.+|-.-|
T Consensus 8 ~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~ 43 (96)
T PRK08178 8 NVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLP 43 (96)
T ss_pred CEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEee
Confidence 566777889999999999999999999999985544
No 39
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.15 E-value=0.033 Score=39.21 Aligned_cols=33 Identities=12% Similarity=0.244 Sum_probs=30.0
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
|.+..+|+||.|.++.+.+++.|+|+..++++.
T Consensus 2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~ 34 (74)
T cd04887 2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVE 34 (74)
T ss_pred EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEE
Confidence 567789999999999999999999999998765
No 40
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=95.09 E-value=0.025 Score=39.67 Aligned_cols=27 Identities=33% Similarity=0.546 Sum_probs=24.2
Q ss_pred CCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 211 EGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 211 ~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
|+||.|.++++.|.+||+|+.+|..-|
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~ 27 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGP 27 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeee
Confidence 689999999999999999999998766
No 41
>cd04926 ACT_ACR_4 C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.01 E-value=0.056 Score=38.49 Aligned_cols=35 Identities=14% Similarity=0.320 Sum_probs=29.7
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
|.+.+..+|+||.|+++.+.|+++|+|+.+....+
T Consensus 2 tri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t 36 (72)
T cd04926 2 VRLELRTEDRVGLLSDVTRVFRENGLTVTRAEIST 36 (72)
T ss_pred eEEEEEECCccCHHHHHHHHHHHCCcEEEEEEEec
Confidence 45677889999999999999999999997765443
No 42
>cd04899 ACT_ACR-UUR-like_2 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the second and fourth ACT domains of a novel protein composed almost entirely of ACT domain repeats, the ACR protein. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=94.84 E-value=0.061 Score=37.30 Aligned_cols=36 Identities=25% Similarity=0.351 Sum_probs=31.2
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
|.|.+..+|+||.|.++.+.|+.+++|+.++..++.
T Consensus 1 ~~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~ 36 (70)
T cd04899 1 TVLELTALDRPGLLADVTRVLAELGLNIHSAKIATL 36 (70)
T ss_pred CEEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEec
Confidence 345667799999999999999999999999887754
No 43
>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=94.58 E-value=0.067 Score=38.68 Aligned_cols=30 Identities=27% Similarity=0.401 Sum_probs=26.0
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
|.|-+..+|+||-|+++.+.|++.|+++.+
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~~ 31 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCITK 31 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEEE
Confidence 455567799999999999999999999864
No 44
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=94.43 E-value=0.073 Score=37.43 Aligned_cols=33 Identities=27% Similarity=0.390 Sum_probs=29.8
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+|.+..+|+||.|.++++.+++.|+|+..+.+.
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~ 34 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQN 34 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeC
Confidence 567788999999999999999999999999763
No 45
>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains. The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=94.43 E-value=0.069 Score=37.12 Aligned_cols=34 Identities=26% Similarity=0.473 Sum_probs=29.8
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
|.+...|+||.|.++++.|+++++|+.++.+++.
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~ 36 (79)
T cd04881 3 LRLTVKDKPGVLAKITGILAEHGISIESVIQKEA 36 (79)
T ss_pred EEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEccc
Confidence 4566789999999999999999999999987654
No 46
>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD. This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t
Probab=94.40 E-value=0.084 Score=36.22 Aligned_cols=34 Identities=18% Similarity=0.275 Sum_probs=29.8
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
.|.+..+|+||.|+++.+.|+.+|+|+..+....
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~ 35 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARIST 35 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEee
Confidence 4567789999999999999999999998887654
No 47
>cd04906 ACT_ThrD-I_1 First of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the first of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=94.30 E-value=0.038 Score=40.69 Aligned_cols=26 Identities=27% Similarity=0.436 Sum_probs=22.2
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCce
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREIN 229 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iN 229 (241)
.+.+.+||+||+|.++|+.++..+||
T Consensus 3 vl~v~ipD~PG~L~~ll~~l~~anI~ 28 (85)
T cd04906 3 LLAVTIPERPGSFKKFCELIGPRNIT 28 (85)
T ss_pred EEEEecCCCCcHHHHHHHHhCCCcee
Confidence 36678899999999999999966666
No 48
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=94.27 E-value=0.058 Score=42.85 Aligned_cols=34 Identities=21% Similarity=0.452 Sum_probs=29.8
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
+.-+.+.++|+||+|.+++++|..++||+--|.-
T Consensus 69 ~dVlaVEmeD~PG~l~~I~~vl~d~diNldYiYA 102 (142)
T COG4747 69 TDVLAVEMEDVPGGLSRIAEVLGDADINLDYIYA 102 (142)
T ss_pred eeEEEEEecCCCCcHHHHHHHHhhcCcCceeeee
Confidence 4456788899999999999999999999988764
No 49
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=94.20 E-value=0.034 Score=38.39 Aligned_cols=33 Identities=24% Similarity=0.426 Sum_probs=28.9
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
+++...|+||.|.++++.|+++|+|+..+.+++
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~ 34 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQT 34 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccC
Confidence 456678999999999999999999998887765
No 50
>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=94.11 E-value=0.077 Score=38.68 Aligned_cols=28 Identities=14% Similarity=0.131 Sum_probs=24.6
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceee
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLT 231 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt 231 (241)
.|-+..+||||-||++...|++.|+++.
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~ 29 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQIS 29 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEE
Confidence 3456779999999999999999999985
No 51
>PRK00194 hypothetical protein; Validated
Probab=93.44 E-value=0.12 Score=38.00 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=29.7
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+-.+.+.-+|+||.+.++.+.|+.+|+|+..+++.
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~ 37 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQT 37 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhH
Confidence 34556666899999999999999999999988764
No 52
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=93.31 E-value=0.15 Score=36.22 Aligned_cols=33 Identities=15% Similarity=0.315 Sum_probs=29.9
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
|.+...|++|.|.+++..+++.|+|+.++++++
T Consensus 3 l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~ 35 (74)
T cd04877 3 LEITCEDRLGITQEVLDLLVEHNIDLRGIEIDP 35 (74)
T ss_pred EEEEEEccchHHHHHHHHHHHCCCceEEEEEec
Confidence 556668999999999999999999999999876
No 53
>cd04875 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase). This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=93.18 E-value=0.16 Score=36.02 Aligned_cols=32 Identities=13% Similarity=0.201 Sum_probs=28.5
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
|.+.-+|+||-+.++.+.|+.+|+|+..++++
T Consensus 2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~ 33 (74)
T cd04875 2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQF 33 (74)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeee
Confidence 34556899999999999999999999999876
No 54
>PRK04435 hypothetical protein; Provisional
Probab=93.11 E-value=0.16 Score=41.47 Aligned_cols=35 Identities=23% Similarity=0.267 Sum_probs=32.5
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
.+++|.+.++|+||.|.++++.+++.|+|+..|..
T Consensus 68 r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q 102 (147)
T PRK04435 68 KIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQ 102 (147)
T ss_pred cEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEE
Confidence 47889999999999999999999999999999975
No 55
>cd04872 ACT_1ZPV ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein. This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=92.89 E-value=0.16 Score=37.40 Aligned_cols=34 Identities=12% Similarity=0.161 Sum_probs=29.3
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
-.+.+.-+|+||-++++.+.|+.+|+|+..++..
T Consensus 2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~ 35 (88)
T cd04872 2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQT 35 (88)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhH
Confidence 3566677999999999999999999999888653
No 56
>PRK08198 threonine dehydratase; Provisional
Probab=92.77 E-value=0.49 Score=44.52 Aligned_cols=36 Identities=25% Similarity=0.239 Sum_probs=32.0
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
....+.+.++|+||.|.++|+.++..|.|+..|.-+
T Consensus 326 r~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~ 361 (404)
T PRK08198 326 RYLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHD 361 (404)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEE
Confidence 356888899999999999999999999999988654
No 57
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=92.28 E-value=0.19 Score=32.98 Aligned_cols=32 Identities=25% Similarity=0.302 Sum_probs=27.9
Q ss_pred EEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 206 VFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 206 ~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
.+..+|+||.|.++++.|+++++|+..++...
T Consensus 2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~ 33 (71)
T cd04876 2 RVEAIDRPGLLADITTVIAEEKINILSVNTRT 33 (71)
T ss_pred EEEEeccCcHHHHHHHHHHhCCCCEEEEEeEE
Confidence 35678999999999999999999999887654
No 58
>PRK06382 threonine dehydratase; Provisional
Probab=91.95 E-value=0.21 Score=47.27 Aligned_cols=35 Identities=20% Similarity=0.159 Sum_probs=32.4
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
-++.|.+.++|+||.|.++++.|+..++|+++|+-
T Consensus 329 ~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~ 363 (406)
T PRK06382 329 QLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEV 363 (406)
T ss_pred CEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEE
Confidence 47788899999999999999999999999998886
No 59
>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=91.89 E-value=0.26 Score=35.10 Aligned_cols=30 Identities=23% Similarity=0.262 Sum_probs=26.3
Q ss_pred EecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 207 FTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 207 ~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+.=+||||-++++-+.|+.+|+|+..++++
T Consensus 4 v~G~DrpGiv~~vt~~la~~~~nI~dl~~~ 33 (75)
T cd04870 4 VTGPDRPGLTSALTEVLAAHGVRILDVGQA 33 (75)
T ss_pred EEcCCCCCHHHHHHHHHHHCCCCEEecccE
Confidence 334899999999999999999999998654
No 60
>TIGR01127 ilvA_1Cterm threonine dehydratase, medium form. A form of threonine dehydratase with two copies of the C-terminal domain Pfam:PF00585 is described by TIGR01124. This model describes a phylogenetically distinct form with a single copy of pfam00585. This form branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any pfam00585 domain. Many members of this model are found in species with other Ile biosynthetic enzymes.
Probab=91.82 E-value=0.24 Score=46.15 Aligned_cols=35 Identities=29% Similarity=0.310 Sum_probs=31.1
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+..|.+.++|+||.|.++++.+++.+.|++.|.-+
T Consensus 305 ~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~ 339 (380)
T TIGR01127 305 KVRIETVLPDRPGALYHLLESIAEARANIVKIDHD 339 (380)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEee
Confidence 44788899999999999999999999999998543
No 61
>cd04900 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD is the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=91.59 E-value=0.33 Score=34.38 Aligned_cols=29 Identities=10% Similarity=0.321 Sum_probs=25.8
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
.+.+..+|+||-|+++-+.|+.+|+|+..
T Consensus 3 ~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~ 31 (73)
T cd04900 3 EVFIYTPDRPGLFARIAGALDQLGLNILD 31 (73)
T ss_pred EEEEEecCCCCHHHHHHHHHHHCCCCeEE
Confidence 45667789999999999999999999875
No 62
>PRK08577 hypothetical protein; Provisional
Probab=91.46 E-value=0.41 Score=38.31 Aligned_cols=37 Identities=19% Similarity=0.363 Sum_probs=32.5
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
...|.+...|+||.|.++++.|+++++|+..+.++..
T Consensus 56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~ 92 (136)
T PRK08577 56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEEL 92 (136)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEe
Confidence 5667788899999999999999999999999877653
No 63
>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=91.07 E-value=0.43 Score=34.75 Aligned_cols=29 Identities=7% Similarity=0.150 Sum_probs=25.3
Q ss_pred EEEEEecCCCchHHHHHHHHHHHCCceee
Q 036073 203 TSIVFTLDEGPGVLTKALAVFALREINLT 231 (241)
Q Consensus 203 tsi~~~~~~~pGaL~~~L~~fa~~~iNLt 231 (241)
|.+-+..+||||-|+++...|.+.|+++.
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~ 30 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVF 30 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEE
Confidence 44556779999999999999999999985
No 64
>PRK08526 threonine dehydratase; Provisional
Probab=91.00 E-value=0.82 Score=43.36 Aligned_cols=177 Identities=18% Similarity=0.152 Sum_probs=90.6
Q ss_pred HHHHHHHcCCcceEEEeeecccccceeccccccc--cCCeEEEEEEEEee-ee--eeecCCCCCcCCeeEEE----e---
Q 036073 47 EAFKAVELWLAEKAILPIENSSGGSIHHNYDLLL--RHRLHIVGEVQFVA-NF--CLLALPGIREEKLKCVL----S--- 114 (241)
Q Consensus 47 ~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~--~~~l~I~~E~~l~I-~~--~L~~~~g~~~~~i~~V~----S--- 114 (241)
|+++.+ ++.|+-|+|+- ..|.+.-+...+. ..+.+|+|--.-.- .+ .+-..+....+.+.++. .
T Consensus 161 EI~eq~--~~~D~vvvpvG--gGGl~aGia~~~k~~~p~~kvigVep~~~~~~~~s~~~g~~~~~~~~~tiadgiav~~~ 236 (403)
T PRK08526 161 EMLDEI--SDLDMVVVPVG--GGGLISGIASAAKQINPNIKIIGVGAKGAPAMYESFHAKKIINSKSVRTIADGIAVRDA 236 (403)
T ss_pred HHHHhc--CCCCEEEEecC--hHHHHHHHHHHHHHhCCCCEEEEEEECCCChHHHHHHcCCcccCCCCCceeccccCCCC
Confidence 445544 35899999984 4566655555554 34566665433111 00 11110101122232221 1
Q ss_pred cHHHHHHHHHHHHhcCCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCceeecccCCCCCCceeEEEEeeCCCC
Q 036073 115 HPQALASSDIVQTQLGVARENIDDTASAAQYVASNGLRDAGVVASARAAEIYGLNILADRIQDDPDNITRFLVLARDPIM 194 (241)
Q Consensus 115 Hpqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~ 194 (241)
-|..+..|++++++ +..+.-....+|.+.+.+.. + ..+.+..|+-+-+|.--...+ ..+.+=-++++-....
T Consensus 237 ~~~~~~~~~~~vd~--~v~V~d~ei~~A~~~l~~~~--g-i~ve~aga~~lAall~~~~~~---~~~~~Vv~ilsGGnid 308 (403)
T PRK08526 237 SPINLAIILECVDD--FVQVDDEEIANAILFLLEKQ--K-IVVEGAGAASVAALLHQKIDL---KKGKKIGVVLSGGNID 308 (403)
T ss_pred CHHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhc--C-cEeeHHHHHHHHHHHhCcccc---ccCCeEEEEECCCCCC
Confidence 16666666665542 22233344555666666542 1 223444444444443111111 1222222333332211
Q ss_pred CC----------CCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 195 PR----------TDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 195 ~~----------~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
.. -...-+..+.+.+||+||+|.++++.+...+.|++.|+=
T Consensus 309 ~~~~~~i~~~~l~~~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~ 359 (403)
T PRK08526 309 VQMLNIIIEKGLIKSYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDY 359 (403)
T ss_pred HHHHHHHHHHHHHhcCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEE
Confidence 10 012236778889999999999999999999999998764
No 65
>PRK06545 prephenate dehydrogenase; Validated
Probab=90.54 E-value=0.27 Score=45.69 Aligned_cols=34 Identities=15% Similarity=0.369 Sum_probs=30.5
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
-..+.+.+||+||.|.+++..++..|||+..|+-
T Consensus 290 ~~~~~v~v~d~pg~~~~~~~~~~~~~i~i~~~~i 323 (359)
T PRK06545 290 FYDLYVDVPDEPGVIARVTAILGEEGISIENLRI 323 (359)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHcCCCeeccee
Confidence 3567788899999999999999999999998875
No 66
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=90.45 E-value=0.42 Score=34.24 Aligned_cols=31 Identities=23% Similarity=0.389 Sum_probs=23.3
Q ss_pred EEEec--CCCchHHHHHHHHHHHCCceeeeeee
Q 036073 205 IVFTL--DEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 205 i~~~~--~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
+++++ +|+||-++.+.+.++++|.|+..++-
T Consensus 3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~ 35 (76)
T PF13740_consen 3 LVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQ 35 (76)
T ss_dssp EEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEE
T ss_pred EEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEE
Confidence 44544 89999999999999999999977654
No 67
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=90.33 E-value=0.42 Score=38.67 Aligned_cols=34 Identities=26% Similarity=0.462 Sum_probs=31.2
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
.+.+|.+.+.||.|.|.++|+..+++++|...|.
T Consensus 71 ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~ 104 (150)
T COG4492 71 RIITLSLSLEDRVGILSDVLDVIAREEINVLTIH 104 (150)
T ss_pred eEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEe
Confidence 4778999999999999999999999999988775
No 68
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=90.26 E-value=0.32 Score=41.96 Aligned_cols=84 Identities=14% Similarity=0.164 Sum_probs=58.2
Q ss_pred CccEEEEeCCCCcHHHHHHHhhC-CC--------CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccc--
Q 036073 12 TKVRISFKGSPGSFTEDAALKAY-PN--------CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLL-- 80 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~-~~--------~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~-- 80 (241)
...+|++-.|..+.++...+.++ .+ .+.++..+.+.++.+|.+|++|.|+++- .+++.+.
T Consensus 104 ~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~~Da~~~~~---------~~~~~~~~~ 174 (243)
T PF12974_consen 104 KGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGKADAAAIPS---------DAFERLEAE 174 (243)
T ss_dssp GGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTSSSEEEEEH---------HHHHHHHHH
T ss_pred CCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCCccEEEEec---------hhHHHHHHc
Confidence 45689987766555577777655 32 2456788999999999999999999873 3444443
Q ss_pred ----cCCeEEEEEEEEeeeeeeecCCCC
Q 036073 81 ----RHRLHIVGEVQFVANFCLLALPGI 104 (241)
Q Consensus 81 ----~~~l~I~~E~~l~I~~~L~~~~g~ 104 (241)
..+++|+++...-..+.++++++.
T Consensus 175 ~~~~~~~~rvl~~s~~~p~~~~~~~~~~ 202 (243)
T PF12974_consen 175 GPDIPSQLRVLWTSPPYPNWPLVASPDL 202 (243)
T ss_dssp -HHHHTTEEEEEEEEEEE--EEEEETTS
T ss_pred cCcccccEEEEEEeCCCCCcEEEEeCCC
Confidence 246999999887777888887764
No 69
>PRK08639 threonine dehydratase; Validated
Probab=90.09 E-value=0.94 Score=43.05 Aligned_cols=35 Identities=20% Similarity=0.393 Sum_probs=28.9
Q ss_pred ceEEEEEecCCCchHHHHHHH-HHHHCCceeeeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALA-VFALREINLTKVFVA 236 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~-~fa~~~iNLt~IeSR 236 (241)
-+..+.|.+|++||+|.++|+ .+.... |++.|+-|
T Consensus 335 r~~~~~v~ipdrPGaL~~~l~~i~~~~~-NI~~~~~~ 370 (420)
T PRK08639 335 LKHYFIVNFPQRPGALREFLDDVLGPND-DITRFEYL 370 (420)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCC-cEEEEEEe
Confidence 477888999999999999999 555444 99988765
No 70
>cd04869 ACT_GcvR_2 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the second of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR in
Probab=90.06 E-value=0.55 Score=33.45 Aligned_cols=32 Identities=19% Similarity=0.396 Sum_probs=28.1
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+.+.-+|+||-+.++-+.|+.+|+|+..+.+.
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~ 33 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTE 33 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEee
Confidence 34566899999999999999999999999774
No 71
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=89.44 E-value=9.9 Score=33.52 Aligned_cols=144 Identities=12% Similarity=0.073 Sum_probs=75.7
Q ss_pred CCccEEEEeCCCCcH--HHH--HHHhhCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeE
Q 036073 11 GTKVRISFKGSPGSF--TED--AALKAYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLH 85 (241)
Q Consensus 11 ~~~~~ia~LGp~Gtf--S~~--Aa~~~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~ 85 (241)
.+..+|+....-+.+ .+. ...+.+|+.++.... +.+++++.+.+|++|+||++......+... ..|.+.++.
T Consensus 90 ~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~ 166 (305)
T PRK11151 90 SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIE---VPLFDEPML 166 (305)
T ss_pred CceEEEEecchhHHHHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCeEE---EEeccCcEE
Confidence 345667765443321 111 123346777665444 589999999999999999876544333221 223333433
Q ss_pred EEEEEEEeeeeeeecCCCCCcCCee--EEEecHHH---HHHHHHHHHhcCC--c-eEeccCHHHHHHHHHhcCCCCeEEe
Q 036073 86 IVGEVQFVANFCLLALPGIREEKLK--CVLSHPQA---LASSDIVQTQLGV--A-RENIDDTASAAQYVASNGLRDAGVV 157 (241)
Q Consensus 86 I~~E~~l~I~~~L~~~~g~~~~~i~--~V~SHpqa---l~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI 157 (241)
++. +-+|-+...+..+++++. ..++++.. ..+..+|+...+. . ...++|...+.+.++++ ...+|
T Consensus 167 ~~~----~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~i 239 (305)
T PRK11151 167 LAV----YEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAG---SGITL 239 (305)
T ss_pred EEe----cCCCCcccCCccCHHHhcCCCeEeecCCccHHHHHHHHHHHCCCCCCceEEeccHHHHHHHHHcC---CCEEE
Confidence 322 333444332223333332 12222221 2344455655443 2 34567777777777653 45788
Q ss_pred cCHhhHH
Q 036073 158 ASARAAE 164 (241)
Q Consensus 158 ~s~~aa~ 164 (241)
.+...+.
T Consensus 240 lp~~~~~ 246 (305)
T PRK11151 240 LPALAVP 246 (305)
T ss_pred eeHHhhh
Confidence 8887664
No 72
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=89.00 E-value=3.4 Score=33.70 Aligned_cols=50 Identities=28% Similarity=0.274 Sum_probs=40.0
Q ss_pred CccEEEEeCCCCcHHHHHHHhhCC-CCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDAALKAYP-NCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~~-~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
...+|++. .|++........++ +.+++.+.+.++++++|.+|++|+.+++
T Consensus 109 ~~~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~ 159 (225)
T PF00497_consen 109 KGKRIGVV--RGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVD 159 (225)
T ss_dssp TTSEEEEE--TTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEE
T ss_pred cCcccccc--cchhHHHHhhhhccchhhhcccccHHHHHHHHhcCCeeeeecc
Confidence 33578865 56666656666665 7888999999999999999999999986
No 73
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=88.87 E-value=16 Score=32.44 Aligned_cols=148 Identities=14% Similarity=0.075 Sum_probs=79.1
Q ss_pred CccEEEEeC-CCCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceecccccccc--CCe
Q 036073 12 TKVRISFKG-SPGSFTEDAALKAYP----NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLR--HRL 84 (241)
Q Consensus 12 ~~~~ia~LG-p~GtfS~~Aa~~~~~----~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~--~~l 84 (241)
...|||+++ |....=+.+...++. +.+++.+++..+..+|+.+|++|.+..= ..........+ .++
T Consensus 18 ~~l~vG~~~~~~~~~~~~~~~~~~~~~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~q-------~~~~l~~~~~~~g~~l 90 (258)
T TIGR00363 18 LHIKVGVISGAEQQVAEVAAKVAKEKYGLDVELVEFNDYALPNEAVSKGDLDANAFQ-------HKPYLDQDAKAKGYKL 90 (258)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCEEEEEEeCCcHHHHHHHHcCCCCeEecC-------CHHHHHHHHHhCCCcE
Confidence 468999984 443343445555553 2688999999999999999999987631 11111111122 345
Q ss_pred EEEEEEEEeeeeeeecCCCCCcCCee---EEEec--HHHHHHHHHHHHhcC-----------------------CceEec
Q 036073 85 HIVGEVQFVANFCLLALPGIREEKLK---CVLSH--PQALASSDIVQTQLG-----------------------VARENI 136 (241)
Q Consensus 85 ~I~~E~~l~I~~~L~~~~g~~~~~i~---~V~SH--pqal~Qc~~fl~~~~-----------------------~~~~~~ 136 (241)
.+++-..+ ....+...+=.+++|++ +|.-. |.-.++.-..|.+.| ++++..
T Consensus 91 v~v~~~~~-~p~~~ys~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel 169 (258)
T TIGR00363 91 VAVGNTFV-YPLAGYSKKIKNVNELQDGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITEL 169 (258)
T ss_pred EEEeeeEE-ecccccCcCCCCHHHcCCCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEc
Confidence 55553322 11244444334667774 55433 333344444555533 344444
Q ss_pred cCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCce
Q 036073 137 DDTASAAQYVASNGLRDAGVVASARAAEIYGLNI 170 (241)
Q Consensus 137 ~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~i 170 (241)
.. +..++.+.++ .-.||+....-+...||..
T Consensus 170 ~~-~~~~~al~~g--~vDaa~v~~~~~~~agl~~ 200 (258)
T TIGR00363 170 ET-SQLPRALDDP--KVDLAVINTTYAGQVGLNP 200 (258)
T ss_pred CH-HHHHHHhhcc--cccEEEEChHHHHHcCCCc
Confidence 43 3333444332 2345666555666667763
No 74
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=87.94 E-value=1.5 Score=33.88 Aligned_cols=80 Identities=13% Similarity=0.018 Sum_probs=52.9
Q ss_pred cEEEEeCCCCcHHHHHHHhhCCC-----------CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccC
Q 036073 14 VRISFKGSPGSFTEDAALKAYPN-----------CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRH 82 (241)
Q Consensus 14 ~~ia~LGp~GtfS~~Aa~~~~~~-----------~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~ 82 (241)
.+|+++ .||+.+..++++.+. .+++.+++..+++.+|.+|+ |..+.. ++........ ..
T Consensus 14 ~~vgv~--~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d--~~~~~~~~~~-----~~ 83 (134)
T smart00079 14 IEYGTI--RGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLME--STYLDYELSQ-----NC 83 (134)
T ss_pred ccceEe--cCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEee--hHhHHHHHhC-----CC
Confidence 678886 899999998876553 25678999999999999999 866654 2222111110 23
Q ss_pred CeEEEEEEEEeeeeeeecCCC
Q 036073 83 RLHIVGEVQFVANFCLLALPG 103 (241)
Q Consensus 83 ~l~I~~E~~l~I~~~L~~~~g 103 (241)
++.++++..-+-.++++.++|
T Consensus 84 ~~~~~~~~~~~~~~~ia~~k~ 104 (134)
T smart00079 84 DLMTVGENFGRKGYGIAFPKG 104 (134)
T ss_pred CeEEcCcccCCCceEEEecCC
Confidence 466666544444566666655
No 75
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=87.71 E-value=1.9 Score=36.68 Aligned_cols=49 Identities=12% Similarity=0.210 Sum_probs=40.5
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..+||+. .|++.+....+.+++.+.+++++..+++.+|.+|++|+.+.+
T Consensus 126 g~~Igv~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~grvDa~i~~ 174 (243)
T PRK15007 126 GKKVGVQ--NGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGD 174 (243)
T ss_pred CCeEEEe--cCcHHHHHHHHhCCCCeEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 4578875 677777666666778888999999999999999999999875
No 76
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=87.33 E-value=3.5 Score=32.63 Aligned_cols=51 Identities=22% Similarity=0.308 Sum_probs=39.2
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEeee
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILPIE 65 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 65 (241)
..+|++.. |+........+.++.+.+.+.+..+++.+|.+|++|+++++-.
T Consensus 106 g~~i~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~ 156 (219)
T smart00062 106 GKKVAVVA--GTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADAP 156 (219)
T ss_pred CCEEEEec--CccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEeccH
Confidence 35788763 6555555555556678899999999999999999999998633
No 77
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=87.26 E-value=1.6 Score=37.12 Aligned_cols=50 Identities=8% Similarity=0.148 Sum_probs=41.6
Q ss_pred CccEEEEeCCCCcHHHHHHHhhCC-CCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDAALKAYP-NCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~~-~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
...+|++. .|+..+.....+++ +.+++.+.+.++++++|.+|++|+.+..
T Consensus 130 ~g~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~ 180 (250)
T TIGR01096 130 DGKTVGVQ--SGTTHEQYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTD 180 (250)
T ss_pred CCCEEEEe--cCchHHHHHHHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 34678874 68877777777777 7788999999999999999999999974
No 78
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=87.24 E-value=4.4 Score=34.87 Aligned_cols=138 Identities=12% Similarity=-0.002 Sum_probs=71.7
Q ss_pred cEEEEeCCCCcHHHH-HH-HhhCC------CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeE
Q 036073 14 VRISFKGSPGSFTED-AA-LKAYP------NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLH 85 (241)
Q Consensus 14 ~~ia~LGp~GtfS~~-Aa-~~~~~------~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~ 85 (241)
.||||+.. +..... |. +.+|. +.+++...+..++++++.+|++|+|++.....+ .. .-...++.
T Consensus 1 l~vg~~~~-~~~~~~~a~~~g~f~~~g~~l~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~----~~---~~~g~~~~ 72 (288)
T TIGR01728 1 VRIGYQKN-GHSALALAKEKGLLEKELGKTKVEWVEFPAGPPALEALGAGSLDFGYIGPGPAL----FA---YAAGADIK 72 (288)
T ss_pred CeEEecCC-CchHHHHHHHhCHHHHhhCCceEEEEecCCCcHHHHHHhcCCccccccCCcHHH----HH---HhcCCCEE
Confidence 37899865 333322 32 23442 356778888889999999999999986533111 10 00113455
Q ss_pred EEEEEEEeeeeeeecCCCC---CcCCee--EEEecH--HHHHHHHHHHHhcCCc---e-EeccCHHHHHHHHHhcCCCCe
Q 036073 86 IVGEVQFVANFCLLALPGI---REEKLK--CVLSHP--QALASSDIVQTQLGVA---R-ENIDDTASAAQYVASNGLRDA 154 (241)
Q Consensus 86 I~~E~~l~I~~~L~~~~g~---~~~~i~--~V~SHp--qal~Qc~~fl~~~~~~---~-~~~~sTa~Aa~~v~~~~~~~~ 154 (241)
+++-..-.-..+++++++. +++|++ +|...+ .......++|++.|+. . ....+..++...+..++ -.
T Consensus 73 ~i~~~~~~~~~~~v~~~~~~i~s~~dL~Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~--vd 150 (288)
T TIGR01728 73 AVGLVSDNKATAIVVIKGSPIRTVADLKGKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQ--VD 150 (288)
T ss_pred EEEEecCCCceEEEECCCCCCCCHHHcCCCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCC--CC
Confidence 5554332123555655432 233432 454321 1223445577665542 2 22245566667666542 33
Q ss_pred EEecCHh
Q 036073 155 GVVASAR 161 (241)
Q Consensus 155 aAI~s~~ 161 (241)
+++.+..
T Consensus 151 a~~~~~p 157 (288)
T TIGR01728 151 AWAIWEP 157 (288)
T ss_pred EEEeccc
Confidence 5555443
No 79
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=87.05 E-value=0.71 Score=39.43 Aligned_cols=32 Identities=13% Similarity=0.387 Sum_probs=28.1
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+.+.-+|+||-++++-+.|+.+|||+..+.++
T Consensus 98 v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~ 129 (190)
T PRK11589 98 VQVEVADSPHLIERFTALFDSHHMNIAELVSR 129 (190)
T ss_pred EEEEECCCCCHHHHHHHHHHHcCCChhheEEe
Confidence 33444899999999999999999999999986
No 80
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=87.01 E-value=1.7 Score=36.64 Aligned_cols=31 Identities=19% Similarity=0.400 Sum_probs=27.7
Q ss_pred EecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 207 FTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 207 ~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
+...||||-+.++-+-|..+||||-.++||-
T Consensus 97 v~a~DrpgIv~~~T~lf~~~~inie~L~~~~ 127 (176)
T COG2716 97 VDANDRPGIVEEFTALFDGHGINIENLVSRT 127 (176)
T ss_pred EEecCCccHHHHHHHHHHhcCCchhhceeee
Confidence 3447999999999999999999999999874
No 81
>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre
Probab=86.88 E-value=13 Score=29.17 Aligned_cols=123 Identities=15% Similarity=0.091 Sum_probs=62.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe--
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL-- 109 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i-- 109 (241)
.+|+.++... .+..++++.+.+|++|+|+..-.....+. ....|.+..+.++. +-.|-+......+++++
T Consensus 26 ~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~pl~~~~~~~~~~l~~ 98 (200)
T cd08411 26 AYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGL---EEEPLFDEPFLLAV----PKDHPLAKRKSVTPEDLAG 98 (200)
T ss_pred HCCCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCCCCCc---eEEEeeccceEEEe----cCCCCccccCccCHHHHcC
Confidence 3566655443 36789999999999999997533221111 11222233332222 22232222222222222
Q ss_pred -eEEE-ec-HHHHHHHHHHHHhcCC--c-eEeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 110 -KCVL-SH-PQALASSDIVQTQLGV--A-RENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 110 -~~V~-SH-pqal~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
..|. +. .....+..+|+.+.+. . ...++|...+.+++.++ ...|+.+...++.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 157 (200)
T cd08411 99 ERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAG---LGITLLPELAVPS 157 (200)
T ss_pred CceEecCCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CCEEEeCHHHhcc
Confidence 2232 11 1123344556655543 2 34566777777777764 4578888887764
No 82
>cd04891 ACT_AK-LysC-DapG-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the first and third, of four, ACT domains present in cyanobacteria AK. Also included are the N-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase isoenzyme AKI found in Bacilli (Bacillus subtilis strain 168), Clostridia, and Actinobacteria bacterial species. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=86.72 E-value=1.4 Score=28.65 Aligned_cols=29 Identities=24% Similarity=0.358 Sum_probs=25.2
Q ss_pred EecCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 207 FTLDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 207 ~~~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
+..++.||.+.++++.|++++||+..|..
T Consensus 6 ~~~~~~~~~~~~i~~~L~~~~i~i~~i~~ 34 (61)
T cd04891 6 KGVPDKPGVAAKIFSALAEAGINVDMIVQ 34 (61)
T ss_pred ecCCCCCcHHHHHHHHHHHcCCcEEEEEE
Confidence 34578999999999999999999988754
No 83
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=86.68 E-value=14 Score=29.05 Aligned_cols=121 Identities=19% Similarity=0.102 Sum_probs=64.6
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCeeE-
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLKC- 111 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~~- 111 (241)
+|+.++... .+-.++.+.+.+|++|+|+..-.+...+. ....|.+..+.++. +-.|-+.. +..+++++..
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~~~~~-~~~~~~~L~~~ 97 (200)
T cd08417 26 APGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGL---RSQPLFEDRFVCVA----RKDHPLAG-GPLTLEDYLAA 97 (200)
T ss_pred CCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccCCCcc---chhhhhcCceEEEe----cCCCcccc-cccCHHHHhCC
Confidence 466554333 45678999999999999998644332221 12233344444433 33343332 2233444432
Q ss_pred --E-EecHH-HHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 112 --V-LSHPQ-ALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 112 --V-~SHpq-al~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
| +.+.. ......+|+.+.+.. . ..++|...+.+.+..+ ...++.+...++.
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08417 98 PHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGT---DLIATVPRRLAEA 155 (200)
T ss_pred CeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcC---CeeeeccHHHHHh
Confidence 2 33322 233456677766543 2 3455665566666653 4577888776654
No 84
>cd04925 ACT_ACR_2 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=86.55 E-value=1.1 Score=31.88 Aligned_cols=30 Identities=30% Similarity=0.445 Sum_probs=25.4
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeee
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKV 233 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~I 233 (241)
.|-+..+|+||-|+++-+.|+.+|+|+..-
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A 31 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVEA 31 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEEE
Confidence 344566899999999999999999998753
No 85
>cd04913 ACT_AKii-LysC-BS-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is fee
Probab=85.86 E-value=1.3 Score=30.33 Aligned_cols=28 Identities=25% Similarity=0.402 Sum_probs=24.4
Q ss_pred EecCCCchHHHHHHHHHHHCCceeeeee
Q 036073 207 FTLDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 207 ~~~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
+.++++||.+.++++.|++.|||+-.+.
T Consensus 7 ~~~~~~~g~~~~i~~~L~~~~I~i~~i~ 34 (75)
T cd04913 7 RGVPDKPGVAAKIFGALAEANINVDMIV 34 (75)
T ss_pred CCCCCCCcHHHHHHHHHHHcCCeEEEEE
Confidence 3457899999999999999999997664
No 86
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=85.81 E-value=16 Score=29.03 Aligned_cols=120 Identities=12% Similarity=0.065 Sum_probs=59.6
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCC-CCCcCCe--
Q 036073 34 YPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALP-GIREEKL-- 109 (241)
Q Consensus 34 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~-g~~~~~i-- 109 (241)
+|+.++.... +-.++.+.+.+|++|+|+........|... ..|.+..+.++ .+-.|-|...+ ..+++|+
T Consensus 27 ~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~hpl~~~~~~i~~~dL~~ 99 (203)
T cd08445 27 APDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRR---IVLREEPLVVA----LPAGHPLAQEKAPLTLAQLAD 99 (203)
T ss_pred CCCeEEEEEeCChHHHHHHHHcCCCcEEEecCCCCCCCcee---EEEEeccEEEE----eeCCCCCccCCCCcCHHHhcC
Confidence 5776554443 468999999999999999642211111111 11122222222 23334443332 2333332
Q ss_pred -eEEEecHH---H-HHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeEEecCHhhH
Q 036073 110 -KCVLSHPQ---A-LASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAGVVASARAA 163 (241)
Q Consensus 110 -~~V~SHpq---a-l~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 163 (241)
..|.-... . ..+..+|+.+.+. +. ..++|.....++++.+ ...++.+...+
T Consensus 100 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 158 (203)
T cd08445 100 EPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAG---EGVTLVPASVQ 158 (203)
T ss_pred CCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcC---CCeEEehHHhh
Confidence 33331111 1 2345567766543 22 3456666666677654 34677777544
No 87
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=85.60 E-value=1.8 Score=45.88 Aligned_cols=49 Identities=14% Similarity=0.160 Sum_probs=42.8
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..+|+. +.|++.+...++.+|+.+++.++|..+++++|.+|++|..|..
T Consensus 164 ~~~i~~--~~g~~~~~~~~~~~p~~~i~~~~s~~~al~av~~G~~Da~i~~ 212 (1197)
T PRK09959 164 PVNIAR--VANYPPDEVIHQSFPKATIISFTNLYQALASVSAGQNDYFIGS 212 (1197)
T ss_pred CeEEEE--eCCCCCHHHHHHhCCCCEEEeCCCHHHHHHHHHcCCCCEEEcc
Confidence 456776 4588888888889999999999999999999999999998865
No 88
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=85.46 E-value=1.4 Score=31.63 Aligned_cols=27 Identities=15% Similarity=0.250 Sum_probs=23.7
Q ss_pred EEecCCCchHHHHHHHHHHHCCceeee
Q 036073 206 VFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 206 ~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
-+..+|+||-|+++.+.|+.+|+|+..
T Consensus 4 ei~~~Dr~gLfa~i~~~l~~~~l~I~~ 30 (76)
T cd04927 4 KLFCSDRKGLLHDVTEVLYELELTIER 30 (76)
T ss_pred EEEECCCCCHHHHHHHHHHHCCCeEEE
Confidence 345589999999999999999999864
No 89
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=85.44 E-value=2.6 Score=33.59 Aligned_cols=50 Identities=26% Similarity=0.336 Sum_probs=40.0
Q ss_pred CccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
...+|++. .|+..+....+.++..+++.+.+.++++++|.+|++|++++.
T Consensus 104 ~g~~i~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 153 (218)
T cd00134 104 KGKKVAVQ--KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVD 153 (218)
T ss_pred CCCEEEEE--cCchHHHHHHHhCCcccEEEeCCHHHHHHHHHcCCccEEEec
Confidence 34678877 566666666666666778999999999999999999998875
No 90
>PRK07334 threonine dehydratase; Provisional
Probab=85.28 E-value=1.4 Score=41.58 Aligned_cols=38 Identities=18% Similarity=0.265 Sum_probs=34.7
Q ss_pred CceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 200 PFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 200 ~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
...+.|.+...|+||.|.++++.+++.++|+.++.++.
T Consensus 324 ~y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~ 361 (403)
T PRK07334 324 GRLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQR 361 (403)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEe
Confidence 35789999999999999999999999999999999874
No 91
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=84.94 E-value=1.5 Score=46.55 Aligned_cols=49 Identities=16% Similarity=0.154 Sum_probs=43.4
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..|||. +.|++.+....+.+|+.+++.+++.++++.+|.+|++|.+|.+
T Consensus 407 g~~vav--~~g~~~~~~~~~~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~ 455 (1197)
T PRK09959 407 GMKVAI--PYYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDALVAT 455 (1197)
T ss_pred CCEEEE--eCCcchHHHHHHHCCCcEEEEcCCHHHHHHHHHcCCCCEEehh
Confidence 467888 5788888888888999999999999999999999999999865
No 92
>cd08452 PBP2_AlsR The C-terminal substrate binding domain of LysR-type trnascriptional regulator AlsR, which regulates acetoin formation under stationary phase growth conditions; contains the type 2 periplasmic binding fold. AlsR is responsible for activating the expression of the acetoin operon (alsSD) in response to inducing signals such as glucose and acetate. Like many other LysR family proteins, AlsR is transcribed divergently from the alsSD operon. The alsS gene encodes acetolactate synthase, an enzyme involved in the production of acetoin in cells of stationary-phase. AlsS catalyzes the conversion of two pyruvate molecules to acetolactate and carbon dioxide. Acetolactate is then converted to acetoin at low pH by acetolactate decarboxylase which encoded by the alsD gene. Acetoin is an important physiological metabolite excreted by many microorganisms grown on glucose or other fermentable carbon sources. This substrate-binding domain shows significant homology to the type 2 perip
Probab=84.74 E-value=18 Score=28.66 Aligned_cols=122 Identities=7% Similarity=-0.030 Sum_probs=60.4
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcC---C
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREE---K 108 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~---~ 108 (241)
.+|+.++.-. .+..++.+.+.+|++|+|++.-.....|.. ...|.+..+.+ ..+-.|-+......+++ +
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~l----v~~~~hpl~~~~~~~~~~L~~ 97 (197)
T cd08452 25 KFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALH---IETVQSSPCVL----ALPKQHPLASKEEITIEDLRD 97 (197)
T ss_pred HCCCcEEEEEecChHHHHHHHHCCCccEEEeeCCCCCCCee---EEEeeeccEEE----EEeCCCccccCCCCCHHHhcC
Confidence 4677655433 367889999999999999975221111111 11122222222 22334444332222333 3
Q ss_pred eeEEEecHH----HHHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 109 LKCVLSHPQ----ALASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 109 i~~V~SHpq----al~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
...|..... ...+..+|+.+.+. .. ..++|...+...++.+ ...++.+...+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 157 (197)
T cd08452 98 EPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAG---IGVTFVPSSAKK 157 (197)
T ss_pred CCEEeccCCcchhHHHHHHHHHHHcCCCccceeecccHHHHHHHHHcC---CCEEEchHHHhh
Confidence 333332211 23344556666543 22 3456666666666653 346777776544
No 93
>PRK11260 cystine transporter subunit; Provisional
Probab=84.58 E-value=2.7 Score=36.52 Aligned_cols=49 Identities=6% Similarity=0.091 Sum_probs=41.0
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..+|+. ..|+..+......+++.++..+++..+++++|.+|++|+.+.+
T Consensus 149 g~~Igv--~~G~~~~~~l~~~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d 197 (266)
T PRK11260 149 GKKVGV--GLGTNYEQWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVD 197 (266)
T ss_pred CCEEEE--ecCCcHHHHHHHhCCCCceEecCCHHHHHHHHHcCCCCEEEec
Confidence 356776 6787777777777888889999999999999999999999874
No 94
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic, long form. Forms scoring between the trusted and noise cutoff tend to branch with this subgroup of threonine ammonia-lyase phylogenetically but have only a single copy of the C-terminal domain.
Probab=84.17 E-value=3.9 Score=39.95 Aligned_cols=176 Identities=16% Similarity=0.209 Sum_probs=87.0
Q ss_pred HHHHHHHHcCCcceEEEeeecccccceecccccccc--CCeEEEEEEEEeeeeeeec--CCC--CCcCCe---------e
Q 036073 46 EEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLR--HRLHIVGEVQFVANFCLLA--LPG--IREEKL---------K 110 (241)
Q Consensus 46 ~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~--~~l~I~~E~~l~I~~~L~~--~~g--~~~~~i---------~ 110 (241)
.|+++.+. +..|+-|+|+= ..|.+.-+...|.+ .+.+|+|--...-. ++.. ..| ..++.+ +
T Consensus 157 ~EI~~q~~-~~~D~vvvpvG--gGGliaGia~~lk~~~p~~kVIgVep~~~~-~~~~s~~~g~~~~~~~~~t~adgiav~ 232 (499)
T TIGR01124 157 LEILRQVA-NPLDAVFVPVG--GGGLAAGVAALIKQLMPEIKVIGVEPTDSD-CMKQALDAGEPVDLDQVGLFADGVAVK 232 (499)
T ss_pred HHHHHhCC-CCCCEEEEccC--ccHHHHHHHHHHHHhCCCCEEEEEEECCCh-HHHHHHhcCCceeCCCCCCccCcccCC
Confidence 34555543 36899999965 45555555444432 45666664432110 1100 011 011111 1
Q ss_pred EEEecHHHHHHHHHHHHhcCCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCceeecccCCCCCCceeEEEEee
Q 036073 111 CVLSHPQALASSDIVQTQLGVARENIDDTASAAQYVASNGLRDAGVVASARAAEIYGLNILADRIQDDPDNITRFLVLAR 190 (241)
Q Consensus 111 ~V~SHpqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~d~~~N~TRF~vl~~ 190 (241)
.+ =+..+.-|++++.+ +-.+.......|.+.+.+.. ..-+.+..|+-+.+|.-+.+... . .+.+=-+|++-
T Consensus 233 ~~--g~~~~~~~~~~vd~--vv~V~d~ei~~ai~~l~~~~---gii~EpagA~~lAal~~~~~~~~-~-~~~~vv~i~sG 303 (499)
T TIGR01124 233 RV--GDETFRLCQQYLDD--IVTVDTDEVCAAIKDLFEDT---RAVAEPAGALALAGLKKYVALHG-I-RGQTLVAILSG 303 (499)
T ss_pred Cc--cHHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhc---CcEEechHHHHHHHHHHhhhhcC-C-CCCeEEEEECC
Confidence 11 13455555554432 11223333555666666532 12334445555666654433221 1 13332223332
Q ss_pred CCCCCC----------CCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 191 DPIMPR----------TDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 191 ~~~~~~----------~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
...... -.......+.+.+|++||+|.++++.+..+ |+|.++=|
T Consensus 304 ~n~~~~~l~~~~~r~~~~~~re~~l~V~iPerPGal~~f~~~i~~~--nItef~yr 357 (499)
T TIGR01124 304 ANMNFHRLRYVSERCELGEQREALLAVTIPEQPGSFLKFCELLGNR--NITEFNYR 357 (499)
T ss_pred CCCCHHHHHHHHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhhc--ceEEEEEE
Confidence 221110 012347788899999999999999999975 77766544
No 95
>cd04907 ACT_ThrD-I_2 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=83.77 E-value=2.1 Score=31.37 Aligned_cols=32 Identities=28% Similarity=0.349 Sum_probs=25.9
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+.|+.|.|||||.+.|+.+. .+-|+|.++=|
T Consensus 3 ~~~v~iPErpGal~~Fl~~l~-p~~~ITeF~YR 34 (81)
T cd04907 3 LFRFEFPERPGALKKFLNELL-PKWNITLFHYR 34 (81)
T ss_pred EEEEEcCCCCCHHHHHHHHhC-CCCeEeEEEEe
Confidence 467889999999999999994 26777776644
No 96
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=83.56 E-value=2.8 Score=35.91 Aligned_cols=49 Identities=12% Similarity=0.076 Sum_probs=39.5
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..+|++. .|+..+.-..+.+++.+++.+++.++++++|.+|++|+.+..
T Consensus 131 g~~I~v~--~g~~~~~~l~~~~~~~~i~~~~~~~~~~~~L~~grvDa~i~~ 179 (247)
T PRK09495 131 GKVVAVK--SGTGSVDYAKANIKTKDLRQFPNIDNAYLELGTGRADAVLHD 179 (247)
T ss_pred CCEEEEe--cCchHHHHHHhcCCCCceEEcCCHHHHHHHHHcCceeEEEeC
Confidence 4578864 477777666666777788899999999999999999988853
No 97
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=83.30 E-value=20 Score=28.18 Aligned_cols=121 Identities=12% Similarity=0.041 Sum_probs=61.3
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcceEEEeeecc--c-ccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe
Q 036073 34 YPNCETIPCD-EFEEAFKAVELWLAEKAILPIENS--S-GGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL 109 (241)
Q Consensus 34 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS--~-~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i 109 (241)
+|+.++.... +-.+..+.+.+|++|+|+..-... . .|. ....|.+..+.+ ..+-.|-+...+..+++++
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~---~~~~l~~~~~~~----v~~~~hp~~~~~~i~~~~L 98 (200)
T cd08453 26 YPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAPPAL---AYRPLLSEPLVL----AVPAAWAAEGGAPLALAAV 98 (200)
T ss_pred CCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCcccCCCcce---eEEEeeeCceEE----EEECCCccccCCCCCHHHh
Confidence 5776654443 467889999999999999742211 0 111 112223333333 2233344433322333333
Q ss_pred ---eEEEec-H---HHHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 110 ---KCVLSH-P---QALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 110 ---~~V~SH-p---qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
.-|... . .......+|+.+.+.. . ..++|...+.+.++.+ ...++.+...++
T Consensus 99 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08453 99 AAEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAG---MGVALVPASLRN 160 (200)
T ss_pred ccCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcC---CcEEEeEhHHhh
Confidence 334322 1 1234567788776543 3 2345555555556553 356777776543
No 98
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=82.49 E-value=13 Score=32.16 Aligned_cols=144 Identities=13% Similarity=0.064 Sum_probs=78.8
Q ss_pred CCccEEEEeCCCCcHHHHHHHh--hCC----CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCe
Q 036073 11 GTKVRISFKGSPGSFTEDAALK--AYP----NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRL 84 (241)
Q Consensus 11 ~~~~~ia~LGp~GtfS~~Aa~~--~~~----~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l 84 (241)
....||||+...+.+.-..|.. +|. +.+++.+.+-.++.+++.+|++|++.+ ......+.-.-. .-...++
T Consensus 5 ~~~l~ig~~~~~~~~p~~~a~~~g~f~~~G~~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~--~~~~~~~ 81 (252)
T PF13379_consen 5 PTTLRIGYLPGPDYAPLYVAQEKGLFEKEGLDVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGA--GGPDVDI 81 (252)
T ss_dssp ESEEEEEETSSGGGHHHHHHHHTTHHHHTTSCEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTT--TT----E
T ss_pred CcEEEEEeecchHHHHHHHHHHcChHHHcCCEEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCC--CCcccce
Confidence 4568999986555444444432 442 367899999999999999999999998 443332221110 0001133
Q ss_pred EEEEEEEEeee-eeeecCC------C-CCcCCe---------eEEEe-cHHH--HHHHHHHHHhcC------CceEeccC
Q 036073 85 HIVGEVQFVAN-FCLLALP------G-IREEKL---------KCVLS-HPQA--LASSDIVQTQLG------VARENIDD 138 (241)
Q Consensus 85 ~I~~E~~l~I~-~~L~~~~------g-~~~~~i---------~~V~S-Hpqa--l~Qc~~fl~~~~------~~~~~~~s 138 (241)
.+++-. ... ..+++++ + .+++|+ ++|.. ++-. .-..+.+|++.+ ++++....
T Consensus 82 ~~~~~~--~~~g~~lvv~~~~~~~~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~ 159 (252)
T PF13379_consen 82 VVLAGL--SQNGNALVVRNDLKDASDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP 159 (252)
T ss_dssp EEEEEC--SBSSEEEEECGGGTTCSTTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G
T ss_pred EEeecc--CCCceEEEEcCccccCCCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH
Confidence 333222 222 3455543 2 245555 46665 5433 334678898753 34455555
Q ss_pred HHHHHHHHHhcCCCCeEEecCHh
Q 036073 139 TASAAQYVASNGLRDAGVVASAR 161 (241)
Q Consensus 139 Ta~Aa~~v~~~~~~~~aAI~s~~ 161 (241)
.++...+.+++ -+.+++..+.
T Consensus 160 -~~~~~al~~g~-iDa~~~~eP~ 180 (252)
T PF13379_consen 160 -PEMVAALRAGE-IDAAVLWEPF 180 (252)
T ss_dssp -HHHHHHHHTTS--SEEEEETTH
T ss_pred -HHHHHHHhCCC-cCEEEecCCH
Confidence 67777666653 4445554444
No 99
>cd04932 ACT_AKiii-LysC-EC_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=82.14 E-value=2.4 Score=30.44 Aligned_cols=27 Identities=19% Similarity=0.359 Sum_probs=24.7
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
+++.||.+.++++.|+++|||+-.|-+
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~VDmI~~ 37 (75)
T cd04932 11 MLHAQGFLAKVFGILAKHNISVDLITT 37 (75)
T ss_pred CCCCcCHHHHHHHHHHHcCCcEEEEee
Confidence 578899999999999999999999854
No 100
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=81.74 E-value=7.9 Score=34.54 Aligned_cols=54 Identities=9% Similarity=0.050 Sum_probs=35.3
Q ss_pred CCCCCccEEEEeCCCCcHHHHHHHh-h----CCC--CceeecCCHHHHHHHHHcCCcceEEE
Q 036073 8 PNDGTKVRISFKGSPGSFTEDAALK-A----YPN--CETIPCDEFEEAFKAVELWLAEKAIL 62 (241)
Q Consensus 8 ~~~~~~~~ia~LGp~GtfS~~Aa~~-~----~~~--~~~~~~~s~~~v~~av~~g~~d~gVv 62 (241)
.......||||+.. ......+-.. + +++ .+++...+-.++++++.+|++|+|+.
T Consensus 23 ~~~~~~lrIg~~~~-~~~~~l~~~~~~~~~~~p~v~ie~~~~~~~~~~~~aL~~G~iDia~~ 83 (314)
T PRK11553 23 ESSPEALRIGYQKG-SIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGST 83 (314)
T ss_pred cCCCCeEEEEeCCC-chHHHHHHhhCHHHHhCCCCeeEEEECCCcHHHHHHHHcCCCCEEcc
Confidence 34456789999742 2222222211 2 344 45667767789999999999999985
No 101
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=81.27 E-value=10 Score=33.71 Aligned_cols=122 Identities=17% Similarity=-0.001 Sum_probs=66.4
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCeeE
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLKC 111 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~~ 111 (241)
.+|+.++.... +-.++++.+.+|++|+|+++-+-...+.. ...|.+..+.++ .+.+|-+. ....+++++..
T Consensus 137 ~~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~l~---~~~l~~~~~~lv----~~~~hpl~-~~~~~~~~L~~ 208 (314)
T PRK09508 137 IAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFT---SVPLFKDELVLV----ASKNHPRI-KGPITEEQLYN 208 (314)
T ss_pred hCCCcEEEEEeCcchhHHHHHhcCCccEEEecCCCCccccc---eeeeecCceEEE----EcCCCCcc-CCCCCHHHHhh
Confidence 35776654433 46888999999999999987542222111 112223333332 23344443 22234444431
Q ss_pred ----EEecHHHHHHHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 112 ----VLSHPQALASSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 112 ----V~SHpqal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
++.++....+..+|+.+.+.. ...++|.......+..+ ...++.+...++.
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 266 (314)
T PRK09508 209 EQHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQT---HLVAIAPRWLAEE 266 (314)
T ss_pred CCCEEecCCCCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhC---ChHHHHHHHHHHH
Confidence 233333334456777766543 24566666677777654 3467888777654
No 102
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=80.51 E-value=2.3 Score=32.15 Aligned_cols=25 Identities=16% Similarity=0.315 Sum_probs=23.4
Q ss_pred CCCchHHHHHHHHHHHCCceeeeee
Q 036073 210 DEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 210 ~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
.||||--+.+-.+|+++|+|+-.|+
T Consensus 11 kDr~GIva~is~vLAe~~vNIldis 35 (90)
T COG3830 11 KDRVGIVAAVSRVLAEHGVNILDIS 35 (90)
T ss_pred CCCCchhHHHHHHHHHcCCcEEEHH
Confidence 7999999999999999999998775
No 103
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=80.50 E-value=25 Score=27.35 Aligned_cols=122 Identities=14% Similarity=0.040 Sum_probs=60.7
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCc---CC
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIRE---EK 108 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~---~~ 108 (241)
.+|+.++... .+-.++++.+.+|++|+|++.-.....|.. ...|.+..+.+ ..+-.|-|...+..++ .+
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08412 25 AYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIA---FEPLARLPPYV----WLPADHPLAGKDEVSLADLAA 97 (198)
T ss_pred HCCCcEEEEEECCHHHHHHHHHcCCCcEEEEcCCCCCcccc---eeeeeccceEE----EecCCCCCCCCCcCCHHHHcC
Confidence 4577654433 457889999999999999985332211111 11122222211 1233444433222222 33
Q ss_pred eeEEE-ecHHHHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 109 LKCVL-SHPQALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 109 i~~V~-SHpqal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
...|. .......+-.+|+.+.+.. . ..++|...+.+.+..+ ...++.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (198)
T cd08412 98 EPLILLDLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANG---LGYSLLNDRPYR 154 (198)
T ss_pred CcEEecCchhHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CCEEEeeccccc
Confidence 33343 2222233345566665543 2 3456666666666653 347788876654
No 104
>cd08462 PBP2_NodD The C-terminal substsrate binding domain of NodD family of LysR-type transcriptional regulators that regulates the expression of nodulation (nod) genes; contains the type 2 periplasmic binding fold. The nodulation (nod) genes in soil bacteria play important roles in the development of nodules. nod genes are involved in synthesis of Nod factors that are required for bacterial entry into root hairs. Thirteen nod genes have been identified and are classified into five transcription units: nodD, nodABCIJ, nodFEL, nodMNT, and nodO. NodD is negatively auto-regulates its own expression of nodD gene, while other nod genes are inducible and positively regulated by NodD in the presence of flavonoids released by plant roots. This substrate-binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. T
Probab=80.49 E-value=26 Score=27.78 Aligned_cols=32 Identities=13% Similarity=0.002 Sum_probs=23.2
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCcceEEEee
Q 036073 33 AYPNCETIPCDEFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 33 ~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPi 64 (241)
.+|+.++.....-.+.++.+.+|++|+|+++-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~l~~g~~D~~i~~~ 56 (200)
T cd08462 25 EAPGVRFELLPPDDQPHELLERGEVDLLIAPE 56 (200)
T ss_pred HCCCCEEEEecCChhHHHHHhcCCeeEEEecC
Confidence 35776554443223999999999999999863
No 105
>cd04914 ACT_AKi-DapG-BS_1 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the N-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria, bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive aspartokinase isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The B. subtilis AKI is tetrameric consisting of two alpha and
Probab=80.46 E-value=2.6 Score=29.43 Aligned_cols=27 Identities=11% Similarity=0.153 Sum_probs=24.1
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+++.||.+.++++.++++|||+-.| ++
T Consensus 9 ~~~~~~~~a~if~~La~~~InvDmI-~~ 35 (67)
T cd04914 9 KDNENDLQQRVFKALANAGISVDLI-NV 35 (67)
T ss_pred CCCCccHHHHHHHHHHHcCCcEEEE-Ee
Confidence 4677999999999999999999999 44
No 106
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=80.38 E-value=3.5 Score=29.52 Aligned_cols=31 Identities=16% Similarity=0.176 Sum_probs=26.1
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
|.+.-||+||-.+++-+.++++|.|+..+..
T Consensus 4 ltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q 34 (77)
T cd04893 4 ISALGTDRPGILNELTRAVSESGCNILDSRM 34 (77)
T ss_pred EEEEeCCCChHHHHHHHHHHHcCCCEEEcee
Confidence 3445599999999999999999999987643
No 107
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=80.23 E-value=13 Score=31.59 Aligned_cols=124 Identities=22% Similarity=0.234 Sum_probs=71.8
Q ss_pred HHHHHHHHHcCCcceEEEeeecccccc--eeccccccccCCeEEEEEEEEeeeeeeecCCC-----CCcCCe---eEEEe
Q 036073 45 FEEAFKAVELWLAEKAILPIENSSGGS--IHHNYDLLLRHRLHIVGEVQFVANFCLLALPG-----IREEKL---KCVLS 114 (241)
Q Consensus 45 ~~~v~~av~~g~~d~gVvPiENS~~G~--V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g-----~~~~~i---~~V~S 114 (241)
=.+.+.++.+|++|.|.+-+-..-.|. +....++|...++.++.-.. =+..|+.++| .+++|+ ...+-
T Consensus 20 S~~gl~~L~~g~~~iAg~h~~~~~~~~~n~~~~~~~l~g~~~v~v~~~~--r~~Gl~v~~~np~~i~~~~dL~~~~~r~v 97 (193)
T PF12727_consen 20 SRAGLSALARGEADIAGIHLPDPESGEYNIPFVRRLLPGIEVVLVRLAR--REQGLIVRPGNPKGITSLEDLADPGLRFV 97 (193)
T ss_pred CHHHHHHHHCCCceEEEecCCCCcccccchHHHHHhcCCCcEEEEeeeE--EeeeEEEeCCCCccCCCHHHhccCCcEEE
Confidence 345678889999999998554332222 22223333333444432222 2356777777 345555 22333
Q ss_pred cHHHHHHHHHHHHh----cCC-----c--eEeccCHHHHHHHHHhcCCCCeEEecCHhhHHh-cCCceee
Q 036073 115 HPQALASSDIVQTQ----LGV-----A--RENIDDTASAAQYVASNGLRDAGVVASARAAEI-YGLNILA 172 (241)
Q Consensus 115 Hpqal~Qc~~fl~~----~~~-----~--~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~-ygL~il~ 172 (241)
-.|.=.=.+.+|++ .++ . .....|..+.|..|+.+ ...++++...+|+. |||..+-
T Consensus 98 nR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G--~AD~G~g~~~~A~~~~gL~Fvp 165 (193)
T PF12727_consen 98 NRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASG--KADAGIGIRAAAEEFYGLDFVP 165 (193)
T ss_pred ECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcC--CCCEEeehHHHHHhhcCCCcEE
Confidence 33333335666654 222 1 13456677778888876 46789999999975 7999874
No 108
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=80.09 E-value=5.2 Score=34.97 Aligned_cols=96 Identities=9% Similarity=0.026 Sum_probs=55.2
Q ss_pred CccEEEEeCCCCcHHHHHHHhhC----CCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEE
Q 036073 12 TKVRISFKGSPGSFTEDAALKAY----PNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIV 87 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~----~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~ 87 (241)
...+||+ ..||..+....++. ...+++.+++..+++++|.+|++|..+..- ....+. .+....++
T Consensus 147 ~g~~V~v--~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~d~-~~~~~~--------~~~~~~~~ 215 (259)
T PRK11917 147 KGANIGV--AQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDK-SILLGY--------VDDKSEIL 215 (259)
T ss_pred CCCeEEE--ecCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEecH-HHHHHh--------hhcCCeec
Confidence 3467888 45665554433322 234677889999999999999999876531 111111 11222333
Q ss_pred EEEEEeeeeeeecCCCCCcCCeeEEEecHHHHHHHHHHHHhc
Q 036073 88 GEVQFVANFCLLALPGIREEKLKCVLSHPQALASSDIVQTQL 129 (241)
Q Consensus 88 ~E~~l~I~~~L~~~~g~~~~~i~~V~SHpqal~Qc~~fl~~~ 129 (241)
.+..-+..++++.+++ +++-..+..++|.++
T Consensus 216 ~~~~~~~~~~~a~~k~-----------~~~l~~~ln~~l~~~ 246 (259)
T PRK11917 216 PDSFEPQSYGIVTKKD-----------DPAFAKYVDDFVKEH 246 (259)
T ss_pred CCcCCCCceEEEEeCC-----------CHHHHHHHHHHHHHH
Confidence 3333333445555554 466677777777654
No 109
>TIGR02079 THD1 threonine dehydratase. This model represents threonine dehydratase, the first step in the pathway converting threonine into isoleucine. At least two other clades of biosynthetic threonine dehydratases have been characterized by models TIGR01124 and TIGR01127. Those sequences described by this model are exclusively found in species containg the rest of the isoleucine pathway and which are generally lacking in members of the those other two clades of threonine dehydratases. Members of this clade are also often gene clustered with other elements of the isoleucine pathway.
Probab=79.52 E-value=2.9 Score=39.69 Aligned_cols=36 Identities=17% Similarity=0.218 Sum_probs=28.8
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
-+..+.|.+|++||+|.++|+.....+-|++.++-|
T Consensus 324 r~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~y~ 359 (409)
T TIGR02079 324 LKHYFIVRFPQRPGALREFLNDVLGPNDDITRFEYT 359 (409)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEee
Confidence 367788999999999999999444444499988765
No 110
>cd04935 ACT_AKiii-DAPDC_1 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. This CD includes the first of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=78.24 E-value=2.9 Score=30.04 Aligned_cols=27 Identities=19% Similarity=0.244 Sum_probs=24.5
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
.++.||.+.++++.|++++||.-.|-+
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~vDmI~~ 37 (75)
T cd04935 11 MWQQVGFLADVFAPFKKHGVSVDLVST 37 (75)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe
Confidence 467899999999999999999999865
No 111
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=77.07 E-value=5.5 Score=35.51 Aligned_cols=135 Identities=16% Similarity=0.104 Sum_probs=75.8
Q ss_pred CCCCccEEEEeCCCCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHcCCcceEEEeeecc----cccceecc-----
Q 036073 9 NDGTKVRISFKGSPGSFTEDAALKAYP----NCETIPCDEFEEAFKAVELWLAEKAILPIENS----SGGSIHHN----- 75 (241)
Q Consensus 9 ~~~~~~~ia~LGp~GtfS~~Aa~~~~~----~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS----~~G~V~~t----- 75 (241)
....+.++|..|+ |+.+|.++..+.. +.+.+|+++-.+.+.++..|++|.++...-+. -.|.+...
T Consensus 102 ~~p~~~~~g~~g~-g~~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~~~~~~~~~~G~~k~Lav~~~ 180 (274)
T PF03401_consen 102 ANPGKLTFGSSGP-GSSDHLAAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSPGEALPYVEAGDLKPLAVFSD 180 (274)
T ss_dssp CSCCC-EEEESST-TSHHHHHHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHTTSEEEEEECSS
T ss_pred hCCCCeEEEecCC-CchHHHHHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecHHHHHHHHhCCCceEEEEecC
Confidence 3455678888875 8999988876552 36789999999999999999999999765433 23443311
Q ss_pred --cccccc------CCeEEEEEEEEeeeeeeecCCCCCcCCeeEEEecHHH---HHHHHHHHHhcCCceEeccCHHHHHH
Q 036073 76 --YDLLLR------HRLHIVGEVQFVANFCLLALPGIREEKLKCVLSHPQA---LASSDIVQTQLGVARENIDDTASAAQ 144 (241)
Q Consensus 76 --~d~L~~------~~l~I~~E~~l~I~~~L~~~~g~~~~~i~~V~SHpqa---l~Qc~~fl~~~~~~~~~~~sTa~Aa~ 144 (241)
++.|.+ .++ .++.+...+.+++++|++.+-+.++..--+. ....++|+++.++... ..+..+..+
T Consensus 181 ~r~~~~pdvPT~~E~G~---~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~~g~~~~-~~~~~~~~~ 256 (274)
T PF03401_consen 181 ERSPALPDVPTFKEQGY---PDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEKMGLEPV-YMDGEEFDA 256 (274)
T ss_dssp S-BTTCTTS-BTTTTT----TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHHHTEEEE-CESHHHHHH
T ss_pred ccccccCCCCCHHHhCc---cceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHHCCCcCC-CCCHHHHHH
Confidence 111111 111 0233455678888888754333332222222 2223445555555443 555666666
Q ss_pred HHHh
Q 036073 145 YVAS 148 (241)
Q Consensus 145 ~v~~ 148 (241)
.+.+
T Consensus 257 ~l~~ 260 (274)
T PF03401_consen 257 FLAE 260 (274)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6655
No 112
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=76.94 E-value=33 Score=26.68 Aligned_cols=122 Identities=14% Similarity=0.065 Sum_probs=60.3
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecc--cccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENS--SGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL 109 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS--~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i 109 (241)
.+|+.++... .+..++.+.+.+|++|+|++..... ..|.. ...|.+..+.++ .+-+|-+...+..+++|+
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~~l~~~~~~~~~dL 97 (201)
T cd08435 25 RHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLA---SEELADEPLVVV----ARPGHPLARRARLTLADL 97 (201)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCCCCcE---EEEcccCcEEEE----EeCCCcCcccCCcCHHHH
Confidence 3577655433 4678899999999999999753211 12211 112223333332 223343433222333333
Q ss_pred e---EEEe-cHH-HHHHHHHHHHhcCCc---e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 110 K---CVLS-HPQ-ALASSDIVQTQLGVA---R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 110 ~---~V~S-Hpq-al~Qc~~fl~~~~~~---~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
. -|.. ... -.....+|+++.+.. . ..+++...+.+.+.++ ...++.+...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08435 98 ADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARS---DMLAVLPRSVAE 158 (201)
T ss_pred hcCCEEecCCCCcHHHHHHHHHHHcCCCCCCceEEEccHHHHHHHHhcC---CeEEEeEHHHhh
Confidence 2 2221 111 122345556655432 2 3345555555666653 357888887665
No 113
>cd04933 ACT_AK1-AT_1 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the first of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine. This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. Like the Escherichia coli AKIII (LysC), Arabidopsis AK1 binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. A loop in common is involved in the binding of both Lys and S-adenosylmethionine providing an explanation for the synergistic inhibition by these effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=75.59 E-value=3.7 Score=29.93 Aligned_cols=27 Identities=22% Similarity=0.292 Sum_probs=24.6
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
.++.||.+.++++.|+++|||.-.|-+
T Consensus 11 ~~~~~g~~a~IF~~La~~~InVDmI~q 37 (78)
T cd04933 11 MLGQYGFLAKVFSIFETLGISVDVVAT 37 (78)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe
Confidence 467899999999999999999999865
No 114
>PRK12483 threonine dehydratase; Reviewed
Probab=75.59 E-value=8 Score=38.06 Aligned_cols=179 Identities=15% Similarity=0.149 Sum_probs=86.6
Q ss_pred HHHHHHHHcCCcceEEEeeecccccceeccccccc--cCCeEEEEEEEEeee---eeeecCCCCCcCCeeEEEe-----c
Q 036073 46 EEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLL--RHRLHIVGEVQFVAN---FCLLALPGIREEKLKCVLS-----H 115 (241)
Q Consensus 46 ~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~--~~~l~I~~E~~l~I~---~~L~~~~g~~~~~i~~V~S-----H 115 (241)
.|+++.+. +..|+-|+|+= ..|.+.-....+. ..+.+|+|--.-.-. ..+-..+...++++.++.. .
T Consensus 177 ~EI~eQ~~-~~~D~VvvpvG--gGGliaGia~~~K~~~p~vkVIGVep~~a~~~~~sl~~g~~~~~~~~~t~adGiav~~ 253 (521)
T PRK12483 177 MEILRQHP-GPLDAIFVPVG--GGGLIAGIAAYVKYVRPEIKVIGVEPDDSNCLQAALAAGERVVLGQVGLFADGVAVAQ 253 (521)
T ss_pred HHHHHHhC-CCCCEEEEecC--ccHHHHHHHHHHHHhCCCCEEEEEEeCCCchhhHHHhcCCcccCCCCCceeceeccCC
Confidence 35555553 25899999985 3555554444443 345777665432110 0111111111222222111 1
Q ss_pred --HHHHHHHHHHHHhcCCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCceeecccCCCCCCceeEEEEeeCCC
Q 036073 116 --PQALASSDIVQTQLGVARENIDDTASAAQYVASNGLRDAGVVASARAAEIYGLNILADRIQDDPDNITRFLVLARDPI 193 (241)
Q Consensus 116 --pqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~d~~~N~TRF~vl~~~~~ 193 (241)
+..+.-|++++.. +-.+.-.....|.+.+.+.. ..-+.+..|+-+.+|.-+..... . .+.+=-+|++-...
T Consensus 254 ~g~~~~~~~~~~vd~--vv~Vse~ei~~ai~~l~~~~---~i~vEpagAaalAal~~~~~~~~-~-~g~~VV~IlsGgNi 326 (521)
T PRK12483 254 IGEHTFELCRHYVDE--VVTVSTDELCAAIKDIYDDT---RSITEPAGALAVAGIKKYAEREG-I-EGQTLVAIDSGANV 326 (521)
T ss_pred CCHHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhC---CcEEeHHHHHHHHHHHHHHHhcC-C-CCCEEEEEeCCCCC
Confidence 2334444333321 11222333455566666532 12344445555555543322111 0 12333334443322
Q ss_pred CCC----------CCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 194 MPR----------TDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 194 ~~~----------~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
... -...-+..+.+.+|++||+|.+++..+..+ |++.++=|
T Consensus 327 d~~~l~~i~~r~l~~~~r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~ 377 (521)
T PRK12483 327 NFDRLRHVAERAELGEQREAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYR 377 (521)
T ss_pred CHHHHHHHHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEE
Confidence 110 012347788899999999999999999988 88877654
No 115
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=75.49 E-value=47 Score=29.45 Aligned_cols=33 Identities=15% Similarity=0.145 Sum_probs=24.6
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCcceEEEeeec
Q 036073 34 YPNCETIP-CDEFEEAFKAVELWLAEKAILPIEN 66 (241)
Q Consensus 34 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiEN 66 (241)
+|+.++.- ..+-.++++++.+|++|+|+++..+
T Consensus 123 ~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~ 156 (312)
T PRK10341 123 FPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSN 156 (312)
T ss_pred CCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCc
Confidence 56665533 3356899999999999999987543
No 116
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=75.49 E-value=54 Score=28.44 Aligned_cols=121 Identities=15% Similarity=0.012 Sum_probs=61.1
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCC-CCcC---C
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPG-IREE---K 108 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g-~~~~---~ 108 (241)
+|+.++... .+..++.+.+.+|++|+|+.+......+... ..|.+..+.++ .+-+|-|...+. .+++ +
T Consensus 117 ~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~~----~~~~~pl~~~~~~i~~~~L~~ 189 (296)
T PRK11242 117 YPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA---QPLFTETLALV----VGRHHPLAARRKALTLDELAD 189 (296)
T ss_pred CCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCCCCcceeE---EEeeeccEEEE----EcCCCcccccCCCcCHHHHhC
Confidence 466665554 4568899999999999999865433332221 12223333322 222232322211 2222 2
Q ss_pred eeEEEecHHH--HHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 109 LKCVLSHPQA--LASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 109 i~~V~SHpqa--l~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
-..|.-.+.. ...-.+|+.+.+.+ . ..++|-..+.+.+..+ ...++.++..++
T Consensus 190 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 247 (296)
T PRK11242 190 EPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG---RLATLLPAAIAR 247 (296)
T ss_pred CCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhC---CeEEEeehhhcc
Confidence 2334333332 22335566665543 2 3455555566666654 346777776554
No 117
>PRK09224 threonine dehydratase; Reviewed
Probab=74.94 E-value=9.6 Score=37.23 Aligned_cols=34 Identities=21% Similarity=0.256 Sum_probs=28.2
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+..+.+.+|++||+|.++++.+. +-|+|.++=|
T Consensus 327 re~~l~v~iPerPGaL~~f~~~l~--~~nItef~yr 360 (504)
T PRK09224 327 REALLAVTIPEEPGSFLKFCELLG--GRNVTEFNYR 360 (504)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhc--cCcEEEEEEE
Confidence 467888999999999999999999 5677766644
No 118
>cd04912 ACT_AKiii-LysC-EC-like_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC) and plants, (Zea mays Ask1, Ask2, and Arabidopsis thaliana AK1). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Like the A. thaliana AK1 (AK1-AT), the E. coli AKIII (LysC) has two bound feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The lysine-sensitive plant isoenzyme is synergistically inhibited by S-adenosylmethionine. A homolog of this group appears to be the Saccharomyces cerevisiae AK (Hom3) which clusters with this group as well. Members of this CD
Probab=74.29 E-value=5.5 Score=28.24 Aligned_cols=30 Identities=17% Similarity=0.326 Sum_probs=25.5
Q ss_pred ecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 208 TLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 208 ~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
.+++.||.+.++++.|+++|||+-.+-+.+
T Consensus 10 ~l~~~~g~~~~if~~L~~~~I~v~~i~~s~ 39 (75)
T cd04912 10 RMLGAHGFLAKVFEIFAKHGLSVDLISTSE 39 (75)
T ss_pred CCCCCccHHHHHHHHHHHcCCeEEEEEcCC
Confidence 346789999999999999999998886544
No 119
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.
Probab=74.26 E-value=7.3 Score=34.11 Aligned_cols=49 Identities=20% Similarity=0.129 Sum_probs=38.8
Q ss_pred ccEEEEeCCCCcHHHHHHHhh-CCCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSFTEDAALKA-YPNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~-~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..+||. +.|++.+...... ++..+++.+++.++++++|.+|++|+.+..
T Consensus 144 g~~Igv--~~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d 193 (275)
T TIGR02995 144 DAKIAA--PGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGRADAYSLT 193 (275)
T ss_pred CceEEE--eCCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCCCCEEecC
Confidence 367885 5777777766653 455678899999999999999999988874
No 120
>cd08450 PBP2_HcaR The C-terminal substrate binding domain of LysR-type transcriptional regulator HcaR in involved in 3-phenylpropionic acid catabolism, contains the type2 periplasmic binding fold. HcaR, a member of the LysR family of transcriptional regulators, controls the expression of the hcA1, A2, B, C, and D operon, encoding for the 3-phenylpropionate dioxygenase complex and 3-phenylpropionate-2',3'-dihydrodiol dehydrogenase, that oxidizes 3-phenylpropionate to 3-(2,3-dihydroxyphenyl) propionate. Dioxygenases play an important role in protecting the cell against the toxic effects of dioxygen. The expression of hcaR is negatively auto-regulated, as for other members of the LysR family, and is strongly repressed in the presence of glucose. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=74.21 E-value=39 Score=26.25 Aligned_cols=32 Identities=9% Similarity=-0.070 Sum_probs=24.3
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEee
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPi 64 (241)
.+|+.++.... +-.++++.+.+|++|+|++..
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08450 25 EHPDLDVELSSLFSPQLAEALMRGKLDVAFMRP 57 (196)
T ss_pred hCCCcEEEEEecChHHHHHHHhcCCccEEEEeC
Confidence 35776655444 467899999999999999753
No 121
>cd04928 ACT_TyrKc Uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains. This CD includes a novel, yet uncharacterized, N-terminal ACT domain of an Arabidopsis/Oryza predicted tyrosine kinase and other related ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=73.43 E-value=5.1 Score=28.56 Aligned_cols=28 Identities=18% Similarity=0.402 Sum_probs=24.7
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
+++..+|+||-+.++-+.|+.+|+|+-.
T Consensus 4 I~V~~~Dr~gLFa~iag~L~~~~LnI~~ 31 (68)
T cd04928 4 ITFAAGDKPKLLSQLSSLLGDLGLNIAE 31 (68)
T ss_pred EEEEECCCcchHHHHHHHHHHCCCceEE
Confidence 5566689999999999999999999865
No 122
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=73.35 E-value=6.4 Score=40.85 Aligned_cols=37 Identities=11% Similarity=0.135 Sum_probs=32.4
Q ss_pred CceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 200 PFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 200 ~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+.|.+-+..+|+||-|+++.+.|+.+|||+......
T Consensus 777 ~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~ 813 (850)
T TIGR01693 777 RKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKIT 813 (850)
T ss_pred CCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEE
Confidence 3578888899999999999999999999999876553
No 123
>PF00497 SBP_bac_3: Bacterial extracellular solute-binding proteins, family 3; InterPro: IPR001638 Bacterial high affinity transport systems are involved in active transport of solutes across the cytoplasmic membrane. The protein components of these traffic systems include one or two transmembrane protein components, one or two membrane-associated ATP-binding proteins (ABC transporters; see IPR003439 from INTERPRO) and a high affinity periplasmic solute-binding protein. The latter are thought to bind the substrate in the vicinity of the inner membrane, and to transfer it to a complex of inner membrane proteins for concentration into the cytoplasm. In Gram-positive bacteria which are surrounded by a single membrane and have therefore no periplasmic region, the equivalent proteins are bound to the membrane via an N-terminal lipid anchor. These homologue proteins do not play an integral role in the transport process per se, but probably serve as receptors to trigger or initiate translocation of the solute throught the membrane by binding to external sites of the integral membrane proteins of the efflux system. In addition, at least some solute-binding proteins function in the initiation of sensory transduction pathways. On the basis of sequence similarities, the vast majority of these solute-binding proteins can be grouped [] into eight families or clusters, which generally correlate with the nature of the solute bound. Family 3 groups together specific amino acids and opine-binding periplasmic proteins and a periplasmic homologue with catalytic activity.; GO: 0005215 transporter activity, 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 3N26_A 3QAX_A 3I6V_A 2VHA_B 2IA4_B 2Q89_A 2Q88_A 2YJP_C 1II5_A 1IIW_A ....
Probab=73.11 E-value=18 Score=29.34 Aligned_cols=123 Identities=14% Similarity=0.115 Sum_probs=69.5
Q ss_pred HHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCC--
Q 036073 27 EDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGI-- 104 (241)
Q Consensus 27 ~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~-- 104 (241)
.+.+.+.--+.++++. ++.++++++.+|++|.++-++..+. +. ...+.... -+....+.++.+++.
T Consensus 30 ~~i~~~~g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~--------~r--~~~~~~s~-p~~~~~~~~~~~~~~~~ 97 (225)
T PF00497_consen 30 RAIAKRLGIKIEFVPM-PWSRLLEMLENGKADIIIGGLSITP--------ER--AKKFDFSD-PYYSSPYVLVVRKGDAP 97 (225)
T ss_dssp HHHHHHHTCEEEEEEE-EGGGHHHHHHTTSSSEEESSEB-BH--------HH--HTTEEEES-ESEEEEEEEEEETTSTC
T ss_pred HHHHhhcccccceeec-ccccccccccccccccccccccccc--------cc--cccccccc-cccchhheeeecccccc
Confidence 3444443224678888 9999999999999999874444322 21 11222222 223334555555441
Q ss_pred ---C---cCCe--eEEEecHHHHHHHHHHHHh-c--CCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 105 ---R---EEKL--KCVLSHPQALASSDIVQTQ-L--GVARENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 105 ---~---~~~i--~~V~SHpqal~Qc~~fl~~-~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
+ ++++ ++|..-.-.. -.++|.+ . +.+.+.+.|..++.+++..+ +-.++|.....+..
T Consensus 98 ~~~~~~~~~dl~~~~i~~~~g~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~i~~~~~~~~ 165 (225)
T PF00497_consen 98 PIKTIKSLDDLKGKRIGVVRGSS--YADYLKQQYPSNINIVEVDSPEEALEALLSG--RIDAFIVDESTAEY 165 (225)
T ss_dssp STSSHSSGGGGTTSEEEEETTSH--HHHHHHHHTHHTSEEEEESSHHHHHHHHHTT--SSSEEEEEHHHHHH
T ss_pred ccccccchhhhcCcccccccchh--HHHHhhhhccchhhhcccccHHHHHHHHhcC--Ceeeeeccchhhhh
Confidence 1 2244 2333333222 1223433 1 67778889999999998875 45578877765543
No 124
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=73.08 E-value=40 Score=26.28 Aligned_cols=123 Identities=16% Similarity=0.128 Sum_probs=62.6
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee-
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK- 110 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~- 110 (241)
.+|+.++.-.. +-.++.+.+.+|++|+|++.......+.. ...|.+..+.++. +-+|-+.. +..+++++.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~---~~~l~~~~~~lv~----~~~~p~~~-~~~~~~~L~~ 96 (198)
T cd08461 25 EAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLR---SRPLFEERYVCVT----RRGHPLLQ-GPLSLDQFCA 96 (198)
T ss_pred HCCCcEEEEeeCCcccHHHHHhcCCCcEEEecCccCCccce---eeeeecCcEEEEE----cCCChhhc-CCCCHHHHhh
Confidence 35776654443 45678999999999999975332212211 1122233333332 22232222 222333222
Q ss_pred --EEEecHH---HHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHhc
Q 036073 111 --CVLSHPQ---ALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAEIY 166 (241)
Q Consensus 111 --~V~SHpq---al~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y 166 (241)
-|.-++. --.+-.+|+.+.+.+ . ..++|...+...+..+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~ 157 (198)
T cd08461 97 LDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAAT---DMVAFVPSRLVPNL 157 (198)
T ss_pred CCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcC---CeEEEchHHHHHhh
Confidence 2332221 112356677765543 2 3456666666666653 46888888777654
No 125
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=73.08 E-value=43 Score=26.19 Aligned_cols=109 Identities=15% Similarity=0.131 Sum_probs=59.6
Q ss_pred CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCC---CcCCe--eE
Q 036073 37 CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGI---REEKL--KC 111 (241)
Q Consensus 37 ~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~---~~~~i--~~ 111 (241)
.++++. +..++.+++.+|++|+++.+..+..+.. ..+ ..........+.++.+++. +++|+ ++
T Consensus 41 ~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~~-----~~~------~~~~~~~~~~~~~~~~~~~~~~~~~dL~g~~ 108 (219)
T smart00062 41 VEFVEV-SFDNLLTALKSGKIDVVAAGMTITPERA-----KQV------DFSDPYYKSGQVILVRKDSPIKSLEDLKGKK 108 (219)
T ss_pred EEEEec-cHHHHHHHHHCCcccEEeccccCCHHHH-----hhe------eeccceeeceeEEEEecCCCCCChHHhCCCE
Confidence 577787 8899999999999999997643221110 000 0111112223455555543 23333 23
Q ss_pred EEecHHHHHHHHHHHHhc--CCceEeccCHHHHHHHHHhcCCCCeEEecCHh
Q 036073 112 VLSHPQALASSDIVQTQL--GVARENIDDTASAAQYVASNGLRDAGVVASAR 161 (241)
Q Consensus 112 V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~ 161 (241)
|..-. . .-...++... +...+...+..++.+.+..+ +-.+++....
T Consensus 109 i~~~~-g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~ 156 (219)
T smart00062 109 VAVVA-G-TTGEELLKKLYPEAKIVSYDSQAEALAALKAG--RADAAVADAP 156 (219)
T ss_pred EEEec-C-ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcC--cccEEEeccH
Confidence 33322 1 1233555554 56677777888888888765 3345665554
No 126
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=72.96 E-value=18 Score=34.89 Aligned_cols=49 Identities=16% Similarity=0.141 Sum_probs=36.4
Q ss_pred ccEEEEeCCCCcHHHHHHHh---hCCCCc--eeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSFTEDAALK---AYPNCE--TIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~---~~~~~~--~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..+|++. .||..++...+ .+++.. .+.+.+.++++++|.+|++|+.|+.
T Consensus 149 Gk~I~V~--~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d 202 (482)
T PRK10859 149 GGTLTVA--AGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIAD 202 (482)
T ss_pred CCeEEEE--CCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEEC
Confidence 3578874 67777766543 345543 4567899999999999999999974
No 127
>PF00585 Thr_dehydrat_C: C-terminal regulatory domain of Threonine dehydratase; InterPro: IPR001721 Threonine dehydratases including Serine/threonine dehydratase (see IPR001926 from INTERPRO) contain a common C-terminal region that may have a regulatory role. Some members contain two copies of this region [].; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process; PDB: 1TDJ_A 3IAU_A.
Probab=72.88 E-value=1.9 Score=32.30 Aligned_cols=35 Identities=23% Similarity=0.368 Sum_probs=24.8
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+..+.|.+|.+||+|.+.|+.+..+. |+|.++=|
T Consensus 9 ~E~~~~v~~PE~pGal~~F~~~l~~~~-nITeF~YR 43 (91)
T PF00585_consen 9 REALFAVEFPERPGALKRFLDALGPRN-NITEFHYR 43 (91)
T ss_dssp -EEEEEEE--BSTTHCHHHHHCCSSSE--EEEEEEE
T ss_pred CEEEEEEECCCCccHHHHHHHHhCCCc-eEEEEEEc
Confidence 467888999999999999999886655 46665543
No 128
>PLN02550 threonine dehydratase
Probab=72.67 E-value=9.7 Score=38.13 Aligned_cols=178 Identities=12% Similarity=0.096 Sum_probs=86.9
Q ss_pred HHHHHHHcCCcceEEEeeecccccceeccccccc--cCCeEEEEEEEEee---eeeeecCCCCCcCCeeE----EEe---
Q 036073 47 EAFKAVELWLAEKAILPIENSSGGSIHHNYDLLL--RHRLHIVGEVQFVA---NFCLLALPGIREEKLKC----VLS--- 114 (241)
Q Consensus 47 ~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~--~~~l~I~~E~~l~I---~~~L~~~~g~~~~~i~~----V~S--- 114 (241)
|+++.+. +..|+-|+|+- ..|.+.-....+. ..+++|+|--.-.- ...+...+-+.++.+.+ +..
T Consensus 250 EI~eQl~-~~~D~VvvpVG--gGGLiaGia~~lK~l~p~vkVIGVEp~~a~~~~~s~~~G~~v~~~~~~tiAdGiav~~~ 326 (591)
T PLN02550 250 EIVRQHQ-GPLHAIFVPVG--GGGLIAGIAAYVKRVRPEVKIIGVEPSDANAMALSLHHGERVMLDQVGGFADGVAVKEV 326 (591)
T ss_pred HHHHHcC-CCCCEEEEEeC--hhHHHHHHHHHHHHhCCCCEEEEEEECCChHHHHHHhcCCccccCCCCCccceeecCCC
Confidence 4444442 25899999985 3555555555443 35677776544221 00111111111221111 111
Q ss_pred cHHHHHHHHHHHHhcCCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCceeecccCCCCCCceeEEEEeeCCCC
Q 036073 115 HPQALASSDIVQTQLGVARENIDDTASAAQYVASNGLRDAGVVASARAAEIYGLNILADRIQDDPDNITRFLVLARDPIM 194 (241)
Q Consensus 115 Hpqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~ 194 (241)
=++.+.-|++++.. +-.+......+|.+.+.+.. ...+-+..|+-+.+|.-..+... .+ +.+=-++++-....
T Consensus 327 G~~t~~i~~~~vD~--vV~Vsd~eI~~Ai~~l~e~~---givvEpAGA~alAall~~~~~~~-~~-g~~Vv~vlsGgNid 399 (591)
T PLN02550 327 GEETFRLCRELVDG--VVLVSRDAICASIKDMFEEK---RSILEPAGALALAGAEAYCKYYG-LK-DENVVAITSGANMN 399 (591)
T ss_pred CHHHHHHHHhhCCE--EEEECHHHHHHHHHHHHHHC---CCEEeHHHHHHHHHHHHHHHhcC-CC-CCeEEEEecCCCCC
Confidence 13445555544432 22233445666777777642 12233334444555543332111 11 22222233322211
Q ss_pred CC----------CCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 195 PR----------TDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 195 ~~----------~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.. -...-+..+.+.+|++||+|.+++..+... |++.++=|
T Consensus 400 ~~~l~~v~~~~~~~~~r~~~~~v~ipd~pG~l~~~~~~l~~~--ni~~~~~~ 449 (591)
T PLN02550 400 FDRLRIVTELADVGRQQEAVLATFMPEEPGSFKRFCELVGPM--NITEFKYR 449 (591)
T ss_pred HHHHHHHHHHHHhccCCEEEEEEEcCCCCCHHHHHHHHhhhh--cceEEEEE
Confidence 10 012235678889999999999999999986 88877644
No 129
>cd08459 PBP2_DntR_NahR_LinR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that are involved in the catabolism of dinitrotoluene, naphthalene and gamma-hexachlorohexane; contains the type 2 periplasmic binding fold. This CD includes LysR-like bacterial transcriptional regulators, DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. DntR from Burkholderia species controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The active form of DntR is homotetrameric, consisting of a dimer of dimers. NahR is a salicylate-dependent transcription activator of the nah and sal operons for naphthalene degradation. Salicylic acid is an intermediate o
Probab=72.21 E-value=45 Score=26.13 Aligned_cols=121 Identities=15% Similarity=0.113 Sum_probs=60.5
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe---
Q 036073 34 YPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL--- 109 (241)
Q Consensus 34 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i--- 109 (241)
+|+.++.... +..++.+.+.+|++|+|+.+......+ + ....|.+..+.+ ..+-+|-+...+ .+++++
T Consensus 26 ~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~-l--~~~~l~~~~~~~----v~~~~~~l~~~~-i~~~~L~~~ 97 (201)
T cd08459 26 APGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAG-F--FQQRLFRERYVC----LVRKDHPRIGST-LTLEQFLAA 97 (201)
T ss_pred CCCCeEEEEecCccCHHHHhhCCCceEEEEcCCCCccc-c--eEEEeecCceEE----EEcCCCccccCC-cCHHHHhhC
Confidence 5766554443 446888999999999999864321111 1 111222333322 233344333221 333332
Q ss_pred eEEEecH--HHHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 110 KCVLSHP--QALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 110 ~~V~SHp--qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
..|...+ ....+.++|+.+++.. . ..++|.....+.+..+ ...++.+...++.
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (201)
T cd08459 98 RHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQT---DLVATVPERLARL 155 (201)
T ss_pred CcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcC---CEEEecHHHHHHH
Confidence 2233222 1223456677766543 3 3344444444555543 4688888877664
No 130
>cd08446 PBP2_Chlorocatechol The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of LysR-type regulators CbnR, ClcR and TfdR, which are involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. In soil bacterium Pseudomonas putida, the 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR for activation. TfdR is involved in the activation of tf
Probab=71.73 E-value=46 Score=25.96 Aligned_cols=122 Identities=14% Similarity=0.069 Sum_probs=59.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcC---C
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREE---K 108 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~---~ 108 (241)
.+|+.++.-. .+..++.+.+.+|++|+|+.+-.....+... ..|.+..+.+ ..+-+|-+...+..+++ +
T Consensus 26 ~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----v~~~~~pl~~~~~~~~~~l~~ 98 (198)
T cd08446 26 ARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAV---ENVAQERLYL----AVPKSHPLAARPAVSLADLRN 98 (198)
T ss_pred HCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecCCCCCCcee---EEeeeccEEE----EEeCCCCcccCCccCHHHHcC
Confidence 4577655433 3567888999999999999753221111111 1122222222 22233333322212222 3
Q ss_pred eeEEE-ecH---HHHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 109 LKCVL-SHP---QALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 109 i~~V~-SHp---qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
...|. ... ....+..+|+.+.+.. . ..++|.....+.++.+ ...++.+...++
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (198)
T cd08446 99 EPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAG---FGVCIVPESVAA 158 (198)
T ss_pred CCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcC---CcEEEchhhhhc
Confidence 33343 121 1123445566665432 2 3466666666667653 357777776544
No 131
>cd08440 PBP2_LTTR_like_4 TThe C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse funct
Probab=71.68 E-value=44 Score=25.69 Aligned_cols=121 Identities=17% Similarity=0.088 Sum_probs=58.9
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe---
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL--- 109 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i--- 109 (241)
+|+.++.-. .+..++.+.+.+|++|+|+..-.....|.. ...|.+..+.++ .+-+|-+...+..+++++
T Consensus 26 ~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~pl~~~~~~~~~~l~~~ 98 (197)
T cd08440 26 HPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLE---FEPLLRDPFVLV----CPKDHPLARRRSVTWAELAGY 98 (197)
T ss_pred CCCcEEEEEeCChHHHHHHHHcCCccEEEEeCCCCCCCee---EEEeecccEEEE----ecCCCCcccCCccCHHHHccC
Confidence 576655433 356889999999999999985321111111 111222232222 222333322222233333
Q ss_pred eEE-EecHHH-HHHHHHHHHhcCC--c-eEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 110 KCV-LSHPQA-LASSDIVQTQLGV--A-RENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 110 ~~V-~SHpqa-l~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+.| +.+... .....+|+.+.+. + ...++|...+.+.+.++ ...++.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (197)
T cd08440 99 PLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAG---LGVAVLPALALP 155 (197)
T ss_pred CEEecCCCccHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEcchhHHH
Confidence 223 222211 2234455655543 2 23456666666666653 457788876554
No 132
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=71.20 E-value=75 Score=28.25 Aligned_cols=144 Identities=10% Similarity=0.035 Sum_probs=68.2
Q ss_pred CCccEEEEeCCCCcH-HHHHH---HhhCCCCceee-cCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeE
Q 036073 11 GTKVRISFKGSPGSF-TEDAA---LKAYPNCETIP-CDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLH 85 (241)
Q Consensus 11 ~~~~~ia~LGp~Gtf-S~~Aa---~~~~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~ 85 (241)
.+..+||+...-+.+ --... .+.+|+.++.. ..+-.++++.+.+|++|+|+.+-.......+ ....|.+..+.
T Consensus 92 ~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l--~~~~l~~~~~~ 169 (316)
T PRK12679 92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQL--VAFPWFRWHHS 169 (316)
T ss_pred CceEEEEechHhhhcchHHHHHHHHHHCCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCCCCc--eEEEccCCcEE
Confidence 345677775333222 11111 22356655543 3457789999999999999974221000001 11112222222
Q ss_pred EEEEEEEeeeeeeecCCCCCcCCe---eEEEecHH--HHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEe
Q 036073 86 IVGEVQFVANFCLLALPGIREEKL---KCVLSHPQ--ALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVV 157 (241)
Q Consensus 86 I~~E~~l~I~~~L~~~~g~~~~~i---~~V~SHpq--al~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI 157 (241)
+.++..|-|......+++++ +.|.-++. .-....+|+...+.. . ..++|.......+.++ ...++
T Consensus 170 ----~v~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g---~Gi~~ 242 (316)
T PRK12679 170 ----LLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALG---LGIGL 242 (316)
T ss_pred ----EEecCCCccccCCCCCHHHHhCCCeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcC---CcEEE
Confidence 23355555443222333333 33332221 223455677665543 2 3445555555566543 34667
Q ss_pred cCHhhH
Q 036073 158 ASARAA 163 (241)
Q Consensus 158 ~s~~aa 163 (241)
.+..++
T Consensus 243 lp~~~~ 248 (316)
T PRK12679 243 VAEQSS 248 (316)
T ss_pred eccccc
Confidence 666544
No 133
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=70.63 E-value=48 Score=25.78 Aligned_cols=121 Identities=16% Similarity=0.059 Sum_probs=60.7
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe---
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL--- 109 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i--- 109 (241)
+|+.++... .+.+++.+.+.+|++|+|+..-.....+.. ...|.+..+.++ .+-+|-+...+..+++++
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~hpl~~~~~~~~~~l~~~ 98 (199)
T cd08426 26 YPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIR---VHSRQPAPIGAV----VPPGHPLARQPSVTLAQLAGY 98 (199)
T ss_pred CCCeEEEEEeCCcHHHHHHHHCCCccEEEecCCCCCCCeE---EEeeccCcEEEE----ecCCCCcccCCccCHHHHhCC
Confidence 466555443 356889999999999999975332222211 122222333222 233333332222223322
Q ss_pred eEEEecH--HHHHHHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 110 KCVLSHP--QALASSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 110 ~~V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
..|.-.+ .......+|+.+.+.. ...++|...+...+..+ ...++.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (199)
T cd08426 99 PLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAG---GGISLLTELAVR 155 (199)
T ss_pred CeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcC---CCEEEEchHhhh
Confidence 3333221 1123345666665432 23466666666777654 357788876554
No 134
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=70.37 E-value=78 Score=28.10 Aligned_cols=143 Identities=11% Similarity=-0.006 Sum_probs=68.9
Q ss_pred CCccEEEEeCCCCcH-HHHHHHh---hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceecccc--ccccCC
Q 036073 11 GTKVRISFKGSPGSF-TEDAALK---AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYD--LLLRHR 83 (241)
Q Consensus 11 ~~~~~ia~LGp~Gtf-S~~Aa~~---~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d--~L~~~~ 83 (241)
.+..+||.....+.+ -...... .+|+.++... .+..++++.+.+|++|+|+.+-.+.. ...++ -|.+..
T Consensus 92 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~----~~~l~~~~l~~~~ 167 (313)
T PRK12684 92 QGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIAD----YKELVSLPCYQWN 167 (313)
T ss_pred CCeEEEEechHHHHHHhHHHHHHHHHHCCCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCC----CCCceEEEeccce
Confidence 445677775443332 1122222 2466655443 46789999999999999998622111 11111 111222
Q ss_pred eEEEEEEEEeeeeeeecCCCCCcCC---eeEEEecH-H-HHHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeE
Q 036073 84 LHIVGEVQFVANFCLLALPGIREEK---LKCVLSHP-Q-ALASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAG 155 (241)
Q Consensus 84 l~I~~E~~l~I~~~L~~~~g~~~~~---i~~V~SHp-q-al~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~a 155 (241)
+.+ ..+..|-+......++++ ..-|.-.. . --.+..+|++..+. +. ..++|.......|..+ ...
T Consensus 168 ~~~----v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gv 240 (313)
T PRK12684 168 HCV----VVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELG---LGV 240 (313)
T ss_pred EEE----EeCCCCccccCCCcCHHHHhcCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhC---Cce
Confidence 222 234444443322222222 23232111 1 12345666666543 33 4556666666677654 235
Q ss_pred EecCHhhHH
Q 036073 156 VVASARAAE 164 (241)
Q Consensus 156 AI~s~~aa~ 164 (241)
++.+..+++
T Consensus 241 ~~lp~~~~~ 249 (313)
T PRK12684 241 GIVADMAFD 249 (313)
T ss_pred EEeehhhcc
Confidence 666655544
No 135
>cd04936 ACT_AKii-LysC-BS-like_2 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis strain 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive AK isoenzymes. The B. subtilis strain 168 AKII is induced by methionine and repressed and inhibited by lysine. Although C. glutamicum is known to contain a single AK, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regu
Probab=70.33 E-value=5.9 Score=26.07 Aligned_cols=30 Identities=23% Similarity=0.413 Sum_probs=25.8
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
+++.||.+.++++.+++++||+-.|.+.+.
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~s~~ 39 (63)
T cd04936 10 MRSHPGVAAKMFEALAEAGINIEMISTSEI 39 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEccCc
Confidence 567899999999999999999988875543
No 136
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=69.24 E-value=83 Score=27.93 Aligned_cols=120 Identities=12% Similarity=-0.031 Sum_probs=60.5
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCcceEEEeeecc-cccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe--
Q 036073 34 YPNCETIP-CDEFEEAFKAVELWLAEKAILPIENS-SGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL-- 109 (241)
Q Consensus 34 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS-~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i-- 109 (241)
+|+.++.- ..+..++.+.|.+|++|+|+.+-... ..+. ...-|.+..+. +..+..|-|...+..+++++
T Consensus 119 ~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~l---~~~~l~~~~~~----~v~~~~hpl~~~~~~~~~~L~~ 191 (309)
T PRK12683 119 FPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDL---VSFPYYSWHHV----VVVPKGHPLTGRENLTLEAIAE 191 (309)
T ss_pred CCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCCc---eEEEcccCeEE----EEecCCCCcccCCccCHHHHhc
Confidence 57765543 34678999999999999999752211 1111 11122233332 23455555544333333333
Q ss_pred -eEEEecH--HHHHHHHHHHHhcCCce---EeccCHHHHHHHHHhcCCCCeEEecCHhhH
Q 036073 110 -KCVLSHP--QALASSDIVQTQLGVAR---ENIDDTASAAQYVASNGLRDAGVVASARAA 163 (241)
Q Consensus 110 -~~V~SHp--qal~Qc~~fl~~~~~~~---~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 163 (241)
..|.-.+ .--.+...|+.+.+... ..++|.......+..+ ...++.+...+
T Consensus 192 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~ 248 (309)
T PRK12683 192 YPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELG---MGVGIVAAMAY 248 (309)
T ss_pred CCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhC---CCeEEeehhhc
Confidence 3343211 12455677777765432 3345554445555543 23555555443
No 137
>TIGR02424 TF_pcaQ pca operon transcription factor PcaQ. Members of this family are LysR-family transcription factors associated with operons for catabolism of protocatechuate. Members occur only in Proteobacteria.
Probab=68.81 E-value=79 Score=27.53 Aligned_cols=122 Identities=16% Similarity=0.150 Sum_probs=61.8
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEeeeccc--ccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSS--GGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL 109 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~--~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i 109 (241)
.+|+.++.... +-.++++.+.+|++|+|++...+.. .+.. ..-|.+..+.++ .+-.|-|...+..+++|+
T Consensus 118 ~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~---~~~l~~~~~~~~----~~~~hpl~~~~~i~~~dL 190 (300)
T TIGR02424 118 RAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGLS---FEHLYNEPVVFV----VRAGHPLLAAPSLPVASL 190 (300)
T ss_pred hCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCccccccee---eeeecCCceEEE----EcCCCccccCCCCCHHHH
Confidence 35776554443 6678999999999999997543221 1111 111223333222 122343433332233333
Q ss_pred eE--EEecHHH---HHHHHHHHHhcCCc----eEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 110 KC--VLSHPQA---LASSDIVQTQLGVA----RENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 110 ~~--V~SHpqa---l~Qc~~fl~~~~~~----~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
.. .+..+.. ......|+.+++.. ...+.|......++.++ ...++.+...++
T Consensus 191 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 251 (300)
T TIGR02424 191 ADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQES---DAIWIISRGVVA 251 (300)
T ss_pred hCCCEEecCCCCchHHHHHHHHHHCCCCCCCceEEeccHHHHHHHHHhC---CceEeCcHHHHh
Confidence 21 2222222 23345677765432 24566666666666654 346777776664
No 138
>cd08413 PBP2_CysB_like The C-terminal substrate domain of LysR-type transcriptional regulators CysB-like contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-bi
Probab=68.39 E-value=57 Score=25.74 Aligned_cols=122 Identities=16% Similarity=0.009 Sum_probs=60.9
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecc-cccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe-
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENS-SGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL- 109 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS-~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i- 109 (241)
.+|+.++.... +-.++.+.+.+|++|+|+.+-... ..+.. ...|.+..+. +..+.+|-|......+++++
T Consensus 25 ~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~~l~~~~~~----~v~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08413 25 RYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLV---TLPCYRWNHC----VIVPPGHPLADLGPLTLEDLA 97 (198)
T ss_pred hCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCcE---EEEeeeeeEE----EEecCCCcccccCCCCHHHHh
Confidence 35776555444 456889999999999999852111 11111 1111222222 12334454443333343333
Q ss_pred --eEEEec-H-HHHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 110 --KCVLSH-P-QALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 110 --~~V~SH-p-qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+.|.-. . .-..+-++|+++.+.. . ..++|......+++.+ ...++.+....+
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08413 98 QYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLG---LGVGIIAEMAYD 156 (198)
T ss_pred cCCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhC---CCEEEccccccC
Confidence 233321 1 1234456677665542 2 3456666666677654 346777765443
No 139
>PF13840 ACT_7: ACT domain ; PDB: 3S1T_A 1ZHV_A 3AB4_K 3AB2_O 2DTJ_A 3AAW_A 2RE1_B 3MAH_A 1ZVP_D.
Probab=67.93 E-value=14 Score=25.48 Aligned_cols=25 Identities=28% Similarity=0.381 Sum_probs=21.8
Q ss_pred CCchHHHHHHHHHHHCCceeeeeee
Q 036073 211 EGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 211 ~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
+.||.+.++++.+++.|||+-.|-|
T Consensus 19 ~~~Gv~a~i~~~La~~~I~i~~isS 43 (65)
T PF13840_consen 19 DVPGVAAKIFSALAEAGINIFMISS 43 (65)
T ss_dssp TSHHHHHHHHHHHHHTTS-ECEEEE
T ss_pred CcccHHHHHHHHHHHCCCCEEEEEE
Confidence 5999999999999999999987764
No 140
>cd08421 PBP2_LTTR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=67.86 E-value=55 Score=25.40 Aligned_cols=122 Identities=15% Similarity=0.025 Sum_probs=60.1
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee-
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK- 110 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~- 110 (241)
.+|+.++... .+-.++.+.+.+|++|+|++.-.-...+. ....|.+..+.++ .+-.|-+...+..+++++.
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~ 97 (198)
T cd08421 25 AHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGL---ETRPYRTDRLVVV----VPRDHPLAGRASVAFADTLD 97 (198)
T ss_pred HCCCceEEEEecCcHHHHHHHhcCCceEEEEecCCCCCCc---EEEEeecCcEEEE----eCCCCCccccCCCCHHHhcC
Confidence 3577655443 35688999999999999998532111111 1122223333322 1223333322223333332
Q ss_pred --EEEecHH--HHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 111 --CVLSHPQ--ALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 111 --~V~SHpq--al~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
-|.-.+. ...+..+++.+.+.+ . ..++|...+...+..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08421 98 HDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAG---LGIGIVPESAAR 155 (198)
T ss_pred CceEeecCCcchHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CCeEEccchhhh
Confidence 2321111 122344555554543 2 3456666666666653 457788877665
No 141
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=67.83 E-value=14 Score=37.71 Aligned_cols=38 Identities=16% Similarity=0.174 Sum_probs=33.5
Q ss_pred CceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 200 PFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 200 ~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
...+.|.+...|++|.|.++...++..++|+.++.++.
T Consensus 624 ~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~ 661 (702)
T PRK11092 624 EFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEE 661 (702)
T ss_pred eeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEE
Confidence 35677778889999999999999999999999998754
No 142
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=67.76 E-value=10 Score=33.80 Aligned_cols=47 Identities=13% Similarity=0.092 Sum_probs=37.9
Q ss_pred eCCCCcHHHHHHHhhC--C--CCceeecCCHHHHHHHHHcCCcceEEEeee
Q 036073 19 KGSPGSFTEDAALKAY--P--NCETIPCDEFEEAFKAVELWLAEKAILPIE 65 (241)
Q Consensus 19 LGp~GtfS~~Aa~~~~--~--~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 65 (241)
.-|.|-|+.++..+.- . ...++.-.+.++++..|++|++|+|+|=.-
T Consensus 145 ~~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~s 195 (258)
T COG0725 145 TVPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYVS 195 (258)
T ss_pred CCCchHHHHHHHHHhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEEE
Confidence 3478999999987532 1 246789999999999999999999998543
No 143
>cd04934 ACT_AK-Hom3_1 CT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydro
Probab=67.62 E-value=7.2 Score=27.84 Aligned_cols=26 Identities=12% Similarity=0.253 Sum_probs=23.5
Q ss_pred CCCchHHHHHHHHHHHCCceeeeeee
Q 036073 210 DEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 210 ~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
...||.+.++++.|+++|||+-.|-+
T Consensus 12 ~~~~g~~~~If~~la~~~I~vd~I~~ 37 (73)
T cd04934 12 SLSHGFLARIFAILDKYRLSVDLIST 37 (73)
T ss_pred ccccCHHHHHHHHHHHcCCcEEEEEe
Confidence 45799999999999999999999865
No 144
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=67.58 E-value=60 Score=25.68 Aligned_cols=141 Identities=11% Similarity=0.013 Sum_probs=68.0
Q ss_pred cEEEEeCCCCcH--HHH--HHHhhCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEE
Q 036073 14 VRISFKGSPGSF--TED--AALKAYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVG 88 (241)
Q Consensus 14 ~~ia~LGp~Gtf--S~~--Aa~~~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~ 88 (241)
.+||+....+.+ ... +.++.+|+.++.... +.+++++++.+|++|+|+++-.....|.... .|.+..+.++
T Consensus 3 l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~l~~~---~l~~~~~~~~- 78 (198)
T cd08485 3 LRVAYFGTVVLHTLPLLLRQLLSVAPSATVSLTQMSKNRQIEALDAGTIDIGFGRFYPYQEGVVVR---NVTNERLFLG- 78 (198)
T ss_pred EEEEEeccchhHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHcCCccEEEecCCCCCCCeEEE---EeeccceEEE-
Confidence 466665444332 221 112335777665543 6778999999999999998522111222211 1223333322
Q ss_pred EEEEeeeeeeecCCCCCcCCe---eEEE-ecHH---HHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEec
Q 036073 89 EVQFVANFCLLALPGIREEKL---KCVL-SHPQ---ALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVA 158 (241)
Q Consensus 89 E~~l~I~~~L~~~~g~~~~~i---~~V~-SHpq---al~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~ 158 (241)
.+-.|.+......+++++ ..|. .+.. .-.+-.+|+.+.+.. . ..++|......+++.+ ...++.
T Consensus 79 ---~~~~~~~~~~~~v~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~ 152 (198)
T cd08485 79 ---AQKSRARSFGEQVHCSALRNEPLILFPREGRPSFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAG---VGVTIV 152 (198)
T ss_pred ---eCCCCccccCCCcCHHHHhcCCeEecCCCCCccHHHHHHHHHHHcCCCcceEEEcCcHHHHHHHHHcC---CceEEC
Confidence 223333322222333333 3332 2211 122333466655432 2 3456666666667654 346777
Q ss_pred CHhhHH
Q 036073 159 SARAAE 164 (241)
Q Consensus 159 s~~aa~ 164 (241)
+...++
T Consensus 153 p~~~~~ 158 (198)
T cd08485 153 PETVAM 158 (198)
T ss_pred cchhhc
Confidence 776544
No 145
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=67.41 E-value=15 Score=37.55 Aligned_cols=39 Identities=21% Similarity=0.215 Sum_probs=34.8
Q ss_pred CceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 200 PFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 200 ~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
.....|.+...|++|.|.++++.+++.++|+.++.++..
T Consensus 625 ~f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~ 663 (701)
T COG0317 625 VYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSD 663 (701)
T ss_pred ceEEEEEEEEccccchHHHHHHHHHhCCCceEEeecccc
Confidence 457778888899999999999999999999999988763
No 146
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=67.26 E-value=12 Score=31.91 Aligned_cols=89 Identities=9% Similarity=-0.033 Sum_probs=51.1
Q ss_pred CccEEEEeCCCCcHHHHHH----HhhCC------CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceecccccccc
Q 036073 12 TKVRISFKGSPGSFTEDAA----LKAYP------NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLR 81 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa----~~~~~------~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~ 81 (241)
...||++.+|.++..+... .+..+ ..+++...+..+++++|.+|++|.++.+-. ...+...+..+ ..
T Consensus 140 ~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~~Da~~~~~~-~~~~~~~~~~~--~~ 216 (254)
T TIGR01098 140 KGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGKVDAATNNSS-AIGRLKKRGPS--DM 216 (254)
T ss_pred cCCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCCCCeEEecHH-HHHHHHHhCcc--ch
Confidence 3468999887654433322 22222 145677778999999999999999998732 22222211111 01
Q ss_pred CCeEEEEEEEEeeeeeeecCCC
Q 036073 82 HRLHIVGEVQFVANFCLLALPG 103 (241)
Q Consensus 82 ~~l~I~~E~~l~I~~~L~~~~g 103 (241)
.++.+.++-.....+.++.+++
T Consensus 217 ~~~~~~~~~~~~~~~~~~~~~~ 238 (254)
T TIGR01098 217 KKVRVIWKSPLIPNDPIAVRKD 238 (254)
T ss_pred hheEEEEecCCCCCCCEEEECC
Confidence 2567777644333455555554
No 147
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=67.21 E-value=93 Score=27.75 Aligned_cols=108 Identities=14% Similarity=0.116 Sum_probs=61.8
Q ss_pred CccEEEEe-CCCCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceecccc-ccc--cCC
Q 036073 12 TKVRISFK-GSPGSFTEDAALKAYP----NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYD-LLL--RHR 83 (241)
Q Consensus 12 ~~~~ia~L-Gp~GtfS~~Aa~~~~~----~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d-~L~--~~~ 83 (241)
...|||+. +|.....+.+...++. +.+++.+.+..+.++++.+|++|.... ..+. .++ .+. ..+
T Consensus 31 ~~I~IG~~~~~~~~~~~~~~~~l~~~~G~~Vel~~f~~~~~~~~ALa~GdID~~~~-----qh~~---~l~~~~~~~g~~ 102 (271)
T PRK11063 31 NHIKVGVIVGAEQQVAEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAF-----QHKP---YLDQQIKDRGYK 102 (271)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHcCCcceecc-----cCHH---HHHHHHHHcCCc
Confidence 35899997 5554444444444432 368899999999999999999998762 1111 111 111 235
Q ss_pred eEEEEEEEE-eeeeeeecCCCCCcCCee---EEEec--HHHHHHHHHHHHhc
Q 036073 84 LHIVGEVQF-VANFCLLALPGIREEKLK---CVLSH--PQALASSDIVQTQL 129 (241)
Q Consensus 84 l~I~~E~~l-~I~~~L~~~~g~~~~~i~---~V~SH--pqal~Qc~~fl~~~ 129 (241)
+.+++-..+ |+ .+....=.+++|++ +|... |.-.+.+-.+|.+.
T Consensus 103 l~~~~~~~vvp~--~~ys~~i~si~DL~~Gk~IAip~d~~n~~r~L~lL~~~ 152 (271)
T PRK11063 103 LVAVGNTFVYPI--AGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKV 152 (271)
T ss_pred EEEEeEEEEEEe--eccccCCCCHHHhcCCCEEEecCCCccHHHHHHHHHHC
Confidence 666655433 43 22222223556664 66544 55556666667663
No 148
>cd08460 PBP2_DntR_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=66.66 E-value=19 Score=28.47 Aligned_cols=121 Identities=17% Similarity=0.063 Sum_probs=61.3
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee--
Q 036073 33 AYPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK-- 110 (241)
Q Consensus 33 ~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~-- 110 (241)
.+|+.++.......++.+.+.+|++|+|+........+. ....|.+..+.+ ..+-+|-|... ..+++|+.
T Consensus 25 ~~P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~~----v~~~~hpl~~~-~~~l~dl~~~ 96 (200)
T cd08460 25 EAPGVRLRFVPESDKDVDALREGRIDLEIGVLGPTGPEI---RVQTLFRDRFVG----VVRAGHPLARG-PITPERYAAA 96 (200)
T ss_pred HCCCCEEEEecCchhHHHHHHCCCccEEEecCCCCCcch---heeeeeccceEE----EEeCCCCCCCC-CCCHHHHhcC
Confidence 357766554433338899999999999997432111111 112222333322 22334444322 22333333
Q ss_pred -EEE-ecHH-HHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 111 -CVL-SHPQ-ALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 111 -~V~-SHpq-al~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
.|. +... .-.+..+|+.+.+.. . ..++|...+..+++.+ ...++.+...++
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 153 (200)
T cd08460 97 PHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGS---DLIALVPERVTA 153 (200)
T ss_pred CCEEEecCCCCcchHHHHHHhcCCceeEEEEcCcHHHHHHHHhcC---CHHHHHHHHHHH
Confidence 222 2211 124467777776543 2 4466666677777654 346777776554
No 149
>PRK06349 homoserine dehydrogenase; Provisional
Probab=66.63 E-value=7.2 Score=37.17 Aligned_cols=33 Identities=27% Similarity=0.501 Sum_probs=28.1
Q ss_pred EEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 205 IVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 205 i~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
|.+.+.|+||.|.++-+.|++++||+.++...+
T Consensus 351 lRl~v~d~pGvLa~I~~~f~~~~vsI~si~q~~ 383 (426)
T PRK06349 351 LRLLVADKPGVLAKIAAIFAENGISIESILQKG 383 (426)
T ss_pred EEEEecCCcchHHHHHHHHhhcCccEEEEEecc
Confidence 334557999999999999999999999887655
No 150
>cd04868 ACT_AK-like ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes each of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). Typically, AK consists of two ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Aspartokinase is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. One mechanism for the regulation of this pathway is by the production of several isoenzymes of aspartokinase with different repressors and allosteric inhibitors. Pairs of ACT domains are proposed to specifically bind am
Probab=66.25 E-value=8.7 Score=24.35 Aligned_cols=26 Identities=27% Similarity=0.373 Sum_probs=23.2
Q ss_pred CCchHHHHHHHHHHHCCceeeeeeee
Q 036073 211 EGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 211 ~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+.||.+.++|+.|++++||+..+..-
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~~~ 37 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMISQS 37 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEEcC
Confidence 57999999999999999999888653
No 151
>PRK05007 PII uridylyl-transferase; Provisional
Probab=66.13 E-value=8.8 Score=40.17 Aligned_cols=33 Identities=21% Similarity=0.289 Sum_probs=29.3
Q ss_pred CceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 200 PFKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 200 ~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
.+.|.|-+..+|+||-|+++..+|.+.|||+..
T Consensus 806 ~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~ 838 (884)
T PRK05007 806 DRRSYMELIALDQPGLLARVGKIFADLGISLHG 838 (884)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEE
Confidence 357888889999999999999999999999853
No 152
>cd04923 ACT_AK-LysC-DapG-like_2 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the second and fourth, of four, ACT domains present in cyanobacteria AK. Also included are the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase isoenzyme AKI found in Bacilli (B. subtilis strain 168), Clostridia, and Actinobacteria bacterial species. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=66.09 E-value=7.1 Score=25.67 Aligned_cols=29 Identities=24% Similarity=0.387 Sum_probs=25.1
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
+++.||.+.++++.+++.+||+-.|.+..
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~s~ 38 (63)
T cd04923 10 MRSHPGVAAKMFKALAEAGINIEMISTSE 38 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEccC
Confidence 56789999999999999999998886543
No 153
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=66.05 E-value=65 Score=25.53 Aligned_cols=140 Identities=11% Similarity=0.013 Sum_probs=69.7
Q ss_pred cEEEEeCCCCcHH-HHH---HHhhCCCCceee-cCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEE
Q 036073 14 VRISFKGSPGSFT-EDA---ALKAYPNCETIP-CDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVG 88 (241)
Q Consensus 14 ~~ia~LGp~GtfS-~~A---a~~~~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~ 88 (241)
.+||+-...+++- -.+ -++.+|+.++.- ..+..++.+.+.+|++|+|++.-..-..|. ....|.+..+.+
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~~~~~---~~~~l~~~~~~l-- 77 (198)
T cd08486 3 LSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGI---EIVNIAQEDLYL-- 77 (198)
T ss_pred EEEEEechhhHHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCCCCce---EEEEEeeccEEE--
Confidence 5677665544321 111 123357765432 356789999999999999997422111111 011122223222
Q ss_pred EEEEeeeeeeecCCCCCcCCe---eEEEecH----HHHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEec
Q 036073 89 EVQFVANFCLLALPGIREEKL---KCVLSHP----QALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVA 158 (241)
Q Consensus 89 E~~l~I~~~L~~~~g~~~~~i---~~V~SHp----qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~ 158 (241)
.++-+|-+......+++|+ .-|.-.+ .-..+..+++.+.+.. . ..+++......+++.+ ...+|.
T Consensus 78 --v~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~l 152 (198)
T cd08486 78 --AVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG---AASSIV 152 (198)
T ss_pred --EecCCCccccCCcccHHHHcCCCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---ceEEEc
Confidence 2233444433333444444 3343222 2345677777776533 3 3355555555555543 457777
Q ss_pred CHhhH
Q 036073 159 SARAA 163 (241)
Q Consensus 159 s~~aa 163 (241)
+..++
T Consensus 153 p~~~~ 157 (198)
T cd08486 153 PASVA 157 (198)
T ss_pred chhhc
Confidence 76543
No 154
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=65.95 E-value=1e+02 Score=27.76 Aligned_cols=145 Identities=16% Similarity=0.057 Sum_probs=74.7
Q ss_pred CCccEEEEeCCCCcHH-HHHH---HhhCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeE
Q 036073 11 GTKVRISFKGSPGSFT-EDAA---LKAYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLH 85 (241)
Q Consensus 11 ~~~~~ia~LGp~GtfS-~~Aa---~~~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~ 85 (241)
.+..+||+...-+++- -... .+.+|+.++.... +.+++.+++.+|++|+|+++-.+...+... ...|.+..+.
T Consensus 92 ~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~~ 169 (327)
T PRK12680 92 QGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGI--AVPLYRWRRL 169 (327)
T ss_pred ceEEEEEecchhHHHhhHHHHHHHHHHCCCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCCcce--EEEeeccceE
Confidence 4567788766555432 1222 2235776665443 568999999999999999863211111111 1122233332
Q ss_pred EEEEEEEeeeeeeecC-CCCCcCCe---eEEEecH-HHH-HHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEE
Q 036073 86 IVGEVQFVANFCLLAL-PGIREEKL---KCVLSHP-QAL-ASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGV 156 (241)
Q Consensus 86 I~~E~~l~I~~~L~~~-~g~~~~~i---~~V~SHp-qal-~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aA 156 (241)
+.++..|-|... ...+++|+ .-|.--+ ... ....+|+...+.. . ..++|......++..+ ...+
T Consensus 170 ----l~~~~~hpl~~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G---~Gia 242 (327)
T PRK12680 170 ----VVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAG---LGVG 242 (327)
T ss_pred ----EEEeCCChhhccCCCCCHHHHhcCCEEEecCCCchHHHHHHHHHHCCCCCcEEEEECCHHHHHHHHHcC---CCEE
Confidence 234555655532 22333333 3333222 122 4466777776543 2 3455555566666653 3466
Q ss_pred ecCHhhHH
Q 036073 157 VASARAAE 164 (241)
Q Consensus 157 I~s~~aa~ 164 (241)
+.+..+++
T Consensus 243 ~lp~~~~~ 250 (327)
T PRK12680 243 LLAEMAVN 250 (327)
T ss_pred Eeechhcc
Confidence 77666554
No 155
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=65.88 E-value=84 Score=26.75 Aligned_cols=138 Identities=17% Similarity=0.138 Sum_probs=69.6
Q ss_pred CccEEEEeCCCCcHHHHHHHh---hCCCCceee-cCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEE
Q 036073 12 TKVRISFKGSPGSFTEDAALK---AYPNCETIP-CDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIV 87 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~---~~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~ 87 (241)
+..+||+.++ + +--.+... .+|+.++.. ..+..++++.+.+|++|+|++.......+. ....|.+..+.++
T Consensus 87 ~~l~ig~~~~-~-~~~~~l~~~~~~~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~lv 161 (279)
T TIGR03339 87 GSLRIAATAP-Y-YVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRL---DRVVLGNDPLVAV 161 (279)
T ss_pred eEEEEeCchH-H-HHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEecccCCCce---EEEEcCCceEEEE
Confidence 5577887643 1 22222222 346665543 357889999999999999998533222211 1112222222222
Q ss_pred EEEEEeeeeeeecCCCCCcCC---eeEEEecH--HHHHHHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCeEEecC
Q 036073 88 GEVQFVANFCLLALPGIREEK---LKCVLSHP--QALASSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDAGVVAS 159 (241)
Q Consensus 88 ~E~~l~I~~~L~~~~g~~~~~---i~~V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s 159 (241)
. +-+|-|...+..++++ ...|...+ .......+|+.+.+.. ...++|...+.+.+..+ ...++.+
T Consensus 162 ~----s~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp 234 (279)
T TIGR03339 162 V----HRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAG---LGVSVVS 234 (279)
T ss_pred E----CCCCccccCCCcCHHHHhCCCeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcC---CCEEEcc
Confidence 1 2223233222233333 33343222 1234567788776533 24467766666677653 3456766
Q ss_pred Hh
Q 036073 160 AR 161 (241)
Q Consensus 160 ~~ 161 (241)
..
T Consensus 235 ~~ 236 (279)
T TIGR03339 235 AA 236 (279)
T ss_pred hh
Confidence 64
No 156
>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa
Probab=65.84 E-value=8 Score=25.86 Aligned_cols=26 Identities=19% Similarity=0.400 Sum_probs=23.2
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
+++.||.+.++++.|++.|||+-.|.
T Consensus 11 ~~~~~~~~~~i~~~l~~~~I~v~~i~ 36 (66)
T cd04922 11 MAGTPGVAATFFSALAKANVNIRAIA 36 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 46789999999999999999997774
No 157
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=65.10 E-value=1e+02 Score=27.51 Aligned_cols=122 Identities=16% Similarity=0.122 Sum_probs=64.8
Q ss_pred hhCCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCeeE
Q 036073 32 KAYPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLKC 111 (241)
Q Consensus 32 ~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~~ 111 (241)
+.+|+.++... ...++++.+.+|++|+|+.+-.....|... ..|.+..+.+ ..+-+|-|... ..+++|+..
T Consensus 141 ~~~P~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~l----v~~~~hpl~~~-~~~~~dL~~ 211 (317)
T PRK11482 141 THYPQLLLRNI-PISDAENQLSQFQTDLIIDTHSCSNRTIQH---HVLFTDNVVL----VCRQGHPLLSL-EDDEETLDN 211 (317)
T ss_pred HHCCCCEEEEe-cchhHHHHHHCCCcCEEEeccCCCCCceEE---EEEecCcEEE----EEeCCCCccCC-CCCHHHHhh
Confidence 34577665432 446889999999999999875433333222 2233334433 23445555432 345566542
Q ss_pred -----EEecHHHHHHHHHHHHhc--CCce-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 112 -----VLSHPQALASSDIVQTQL--GVAR-ENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 112 -----V~SHpqal~Qc~~fl~~~--~~~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
|..........++++.+. .... ..+.|.......++.+ ...+|.+...+..
T Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~ilp~~~~~~ 270 (317)
T PRK11482 212 AEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASS---DMLGIMPSRFYNL 270 (317)
T ss_pred CCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcC---CeeEEeHHHHHHH
Confidence 222222222345555553 2232 3445555556666653 4577888876654
No 158
>cd04937 ACT_AKi-DapG-BS_2 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive AK isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The BS AKI is tetrameric consisting of two alpha and two beta subunits; th
Probab=65.06 E-value=7 Score=26.67 Aligned_cols=28 Identities=18% Similarity=0.342 Sum_probs=24.2
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+.+.||.+.++++.|++.|||+..+-.+
T Consensus 11 ~~~~~gi~~~if~aL~~~~I~v~~~~~S 38 (64)
T cd04937 11 IRGVPGVMAKIVGALSKEGIEILQTADS 38 (64)
T ss_pred ccCCcCHHHHHHHHHHHCCCCEEEEEcC
Confidence 4578999999999999999999877643
No 159
>cd04924 ACT_AK-Arch_2 ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). Included in this CD is the second of two ACT domains of a monofunctional aspartokinase found mostly in Archaea species (ACT_AK-Arch_2). The first or N-terminal ACT domain of these proteins cluster with the ThrA-like ACT 1 domains (ACT_AKi-HSDH-ThrA-like_1) which includes the threonine-sensitive archaeal Methanococcus jannaschii aspartokinase ACT 1 domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=65.00 E-value=8.6 Score=25.65 Aligned_cols=26 Identities=19% Similarity=0.363 Sum_probs=23.0
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
+++.||.+.++++.|+++|||+-.|.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~ 36 (66)
T cd04924 11 MRGTPGVAGRVFGALGKAGINVIMIS 36 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 46789999999999999999997764
No 160
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=64.92 E-value=7.8 Score=34.81 Aligned_cols=33 Identities=27% Similarity=0.445 Sum_probs=28.7
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKV 233 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~I 233 (241)
.|-.|-+-+.|+||.|.++=++|+.||.|+-++
T Consensus 76 krHvinclVqnEpGvlsRisGvlAaRGfNIdSL 108 (309)
T KOG2663|consen 76 KRHVINCLVQNEPGVLSRISGVLAARGFNIDSL 108 (309)
T ss_pred cceeEEEEecCCchHHHHHHHHHHhccCCchhe
Confidence 466777778999999999999999999998654
No 161
>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Probab=64.70 E-value=17 Score=36.94 Aligned_cols=37 Identities=16% Similarity=0.231 Sum_probs=32.9
Q ss_pred CceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 200 PFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 200 ~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
...+.|.+...|++|.|.++.+.++..++|+.++..+
T Consensus 608 ~f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~ 644 (683)
T TIGR00691 608 RFIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTK 644 (683)
T ss_pred eeEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeE
Confidence 3567788888999999999999999999999998864
No 162
>cd04890 ACT_AK-like_1 ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the first of two ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids, lysine, threonine, methionine, and isoleucine. This CD, includes the first ACT domain of the Escherichia coli (EC) isoenzyme, AKIII (LysC) and the Arabidopsis isoenzyme, asparate kinase 1, both enzymes monofunctional and involved in lysine synthesis, as well as the the first ACT domain of Bacillus subtilis (BS) isoenzyme, AKIII (YclM), and of the Saccharomyces cerevisiae AK (Hom3). Also included are the first ACT domains of the Methylomicrobium alcaliphilum AK, the first enzyme of the ectoine biosynthetic pathway. Members of this CD bel
Probab=63.90 E-value=9.8 Score=25.45 Aligned_cols=26 Identities=15% Similarity=0.263 Sum_probs=23.5
Q ss_pred CCCchHHHHHHHHHHHCCceeeeeee
Q 036073 210 DEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 210 ~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
+++||...++++.|++++||.-.|.+
T Consensus 11 ~~~~~~~~~if~~l~~~~i~v~~i~t 36 (62)
T cd04890 11 NGEVGFLRKIFEILEKHGISVDLIPT 36 (62)
T ss_pred CcccCHHHHHHHHHHHcCCeEEEEec
Confidence 56899999999999999999998854
No 163
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=63.69 E-value=20 Score=36.92 Aligned_cols=52 Identities=13% Similarity=0.201 Sum_probs=39.0
Q ss_pred eeEEEEeeCCCCCCCCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 183 TRFLVLARDPIMPRTDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 183 TRF~vl~~~~~~~~~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
-|++-+.+.... .....+.|.+...|++|.|.++...++..++|+..+.++.
T Consensus 650 eR~I~V~W~~~~---~~~~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~ 701 (743)
T PRK10872 650 ERIVDAVWGESY---SSGYSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRS 701 (743)
T ss_pred ceEEEeEecCCC---CceeEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEE
Confidence 355555553211 1135667888889999999999999999999999998764
No 164
>cd04919 ACT_AK-Hom3_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydrodynamic size. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=63.63 E-value=9.3 Score=25.70 Aligned_cols=26 Identities=15% Similarity=0.270 Sum_probs=22.8
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
++++||.+.++++.|++.|||+-.|.
T Consensus 11 ~~~~~~~~~~if~~L~~~~I~v~~i~ 36 (66)
T cd04919 11 MKNMIGIAGRMFTTLADHRINIEMIS 36 (66)
T ss_pred CCCCcCHHHHHHHHHHHCCCCEEEEE
Confidence 35689999999999999999997764
No 165
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=63.52 E-value=11 Score=39.19 Aligned_cols=33 Identities=21% Similarity=0.275 Sum_probs=29.2
Q ss_pred CceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 200 PFKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 200 ~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
.+.|.|=+..+|+||-|+++.++|.+.||++..
T Consensus 781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~ 813 (854)
T PRK01759 781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLLN 813 (854)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEE
Confidence 357888888999999999999999999999853
No 166
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=62.44 E-value=72 Score=24.83 Aligned_cols=123 Identities=17% Similarity=0.099 Sum_probs=61.6
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe--
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL-- 109 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i-- 109 (241)
.+|+.++... .+..++.+.+.+|++|+|++--.....+. ....|.+..+.++. +-.|-+.. ...+++++
T Consensus 25 ~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~lv~----~~~~~~~~-~~~~~~~L~~ 96 (200)
T cd08466 25 LAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSF---KSELLFEDELVCVA----RKDHPRIQ-GSLSLEQYLA 96 (200)
T ss_pred HCCCCEEEEecCchHhHHHHHHcCCccEEEecccCCCCCc---eeeeecccceEEEE----eCCCCCCC-CCcCHHHHhh
Confidence 3577665444 35678999999999999997421111111 11223333433332 22333322 12344444
Q ss_pred -eEEEecHHH-HHHHHHHHHhcCC---c-eEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhc
Q 036073 110 -KCVLSHPQA-LASSDIVQTQLGV---A-RENIDDTASAAQYVASNGLRDAGVVASARAAEIY 166 (241)
Q Consensus 110 -~~V~SHpqa-l~Qc~~fl~~~~~---~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y 166 (241)
..+.-.+.. ..+-.+|+.+.+. + ...++|.....+.++.+ ...++.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~~ 156 (200)
T cd08466 97 EKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQT---DLIAIAPRWLADQY 156 (200)
T ss_pred CCcEEecCCCCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCC---CeehhhHHHHHHHh
Confidence 223222221 1234556655543 2 23455555555666543 45778887766543
No 167
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=62.05 E-value=76 Score=24.92 Aligned_cols=123 Identities=19% Similarity=0.065 Sum_probs=66.0
Q ss_pred hCCCCcee-ecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe--
Q 036073 33 AYPNCETI-PCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL-- 109 (241)
Q Consensus 33 ~~~~~~~~-~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i-- 109 (241)
.+|+.++. ...+..++.+.+.+|++|+|+........|... ..|.+..+. +..+-+|-|...+..+++++
T Consensus 31 ~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----~~~~~~~pl~~~~~i~~~dL~~ 103 (209)
T PF03466_consen 31 RHPNIRIEIREGDSDELIEALRSGELDLAITFGPPPPPGLES---EPLGEEPLV----LVVSPDHPLAQKKPITLEDLAD 103 (209)
T ss_dssp HSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSSSSTTEEE---EEEEEEEEE----EEEETTSGGGTTSSSSGGGGTT
T ss_pred HCCCcEEEEEeccchhhhHHHhcccccEEEEEeecccccccc---ccccceeee----eeeeccccccccccchhhhhhh
Confidence 35775543 335558999999999999999875531111111 011111111 11222333333333333433
Q ss_pred -eEEEec--HHHHHHHHHHHHhcCCce---EeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 110 -KCVLSH--PQALASSDIVQTQLGVAR---ENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 110 -~~V~SH--pqal~Qc~~fl~~~~~~~---~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
..|.-. ..-..+..+|+.+.+... ..++|...+...+.++ ...++.+...++.
T Consensus 104 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 162 (209)
T PF03466_consen 104 YPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASG---DGIAILPDSLAQD 162 (209)
T ss_dssp SEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTT---SEBEEEEHHHHHH
T ss_pred ccccccccccccccccccccccccccccccccccchhhhccccccc---cceeecCcccccc
Confidence 344422 224566666777666532 4567777777777653 5688888887643
No 168
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=61.92 E-value=19 Score=32.47 Aligned_cols=51 Identities=24% Similarity=0.211 Sum_probs=37.2
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEeee
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILPIE 65 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 65 (241)
..|||.-|+-= -++.-.+.++|+.++++. -|+++..||.+|++|.|++=.|
T Consensus 95 ~~rvavpG~~T-TA~lL~rl~~p~~~~V~m-~fdeI~~Avl~G~VDaGvlIHE 145 (272)
T COG2107 95 GKRVAVPGEMT-TAALLFRLAYPKAEIVYM-PFDEIIPAVLEGKVDAGVLIHE 145 (272)
T ss_pred cceEecCCccc-HHHHHHHHhCCCceEEEe-eHHHHHHHHHcCCCccceEEee
Confidence 45677665532 234444556788887765 5999999999999999998776
No 169
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=61.72 E-value=73 Score=24.64 Aligned_cols=33 Identities=21% Similarity=0.234 Sum_probs=24.4
Q ss_pred hhCCCCceeecC-CHHHHHHHHHcCCcceEEEee
Q 036073 32 KAYPNCETIPCD-EFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 32 ~~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPi 64 (241)
+.+|+.++.... +-+++++.+.+|++|+|+++.
T Consensus 25 ~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~ 58 (199)
T cd08451 25 EAYPDVELTLEEANTAELLEALREGRLDAAFVRP 58 (199)
T ss_pred HHCCCcEEEEecCChHHHHHHHHCCCccEEEEec
Confidence 346776554433 567889999999999999863
No 170
>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.
Probab=60.66 E-value=21 Score=29.84 Aligned_cols=50 Identities=14% Similarity=0.022 Sum_probs=34.3
Q ss_pred CccEEEEeCCCCcHHHHHHHhhCCCCcee---------ecCCHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDAALKAYPNCETI---------PCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~~~~~~~---------~~~s~~~v~~av~~g~~d~gVvP 63 (241)
...+||. +.|+..+....+.....+.. ...|..+++.+|.+|++|.+++.
T Consensus 103 ~g~~V~v--~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~ 161 (232)
T TIGR03871 103 KKLRIGV--FAGTPPAHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVW 161 (232)
T ss_pred cCCeEEE--EcCChHHHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEec
Confidence 3467887 45888877665432111111 23488999999999999999985
No 171
>PRK05092 PII uridylyl-transferase; Provisional
Probab=60.63 E-value=14 Score=38.96 Aligned_cols=35 Identities=17% Similarity=0.205 Sum_probs=30.3
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
+.|.|.+..+|+||-|+++.+.|+..|||+..-..
T Consensus 842 ~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I 876 (931)
T PRK05092 842 RFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHI 876 (931)
T ss_pred CeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEE
Confidence 35778888899999999999999999999976543
No 172
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=60.57 E-value=16 Score=31.18 Aligned_cols=49 Identities=22% Similarity=0.269 Sum_probs=38.4
Q ss_pred ccEEEEeCCCCcH--HHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSF--TEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~Gtf--S~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..+|+.+ .||. .+.......+..+++.+++..+++.++.+|++|..+..
T Consensus 146 gk~v~v~--~gt~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d 196 (275)
T COG0834 146 GKKVGVQ--LGTTDEAEEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSD 196 (275)
T ss_pred CCEEEEE--cCcchhHHHHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcc
Confidence 3567665 6766 55555555566899999999999999999999999974
No 173
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=60.32 E-value=1e+02 Score=25.94 Aligned_cols=123 Identities=15% Similarity=0.088 Sum_probs=61.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCC-C---CCcC
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALP-G---IREE 107 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~-g---~~~~ 107 (241)
.+|+.++... .+.+++.+.+.+|++|+|++...+...+.+ ....|....+.++. +-+|.+.... . .++.
T Consensus 92 ~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~--~~~~l~~~~~~~v~----~~~~~~~~~~~~~~~~~l~ 165 (269)
T PRK11716 92 EHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASV--AFSPIDEIPLVLIA----PALPCPVRQQLSQEKPDWS 165 (269)
T ss_pred HCCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcce--EEEEcccceEEEEE----cCCcchhhhccccchhhHh
Confidence 3566655433 577899999999999999985433222211 11223333433332 3333222111 1 1233
Q ss_pred CeeEEE-ecHHHHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 108 KLKCVL-SHPQALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 108 ~i~~V~-SHpqal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+..-|. +.......-.+|+.+.+.. . ..++|.......+.++ ...++.+...++
T Consensus 166 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 223 (269)
T PRK11716 166 RIPFILPEHGPARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALG---CGVGLLPEVVLE 223 (269)
T ss_pred hCCeeecCCCchHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcC---CCeEeccHHHhh
Confidence 333333 1111122334566665432 2 3455555555566653 357888887665
No 174
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=59.58 E-value=79 Score=24.32 Aligned_cols=30 Identities=23% Similarity=0.015 Sum_probs=23.0
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEe
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 63 (241)
+|+.++.-. .+-.++++.+.+|++|+|++.
T Consensus 26 ~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~ 56 (197)
T cd08438 26 YPNIELELVEYGGKKVEQAVLNGELDVGITV 56 (197)
T ss_pred CcCeEEEEEEcCcHHHHHHHHcCCCCEEEEe
Confidence 566554433 467889999999999999975
No 175
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=59.04 E-value=1.2e+02 Score=26.29 Aligned_cols=122 Identities=10% Similarity=0.003 Sum_probs=62.7
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCc---CC
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIRE---EK 108 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~---~~ 108 (241)
.+|+.++.... +.+++++.+.+|++|+|++.-.....+ -....|.+..+.++ .+-.|-|......++ .+
T Consensus 115 ~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~---l~~~~l~~~~~~~v----~~~~~pl~~~~~i~~~~L~~ 187 (296)
T PRK09906 115 RHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDE---IDYLELLDEPLVVV----LPVDHPLAHEKEITAAQLDG 187 (296)
T ss_pred HCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecCCCCCCC---ceEEEEecccEEEE----ecCCCccccCCCcCHHHHcC
Confidence 45776655433 568899999999999999864321111 11223333444333 223333432222222 33
Q ss_pred eeEEEecH---HH-HHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 109 LKCVLSHP---QA-LASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 109 i~~V~SHp---qa-l~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
..-|.--+ .. ..+..+|+...++. . ..++|.......++.+ ...++.+...++
T Consensus 188 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g~~~~p~~~~~ 247 (296)
T PRK09906 188 VNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG---LGCTIIPGYMNN 247 (296)
T ss_pred CCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcEEEeeHHHhh
Confidence 34443211 12 34456777766543 2 3456665666666653 346666665443
No 176
>cd08437 PBP2_MleR The substrate binding domain of LysR-type transcriptional regulator MleR which required for malolactic fermentation, contains type 2 periplasmic binidning fold. MleR, a transcription activator of malolactic fermentation system, is found in gram-positive bacteria and belongs to the lysR family of bacterial transcriptional regulators. The mleR gene is required for the expression and induction of malolactic fermentation. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplasmically located ATPase dom
Probab=58.89 E-value=85 Score=24.45 Aligned_cols=122 Identities=11% Similarity=-0.002 Sum_probs=59.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeeccc-ccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSS-GGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK 110 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~-~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~ 110 (241)
.+|+.++... .+-.++.+.+.+|++|+|++.-.... .+.+ ....|.+..+.++ .+-+|-|......+++|+.
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l--~~~~l~~~~~~~~----~~~~hpl~~~~~i~~~dL~ 98 (198)
T cd08437 25 TGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSAL--HSKIIKTQHFMII----VSKDHPLAKAKKVNFADLK 98 (198)
T ss_pred hCCceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCcccc--eEEEeecceEEEE----ecCCCcccccCcccHHHHc
Confidence 3577655443 36788999999999999997532110 1100 1122223333332 2233433332223333333
Q ss_pred ---EEE-ecHH-HHHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeEEecCHhhH
Q 036073 111 ---CVL-SHPQ-ALASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAGVVASARAA 163 (241)
Q Consensus 111 ---~V~-SHpq-al~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 163 (241)
.|. .... --.+..+|+.+.+. +. ..++|.....++++++ ...++.+...+
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 156 (198)
T cd08437 99 KENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVREN---VGIGFLTDIAV 156 (198)
T ss_pred CCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CcEEEEEhhhc
Confidence 232 1111 12445566666553 23 3455555555666653 34677776544
No 177
>cd04916 ACT_AKiii-YclM-BS_2 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. B. subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from B. subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=58.88 E-value=13 Score=24.83 Aligned_cols=26 Identities=27% Similarity=0.335 Sum_probs=23.1
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
+++.||.+.++++.+++.|||+-.|.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~i~v~~i~ 36 (66)
T cd04916 11 MKNTVGVSARATAALAKAGINIRMIN 36 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 46789999999999999999997774
No 178
>TIGR00719 sda_beta L-serine dehydratase, iron-sulfur-dependent, beta subunit. This family of enzymes is not homologous to the pyridoxal phosphate-dependent threonine deaminases and eukaryotic serine deaminases.
Probab=58.82 E-value=15 Score=31.61 Aligned_cols=33 Identities=18% Similarity=0.267 Sum_probs=28.3
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeee
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
-.+|++.=.|+||.+.++-..|.+++||+....
T Consensus 148 g~~L~~~~~D~PG~Ig~vg~~Lg~~~iNIa~m~ 180 (208)
T TIGR00719 148 HPAILLEHNDKFGTIAGVANLLAGFEINIEHLE 180 (208)
T ss_pred ccEEEEEeCCCCChHHHHHHHHHhCCccEEEEE
Confidence 346777778999999999999999999997653
No 179
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=58.62 E-value=30 Score=29.84 Aligned_cols=50 Identities=10% Similarity=0.126 Sum_probs=37.6
Q ss_pred CccEEEEeCCCCcHHHHHHHhhCC--CCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDAALKAYP--NCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~~--~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
...+||+ +.|+..+.-....+. +.+++...+.++++++|.+|++|+.+..
T Consensus 132 ~g~~Igv--~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 132 KGKHVGV--LQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred CCCEEEE--ecCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeC
Confidence 4467887 478776554444333 3678889999999999999999998864
No 180
>PF12916 DUF3834: Protein of unknown function (DUF3834); InterPro: IPR024533 This family is likely to be related to solute-binding lipo-proteins.; PDB: 3MST_A.
Probab=58.28 E-value=20 Score=30.87 Aligned_cols=72 Identities=22% Similarity=0.194 Sum_probs=43.2
Q ss_pred CccEEEEeCCCCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccc-cccccCCeEE
Q 036073 12 TKVRISFKGSPGSFTEDAALKAYP----NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNY-DLLLRHRLHI 86 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~~----~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~-d~L~~~~l~I 86 (241)
+..||++.= +||=.+.=++.+.. ..+++..++..++++++++|++|-|||+-+ +.. .+++ |+|.+.++++
T Consensus 67 ~~~rI~vwR-kGsaADvl~Ral~d~~~~~~EvVytdD~~~i~~Ml~~g~vdsAVv~~~--~~~--G~~fEdl~~~~g~~~ 141 (201)
T PF12916_consen 67 GKPRIAVWR-KGSAADVLTRALLDLKGIKAEVVYTDDMSEIVKMLNEGEVDSAVVGSE--FSK--GETFEDLLGSLGLYA 141 (201)
T ss_dssp TSSEEEESS-TTSHHHHHHHHHHHHH--T-EEEE---HHHHHHHHHTT-E--EEEETT--T-----EEHHHHHHHTT---
T ss_pred CCceEEEEe-cccHHHHHHHHHHhhccccceeEEecCHHHHHHHHhcCceeeeeecch--hcc--chhHHHHHhhcCCCC
Confidence 446888885 89988877665542 479999999999999999999999999943 332 3444 4556677766
Q ss_pred EE
Q 036073 87 VG 88 (241)
Q Consensus 87 ~~ 88 (241)
=|
T Consensus 142 Pg 143 (201)
T PF12916_consen 142 PG 143 (201)
T ss_dssp --
T ss_pred Ch
Confidence 43
No 181
>cd08468 PBP2_Pa0477 The C-terminal substrate biniding domain of an uncharacterized LysR-like transcriptional regulator Pa0477 related to DntR, contains the type 2 periplasmic binding fold. LysR-type transcriptional regulator Pa0477 is related to DntR, which controls genes encoding enzymes for oxidative degradation of the nitro-aromatic compound 2,4-dinitrotoluene. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their spec
Probab=57.82 E-value=92 Score=24.53 Aligned_cols=32 Identities=13% Similarity=-0.113 Sum_probs=24.5
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEee
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPi 64 (241)
.+|+.++... .+-.++.+.+.+|++|+|++.-
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (202)
T cd08468 25 LAPSVRLNLVHAEQKLPLDALLAGEIDFALGYS 57 (202)
T ss_pred hCCCCEEEEEECChHhHHHHHHCCCccEEEecc
Confidence 3577665444 4678999999999999999753
No 182
>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....
Probab=57.57 E-value=1.1e+02 Score=25.22 Aligned_cols=105 Identities=12% Similarity=0.020 Sum_probs=65.2
Q ss_pred CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcC---Ce--eE
Q 036073 37 CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREE---KL--KC 111 (241)
Q Consensus 37 ~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~---~i--~~ 111 (241)
.+++...+-.++++++.+|++|+|+......+ ...=...++++++...-.-...|+++++..++ |+ |+
T Consensus 23 ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~-------~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DLkGK~ 95 (216)
T PF09084_consen 23 VEIVFFGGGGDVLEALASGKADIAVAGPDAVL-------FARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADLKGKK 95 (216)
T ss_dssp EEEEEESSHHHHHHHHHTTSHSEEEEECHHHH-------HHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGGTTSE
T ss_pred EEEEEecChhHHHHHHhcCCceEEeccchHHH-------HHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHhCCCE
Confidence 68899999999999999999999997644222 11112356788877665555678877764333 33 36
Q ss_pred EEecH--HHHHHHHHHHHhcCC-----ceEeccCHHHHHHHHHhc
Q 036073 112 VLSHP--QALASSDIVQTQLGV-----ARENIDDTASAAQYVASN 149 (241)
Q Consensus 112 V~SHp--qal~Qc~~fl~~~~~-----~~~~~~sTa~Aa~~v~~~ 149 (241)
|...+ .....-+.+|+++++ +.+.. +....+..+.++
T Consensus 96 i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~-~~~~~~~al~~g 139 (216)
T PF09084_consen 96 IGVSRGSSSEYFLRALLKKNGIDPDDVKIVNL-GPPELAQALLSG 139 (216)
T ss_dssp EEESTTSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTT
T ss_pred EEEecCcchhHHHHHHHHHhccccccceeeee-ehhhhhhhhhcC
Confidence 66555 344556677877654 33333 345555555554
No 183
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=57.50 E-value=49 Score=31.86 Aligned_cols=50 Identities=20% Similarity=0.177 Sum_probs=33.7
Q ss_pred ccEEEEeCCCCcHHH----------HHHHhhC---C-CCceeecCCHHHHHHHHHcCCcceEEE
Q 036073 13 KVRISFKGSPGSFTE----------DAALKAY---P-NCETIPCDEFEEAFKAVELWLAEKAIL 62 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~----------~Aa~~~~---~-~~~~~~~~s~~~v~~av~~g~~d~gVv 62 (241)
..+|++..++.+|-. .-++.+. + ..+++...++++++.++++|++|+++.
T Consensus 44 ~LrVg~~~~P~~~~~~~~~~~G~~~DLl~~ia~~LGv~~e~v~~~~~~~ll~aL~~G~iDi~~~ 107 (482)
T PRK10859 44 ELRVGTINSPLTYYIGNDGPTGFEYELAKRFADYLGVKLEIKVRDNISQLFDALDKGKADLAAA 107 (482)
T ss_pred EEEEEEecCCCeeEecCCCcccHHHHHHHHHHHHhCCcEEEEecCCHHHHHHHHhCCCCCEEec
Confidence 467887766665532 1122221 2 356777889999999999999997653
No 184
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=57.50 E-value=19 Score=32.40 Aligned_cols=50 Identities=16% Similarity=0.183 Sum_probs=39.1
Q ss_pred CccEEEEeCCCCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDAALKAYP----NCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~~----~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
...+||. ..||.++...+.+.+ +.+++.+.+.++++++|.+|++|+.+..
T Consensus 152 ~Gk~V~v--~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~d 205 (302)
T PRK10797 152 KGKAVVV--TSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMD 205 (302)
T ss_pred CCCEEEE--eCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEcc
Confidence 3457876 478887776665543 4678999999999999999999998753
No 185
>cd04921 ACT_AKi-HSDH-ThrA-like_1 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the first of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pat
Probab=57.27 E-value=21 Score=24.91 Aligned_cols=27 Identities=19% Similarity=0.304 Sum_probs=23.3
Q ss_pred ecCCCchHHHHHHHHHHHCCceeeeee
Q 036073 208 TLDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 208 ~~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
.+.+.+|.+.++++.|++.+||+-.+.
T Consensus 10 ~~~~~~~~~~~i~~~L~~~~I~v~~i~ 36 (80)
T cd04921 10 GMVGVPGIAARIFSALARAGINVILIS 36 (80)
T ss_pred CCCCCccHHHHHHHHHHHCCCcEEEEE
Confidence 346789999999999999999997664
No 186
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=56.05 E-value=1.4e+02 Score=25.94 Aligned_cols=114 Identities=8% Similarity=-0.027 Sum_probs=57.7
Q ss_pred hCCCCcee-ecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCC-ee
Q 036073 33 AYPNCETI-PCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEK-LK 110 (241)
Q Consensus 33 ~~~~~~~~-~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~-i~ 110 (241)
.+|+.++. -.....++++.+.+|++|+|+........+ +..+......+++++.++..+.. -.
T Consensus 114 ~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~---------------l~~~~l~~~~~~~v~~~~~~~~~~~~ 178 (275)
T PRK03601 114 NQEALQFEARIAQRQSLVKQLHERQLDLLITTEAPKMDE---------------FSSQLLGHFTLALYTSAPSKKKSELN 178 (275)
T ss_pred hCCCcEEEEEECChHHHHHHHHcCCCCEEEEcCCCccCC---------------ccEEEecceeEEEEecCchhhcccCC
Confidence 45776653 355677899999999999999753321111 11222222334444443321111 11
Q ss_pred EE-EecHHHHHHHHHHHHhcCC-ceEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 111 CV-LSHPQALASSDIVQTQLGV-ARENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 111 ~V-~SHpqal~Qc~~fl~~~~~-~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
.| +..+..+.+-..++...+. ....++|.....+.++.+ ...++++...++
T Consensus 179 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~~~p~~~~~ 231 (275)
T PRK03601 179 YIRLEWGADFQQHEAGLIGADEVPILTTSSAELARQLLATL---NGCAFLPVHWAK 231 (275)
T ss_pred eEEccCCccHhHHHHHhcccCCcceEEeCcHHHHHHHHHhC---CCEEEEcHHHHh
Confidence 11 1122223322222222222 235566777777777764 457888887664
No 187
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=55.76 E-value=99 Score=24.30 Aligned_cols=122 Identities=13% Similarity=0.032 Sum_probs=61.6
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeee-cccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCc---C
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIE-NSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIRE---E 107 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiE-NS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~---~ 107 (241)
.+|+.++... .+-.++.+.+.+|++|+|+..-. +...+.. ...|.+..+. +..+..|-|...+..++ .
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~~l~~~~~~----~~~~~~hpl~~~~~~~~~~l~ 97 (198)
T cd08444 25 QFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPELV---SFPYYDWHHH----IIVPVGHPLESITPLTIETIA 97 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEeccccCCCcCcE---Eeecccccee----EEecCCCccccCCCcCHHHHh
Confidence 3577655443 35678899999999999997411 0011110 1111122211 23344454443222233 3
Q ss_pred CeeEEEecHH-H-HHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 108 KLKCVLSHPQ-A-LASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 108 ~i~~V~SHpq-a-l~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+...|.-++. . -.++.+|+.+.+. +. ..++|.....+++.++ ...++.+...++
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08444 98 KWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLG---MGIGIVAEMAFE 156 (198)
T ss_pred CCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcC---CcEEeccHHHHh
Confidence 3444443322 1 2345677776554 22 3456666666666653 346777776554
No 188
>cd08425 PBP2_CynR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator CynR, contains the type 2 periplasmic binding fold. CynR is a LysR-like transcriptional regulator of the cyn operon, which encodes genes that allow cyanate to be used as a sole source of nitrogen. The operon includes three genes in the following order: cynT (cyanate permease), cynS (cyanase), and cynX (a protein of unknown function). CynR negatively regulates its own expression independently of cyanate. CynR binds to DNA and induces bending of DNA in the presence or absence of cyanate, but the amount of bending is decreased by cyanate. The CynR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding
Probab=55.42 E-value=96 Score=24.03 Aligned_cols=121 Identities=16% Similarity=0.032 Sum_probs=60.0
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCC-CCCcCCee-
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALP-GIREEKLK- 110 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~-g~~~~~i~- 110 (241)
+|+.++... .+..++.+.+.+|++|+|+..-.....+.. ...|.+..+.++ .+-.|-+.... ..+++|+.
T Consensus 27 ~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~dL~~ 99 (197)
T cd08425 27 YPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDID---AQPLFDERLALV----VGATHPLAQRRTALTLDDLAA 99 (197)
T ss_pred CCCcEEEEEECcHHHHHHHHHcCCccEEEEecCCCCCCcE---EEEeccccEEEE----ecCCCchhHhcccCCHHHHhc
Confidence 566554433 356789999999999999975332111111 112222232222 22233332221 13333332
Q ss_pred --EEE-ec-HHHHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 111 --CVL-SH-PQALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 111 --~V~-SH-pqal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
-|. .. ........+|+.+.+.. . ..++|.......++++ ...++.+...++
T Consensus 100 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08425 100 EPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRG---RLATILPDAIAR 157 (197)
T ss_pred CCcEecCCCccHHHHHHHHHHHcCCCeeeEEeeCcHHHHHHHHhcC---CcEEeechhhhc
Confidence 232 11 12233456677766543 2 3456666666666654 346777776543
No 189
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=54.91 E-value=67 Score=27.34 Aligned_cols=113 Identities=12% Similarity=0.131 Sum_probs=63.9
Q ss_pred CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccc-cCCeEEEEEEEE-----eeeeeeecCCCC---CcC
Q 036073 37 CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLL-RHRLHIVGEVQF-----VANFCLLALPGI---REE 107 (241)
Q Consensus 37 ~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~-~~~l~I~~E~~l-----~I~~~L~~~~g~---~~~ 107 (241)
.++++..++.+..+++.+|++|+++++-. .+-.+. +.++..++...- ...-.++++++. +++
T Consensus 31 v~~~~~~~~~~~~~~l~~g~~D~~~~~~~---------~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds~i~~l~ 101 (243)
T PF12974_consen 31 VELVPADDYAEFIEALRSGEIDLAFMGPL---------PYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADSPITSLA 101 (243)
T ss_dssp EEEE--SSHHHHHHHHHTTS-SEEE--HH---------HHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTSS--SHH
T ss_pred EEEEEcCCHHHHHHHHHcCCccEEEECcH---------HHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCCCCCChh
Confidence 67899999999999999999999997611 222222 346666666655 334456666654 344
Q ss_pred Ce---eEEEecHHH---HHHHHHHH-HhcCC------ceEeccCHHHHHHHHHhcCCCCeEEecC
Q 036073 108 KL---KCVLSHPQA---LASSDIVQ-TQLGV------ARENIDDTASAAQYVASNGLRDAGVVAS 159 (241)
Q Consensus 108 ~i---~~V~SHpqa---l~Qc~~fl-~~~~~------~~~~~~sTa~Aa~~v~~~~~~~~aAI~s 159 (241)
|+ +-.+..|.. .--.+.+| ++.|+ +.+.+.+-..+++.+..+ .-+.+++.+
T Consensus 102 dL~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G-~~Da~~~~~ 165 (243)
T PF12974_consen 102 DLKGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNG-KADAAAIPS 165 (243)
T ss_dssp HHGGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTT-SSSEEEEEH
T ss_pred hcCCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcC-CccEEEEec
Confidence 55 334555553 34456667 56543 445666777778887765 344455444
No 190
>PRK03381 PII uridylyl-transferase; Provisional
Probab=54.70 E-value=20 Score=36.95 Aligned_cols=33 Identities=12% Similarity=0.216 Sum_probs=28.8
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeee
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
.|.|.+..+|+||-|+++-+.|+..|+|+..-.
T Consensus 707 ~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~Ak 739 (774)
T PRK03381 707 ATVLEVRAADRPGLLARLARALERAGVDVRWAR 739 (774)
T ss_pred eEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEE
Confidence 577777889999999999999999999997643
No 191
>cd08443 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding speci
Probab=53.77 E-value=1.1e+02 Score=24.14 Aligned_cols=123 Identities=15% Similarity=0.041 Sum_probs=59.6
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCeeE
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLKC 111 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~~ 111 (241)
.+|+.++.-. .+..++.+.+.+|++|+|+..-.-.....+ ....|.+.++.++ .+-+|-+......+++++..
T Consensus 25 ~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~--~~~~l~~~~~~~v----~~~~hpl~~~~~i~~~~l~~ 98 (198)
T cd08443 25 RYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDL--ITLPCYHWNRCVV----VKRDHPLADKQSISIEELAT 98 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccccccCCc--eEeeeeeceEEEE----EcCCCccccCCCCCHHHHhc
Confidence 4677655443 467889999999999999974210001111 0111222233222 22234443322233333331
Q ss_pred --EEecHH--H-HHHHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 112 --VLSHPQ--A-LASSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 112 --V~SHpq--a-l~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
..+.+. . .....+|+++.+.. ...+++.....+.++.+ ...|+.+...++
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~~p~~~~~ 156 (198)
T cd08443 99 YPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLG---LGVGVIASMAYD 156 (198)
T ss_pred CCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CcEEEeeccccc
Confidence 222222 2 22334556555543 23456666666666654 346666665443
No 192
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=53.76 E-value=1.5e+02 Score=25.78 Aligned_cols=118 Identities=13% Similarity=-0.040 Sum_probs=58.0
Q ss_pred CCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe---e
Q 036073 34 YPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL---K 110 (241)
Q Consensus 34 ~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i---~ 110 (241)
+|+.++....+ +..+.+.+|++|+|++..+....|.... .|.+..+.++ .+-.|.+......+++|+ .
T Consensus 120 ~p~i~i~l~~~--~~~~~l~~g~~Dl~i~~~~~~~~~l~~~---~l~~~~~~~~----~~~~~~~~~~~~i~~~dL~~~p 190 (297)
T PRK11139 120 HPDIDVRLKAV--DRLEDFLRDDVDVAIRYGRGNWPGLRVE---KLLDEYLLPV----CSPALLNGGKPLKTPEDLARHT 190 (297)
T ss_pred CCCceEEEEeC--CChhhhccCCCCEEEEeCCCCCCCceEE---EeccceeEEE----eCHHHhcccCCCCCHHHhhcCc
Confidence 46644333222 3357788999999998765433332211 2223333322 233343333333344433 3
Q ss_pred EEEecHHHHHHHHHHHHhcCC---c---eEeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 111 CVLSHPQALASSDIVQTQLGV---A---RENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 111 ~V~SHpqal~Qc~~fl~~~~~---~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
.|...+ .....+|+...+. . ...+++...+...+..+ ...++.+...++.
T Consensus 191 ~i~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 246 (297)
T PRK11139 191 LLHDDS--REDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG---QGVALGNRVLAQP 246 (297)
T ss_pred eEeecC--cccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhC---CCeEecchhhhHH
Confidence 343322 2345667776433 2 23455555555555543 3567777766654
No 193
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=53.59 E-value=1e+02 Score=23.71 Aligned_cols=31 Identities=16% Similarity=0.118 Sum_probs=23.3
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEee
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPi 64 (241)
+|+.++.-. .+..++.+.+.+|++|+|++.-
T Consensus 26 ~p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08414 26 YPDVELELREMTTAEQLEALRAGRLDVGFVRP 57 (197)
T ss_pred CCCcEEEEecCChHHHHHHHHcCCccEEEEcC
Confidence 466555433 3568899999999999999853
No 194
>cd04892 ACT_AK-like_2 ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the second of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). The exception in this group, is the inclusion of the first ACT domain of the bifunctional aspartokinase - homoserine dehydrogenase-like enzyme group (ACT_AKi-HSDH-ThrA-like_1) which includes the monofunctional, threonine-sensitive, aspartokinase found in Methanococcus jannaschii and other related archaeal species. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. AK is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. One mechanism for the regulation of this pathway is by the production of several isoenzymes of AK with different repressors an
Probab=53.52 E-value=18 Score=23.33 Aligned_cols=26 Identities=23% Similarity=0.409 Sum_probs=23.0
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
..+.+|.+.++++.|++++|++-.+.
T Consensus 10 ~~~~~~~~~~i~~~l~~~~i~v~~i~ 35 (65)
T cd04892 10 MRGTPGVAARIFSALAEAGINIIMIS 35 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEE
Confidence 45789999999999999999998874
No 195
>PRK03059 PII uridylyl-transferase; Provisional
Probab=53.24 E-value=22 Score=37.14 Aligned_cols=32 Identities=16% Similarity=0.256 Sum_probs=28.7
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
+.|.|.+..+|+||-|+++-++|+..|+|+..
T Consensus 785 ~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~ 816 (856)
T PRK03059 785 QYYILSVSANDRPGLLYAIARVLAEHRVSVHT 816 (856)
T ss_pred CEEEEEEEeCCcchHHHHHHHHHHHCCCeEEE
Confidence 46778788899999999999999999999864
No 196
>cd08420 PBP2_CysL_like C-terminal substrate binding domain of LysR-type transcriptional regulator CysL, which activates the transcription of the cysJI operon encoding sulfite reductase, contains the type 2 periplasmic binding fold. CysL, also known as YwfK, is a regular of sulfur metabolism in Bacillus subtilis. Sulfur is required for the synthesis of proteins and essential cofactors in all living organism. Sulfur can be assimilated either from inorganic sources (sulfate and thiosulfate), or from organic sources (sulfate esters, sulfamates, and sulfonates). CysL activates the transcription of the cysJI operon encoding sulfite reductase, which reduces sulfite to sulfide. Both cysL mutant and cysJI mutant are unable to grow using sulfate or sulfite as the sulfur source. Like other LysR-type regulators, CysL also negatively regulates its own transcription. In Escherichia coli, three LysR-type activators are involved in the regulation of sulfur metabolism: CysB, Cbl and MetR. The topology
Probab=52.57 E-value=1e+02 Score=23.57 Aligned_cols=121 Identities=14% Similarity=0.089 Sum_probs=60.9
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCC---e
Q 036073 34 YPNCETIP-CDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEK---L 109 (241)
Q Consensus 34 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~---i 109 (241)
+|+.++.. ..+..++.+++.+|++|+|++.......+.. ...|.+..+.++ .+-.|-+......++++ .
T Consensus 26 ~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~~~~~~~~i~~~~l~~~ 98 (201)
T cd08420 26 YPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLI---VEPFAEDELVLV----VPPDHPLAGRKEVTAEELAAE 98 (201)
T ss_pred CCCceEEEEeCCcHHHHHHHHCCCccEEEecCCCCCcceE---EEeecCccEEEE----ecCCCCccccCccCHHHHhcC
Confidence 56655433 3466789999999999999985433222211 112223333332 22233332222222333 3
Q ss_pred eEEEecHH--HHHHHHHHHHhcC-----Cc-eEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 110 KCVLSHPQ--ALASSDIVQTQLG-----VA-RENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 110 ~~V~SHpq--al~Qc~~fl~~~~-----~~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
..|.-.+. -..+..+|+.+.+ .. ...+++...+.+.++++ ...++.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08420 99 PWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAG---LGISILSRLAVR 158 (201)
T ss_pred CEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcC---CCEEEeeHHHHH
Confidence 33332221 1234556666432 12 24456666666677653 457888876654
No 197
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=52.54 E-value=1e+02 Score=23.55 Aligned_cols=33 Identities=12% Similarity=0.051 Sum_probs=24.4
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeee
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIE 65 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiE 65 (241)
.+|+.++.-. .+-.++.+.+.+|++|+|+..-.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (194)
T cd08436 25 RHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLP 58 (194)
T ss_pred HCCCcEEEEecCCHHHHHHHHHcCCccEEEEecC
Confidence 4577655433 35678999999999999998643
No 198
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=52.25 E-value=1.2e+02 Score=24.02 Aligned_cols=32 Identities=13% Similarity=-0.060 Sum_probs=24.5
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCcceEEEeee
Q 036073 34 YPNCETIP-CDEFEEAFKAVELWLAEKAILPIE 65 (241)
Q Consensus 34 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiE 65 (241)
+|+.++.. ..+..++++.+.+|++|+|+...+
T Consensus 26 ~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~ 58 (200)
T cd08465 26 APGIDLAVSQASREAMLAQVADGEIDLALGVFP 58 (200)
T ss_pred CCCcEEEEecCChHhHHHHHHCCCccEEEeccc
Confidence 57766533 346789999999999999997543
No 199
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=51.29 E-value=18 Score=33.32 Aligned_cols=52 Identities=8% Similarity=-0.043 Sum_probs=39.1
Q ss_pred CCCCccEEEEeCCCCcHHHHHHHhhCC-------CCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 9 NDGTKVRISFKGSPGSFTEDAALKAYP-------NCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 9 ~~~~~~~ia~LGp~GtfS~~Aa~~~~~-------~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
.+-.-.|||+ +.||.+|....+.+. +.++++.. ..+...++.+|++|.++++
T Consensus 102 aDLKGKkIav--~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~-~~d~~aAl~~G~VDAa~~~ 160 (328)
T TIGR03427 102 ADLKGQKVNL--VELSVSHYLLARALESVGLSEKDVKVVNTS-DADIVAAFITKDVTAVVTW 160 (328)
T ss_pred HHcCCCEEec--cCCChHHHHHHHHHHHcCCCHHHeEEEeCC-hHHHHHHHhcCCCcEEEEc
Confidence 3445578997 689999966555431 36788875 4889999999999999874
No 200
>PRK09224 threonine dehydratase; Reviewed
Probab=51.23 E-value=18 Score=35.28 Aligned_cols=35 Identities=23% Similarity=0.294 Sum_probs=29.8
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
+.-.+.|..|.|||+|.+.|+.+. -+-|+|.+|=|
T Consensus 422 ~e~~~~~~fPerpGal~~Fl~~l~-~~~~It~f~Yr 456 (504)
T PRK09224 422 DERLYRFEFPERPGALLKFLSTLG-THWNISLFHYR 456 (504)
T ss_pred ceEEEEEeCCCCCCHHHHHHHhcC-CCCeeEEEEEc
Confidence 455677899999999999999887 77899988865
No 201
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.12 E-value=12 Score=34.59 Aligned_cols=93 Identities=17% Similarity=0.040 Sum_probs=61.3
Q ss_pred CCCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccc---cCCeEE------E
Q 036073 21 SPGSFTEDAALKAYP----NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLL---RHRLHI------V 87 (241)
Q Consensus 21 p~GtfS~~Aa~~~~~----~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~---~~~l~I------~ 87 (241)
-.||+.|.+...++. +.+.+|++...+++.++..|++|.++.=+-++....=.-++.+|. +..+.. .
T Consensus 157 g~Gs~dhl~~~~~~k~~Gi~~~~Vpy~g~gea~taLlgg~v~a~~~~~se~~~~vksG~lr~Lav~s~eRl~~~pdvPT~ 236 (319)
T COG3181 157 GLGSADHLAGALFAKAAGIKITYVPYKGGGEALTALLGGHVDAGSTNLSELLSQVKSGTLRLLAVFSEERLPGLPDVPTL 236 (319)
T ss_pred CCCcHHHHHHHHHHHHhCCceeEEeecCccHHHHHHhcCceeeeecChhhhhhhhccCceEEEEeechhhcCCCCCCCCh
Confidence 368999999887663 468899999999999999999999987654333322222445443 111111 1
Q ss_pred EE----EEEeeeeeeecCCCCCcCCeeEEE
Q 036073 88 GE----VQFVANFCLLALPGIREEKLKCVL 113 (241)
Q Consensus 88 ~E----~~l~I~~~L~~~~g~~~~~i~~V~ 113 (241)
.| +.+++.+.+.+.+|++.+.|.++.
T Consensus 237 ~E~G~~~~~~~wrgvfap~g~~~e~~~~~~ 266 (319)
T COG3181 237 KEQGYDVVMSIWRGVFAPAGTPDEIIAKLS 266 (319)
T ss_pred HhcCCceeeeeeeEEEeCCCCCHHHHHHHH
Confidence 11 226777888888998765555443
No 202
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=50.98 E-value=1.1e+02 Score=23.60 Aligned_cols=122 Identities=19% Similarity=0.090 Sum_probs=60.1
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcC---C
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREE---K 108 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~---~ 108 (241)
.+|+.++... .+-.++.+.+.+|++|+|+..-.+...+. ....|.+..+.++ .+-+|-+...+..+++ +
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~---~~~~l~~~~~~~~----~~~~~~~~~~~~~~~~~l~~ 97 (198)
T cd08433 25 RYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGL---STEPLLEEDLFLV----GPADAPLPRGAPVPLAELAR 97 (198)
T ss_pred HCCCcEEEEEecCcHHHHHHHhCCCCcEEEEeCCCCCCCe---eEEEeccccEEEE----ecCCCccccCCCCCHHHhCC
Confidence 3566655443 35678899999999999997432221111 1111222222221 2233333222222322 2
Q ss_pred eeEEE-ecHHH-HHHHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 109 LKCVL-SHPQA-LASSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 109 i~~V~-SHpqa-l~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
...|. .+... .....+|+.+.+.+ ...++|...+.+.++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08433 98 LPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAG---LGYTILPASAVA 155 (198)
T ss_pred CceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcC---CcEEEcchhhhh
Confidence 23332 22222 23455666665543 24466666666677653 356777766543
No 203
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=50.85 E-value=1.1e+02 Score=23.54 Aligned_cols=120 Identities=14% Similarity=0.062 Sum_probs=60.5
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEeeeccc--ccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSS--GGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK 110 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~--~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~ 110 (241)
+|+.++... .+..++.+.+.+|++|+|+....... .+. ....|.+..+.++.- -+|-+.. + .+++++.
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~~~l~~~~~~~v~~----~~~~~~~-~-~~~~~l~ 96 (201)
T cd08418 26 FPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKEL---ISEPLFESDFVVVAR----KDHPLQG-A-RSLEELL 96 (201)
T ss_pred CCCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCCCCcce---eEEeecCCceEEEeC----CCCcccc-C-CCHHHHc
Confidence 566554433 35678999999999999997432111 111 111222333333222 1222211 1 1233332
Q ss_pred ---EEEec--HHHHHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 111 ---CVLSH--PQALASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 111 ---~V~SH--pqal~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
.|... ........+|+.+.+. +. ..++|......+++++ ...|+.+...++.
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 156 (201)
T cd08418 97 DASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKA---DFLTILSRDMGRG 156 (201)
T ss_pred CCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhC---CEEEEeEHHHhhh
Confidence 23321 2233445667766543 22 4456666666777754 4578888776653
No 204
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=50.79 E-value=48 Score=28.48 Aligned_cols=50 Identities=10% Similarity=0.131 Sum_probs=36.7
Q ss_pred CccEEEEeCCCCcHHHHHHHhhC--CCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDAALKAY--PNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~--~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
...+||+. .|++.++-...++ .+.+++...+.++++++|.+|++|+.+..
T Consensus 132 ~g~~Igv~--~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~ 183 (259)
T PRK15437 132 KGKRVGVL--QGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQD 183 (259)
T ss_pred CCCEEEEe--cCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEec
Confidence 44678874 5776554444333 24678899999999999999999998753
No 205
>TIGR00656 asp_kin_monofn aspartate kinase, monofunctional class. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. The protein slr0657 from Synechocystis PCC6803 is extended by a duplication of the C-terminal region corresponding to the beta chain. Incorporation of a second copy of the C-terminal domain may be quite common in this subgroup of aspartokinases.
Probab=50.51 E-value=81 Score=29.45 Aligned_cols=96 Identities=18% Similarity=0.102 Sum_probs=57.9
Q ss_pred CceEeccCHHHHHHHHHhcCCCCeEEecCHh---hHHhcCCceeecccCCCCCCceeEEEEeeCCCC-CC-C---CCCce
Q 036073 131 VARENIDDTASAAQYVASNGLRDAGVVASAR---AAEIYGLNILADRIQDDPDNITRFLVLARDPIM-PR-T---DKPFK 202 (241)
Q Consensus 131 ~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~---aa~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~-~~-~---~~~~k 202 (241)
++.+..-|..+|.++...+ +-+-.+. .|..++.++.-.+..+.. --|.. .+.... +. . ...+.
T Consensus 190 a~~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~a~~~~i~i~i~~~~~~~-~gT~I---~~~~~~~~~v~~I~~~~~v 260 (401)
T TIGR00656 190 AKRIDKISYEEALELATFG-----AKVLHPRTVEPAMRSGVPIEVRSSFDPE-EGTLI---TNSMENPPLVKGIALRKNV 260 (401)
T ss_pred cEECCccCHHHHHHHHHcC-----CcccCHHHHHHHHHCCCeEEEEECCCCC-CCeEE---EeCcccCCceEEEEEECCE
Confidence 3455666777787776542 2233333 345689998887765533 23333 222111 10 0 11234
Q ss_pred EEEEEe---cCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 203 TSIVFT---LDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 203 tsi~~~---~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
+.+.+. +.++||.+.++++.|++++||+-.|..
T Consensus 261 a~vsv~g~~~~~~~g~~~~if~~L~~~~I~i~~i~~ 296 (401)
T TIGR00656 261 TRVTVHGLGMLGKRGFLARIFGALAERNINVDLISQ 296 (401)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHcCCcEEEEEc
Confidence 444443 678999999999999999999988765
No 206
>PRK04374 PII uridylyl-transferase; Provisional
Probab=50.43 E-value=26 Score=36.75 Aligned_cols=32 Identities=19% Similarity=0.422 Sum_probs=28.6
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
+.|.|.+..+|+||-|+++-++|+..|+|+..
T Consensus 795 ~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~ 826 (869)
T PRK04374 795 RRTRISLVAPDRPGLLADVAHVLRMQHLRVHD 826 (869)
T ss_pred CeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEE
Confidence 46777788899999999999999999999864
No 207
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=50.18 E-value=1.4e+02 Score=26.38 Aligned_cols=125 Identities=10% Similarity=-0.020 Sum_probs=60.9
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCcceEEEeeeccc----ccce----eccccccccCCeEEEEEEEEeeeeeeecCCCC
Q 036073 33 AYPNCETIPCDEFEEAFKAVELWLAEKAILPIENSS----GGSI----HHNYDLLLRHRLHIVGEVQFVANFCLLALPGI 104 (241)
Q Consensus 33 ~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~----~G~V----~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~ 104 (241)
.+|+.++.....-.++.+.+.+|++|+|++. .+.. .|.. ......|.+..+. +.++-+|-+.. ...
T Consensus 122 ~~P~v~v~i~~~~~~~~~~l~~g~~D~~i~~-~~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~v~~~~hp~~~-~~~ 195 (319)
T PRK10216 122 RYPQATIKLRNWDYDSLDAITRGEVDIGFTG-RESHPRSRELLSLLPLAIDFEVLFSDLPC----VWLRKDHPALH-EEW 195 (319)
T ss_pred HCCCCEEEEEeCCcchHHHHhcCCccEEEec-CCCCccccccccccccccceeeeeecceE----EEEeCCCCccC-CCC
Confidence 3576544333322357899999999999984 2111 1110 0011111122222 22344454322 222
Q ss_pred CcCCe---eEEEecH--HHHHHHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 105 REEKL---KCVLSHP--QALASSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 105 ~~~~i---~~V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+++|+ ..|.--+ ....+..+++.+.+.+ ...++|.......++.++ ....+|.+..+++
T Consensus 196 ~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~-~~gi~ilp~~~~~ 262 (319)
T PRK10216 196 NLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPEFEQSLFMAAQPD-HLLLATAPRYCQY 262 (319)
T ss_pred CHHHHhhCCCeEecCCCCCcchHHHHHHHhCCccceEEECCcHHHHHHHHHcCC-cceEeccHHHHHH
Confidence 33332 2333211 1233567777776543 345667777777777531 2357888886543
No 208
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=50.13 E-value=1.2e+02 Score=23.50 Aligned_cols=122 Identities=13% Similarity=0.008 Sum_probs=59.1
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee-
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK- 110 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~- 110 (241)
.+|+.++.-.. +-.++.+.+.+|++|+|+..-.....+. ....|.+..+.++ .+-+|-+. ....+++++.
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~~~~-~~~~~~~~l~~ 96 (200)
T cd08464 25 EAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWL---KREVLYTEGYACL----FDPQQLSL-SAPLTLEDYVA 96 (200)
T ss_pred HCCCcEEEEecCCcccHHHHHhcCcccEEEecCCCCcccc---eeeeecccceEEE----EeCCCccc-cCCCCHHHHhc
Confidence 35776654443 4557789999999999997532111111 1112223333222 22223221 1122333322
Q ss_pred --EE-EecHHH-HHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 111 --CV-LSHPQA-LASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 111 --~V-~SHpqa-l~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
.+ +.+... .....+|+.+.+.. . ..++|.......+..+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 155 (200)
T cd08464 97 RPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGT---PLIATVPARLARA 155 (200)
T ss_pred CCcEEecCCCCCcchHHHHHHHcCCCcceEEEcCchhhHHHHHcCC---CceeecHHHHHHH
Confidence 22 222111 23345677766543 2 3445555444555443 4588999887764
No 209
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=49.80 E-value=27 Score=29.21 Aligned_cols=33 Identities=21% Similarity=0.317 Sum_probs=27.7
Q ss_pred EEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 204 SIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 204 si~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+..+..+.||-|..+++.+++|||+..-+-|+
T Consensus 97 ei~~~~~~~pgi~A~V~~~iak~gi~Irqi~~~ 129 (167)
T COG2150 97 EIYPEDARYPGILAGVASLIAKRGISIRQIISE 129 (167)
T ss_pred EEEeccCCCccHHHHHHHHHHHcCceEEEEecC
Confidence 344445689999999999999999999888775
No 210
>cd08416 PBP2_MdcR The C-terminal substrate-binding domian of LysR-type transcriptional regulator MdcR, which involved in the malonate catabolism contains the type 2 periplasmic binding fold. This family includes the C-terminal substrate binding domain of LysR-type transcriptional regulator (LTTR) MdcR that controls the expression of the malonate decarboxylase (mdc) genes. Like other members of the LTTRs, MdcR is a positive regulatory protein for its target promoter and composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins (PBP2). The PBP2 are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these dom
Probab=49.04 E-value=1.2e+02 Score=23.38 Aligned_cols=122 Identities=15% Similarity=0.051 Sum_probs=60.3
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecc--cccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcC--
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENS--SGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREE-- 107 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS--~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~-- 107 (241)
.+|+.++.-. .+-.++.+.+.+|++|+|+...... -.+.. ...|.+..+.+ ..+-.|-+...+..+++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~l~---~~~l~~~~~~~----v~~~~hp~~~~~~~~~~~L 97 (199)
T cd08416 25 RRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDFE---VVPLFEDDIFL----AVPATSPLAASSEIDLRDL 97 (199)
T ss_pred hCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCCCCCeE---EEEeecceEEE----EECCCCcccccCccCHHHh
Confidence 3577655443 3556789999999999999864321 11111 11122222222 22334444332222333
Q ss_pred -CeeEEE-ecHHH-HHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 108 -KLKCVL-SHPQA-LASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 108 -~i~~V~-SHpqa-l~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+...|. +.... .....+++.+.+. +. ..++|...+.+.++++ ...++.+...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (199)
T cd08416 98 KDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGG---VGYALLPGRIAD 157 (199)
T ss_pred cCCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcC---CcEEEechhhhh
Confidence 333333 22221 2234556665543 22 3456666666667653 346777776554
No 211
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=47.70 E-value=1.3e+02 Score=23.13 Aligned_cols=121 Identities=16% Similarity=0.111 Sum_probs=59.6
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCC---e
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEK---L 109 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~---i 109 (241)
+|+.++... .+-.++.+.+.+|++|+|+..-.....+.. ...|.+..+.++. +-+|-|...+..++++ .
T Consensus 25 ~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~~~----~~~~~l~~~~~~~~~~l~~~ 97 (197)
T cd08419 25 HPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLV---AEPFLDNPLVVIA----PPDHPLAGQKRIPLERLARE 97 (197)
T ss_pred CCCceEEEEECCHHHHHHHHhcCCccEEEecCCCCCCCeE---EEEeccCCEEEEe----cCCCCCcCCCCcCHHHHhCC
Confidence 576655433 467788999999999999974321111111 1122222322221 1222222221222222 2
Q ss_pred eEEEecH--HHHHHHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 110 KCVLSHP--QALASSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 110 ~~V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
..|.-.+ .-..+-.+|+.+.+.+ ...++|...+.+.++++ ...++.+...++
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (197)
T cd08419 98 PFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAG---LGLSVLSLHTLA 154 (197)
T ss_pred CcEEecCCCcHHHHHHHHHHHCCCCcceEEEECCHHHHHHHHHhC---CceEeecHHHHH
Confidence 2333111 1123455666665532 24466666677777764 346777877664
No 212
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=47.66 E-value=1.3e+02 Score=23.17 Aligned_cols=31 Identities=16% Similarity=0.008 Sum_probs=23.5
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEee
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPi 64 (241)
+|+.++... .+..+..+.+.+|++|+|++..
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08449 26 YPNVTVRFHELSPEAQKAALLSKRIDLGFVRF 57 (197)
T ss_pred CCCeEEEEEECCHHHHHHHHhCCCccEEEecc
Confidence 576655433 3578899999999999999754
No 213
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=47.18 E-value=1.3e+02 Score=23.15 Aligned_cols=122 Identities=13% Similarity=0.037 Sum_probs=57.7
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe--
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL-- 109 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i-- 109 (241)
.+|+.++.-.. +-.++.+.+.+|++|+|+..-.....+.. ...|.+..+.+ ..+-+|-+...+..+++++
T Consensus 25 ~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08456 25 RHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIE---RERLLRIDGVC----VLPPGHRLAVKKVLTPSDLEG 97 (196)
T ss_pred HCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCee---EEEeeccCeEE----EecCCCchhccCccCHHHcCC
Confidence 35765544333 45678899999999999975322111111 11122222222 1222333332222233333
Q ss_pred -eEEE-ecHHH-HHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 110 -KCVL-SHPQA-LASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 110 -~~V~-SHpqa-l~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
..|. .+... .....+|+.+.+.. . ..++|...+.+.+.++ ...++.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (196)
T cd08456 98 EPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAG---VGVSVVNPLTAL 155 (196)
T ss_pred CcEEEecCCcchHHHHHHHHHHCCCCcceEEEEccHHHHHHHHHcC---CeEEEeChhhhc
Confidence 3333 22222 22345566655533 2 3445555556666653 356677766554
No 214
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=47.12 E-value=1.7e+02 Score=24.45 Aligned_cols=114 Identities=11% Similarity=0.141 Sum_probs=58.1
Q ss_pred CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCC----CcCCee-
Q 036073 36 NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGI----REEKLK- 110 (241)
Q Consensus 36 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~----~~~~i~- 110 (241)
+.++++ .+..++++++.+|++|+++.++..+.+-. ..+.... -.......++.+++. ++++++
T Consensus 64 ~~~~~~-~~~~~~~~~l~~G~~D~~~~~~~~~~~r~----------~~~~~s~-p~~~~~~~~~~~~~~~~~~~~~dl~g 131 (250)
T TIGR01096 64 KCKFVE-QNFDGLIPSLKAKKVDAIMATMSITPKRQ----------KQIDFSD-PYYATGQGFVVKKGSDLAKTLEDLDG 131 (250)
T ss_pred eEEEEe-CCHHHHHHHHhCCCcCEEEecCccCHHHh----------hcccccc-chhcCCeEEEEECCCCcCCChHHcCC
Confidence 357777 46899999999999999875432221110 0010000 001112223333221 122221
Q ss_pred -EEEecHHHHHHHHHHHHhc---CCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 111 -CVLSHPQALASSDIVQTQL---GVARENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 111 -~V~SHpqal~Qc~~fl~~~---~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
+|-. .....+. .++.+. +.+.+.+.|..++.+.+..+ +-.++|.....+..
T Consensus 132 ~~i~~-~~g~~~~-~~l~~~~~~~~~~~~~~s~~~~~~~L~~g--~vD~~v~~~~~~~~ 186 (250)
T TIGR01096 132 KTVGV-QSGTTHE-QYLKDYFKPGVDIVEYDSYDNANMDLKAG--RIDAVFTDASVLAE 186 (250)
T ss_pred CEEEE-ecCchHH-HHHHHhccCCcEEEEcCCHHHHHHHHHcC--CCCEEEeCHHHHHH
Confidence 2221 1112221 344442 56677788899999988875 44577777665543
No 215
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=46.72 E-value=1.3e+02 Score=23.08 Aligned_cols=31 Identities=19% Similarity=0.066 Sum_probs=23.1
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcceEEEee
Q 036073 34 YPNCETIPCD-EFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 34 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPi 64 (241)
+|+.++.... +-.++.+.+.+|++|+|++.-
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (200)
T cd08423 26 HPGLEVRLREAEPPESLDALRAGELDLAVVFD 57 (200)
T ss_pred CCCCeEEEEeCCHHHHHHHHhcCCccEEEEec
Confidence 4665544333 467889999999999999853
No 216
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=46.13 E-value=2.1e+02 Score=25.14 Aligned_cols=136 Identities=12% Similarity=-0.056 Sum_probs=68.3
Q ss_pred EEEEeCCCCcHHHHHHHh-hCC-----CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEE
Q 036073 15 RISFKGSPGSFTEDAALK-AYP-----NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVG 88 (241)
Q Consensus 15 ~ia~LGp~GtfS~~Aa~~-~~~-----~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~ 88 (241)
+|+|+=.. +--..|-.+ +|. +++++.+.+-.++++++.+|++|+++...... +. ..-...++.++.
T Consensus 2 ~~~~~~~~-~p~~va~~~G~~~k~~Gl~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~~~----~~---a~~~g~~~~~v~ 73 (300)
T TIGR01729 2 TVGYQTIV-EPFKVAQADGAAAKEAGATIDWRKFDSGADISTALASGNVPIGVIGSSPL----AA---AASRGVPIELFW 73 (300)
T ss_pred EEEecCCC-CHHHHHHHcCchHHhcCCeeEEEecCcHHHHHHHHHcCCCCEeccCCCHH----HH---HHHCCCCeEEEE
Confidence 68886322 322333322 331 36788999989999999999999997532110 00 000122344332
Q ss_pred EEE-EeeeeeeecCCCC---CcCCee--EEEecHHH--HHHHHHHHHhcCC-----ceEeccCHHHHHHHHHhcCCCCeE
Q 036073 89 EVQ-FVANFCLLALPGI---REEKLK--CVLSHPQA--LASSDIVQTQLGV-----ARENIDDTASAAQYVASNGLRDAG 155 (241)
Q Consensus 89 E~~-l~I~~~L~~~~g~---~~~~i~--~V~SHpqa--l~Qc~~fl~~~~~-----~~~~~~sTa~Aa~~v~~~~~~~~a 155 (241)
-.. ..-...|+++++. +++|++ +|..++-. ...-..||++.+. +.+.. +..+++..+..+ .-+++
T Consensus 74 ~~~~~~~~~~lv~~~~s~I~s~~DLkGK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~G-~vDa~ 151 (300)
T TIGR01729 74 ILDNIGKSEALVAREGSGIEKPEDLKGKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQRG-DIDAA 151 (300)
T ss_pred EeccCCccceEEecCCCCCCChhHcCCCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHcC-CcCEE
Confidence 111 1113567777663 334443 55543321 2223467876553 33333 344555555554 23444
Q ss_pred EecCH
Q 036073 156 VVASA 160 (241)
Q Consensus 156 AI~s~ 160 (241)
++..+
T Consensus 152 ~~~~p 156 (300)
T TIGR01729 152 YVWPP 156 (300)
T ss_pred EEecH
Confidence 44444
No 217
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=45.94 E-value=2.1e+02 Score=25.14 Aligned_cols=53 Identities=15% Similarity=0.122 Sum_probs=33.4
Q ss_pred CCccEEEEeCCCCcH-HHHHHH---hhCCCCceeec-CCHHHHHHHHHcCCcceEEEe
Q 036073 11 GTKVRISFKGSPGSF-TEDAAL---KAYPNCETIPC-DEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 11 ~~~~~ia~LGp~Gtf-S~~Aa~---~~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 63 (241)
.+..+||.....+++ --.... +.+|+.++.-. .+.+++++.+.+|++|+|+.+
T Consensus 92 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~ 149 (309)
T PRK12682 92 SGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAT 149 (309)
T ss_pred CCeEEEeeCchHHHHHHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHcCCccEEEec
Confidence 455778776544332 111111 23577665443 457899999999999999975
No 218
>cd08483 PBP2_HvrB The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold. The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transp
Probab=45.75 E-value=64 Score=24.90 Aligned_cols=116 Identities=10% Similarity=-0.042 Sum_probs=57.5
Q ss_pred CCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCe---e
Q 036073 34 YPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKL---K 110 (241)
Q Consensus 34 ~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i---~ 110 (241)
+|+.++.... .+..+.+.+|++|+|+..-.-...|. ....|.+..+.++. +-+| +......+++++ +
T Consensus 26 ~P~i~l~~~~--~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~-~~~~~~~~~~~L~~~~ 95 (190)
T cd08483 26 HPEIELSLLP--SADLVDLRPDGIDVAIRYGNGDWPGL---ESEPLTAAPFVVVA----APGL-LGDRKVDSLADLAGLP 95 (190)
T ss_pred CCCceEEEEe--cCCcCCCCCCCcCEEEEecCCCCCCc---EEEeecccceEeee----CHHH-HhhCCCCCHHHHhcCc
Confidence 5665544332 23467789999999998532111221 12233344444332 2334 333222333333 3
Q ss_pred EEEecHHHHHHHHHHHHhcCCc-----eEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 111 CVLSHPQALASSDIVQTQLGVA-----RENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 111 ~V~SHpqal~Qc~~fl~~~~~~-----~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
.|. +.. .....+|+.+.+.. ...++|.....+.+..+ ...++.+...++
T Consensus 96 ~i~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~~ 149 (190)
T cd08483 96 WLQ-ERG-TNEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAG---LGLSIQARALVE 149 (190)
T ss_pred eec-cCC-chHHHHHHHHcCCCcccccCceeCcHHHHHHHHHcC---CcEEeecHHhhH
Confidence 333 221 12346777765542 23456666666666653 357777776554
No 219
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=45.73 E-value=2.1e+02 Score=25.08 Aligned_cols=53 Identities=13% Similarity=0.034 Sum_probs=35.9
Q ss_pred CCccEEEEeCCCCc-HHHHHH---HhhCCCCceeecC-CHHHHHHHHHcCCcceEEEe
Q 036073 11 GTKVRISFKGSPGS-FTEDAA---LKAYPNCETIPCD-EFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 11 ~~~~~ia~LGp~Gt-fS~~Aa---~~~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvP 63 (241)
.+..+||..+..+. +-.... .+.+|+.++.... +..++.+.+.+|++|+|+.+
T Consensus 94 ~g~l~ig~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 94 RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred CceEEEEEcCcchHhHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEEc
Confidence 45688988877664 322222 2335776654433 57888999999999999974
No 220
>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h
Probab=45.55 E-value=1.4e+02 Score=23.13 Aligned_cols=120 Identities=10% Similarity=-0.005 Sum_probs=59.2
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCC---
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEK--- 108 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~--- 108 (241)
.+|+.++.... +-+++++.+.+|++|+|++.......+.. ...|.+..+.+ ..+-.|.+...+..+++|
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08457 25 LRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGF---LIETRSLPAVV----AVPMGHPLAQLDVVSPQDLAG 97 (196)
T ss_pred HCCCeEEEEEecCcHHHHHHHHcCCccEEEeccCCCCCCcE---EEEeccCCeEE----EeeCCCccccCCccCHHHhCC
Confidence 35776554433 34788999999999999986432211111 11122223222 223344444333333333
Q ss_pred eeEEE-ecHH-HHHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeEEecCHhh
Q 036073 109 LKCVL-SHPQ-ALASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAGVVASARA 162 (241)
Q Consensus 109 i~~V~-SHpq-al~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~a 162 (241)
.+.|. ++.. ......+|+.+.+. .. ..++|...+.+.++.+ ...++.+...
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~ 153 (196)
T cd08457 98 ERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREG---LGIAIIDPAT 153 (196)
T ss_pred CceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcC---CeEEEEChHH
Confidence 33343 2222 22445666766543 22 3455555555566553 3456665543
No 221
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=45.09 E-value=35 Score=35.86 Aligned_cols=32 Identities=19% Similarity=0.300 Sum_probs=28.2
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
+-|.|.+..+|+||-|+++-++|+..|+|+..
T Consensus 813 ~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~ 844 (895)
T PRK00275 813 PVTVLEIIAPDRPGLLARIGRIFLEFDLSLQN 844 (895)
T ss_pred CeEEEEEEECCCCCHHHHHHHHHHHCCCEEEE
Confidence 46777788899999999999999999999853
No 222
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=44.14 E-value=2.1e+02 Score=24.63 Aligned_cols=144 Identities=13% Similarity=0.063 Sum_probs=71.6
Q ss_pred CCccEEEEeCCCCc-HHHH---HHHhhCCCCceee-cCCHHHHHHHHHcCCcceEEEeee-cc-cccceeccccccccCC
Q 036073 11 GTKVRISFKGSPGS-FTED---AALKAYPNCETIP-CDEFEEAFKAVELWLAEKAILPIE-NS-SGGSIHHNYDLLLRHR 83 (241)
Q Consensus 11 ~~~~~ia~LGp~Gt-fS~~---Aa~~~~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiE-NS-~~G~V~~t~d~L~~~~ 83 (241)
.+..+||+...-+. +-.. +..+.+|+.++.- ..+-.++++.+.+|++|+|++.-. .. ..+. ....|.+..
T Consensus 96 ~~~l~I~~~~~~~~~~l~~~l~~f~~~~p~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~l---~~~~l~~~~ 172 (294)
T PRK09986 96 AGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGF---TSRRLHESA 172 (294)
T ss_pred cceEEEEEehHHhHHHHHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHcCCCCEEEecCCccCCCCCe---EEEEeeccc
Confidence 45678887654442 1111 2223356655433 345688999999999999997311 00 0111 111122222
Q ss_pred eEEEEEEEEeeeeeeecCCCCCcCCee---EEEecH--HHHH-HHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCe
Q 036073 84 LHIVGEVQFVANFCLLALPGIREEKLK---CVLSHP--QALA-SSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDA 154 (241)
Q Consensus 84 l~I~~E~~l~I~~~L~~~~g~~~~~i~---~V~SHp--qal~-Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~ 154 (241)
+.+ ..+-+|-+...+..+++++. .|...+ ..+. +..+|+.+.+.. ...++|.......++.+ ..
T Consensus 173 ~~~----v~~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g 245 (294)
T PRK09986 173 FAV----AVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG---IG 245 (294)
T ss_pred EEE----EEcCCCCcccCCccCHHHHcCCCEEecCCCchhHHHHHHHHHHHCCCCCceeeecCCHHHHHHHHHcC---Ce
Confidence 222 22333434333333444443 344322 2233 555556555432 23466666666666653 45
Q ss_pred EEecCHhhHH
Q 036073 155 GVVASARAAE 164 (241)
Q Consensus 155 aAI~s~~aa~ 164 (241)
.++.++..++
T Consensus 246 i~~l~~~~~~ 255 (294)
T PRK09986 246 ITLLPDSYAQ 255 (294)
T ss_pred EEEccHHHhh
Confidence 7788877654
No 223
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=43.94 E-value=31 Score=31.08 Aligned_cols=142 Identities=11% Similarity=0.011 Sum_probs=72.8
Q ss_pred CCCccEEEEeCCCCcHHHHHH-HhhC-C----CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCC
Q 036073 10 DGTKVRISFKGSPGSFTEDAA-LKAY-P----NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHR 83 (241)
Q Consensus 10 ~~~~~~ia~LGp~GtfS~~Aa-~~~~-~----~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~ 83 (241)
.....||+|....+-| ..|- +.+| . +++++.+.+-.++++++.+|++|+|++.....+... ....+
T Consensus 21 ~~~~v~~~y~~~~~~~-~vA~~~g~f~~~~Gl~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~~~a~-------~~g~~ 92 (320)
T PRK11480 21 QAVNVTVAYQTSAEPA-KVAQADNTFAKESGATVDWRKFDSGASIVRALASGDVQIGNLGSSPLAVAA-------SQQVP 92 (320)
T ss_pred CCCeEEEEecCCCcHH-HHHHHcCchHHHcCCeeEEEEeCCHHHHHHHHHCCCCCEECcCchHHHHHH-------HCCCC
Confidence 3567899998532222 2221 2234 2 368899999999999999999999987543211100 11223
Q ss_pred eEEEEEEE-EeeeeeeecCCCC-CcCCe--eEEEecHHH--HHHHHHHHHhcCC-----ceEeccCHHHHHHHHHhcCCC
Q 036073 84 LHIVGEVQ-FVANFCLLALPGI-REEKL--KCVLSHPQA--LASSDIVQTQLGV-----ARENIDDTASAAQYVASNGLR 152 (241)
Q Consensus 84 l~I~~E~~-l~I~~~L~~~~g~-~~~~i--~~V~SHpqa--l~Qc~~fl~~~~~-----~~~~~~sTa~Aa~~v~~~~~~ 152 (241)
+.+++-.. ......|+++++. +++|+ |+|...+-. ...-..||++.|+ +.+... ...++..+..+ .-
T Consensus 93 ~~~v~~~~~~~~~~~lv~~~~I~s~~DLkGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~-~~~~~~Al~~G-~V 170 (320)
T PRK11480 93 IEVFLLASKLGNSEALVVKKTISKPEDLIGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQ-PPAIIAAWQRG-DI 170 (320)
T ss_pred eEEEEeeccCCcceEEEecCCCCChHHcCCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECC-cHHHHHHHHcC-Cc
Confidence 44333211 1222456665543 34444 356543211 1234567877654 333333 34455555544 23
Q ss_pred CeEEecCHh
Q 036073 153 DAGVVASAR 161 (241)
Q Consensus 153 ~~aAI~s~~ 161 (241)
+++++..+.
T Consensus 171 DAa~~~~p~ 179 (320)
T PRK11480 171 DGAYVWAPA 179 (320)
T ss_pred CEEEEcchH
Confidence 444444443
No 224
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=43.93 E-value=2.6e+02 Score=25.64 Aligned_cols=130 Identities=12% Similarity=-0.016 Sum_probs=67.5
Q ss_pred CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEE-EeeeeeeecCCCCCcCCe--eEE
Q 036073 36 NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQ-FVANFCLLALPGIREEKL--KCV 112 (241)
Q Consensus 36 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~-l~I~~~L~~~~g~~~~~i--~~V 112 (241)
+++++.+++-.++++++.+|++|+|.+--.-++..... ...+++|+.-.. -.-...|++++..+++|+ |+|
T Consensus 36 ~Ve~~~f~~~~~~l~Al~aG~iD~~~~g~~~~~~~~~a------~g~~~~iv~v~~~~~g~~~ivv~~i~svaDLKGKkI 109 (328)
T TIGR03427 36 TIEVVQINDYVESINQYTAGKFDGCTMTNMDALTIPAA------GGVDTTALIVGDFSNGNDGIVLKGGKSLADLKGQKV 109 (328)
T ss_pred eEEEEECCChHHHHHHHHcCCCCEEeecCHHHHHHHHh------CCCCeEEEEEEccCCCceEEEECCCCCHHHcCCCEE
Confidence 36889999999999999999999986521100000000 012222222111 111234555555567777 477
Q ss_pred EecHHHHHH--HHHHHHhcC-----CceEeccCHHHHHHHHHhcCCCCeEEecCHhhH---HhcCCceeec
Q 036073 113 LSHPQALAS--SDIVQTQLG-----VARENIDDTASAAQYVASNGLRDAGVVASARAA---EIYGLNILAD 173 (241)
Q Consensus 113 ~SHpqal~Q--c~~fl~~~~-----~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa---~~ygL~il~~ 173 (241)
..+.-...+ ..+.|++.| ++.+.... +.+...+..+ .-+++++-.+... +..|.++|..
T Consensus 110 av~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~~-~d~~aAl~~G-~VDAa~~~eP~~s~~~~~~g~~~l~~ 178 (328)
T TIGR03427 110 NLVELSVSHYLLARALESVGLSEKDVKVVNTSD-ADIVAAFITK-DVTAVVTWNPQLSEIKAQPGANEVFD 178 (328)
T ss_pred eccCCChHHHHHHHHHHHcCCCHHHeEEEeCCh-HHHHHHHhcC-CCcEEEEcCchHHHHHhCCCcEEecc
Confidence 655444332 344556544 45555543 4444444443 3455555444433 2246666654
No 225
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=43.70 E-value=1e+02 Score=24.05 Aligned_cols=113 Identities=12% Similarity=0.147 Sum_probs=60.2
Q ss_pred CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCC---cCCee--
Q 036073 36 NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIR---EEKLK-- 110 (241)
Q Consensus 36 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~---~~~i~-- 110 (241)
+.++++.. ..++.+++.+|++|+++.+....-+.. ..+ .. ......-.+.++++++.. ++|++
T Consensus 39 ~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~~~--~~~--------~~-~~~~~~~~~~~~~~~~~~~~~~~dl~g~ 106 (218)
T cd00134 39 KVKFVEVD-WDGLITALKSGKVDLIAAGMTITPERA--KQV--------DF-SDPYYKSGQVILVKKGSPIKSVKDLKGK 106 (218)
T ss_pred eEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHHHH--hhc--------cC-cccceeccEEEEEECCCCCCChHHhCCC
Confidence 35677777 789999999999999998752111110 000 00 011222234555554432 22322
Q ss_pred EEEecHHHHHHHHHHHHhc--CCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 111 CVLSHPQALASSDIVQTQL--GVARENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 111 ~V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+|..- .. .-...++.+. ......+.+..++.+.+..+ ...+++.....+.
T Consensus 107 ~i~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~~~~ 158 (218)
T cd00134 107 KVAVQ-KG-STAEKYLKKALPEAKVVSYDDNAEALAALENG--RADAVIVDEIALA 158 (218)
T ss_pred EEEEE-cC-chHHHHHHHhCCcccEEEeCCHHHHHHHHHcC--CccEEEeccHHHH
Confidence 22211 11 1123445443 35567788888889988875 3456666655444
No 226
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=43.62 E-value=1.5e+02 Score=22.93 Aligned_cols=142 Identities=17% Similarity=0.070 Sum_probs=68.8
Q ss_pred cEEEEeCCCCcH--HHHH--HHhhCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEE
Q 036073 14 VRISFKGSPGSF--TEDA--ALKAYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVG 88 (241)
Q Consensus 14 ~~ia~LGp~Gtf--S~~A--a~~~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~ 88 (241)
.+||+-..-+.+ .... ..+.+|+.++... .+-.++.+.+.+|++|+|+..-.....+. ....|.+..+.++
T Consensus 2 l~Ig~~~~~~~~~~~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~~- 77 (198)
T cd08441 2 LRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGI---AYEPLFDYEVVLV- 77 (198)
T ss_pred EEEEeeccchhhhhHHHHHHHHHhCCCeEEEEEeCCchhHHHHHHcCCceEEEecCCcCCCCc---EEEEccCCcEEEE-
Confidence 466766554432 1111 1223577655444 35578899999999999997421111111 1112223333222
Q ss_pred EEEEeeeeeeecCCCCCcCCee---EEE-ecHH-HHHHHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCeEEecCH
Q 036073 89 EVQFVANFCLLALPGIREEKLK---CVL-SHPQ-ALASSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDAGVVASA 160 (241)
Q Consensus 89 E~~l~I~~~L~~~~g~~~~~i~---~V~-SHpq-al~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~ 160 (241)
.+..|-+......+++++. .|. .+.. ......+|+.+.+.. ...++|...+.+.++.+ ...++.+.
T Consensus 78 ---~~~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~ 151 (198)
T cd08441 78 ---VAPDHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASG---RGVAALPN 151 (198)
T ss_pred ---EcCCCChHHcccCCHHHhcCCceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhC---CcEEEeeH
Confidence 2333434332223333333 232 1111 123345677665532 24566666666666654 34677777
Q ss_pred hhHHh
Q 036073 161 RAAEI 165 (241)
Q Consensus 161 ~aa~~ 165 (241)
..++.
T Consensus 152 ~~~~~ 156 (198)
T cd08441 152 WAVRE 156 (198)
T ss_pred HHHHH
Confidence 65543
No 227
>KOG4028 consensus Uncharacterized conserved protein [Function unknown]
Probab=43.06 E-value=22 Score=28.94 Aligned_cols=34 Identities=18% Similarity=0.182 Sum_probs=25.2
Q ss_pred cEEEEeCCCCcHHHHHHHhhCCC-CceeecCCHHH
Q 036073 14 VRISFKGSPGSFTEDAALKAYPN-CETIPCDEFEE 47 (241)
Q Consensus 14 ~~ia~LGp~GtfS~~Aa~~~~~~-~~~~~~~s~~~ 47 (241)
..-+.--|+||+.|+-+.++.++ .++..-+++++
T Consensus 108 la~~~wrp~gswreel~~~~vggg~ql~~~~ai~~ 142 (175)
T KOG4028|consen 108 LACGCWRPKGSWREELAHAFVGGGLQLLHGDAIED 142 (175)
T ss_pred ecccccCCCCcHHHHHHHHHhcCCceeeccccccC
Confidence 44566779999999999998864 56666555544
No 228
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=42.94 E-value=32 Score=30.96 Aligned_cols=51 Identities=20% Similarity=-0.032 Sum_probs=35.4
Q ss_pred CCCccEEEEeCCCCcHHHHHHHhhC---C----CCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 10 DGTKVRISFKGSPGSFTEDAALKAY---P----NCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 10 ~~~~~~ia~LGp~GtfS~~Aa~~~~---~----~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
+...+||++ |.|+.+|.....++ + +.++++.. ..+...++.+|++|.+++.
T Consensus 119 DLkGK~Iav--~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~-~~~~~~Al~~G~VDAa~~~ 176 (320)
T PRK11480 119 DLIGKRIAV--PFISTTHYSLLAALKHWGIKPGQVEIVNLQ-PPAIIAAWQRGDIDGAYVW 176 (320)
T ss_pred HcCCCEEec--CCCCchHHHHHHHHHHcCCCHhheEEEECC-cHHHHHHHHcCCcCEEEEc
Confidence 344578998 56777775544333 1 24566655 6889999999999988875
No 229
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=42.69 E-value=1.5e+02 Score=22.67 Aligned_cols=123 Identities=13% Similarity=0.003 Sum_probs=60.4
Q ss_pred hhCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcC---
Q 036073 32 KAYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREE--- 107 (241)
Q Consensus 32 ~~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~--- 107 (241)
+.+|+.++.-. .+..+..+.+.+|++|+|+..-.....+ -....|.+..+.++ .+-+|-+...+..+++
T Consensus 24 ~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~---~~~~~l~~~~~~~v----~~~~~~l~~~~~~~~~~l~ 96 (196)
T cd08415 24 ARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPG---LESEPLASGRAVCV----LPPGHPLARKDVVTPADLA 96 (196)
T ss_pred HHCCCcEEEEEecchHHHHHHHHcCCccEEEEeCCCCCCc---ceeeeecccceEEE----EcCCCChHhcCccCHHHhc
Confidence 34677655433 3567899999999999999863221111 11112222232221 1222323222222222
Q ss_pred CeeEEEe-cH-HHHHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 108 KLKCVLS-HP-QALASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 108 ~i~~V~S-Hp-qal~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+-..|.- +. ....+..+|+.+.+. +. ..++|.....+.+..+ ...++.+...++
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 155 (196)
T cd08415 97 GEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAG---LGVAIVDPLTAA 155 (196)
T ss_pred CCcEEEeCCCccHHHHHHHHHHHcCCCceEEEEEeHHHHHHHHHHcC---CCeEEechhhhh
Confidence 3333332 22 223455667766553 22 3455665566666653 346777776544
No 230
>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....
Probab=42.38 E-value=72 Score=26.29 Aligned_cols=55 Identities=18% Similarity=0.022 Sum_probs=37.5
Q ss_pred CCCCccEEEEeCCCCcHHHHHHHhhC---C----CCceeecCCHHHHHHHHHcCCcceEEEeeec
Q 036073 9 NDGTKVRISFKGSPGSFTEDAALKAY---P----NCETIPCDEFEEAFKAVELWLAEKAILPIEN 66 (241)
Q Consensus 9 ~~~~~~~ia~LGp~GtfS~~Aa~~~~---~----~~~~~~~~s~~~v~~av~~g~~d~gVvPiEN 66 (241)
.+....||++.+ |+.++.-.+.++ + +.+++... ..+...++.+|++|.+++..++
T Consensus 89 ~DLkGK~i~v~~--~s~~~~~~~~~l~~~g~~~~~v~~v~~~-~~~~~~al~~g~vDa~~~~~~~ 150 (216)
T PF09084_consen 89 ADLKGKKIGVSR--GSSSEYFLRALLKKNGIDPDDVKIVNLG-PPELAQALLSGQVDAAILWYPP 150 (216)
T ss_dssp GGGTTSEEEEST--TSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTTSSSEEEEEEEC
T ss_pred HHhCCCEEEEec--CcchhHHHHHHHHHhccccccceeeeee-hhhhhhhhhcCCCCEEEEccCC
Confidence 334457899776 777776555433 2 25666665 5677779999999999977776
No 231
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=42.10 E-value=1.7e+02 Score=22.98 Aligned_cols=122 Identities=16% Similarity=0.079 Sum_probs=60.5
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee-
Q 036073 33 AYPNCETIPCD-EFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK- 110 (241)
Q Consensus 33 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~- 110 (241)
.+|+.++.... +-.++.+.+.+|++|+|+.....- .+.+. ...|.+.++.++ .+-.|-|... ..+++|+.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~-~~~~~--~~~l~~~~~~~v----~~~~h~l~~~-~~~~~dL~~ 96 (200)
T cd08467 25 RAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVP-PDGLV--VRRLYDDGFACL----VRHGHPALAQ-EWTLDDFAT 96 (200)
T ss_pred hCCCCEEEEecCCcccHHHHhhCCCcCEEEecCCCC-Cccce--eEEeeeccEEEE----EcCCCccccC-CCCHHHHhC
Confidence 35777665554 445889999999999999742111 11111 112223333222 2334444322 23333322
Q ss_pred --EEEecH--HHHHHHHHHHHhcCCc---eEeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 111 --CVLSHP--QALASSDIVQTQLGVA---RENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 111 --~V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
.|.-.. ....+..+|+++.+.. ...++|.....+.++.+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08467 97 LRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAAT---DLIATVPRRVATQ 155 (200)
T ss_pred CCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcC---CeEEeeHHHHHHH
Confidence 222111 1112344566665543 24456666666667653 4577888766654
No 232
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=41.89 E-value=34 Score=35.55 Aligned_cols=32 Identities=16% Similarity=0.321 Sum_probs=28.1
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
.-|-|.+..+|+||-|+++.+.|+.+|+|+..
T Consensus 667 ~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~ 698 (850)
T TIGR01693 667 GGTEVFIYAPDQPGLFAKVAGALAMLSLSVHD 698 (850)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEE
Confidence 35777788899999999999999999999854
No 233
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=41.76 E-value=1.6e+02 Score=22.54 Aligned_cols=122 Identities=9% Similarity=-0.025 Sum_probs=59.9
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCeeE
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLKC 111 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~~ 111 (241)
.+|+.++.-. .+-+++.+.+.+|++|+|++.-..-..+... ..|.+..+.++. +-+|-+... -.++.+...
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v~----~~~~~~~~~-~~~l~~~~~ 96 (193)
T cd08442 25 RYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQ---EPVFQEELVLVS----PKGHPPVSR-AEDLAGSTL 96 (193)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEEeCCCCCCCcEE---EEeecCcEEEEe----cCCCccccc-HHHhCCCce
Confidence 3577655443 3567889999999999999752211111111 111222222211 112222110 001223333
Q ss_pred EEec-H-HHHHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 112 VLSH-P-QALASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 112 V~SH-p-qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
|.-. . ....+...|+.+.+.. . ..++|...+...+.++ ...++.+...++.
T Consensus 97 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 152 (193)
T cd08442 97 LAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAG---MGIALLPRSVLDS 152 (193)
T ss_pred EEecCCCcHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHhC---CcEEEcCHHHHhh
Confidence 3211 1 1234466777776533 2 3456666666666653 3577888876653
No 234
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=40.93 E-value=81 Score=27.71 Aligned_cols=56 Identities=20% Similarity=0.079 Sum_probs=39.5
Q ss_pred CCCCccEEEEeCCCCcHHHHH---HHhh---CCCC--ceeecCCHHHHHHHHHcCCcceEEEee
Q 036073 9 NDGTKVRISFKGSPGSFTEDA---ALKA---YPNC--ETIPCDEFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 9 ~~~~~~~ia~LGp~GtfS~~A---a~~~---~~~~--~~~~~~s~~~v~~av~~g~~d~gVvPi 64 (241)
......+|+...+.|+|--.+ ++.+ +++. ++++..+-.+.+++|.+|++|++++..
T Consensus 27 ~~~~~l~Ig~~~~~~~~~~~~~~la~~~~~~~~~i~v~~~~~~~~~~~~~~l~~G~~D~~~~~~ 90 (320)
T TIGR02122 27 GEPTFVTIGTGGTGGVYYPIGGAIAQLINKKSGKLRVRVQSTGGSVENVNLLEAGEADLAIVQS 90 (320)
T ss_pred CCCceEEEEeCCCCCChHHHHHHHHHHHhccCCCeeEEEEeCcchHHHHHHHhCCCCcEEEEcc
Confidence 445678999999999865432 2222 2433 455556677899999999999999863
No 235
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=40.62 E-value=1.7e+02 Score=22.46 Aligned_cols=31 Identities=19% Similarity=0.086 Sum_probs=23.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEe
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 63 (241)
.+|+.++... .+.+++.+.+.+|++|+|+..
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (195)
T cd08427 25 RHPDLEVHIVPGLSAELLARVDAGELDAAIVV 56 (195)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCCCEEEEc
Confidence 3577665443 356889999999999999985
No 236
>TIGR01098 3A0109s03R phosphate/phosphite/phosphonate ABC transporters, periplasmic binding protein. A subset of this model in which nearly all members exhibit genomic context with elements of phosphonate metabolism, particularly the C-P lyase system has been built (TIGR03431) as an equivalog. Nevertheless, there are members of this subfamily (TIGR01098) which show up sporadically on a phylogenetic tree that also show phosphonate context and are most likely competent to transport phosphonates.
Probab=40.52 E-value=2.2e+02 Score=23.93 Aligned_cols=54 Identities=4% Similarity=0.008 Sum_probs=36.9
Q ss_pred CCccEEEEeCCCCcHHHH----HHHhhC-----CCCceeecCCHHHHHHHHHcCCcceEEEee
Q 036073 11 GTKVRISFKGSPGSFTED----AALKAY-----PNCETIPCDEFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 11 ~~~~~ia~LGp~GtfS~~----Aa~~~~-----~~~~~~~~~s~~~v~~av~~g~~d~gVvPi 64 (241)
....+||+.+....+... ...+++ -+.++++..++.+.++++.+|++|+++...
T Consensus 31 ~~~l~vg~~~~~~~~~~~~~~~~l~~~l~~~~g~~v~~~~~~~~~~~~~~l~~g~~Di~~~~~ 93 (254)
T TIGR01098 31 PKELNFGILPGENASNLTRRWEPLADYLEKKLGIKVQLFVATDYSAVIEAMRFGRVDIAWFGP 93 (254)
T ss_pred CCceEEEECCCCCHHHHHHHHHHHHHHHHHHhCCcEEEEeCCCHHHHHHHHHcCCccEEEECc
Confidence 446899998754433321 111122 135677788999999999999999998654
No 237
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=40.37 E-value=1.7e+02 Score=22.42 Aligned_cols=31 Identities=16% Similarity=0.087 Sum_probs=23.5
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEe
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 63 (241)
.+|+.++... .+-.++.+.+.+|++|+|+..
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~ 56 (197)
T cd08448 25 EYPGIEVALHEMSSAEQIEALLRGELDLGFVH 56 (197)
T ss_pred HCCCCeEEEEeCCHHHHHHHHHcCCcceEEEe
Confidence 4577655432 357889999999999999974
No 238
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=40.29 E-value=2.4e+02 Score=24.33 Aligned_cols=150 Identities=12% Similarity=0.034 Sum_probs=80.3
Q ss_pred EeCCCCcHHHHHHHhhCC--------CC--ceeecC---CHHHHHHHHHcCCcceEEEeeecccccce-----------e
Q 036073 18 FKGSPGSFTEDAALKAYP--------NC--ETIPCD---EFEEAFKAVELWLAEKAILPIENSSGGSI-----------H 73 (241)
Q Consensus 18 ~LGp~GtfS~~Aa~~~~~--------~~--~~~~~~---s~~~v~~av~~g~~d~gVvPiENS~~G~V-----------~ 73 (241)
..-|+|+...++...+.. .. ++.|-. .-.+++++|.+|.+|+++++.-+.. +.+ .
T Consensus 3 ~~~p~~~~~~~~~~~f~~~v~e~t~G~v~v~~~~~g~Lg~~~e~~~~v~~G~~d~~~~~~~~~~-~~~p~~~~~~lP~~~ 81 (257)
T TIGR00787 3 HNAARSSPKHKAAEKFAKLVNEKTNGEIKISVFPSSQLGSDRAMLEALQGGALDMTAPSSSKFG-PLVPELAVFDLPFLF 81 (257)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHcCCeEEEEEcCCCCCCChHHHHHHHhCCCccEEeccccccc-ccCcchhhccCCeec
Confidence 345888888888776531 12 233322 4589999999999999986532111 100 0
Q ss_pred cc-------cc---------ccccCCeEEEEEEEEeeeeeeec---CCCCCcCCee--EEEecHHHHHHHHHHHHhcCCc
Q 036073 74 HN-------YD---------LLLRHRLHIVGEVQFVANFCLLA---LPGIREEKLK--CVLSHPQALASSDIVQTQLGVA 132 (241)
Q Consensus 74 ~t-------~d---------~L~~~~l~I~~E~~l~I~~~L~~---~~g~~~~~i~--~V~SHpqal~Qc~~fl~~~~~~ 132 (241)
.+ ++ .+.+.++.+.+-. +..+.++. .|=.+++|++ +|...+-.. -.++++..++.
T Consensus 82 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~--~~g~~~~~~~~~~i~s~~Dl~G~kir~~~~~~--~~~~~~~~Ga~ 157 (257)
T TIGR00787 82 RDYNHVHKVLDGEVGKALKKSLEKKGLKGLAYW--DNGFRQFTSSKKPITKPEDLKGLKIRIPNSPM--NEAQFKALGAN 157 (257)
T ss_pred CCHHHHHHHHcCHHHHHHHHHHHHcCcEEEeec--CCceeEeeeCCCccCChHHhCCCEEecCCCHH--HHHHHHHcCCc
Confidence 01 11 1223456666533 23333333 2223556654 455443221 35677777766
Q ss_pred eEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCceeeccc
Q 036073 133 RENIDDTASAAQYVASNGLRDAGVVASARAAEIYGLNILADRI 175 (241)
Q Consensus 133 ~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I 175 (241)
.+ .-+.++.-..+..+ .-.+++.+......++|.-+.+.+
T Consensus 158 ~v-~~~~~e~~~aL~~G--~vDg~~~~~~~~~~~~~~ev~~y~ 197 (257)
T TIGR00787 158 PE-PMAFSEVYTALQTG--VVDGQENPLSNVYSSKFYEVQKYL 197 (257)
T ss_pred cc-ccCHHHHHHHHHcC--CcccccCCHHHHhhcchhhhcchh
Confidence 55 44555666655544 235677777666666665454443
No 239
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=39.69 E-value=1.3e+02 Score=22.97 Aligned_cols=119 Identities=10% Similarity=-0.059 Sum_probs=54.4
Q ss_pred CCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee---
Q 036073 34 YPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK--- 110 (241)
Q Consensus 34 ~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~--- 110 (241)
+|+.++.....- -.+.+.+|++|+|++...+...+. ....|.+..+.++ .+-+| +...+..+++|+.
T Consensus 26 ~P~i~i~i~~~~--~~~~l~~~~~Dl~l~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~-~~~~~~~~~~dl~~~~ 95 (194)
T cd08481 26 HPDITVNLVTRD--EPFDFSQGSFDAAIHFGDPVWPGA---ESEYLMDEEVVPV----CSPAL-LAGRALAAPADLAHLP 95 (194)
T ss_pred CCCceEEEEecc--cccCcccCCCCEEEEcCCCCCCCc---cceecccCeeeec----CCHHH-HhcCCCCcHHHHhhCc
Confidence 566554333211 124688999999998644322221 1122333333222 22233 2222223343332
Q ss_pred EEEecHHHHHHHHHHHHhcCCc------eEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhc
Q 036073 111 CVLSHPQALASSDIVQTQLGVA------RENIDDTASAAQYVASNGLRDAGVVASARAAEIY 166 (241)
Q Consensus 111 ~V~SHpqal~Qc~~fl~~~~~~------~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y 166 (241)
-|. .......-.+|+.+.+.+ ...+++...+.+.++.+ ...++.++..++.+
T Consensus 96 ~i~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~~~~ 153 (194)
T cd08481 96 LLQ-QTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAG---LGVALLPRFLIEEE 153 (194)
T ss_pred eEe-cCCCCcCHHHHHHHcCCCCCCccCceEeccHHHHHHHHHhC---CCeEEecHHHHHHH
Confidence 222 110011235566665432 12345555566666653 45788888766543
No 240
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=39.22 E-value=53 Score=28.98 Aligned_cols=50 Identities=12% Similarity=-0.087 Sum_probs=33.5
Q ss_pred CCccEEEEeCCCCcHHHHHHHhhC---C----CCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 11 GTKVRISFKGSPGSFTEDAALKAY---P----NCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 11 ~~~~~ia~LGp~GtfS~~Aa~~~~---~----~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
....|||+ +.||-+|.-...++ + +.++++. ...+...++.+|++|.++++
T Consensus 98 LkGK~Igv--~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~G~vDa~~~~ 154 (300)
T TIGR01729 98 LKGKNVAV--PFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQRGDIDAAYVW 154 (300)
T ss_pred cCCCEEEe--CCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHcCCcCEEEEe
Confidence 34568998 56666665433332 1 2455555 46789999999999988875
No 241
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=39.14 E-value=47 Score=29.25 Aligned_cols=50 Identities=24% Similarity=0.229 Sum_probs=37.4
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCCC-------CceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSFTEDAALKAYPN-------CETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~~-------~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..+|++ |+.|+.++....+++.. ...+.+.+..+++.++.+|++|.++..
T Consensus 141 gk~v~~-~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 141 GKRVAV-GAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred CCEEec-CCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEEe
Confidence 356765 56788888776665531 224678899999999999999999976
No 242
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=38.83 E-value=54 Score=29.11 Aligned_cols=51 Identities=16% Similarity=0.081 Sum_probs=35.8
Q ss_pred CCCccEEEEeCCCCcHHHHHHHhhCCC-------CceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 10 DGTKVRISFKGSPGSFTEDAALKAYPN-------CETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 10 ~~~~~~ia~LGp~GtfS~~Aa~~~~~~-------~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
+-...+|++ +.||.+|.....++.. .+++ ..+..+...++.+|++|.+++.
T Consensus 126 dL~Gk~I~~--~~gs~~~~~l~~~l~~~g~~~~dv~~v-~~~~~~~~~al~~G~vDa~~~~ 183 (314)
T PRK11553 126 DLKGHKVAF--QKGSSSHNLLLRALRKAGLKFTDIQPT-YLTPADARAAFQQGNVDAWAIW 183 (314)
T ss_pred HhCCCEEee--cCCCcHHHHHHHHHHHcCCCHHHeEEE-ecChHHHHHHHHcCCCCEEEEc
Confidence 334467887 5688888776665532 2333 4477888999999999998873
No 243
>PRK06635 aspartate kinase; Reviewed
Probab=38.69 E-value=52 Score=30.79 Aligned_cols=29 Identities=24% Similarity=0.387 Sum_probs=25.6
Q ss_pred ecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 208 TLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 208 ~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+++.||.+.++++.|+++|||+..|.+.
T Consensus 349 ~~~~~~g~~a~i~~~La~~~Ini~~i~ss 377 (404)
T PRK06635 349 GMRSHPGVAAKMFEALAEEGINIQMISTS 377 (404)
T ss_pred CCCCCchHHHHHHHHHHHCCCCEEEEEec
Confidence 35789999999999999999999988653
No 244
>cd04918 ACT_AK1-AT_2 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the second of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine (SAM). This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. In its inactive state, Arabidopsis AK1 binds the effectors lysine and SAM (two molecules each) at the interface of two ACT1 domain subunits. The second ACT domain (ACT2), this CD, does not interact with an effector. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=38.64 E-value=61 Score=21.99 Aligned_cols=26 Identities=15% Similarity=0.312 Sum_probs=22.4
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
+...||.+.++++.|++.|||+-.|-
T Consensus 10 ~~~~~~~~~~i~~aL~~~~I~v~~i~ 35 (65)
T cd04918 10 VQRSSLILERAFHVLYTKGVNVQMIS 35 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 44568999999999999999997665
No 245
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=37.94 E-value=2.6e+02 Score=23.96 Aligned_cols=53 Identities=13% Similarity=0.204 Sum_probs=33.1
Q ss_pred CCccEEEEeCCCCcHH-HHH---HHhhCCCCceee-cCCHHHHHHHHHcCCcceEEEe
Q 036073 11 GTKVRISFKGSPGSFT-EDA---ALKAYPNCETIP-CDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 11 ~~~~~ia~LGp~GtfS-~~A---a~~~~~~~~~~~-~~s~~~v~~av~~g~~d~gVvP 63 (241)
.+..+|+.....+.+= -.+ .++.+|+.++.- ..+-.++++.+.+|++|+|+++
T Consensus 88 ~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~ 145 (290)
T PRK10837 88 NGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIE 145 (290)
T ss_pred CCeEEEEecchhHhhhhHHHHHHHHHHCCCceEEEEECCHHHHHHHHHhCCceEEEec
Confidence 3456777665443321 111 123357765443 3577889999999999999985
No 246
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=37.56 E-value=30 Score=32.83 Aligned_cols=34 Identities=24% Similarity=0.466 Sum_probs=27.9
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
.-+|++.=.|+||.+.++++.+++++||+..+..
T Consensus 338 ~~rlii~h~d~pG~ia~it~~l~~~~iNI~~m~~ 371 (409)
T PRK11790 338 GHRLLHIHENRPGVLAAINQIFAEQGINIAAQYL 371 (409)
T ss_pred CceEEEEeCCCCCHHHHHHHHHHhcCCCHHHhee
Confidence 4566665679999999999999999999965543
No 247
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=36.94 E-value=34 Score=33.55 Aligned_cols=75 Identities=19% Similarity=0.209 Sum_probs=47.9
Q ss_pred HhhHHhcCCceeecc--cCCCCCCceeEEEEeeCCCC------CCC--------------CCCceEEEEEecCCCchHHH
Q 036073 160 ARAAEIYGLNILADR--IQDDPDNITRFLVLARDPIM------PRT--------------DKPFKTSIVFTLDEGPGVLT 217 (241)
Q Consensus 160 ~~aa~~ygL~il~~~--I~d~~~N~TRF~vl~~~~~~------~~~--------------~~~~ktsi~~~~~~~pGaL~ 217 (241)
..-|+-.|+++-... ..+...|.-++.+-+..... -.. -..+..+|++.-.|+||.+.
T Consensus 388 ~~iA~e~GI~~~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~ggg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I~ 467 (526)
T PRK13581 388 PLLAKERGIEVEESKSEESPDYSNLITVTVTTDDGERSVAGTVFGDGEPRIVEIDGYRVDAKPEGHMLIIRNRDRPGVIG 467 (526)
T ss_pred HHHHHHcCCEEEEEEecCCCCCCCEEEEEEEeCCeEEEEEEEEecCCceEEEEECCEEEEeeCCceEEEEEeCCcCChhH
Confidence 356788888875432 33335676676654433110 000 01234566777789999999
Q ss_pred HHHHHHHHCCceeeeee
Q 036073 218 KALAVFALREINLTKVF 234 (241)
Q Consensus 218 ~~L~~fa~~~iNLt~Ie 234 (241)
.+...|+.++||+....
T Consensus 468 ~v~~~L~~~~iNIa~m~ 484 (526)
T PRK13581 468 KVGTLLGEAGINIAGMQ 484 (526)
T ss_pred HHHHHHhhcCCCchhcE
Confidence 99999999999996654
No 248
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=36.62 E-value=35 Score=23.21 Aligned_cols=30 Identities=20% Similarity=0.207 Sum_probs=24.5
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeeeeecc
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVFVARV 238 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~IeSRP~ 238 (241)
+.+.||.+.++++.|++.+|++-..-.+.+
T Consensus 10 ~~~~~gv~~~~~~~L~~~~i~~i~~~~s~~ 39 (63)
T cd04920 10 IRSLLHKLGPALEVFGKKPVHLVSQAANDL 39 (63)
T ss_pred cccCccHHHHHHHHHhcCCceEEEEeCCCC
Confidence 457899999999999999999877655543
No 249
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=35.89 E-value=1.1e+02 Score=26.22 Aligned_cols=47 Identities=15% Similarity=-0.007 Sum_probs=32.6
Q ss_pred EEEEeCCCCcHHHHHHHhhCC-------CCceeecC---------CHHHHHHHHHcCCcceEEEe
Q 036073 15 RISFKGSPGSFTEDAALKAYP-------NCETIPCD---------EFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 15 ~ia~LGp~GtfS~~Aa~~~~~-------~~~~~~~~---------s~~~v~~av~~g~~d~gVvP 63 (241)
+||.+ .||..+..+.++.. ..+++.+. +..+++.+|.+|++|..+..
T Consensus 108 ~vgv~--~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aL~~GrvDa~i~~ 170 (246)
T TIGR03870 108 KIGVI--FGSPAETMLKQIGRYEDNFAYLYSLVNFKSPRNQYTQIDPRKLVSEVATGKADLAVAF 170 (246)
T ss_pred eEEEe--cCChHHHHHHhcCccccccccccccccccCcccccccCCHHHHHHHHHcCCCCEEEee
Confidence 88876 58888887765431 01222222 46889999999999999875
No 250
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=35.50 E-value=46 Score=34.65 Aligned_cols=33 Identities=27% Similarity=0.286 Sum_probs=29.2
Q ss_pred CceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 200 PFKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 200 ~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
+++|.+=+.-.|+||.|+.+.++|+..++++-+
T Consensus 789 ~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~ 821 (867)
T COG2844 789 NDKTVLEVRALDRPGLLAALAGVFADLGLSLHS 821 (867)
T ss_pred CCceEEEEEeCCcccHHHHHHHHHHhcccceee
Confidence 357888888899999999999999999998854
No 251
>PRK09084 aspartate kinase III; Validated
Probab=34.73 E-value=2.9e+02 Score=26.56 Aligned_cols=99 Identities=15% Similarity=0.134 Sum_probs=58.4
Q ss_pred CceEeccCHHHHHHHHHhcCCCCeEEecCHh--hHHhcCCceeecccCCCCCCceeEEEEeeCCCCCC----CCCCceEE
Q 036073 131 VARENIDDTASAAQYVASNGLRDAGVVASAR--AAEIYGLNILADRIQDDPDNITRFLVLARDPIMPR----TDKPFKTS 204 (241)
Q Consensus 131 ~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~--aa~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~~~----~~~~~kts 204 (241)
++.+..-|-.+|.++..-+ .-.+-+.. .+..+|..+.-.+..|...--|.+- ......+. ....+-+.
T Consensus 235 a~~i~~is~~ea~ela~~G----a~vlh~~~~~~~~~~~i~i~i~~~~~~~~~GT~I~--~~~~~~~~v~~it~~~~i~l 308 (448)
T PRK09084 235 AKRIDEISFEEAAEMATFG----AKVLHPATLLPAVRSNIPVFVGSSKDPEAGGTWIC--NDTENPPLFRAIALRRNQTL 308 (448)
T ss_pred CeEcccCCHHHHHHHHhCC----CcccCHHHHHHHHHcCCcEEEEeCCCCCCCceEEe--cCCCCCCeeEEEEeeCCEEE
Confidence 4556666677777765532 22233332 3567889988887765443445542 11111110 01123334
Q ss_pred EEEe---cCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 205 IVFT---LDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 205 i~~~---~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
+.+. ..+.||.+.++++.|++++||.-.|.|
T Consensus 309 Itv~~~~~~~~~g~~a~if~~l~~~~I~Vd~I~s 342 (448)
T PRK09084 309 LTLHSLNMLHARGFLAEVFGILARHKISVDLITT 342 (448)
T ss_pred EEEecCCCCccccHHHHHHHHHHHcCCeEEEEec
Confidence 4443 246899999999999999999988865
No 252
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=33.90 E-value=3.4e+02 Score=24.12 Aligned_cols=143 Identities=17% Similarity=0.113 Sum_probs=68.6
Q ss_pred CccEEEEeCCCCcH-HHHHH---HhhCCCCceee-cCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEE
Q 036073 12 TKVRISFKGSPGSF-TEDAA---LKAYPNCETIP-CDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHI 86 (241)
Q Consensus 12 ~~~~ia~LGp~Gtf-S~~Aa---~~~~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I 86 (241)
+..+||.....+++ =.... ++.+|+.++.. ..+-.++.+.+.+|++|+|+++-.--..+.. +..|.+..+.+
T Consensus 89 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~l 165 (317)
T PRK15421 89 TRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLH---YSPMFDYEVRL 165 (317)
T ss_pred eeEEEEecccchHHHHHHHHHHHHHHCCCceEEEEeCccHHHHHHHHCCCcCEEEecCcccCCCce---EEEeccceEEE
Confidence 45677775433321 11111 12356665543 3356788999999999999975210011111 11222223322
Q ss_pred EEEEEEeeeeeeecCCCCCcCCee---EEE--ecHHHHHHHHHHHHhcCCc--eEeccCHHHHHHHHHhcCCCCeEEecC
Q 036073 87 VGEVQFVANFCLLALPGIREEKLK---CVL--SHPQALASSDIVQTQLGVA--RENIDDTASAAQYVASNGLRDAGVVAS 159 (241)
Q Consensus 87 ~~E~~l~I~~~L~~~~g~~~~~i~---~V~--SHpqal~Qc~~fl~~~~~~--~~~~~sTa~Aa~~v~~~~~~~~aAI~s 159 (241)
.++..|-+......+++++. .|. .+.........|+.+.+.+ ...++|.....+.+..+ ...++.+
T Consensus 166 ----v~~~~hpl~~~~~i~~~~L~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~i~p 238 (317)
T PRK15421 166 ----VLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAAR---MGIAALP 238 (317)
T ss_pred ----EEcCCCCccccCcCCHHHhCCCcEEecCCchhhHHHHHHHHHHhCCCCceeecCCHHHHHHHHHhC---CcEEEec
Confidence 23334444333333334332 232 1122234455566665543 33456666666666654 3456777
Q ss_pred HhhHH
Q 036073 160 ARAAE 164 (241)
Q Consensus 160 ~~aa~ 164 (241)
...++
T Consensus 239 ~~~~~ 243 (317)
T PRK15421 239 HWVVE 243 (317)
T ss_pred chhcc
Confidence 66443
No 253
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=33.74 E-value=1.2e+02 Score=26.06 Aligned_cols=50 Identities=18% Similarity=0.127 Sum_probs=35.9
Q ss_pred CccEEEEeCCCCcHHHHHHHhhC------C--CCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDAALKAY------P--NCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~------~--~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
...+|+ ..++||-+|...+.++ + +.+++.... .+...++.+|++|.++++
T Consensus 120 kGk~i~-~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~iDa~~~~ 177 (252)
T PF13379_consen 120 KGKKIA-VPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGEIDAAVLW 177 (252)
T ss_dssp STEEEE-ESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-SEEEEE
T ss_pred CCcEEE-EcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCCcCEEEec
Confidence 345666 4577888887776554 2 367888888 999999999999999985
No 254
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=33.63 E-value=2.6e+02 Score=29.28 Aligned_cols=100 Identities=11% Similarity=0.060 Sum_probs=60.3
Q ss_pred CceEeccCHHHHHHHHHhcCCCCeEEecCHhhH---HhcCCceeecccCCCCCCceeEEEEeeCCCCCC----CCCCceE
Q 036073 131 VARENIDDTASAAQYVASNGLRDAGVVASARAA---EIYGLNILADRIQDDPDNITRFLVLARDPIMPR----TDKPFKT 203 (241)
Q Consensus 131 ~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa---~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~~~----~~~~~kt 203 (241)
++.+..-|..+|.+++..+ |.+-.+.|+ ..+|..+...+..+....-|..- ......+. ....+-+
T Consensus 251 a~~i~~ls~~e~~el~~~g-----~~v~~~~a~~~a~~~~i~i~v~~~~~~~~~gT~I~--~~~~~~~~v~~It~~~~v~ 323 (861)
T PRK08961 251 ARLLTRLDYDEAQEIATTG-----AKVLHPRSIKPCRDAGIPMAILDTERPDLSGTSID--GDAEPVPGVKAISRKNGIV 323 (861)
T ss_pred ceEecccCHHHHHHHHHCC-----CeEECHHHHHHHHHCCCCEEEEeCCCCCCCccEEe--CCCCCCCcceeEEEECCEE
Confidence 4556666667777765532 455555554 45799988877665443444432 11111110 1122344
Q ss_pred EEEEe---cCCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 204 SIVFT---LDEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 204 si~~~---~~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
.+.+. ..+.||.+.++++.|++++||.-.|.|-.
T Consensus 324 lItv~~~~~~~~~g~~a~if~~la~~~I~Vd~I~sse 360 (861)
T PRK08961 324 LVSMETIGMWQQVGFLADVFTLFKKHGLSVDLISSSE 360 (861)
T ss_pred EEEEecCCccccccHHHHHHHHHHHcCCeEEEEEcCC
Confidence 44442 35789999999999999999999886543
No 255
>PRK06291 aspartate kinase; Provisional
Probab=33.56 E-value=4.4e+02 Score=25.32 Aligned_cols=97 Identities=11% Similarity=-0.026 Sum_probs=56.7
Q ss_pred CceEeccCHHHHHHHHHhcCCCCeEEecCHhhH---HhcCCceeecccCCCCCCceeEEEEeeCC-CCCC----CCCCce
Q 036073 131 VARENIDDTASAAQYVASNGLRDAGVVASARAA---EIYGLNILADRIQDDPDNITRFLVLARDP-IMPR----TDKPFK 202 (241)
Q Consensus 131 ~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa---~~ygL~il~~~I~d~~~N~TRF~vl~~~~-~~~~----~~~~~k 202 (241)
.+.+..-|..+|.++..- + +-+-.+.|+ ..+|+++.-.+..+....-|..- .... ..+. ....+-
T Consensus 249 a~~i~~l~~~ea~~l~~~----G-~~v~~~~a~~~~~~~~i~i~i~~~~~~~~~gt~i~--~~~~~~~~~V~~It~~~~v 321 (465)
T PRK06291 249 ARVIPKISYIEAMELSYF----G-AKVLHPRTIEPAMEKGIPVRVKNTFNPEFPGTLIT--SDSESSKRVVKAVTLIKNV 321 (465)
T ss_pred CeEccccCHHHHHHHHhC----C-CcccCHHHHHHHHHcCCcEEEecCCCCCCCceEEE--ecccccCcccceEEeeCCE
Confidence 344555566666666432 1 234444443 45899998888766444455442 2111 1000 012233
Q ss_pred EEEEEe---cCCCchHHHHHHHHHHHCCceeeeee
Q 036073 203 TSIVFT---LDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 203 tsi~~~---~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
+.+.+. ..+.||.+.++++.|+++|||+-.|-
T Consensus 322 alIsI~g~~m~~~~g~~arvf~~L~~~gI~V~mIs 356 (465)
T PRK06291 322 ALINISGAGMVGVPGTAARIFSALAEEGVNVIMIS 356 (465)
T ss_pred EEEEEeCCCCCCCccHHHHHHHHHHHCCCcEEEEE
Confidence 444442 34789999999999999999997774
No 256
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=33.53 E-value=3e+02 Score=23.42 Aligned_cols=28 Identities=4% Similarity=0.189 Sum_probs=22.5
Q ss_pred CCceeecCCHHHHHHHHHcCCcceEEEee
Q 036073 36 NCETIPCDEFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 36 ~~~~~~~~s~~~v~~av~~g~~d~gVvPi 64 (241)
+.++++. ++..+++++++|++|.++-++
T Consensus 66 ~i~~~~~-pw~~~~~~l~~g~~D~~~~~~ 93 (259)
T PRK15437 66 QCTFVEN-PLDALIPSLKAKKIDAIMSSL 93 (259)
T ss_pred ceEEEeC-CHHHHHHHHHCCCCCEEEecC
Confidence 4677775 599999999999999776554
No 257
>KOG1250 consensus Threonine/serine dehydratases [Amino acid transport and metabolism]
Probab=33.52 E-value=65 Score=30.97 Aligned_cols=110 Identities=12% Similarity=0.119 Sum_probs=60.0
Q ss_pred HHHHHHHHHhcC--CceEeccCHHHHHHHHHhcC-----CCCeEEecCHhhHHhcCCce--eecccCCCCCCceeE--EE
Q 036073 119 LASSDIVQTQLG--VARENIDDTASAAQYVASNG-----LRDAGVVASARAAEIYGLNI--LADRIQDDPDNITRF--LV 187 (241)
Q Consensus 119 l~Qc~~fl~~~~--~~~~~~~sTa~Aa~~v~~~~-----~~~~aAI~s~~aa~~ygL~i--l~~~I~d~~~N~TRF--~v 187 (241)
=.|.=+...++. ...+.-.+-+.|.+.+.+.+ ..+.+|++.-...+.++|+. +-...+-..-|+|++ ++
T Consensus 284 g~~tf~~a~~~~d~vvvV~~~ei~aaI~~l~edek~vvEpAgaaaLaai~~~~~~~lk~~~vv~ilsG~n~~~~~L~~vi 363 (457)
T KOG1250|consen 284 GENTFELAQKLVDRVVVVEDDEIAAAILRLFEDEKMVVEPAGAAALAAIYSGKLNHLKGKKVVSILSGGNIDFDSLGRVI 363 (457)
T ss_pred hHHHHHHHHhcCceEEEeccHHHHHHHHHHHHhhhheeccchHHHHHHHHhccccccCCceEEeecccCCCCccccccee
Confidence 334444444442 23344455666666666643 12345565555555565553 224455556677776 32
Q ss_pred EeeCCCCCCCCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeee
Q 036073 188 LARDPIMPRTDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKV 233 (241)
Q Consensus 188 l~~~~~~~~~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~I 233 (241)
. +... ....-..+...++++||...++-+....++++.-.|
T Consensus 364 e-ra~~----g~~~~v~l~v~l~d~pG~~~~l~~~i~~~~~se~~~ 404 (457)
T KOG1250|consen 364 E-RACA----GSNREVRLLVALPDRPGGFNKLTELIGPLSVSEKDI 404 (457)
T ss_pred E-Eeec----cCCceEeeeeecccCCCcchhhHHhhcccccchhhh
Confidence 2 2111 111123456678999999998888877777765443
No 258
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=33.25 E-value=56 Score=34.18 Aligned_cols=32 Identities=9% Similarity=0.221 Sum_probs=28.2
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
+-|.|.+..+|+||-|+++-++|+.+|+|+..
T Consensus 676 ~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~ 707 (854)
T PRK01759 676 GGTEIFIYCQDQANLFLKVVSTIGAKKLSIHD 707 (854)
T ss_pred CeEEEEEEecCCccHHHHHHHHHHHCCCeEEE
Confidence 35777788899999999999999999999854
No 259
>cd04915 ACT_AK-Ectoine_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinas
Probab=32.61 E-value=51 Score=22.64 Aligned_cols=24 Identities=33% Similarity=0.433 Sum_probs=20.9
Q ss_pred CchHHHHHHHHHHHCCceeeeeee
Q 036073 212 GPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 212 ~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
.||.+.++++.+++.|||+-.|-.
T Consensus 14 ~~gv~~ki~~~L~~~~I~v~~i~~ 37 (66)
T cd04915 14 TPGVLARGLAALAEAGIEPIAAHQ 37 (66)
T ss_pred cchHHHHHHHHHHHCCCCEEEEEe
Confidence 799999999999999999965543
No 260
>PRK05007 PII uridylyl-transferase; Provisional
Probab=32.57 E-value=59 Score=34.15 Aligned_cols=32 Identities=16% Similarity=0.152 Sum_probs=27.8
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
+-|.+.+..+|+||-|+++.+.|+.+|+|+-.
T Consensus 700 ~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~ 731 (884)
T PRK05007 700 GGTEIFIWSPDRPYLFAAVCAELDRRNLSVHD 731 (884)
T ss_pred CeEEEEEEecCCcCHHHHHHHHHHHCCCEEEE
Confidence 35677777899999999999999999999864
No 261
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=32.51 E-value=3.6e+02 Score=24.01 Aligned_cols=50 Identities=12% Similarity=0.036 Sum_probs=37.9
Q ss_pred CccEEEEe-CCCCcHHHHHHHhhCC--C--CceeecCCHHHHHHHHHcCCcceEE
Q 036073 12 TKVRISFK-GSPGSFTEDAALKAYP--N--CETIPCDEFEEAFKAVELWLAEKAI 61 (241)
Q Consensus 12 ~~~~ia~L-Gp~GtfS~~Aa~~~~~--~--~~~~~~~s~~~v~~av~~g~~d~gV 61 (241)
...+||+. ||...+.+.+...... + .+++.++......+++.+|++|..+
T Consensus 32 ~tLkVG~~~~~~~~~~e~a~~~~k~~~G~~Velv~fsd~~~~n~AL~~G~ID~n~ 86 (272)
T PRK09861 32 KHIKVGVINGAEQDVAEVAKKVAKEKYGLDVELVGFSGSLLPNDATNHGELDANV 86 (272)
T ss_pred CcEEEEEcCCchHHHHHHHHHHHHHcCCCeEEEEecCchhhHHHHHHcCCcceeh
Confidence 45899996 7777777766554322 3 5777888888888999999999987
No 262
>TIGR00656 asp_kin_monofn aspartate kinase, monofunctional class. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. The protein slr0657 from Synechocystis PCC6803 is extended by a duplication of the C-terminal region corresponding to the beta chain. Incorporation of a second copy of the C-terminal domain may be quite common in this subgroup of aspartokinases.
Probab=32.34 E-value=44 Score=31.21 Aligned_cols=29 Identities=17% Similarity=0.331 Sum_probs=25.3
Q ss_pred ecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 208 TLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 208 ~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+.++||.+.++++.|+..|||+..+-+.
T Consensus 346 ~~~~~~g~~a~i~~~L~~~gIni~~i~~s 374 (401)
T TIGR00656 346 GMVGAPGVASEIFSALEEKNINILMIGSS 374 (401)
T ss_pred CcccCccHHHHHHHHHHHCCCcEEEEEcC
Confidence 34689999999999999999999887654
No 263
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=32.12 E-value=2.3e+02 Score=21.67 Aligned_cols=124 Identities=14% Similarity=0.040 Sum_probs=61.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCC-CCC---cC
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALP-GIR---EE 107 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~-g~~---~~ 107 (241)
.+|+.++.-. .+..++++.+.+|++|+|+..-.......+ ....|.+..+.+ ..+-+|-+...+ ..+ +.
T Consensus 25 ~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l--~~~~l~~~~~~~----~~~~~~~~~~~~~~~~~~~l~ 98 (199)
T cd08430 25 QHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARL--AFLPLATSPLVF----IAPNIACAVTQQLSQGEIDWS 98 (199)
T ss_pred HCCCceEEEEeCCHHHHHHHHHCCCCCEEEEecCCCCCccc--EEEeeccceEEE----EEeCCchhhhhhccccccccc
Confidence 4677665444 467789999999999999975221111111 112222333322 234444443221 112 33
Q ss_pred CeeEEEecHH-HHHHHHHHHHhcCC--ce-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 108 KLKCVLSHPQ-ALASSDIVQTQLGV--AR-ENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 108 ~i~~V~SHpq-al~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
+...|...+. ......+|+.+.+. +. ..++|.....+.+.++ ...|+.+...++.
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~lp~~~~~~ 157 (199)
T cd08430 99 RLPFILPERGLARERLDQWFRRRGIKPNIYAQVAGHEAIVSMVALG---CGVGIVPELVLDN 157 (199)
T ss_pred cCCeEEccCChHHHHHHHHHHHcCCCCCeeEEEccHHHHHHHHHhC---CeEEEccHHHhhh
Confidence 3334432111 12334567766553 32 3345554455555543 4578888876653
No 264
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=31.57 E-value=56 Score=23.48 Aligned_cols=78 Identities=13% Similarity=0.149 Sum_probs=50.5
Q ss_pred EEecHHHHHHHHHHHHhcCC-ceEeccCHHHHHHHHHhcCCCCeEEecCHhhHHhcCCceeecccCCCCCCceeEEEEee
Q 036073 112 VLSHPQALASSDIVQTQLGV-ARENIDDTASAAQYVASNGLRDAGVVASARAAEIYGLNILADRIQDDPDNITRFLVLAR 190 (241)
Q Consensus 112 V~SHpqal~Qc~~fl~~~~~-~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~d~~~N~TRF~vl~~ 190 (241)
|-.||.-..-.+++|+..+. ....+.|..++.+.+.+.. ++ .+|..-......|++++. .|.... ..+++++++.
T Consensus 4 vd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~~-~d-~iiid~~~~~~~~~~~~~-~i~~~~-~~~~ii~~t~ 79 (112)
T PF00072_consen 4 VDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLKKHP-PD-LIIIDLELPDGDGLELLE-QIRQIN-PSIPIIVVTD 79 (112)
T ss_dssp EESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHST-ES-EEEEESSSSSSBHHHHHH-HHHHHT-TTSEEEEEES
T ss_pred EECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhcccC-ce-EEEEEeeecccccccccc-cccccc-ccccEEEecC
Confidence 44577788888899997788 6677788888888886653 44 344333223344555443 343333 7899999986
Q ss_pred CCC
Q 036073 191 DPI 193 (241)
Q Consensus 191 ~~~ 193 (241)
...
T Consensus 80 ~~~ 82 (112)
T PF00072_consen 80 EDD 82 (112)
T ss_dssp STS
T ss_pred CCC
Confidence 643
No 265
>COG3482 Uncharacterized conserved protein [Function unknown]
Probab=31.56 E-value=65 Score=28.45 Aligned_cols=46 Identities=20% Similarity=0.229 Sum_probs=34.1
Q ss_pred cEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCcceEEE
Q 036073 14 VRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEAFKAVELWLAEKAIL 62 (241)
Q Consensus 14 ~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVv 62 (241)
++|.|.|| |-||..+++.. +.+..|-.-..+++.+|..|-.-.++|
T Consensus 2 ~~vvf~Gp--ti~~~~~~~v~-~~~~~~Pa~~g~~~~av~~~~~~i~ii 47 (237)
T COG3482 2 GPVVFAGP--TISHADAEKVL-DAIYLPPAAQGDVLSAVQRGPAAIGII 47 (237)
T ss_pred CceeecCC--CccHHHHHhhh-cccccCchhhhhHHHHHHhcCceEEEe
Confidence 34999999 57777887655 556667777889999999985555543
No 266
>PF14503 YhfZ_C: YhfZ C-terminal domain; PDB: 2OZZ_B.
Probab=30.98 E-value=3.2e+02 Score=24.12 Aligned_cols=112 Identities=13% Similarity=0.093 Sum_probs=59.7
Q ss_pred ceeecCCHHHHHHHHHcCCcceEEEeeecccccceecccccccc-CCeEEEEEEE---EeeeeeeecCCCCCcCCe---e
Q 036073 38 ETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLR-HRLHIVGEVQ---FVANFCLLALPGIREEKL---K 110 (241)
Q Consensus 38 ~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~-~~l~I~~E~~---l~I~~~L~~~~g~~~~~i---~ 110 (241)
.+..++--..=+++|.+|..||+||-- ......+.+ .++.|+-++- ..=.|.|+.+.+ ..+.| .
T Consensus 45 ~~aymRGa~~Rie~l~~g~yDfaVvS~--------lAA~~~i~~~~~l~i~~~fG~~sYvs~Hvli~~~~-~~~~i~dGm 115 (232)
T PF14503_consen 45 NFAYMRGAENRIEALKNGRYDFAVVSK--------LAAEHYIEEGEDLEIVLEFGPGSYVSEHVLIFRDG-EKKEIEDGM 115 (232)
T ss_dssp EEEE-S-HHHHHHHHHTTS-SEEEEEH--------HHHCCCCCC-SSEEEEEE--TTSSS--EEEEEETT--GGG-----
T ss_pred EEEeeccchHHHHHHHhCCcceEeehH--------HHHHHHHhhccCeEEEEeeCCCCcccceEEEEecC-Cccceeeee
Confidence 456777777789999999999999841 111122333 4566665553 233588887766 34556 8
Q ss_pred EEEecHHHHHHHHHHHHh---cCCceEeccCHHHHHHHHHhcCCCCeEEecCHh
Q 036073 111 CVLSHPQALASSDIVQTQ---LGVARENIDDTASAAQYVASNGLRDAGVVASAR 161 (241)
Q Consensus 111 ~V~SHpqal~Qc~~fl~~---~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~ 161 (241)
+|-=-+.-..|+.---.. +++++++. +..+-.+.+.++. =.|||-+..
T Consensus 116 RVGiD~~S~Dq~~LT~~~~~gk~Ve~Vei-~Y~q~~~~l~~g~--IDA~IWN~d 166 (232)
T PF14503_consen 116 RVGIDPSSIDQKILTEAEFEGKNVEFVEI-PYNQLLELLRSGE--IDAAIWNYD 166 (232)
T ss_dssp EEEE-TT-HHHHHHHHHHHTTS--EEEE---HHHHHHHHHHTS----EEEEE--
T ss_pred EeecCCCCccHHHHHHHHhCCCceEEEEe-cHHHHHHHHHCCC--ccEEEECCc
Confidence 998888888887533222 35666665 3566667776652 358886554
No 267
>PRK09034 aspartate kinase; Reviewed
Probab=30.62 E-value=4.7e+02 Score=25.08 Aligned_cols=98 Identities=14% Similarity=0.009 Sum_probs=58.5
Q ss_pred CCceEeccCHHHHHHHHHhcCCCCeEEecCHhh---HHhcCCceeecccCCCCCCceeEEEEeeCCCCC-C-----CCCC
Q 036073 130 GVARENIDDTASAAQYVASNGLRDAGVVASARA---AEIYGLNILADRIQDDPDNITRFLVLARDPIMP-R-----TDKP 200 (241)
Q Consensus 130 ~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~a---a~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~~-~-----~~~~ 200 (241)
+++.+..-|-.+|.++..-+ |-+-.+.| |..+++.+.-.+..+....-|..- ....... . ....
T Consensus 234 ~A~~l~~lsy~Ea~ela~~G-----akvlhp~ai~~a~~~~Ipi~v~~~~~p~~~GT~I~--~~~~~~~~~~Vk~It~~~ 306 (454)
T PRK09034 234 NPKSIKEITYREMRELSYAG-----FSVFHDEALIPAYRGGIPINIKNTNNPEDPGTLIV--PDRDNKNKNPITGIAGDK 306 (454)
T ss_pred CCeECCccCHHHHHHHHhCC-----cccCCHHHHHHHHHcCCCEEEEcCCCCCCCccEEE--eccccCccccceEEEecC
Confidence 34556667778888876432 22333332 356899999888776544455442 2211110 0 0112
Q ss_pred ceEEEEEe---cCCCchHHHHHHHHHHHCCceeeeee
Q 036073 201 FKTSIVFT---LDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 201 ~ktsi~~~---~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
+-+.|.+. .+++||.+.++++.|+++|||.-.|.
T Consensus 307 ~i~~Itv~~~~~~~~~g~~a~if~~la~~~I~Vd~i~ 343 (454)
T PRK09034 307 GFTSIYISKYLMNREVGFGRKVLQILEDHGISYEHMP 343 (454)
T ss_pred CEEEEEEccCCCCCCccHHHHHHHHHHHcCCeEEEEc
Confidence 23344333 35679999999999999999988773
No 268
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=29.73 E-value=2.1e+02 Score=21.81 Aligned_cols=119 Identities=15% Similarity=0.005 Sum_probs=54.6
Q ss_pred CCCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee---
Q 036073 34 YPNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK--- 110 (241)
Q Consensus 34 ~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~--- 110 (241)
+|+.++.....- ..+.+.+|++|+|++..+....+.. ...|.+..+.++ .+-+| ...++..+++++.
T Consensus 26 ~P~v~i~~~~~~--~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~-~~~~~~i~~~~l~~~~ 95 (194)
T cd08432 26 HPDIDLRLSTSD--RLVDFAREGIDLAIRYGDGDWPGLE---AERLMDEELVPV----CSPAL-LAGLPLLSPADLARHT 95 (194)
T ss_pred CCCeEEEEEecC--CccccccccccEEEEecCCCCCCcc---eEEccCCcEEEe----cCHHH-HHhcCCCCHHHhhcCc
Confidence 466544333321 4677899999999986443222211 122223333222 12223 2222233444443
Q ss_pred EEE-ecHH-HHHHHHHHHHhcCC--c-eEeccCHHHHHHHHHhcCCCCeEEecCHhhHHh
Q 036073 111 CVL-SHPQ-ALASSDIVQTQLGV--A-RENIDDTASAAQYVASNGLRDAGVVASARAAEI 165 (241)
Q Consensus 111 ~V~-SHpq-al~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 165 (241)
.|. +... ......+++...+. . ...++|.......++.+ ...++.+...++.
T Consensus 96 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 152 (194)
T cd08432 96 LLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAG---LGVALAPRALVAD 152 (194)
T ss_pred eEEecCcccccHHHHhcCCeeccccCCeEEECCHHHHHHHHHhC---CCeEEeeHHHhhh
Confidence 232 1111 11222222222222 2 24556666666777764 3578888876653
No 269
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=29.31 E-value=1e+02 Score=27.15 Aligned_cols=105 Identities=14% Similarity=0.139 Sum_probs=65.3
Q ss_pred cEEEEe-CCCCcHHHHHHHhhCC---CCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccc------cCC
Q 036073 14 VRISFK-GSPGSFTEDAALKAYP---NCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLL------RHR 83 (241)
Q Consensus 14 ~~ia~L-Gp~GtfS~~Aa~~~~~---~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~------~~~ 83 (241)
.|||+. ||....=+.+...+-. ..+++.+++..+.-.||.+|++|.-+.= ..-.|. ..+
T Consensus 1 ikIG~~~~~~~~i~~~v~~~~~~~Gi~vevv~f~D~~~~N~AL~~G~iDaN~fQ-----------h~~yl~~~n~~~~~~ 69 (237)
T PF03180_consen 1 IKIGVTPGPDAEILEAVKEKLKKKGIDVEVVEFSDYVQPNEALADGEIDANFFQ-----------HIPYLEQFNKENGYN 69 (237)
T ss_dssp EEEEEETTCHHHHHHHHHHHHHHTTEEEEEEEESSTTHHHHHHHTTSSSEEEEE-----------EHHHHHHHHHHHT--
T ss_pred CEEEEeCCCHHHHHHHHHHHHHhcCCeEEEEEecchhhcChHHHCCCcceeccC-----------CHHHHHHHHHHCCCc
Confidence 378887 4544443433332222 2688999999999999999999987642 333332 256
Q ss_pred eEEEEEEEEeeeeeeecCCCCCcCCee---E--EEecHHHHHHHHHHHHhcC
Q 036073 84 LHIVGEVQFVANFCLLALPGIREEKLK---C--VLSHPQALASSDIVQTQLG 130 (241)
Q Consensus 84 l~I~~E~~l~I~~~L~~~~g~~~~~i~---~--V~SHpqal~Qc~~fl~~~~ 130 (241)
|..++.+++. .+.|.+.+-.++++|. + |-.-|.-.++.-..|.+.|
T Consensus 70 L~~v~~~~~~-p~glYS~k~~sl~~lp~Ga~VaIpnD~sN~~RaL~lLq~aG 120 (237)
T PF03180_consen 70 LVPVGPTYIE-PMGLYSKKYKSLDDLPDGATVAIPNDPSNQARALKLLQEAG 120 (237)
T ss_dssp EEEEEEEEE----EEEESSSSSGGGS-TTEEEEEESSHHHHHHHHHHHHHTT
T ss_pred EEEecceeEE-eEEEeecccCchhhcCCCCEEEEeCCccchhHHHHHHHhCC
Confidence 8888876665 4888887777777776 2 4455555666666666644
No 270
>TIGR00657 asp_kinases aspartate kinase. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. This may be a feature of a number of closely related forms, including a paralog from B. subtilis.
Probab=28.12 E-value=98 Score=29.44 Aligned_cols=29 Identities=24% Similarity=0.428 Sum_probs=25.5
Q ss_pred ecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 208 TLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 208 ~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+.+.||.+.++++.|+++|||+..|.+.
T Consensus 387 ~~~~~~g~~a~if~~La~~~Inv~~i~~s 415 (441)
T TIGR00657 387 GMKSAPGVASKIFEALAQNGINIEMISSS 415 (441)
T ss_pred CCCCCCchHHHHHHHHHHCCCCEEEEEec
Confidence 35688999999999999999999998653
No 271
>PLN02550 threonine dehydratase
Probab=26.57 E-value=67 Score=32.25 Aligned_cols=57 Identities=23% Similarity=0.266 Sum_probs=37.1
Q ss_pred cccCCCCCC--ceeEEEEeeCCCCCCCCCCceEEEEEecCCCchHHHHHHHHHHHCCceeeeeeee
Q 036073 173 DRIQDDPDN--ITRFLVLARDPIMPRTDKPFKTSIVFTLDEGPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 173 ~~I~d~~~N--~TRF~vl~~~~~~~~~~~~~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
.+++|++.- +=||++=+|... .+--.+.|++|.|||+|.+.|+.|..+ -|+|.++=|
T Consensus 485 ~~l~~~~~~~~~LR~v~g~ra~~------~~E~l~~v~fPErpGAl~~Fl~~lg~~-~nITeF~YR 543 (591)
T PLN02550 485 VNLTSNDLVKDHLRYLMGGRAIV------KDELLYRFVFPERPGALMKFLDAFSPR-WNISLFHYR 543 (591)
T ss_pred EeCCCChHHhhhhhheecccccc------CceEEEEEEecCcCCHHHHHHHhhCCC-CceeeEEee
Confidence 456776553 446665345422 124577899999999999999988752 355555443
No 272
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=26.53 E-value=1.6e+02 Score=25.68 Aligned_cols=52 Identities=12% Similarity=-0.039 Sum_probs=32.0
Q ss_pred CccEEEEeCCCCcHHHHH-HHhh---CCC-----CceeecC-CHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDA-ALKA---YPN-----CETIPCD-EFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~A-a~~~---~~~-----~~~~~~~-s~~~v~~av~~g~~d~gVvP 63 (241)
...||++.+|..+..... ...+ .+- ...+.+. +..+++.+|.+|++|.++++
T Consensus 134 ~Gk~v~~~~~~s~~~~~~~~~~l~~~~g~~~~~~~~~v~~~~~~~~~~~al~~G~vDa~~~~ 195 (288)
T TIGR03431 134 KGKTFGFVDPNSTSGFLVPSYYLFKKNGIKPKEYFKKVTFSGSHEAAILAVANGTVDAATTN 195 (288)
T ss_pred CCCEEEeeCCCcchhhHHHHHHHHHhcCCChHHhHHhheecCchHHHHHHHHcCCCCeEecc
Confidence 357899987554432221 1111 111 1223344 78999999999999999975
No 273
>PRK06635 aspartate kinase; Reviewed
Probab=26.48 E-value=71 Score=29.87 Aligned_cols=27 Identities=19% Similarity=0.427 Sum_probs=24.3
Q ss_pred cCCCchHHHHHHHHHHHCCceeeeeee
Q 036073 209 LDEGPGVLTKALAVFALREINLTKVFV 235 (241)
Q Consensus 209 ~~~~pGaL~~~L~~fa~~~iNLt~IeS 235 (241)
..++||.|.++++.|+++|||+-.|.+
T Consensus 270 ~~~~~g~l~~i~~~L~~~~I~i~~is~ 296 (404)
T PRK06635 270 VPDKPGIAAQIFGALAEANINVDMIVQ 296 (404)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEe
Confidence 578999999999999999999987754
No 274
>PRK08210 aspartate kinase I; Reviewed
Probab=26.48 E-value=75 Score=29.79 Aligned_cols=95 Identities=12% Similarity=0.002 Sum_probs=52.5
Q ss_pred ceEeccCHHHHHHHHHhcCCCCeEEecCHhh---HHhcCCceeecccCCCCCCceeEEEEeeCCCC-----CCC------
Q 036073 132 ARENIDDTASAAQYVASNGLRDAGVVASARA---AEIYGLNILADRIQDDPDNITRFLVLARDPIM-----PRT------ 197 (241)
Q Consensus 132 ~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~a---a~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~-----~~~------ 197 (241)
+.++.-|..++.++...+ +-+-.+.| +..+|.++.-.+..+... -|..- ...+.. ...
T Consensus 195 ~~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~~~~~~i~i~i~~~~~~~~-gT~I~--~~~~~~~~~~~~~~~v~~It 266 (403)
T PRK08210 195 RLLDVVSYNEVFQMAYQG-----AKVIHPRAVEIAMQANIPLRIRSTYSDSP-GTLIT--SLGDAKGGIDVEERLITGIA 266 (403)
T ss_pred eECCccCHHHHHHHHHCC-----ccccCHHHHHHHHHCCCeEEEEecCCCcC-CcEEE--ecCccccccccccCceEEEE
Confidence 334445556666655432 22333333 456788888877765322 34331 211110 000
Q ss_pred CCCceEEEEEe-cCCCchHHHHHHHHHHHCCceeeeee
Q 036073 198 DKPFKTSIVFT-LDEGPGVLTKALAVFALREINLTKVF 234 (241)
Q Consensus 198 ~~~~ktsi~~~-~~~~pGaL~~~L~~fa~~~iNLt~Ie 234 (241)
...+-+.+.+. .++.||.|.++++.|+++|||+-.|.
T Consensus 267 ~~~~i~~isv~~~~~~~g~la~If~~L~~~~I~i~~i~ 304 (403)
T PRK08210 267 HVSNVTQIKVKAKENAYDLQQEVFKALAEAGISVDFIN 304 (403)
T ss_pred EcCCcEEEEEecCCCcchHHHHHHHHHHHcCCeEEEEE
Confidence 01223344333 34569999999999999999998773
No 275
>TIGR03431 PhnD phosphonate ABC transporter, periplasmic phosphonate binding protein. Note that this model does not identify all phnD-subfamily genes with evident phosphonate context, but all sequences above the trusted context may be inferred to bind phosphonate compounds even in the absence of such context. Furthermore, there is ample evidence to suggest that many other members of the TIGR01098 subfamily have a different primary function.
Probab=25.74 E-value=2e+02 Score=25.08 Aligned_cols=52 Identities=2% Similarity=-0.008 Sum_probs=36.6
Q ss_pred CccEEEEeCCCCcHHHHHH-H---hhC----C-CCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 12 TKVRISFKGSPGSFTEDAA-L---KAY----P-NCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa-~---~~~----~-~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
...+|++.++.+.-..... . +++ + +.+++...++.+.+.++.+|++|+++..
T Consensus 27 ~~l~vg~~~~~~~~~~~~~~~~l~~~l~~~~g~~v~~~~~~~~~~~~~al~~g~~D~~~~~ 87 (288)
T TIGR03431 27 KELNFGIIPTENASDLKQRWEPLADYLSKKLGVKVKLFFATDYAGVIEGMRFGKVDIAWYG 87 (288)
T ss_pred CeEEEEEcCCCCHHHHHHHHHHHHHHHHHHhCCcEEEEeCCCHHHHHHHHHcCCccEEEEC
Confidence 5689999998765432221 1 112 1 2456678899999999999999999854
No 276
>cd00404 Aconitase_swivel Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The aconitase family contains the following proteins: - Iron-responsive element binding protein (IRE-BP). IRE-BP is a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid.
Probab=25.67 E-value=52 Score=24.68 Aligned_cols=49 Identities=24% Similarity=0.337 Sum_probs=37.4
Q ss_pred cEEEEeCC---CCcHHHHHHHhhC-CCCceeecCCHHHHHHHHHcCCcceEEEeee
Q 036073 14 VRISFKGS---PGSFTEDAALKAY-PNCETIPCDEFEEAFKAVELWLAEKAILPIE 65 (241)
Q Consensus 14 ~~ia~LGp---~GtfS~~Aa~~~~-~~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 65 (241)
..|-..|. .||..|.|+.... -+.+.+-..+|..+|. ++....|++|++
T Consensus 16 ~~iiVaG~nfG~GSSRE~A~~al~~~Gi~aVia~sfa~If~---rN~~n~Gll~l~ 68 (88)
T cd00404 16 PGVVIGDENYGTGSSREHAALELRLLGGRAVIAKSFARIFF---RNLVDQGLLPLE 68 (88)
T ss_pred CEEEEecCCeecCCCHHHHHHHHHHhCCCEEEEeCHHHHHH---hhHHhcCCceEE
Confidence 34666664 6999999998643 3578899999999995 455678899986
No 277
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=25.66 E-value=4.5e+02 Score=22.86 Aligned_cols=145 Identities=10% Similarity=-0.038 Sum_probs=68.6
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEeeec--ccccceeccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCee
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILPIEN--SSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGIREEKLK 110 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiEN--S~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~~~~~i~ 110 (241)
+|+.++.-. .+-+++.+.+.+|++|+|+..... .....+ ....|.+..+.++. +-.|-+.. .-..+.+..
T Consensus 119 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l--~~~~l~~~~~~~~~----~~~~~~~~-~~~~l~~~~ 191 (296)
T PRK11062 119 DESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEGL--FSKKLGECGVSFFC----TNPLPEKP-FPACLEERR 191 (296)
T ss_pred CCceEEEEEeCCHHHHHHHHHcCCCCEEEecCCCccccccch--hhhhhhccCcceEe----cCCCcccc-ChHHHhcCC
Confidence 466655433 477899999999999999974221 101111 11122233332221 11221111 001122333
Q ss_pred EEEec-HHH-HHHHHHHHHhcCCc--e-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHhc----CCceeecccCCCCCC
Q 036073 111 CVLSH-PQA-LASSDIVQTQLGVA--R-ENIDDTASAAQYVASNGLRDAGVVASARAAEIY----GLNILADRIQDDPDN 181 (241)
Q Consensus 111 ~V~SH-pqa-l~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y----gL~il~~~I~d~~~N 181 (241)
.|... ... ..+-.+|+...+.. . ..++|.......+.++ ...++.+...++.+ +|..+. +...-
T Consensus 192 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~~~~~~l~~l~----~~~~~ 264 (296)
T PRK11062 192 LLIPGRRTMLGRKLLNWFNSQGLNVEILGEFDDAALMKAFGAYH---DAIFVAPSLYAQDFYADHSVVEIG----RVDNV 264 (296)
T ss_pred eeecCCCchHHHHHHHHHHHcCCCceeeeeeCcHHHHHHHHHcC---CceEECCHHHHHHHHHcCCeEEcC----Ccccc
Confidence 33221 111 23345667665543 2 2455555555555543 45788888877643 244332 11223
Q ss_pred ceeEEEEeeCC
Q 036073 182 ITRFLVLARDP 192 (241)
Q Consensus 182 ~TRF~vl~~~~ 192 (241)
...|.++.++.
T Consensus 265 ~~~~~lv~~~~ 275 (296)
T PRK11062 265 KEEYHVIFAER 275 (296)
T ss_pred ceEEEEEEecC
Confidence 45666666543
No 278
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=25.58 E-value=3.1e+02 Score=20.98 Aligned_cols=30 Identities=13% Similarity=0.146 Sum_probs=23.1
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcceEEEe
Q 036073 34 YPNCETIPC-DEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 34 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 63 (241)
+|+.++... .+..++.+.+.+|++|+|+..
T Consensus 26 ~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~ 56 (198)
T cd08447 26 LPDVDLVLREMVTTDQIEALESGRIDLGLLR 56 (198)
T ss_pred CCCeEEEEEeCCHHHHHHHHHcCCceEEEec
Confidence 466555432 367899999999999999974
No 279
>cd04911 ACT_AKiii-YclM-BS_1 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Bacillus subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from Bacillus subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=25.56 E-value=71 Score=23.21 Aligned_cols=24 Identities=17% Similarity=0.235 Sum_probs=20.9
Q ss_pred CCCchHHHHHHHHHHHCCceeeee
Q 036073 210 DEGPGVLTKALAVFALREINLTKV 233 (241)
Q Consensus 210 ~~~pGaL~~~L~~fa~~~iNLt~I 233 (241)
..+.|-+.++|++|.++||+.-.+
T Consensus 12 n~evGF~rk~L~I~E~~~is~Eh~ 35 (76)
T cd04911 12 NREVGFGRKLLSILEDNGISYEHM 35 (76)
T ss_pred cchhcHHHHHHHHHHHcCCCEeee
Confidence 567899999999999999987554
No 280
>PRK12483 threonine dehydratase; Reviewed
Probab=25.23 E-value=63 Score=31.87 Aligned_cols=29 Identities=31% Similarity=0.447 Sum_probs=23.2
Q ss_pred eEEEEEecCCCchHHHHHHHHHHH-CCcee
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFAL-REINL 230 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~-~~iNL 230 (241)
-..+.|++|.+||+|.+.|+.+.. ++|.+
T Consensus 440 E~~~~v~iPE~pGa~~~f~~~l~~~~niTe 469 (521)
T PRK12483 440 ERLFRFEFPERPGALMKFLSRLGPRWNISL 469 (521)
T ss_pred eEEEEEEcCCCCcHHHHHHHHhCCCcceee
Confidence 346778999999999999999986 35543
No 281
>cd01580 AcnA_IRP_Swivel Aconitase A swivel domain. This is the major form of the TCA cycle enzyme aconitate hydratase, also known as aconitase and citrate hydro-lyase. It includes bacterial and archaeal aconitase A, and the eukaryotic cytosolic form of aconitase. This group also includes sequences that have been shown to act as an iron-responsive element (IRE) binding protein in animals and may have the same role in other eukaryotes. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism.
Probab=24.98 E-value=63 Score=27.24 Aligned_cols=59 Identities=22% Similarity=0.349 Sum_probs=38.9
Q ss_pred EEEeCC---CCcHHHHHHHhhC-CCCceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccc
Q 036073 16 ISFKGS---PGSFTEDAALKAY-PNCETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDL 78 (241)
Q Consensus 16 ia~LGp---~GtfS~~Aa~~~~-~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~ 78 (241)
|-..|. .||..|.||.... -+...+-..||..++.. +-+..|++|++ -..+...+++.+
T Consensus 99 IIvaG~nfG~GSSRE~Aa~~~~~lGi~aVIA~SFarI~~~---Nli~~Gllpl~-~~~~~~~~~l~l 161 (171)
T cd01580 99 VILAGKEYGSGSSRDWAAKGPFLLGVKAVIAESFERIHRS---NLVGMGILPLQ-FPPGENADSLGL 161 (171)
T ss_pred EEEccCcccCCCcHHHHHHHHHHhCCCEEEEccHHHHHHh---hHhhcCcceEE-eCCccCHHhhCC
Confidence 445555 4777777776433 34678899999999954 44667899985 334555555544
No 282
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=24.89 E-value=3.5e+02 Score=21.40 Aligned_cols=31 Identities=10% Similarity=-0.111 Sum_probs=22.5
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCcceEEEee
Q 036073 34 YPNCETIP-CDEFEEAFKAVELWLAEKAILPI 64 (241)
Q Consensus 34 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPi 64 (241)
+|+.++.- ..+-.++.+.+.+|++|+|+...
T Consensus 26 ~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 26 APGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred CCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 56654432 23566889999999999999853
No 283
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=24.87 E-value=4.3e+02 Score=22.44 Aligned_cols=112 Identities=14% Similarity=0.175 Sum_probs=57.9
Q ss_pred CceeecCCHHHHHHHHHcCCcceEEEeeecccccceeccccccccCCeEEEEEEEEeeeeeeecCCCC----CcCCee--
Q 036073 37 CETIPCDEFEEAFKAVELWLAEKAILPIENSSGGSIHHNYDLLLRHRLHIVGEVQFVANFCLLALPGI----REEKLK-- 110 (241)
Q Consensus 37 ~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~g~----~~~~i~-- 110 (241)
.++++. ++++++++++.|++|.++-++.-+ -+. +..+....-+ +.....++++++. +++++.
T Consensus 67 ~~~~~~-~~~~~~~~l~~g~~Di~~~~~~~t--------~eR--~~~~~fs~p~-~~~~~~~~~~~~~~~~~~~~dl~g~ 134 (260)
T PRK15010 67 CTWVAS-DFDALIPSLKAKKIDAIISSLSIT--------DKR--QQEIAFSDKL-YAADSRLIAAKGSPIQPTLDSLKGK 134 (260)
T ss_pred eEEEeC-CHHHHHHHHHCCCCCEEEecCcCC--------HHH--Hhhcccccce-EeccEEEEEECCCCCCCChhHcCCC
Confidence 456664 689999999999999776433211 110 0111111111 1233455555442 122222
Q ss_pred EEEecHHHHHHHHHHHHh----cCCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 111 CVLSHPQALASSDIVQTQ----LGVARENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 111 ~V~SHpqal~Qc~~fl~~----~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+|--..-... ..|+.+ .++..+.+.+..++.+++..+ +-.+.|++...+.
T Consensus 135 ~Igv~~gs~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--riDa~i~d~~~~~ 188 (260)
T PRK15010 135 HVGVLQGSTQ--EAYANETWRSKGVDVVAYANQDLVYSDLAAG--RLDAALQDEVAAS 188 (260)
T ss_pred EEEEecCchH--HHHHHHhcccCCceEEecCCHHHHHHHHHcC--CccEEEeCcHHHH
Confidence 2322221111 134432 356667777777778888765 3457777765543
No 284
>PRK07377 hypothetical protein; Provisional
Probab=24.50 E-value=1.1e+02 Score=26.08 Aligned_cols=31 Identities=10% Similarity=-0.069 Sum_probs=26.6
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 33 AYPNCETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 33 ~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
|+-..+++++++.+++.+++.+|++|.++.+
T Consensus 106 y~~rlElv~y~~~~~l~~aL~~~eVh~~c~~ 136 (184)
T PRK07377 106 YHLRLELVVYPDLQALEQALRDKEVHAICLE 136 (184)
T ss_pred hCceeeEEecCCHHHHHHHHhcCCccEEecC
Confidence 3345789999999999999999999988764
No 285
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a vari
Probab=23.64 E-value=1.1e+02 Score=23.61 Aligned_cols=31 Identities=13% Similarity=0.151 Sum_probs=23.4
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcceEEEe
Q 036073 33 AYPNCETIPC-DEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 33 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 63 (241)
.+|+.++... .+-.++++.+.+|++|+|++.
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~~~~Dl~i~~ 56 (185)
T cd08439 25 VYPRLAIEVVCKRTPRLMEMLERGEVDLALIT 56 (185)
T ss_pred HCCCeEEEEEECChHHHHHHHHCCCCcEEEEe
Confidence 3577655443 356789999999999999985
No 286
>PRK03381 PII uridylyl-transferase; Provisional
Probab=23.48 E-value=96 Score=32.06 Aligned_cols=31 Identities=23% Similarity=0.402 Sum_probs=26.9
Q ss_pred eEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 202 KTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 202 ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
-|.+.+..+|+||-++++-++|+.+|+|+-.
T Consensus 599 ~~~V~V~~~DrpGLfa~i~~vL~~~glnI~d 629 (774)
T PRK03381 599 MVEVTVVAPDRRGLLSKAAGVLALHRLRVRS 629 (774)
T ss_pred eEEEEEEecCCccHHHHHHHHHHHCCCeEEE
Confidence 4666677799999999999999999999854
No 287
>PRK13584 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=23.45 E-value=3.3e+02 Score=23.59 Aligned_cols=149 Identities=15% Similarity=0.136 Sum_probs=82.1
Q ss_pred cEEEEeCCCCcHHHHHHHhhCC-C------------Ccee--------ecCCHHHHHHHHHcCCcceEEEeeecccccce
Q 036073 14 VRISFKGSPGSFTEDAALKAYP-N------------CETI--------PCDEFEEAFKAVELWLAEKAILPIENSSGGSI 72 (241)
Q Consensus 14 ~~ia~LGp~GtfS~~Aa~~~~~-~------------~~~~--------~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V 72 (241)
++||. |+|.-++.+...+-. + -+++ .+---.|+-.-|+.|.+|+||+=
T Consensus 2 l~iAl--pKGRL~e~~~~ll~~aG~~~~~~~~~~~~R~L~~~~~~i~~~~~r~~DIp~yV~~G~aDlGI~G--------- 70 (204)
T PRK13584 2 LRIAI--AKGRLMDSLINYLDVIEYTTLSETLKNRERQLLLSVDNIECILVKGSDVPIYVEQGMADIGIVG--------- 70 (204)
T ss_pred EEEEe--cCcccHHHHHHHHHHcCCCcccccCccCCcceeccCCCeEEEEECHHHHHHHHhCCCccEEEee---------
Confidence 57787 799988888764310 0 1111 11223578899999999999963
Q ss_pred eccccccccCCeEEEEEEEEeee---eeeecCCCCCcCCeeEEEecHHHHHHHHHHHHhcCCc--eEeccCHHHHHHHHH
Q 036073 73 HHNYDLLLRHRLHIVGEVQFVAN---FCLLALPGIREEKLKCVLSHPQALASSDIVQTQLGVA--RENIDDTASAAQYVA 147 (241)
Q Consensus 73 ~~t~d~L~~~~l~I~~E~~l~I~---~~L~~~~g~~~~~i~~V~SHpqal~Qc~~fl~~~~~~--~~~~~sTa~Aa~~v~ 147 (241)
.|.|.+.+-.+..-..|... ++++++|+. .+.++|.+-..-+. ++|++++|++ .+..+-.-|.|=.+
T Consensus 71 ---~D~l~E~~~~v~el~dLgfG~crl~vA~p~~~--~~~~rVATkyp~it--~~yf~~~Gi~~~ii~l~GsvElaP~~- 142 (204)
T PRK13584 71 ---SDILDERQYNVNNLLNMPFGACHFAVAAKPET--TNYRKIATSYVHTA--ETYFKSKGIDVELIKLNGSVELACVV- 142 (204)
T ss_pred ---eeEeeccCCCeEEEecCCCCcEEEEEEEEcCC--CCceEEEeCcHHHH--HHHHHHcCCeEEEEECCCceeecccc-
Confidence 24444433223333344443 356665543 35577877766554 6799998764 34443333322211
Q ss_pred hcCCCC-eEEe-cCHhhHHhcCCceeecccCCCCCCceeEEE
Q 036073 148 SNGLRD-AGVV-ASARAAEIYGLNILADRIQDDPDNITRFLV 187 (241)
Q Consensus 148 ~~~~~~-~aAI-~s~~aa~~ygL~il~~~I~d~~~N~TRF~v 187 (241)
+.-+ .+=| .+-.--+.+||+++++ |- +-.+|++.
T Consensus 143 --GlAD~IvDiv~TG~TLr~NgL~~~e~-I~---~ssa~LI~ 178 (204)
T PRK13584 143 --DMVDGIVDIVQTGTTLKANGLVEKQH-IS---DINARLIT 178 (204)
T ss_pred --CCccEEEEEECccHHHHHCCCEEEEE-EE---eeEEEEEE
Confidence 1111 1123 3556678899988844 33 23455543
No 288
>cd08431 PBP2_HupR The C-terminal substrate binding domain of LysR-type transcriptional regulator, HupR, which regulates expression of the heme uptake receptor HupA; contains the type 2 periplasmic binding fold. HupR, a member of the LysR family, activates hupA transcription under low-iron conditions in the presence of hemin. The expression of many iron-uptake genes, such as hupA, is regulated at the transcriptional level by iron and an iron-binding repressor protein called Fur (ferric uptake regulation). Under iron-abundant conditions with heme, the active Fur repressor protein represses transcription of the iron-uptake gene hupA, and prevents transcriptional activation via HupR. Under low-iron conditions with heme, the Fur repressor is inactive and transcription of the hupA is allowed. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, p
Probab=23.30 E-value=1e+02 Score=23.84 Aligned_cols=32 Identities=9% Similarity=-0.023 Sum_probs=23.9
Q ss_pred hhCCCCceeecC-CHHHHHHHHHcCCcceEEEe
Q 036073 32 KAYPNCETIPCD-EFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 32 ~~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvP 63 (241)
+.+|+.++.-.. +.+++.+++.+|++|+|++.
T Consensus 24 ~~~P~v~i~i~~~~~~~~~~~l~~g~~D~~i~~ 56 (195)
T cd08431 24 QLNKATRIRLSEEVLGGTWDALASGRADLVIGA 56 (195)
T ss_pred HHCCCCceEEEEeccchHHHHHhCCCCCEEEEe
Confidence 346776654433 45688999999999999975
No 289
>TIGR01327 PGDH D-3-phosphoglycerate dehydrogenase. This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli.
Probab=23.25 E-value=58 Score=31.98 Aligned_cols=75 Identities=16% Similarity=0.183 Sum_probs=46.4
Q ss_pred HhhHHhcCCceeecccCC--CCCCceeEEEEeeCCCC------CCCC--------------CCceEEEEEecCCCchHHH
Q 036073 160 ARAAEIYGLNILADRIQD--DPDNITRFLVLARDPIM------PRTD--------------KPFKTSIVFTLDEGPGVLT 217 (241)
Q Consensus 160 ~~aa~~ygL~il~~~I~d--~~~N~TRF~vl~~~~~~------~~~~--------------~~~ktsi~~~~~~~pGaL~ 217 (241)
...|+-.|+++....... ...|.-++-+-+..... -..+ ..+-.+|++.-.|+||.+.
T Consensus 387 ~~iA~e~GI~v~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~gGg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I~ 466 (525)
T TIGR01327 387 PAVAKERGITVEESKSESSPDYKNYLSVTVTGDSGTVSVAGTVFGGFSPRIVEIDGFHVDLEPEGIMLIILHLDKPGVIG 466 (525)
T ss_pred HHHHHHcCCEEEEEEccCCCCCCCEEEEEEEeCCcEEEEEEEEecCCcEEEEEECCEEEEEecCccEEEEEecCcCCcch
Confidence 466888899986543332 23465555543322110 0000 0123456666689999999
Q ss_pred HHHHHHHHCCceeeeee
Q 036073 218 KALAVFALREINLTKVF 234 (241)
Q Consensus 218 ~~L~~fa~~~iNLt~Ie 234 (241)
++.+.|..++||+....
T Consensus 467 ~v~~~L~~~~iNIa~m~ 483 (525)
T TIGR01327 467 KVGTLLGTAGINIASMQ 483 (525)
T ss_pred HHHhHHhhcCCChHHcE
Confidence 99999999999997653
No 290
>PRK05092 PII uridylyl-transferase; Provisional
Probab=22.94 E-value=1.3e+02 Score=31.76 Aligned_cols=32 Identities=16% Similarity=0.248 Sum_probs=28.1
Q ss_pred ceEEEEEecCCCchHHHHHHHHHHHCCceeee
Q 036073 201 FKTSIVFTLDEGPGVLTKALAVFALREINLTK 232 (241)
Q Consensus 201 ~ktsi~~~~~~~pGaL~~~L~~fa~~~iNLt~ 232 (241)
+-|.+.+..+|+||-|.++.+.|+.+|+|+-.
T Consensus 731 ~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~ 762 (931)
T PRK05092 731 GVTEVTVLAADHPGLFSRIAGACAAAGANIVD 762 (931)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEE
Confidence 35777788899999999999999999999854
No 291
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=22.92 E-value=5.1e+02 Score=22.52 Aligned_cols=140 Identities=16% Similarity=0.116 Sum_probs=75.2
Q ss_pred ccEEEEeCCCCcHHHHHHHhhC--------C---CCcee----------ecCCHHHHHHHHHcCCcceEEEeeecccccc
Q 036073 13 KVRISFKGSPGSFTEDAALKAY--------P---NCETI----------PCDEFEEAFKAVELWLAEKAILPIENSSGGS 71 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~--------~---~~~~~----------~~~s~~~v~~av~~g~~d~gVvPiENS~~G~ 71 (241)
+++||. |+|.-.+.+...+- . +-+++ .+---.|+-.-|+.|.+|+||+=
T Consensus 3 ~l~iAl--pKGRL~e~t~~ll~~aG~~~~~~~~~~R~L~~~~~~~~i~~~~~r~~DIp~yV~~G~~DlGItG-------- 72 (215)
T PRK01686 3 MLTIAL--PKGRILEETLPLLAKAGIDPSEDPDKSRKLIFPTPEPDVRFLLVRATDVPTYVEHGAADLGIVG-------- 72 (215)
T ss_pred cEEEEe--cCcccHHHHHHHHHHcCCCcccCCCCCcceEeecCCCCEEEEEECHHHHHHHHhCCCccEEEee--------
Confidence 467787 69999888765431 0 01111 22234688899999999999963
Q ss_pred eeccccccccCCeEEEEEEEEeee---eeeecCCCCCc------CCeeEEEecHHHHHHHHHHHHhcCCc--eEeccCHH
Q 036073 72 IHHNYDLLLRHRLHIVGEVQFVAN---FCLLALPGIRE------EKLKCVLSHPQALASSDIVQTQLGVA--RENIDDTA 140 (241)
Q Consensus 72 V~~t~d~L~~~~l~I~~E~~l~I~---~~L~~~~g~~~------~~i~~V~SHpqal~Qc~~fl~~~~~~--~~~~~sTa 140 (241)
.|+|.+.+-.+.--..|... .+++++++... ..-++|.+-.--+. ++|++++++. .+..+-..
T Consensus 73 ----~D~l~E~~~~v~~l~dLgfG~crl~vAvp~~~~~~~~~~~~~~~rIATkYp~it--~~yf~~~gv~~~iv~l~Gsv 146 (215)
T PRK01686 73 ----KDVLLEHGKDLYEPLDLGIGKCRMSVAVPPGFDYAPAVKQGPRLRVATKYPNIA--RRYFAEKGEQVEIIKLYGSV 146 (215)
T ss_pred ----eeEeeecCCCeEEEecCCccCEEEEEEEECcccccchhhccCCCEEEeCCHHHH--HHHHHHcCCeEEEEECcCce
Confidence 24444332222222233333 34555544221 12245665555444 5799998764 34443333
Q ss_pred HHHHHHHhcCCCCeEEe----cCHhhHHhcCCceeec
Q 036073 141 SAAQYVASNGLRDAGVV----ASARAAEIYGLNILAD 173 (241)
Q Consensus 141 ~Aa~~v~~~~~~~~aAI----~s~~aa~~ygL~il~~ 173 (241)
|+|=.+ +-+-+| .+-..-+.+||++++.
T Consensus 147 E~aP~~-----GlAD~IvDivsTG~TLr~NgL~~ie~ 178 (215)
T PRK01686 147 ELAPLV-----GLADAIVDIVETGNTLRANGLVEVEE 178 (215)
T ss_pred eecccc-----CCccEEEEeecChHHHHHCcCEEeeE
Confidence 332211 111122 3556678899999863
No 292
>TIGR01728 SsuA_fam ABC transporter, substrate-binding protein, aliphatic sulfonates family. Members of this family are substrate-binding periplasmic proteins of ABC transporters. This subfamily includes SsuA, a member of a transporter operon needed to obtain sulfur from aliphatic sulfonates. Related proteins outside the scope of this model include taurine (NH2-CH2-CH2-S03H) binding proteins, the probable sulfate ester binding protein AtsR, and the probable aromatic sulfonate binding protein AsfC. All these families make sulfur available when Cys and sulfate levels are low. Please note that phylogenetic analysis by neighbor-joining suggests that a number of sequences belonging to this family have been excluded because of scoring lower than taurine-binding proteins.
Probab=22.49 E-value=1.6e+02 Score=25.05 Aligned_cols=48 Identities=17% Similarity=0.020 Sum_probs=31.1
Q ss_pred ccEEEEeCCCCcHHHHHHHhhCC--C-----CceeecCCHHHHHHHHHcCCcceEEEe
Q 036073 13 KVRISFKGSPGSFTEDAALKAYP--N-----CETIPCDEFEEAFKAVELWLAEKAILP 63 (241)
Q Consensus 13 ~~~ia~LGp~GtfS~~Aa~~~~~--~-----~~~~~~~s~~~v~~av~~g~~d~gVvP 63 (241)
..+|++- .|+-++.....++. + .+.++ .+..++..++.+|++|.++++
T Consensus 101 Gk~i~~~--~~~~~~~~~~~~l~~~G~~~~~v~~~~-~~~~~~~~al~~g~vda~~~~ 155 (288)
T TIGR01728 101 GKRIAVP--KGGSGHDLLLRALLKAGLSGDDVTILY-LGPSDARAAFAAGQVDAWAIW 155 (288)
T ss_pred CCEEEec--CCccHHHHHHHHHHHcCCCccceeEEe-cCcHHHHHHHHCCCCCEEEec
Confidence 3578863 45545554444442 1 22333 457899999999999999986
No 293
>COG0040 HisG ATP phosphoribosyltransferase [Amino acid transport and metabolism]
Probab=22.01 E-value=5.1e+02 Score=23.72 Aligned_cols=88 Identities=11% Similarity=-0.009 Sum_probs=53.9
Q ss_pred CccEEEEeCCCCcHHHHHHHhhCCCCceeecCCHHHH-HHHHHcCCcceEEEeeecccccceecc-cccccc--------
Q 036073 12 TKVRISFKGSPGSFTEDAALKAYPNCETIPCDEFEEA-FKAVELWLAEKAILPIENSSGGSIHHN-YDLLLR-------- 81 (241)
Q Consensus 12 ~~~~ia~LGp~GtfS~~Aa~~~~~~~~~~~~~s~~~v-~~av~~g~~d~gVvPiENS~~G~V~~t-~d~L~~-------- 81 (241)
+..|+.+.+|+++. +.....+.+. ..-..+|..+ -+-.+.+..++=++.+.=|+|+....- -|++.+
T Consensus 93 G~crl~vAvp~~~~-~~~~~~l~~~--~rIATkYp~l~~~yf~~~g~~~~Ii~l~GsvE~aP~~GlADaIvDivsTG~TL 169 (290)
T COG0040 93 GGCRLVVAVPEESD-YTSPEDLKGR--LRIATKYPNLARKYFAEKGIDVEIIKLSGSVELAPALGLADAIVDIVSTGTTL 169 (290)
T ss_pred CcEEEEEEecCCcC-ccChhHhcCC--ceEEEccHHHHHHHHHHcCceEEEEEccCcEeeccccCccceEEEeecCCHhH
Confidence 45678888888865 2222222222 1111222222 222355668888998888888764332 455443
Q ss_pred --CCeEEEEEEEEeeeeeeecCCC
Q 036073 82 --HRLHIVGEVQFVANFCLLALPG 103 (241)
Q Consensus 82 --~~l~I~~E~~l~I~~~L~~~~g 103 (241)
.+|.++ |..+.++.+|+++++
T Consensus 170 kaNgL~~i-d~i~~ssa~LI~n~~ 192 (290)
T COG0040 170 KANGLKEI-EVIYDSSARLIVNAK 192 (290)
T ss_pred HHCCCEEE-EEEEeeEEEEEeccc
Confidence 679999 889999999999854
No 294
>PF08212 Lipocalin_2: Lipocalin-like domain; InterPro: IPR000566 Proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids share limited regions of sequence homology and a common tertiary structure architecture [, , , , ]. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing a internal ligand binding site [, ]. The name 'lipocalin' has been proposed [] for this protein family, but cytosolic fatty-acid binding proteins are also included. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these [, ]. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); alpha-1-acid glycoprotein (orosomucoid) []; aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain []; crustacyanin []; epididymal-retinoic acid binding protein (E-RABP) []; insectacyanin; odorant-binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin; probasin (PB), a rat prostatic protein; prostaglandin D synthase (5.3.99.2 from EC) []; purpurin; Von Ebner's gland protein (VEGP) []; and lizard epididymal secretory protein IV (LESP IV) [].; GO: 0005488 binding; PDB: 3EBW_B 1QWD_A 2ACO_A 3MBT_A.
Probab=21.97 E-value=1.3e+02 Score=23.74 Aligned_cols=26 Identities=8% Similarity=0.080 Sum_probs=19.0
Q ss_pred CchHHHHHHHHHHHCCceeeeeeeec
Q 036073 212 GPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 212 ~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
.+-.+.++|+.+++.|+|+++|+--|
T Consensus 117 ~~~~~~~~~~~~~~~G~d~~~l~~~~ 142 (143)
T PF08212_consen 117 SEETYAEILDRAKQQGYDVSKLIWTP 142 (143)
T ss_dssp -HHHHHHHHHHHHHTT--GGGEEE--
T ss_pred CHHHHHHHHHHHHHcCCCHHHeEECC
Confidence 45678999999999999999998654
No 295
>cd04871 ACT_PSP_2 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_2 CD includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains
Probab=21.68 E-value=74 Score=23.09 Aligned_cols=27 Identities=15% Similarity=0.124 Sum_probs=23.6
Q ss_pred CC-CchHHHHHHHHHHHCCceeeeeeee
Q 036073 210 DE-GPGVLTKALAVFALREINLTKVFVA 236 (241)
Q Consensus 210 ~~-~pGaL~~~L~~fa~~~iNLt~IeSR 236 (241)
++ .+|.++++=+.++.+|+|+..|...
T Consensus 7 ~~~~a~~ia~Vs~~lA~~~~NI~~I~~l 34 (84)
T cd04871 7 RPLTAEQLAAVTRVVADQGLNIDRIRRL 34 (84)
T ss_pred CcCCHHHHHHHHHHHHHcCCCHHHHHHh
Confidence 45 7999999999999999999888653
No 296
>smart00094 TR_FER Transferrin.
Probab=21.24 E-value=1.1e+02 Score=28.47 Aligned_cols=28 Identities=29% Similarity=0.356 Sum_probs=25.7
Q ss_pred CCCceeecCCHHHHHHHHHcCCcceEEE
Q 036073 35 PNCETIPCDEFEEAFKAVELWLAEKAIL 62 (241)
Q Consensus 35 ~~~~~~~~~s~~~v~~av~~g~~d~gVv 62 (241)
+..+.+.-.|..++++++.+|++|++.+
T Consensus 27 ~~v~Cv~~~s~~~Ci~~I~~g~AD~a~l 54 (332)
T smart00094 27 PALECVSASSTEECIKAIQKGEADAVTL 54 (332)
T ss_pred CceEEEEcCCHHHHHHHHHCCCCCEEEE
Confidence 3578899999999999999999999998
No 297
>cd04917 ACT_AKiii-LysC-EC_2 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The second ACT domain (ACT2), this CD, is not involved in the binding of heterotrophic effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=21.03 E-value=1.1e+02 Score=20.47 Aligned_cols=28 Identities=11% Similarity=0.107 Sum_probs=21.5
Q ss_pred CCCchHHHHHHHHHHHCCceeeeeeeec
Q 036073 210 DEGPGVLTKALAVFALREINLTKVFVAR 237 (241)
Q Consensus 210 ~~~pGaL~~~L~~fa~~~iNLt~IeSRP 237 (241)
.+.||.+.++++.|+..+++|...-++.
T Consensus 12 ~~~~~v~~~i~~~L~~i~i~~i~~~~s~ 39 (64)
T cd04917 12 SETAGVEKRIFDALEDINVRMICYGASN 39 (64)
T ss_pred cCCcCHHHHHHHHHHhCCeEEEEEecCc
Confidence 4689999999999988777775544443
No 298
>KOG1349 consensus Gpi-anchor transamidase [Posttranslational modification, protein turnover, chaperones]
Probab=20.21 E-value=85 Score=28.44 Aligned_cols=60 Identities=18% Similarity=-0.027 Sum_probs=46.9
Q ss_pred CcCCeeEEEecHHHHHHHHHHHHhcCCceEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 036073 105 REEKLKCVLSHPQALASSDIVQTQLGVARENIDDTASAAQYVASNGLRDAGVVASARAAE 164 (241)
Q Consensus 105 ~~~~i~~V~SHpqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 164 (241)
+.+|+.++-||.-|.+=-+-|=++.--+....-||.+|+.+.-.-..|+..||+|..-++
T Consensus 155 KFqd~eelts~dLadai~qm~e~~Ryneil~miDTCQaasly~~~~sPNVLav~SS~~ge 214 (309)
T KOG1349|consen 155 KFQDAEELTSDDLADAIQQMWEKKRYNEILFMIDTCQAASLYERFYSPNVLAVASSLVGE 214 (309)
T ss_pred ecccHHHhhhHHHHHHHHHHHHhhhhceEEEEeeccchHHHHHhhcCCCeEEEeecccCC
Confidence 689999999999887755555444445677788999999998776678999999886554
Done!