Query 014547
Match_columns 423
No_of_seqs 225 out of 1165
Neff 5.1
Searched_HMMs 46136
Date Fri Mar 29 06:12:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014547.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014547hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02317 arogenate dehydratase 100.0 7.1E-99 2E-103 764.5 39.2 378 26-417 5-382 (382)
2 KOG2797 Prephenate dehydratase 100.0 3.2E-96 7E-101 715.4 25.1 361 21-419 17-377 (377)
3 COG0077 PheA Prephenate dehydr 100.0 2E-88 4.4E-93 663.0 32.7 272 127-413 2-275 (279)
4 PRK11899 prephenate dehydratas 100.0 4.6E-86 9.9E-91 649.7 34.9 271 127-413 4-275 (279)
5 PRK11898 prephenate dehydratas 100.0 1.4E-80 2.9E-85 611.9 34.7 272 127-413 1-278 (283)
6 PRK10622 pheA bifunctional cho 100.0 8.5E-81 1.9E-85 636.4 33.7 274 126-414 102-379 (386)
7 PF00800 PDT: Prephenate dehyd 100.0 9.8E-56 2.1E-60 408.8 19.3 179 130-308 1-181 (181)
8 cd04904 ACT_AAAH ACT domain of 99.8 1.3E-20 2.9E-25 150.9 9.7 73 319-407 1-73 (74)
9 cd04931 ACT_PAH ACT domain of 99.8 2.6E-19 5.6E-24 149.6 10.0 70 315-399 11-80 (90)
10 cd04930 ACT_TH ACT domain of t 99.8 4E-19 8.6E-24 154.7 9.6 75 317-407 40-114 (115)
11 cd04905 ACT_CM-PDT C-terminal 99.8 1.1E-18 2.5E-23 140.7 11.1 80 318-411 1-80 (80)
12 cd04929 ACT_TPH ACT domain of 99.8 5.4E-19 1.2E-23 142.5 8.5 71 319-405 1-71 (74)
13 cd04880 ACT_AAAH-PDT-like ACT 99.8 3.4E-18 7.4E-23 135.9 9.9 75 320-408 1-75 (75)
14 TIGR01268 Phe4hydrox_tetr phen 99.8 2.6E-18 5.5E-23 177.9 11.4 89 317-420 15-107 (436)
15 TIGR01270 Trp_5_monoox tryptop 99.7 2.8E-16 6.1E-21 163.5 11.1 90 315-420 28-134 (464)
16 PRK06034 hypothetical protein; 99.1 1.1E-10 2.4E-15 115.6 8.0 72 128-203 95-169 (279)
17 TIGR01269 Tyr_3_monoox tyrosin 99.0 1.1E-09 2.3E-14 113.9 10.1 89 318-420 37-128 (457)
18 KOG3820 Aromatic amino acid hy 98.8 1.8E-08 3.9E-13 103.1 8.8 89 317-421 35-130 (461)
19 PRK08818 prephenate dehydrogen 98.6 8E-08 1.7E-12 99.0 8.2 66 317-398 294-360 (370)
20 cd04886 ACT_ThrD-II-like C-ter 98.0 6.4E-05 1.4E-09 57.1 9.2 68 322-402 2-69 (73)
21 PF01842 ACT: ACT domain; Int 97.9 6.6E-05 1.4E-09 56.7 8.5 38 319-356 1-38 (66)
22 cd04882 ACT_Bt0572_2 C-termina 97.2 0.0023 4.9E-08 48.3 8.0 60 321-401 2-61 (65)
23 PRK06737 acetolactate synthase 97.1 0.0044 9.6E-08 50.7 9.6 71 319-406 3-73 (76)
24 cd04878 ACT_AHAS N-terminal AC 97.1 0.0059 1.3E-07 46.0 9.7 67 320-403 2-68 (72)
25 cd04874 ACT_Af1403 N-terminal 97.1 0.0054 1.2E-07 46.5 9.0 63 320-401 2-64 (72)
26 cd04884 ACT_CBS C-terminal ACT 97.0 0.0045 9.8E-08 48.6 8.5 65 321-400 2-66 (72)
27 cd04883 ACT_AcuB C-terminal AC 96.9 0.0082 1.8E-07 46.4 8.9 64 319-401 2-65 (72)
28 PF13710 ACT_5: ACT domain; PD 96.8 0.0078 1.7E-07 47.1 7.7 62 327-405 1-62 (63)
29 cd04888 ACT_PheB-BS C-terminal 96.7 0.02 4.2E-07 44.7 9.5 73 320-408 2-76 (76)
30 PF13291 ACT_4: ACT domain; PD 96.6 0.018 4E-07 45.9 9.2 70 316-401 4-73 (80)
31 cd02116 ACT ACT domains are co 96.6 0.013 2.8E-07 40.2 7.4 58 322-397 2-59 (60)
32 cd04902 ACT_3PGDH-xct C-termin 96.6 0.012 2.5E-07 45.4 7.6 61 321-397 2-62 (73)
33 TIGR01127 ilvA_1Cterm threonin 96.5 0.18 3.8E-06 51.9 17.7 219 160-404 140-378 (380)
34 cd04903 ACT_LSD C-terminal ACT 96.5 0.017 3.8E-07 43.4 7.7 62 321-401 2-63 (71)
35 PRK11895 ilvH acetolactate syn 96.4 0.032 6.9E-07 51.7 10.4 71 319-406 3-73 (161)
36 TIGR00119 acolac_sm acetolacta 96.4 0.034 7.3E-07 51.4 10.3 71 320-407 3-73 (157)
37 cd04908 ACT_Bt0572_1 N-termina 96.2 0.032 6.9E-07 43.1 8.1 34 321-354 4-37 (66)
38 CHL00100 ilvH acetohydroxyacid 96.2 0.032 6.9E-07 52.4 9.2 73 319-408 3-75 (174)
39 cd04909 ACT_PDH-BS C-terminal 96.2 0.041 8.8E-07 42.4 8.3 64 320-401 3-66 (69)
40 PRK11152 ilvM acetolactate syn 96.1 0.049 1.1E-06 44.5 9.0 67 318-402 3-69 (76)
41 cd04879 ACT_3PGDH-like ACT_3PG 96.1 0.031 6.8E-07 41.8 7.4 62 321-401 2-63 (71)
42 PRK08198 threonine dehydratase 96.0 0.24 5.2E-06 51.4 15.8 220 160-407 162-403 (404)
43 cd04901 ACT_3PGDH C-terminal A 95.9 0.021 4.5E-07 43.7 5.8 60 321-401 2-61 (69)
44 PRK13562 acetolactate synthase 95.9 0.079 1.7E-06 44.3 9.2 71 319-406 3-74 (84)
45 PRK08526 threonine dehydratase 95.8 0.58 1.3E-05 49.1 17.6 209 170-404 168-399 (403)
46 PRK04435 hypothetical protein; 95.8 0.1 2.2E-06 47.4 10.5 77 317-409 68-146 (147)
47 cd04896 ACT_ACR-like_3 ACT dom 95.8 0.054 1.2E-06 44.2 7.7 63 321-398 3-69 (75)
48 cd04887 ACT_MalLac-Enz ACT_Mal 95.7 0.09 2E-06 40.8 8.6 69 321-407 2-70 (74)
49 cd04885 ACT_ThrD-I Tandem C-te 95.6 0.042 9E-07 42.9 6.4 62 322-401 2-63 (68)
50 PRK08178 acetolactate synthase 95.4 0.15 3.2E-06 43.7 9.5 72 318-407 8-79 (96)
51 cd04881 ACT_HSDH-Hom ACT_HSDH_ 95.4 0.13 2.8E-06 39.4 8.5 64 321-400 3-66 (79)
52 PRK00194 hypothetical protein; 95.3 0.11 2.4E-06 42.4 8.1 36 318-353 3-38 (90)
53 cd04870 ACT_PSP_1 CT domains f 95.2 0.16 3.4E-06 40.4 8.6 62 323-399 4-65 (75)
54 cd04872 ACT_1ZPV ACT domain pr 95.1 0.13 2.9E-06 42.0 8.0 67 319-400 2-69 (88)
55 PRK08639 threonine dehydratase 94.9 1.6 3.4E-05 46.0 17.4 74 317-407 335-409 (420)
56 cd04876 ACT_RelA-SpoT ACT dom 94.9 0.34 7.3E-06 34.9 9.1 63 322-401 2-64 (71)
57 cd04877 ACT_TyrR N-terminal AC 94.8 0.19 4E-06 39.8 7.9 59 321-400 3-61 (74)
58 TIGR01124 ilvA_2Cterm threonin 94.8 1.2 2.6E-05 48.2 16.4 213 161-407 158-395 (499)
59 cd04906 ACT_ThrD-I_1 First of 94.7 0.23 5E-06 40.6 8.5 69 321-407 4-72 (85)
60 PF13740 ACT_6: ACT domain; PD 94.6 0.21 4.4E-06 40.0 7.8 59 324-398 8-66 (76)
61 cd04899 ACT_ACR-UUR-like_2 C-t 94.6 0.31 6.7E-06 37.3 8.6 36 320-355 2-37 (70)
62 cd04926 ACT_ACR_4 C-terminal 94.6 0.23 5E-06 39.3 7.9 36 319-354 2-37 (72)
63 PRK08577 hypothetical protein; 94.5 0.44 9.5E-06 42.4 10.5 69 318-401 56-124 (136)
64 PRK07334 threonine dehydratase 94.5 1 2.3E-05 46.9 14.7 219 161-406 164-401 (403)
65 cd04873 ACT_UUR-ACR-like ACT d 94.4 0.4 8.7E-06 36.2 8.8 36 320-355 2-37 (70)
66 TIGR02079 THD1 threonine dehyd 94.2 2.7 5.9E-05 44.1 17.1 75 317-407 324-398 (409)
67 PRK09224 threonine dehydratase 94.1 2.9 6.2E-05 45.2 17.4 73 317-407 327-399 (504)
68 cd04895 ACT_ACR_1 ACT domain-c 94.0 0.37 8E-06 39.0 8.1 33 319-351 2-36 (72)
69 COG4492 PheB ACT domain-contai 94.0 0.26 5.6E-06 44.7 7.8 76 317-409 71-149 (150)
70 cd04889 ACT_PDH-BS-like C-term 93.9 0.31 6.8E-06 36.1 7.1 34 322-355 2-35 (56)
71 cd04875 ACT_F4HF-DF N-terminal 93.9 0.64 1.4E-05 36.5 9.2 62 321-399 2-68 (74)
72 PRK12483 threonine dehydratase 93.9 3.6 7.9E-05 44.8 17.8 216 161-408 178-417 (521)
73 PRK06382 threonine dehydratase 93.7 0.42 9E-06 50.0 10.0 35 317-351 329-363 (406)
74 cd04869 ACT_GcvR_2 ACT domains 93.2 0.71 1.5E-05 36.5 8.4 35 321-355 2-36 (81)
75 PLN02550 threonine dehydratase 93.0 2.7 5.9E-05 46.5 15.1 209 170-408 258-488 (591)
76 COG2061 ACT-domain-containing 91.7 1.2 2.5E-05 41.5 8.7 75 317-407 4-79 (170)
77 cd04900 ACT_UUR-like_1 ACT dom 91.6 1.5 3.2E-05 34.5 8.3 34 319-352 2-37 (73)
78 COG4747 ACT domain-containing 91.1 1.1 2.3E-05 40.2 7.5 65 321-409 72-136 (142)
79 cd04935 ACT_AKiii-DAPDC_1 ACT 90.9 1.6 3.4E-05 35.1 7.9 63 325-407 11-74 (75)
80 PRK11589 gcvR glycine cleavage 90.1 1.5 3.2E-05 41.8 8.2 35 321-355 98-132 (190)
81 cd04893 ACT_GcvR_1 ACT domains 89.8 3.6 7.9E-05 32.9 9.2 64 321-400 4-67 (77)
82 cd04932 ACT_AKiii-LysC-EC_1 AC 88.4 4 8.7E-05 32.8 8.5 62 325-406 11-73 (75)
83 cd04897 ACT_ACR_3 ACT domain-c 88.4 3.6 7.8E-05 33.6 8.2 33 319-351 2-36 (75)
84 cd04912 ACT_AKiii-LysC-EC-like 88.1 3.9 8.5E-05 32.4 8.3 56 325-399 11-67 (75)
85 COG2716 GcvR Glycine cleavage 87.4 2.3 5.1E-05 40.1 7.4 74 323-409 97-171 (176)
86 COG0440 IlvH Acetolactate synt 87.2 3.2 7E-05 38.8 8.1 74 318-408 4-77 (163)
87 cd04927 ACT_ACR-like_2 Second 87.0 4.5 9.7E-05 32.4 8.0 26 323-348 5-30 (76)
88 PF12974 Phosphonate-bd: ABC t 87.0 1.7 3.6E-05 41.3 6.4 83 127-218 105-202 (243)
89 TIGR01728 SsuA_fam ABC transpo 86.9 9.4 0.0002 36.1 11.5 138 128-277 1-157 (288)
90 cd04934 ACT_AK-Hom3_1 CT domai 84.8 7.7 0.00017 31.1 8.3 55 327-401 13-67 (73)
91 TIGR00363 lipoprotein, YaeC fa 84.5 45 0.00097 33.0 15.5 149 127-286 19-200 (258)
92 PF00497 SBP_bac_3: Bacterial 84.4 9.7 0.00021 34.0 9.8 48 128-177 111-159 (225)
93 PRK13011 formyltetrahydrofolat 84.4 7.7 0.00017 39.1 10.0 67 319-400 8-76 (286)
94 smart00062 PBPb Bacterial peri 83.6 21 0.00045 30.8 11.2 113 150-278 40-157 (219)
95 PRK11790 D-3-phosphoglycerate 83.1 4.1 8.9E-05 42.9 7.8 63 318-402 338-401 (409)
96 PRK06349 homoserine dehydrogen 82.6 5.1 0.00011 42.3 8.3 64 320-400 350-413 (426)
97 smart00079 PBPe Eukaryotic hom 82.3 6.1 0.00013 33.5 7.3 78 128-217 14-104 (134)
98 cd08452 PBP2_AlsR The C-termin 82.2 31 0.00068 30.0 12.0 32 146-177 24-56 (197)
99 PF13379 NMT1_2: NMT1-like fam 81.8 30 0.00065 33.0 12.6 139 126-273 6-176 (252)
100 COG1707 ACT domain-containing 81.5 5 0.00011 38.1 6.7 60 321-398 5-64 (218)
101 cd08445 PBP2_BenM_CatM_CatR Th 81.4 27 0.00059 30.4 11.3 123 147-279 26-158 (203)
102 cd08417 PBP2_Nitroaromatics_li 80.2 37 0.00081 29.1 12.4 124 147-281 25-155 (200)
103 cd04907 ACT_ThrD-I_2 Second of 80.2 18 0.00039 29.6 9.0 64 320-402 3-66 (81)
104 cd04925 ACT_ACR_2 ACT domain-c 80.0 16 0.00034 28.9 8.4 30 321-350 3-32 (74)
105 cd08453 PBP2_IlvR The C-termin 79.7 32 0.0007 29.7 11.1 125 147-280 25-160 (200)
106 PRK11151 DNA-binding transcrip 79.5 24 0.00052 34.3 11.3 144 126-280 91-246 (305)
107 cd04891 ACT_AK-LysC-DapG-like_ 79.4 13 0.00029 26.5 7.3 30 324-353 7-36 (61)
108 PRK06545 prephenate dehydrogen 78.8 5.5 0.00012 40.9 6.8 40 318-357 290-329 (359)
109 PRK11063 metQ DL-methionine tr 78.2 76 0.0016 31.6 15.6 146 127-285 32-212 (271)
110 PRK09959 hybrid sensory histid 78.1 7.1 0.00015 45.7 8.2 48 128-177 165-212 (1197)
111 PF12727 PBP_like: PBP superfa 78.1 23 0.00049 33.4 10.2 126 159-289 20-166 (193)
112 COG3830 ACT domain-containing 77.6 8 0.00017 32.9 6.2 69 323-406 8-78 (90)
113 PRK15007 putative ABC transpor 77.3 7.1 0.00015 36.4 6.6 48 128-177 127-174 (243)
114 cd08411 PBP2_OxyR The C-termin 76.5 49 0.0011 28.5 12.0 125 147-281 26-157 (200)
115 KOG2663 Acetolactate synthase, 76.4 9.4 0.0002 38.4 7.2 75 315-408 74-150 (309)
116 TIGR01096 3A0103s03R lysine-ar 76.1 6.8 0.00015 36.6 6.1 48 128-177 132-180 (250)
117 PRK13010 purU formyltetrahydro 75.3 15 0.00032 37.2 8.5 65 321-400 12-80 (289)
118 cd08435 PBP2_GbpR The C-termin 75.2 51 0.0011 28.1 13.0 123 147-280 25-158 (201)
119 PF03401 TctC: Tripartite tric 74.9 9.8 0.00021 37.6 7.1 128 126-265 105-261 (274)
120 PRK13581 D-3-phosphoglycerate 74.4 11 0.00023 41.0 7.9 104 276-399 388-514 (526)
121 cd08486 PBP2_CbnR The C-termin 74.1 50 0.0011 29.0 10.9 142 127-278 2-156 (198)
122 PRK11092 bifunctional (p)ppGpp 73.7 21 0.00045 40.5 10.1 69 316-401 624-692 (702)
123 PF00497 SBP_bac_3: Bacterial 73.4 19 0.0004 32.2 8.0 133 133-281 22-165 (225)
124 TIGR01693 UTase_glnD [Protein- 73.2 17 0.00037 41.8 9.4 66 317-397 778-845 (850)
125 cd04913 ACT_AKii-LysC-BS-like_ 73.1 26 0.00057 26.1 7.7 27 324-350 8-34 (75)
126 cd00134 PBPb Bacterial peripla 72.9 11 0.00023 32.8 6.2 48 128-177 106-153 (218)
127 PRK09959 hybrid sensory histid 72.2 5.6 0.00012 46.5 5.4 49 127-177 407-455 (1197)
128 TIGR00691 spoT_relA (p)ppGpp s 72.1 24 0.00053 39.8 10.2 69 316-401 608-676 (683)
129 PRK11480 tauA taurine transpor 72.1 1E+02 0.0023 30.6 13.8 151 112-275 12-177 (320)
130 cd08412 PBP2_PAO1_like The C-t 71.9 62 0.0013 27.6 12.2 124 147-280 25-154 (198)
131 PRK11260 cystine transporter s 71.9 9.6 0.00021 36.5 6.1 48 128-177 150-197 (266)
132 cd04890 ACT_AK-like_1 ACT doma 70.5 16 0.00035 27.3 5.9 51 326-397 11-61 (62)
133 cd08459 PBP2_DntR_NahR_LinR_li 70.4 52 0.0011 28.4 10.0 124 147-281 25-155 (201)
134 PRK09508 leuO leucine transcri 70.1 23 0.00051 34.8 8.5 124 147-281 137-266 (314)
135 TIGR00070 hisG ATP phosphoribo 69.7 36 0.00077 32.3 9.2 110 159-288 49-171 (182)
136 COG0317 SpoT Guanosine polypho 69.7 28 0.00061 39.5 9.9 70 316-402 625-694 (701)
137 TIGR01098 3A0109s03R phosphate 68.9 18 0.00039 34.1 7.2 87 128-217 142-238 (254)
138 PRK10872 relA (p)ppGpp synthet 68.6 27 0.00059 39.9 9.6 70 316-401 664-733 (743)
139 PRK11553 alkanesulfonate trans 67.9 63 0.0014 31.8 11.1 138 127-275 28-183 (314)
140 PRK05092 PII uridylyl-transfer 67.0 25 0.00055 40.9 9.2 35 318-352 843-877 (931)
141 cd08438 PBP2_CidR The C-termin 66.9 79 0.0017 26.8 12.0 31 147-177 25-56 (197)
142 PF00585 Thr_dehydrat_C: C-ter 66.7 13 0.00028 31.0 5.1 67 317-401 9-75 (91)
143 PRK09495 glnH glutamine ABC tr 66.7 15 0.00033 34.6 6.2 47 128-176 132-178 (247)
144 cd08440 PBP2_LTTR_like_4 TThe 66.7 78 0.0017 26.7 11.5 31 147-177 25-56 (197)
145 PRK10341 DNA-binding transcrip 66.5 78 0.0017 31.0 11.4 116 147-279 122-251 (312)
146 smart00062 PBPb Bacterial peri 65.7 17 0.00037 31.3 5.9 49 128-178 107-155 (219)
147 cd04933 ACT_AK1-AT_1 ACT domai 65.3 26 0.00055 28.6 6.4 58 325-401 11-72 (78)
148 TIGR00719 sda_beta L-serine de 65.3 27 0.00058 33.4 7.6 57 318-390 148-205 (208)
149 PRK06027 purU formyltetrahydro 64.8 41 0.0009 33.8 9.2 63 321-400 9-76 (286)
150 PRK05007 PII uridylyl-transfer 64.7 18 0.00039 42.0 7.4 35 317-351 807-843 (884)
151 TIGR01327 PGDH D-3-phosphoglyc 64.5 17 0.00037 39.5 6.8 104 276-399 387-513 (525)
152 PRK11242 DNA-binding transcrip 64.1 75 0.0016 30.4 10.6 145 126-280 91-247 (296)
153 PRK11917 bifunctional adhesin/ 63.9 43 0.00094 32.3 8.9 94 128-243 149-246 (259)
154 cd08436 PBP2_LTTR_like_3 The C 62.6 95 0.0021 26.2 10.4 34 146-179 24-58 (194)
155 TIGR00655 PurU formyltetrahydr 62.6 44 0.00095 33.6 8.8 65 321-400 3-71 (280)
156 TIGR01096 3A0103s03R lysine-ar 62.5 94 0.002 28.8 10.7 116 150-281 64-186 (250)
157 cd08437 PBP2_MleR The substrat 60.8 1.1E+02 0.0024 26.3 12.5 32 147-178 25-57 (198)
158 cd08446 PBP2_Chlorocatechol Th 59.7 1.1E+02 0.0024 26.1 11.8 123 147-279 26-157 (198)
159 cd05466 PBP2_LTTR_substrate Th 59.4 1E+02 0.0022 25.5 12.5 116 147-280 25-155 (197)
160 PRK11482 putative DNA-binding 59.2 1.2E+02 0.0026 30.1 11.2 144 126-281 117-270 (317)
161 cd08461 PBP2_DntR_like_3 The C 58.8 61 0.0013 27.8 8.2 125 147-282 25-157 (198)
162 PRK12683 transcriptional regul 58.3 1.4E+02 0.0031 29.3 11.6 122 147-278 118-247 (309)
163 PF12974 Phosphonate-bd: ABC t 58.3 1.1E+02 0.0025 28.8 10.5 116 150-275 30-165 (243)
164 PRK01759 glnD PII uridylyl-tra 58.2 31 0.00067 39.9 7.7 31 317-347 782-812 (854)
165 cd08457 PBP2_OccR The C-termin 57.1 1.3E+02 0.0027 25.9 11.1 121 147-277 25-152 (196)
166 cd00134 PBPb Bacterial peripla 56.5 56 0.0012 28.2 7.5 116 150-281 39-159 (218)
167 cd08413 PBP2_CysB_like The C-t 56.2 1.3E+02 0.0027 26.2 9.8 124 147-279 25-155 (198)
168 cd08485 PBP2_ClcR The C-termin 56.2 1.4E+02 0.003 26.1 11.2 50 128-177 3-57 (198)
169 cd08414 PBP2_LTTR_aromatics_li 56.0 1.3E+02 0.0027 25.5 14.7 115 148-280 26-157 (197)
170 PRK10859 membrane-bound lytic 56.0 1.3E+02 0.0028 32.1 11.6 114 150-280 81-207 (482)
171 cd08462 PBP2_NodD The C-termin 55.9 1.4E+02 0.003 26.0 12.4 32 147-178 25-56 (200)
172 PF09084 NMT1: NMT1/THI5 like; 55.6 1.6E+02 0.0035 26.7 15.7 108 150-265 22-139 (216)
173 cd08443 PBP2_CysB The C-termin 55.6 1.4E+02 0.0031 26.0 12.0 125 146-279 24-155 (198)
174 COG3283 TyrR Transcriptional r 55.4 33 0.00071 36.6 6.6 70 324-420 6-75 (511)
175 cd04923 ACT_AK-LysC-DapG-like_ 55.3 60 0.0013 23.5 6.5 27 325-351 10-36 (63)
176 PRK10820 DNA-binding transcrip 54.9 32 0.0007 37.3 6.9 58 322-400 4-61 (520)
177 PF03466 LysR_substrate: LysR 54.5 1.4E+02 0.0031 25.7 15.4 116 147-280 31-161 (209)
178 cd08456 PBP2_LysR The C-termin 54.4 1.1E+02 0.0025 25.9 9.1 31 147-177 25-56 (196)
179 TIGR02424 TF_pcaQ pca operon t 54.3 2.1E+02 0.0045 27.5 13.9 124 147-280 118-251 (300)
180 PRK11716 DNA-binding transcrip 54.1 1.9E+02 0.0041 27.0 11.4 146 126-280 67-223 (269)
181 PRK10859 membrane-bound lytic 53.9 1.1E+02 0.0023 32.8 10.5 78 128-216 150-234 (482)
182 PF13840 ACT_7: ACT domain ; P 53.2 73 0.0016 24.6 6.9 33 318-350 8-42 (65)
183 cd08460 PBP2_DntR_like_1 The C 53.0 85 0.0019 27.2 8.2 123 147-280 25-153 (200)
184 cd04868 ACT_AK-like ACT domain 52.9 58 0.0012 22.7 5.9 27 327-353 12-38 (60)
185 cd04936 ACT_AKii-LysC-BS-like_ 52.3 71 0.0015 23.1 6.5 27 325-351 10-36 (63)
186 cd08444 PBP2_Cbl The C-termina 51.5 1.6E+02 0.0035 25.5 11.3 124 147-280 25-156 (198)
187 cd08416 PBP2_MdcR The C-termin 51.4 1.5E+02 0.0033 25.2 11.3 125 147-280 25-157 (199)
188 cd08466 PBP2_LeuO The C-termin 51.3 1.6E+02 0.0034 25.3 10.1 124 147-281 25-155 (200)
189 PRK12684 transcriptional regul 50.8 2.5E+02 0.0055 27.5 12.7 53 125-177 92-149 (313)
190 cd08425 PBP2_CynR The C-termin 50.5 1.6E+02 0.0035 25.1 9.5 32 147-178 26-58 (197)
191 cd08418 PBP2_TdcA The C-termin 50.3 1.6E+02 0.0035 25.1 10.0 123 147-281 25-156 (201)
192 cd08451 PBP2_BudR The C-termin 50.3 1.6E+02 0.0035 25.0 14.1 33 146-178 25-58 (199)
193 cd04892 ACT_AK-like_2 ACT doma 50.1 85 0.0018 22.3 6.6 53 325-400 10-62 (65)
194 TIGR02995 ectoine_ehuB ectoine 50.1 31 0.00067 33.3 5.3 48 128-177 145-193 (275)
195 PRK09495 glnH glutamine ABC tr 49.8 65 0.0014 30.3 7.3 131 134-280 48-184 (247)
196 COG4747 ACT domain-containing 49.8 20 0.00043 32.4 3.5 29 321-349 6-34 (142)
197 PRK04374 PII uridylyl-transfer 49.6 72 0.0016 37.1 8.9 36 317-352 795-832 (869)
198 PRK12680 transcriptional regul 49.1 1.9E+02 0.0042 28.8 11.0 144 126-279 93-249 (327)
199 cd08430 PBP2_IlvY The C-termin 49.0 1.7E+02 0.0036 24.9 12.8 127 146-281 24-157 (199)
200 PRK11260 cystine transporter s 48.9 1.7E+02 0.0037 27.9 10.2 117 150-282 81-204 (266)
201 cd08423 PBP2_LTTR_like_6 The C 48.6 1.7E+02 0.0036 24.8 10.3 32 147-178 25-57 (200)
202 cd08426 PBP2_LTTR_like_5 The C 48.2 1.7E+02 0.0038 24.9 15.3 124 147-280 25-155 (199)
203 cd04937 ACT_AKi-DapG-BS_2 ACT 47.7 80 0.0017 23.9 6.3 33 319-351 4-37 (64)
204 PRK10837 putative DNA-binding 47.7 2.4E+02 0.0051 26.9 10.9 53 126-178 89-146 (290)
205 cd04924 ACT_AK-Arch_2 ACT doma 47.5 97 0.0021 22.7 6.6 27 325-351 11-37 (66)
206 PRK09034 aspartate kinase; Rev 47.5 2.1E+02 0.0046 30.5 11.5 128 245-399 233-372 (454)
207 TIGR01098 3A0109s03R phosphate 46.8 2.5E+02 0.0054 26.3 15.2 143 127-279 33-205 (254)
208 cd08415 PBP2_LysR_opines_like 46.2 1.8E+02 0.004 24.6 12.2 124 146-279 24-154 (196)
209 PRK11589 gcvR glycine cleavage 46.0 93 0.002 29.6 7.7 65 318-399 6-73 (190)
210 cd04911 ACT_AKiii-YclM-BS_1 AC 45.9 70 0.0015 26.3 5.9 57 326-402 12-68 (76)
211 cd08464 PBP2_DntR_like_2 The C 45.5 1.9E+02 0.0041 24.7 9.1 124 147-281 25-155 (200)
212 cd04928 ACT_TyrKc Uncharacteri 45.4 1.6E+02 0.0034 23.6 8.6 32 321-352 4-35 (68)
213 PRK12682 transcriptional regul 45.4 3E+02 0.0065 26.8 14.1 137 126-279 93-248 (309)
214 cd08421 PBP2_LTTR_like_1 The C 45.3 1.9E+02 0.0042 24.6 13.2 31 147-177 25-56 (198)
215 TIGR03871 ABC_peri_MoxJ_2 quin 45.1 47 0.001 30.7 5.5 48 128-177 105-161 (232)
216 cd08468 PBP2_Pa0477 The C-term 45.0 2.1E+02 0.0045 24.8 12.4 120 147-281 25-157 (202)
217 PRK12679 cbl transcriptional r 44.8 2E+02 0.0042 28.4 10.2 143 126-277 93-246 (316)
218 cd04922 ACT_AKi-HSDH-ThrA_2 AC 44.6 1.2E+02 0.0025 22.3 6.7 27 325-351 11-37 (66)
219 PRK00275 glnD PII uridylyl-tra 43.9 97 0.0021 36.2 8.8 35 318-352 814-850 (895)
220 cd04871 ACT_PSP_2 ACT domains 43.5 70 0.0015 26.1 5.6 64 328-399 10-74 (84)
221 PRK03381 PII uridylyl-transfer 43.4 85 0.0019 36.0 8.2 34 318-351 707-740 (774)
222 PF12916 DUF3834: Protein of u 42.9 68 0.0015 31.1 6.2 72 127-202 68-143 (201)
223 PF07485 DUF1529: Domain of Un 42.7 1E+02 0.0022 27.5 7.0 51 330-396 68-118 (123)
224 TIGR00656 asp_kin_monofn aspar 42.2 3.2E+02 0.007 28.2 11.7 98 245-351 188-296 (401)
225 PRK09986 DNA-binding transcrip 41.4 3.2E+02 0.007 26.0 10.9 146 126-280 97-255 (294)
226 cd08449 PBP2_XapR The C-termin 41.3 2.2E+02 0.0048 24.1 14.5 32 147-178 25-57 (197)
227 PRK09906 DNA-binding transcrip 41.3 3.3E+02 0.0071 26.1 14.5 124 146-279 114-246 (296)
228 COG2107 Predicted periplasmic 40.9 63 0.0014 32.7 5.8 50 128-179 96-145 (272)
229 cd08420 PBP2_CysL_like C-termi 40.8 2.2E+02 0.0048 23.9 11.0 123 147-280 25-158 (201)
230 PRK15421 DNA-binding transcrip 40.2 3.5E+02 0.0077 26.7 11.2 144 126-279 89-242 (317)
231 cd04918 ACT_AK1-AT_2 ACT domai 39.9 1.7E+02 0.0036 22.3 7.6 33 318-350 3-35 (65)
232 cd04919 ACT_AK-Hom3_2 ACT doma 39.9 1.5E+02 0.0033 21.9 6.8 27 325-351 11-37 (66)
233 cd08469 PBP2_PnbR The C-termin 39.6 2.7E+02 0.0058 24.6 10.7 32 147-178 25-57 (221)
234 PRK03601 transcriptional regul 39.6 3.5E+02 0.0076 25.9 14.4 116 146-280 113-231 (275)
235 PRK03059 PII uridylyl-transfer 39.1 1.4E+02 0.003 34.7 9.1 36 317-352 785-822 (856)
236 TIGR02995 ectoine_ehuB ectoine 39.1 2.2E+02 0.0047 27.5 9.3 131 134-280 56-198 (275)
237 cd08427 PBP2_LTTR_like_2 The C 38.9 2.4E+02 0.0052 23.8 14.9 118 147-280 25-153 (195)
238 TIGR02122 TRAP_TAXI TRAP trans 38.5 3.7E+02 0.0081 26.0 11.2 55 124-178 28-90 (320)
239 PRK06635 aspartate kinase; Rev 38.3 4.2E+02 0.0092 27.4 11.8 28 325-352 270-297 (404)
240 PRK15010 ABC transporter lysin 38.2 89 0.0019 29.7 6.4 48 128-177 134-183 (260)
241 COG0725 ModA ABC-type molybdat 38.0 55 0.0012 32.5 5.0 46 134-179 146-195 (258)
242 COG0834 HisJ ABC-type amino ac 38.0 52 0.0011 30.8 4.6 48 128-177 147-196 (275)
243 cd08448 PBP2_LTTR_aromatics_li 36.7 2.6E+02 0.0056 23.6 13.3 31 147-177 25-56 (197)
244 KOG3217 Protein tyrosine phosp 36.3 68 0.0015 29.9 4.8 72 333-422 58-138 (159)
245 cd08442 PBP2_YofA_SoxR_like Th 35.5 2.7E+02 0.0059 23.4 11.3 116 147-280 25-151 (193)
246 TIGR01729 taurine_ABC_bnd taur 35.1 4.3E+02 0.0094 25.7 15.1 127 129-265 2-146 (300)
247 PRK08961 bifunctional aspartat 34.8 6.2E+02 0.013 29.5 13.4 129 245-399 249-388 (861)
248 PRK15437 histidine ABC transpo 33.5 2.7E+02 0.0058 26.4 8.8 131 133-279 49-187 (259)
249 cd08465 PBP2_ToxR The C-termin 33.4 2.5E+02 0.0055 24.4 8.1 33 147-179 25-58 (200)
250 PF01193 RNA_pol_L: RNA polyme 33.1 1.5E+02 0.0033 22.9 5.8 63 322-401 2-65 (66)
251 CHL00180 rbcR LysR transcripti 33.1 4.6E+02 0.01 25.4 13.5 52 126-177 95-151 (305)
252 cd04921 ACT_AKi-HSDH-ThrA-like 33.0 2.2E+02 0.0047 22.0 6.8 27 325-351 11-37 (80)
253 PRK05007 PII uridylyl-transfer 32.5 1.5E+02 0.0033 34.6 8.1 35 318-352 701-737 (884)
254 cd04914 ACT_AKi-DapG-BS_1 ACT 32.0 67 0.0014 25.0 3.6 27 325-352 9-35 (67)
255 PRK10797 glutamate and asparta 31.7 83 0.0018 31.3 5.2 47 128-176 154-204 (302)
256 cd08433 PBP2_Nac The C-teminal 31.7 3.2E+02 0.007 23.2 12.2 123 147-279 25-154 (198)
257 PRK10216 DNA-binding transcrip 31.7 5E+02 0.011 25.4 11.3 147 127-280 98-262 (319)
258 PRK09224 threonine dehydratase 30.9 1.3E+02 0.0029 32.6 6.9 35 318-353 423-457 (504)
259 PRK00489 hisG ATP phosphoribos 30.4 5.4E+02 0.012 25.4 10.7 121 150-287 45-174 (287)
260 PRK08210 aspartate kinase I; R 30.2 2.1E+02 0.0046 29.7 8.1 96 246-349 193-303 (403)
261 PRK11062 nhaR transcriptional 30.2 5.1E+02 0.011 25.0 13.1 168 127-308 94-275 (296)
262 PF02566 OsmC: OsmC-like prote 29.9 1.5E+02 0.0032 23.9 5.5 65 333-402 22-86 (100)
263 cd04916 ACT_AKiii-YclM-BS_2 AC 29.2 2.3E+02 0.005 20.7 6.6 26 325-350 11-36 (66)
264 TIGR03427 ABC_peri_uca ABC tra 29.0 6.4E+02 0.014 25.8 17.3 131 150-290 36-179 (328)
265 PRK09791 putative DNA-binding 28.0 5.5E+02 0.012 24.7 13.5 32 147-178 120-152 (302)
266 PF09383 NIL: NIL domain; Int 27.7 91 0.002 24.5 3.8 70 320-407 6-76 (76)
267 cd08419 PBP2_CbbR_RubisCO_like 27.7 3.7E+02 0.008 22.6 14.7 116 147-280 24-154 (197)
268 PRK10797 glutamate and asparta 27.4 6.2E+02 0.013 25.1 11.3 115 150-278 87-208 (302)
269 PRK15437 histidine ABC transpo 27.1 1.7E+02 0.0036 27.9 6.2 48 128-177 134-183 (259)
270 PF01634 HisG: ATP phosphoribo 25.7 5.2E+02 0.011 24.1 8.9 114 160-289 4-130 (163)
271 PRK11139 DNA-binding transcrip 25.1 4E+02 0.0087 25.6 8.6 120 148-281 120-246 (297)
272 PRK01759 glnD PII uridylyl-tra 25.1 2.4E+02 0.0052 32.8 8.0 36 317-352 676-713 (854)
273 cd04915 ACT_AK-Ectoine_2 ACT d 25.0 3.1E+02 0.0068 21.0 6.3 49 328-399 14-62 (66)
274 cd08458 PBP2_NocR The C-termin 24.9 4.5E+02 0.0097 22.6 12.6 31 147-177 25-56 (196)
275 TIGR03339 phn_lysR aminoethylp 24.8 5.8E+02 0.012 23.8 15.3 140 126-277 87-236 (279)
276 PHA03169 hypothetical protein; 24.8 3.5E+02 0.0075 28.9 8.2 69 315-396 320-388 (413)
277 cd08467 PBP2_SyrM The C-termin 24.6 4.6E+02 0.01 22.6 9.0 124 147-281 25-155 (200)
278 PRK06635 aspartate kinase; Rev 23.8 2.2E+02 0.0048 29.4 6.9 28 324-351 349-376 (404)
279 PF11966 SSURE: Fibronectin-bi 23.5 1.6E+02 0.0036 24.5 4.5 38 372-409 18-60 (81)
280 PRK15010 ABC transporter lysin 23.4 6.4E+02 0.014 23.8 12.5 131 134-280 50-188 (260)
281 cd04920 ACT_AKiii-DAPDC_2 ACT 23.4 3.3E+02 0.0072 20.6 6.2 56 319-399 3-59 (63)
282 cd08450 PBP2_HcaR The C-termin 23.4 4.6E+02 0.0099 22.2 15.5 32 147-178 25-57 (196)
283 PF05576 Peptidase_S37: PS-10 23.0 1.2E+02 0.0027 32.7 4.7 103 278-398 12-132 (448)
284 COG2844 GlnD UTP:GlnB (protein 22.8 3E+02 0.0065 32.2 7.9 32 316-347 789-820 (867)
285 TIGR01729 taurine_ABC_bnd taur 22.8 7.1E+02 0.015 24.1 10.7 116 230-353 11-133 (300)
286 TIGR00656 asp_kin_monofn aspar 22.5 2.8E+02 0.006 28.7 7.3 27 324-350 346-372 (401)
287 PRK05925 aspartate kinase; Pro 22.2 9.9E+02 0.021 25.6 11.6 100 245-349 224-332 (440)
288 PRK11013 DNA-binding transcrip 22.1 7.4E+02 0.016 24.1 11.9 122 147-279 119-248 (309)
289 PRK09084 aspartate kinase III; 21.8 9.9E+02 0.022 25.5 11.9 101 245-351 233-342 (448)
290 TIGR01693 UTase_glnD [Protein- 21.6 4.1E+02 0.0088 30.8 9.0 35 317-351 667-703 (850)
291 cd08483 PBP2_HvrB The C-termin 21.5 1.4E+02 0.003 25.3 4.1 119 147-280 25-149 (190)
292 PF09967 DUF2201: VWA-like dom 21.2 90 0.002 27.4 2.9 27 376-402 2-28 (126)
293 cd08441 PBP2_MetR The C-termin 21.1 5.2E+02 0.011 22.0 12.3 143 128-280 2-155 (198)
294 PRK05092 PII uridylyl-transfer 20.6 4.8E+02 0.01 30.7 9.3 33 317-349 731-763 (931)
295 TIGR03427 ABC_peri_uca ABC tra 20.3 1.2E+02 0.0026 31.0 4.0 47 128-177 107-160 (328)
296 cd08481 PBP2_GcdR_like The C-t 20.3 2.9E+02 0.0063 23.3 5.9 122 147-282 25-153 (194)
297 PRK15007 putative ABC transpor 20.0 6.9E+02 0.015 23.0 14.0 133 134-282 45-181 (243)
No 1
>PLN02317 arogenate dehydratase
Probab=100.00 E-value=7.1e-99 Score=764.52 Aligned_cols=378 Identities=71% Similarity=1.097 Sum_probs=346.0
Q ss_pred eeeeecCcccccCCCcccCccchhchhhhhhcccccccCCCCCCcccccccCCCCcccccCccccccccchhhhccCCCC
Q 014547 26 VQCVYRSDSVHFPNGIGCSRTDWQSSCAILSSNVVSQQQSGDKPAEHIAAVNGHKTSIDLNLVPIEHANSAAATASNNKP 105 (423)
Q Consensus 26 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 105 (423)
..|+++..+.+++......|+.||++|+++.+++.++..............+++....+....+... +
T Consensus 5 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------------~ 72 (382)
T PLN02317 5 PPRTPRSGSSSFPARWASRRAAWQSSCAILSSKVRSPEGDAPPSRPAVESSGGAGLVVATQSVSFHR------------D 72 (382)
T ss_pred CCCCCCCCCcccCCCccccchhhhhhcchhhcccccccccccccccccccccccccccccccccccc------------c
Confidence 4567777788889999999999999999999999999988766655555555554333332222221 1
Q ss_pred CCCCCCccccccCCCCCCCCCccEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCc
Q 014547 106 QLPPQKPLTITDLSPAPMHGSQLRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGS 185 (423)
Q Consensus 106 ~~~~~~~~~~~~~~~~~~~~~~~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~ 185 (423)
...+|+||+++++.+.+++++.++||||||+|||||+||.++|++.+++||+||++||++|++|++||||||||||++|+
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~rVaylGp~GtfSe~AA~~~f~~~e~vp~~sf~~vf~AVe~g~ad~gVvPIENS~~Gs 152 (382)
T PLN02317 73 LSGLPRPLSITDLSPSPMHGSKLRVAYQGVPGAYSEAAARKAYPNCEAVPCEQFEAAFQAVELWLADRAVLPIENSLGGS 152 (382)
T ss_pred cccccccccHhhhcccccCCCCcEEEEECCCcCHHHHHHHHhhCcCceeecCCHHHHHHHHHCCCCCEEEEEEeccCccc
Confidence 12679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcccEEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhc
Q 014547 186 IHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLTRVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAAN 265 (423)
Q Consensus 186 V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~ 265 (423)
|.+|||+|.+++++|+||+++||+|||++++|.++++|++||||||||+||++||+++ +++++++.|||+||++|++.
T Consensus 153 V~~t~DlL~~~~l~IvgEv~l~I~h~Ll~~~g~~l~~Ik~VySHPQALaQC~~~L~~~--~~~~~~~~sTA~AA~~Va~~ 230 (382)
T PLN02317 153 IHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEELKRVISHPQALAQCENTLTKL--GVVREAVDDTAGAAKMVAAN 230 (382)
T ss_pred hHHHHHHHhcCCCEEEEEEEEEeeeEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHc--CCeEEEcCCHHHHHHHHHhc
Confidence 9999999999999999999999999999999999999999999999999999999998 57899999999999999988
Q ss_pred CCCCeeEEccHHHHHHcCCceeecCccCCCCCeeEEEEEeeCCCCCCCCCCCeEEEEEEeCCCccHHHHHHHHHHhCCce
Q 014547 266 DLRDTAAIASARAAELYGMQVLEDGIQDDSSNVTRFVMLAREPIIPRTDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNIS 345 (423)
Q Consensus 266 ~~~~~AAIaS~~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~~~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~IN 345 (423)
+.++.|||||+.||++|||+||+++|||.++|+|||+||+|++..+..++.+||||+|+++++||+|+++|++|+.+|||
T Consensus 231 ~~~~~AAIaS~~aA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KTSivfsl~~~pG~L~k~L~~Fa~~~IN 310 (382)
T PLN02317 231 GLRDTAAIASARAAELYGLDILAEGIQDDSDNVTRFLMLAREPIIPRTDRPFKTSIVFSLEEGPGVLFKALAVFALRDIN 310 (382)
T ss_pred CCCCceeecCHHHHHHcCCcchhhhhcCCCCCeeeEEEEecCCcCCCCCCCccEEEEEEcCCCCchHHHHHHHHHHCCCC
Confidence 77889999999999999999999999999999999999999876555556679999999999999999999999999999
Q ss_pred eeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcCceEEEccccCCCCCC
Q 014547 346 LTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTSFLRVLGSYPMDMTPW 417 (423)
Q Consensus 346 LtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~~vrvLGsYp~~~~pw 417 (423)
||||||||.+++|.|++||++.|+++.|+|+|||||+|++.|++++++|++|++++.++|+|||||+++++|
T Consensus 311 LtkIESRP~~~~~~~~~~~~~~~~~~~~eY~FyVD~eg~~~d~~~~~aL~~L~~~~~~lrvLGsYp~~~~~~ 382 (382)
T PLN02317 311 LTKIESRPQRKRPLRVVDDSNSGTAKYFDYLFYVDFEASMADPRAQNALAHLQEFATFLRVLGSYPMDMTPL 382 (382)
T ss_pred EEEEEeeecCCCCccccccccccccccccEEEEEEEEcCcCCHHHHHHHHHHHHhcCeEEEEeeeecCCCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999998
No 2
>KOG2797 consensus Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=3.2e-96 Score=715.42 Aligned_cols=361 Identities=75% Similarity=1.132 Sum_probs=343.5
Q ss_pred cccceeeeeecCcccccCCCcccCccchhchhhhhhcccccccCCCCCCcccccccCCCCcccccCccccccccchhhhc
Q 014547 21 RQFNRVQCVYRSDSVHFPNGIGCSRTDWQSSCAILSSNVVSQQQSGDKPAEHIAAVNGHKTSIDLNLVPIEHANSAAATA 100 (423)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 100 (423)
.....+.|.|+ ++||+|||||++||.++++.. ...+|||....+++++|++.-
T Consensus 17 ~~~~~~~~~~~--------------~~w~~s~~~~~~~v~~~e~~~------~~~~~~~~~~~~~~~~~~~~~------- 69 (377)
T KOG2797|consen 17 PKRVLVECSYR--------------SDWQSSCAILSSKVTSQENSE------SMKVNGHVNGYNTQLVQAKKV------- 69 (377)
T ss_pred ccceeeccCcc--------------cccccchHHHHHHHHhhhccc------ccceecccchhhhhhhhhhhh-------
Confidence 44458889877 899999999999999999866 267899997777999998721
Q ss_pred cCCCCCCCCCCccccccCCCCCCCCCccEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeecc
Q 014547 101 SNNKPQLPPQKPLTITDLSPAPMHGSQLRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVEN 180 (423)
Q Consensus 101 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIEN 180 (423)
. +-|||+..+++.|+||+++..+|+|||++|+|||.||.+.|++++.+||+.|+.+|++|+.+.+||+||||||
T Consensus 70 --~----~~~~pl~~~~l~psp~~~s~lRva~qg~pgaysesaa~ka~pn~~avpc~~f~~afqave~w~vD~AVLPiEN 143 (377)
T KOG2797|consen 70 --R----KAPQPLTSTDLSPSPMHGSTLRVAYQGVPGAYSESAALKAYPNCEAVPCDQFEAAFQAVELWIVDYAVLPIEN 143 (377)
T ss_pred --h----cCCCcchhhhcccCCCCCceEEEEeecCCchhhhhhhhhhcCCcccccHhHHHHHHHHHHHhhccceeeeeec
Confidence 1 2289999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcccEEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHH
Q 014547 181 SLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLTRVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAE 260 (423)
Q Consensus 181 S~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~ 260 (423)
|+.|+|+.+||||.+++++|+||+++||+|||++++|+.++++++|.||||||+||+.||.++.|++.++.++|||+||+
T Consensus 144 S~gGsIhrnYDLLlrh~lhiVgEv~vPvhHCLi~~~gv~~e~~~~VlSHPQal~Qce~~L~~l~~~~~r~a~~dTa~Aa~ 223 (377)
T KOG2797|consen 144 STGGSIHRNYDLLLRHRLHIVGEVQVPVHHCLIALPGVRKEEVVRVLSHPQALGQCECSLTKLGPNAAREAVSDTAGAAE 223 (377)
T ss_pred cCCceeeechHHHhhcchheeeEEecceeeeEecCCCCChhheeeeecCcHHHHHHHHHHHhcccceeeeeccchHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhcCCCCeeEEccHHHHHHcCCceeecCccCCCCCeeEEEEEeeCCCCCCCCCCCeEEEEEEeCCCccHHHHHHHHHH
Q 014547 261 YIAANDLRDTAAIASARAAELYGMQVLEDGIQDDSSNVTRFVMLAREPIIPRTDRPFKTSIVFAHDKGTSVLFKVLSAFA 340 (423)
Q Consensus 261 ~va~~~~~~~AAIaS~~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~~~~~~~KTSivf~l~~~pGaL~~vL~~Fa 340 (423)
.++.++..+.+||+|++||++|||.||+++|||+.+|.|||++|.|++.+|+.++.+||||+|...++||.|+++|++|+
T Consensus 224 ~~s~~~~~d~~AIASe~aA~ly~l~Il~~~IqDd~~NvTRFLmLar~p~ip~t~rl~ktsivf~~~~gp~vLfkvl~vfa 303 (377)
T KOG2797|consen 224 QISASNTADTAAIASERAAELYGLNILEKNIQDDLGNVTRFLMLAREPIIPDTDRLFKTSIVFFREKGPGVLFKVLSVFA 303 (377)
T ss_pred HHHhcccccHHHHHHHHHHHHhcchhhhhhcccccCCeeEEEEEeccCCCCCCCccceeeEEEEeecCCchHHHHHHHHH
Confidence 99999889999999999999999999999999999999999999999999999999999999998889999999999999
Q ss_pred hCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcCceEEEccccCCCCCCCC
Q 014547 341 FRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTSFLRVLGSYPMDMTPWSP 419 (423)
Q Consensus 341 ~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~~vrvLGsYp~~~~pw~p 419 (423)
.|+||||||||||.+..|.|+||| .++|+|+||||||..+.+++.++++.+++++++++|+|||||+++++|.+
T Consensus 304 ~r~inltkIesRP~h~~p~r~v~~-----~k~f~ylFyidfeasmae~~aq~al~~~~e~~sflrvlGsyp~d~t~~~~ 377 (377)
T KOG2797|consen 304 FRSINLTKIESRPFHNRPLRVVDD-----SKNFEYLFYIDFEASMAEPRAQNALGEVQEFTSFLRVLGSYPMDMTYWSK 377 (377)
T ss_pred hhhceeeeeecccccCCCcccccc-----cccccEEEEEEEEeccCcHHHHHHHHHHHHHHHHHHHhcCCccccccCCC
Confidence 999999999999999999999999 47899999999999999999999999999999999999999999999975
No 3
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=2e-88 Score=663.02 Aligned_cols=272 Identities=44% Similarity=0.689 Sum_probs=259.7
Q ss_pred ccEEEEeCCCccHHHHHHhhhCCC-CceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEE
Q 014547 127 QLRVAYQGVPGAYSEAAAGKAYPN-CEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQ 205 (423)
Q Consensus 127 ~~~VayLGP~GTfSh~AA~~~f~~-~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~ 205 (423)
.++|+||||+|||||+||+++|++ .+..||.||+|||++|++|++||||||||||++|+|++|+|+|.+++|+|+||+.
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 579999999999999999999998 7999999999999999999999999999999999999999999999999999999
Q ss_pred EeeeeeeeecCCCCcCcccEEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCc
Q 014547 206 LPVHHCLLALPGVRKEYLTRVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQ 285 (423)
Q Consensus 206 lpI~h~Lla~~g~~l~dIk~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~ 285 (423)
+||+|||+++.+.++++|++|||||||++||++||++++|++++++++|||+||+++++..+...|||||+.||++|||+
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 99999999998889999999999999999999999999999999999999999999999888899999999999999999
Q ss_pred eeecCccCCCCCeeEEEEEeeC-CCCCCCCCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccc
Q 014547 286 VLEDGIQDDSSNVTRFVMLARE-PIIPRTDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDD 364 (423)
Q Consensus 286 ILa~nIqD~~~N~TRFlVLsr~-~~~~~~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~ 364 (423)
||++||||.++|+|||+||+|+ +.. ..+.+.||||+|.++|+||+|+++|++|+.||||||||||||.++++
T Consensus 162 il~~~I~D~~~N~TRF~vl~r~~~~~-~~~~~~kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~~~------ 234 (279)
T COG0077 162 ILAENIEDEPNNRTRFLVLSRRKPPS-VSDGPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTGL------ 234 (279)
T ss_pred hHhhcccCCCCCeEEEEEEeccCCCC-cCCCCceEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCCCC------
Confidence 9999999999999999999985 322 12245799999999999999999999999999999999999999875
Q ss_pred cCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcCceEEEccccCC
Q 014547 365 ANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTSFLRVLGSYPMD 413 (423)
Q Consensus 365 ~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~~vrvLGsYp~~ 413 (423)
|+|+||||++||.+++.+++||++|++.+.++|+|||||..
T Consensus 235 --------~~Y~F~iD~eg~~~~~~v~~AL~el~~~t~~~kilGsYp~~ 275 (279)
T COG0077 235 --------GEYLFFIDIEGHIDDPLVKEALEELKEITEFVKILGSYPSA 275 (279)
T ss_pred --------eeEEEEEEEecCcCcHhHHHHHHHHHhheeEEEEEeecccc
Confidence 99999999999999999999999999999999999999974
No 4
>PRK11899 prephenate dehydratase; Provisional
Probab=100.00 E-value=4.6e-86 Score=649.71 Aligned_cols=271 Identities=41% Similarity=0.613 Sum_probs=256.9
Q ss_pred ccEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEE
Q 014547 127 QLRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQL 206 (423)
Q Consensus 127 ~~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~l 206 (423)
+++||||||+|||||+||+++|++.+++||.||++||++|++|++||||||||||++|+|.+|+|+|.+++++|+||+.+
T Consensus 4 ~~kvaylGp~GsfS~~Aa~~~~~~~~~v~~~s~~~vf~av~~g~~d~gVvPiENS~~G~V~~~~Dll~~~~l~Iv~E~~l 83 (279)
T PRK11899 4 TNRIAFQGEPGANSHLACRDAFPDMEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVADIHHLLPESGLHIVGEYFL 83 (279)
T ss_pred CCEEEEECCCCCHHHHHHHHhcCcCceeecCCHHHHHHHHHCCCCCEEEEEeeccCCccHHHHHHHHhcCCCEEEEEEEE
Confidence 56899999999999999999999889999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeeeecCCCCcCcccEEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCce
Q 014547 207 PVHHCLLALPGVRKEYLTRVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQV 286 (423)
Q Consensus 207 pI~h~Lla~~g~~l~dIk~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~I 286 (423)
||+|||++++|.++++|++||||||||+||++||+++ +++.+++.|||+||++|++.+.++.|||||+.||++|||+|
T Consensus 84 ~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~AAIas~~aa~~YgL~i 161 (279)
T PRK11899 84 PIRHQLMALPGATLEEIKTVHSHPHALGQCRKIIRAL--GLKPVVAADTAGAARLVAERGDPSMAALASRLAAELYGLDI 161 (279)
T ss_pred EeeEEEecCCCCCHHHCeEEEEeHHHHHHHHHHHHHc--CCeEEEcCChHHHHHHHHhcCCCCeeEeCCHHHHHHcCCcc
Confidence 9999999999999999999999999999999999998 57899999999999999988778899999999999999999
Q ss_pred eecCccCCCCCeeEEEEEeeCCCC-CCCCCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCccccccc
Q 014547 287 LEDGIQDDSSNVTRFVMLAREPII-PRTDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDA 365 (423)
Q Consensus 287 La~nIqD~~~N~TRFlVLsr~~~~-~~~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~ 365 (423)
|+++|||.++|+|||+||++++.. +..+..+||||+|.++|+||+|+++|++|+.+|||||||||||.++++
T Consensus 162 l~~~IqD~~~N~TRF~vi~~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~------- 234 (279)
T PRK11899 162 LAENIEDADHNTTRFVVLSREADWAARGDGPIVTTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSF------- 234 (279)
T ss_pred hhhcccCCcccceeEEEEecCCCCCCCCCCCceEEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCC-------
Confidence 999999999999999999998642 222334699999999999999999999999999999999999999865
Q ss_pred CCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcCceEEEccccCC
Q 014547 366 NVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTSFLRVLGSYPMD 413 (423)
Q Consensus 366 ~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~~vrvLGsYp~~ 413 (423)
|+|+||||++||.+|++++++|++|++.+.++|+|||||..
T Consensus 235 -------~~Y~F~id~eg~~~d~~v~~aL~~l~~~~~~~kvLGsYp~~ 275 (279)
T PRK11899 235 -------TATQFYADIEGHPEDRNVALALEELRFFSEEVRILGVYPAH 275 (279)
T ss_pred -------ceEEEEEEEECCCCCHHHHHHHHHHHHhcCcEEEeeeecCc
Confidence 99999999999999999999999999999999999999963
No 5
>PRK11898 prephenate dehydratase; Provisional
Probab=100.00 E-value=1.4e-80 Score=611.94 Aligned_cols=272 Identities=40% Similarity=0.594 Sum_probs=254.6
Q ss_pred ccEEEEeCCCccHHHHHHhhhCCC---CceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcC-CcEEEE
Q 014547 127 QLRVAYQGVPGAYSEAAAGKAYPN---CEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRH-RLHIVG 202 (423)
Q Consensus 127 ~~~VayLGP~GTfSh~AA~~~f~~---~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~-~L~Ivg 202 (423)
+++||||||+|||||+||.++|++ .++++|+||++||++|++|++||||||||||++|+|.+|||+|.++ +++|+|
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 358999999999999999999965 7899999999999999999999999999999999999999999875 899999
Q ss_pred EEEEeeeeeeeecCCCCcCcccEEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHc
Q 014547 203 EVQLPVHHCLLALPGVRKEYLTRVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELY 282 (423)
Q Consensus 203 Ei~lpI~h~Lla~~g~~l~dIk~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelY 282 (423)
|+.+||+|||+++++.. ++|++||||||||+||++||++++|+++.+++.|||+||+++++++..+.|||+|+.||++|
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 99999999999998876 99999999999999999999999899999999999999999998876778999999999999
Q ss_pred CCceeecCccCCCCCeeEEEEEeeCCC-CCCCCCCCeEEEEEEeCC-CccHHHHHHHHHHhCCceeeeeeeeeCCCCCcc
Q 014547 283 GMQVLEDGIQDDSSNVTRFVMLAREPI-IPRTDRPFKTSIVFAHDK-GTSVLFKVLSAFAFRNISLTKIESRPHRNRPIR 360 (423)
Q Consensus 283 gL~ILa~nIqD~~~N~TRFlVLsr~~~-~~~~~~~~KTSivf~l~~-~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~ 360 (423)
||+||++||||.++|+|||++|++++. .+.....+||||+|++++ +||+|+++|++|+.+|||||||||||.++++
T Consensus 160 gL~il~~~I~d~~~N~TRF~vi~~~~~~~~~~~~~~ktslif~l~~~~pGsL~~~L~~F~~~~INLt~IeSRP~~~~~-- 237 (283)
T PRK11898 160 GLEILAEDIQDYPNNRTRFWLLGRKKPPPPLRTGGDKTSLVLTLPNNLPGALYKALSEFAWRGINLTRIESRPTKTGL-- 237 (283)
T ss_pred CCcEehhcCCCCCccceEEEEEEcCcccCCCCCCCCeEEEEEEeCCCCccHHHHHHHHHHHCCCCeeeEecccCCCCC--
Confidence 999999999999999999999999864 222234569999999987 5999999999999999999999999999865
Q ss_pred cccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcCceEEEccccCC
Q 014547 361 LVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTSFLRVLGSYPMD 413 (423)
Q Consensus 361 ~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~~vrvLGsYp~~ 413 (423)
|+|.|||||+|+.++++++++|++|++.+.++|+|||||..
T Consensus 238 ------------~~y~F~vd~eg~~~~~~~~~al~~L~~~~~~~k~LGsY~~~ 278 (283)
T PRK11898 238 ------------GTYFFFIDVEGHIDDVLVAEALKELEALGEDVKVLGSYPVY 278 (283)
T ss_pred ------------ccEEEEEEEEccCCCHHHHHHHHHHHHhcCcEEEEEeeccc
Confidence 99999999999999999999999999999999999999964
No 6
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=100.00 E-value=8.5e-81 Score=636.43 Aligned_cols=274 Identities=37% Similarity=0.578 Sum_probs=256.3
Q ss_pred CccEEEEeCCCccHHHHHHhhhCCC----CceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEE
Q 014547 126 SQLRVAYQGVPGAYSEAAAGKAYPN----CEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIV 201 (423)
Q Consensus 126 ~~~~VayLGP~GTfSh~AA~~~f~~----~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Iv 201 (423)
..++||||||+|||||+||+++|+. ...+||+||++||++|++|++||||||||||++|.|.+|||+|.+++++|+
T Consensus 102 ~~~~va~lGp~GtfSh~Aa~~~~~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~DlL~~~~l~I~ 181 (386)
T PRK10622 102 HSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVLPIENTSSGAINDVYDLLQHTSLSIV 181 (386)
T ss_pred ccceEEEECCCCcHHHHHHHHhhccccccccccCCCCHHHHHHHHHCCCCCEEEEEEecCCceehHHHHHHHhcCCCEEE
Confidence 3578999999999999999998753 234589999999999999999999999999999999999999999999999
Q ss_pred EEEEEeeeeeeeecCCCCcCcccEEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 202 GEVQLPVHHCLLALPGVRKEYLTRVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 202 gEi~lpI~h~Lla~~g~~l~dIk~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
||+.+||+|||++.+|.++++|++||||||||+||++||+++ |+++++++.|||+||++|++.+.++.|||||+.||++
T Consensus 182 ~E~~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~-p~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~aa~~ 260 (386)
T PRK10622 182 GEMTLPIDHCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRY-PHWKIEYTESTAAAMEKVAQANSPHVAALGSEAGGAL 260 (386)
T ss_pred EEEEEEEEEEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHC-CCceEEEcCChHHHHHHHHhcCCCCEEEECCHHHHHH
Confidence 999999999999999999999999999999999999999998 8999999999999999999887778999999999999
Q ss_pred cCCceeecCccCCCCCeeEEEEEeeCCCCCCCCCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCccc
Q 014547 282 YGMQVLEDGIQDDSSNVTRFVMLAREPIIPRTDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRL 361 (423)
Q Consensus 282 YgL~ILa~nIqD~~~N~TRFlVLsr~~~~~~~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~ 361 (423)
|||+||++||||.++|+|||+||++++..+..+.++||||+|.++|+||+|+++|+.|+.+|||||||||||.++++
T Consensus 261 ygL~vl~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~~L~~Fa~~giNLtkIeSRP~~~~~--- 337 (386)
T PRK10622 261 YGLQVLERNLANQQQNITRFIVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTKLESRPIHGNP--- 337 (386)
T ss_pred cCCcChhhcCcCCccccceEEEEecCCCCCCCCCCCcEEEEEEcCCCCcHHHHHHHHHHHcCCCeeEEEeeecCCCC---
Confidence 99999999999999999999999998642333334699999999999999999999999999999999999999875
Q ss_pred ccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcCceEEEccccCCC
Q 014547 362 VDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTSFLRVLGSYPMDM 414 (423)
Q Consensus 362 ~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~~vrvLGsYp~~~ 414 (423)
|+|+||||++||..|++++++|++|++.|.++|+|||||...
T Consensus 338 -----------~~Y~Ffid~eg~~~d~~~~~aL~~l~~~~~~~kvLGsYp~~~ 379 (386)
T PRK10622 338 -----------WEEMFYLDVQANLRSAEMQKALKELGEITRSLKVLGCYPSEN 379 (386)
T ss_pred -----------ceEEEEEEEeCCCCCHHHHHHHHHHHHhcCcEEEeeeecCCc
Confidence 999999999999999999999999999999999999999753
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=9.8e-56 Score=408.80 Aligned_cols=179 Identities=47% Similarity=0.737 Sum_probs=166.4
Q ss_pred EEEeCCCccHHHHHHhhhC--CCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEe
Q 014547 130 VAYQGVPGAYSEAAAGKAY--PNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLP 207 (423)
Q Consensus 130 VayLGP~GTfSh~AA~~~f--~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lp 207 (423)
||||||+|||||+||+++| ++.++++|+||++||++|++|++||||||||||++|.|.+|+|+|.+.+++|+||+.+|
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 67899999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeeecCCCCcCcccEEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCcee
Q 014547 208 VHHCLLALPGVRKEYLTRVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQVL 287 (423)
Q Consensus 208 I~h~Lla~~g~~l~dIk~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~IL 287 (423)
|+|||+++++.++++|++||||||+++||++||++++|+++++.+.||++||++|+..+.++.|||+|+.||++|||+||
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 99999999999999999999999999999999999999999999999999999988877789999999999999999999
Q ss_pred ecCccCCCCCeeEEEEEeeCC
Q 014547 288 EDGIQDDSSNVTRFVMLAREP 308 (423)
Q Consensus 288 a~nIqD~~~N~TRFlVLsr~~ 308 (423)
+++|||.++|+|||+||+|++
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
>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=99.84 E-value=1.3e-20 Score=150.90 Aligned_cols=73 Identities=27% Similarity=0.464 Sum_probs=68.4
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHH
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQ 398 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~ 398 (423)
|||+|+++|+||+|+++|+.|+.+|||||||||||.++++ |+|.|||||+| .+++++++|++|+
T Consensus 1 tsl~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~--------------~~y~Ffvd~~~--~~~~~~~~l~~L~ 64 (74)
T cd04904 1 TSLIFSLKEEVGALARALKLFEEFGVNLTHIESRPSRRNG--------------SEYEFFVDCEV--DRGDLDQLISSLR 64 (74)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCC--------------ceEEEEEEEEc--ChHHHHHHHHHHH
Confidence 6899999999999999999999999999999999999764 99999999999 5678999999999
Q ss_pred hhcCceEEE
Q 014547 399 EFTSFLRVL 407 (423)
Q Consensus 399 ~~~~~vrvL 407 (423)
+.+..+|++
T Consensus 65 ~~~~~~~~~ 73 (74)
T cd04904 65 RVVADVNIL 73 (74)
T ss_pred HhcCeEEEc
Confidence 999999875
No 9
>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=99.80 E-value=2.6e-19 Score=149.59 Aligned_cols=70 Identities=29% Similarity=0.455 Sum_probs=65.2
Q ss_pred CCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHH
Q 014547 315 RPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNAL 394 (423)
Q Consensus 315 ~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL 394 (423)
...||||+|.++|+||+|+++|+.|+.+|||||||||||.++.+ |+|.|||||+|+ .+++++++|
T Consensus 11 ~~~ktslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~--------------~~Y~FfVDieg~-~~~~~~~~l 75 (90)
T cd04931 11 KNGVISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNK--------------DEYEFFINLDKK-SAPALDPII 75 (90)
T ss_pred CCCcEEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCC--------------ceEEEEEEEEcC-CCHHHHHHH
Confidence 34689999999999999999999999999999999999998764 999999999998 689999999
Q ss_pred HHHHh
Q 014547 395 AEVQE 399 (423)
Q Consensus 395 ~eL~~ 399 (423)
++|++
T Consensus 76 ~~L~~ 80 (90)
T cd04931 76 KSLRN 80 (90)
T ss_pred HHHHH
Confidence 99986
No 10
>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=99.79 E-value=4e-19 Score=154.65 Aligned_cols=75 Identities=19% Similarity=0.318 Sum_probs=69.3
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e 396 (423)
+||||+|+++|+||+|+++|+.|+.+|||||||||||+++.+ |+|.|||||+|+.+ +++++|++
T Consensus 40 ~ktSlifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~~~~--------------~eY~FfIdieg~~~--~~~~aL~~ 103 (115)
T cd04930 40 QKATLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSRKEG--------------GDLEVLVRCEVHRS--DLLQLISS 103 (115)
T ss_pred ccEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCCCCC--------------ceEEEEEEEEeCHH--HHHHHHHH
Confidence 589999999999999999999999999999999999998764 89999999999764 69999999
Q ss_pred HHhhcCceEEE
Q 014547 397 VQEFTSFLRVL 407 (423)
Q Consensus 397 L~~~~~~vrvL 407 (423)
|++.+..+++.
T Consensus 104 L~~~~~~~kv~ 114 (115)
T cd04930 104 LRQVAEDVRLT 114 (115)
T ss_pred HHHhcCeeEec
Confidence 99999988763
No 11
>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=99.78 E-value=1.1e-18 Score=140.68 Aligned_cols=80 Identities=49% Similarity=0.832 Sum_probs=75.2
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHH
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEV 397 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL 397 (423)
|+||+|.++|+||+|.++|+.|+++||||++|+|||.+.. .|+|.||||++++.++++++++++.|
T Consensus 1 ~~sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~--------------~~~~~f~vd~~~~~~~~~~~~~l~~l 66 (80)
T cd04905 1 KTSIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGG--------------LWEYVFFIDFEGHIEDPNVAEALEEL 66 (80)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCC--------------CceEEEEEEEECCCCCHHHHHHHHHH
Confidence 5899999999999999999999999999999999999754 38999999999987789999999999
Q ss_pred HhhcCceEEEcccc
Q 014547 398 QEFTSFLRVLGSYP 411 (423)
Q Consensus 398 ~~~~~~vrvLGsYp 411 (423)
++.+.++|+||+||
T Consensus 67 ~~~~~~~~~lG~y~ 80 (80)
T cd04905 67 KRLTEFVKVLGSYP 80 (80)
T ss_pred HHhCCeEEEeeeeC
Confidence 99999999999997
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=99.78 E-value=5.4e-19 Score=142.51 Aligned_cols=71 Identities=24% Similarity=0.351 Sum_probs=64.8
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHH
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQ 398 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~ 398 (423)
|||+|+++|+||+|+++|+.|+.+||||+||||||.+..+ |+|.|||||+|+. .++++++++|+
T Consensus 1 tsl~~~l~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~--------------~~y~F~id~e~~~--~~i~~~l~~l~ 64 (74)
T cd04929 1 TSVIFSLKNEVGGLAKALKLFQELGINVVHIESRKSKRRS--------------SEFEIFVDCECDQ--RRLDELVQLLK 64 (74)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCC--------------ceEEEEEEEEcCH--HHHHHHHHHHH
Confidence 6899999999999999999999999999999999998764 9999999999986 48999999999
Q ss_pred hhcCceE
Q 014547 399 EFTSFLR 405 (423)
Q Consensus 399 ~~~~~vr 405 (423)
+.+...+
T Consensus 65 ~~~~~~~ 71 (74)
T cd04929 65 REVASVN 71 (74)
T ss_pred Hhccccc
Confidence 8876543
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=99.76 E-value=3.4e-18 Score=135.93 Aligned_cols=75 Identities=43% Similarity=0.682 Sum_probs=70.8
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
|++|.++|+||+|.++|+.|+.+|+||++|||||.++.+ |+|.||||++|+..+.++++++++|++
T Consensus 1 sl~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~--------------~~~~f~id~~~~~~~~~~~~~l~~l~~ 66 (75)
T cd04880 1 SLVFSLKNKPGALAKALKVFAERGINLTKIESRPSRKGL--------------WEYEFFVDFEGHIDDPDVKEALEELKR 66 (75)
T ss_pred CEEEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCC--------------ceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 588999999999999999999999999999999998754 899999999998788999999999999
Q ss_pred hcCceEEEc
Q 014547 400 FTSFLRVLG 408 (423)
Q Consensus 400 ~~~~vrvLG 408 (423)
.+.++++||
T Consensus 67 ~~~~~~~lG 75 (75)
T cd04880 67 VTEDVKVLG 75 (75)
T ss_pred hCCeeEECC
Confidence 999999998
No 14
>TIGR01268 Phe4hydrox_tetr phenylalanine-4-hydroxylase, tetrameric form. The member of this family from Drosophila has been described as having both phenylalanine-4-hydroxylase and tryptophan 5-monoxygenase activity (PubMed:1371286). However, a Drosophila member of the tryptophan 5-monoxygenase clade has subsequently been discovered.
Probab=99.76 E-value=2.6e-18 Score=177.93 Aligned_cols=89 Identities=26% Similarity=0.551 Sum_probs=81.4
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e 396 (423)
.||||+|+++|+||+|+++|++|+.+|||||||||||+++.+ |+|.|||||+|+. +++++++|++
T Consensus 15 ~KTSLiFsL~d~pGaL~~vL~vFa~~gINLthIESRPsk~~~--------------~eY~FFVD~eg~~-~~~v~~aL~~ 79 (436)
T TIGR01268 15 AKTSLIFSLKEEAGALAETLKLFQAHDVNLTHIESRPSKTHP--------------GEYEFFVEFDEAS-DRKLEGVIEH 79 (436)
T ss_pred CeEEEEEEcCCCCcHHHHHHHHHHHCCCCeeEEecccCCCCC--------------ccEEEEEEEecCc-cHHHHHHHHH
Confidence 489999999999999999999999999999999999998764 8999999999986 5899999999
Q ss_pred HHhhc-CceEEEccccC-CC--CCCCCC
Q 014547 397 VQEFT-SFLRVLGSYPM-DM--TPWSPS 420 (423)
Q Consensus 397 L~~~~-~~vrvLGsYp~-~~--~pw~p~ 420 (423)
|++.+ ..+++||+-.. +. .||||-
T Consensus 80 Lk~~~~~~vkiLGs~~~~~~~~vpWFPr 107 (436)
T TIGR01268 80 LRQKAEVTVNILSRDNKQNKDSVPWFPR 107 (436)
T ss_pred HHHhccceEEEeCCCCcccccCCCCCCC
Confidence 99999 89999999653 33 799996
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=99.66 E-value=2.8e-16 Score=163.50 Aligned_cols=90 Identities=21% Similarity=0.248 Sum_probs=76.9
Q ss_pred CCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcce-EEEEEEEecCcChHHHHHH
Q 014547 315 RPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFE-YMFYIDFEASMAEVRAQNA 393 (423)
Q Consensus 315 ~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~e-Y~FfID~eg~~~d~~v~~a 393 (423)
+..||||+|+++|+||+|+++|+.|+.+|||||||||||+++.+ |+ |.|||||+|+. .+++++
T Consensus 28 ~~~ktSLIFsL~d~pGaL~~vL~vFa~~gINLThIESRPsk~~~--------------~e~Y~FfVD~Eg~~--~~l~~a 91 (464)
T TIGR01270 28 GVQRLSIIFSLSNVVGDLSKAIAIFQDRHINILHLESRDSKDGT--------------SKTMDVLVDVELFH--YGLQEA 91 (464)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHCCCCEEEEECCcCCCCC--------------CccEEEEEEEEcCH--HHHHHH
Confidence 34699999999999999999999999999999999999998754 89 99999999975 689999
Q ss_pred HHHHHhhcCceEEE-----ccc-----------cCCCCCCCCC
Q 014547 394 LAEVQEFTSFLRVL-----GSY-----------PMDMTPWSPS 420 (423)
Q Consensus 394 L~eL~~~~~~vrvL-----GsY-----------p~~~~pw~p~ 420 (423)
|++|++.+..+.+. +.. .....||||-
T Consensus 92 L~~Lk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~vpWfPr 134 (464)
T TIGR01270 92 MDLLKSGLDVHEVSSPIRPTLIEAQYTEPGSDDATTGVPWFPK 134 (464)
T ss_pred HHHHHHhcccceeccccccccccccccccccccccCCCCCCCC
Confidence 99999988875553 221 2334799996
No 16
>PRK06034 hypothetical protein; Provisional
Probab=99.13 E-value=1.1e-10 Score=115.57 Aligned_cols=72 Identities=15% Similarity=0.093 Sum_probs=59.3
Q ss_pred cEE-EEeCCCccHHHHHHhhhCC-CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhh-cCCcEEEEE
Q 014547 128 LRV-AYQGVPGAYSEAAAGKAYP-NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLL-RHRLHIVGE 203 (423)
Q Consensus 128 ~~V-ayLGP~GTfSh~AA~~~f~-~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~-~~~L~IvgE 203 (423)
.+| +||||+|||||+||+++|+ ..++++|.||++||++|++|++|||||||++. .+.. +-.|. ....+|++-
T Consensus 95 ~~V~a~lG~~gs~s~~AA~~~FG~s~~~~~~~s~~dVf~AV~~g~adyGVVPI~~~-~~~W---W~~L~~~~~~~iiar 169 (279)
T PRK06034 95 FSVHADGSGGEAAMRDSARFHFGFTVPYVPHFSAQAVVEAVARSKGDLGLVSLTSS-DTPW---WGRLEAEGAPKIIAR 169 (279)
T ss_pred ceEEEEeCCccHHHHHHHHHHhccccCCccCCCHHHHHHHHHcCCCCEEEEECCCC-CCcH---HHHhccCCCCeEEEe
Confidence 469 9999999999999999998 46889999999999999999999999999544 3444 44444 445777763
No 17
>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=99.02 E-value=1.1e-09 Score=113.89 Aligned_cols=89 Identities=19% Similarity=0.284 Sum_probs=69.5
Q ss_pred eEEEEEEeCCC-ccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH
Q 014547 318 KTSIVFAHDKG-TSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 318 KTSivf~l~~~-pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e 396 (423)
.++++|.++++ +|+|.++|++|+.++|||+||||||++... - ...+|.|||||+++ +.++.++++.
T Consensus 37 ~~~~~~~~~~~~~g~L~~~l~~f~~~~inl~hiEsr~~~~~~--------~---~~~~~~~~v~~~~~--~~~~~~~~~~ 103 (457)
T TIGR01269 37 MQNNQFYIRTKEISSLHRILKYIETFKLNLVHFETRPTRTLS--------N---ADVDYSCLITLEAN--EINMSLLIES 103 (457)
T ss_pred ceeEEEEeccCcchhHHHHHHHHHHcCCcEEEeecCCccccC--------C---CCCceEEEEEEecc--HhhHHHHHHH
Confidence 57778888754 999999999999999999999999987542 0 12479999999975 5789999999
Q ss_pred HHhhcCce--EEEccccCCCCCCCCC
Q 014547 397 VQEFTSFL--RVLGSYPMDMTPWSPS 420 (423)
Q Consensus 397 L~~~~~~v--rvLGsYp~~~~pw~p~ 420 (423)
|++.+..+ .+++. ..+..||||-
T Consensus 104 l~~~~~~~~~~~~~~-~~~~vpWfPr 128 (457)
T TIGR01269 104 LRGNSFISGINLLNN-QNVKEDWFPK 128 (457)
T ss_pred HHhhhccccccccCC-ccccCCCCCC
Confidence 99876533 33333 3445899996
No 18
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=98.78 E-value=1.8e-08 Score=103.15 Aligned_cols=89 Identities=24% Similarity=0.413 Sum_probs=73.5
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e 396 (423)
-.++++|++++++|+|.++|++|...++||.||||||++... .+|.|||+++... .++.++++.
T Consensus 35 ~~~~~if~~r~~~~~l~~~Lk~f~~~~vnl~HiEsR~s~~~~--------------~~~evlv~~~~~~--~~l~~~i~~ 98 (461)
T KOG3820|consen 35 ARISLIFSLRNKVGALARALKAFEEFHVNLLHIESRPSERRS--------------SGYEVLVELDATR--GQLIQAIEL 98 (461)
T ss_pred ceEEEEEEecccchHHHHHHHHhhhcCceEEEeecccccccC--------------CCceEEEeeccch--hhHHHHHHH
Confidence 478899999999999999999999999999999999997532 4699999999744 589999999
Q ss_pred HHhhcCceEEEccccC-------CCCCCCCCC
Q 014547 397 VQEFTSFLRVLGSYPM-------DMTPWSPSR 421 (423)
Q Consensus 397 L~~~~~~vrvLGsYp~-------~~~pw~p~~ 421 (423)
|++.+..+...-++.. ...||||-.
T Consensus 99 lrq~~~~~~~~s~~~~~~~~~~~~~vpWFPr~ 130 (461)
T KOG3820|consen 99 LRQNHVALSYFSSFNRDLKDNKNTSVPWFPRK 130 (461)
T ss_pred HHHhcccceecccchhhhhhccCCCCCccccc
Confidence 9988766555555432 348999963
No 19
>PRK08818 prephenate dehydrogenase; Provisional
Probab=98.63 E-value=8e-08 Score=99.01 Aligned_cols=66 Identities=23% Similarity=0.256 Sum_probs=55.2
Q ss_pred CeEEEEEEeC-CCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHH
Q 014547 317 FKTSIVFAHD-KGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALA 395 (423)
Q Consensus 317 ~KTSivf~l~-~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~ 395 (423)
.-++|+|.++ |+||+|+++|+.|+.+|||||+||| .+.++ |+|.|||||++..+-..+..+-.
T Consensus 294 ~~~~l~~~v~~d~pG~L~~vl~~la~~~INit~Ies--~~~r~--------------~~y~f~i~~~~~~~~~~~~~~~~ 357 (370)
T PRK08818 294 EPLTLSVYLPEDRPGSLRTLLHVFEQHGVNLSSIHS--SRTPA--------------GELHFRIGFEPGSDRAALARAAA 357 (370)
T ss_pred cceEEEEECCCCCCChHHHHHHHHHHcCcccceEEE--ecccC--------------ceEEEEEEEeccccHHHHHHHHh
Confidence 4689999997 9999999999999999999999999 55443 89999999998655566666666
Q ss_pred HHH
Q 014547 396 EVQ 398 (423)
Q Consensus 396 eL~ 398 (423)
++.
T Consensus 358 ~~~ 360 (370)
T PRK08818 358 EID 360 (370)
T ss_pred hhc
Confidence 654
No 20
>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=97.98 E-value=6.4e-05 Score=57.13 Aligned_cols=68 Identities=12% Similarity=0.056 Sum_probs=54.2
Q ss_pred EEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhc
Q 014547 322 VFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFT 401 (423)
Q Consensus 322 vf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~ 401 (423)
.+.++++||.|.++++.|+..|+|++.|.+++.+..- ..+.+.+++.++.. +...++.+++.|++.+
T Consensus 2 ~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~------------~~~~~~~~i~v~~~-~~~~l~~l~~~l~~~g 68 (73)
T cd04886 2 RVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTL------------PLGEVEVELTLETR-GAEHIEEIIAALREAG 68 (73)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCC------------CCceEEEEEEEEeC-CHHHHHHHHHHHHHcC
Confidence 4678899999999999999999999999998864210 01467888888873 4577889999998876
Q ss_pred C
Q 014547 402 S 402 (423)
Q Consensus 402 ~ 402 (423)
.
T Consensus 69 ~ 69 (73)
T cd04886 69 Y 69 (73)
T ss_pred C
Confidence 3
No 21
>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=97.94 E-value=6.6e-05 Score=56.72 Aligned_cols=38 Identities=13% Similarity=0.186 Sum_probs=34.7
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCC
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRN 356 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~ 356 (423)
+.+.+..+|+||.|.++++.|+++|||+..+++++.+.
T Consensus 1 ~~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~ 38 (66)
T PF01842_consen 1 YRVRVIVPDRPGILADVTEILADHGINIDSISQSSDKD 38 (66)
T ss_dssp EEEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred CEEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence 45777889999999999999999999999999999874
No 22
>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=97.21 E-value=0.0023 Score=48.31 Aligned_cols=60 Identities=12% Similarity=0.120 Sum_probs=44.3
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
+.+.++|+||.|.++++.|+++|+|+.++...+.... ....+++.++. ...+++.|++.
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~---------------~~~~v~~~ve~------~~~~~~~L~~~ 60 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKG---------------GKALLIFRTED------IEKAIEVLQER 60 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCC---------------CeEEEEEEeCC------HHHHHHHHHHC
Confidence 4567899999999999999999999999987665421 13456667664 44666667665
Q ss_pred c
Q 014547 401 T 401 (423)
Q Consensus 401 ~ 401 (423)
.
T Consensus 61 G 61 (65)
T cd04882 61 G 61 (65)
T ss_pred C
Confidence 4
No 23
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=97.15 E-value=0.0044 Score=50.71 Aligned_cols=71 Identities=14% Similarity=0.195 Sum_probs=55.1
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHH
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQ 398 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~ 398 (423)
-+|.+-+.|+||.|.++++.|+.||.|+..|..-|.... .-..+-|-+.| ++..+.++.++|+
T Consensus 3 ~tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te~~---------------~~sriti~~~~--~~~~i~qi~kQL~ 65 (76)
T PRK06737 3 HTFSLVIHNDPSVLLRISGIFARRGYYISSLNLNERDTS---------------GVSEMKLTAVC--TENEATLLVSQLK 65 (76)
T ss_pred EEEEEEEecCCCHHHHHHHHHhccCcceEEEEecccCCC---------------CeeEEEEEEEC--CHHHHHHHHHHHh
Confidence 456677789999999999999999999999998887632 23556666655 5678899999998
Q ss_pred hhcCceEE
Q 014547 399 EFTSFLRV 406 (423)
Q Consensus 399 ~~~~~vrv 406 (423)
+...-+++
T Consensus 66 KLidV~~V 73 (76)
T PRK06737 66 KLINVLQV 73 (76)
T ss_pred CCcCEEEE
Confidence 87654443
No 24
>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=97.13 E-value=0.0059 Score=46.05 Aligned_cols=67 Identities=12% Similarity=0.157 Sum_probs=50.9
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
+|.+...++||.|.+++..|+.+++|+.++...+..+. ....+++.++. .+ ..+..++++|++
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~---------------~~~~~~~~~~~-~~-~~~~~l~~~l~~ 64 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDP---------------GISRITIVVEG-DD-DVIEQIVKQLNK 64 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCC---------------CeEEEEEEEEC-CH-HHHHHHHHHHhC
Confidence 46778889999999999999999999999998765221 12345555554 34 789999999987
Q ss_pred hcCc
Q 014547 400 FTSF 403 (423)
Q Consensus 400 ~~~~ 403 (423)
....
T Consensus 65 ~~~v 68 (72)
T cd04878 65 LVDV 68 (72)
T ss_pred CccE
Confidence 7643
No 25
>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=97.07 E-value=0.0054 Score=46.53 Aligned_cols=63 Identities=13% Similarity=0.168 Sum_probs=47.9
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
.|.+..++++|.|.++++.|+++++|+.++...+... ..+.+++++++. ..+..+++.|++
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~----------------~~~~~~i~~~~~---~~~~~~~~~L~~ 62 (72)
T cd04874 2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIERE----------------GKARIYMELEGV---GDIEELVEELRS 62 (72)
T ss_pred eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccCC----------------CeEEEEEEEecc---ccHHHHHHHHhC
Confidence 4667788999999999999999999999998765432 245567888764 355577777776
Q ss_pred hc
Q 014547 400 FT 401 (423)
Q Consensus 400 ~~ 401 (423)
..
T Consensus 63 ~~ 64 (72)
T cd04874 63 LP 64 (72)
T ss_pred CC
Confidence 54
No 26
>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=97.04 E-value=0.0045 Score=48.55 Aligned_cols=65 Identities=12% Similarity=0.128 Sum_probs=44.5
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
+.+.++|+||.|.++++.|+++|+|+..|...+..... | ....+|.+++.. +..++.+++.|++.
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~---------~-----~~~~~v~v~~e~-~~~~~~i~~~L~~~ 66 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPD---------G-----MRRVFIRVTPMD-RSKENELIEELKAK 66 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCC---------C-----ccEEEEEEEEec-chHHHHHHHHHhCc
Confidence 45688999999999999999999999998765543211 1 223444444422 23467777777655
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=96.91 E-value=0.0082 Score=46.44 Aligned_cols=64 Identities=8% Similarity=0.134 Sum_probs=45.4
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHH
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQ 398 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~ 398 (423)
+.+.+.++|+||.|.++++.|+++++|+.++..-+.... ....++|.+++.. .+ .+++.|+
T Consensus 2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~---------------~~~~v~i~v~~~~-~~---~~~~~L~ 62 (72)
T cd04883 2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEE---------------DNKILVFRVQTMN-PR---PIIEDLR 62 (72)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCC---------------CeEEEEEEEecCC-HH---HHHHHHH
Confidence 357778999999999999999999999999976554321 1345566666522 22 5666676
Q ss_pred hhc
Q 014547 399 EFT 401 (423)
Q Consensus 399 ~~~ 401 (423)
+..
T Consensus 63 ~~G 65 (72)
T cd04883 63 RAG 65 (72)
T ss_pred HCC
Confidence 654
No 28
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=96.76 E-value=0.0078 Score=47.09 Aligned_cols=62 Identities=10% Similarity=0.208 Sum_probs=48.2
Q ss_pred CCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcCceE
Q 014547 327 KGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTSFLR 405 (423)
Q Consensus 327 ~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~~vr 405 (423)
|+||+|.++++.|..||+|+..|..-+.... .-+.+-|.+++. +..+..++++|++...-++
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~---------------~~~riti~v~~~--~~~i~~l~~Ql~KlidV~~ 62 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDP---------------GISRITIVVSGD--DREIEQLVKQLEKLIDVVK 62 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-SST---------------TEEEEEEEEES---CCHHHHHHHHHHCSTTEEE
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecCCC---------------CEEEEEEEEeeC--chhHHHHHHHHhccCCeEe
Confidence 5799999999999999999999999995432 357888888873 4678889999988765443
No 29
>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=96.68 E-value=0.02 Score=44.67 Aligned_cols=73 Identities=18% Similarity=0.190 Sum_probs=49.6
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
+|.+..+++||.|.++++.+++.|+|+..|.+...... .+...|-++.. ..+..+..+++.|++
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~--------------~~~i~~~v~v~--~~~~~l~~l~~~L~~ 65 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHG--------------RANVTISIDTS--TMNGDIDELLEELRE 65 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCC--------------eEEEEEEEEcC--chHHHHHHHHHHHhc
Confidence 56778889999999999999999999999987422110 13445555543 233477788888874
Q ss_pred hc--CceEEEc
Q 014547 400 FT--SFLRVLG 408 (423)
Q Consensus 400 ~~--~~vrvLG 408 (423)
.- ..|+++|
T Consensus 66 i~~V~~v~~~~ 76 (76)
T cd04888 66 IDGVEKVELVG 76 (76)
T ss_pred CCCeEEEEEeC
Confidence 32 3455554
No 30
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=96.63 E-value=0.018 Score=45.90 Aligned_cols=70 Identities=9% Similarity=0.200 Sum_probs=51.7
Q ss_pred CCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHH
Q 014547 316 PFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALA 395 (423)
Q Consensus 316 ~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~ 395 (423)
.+.+.|.+...|+||.|.+++++++..++|+..++.+..+.. ..+.+.++++-. +-..+..+++
T Consensus 4 ~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~---------------~~~~~~l~v~V~-d~~~L~~ii~ 67 (80)
T PF13291_consen 4 SFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDD---------------GTARITLTVEVK-DLEHLNQIIR 67 (80)
T ss_dssp -EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ET---------------TEEEEEEEEEES-SHHHHHHHHH
T ss_pred EEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccC---------------CEEEEEEEEEEC-CHHHHHHHHH
Confidence 478889999999999999999999999999999999987521 134555555532 4478999999
Q ss_pred HHHhhc
Q 014547 396 EVQEFT 401 (423)
Q Consensus 396 eL~~~~ 401 (423)
.|++.-
T Consensus 68 ~L~~i~ 73 (80)
T PF13291_consen 68 KLRQIP 73 (80)
T ss_dssp HHCTST
T ss_pred HHHCCC
Confidence 998654
No 31
>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=96.62 E-value=0.013 Score=40.21 Aligned_cols=58 Identities=24% Similarity=0.260 Sum_probs=43.0
Q ss_pred EEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHH
Q 014547 322 VFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEV 397 (423)
Q Consensus 322 vf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL 397 (423)
.+..++++|.|.++++.|+.+++|+.++.+++.... +...|++.++... .+..++++|
T Consensus 2 ~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~---------------~~~~~~~~~~~~~---~~~~~~~~l 59 (60)
T cd02116 2 TVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGDG---------------GEADIFIVVDGDG---DLEKLLEAL 59 (60)
T ss_pred EEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcCCC---------------CeEEEEEEEechH---HHHHHHHHh
Confidence 456778899999999999999999999998776421 3566777776521 455555554
No 32
>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=96.59 E-value=0.012 Score=45.40 Aligned_cols=61 Identities=11% Similarity=0.143 Sum_probs=43.1
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHH
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEV 397 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL 397 (423)
+++..+++||.|.++++.|+++|+|+..+.+.+.... ......+++++.. .+.+.+.|+++
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~---------------~~~~~~i~v~~~~-~~~~~~~l~~~ 62 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPG---------------GEALMVLSVDEPV-PDEVLEELRAL 62 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCC---------------CEEEEEEEeCCCC-CHHHHHHHHcC
Confidence 4567889999999999999999999999987665321 2455666887633 33444444443
No 33
>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=96.50 E-value=0.18 Score=51.91 Aligned_cols=219 Identities=14% Similarity=0.079 Sum_probs=107.2
Q ss_pred HHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhc--CCcEEEEEEEEeee---eeeeecCCCCcCcccEEE---echh
Q 014547 160 EVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLR--HRLHIVGEVQLPVH---HCLLALPGVRKEYLTRVI---SHPQ 231 (423)
Q Consensus 160 ~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~--~~L~IvgEi~lpI~---h~Lla~~g~~l~dIk~Vy---SHPq 231 (423)
.|+++.+ +..|+-|+|+- ..|.+.-+...|.+ .+++|+|--...-. ..+...+......+.++. .-+.
T Consensus 140 ~Ei~~q~--~~~D~vv~~vG--~Gg~~aGi~~~~k~~~p~~kvigVe~~~~~~~~~~~~~g~~~~~~~~~~~a~g~~~~~ 215 (380)
T TIGR01127 140 LEIMEDI--PDVDTVIVPVG--GGGLISGVASAAKQINPNVKVIGVEAEGAPSMYESLREGKIKAVESVRTIADGIAVKK 215 (380)
T ss_pred HHHHHhC--CCCCEEEEEeC--hHHHHHHHHHHHHHhCCCCEEEEEEECCChHHHHHHHcCCceecCCCCCeecchhCCC
Confidence 3455544 35899999986 56777777766643 46788773332110 001111101111222211 1111
Q ss_pred HHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCceeecCccCCCCCeeEEEEEeeCCCCC
Q 014547 232 ALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQVLEDGIQDDSSNVTRFVMLAREPIIP 311 (423)
Q Consensus 232 AL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~ 311 (423)
+-..+-.++.++.-.+..+.-.....|++.+.+.. +. .+.+.-|+-+.++.-.. .. ..+.+=-++++-- ...
T Consensus 216 ~~~~~~~~~~~~vd~~v~V~d~e~~~a~~~l~~~~--gi-~~e~s~a~~laa~~~~~--~~--~~~~~vv~i~sGG-n~d 287 (380)
T TIGR01127 216 PGDLTFNIIKEYVDDVVTVDEEEIANAIYLLLERH--KI-LAEGAGAAGVAALLEQK--VD--VKGKKIAVVLSGG-NID 287 (380)
T ss_pred ccHHHHHHHHHhCCEEEEECHHHHHHHHHHHHHhc--Ce-EechHHHHHHHHHHhCc--cc--cCCCeEEEEeCCC-CCC
Confidence 22344455555433333332222345555565532 11 22223333333332111 11 1223323333322 111
Q ss_pred C---------C--CCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeee-eCCCCCcccccccCCCCCCcceEEEEE
Q 014547 312 R---------T--DRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESR-PHRNRPIRLVDDANVGTAKHFEYMFYI 379 (423)
Q Consensus 312 ~---------~--~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESR-P~~~~p~~~~~~~~~G~~~~~eY~FfI 379 (423)
. . ....+..|.+.++|+||.|.++++.|+..+.|++.|.-+ ..+..+ . ......|
T Consensus 288 ~d~l~~vi~~gl~~~gr~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~r~~~~~~--------~-----~~~~v~v 354 (380)
T TIGR01127 288 LNLLNKIIEKGLVKSGRKVRIETVLPDRPGALYHLLESIAEARANIVKIDHDRLSKEIP--------P-----GFAMVEI 354 (380)
T ss_pred HHHHHHHHHHHHHhCCCEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeccccCCC--------C-----ceEEEEE
Confidence 0 0 112244788899999999999999999999999998654 222211 1 1334444
Q ss_pred EEecCcChHHHHHHHHHHHhhcCce
Q 014547 380 DFEASMAEVRAQNALAEVQEFTSFL 404 (423)
Q Consensus 380 D~eg~~~d~~v~~aL~eL~~~~~~v 404 (423)
.++.. +...++++++.|++..-.+
T Consensus 355 ~vet~-~~~~~~~i~~~L~~~G~~v 378 (380)
T TIGR01127 355 TLETR-GKEHLDEILKILRDMGYNF 378 (380)
T ss_pred EEEeC-CHHHHHHHHHHHHHcCCcc
Confidence 55442 2456678888888765444
No 34
>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=96.46 E-value=0.017 Score=43.43 Aligned_cols=62 Identities=13% Similarity=0.270 Sum_probs=44.4
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
|.+..+|+||.|.++++.|+++|+|+..+...+.... ......|+++.. .+.+++++|++.
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~---------------~~~~i~i~v~~~----~~~~~i~~l~~~ 62 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKG---------------DQALMVIEVDQP----IDEEVIEEIKKI 62 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCC---------------CeEEEEEEeCCC----CCHHHHHHHHcC
Confidence 5667789999999999999999999999988764211 122344666553 455677777754
Q ss_pred c
Q 014547 401 T 401 (423)
Q Consensus 401 ~ 401 (423)
-
T Consensus 63 ~ 63 (71)
T cd04903 63 P 63 (71)
T ss_pred C
Confidence 4
No 35
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=96.39 E-value=0.032 Score=51.75 Aligned_cols=71 Identities=14% Similarity=0.183 Sum_probs=56.0
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHH
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQ 398 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~ 398 (423)
-.|.+.++|+||.|.++.+.|+.||+|+..+-.-|.... ..+.+.+-+++ ++..+.++.++|.
T Consensus 3 ~~IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~---------------~~sriti~V~~--~~~~i~qi~kQl~ 65 (161)
T PRK11895 3 HTLSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTEDP---------------GLSRMTIVTSG--DEQVIEQITKQLN 65 (161)
T ss_pred EEEEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecCCC---------------CEEEEEEEEEC--CHHHHHHHHHHHh
Confidence 456777899999999999999999999999987777421 24566677776 5688999999998
Q ss_pred hhcCceEE
Q 014547 399 EFTSFLRV 406 (423)
Q Consensus 399 ~~~~~vrv 406 (423)
+.-.-+++
T Consensus 66 KLidV~~V 73 (161)
T PRK11895 66 KLIDVLKV 73 (161)
T ss_pred ccccEEEE
Confidence 87654444
No 36
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=96.36 E-value=0.034 Score=51.36 Aligned_cols=71 Identities=11% Similarity=0.159 Sum_probs=55.6
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
.|.+.++|+||.|.++.+.|+.+|+|+..+-.-|.... ..+.+.|-+++ ++..+.++.++|++
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~---------------~~sriti~V~~--d~~~i~qi~kQl~K 65 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTEDP---------------DLSRMTIVVVG--DDKVLEQITKQLNK 65 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecCCC---------------CEEEEEEEEEC--CHHHHHHHHHHHhc
Confidence 56677889999999999999999999999988777421 24566667766 57889999999988
Q ss_pred hcCceEEE
Q 014547 400 FTSFLRVL 407 (423)
Q Consensus 400 ~~~~vrvL 407 (423)
.-.-+++.
T Consensus 66 li~V~~V~ 73 (157)
T TIGR00119 66 LVDVIKVS 73 (157)
T ss_pred CccEEEEE
Confidence 76544443
No 37
>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=96.23 E-value=0.032 Score=43.10 Aligned_cols=34 Identities=9% Similarity=0.072 Sum_probs=30.5
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeC
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPH 354 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~ 354 (423)
|.+.++|+||.|.+++..|+++|||+..+..-+.
T Consensus 4 i~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~ 37 (66)
T cd04908 4 LSVFLENKPGRLAAVTEILSEAGINIRALSIADT 37 (66)
T ss_pred EEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEec
Confidence 5668899999999999999999999999987654
No 38
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=96.17 E-value=0.032 Score=52.38 Aligned_cols=73 Identities=11% Similarity=0.199 Sum_probs=54.3
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHH
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQ 398 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~ 398 (423)
-.|.+...|+||.|.++.+.|+.||+|+..+...|.... ....+-|.+.++ +..+.++.++|+
T Consensus 3 ~~isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~---------------~~sr~TIvv~~~--~~~ieqL~kQL~ 65 (174)
T CHL00100 3 HTLSVLVEDESGVLTRIAGLFARRGFNIESLAVGPAEQK---------------GISRITMVVPGD--DRTIEQLTKQLY 65 (174)
T ss_pred EEEEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCC---------------CccEEEEEEECC--HHHHHHHHHHHH
Confidence 456667789999999999999999999999999886532 134666777763 333777777887
Q ss_pred hhcCceEEEc
Q 014547 399 EFTSFLRVLG 408 (423)
Q Consensus 399 ~~~~~vrvLG 408 (423)
+.+.-+++-.
T Consensus 66 KLidVl~V~~ 75 (174)
T CHL00100 66 KLVNILKVQD 75 (174)
T ss_pred HHhHhhEEEe
Confidence 7776555443
No 39
>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=96.15 E-value=0.041 Score=42.42 Aligned_cols=64 Identities=14% Similarity=0.034 Sum_probs=44.3
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
.+.+.++++||.|.++++.|+.+|+|+..+...+.+... .....|.++.. .....+++.|++
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~-------------~~~~~i~v~~~-----~~~~~~~~~L~~ 64 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIREGI-------------GGILRISFKTQ-----EDRERAKEILKE 64 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEeecCC-------------cEEEEEEECCH-----HHHHHHHHHHHH
Confidence 356678899999999999999999999999766653211 02345555532 245566777766
Q ss_pred hc
Q 014547 400 FT 401 (423)
Q Consensus 400 ~~ 401 (423)
..
T Consensus 65 ~G 66 (69)
T cd04909 65 AG 66 (69)
T ss_pred cC
Confidence 53
No 40
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=96.12 E-value=0.049 Score=44.55 Aligned_cols=67 Identities=10% Similarity=0.142 Sum_probs=49.6
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHH
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEV 397 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL 397 (423)
|.+|.+.+.|+||+|.++++.|+.||.|+..|.--|.... .-...-+-+ + ++..+..+.++|
T Consensus 3 ~~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~---------------~~sriti~v-~--~~~~i~ql~kQL 64 (76)
T PRK11152 3 QHQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDA---------------QNINIELTV-A--SERPIDLLSSQL 64 (76)
T ss_pred eEEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCC---------------CEEEEEEEE-C--CCchHHHHHHHH
Confidence 4567777889999999999999999999999998886531 112222223 2 467788888888
Q ss_pred HhhcC
Q 014547 398 QEFTS 402 (423)
Q Consensus 398 ~~~~~ 402 (423)
.+.-.
T Consensus 65 ~KL~d 69 (76)
T PRK11152 65 NKLVD 69 (76)
T ss_pred hcCcC
Confidence 87654
No 41
>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=96.11 E-value=0.031 Score=41.81 Aligned_cols=62 Identities=13% Similarity=0.214 Sum_probs=44.4
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
+.+..++++|.|.++++.|+++|+|+.++++.+.... ..+...++++.. ...+++++|++.
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~---------------~~~~~~~~v~~~----~~~~l~~~l~~~ 62 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKG---------------GIAYMVLDVDSP----VPEEVLEELKAL 62 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCC---------------CEEEEEEEcCCC----CCHHHHHHHHcC
Confidence 5567889999999999999999999999998775411 134455566442 244667777654
Q ss_pred c
Q 014547 401 T 401 (423)
Q Consensus 401 ~ 401 (423)
-
T Consensus 63 ~ 63 (71)
T cd04879 63 P 63 (71)
T ss_pred C
Confidence 4
No 42
>PRK08198 threonine dehydratase; Provisional
Probab=96.01 E-value=0.24 Score=51.39 Aligned_cols=220 Identities=12% Similarity=0.065 Sum_probs=113.6
Q ss_pred HHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhc--CCcEEEEEEEEeeeee--eee--cCCC--CcCcccEEEec--
Q 014547 160 EVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLR--HRLHIVGEVQLPVHHC--LLA--LPGV--RKEYLTRVISH-- 229 (423)
Q Consensus 160 ~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~--~~L~IvgEi~lpI~h~--Lla--~~g~--~l~dIk~VySH-- 229 (423)
.|+++.+ ++.|+-|+|+- ..|.+.-....|.+ .+++|+|--. ..| +.. ..|. ....+.++..-
T Consensus 162 ~EI~~q~--~~~d~vv~~vG--~GG~~~Gi~~~~k~~~p~~kiigVe~---~~~~~~~~~~~~g~~~~~~~~~t~a~g~~ 234 (404)
T PRK08198 162 LEILEDL--PDVDTVVVPIG--GGGLISGVATAVKALRPEVRVIGVQA---EGAPAMPESLAAGRPVELESVDTIADGIA 234 (404)
T ss_pred HHHHHhC--CCCCEEEEEeC--HhHHHHHHHHHHHHhCCCCEEEEEEe---CCChHHHHHHHcCCCEecCCCCccccccc
Confidence 3444444 35899999987 56767666666543 4577777322 111 110 0110 11122221110
Q ss_pred -hhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCceeecCccCCCCCeeEEEEEeeCC
Q 014547 230 -PQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQVLEDGIQDDSSNVTRFVMLAREP 308 (423)
Q Consensus 230 -PqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~ 308 (423)
+.+-.++-.++++..-.+..+.-.....|++.+++.. .. .+.+.-|+-+-+|.-+.. + ..+.+=-++++.-.
T Consensus 235 v~~~~~~~~~~~~~~~d~~v~V~d~e~~~a~~~l~~~~--g~-~~e~sga~~lAal~~~~~-~---~~~~~vv~vl~ggn 307 (404)
T PRK08198 235 VKRPGDLTFEIIRELVDDVVTVSDEEIARAILLLLERA--KL-VVEGAGAVSVAALLSGKL-D---VKGKKVVAVLSGGN 307 (404)
T ss_pred cCCcCHHHHHHHHHhCCEEEEECHHHHHHHHHHHHHhc--Ce-EEehHHHHHHHHHHhchh-h---cCCCeEEEEECCCC
Confidence 0001123333444332333333333445666666532 22 223334444444433321 1 22334444444322
Q ss_pred CC--------CCC--CCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeee-CCCCCcccccccCCCCCCcceEEE
Q 014547 309 II--------PRT--DRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRP-HRNRPIRLVDDANVGTAKHFEYMF 377 (423)
Q Consensus 309 ~~--------~~~--~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP-~~~~p~~~~~~~~~G~~~~~eY~F 377 (423)
.. ... .......|.+.++|+||.|.++|+.++..|.|++.|.-+. ..+.| .....+
T Consensus 308 ~~~~~l~~ii~~gl~~~gr~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~~~~~~~-------------~~~~~v 374 (404)
T PRK08198 308 IDVLLLSRVIERGLVAAGRYLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDRFSPDLR-------------LGEVEV 374 (404)
T ss_pred CCHHHHHHHHHhhhhhcCCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEEccCCCC-------------CceEEE
Confidence 10 011 1223568888999999999999999999999999987654 33222 124556
Q ss_pred EEEEecCcChHHHHHHHHHHHhhcCceEEE
Q 014547 378 YIDFEASMAEVRAQNALAEVQEFTSFLRVL 407 (423)
Q Consensus 378 fID~eg~~~d~~v~~aL~eL~~~~~~vrvL 407 (423)
.|.++.. +...+++++++|++..-.++++
T Consensus 375 ~v~ie~~-~~~~~~~l~~~L~~~G~~v~~~ 403 (404)
T PRK08198 375 ELTLETR-GPEHIEEILDALRDAGYEVKVV 403 (404)
T ss_pred EEEEEeC-CHHHHHHHHHHHHHCCCeEEEc
Confidence 6666653 3357788999998877555543
No 43
>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=95.94 E-value=0.021 Score=43.68 Aligned_cols=60 Identities=17% Similarity=0.206 Sum_probs=43.5
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
+++...|+||.|.++++.|+++|+|+.++.+++..+ .-...++++.. .+++++++|++.
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~-----------------~a~~~~~~~~~----~l~~li~~l~~~ 60 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGE-----------------IGYVVIDIDSE----VSEELLEALRAI 60 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCC-----------------EEEEEEEcCCC----CCHHHHHHHHcC
Confidence 456778999999999999999999999987765321 22334466653 455777777764
Q ss_pred c
Q 014547 401 T 401 (423)
Q Consensus 401 ~ 401 (423)
-
T Consensus 61 ~ 61 (69)
T cd04901 61 P 61 (69)
T ss_pred C
Confidence 4
No 44
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=95.86 E-value=0.079 Score=44.29 Aligned_cols=71 Identities=13% Similarity=0.165 Sum_probs=52.3
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEe-cCcChHHHHHHHHHH
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFE-ASMAEVRAQNALAEV 397 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~e-g~~~d~~v~~aL~eL 397 (423)
-.|.+-+.|+||.|.++-+.|..||+|+..|.-=|+... | =..+=|-++ | ++..+.++.++|
T Consensus 3 ~~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~----------~-----iSRmtivv~~~--d~~~ieqI~kQL 65 (84)
T PRK13562 3 RILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQP----------G-----ISNMEIQVDIQ--DDTSLHILIKKL 65 (84)
T ss_pred EEEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCCC----------C-----ceEEEEEEeCC--CHHHHHHHHHHH
Confidence 456666789999999999999999999999988887532 1 123333443 4 567788999999
Q ss_pred HhhcCceEE
Q 014547 398 QEFTSFLRV 406 (423)
Q Consensus 398 ~~~~~~vrv 406 (423)
++.-.-+++
T Consensus 66 ~KlidVikV 74 (84)
T PRK13562 66 KQQINVLTV 74 (84)
T ss_pred hCCccEEEE
Confidence 887654444
No 45
>PRK08526 threonine dehydratase; Provisional
Probab=95.80 E-value=0.58 Score=49.07 Aligned_cols=209 Identities=14% Similarity=0.092 Sum_probs=112.0
Q ss_pred CcCeEEEeeccCCCCchHHHHHHhh--cCCcEEEEEEEEe---eeeeeeecCCCCcCcccEE----Ee---chhHHHHHH
Q 014547 170 IADRAVLPVENSLGGSIHRNYDLLL--RHRLHIVGEVQLP---VHHCLLALPGVRKEYLTRV----IS---HPQALSQCE 237 (423)
Q Consensus 170 ~~d~gVVPIENS~~G~V~~tlDlL~--~~~L~IvgEi~lp---I~h~Lla~~g~~l~dIk~V----yS---HPqAL~QC~ 237 (423)
..|+-|+|+- ..|.+.-+...|. ..+.+|+|--.-. ....+-..+-.....+.++ .. -|..+..|+
T Consensus 168 ~~D~vvvpvG--gGGl~aGia~~~k~~~p~~kvigVep~~~~~~~~s~~~g~~~~~~~~~tiadgiav~~~~~~~~~~~~ 245 (403)
T PRK08526 168 DLDMVVVPVG--GGGLISGIASAAKQINPNIKIIGVGAKGAPAMYESFHAKKIINSKSVRTIADGIAVRDASPINLAIIL 245 (403)
T ss_pred CCCEEEEecC--hHHHHHHHHHHHHHhCCCCEEEEEEECCCChHHHHHHcCCcccCCCCCceeccccCCCCCHHHHHHHH
Confidence 5899999985 5677766666654 3567887732211 0000111110112223222 11 166667666
Q ss_pred HHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCceeecCccCCCCCeeEEEEEeeCCCCCC-----
Q 014547 238 HTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQVLEDGIQDDSSNVTRFVMLAREPIIPR----- 312 (423)
Q Consensus 238 ~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~~----- 312 (423)
+++.+ +..+.-+....|.+.+.+.. +. .+.+.-|+-+-+|.--...+ ..+.+=-++++--.....
T Consensus 246 ~~vd~----~v~V~d~ei~~A~~~l~~~~--gi-~ve~aga~~lAall~~~~~~---~~~~~Vv~ilsGGnid~~~~~~i 315 (403)
T PRK08526 246 ECVDD----FVQVDDEEIANAILFLLEKQ--KI-VVEGAGAASVAALLHQKIDL---KKGKKIGVVLSGGNIDVQMLNII 315 (403)
T ss_pred HhCCE----EEEECHHHHHHHHHHHHHhc--Cc-EeeHHHHHHHHHHHhCcccc---ccCCeEEEEECCCCCCHHHHHHH
Confidence 65542 33333333456666666542 22 22444444444442111112 122333333333221110
Q ss_pred -----CCCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeee-eeCCCCCcccccccCCCCCCcceEEEEEEEecCcC
Q 014547 313 -----TDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIES-RPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMA 386 (423)
Q Consensus 313 -----~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIES-RP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~ 386 (423)
-....+..|.+.++++||+|.++++.+...+.|+++|+= |.....+ + .+-...|.+|.. +
T Consensus 316 ~~~~l~~~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~~~~~--------~-----~~~~~~~~~e~~-~ 381 (403)
T PRK08526 316 IEKGLIKSYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFSTKLD--------Y-----GDAMISITLETK-G 381 (403)
T ss_pred HHHHHHhcCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEeccCCCC--------C-----ccEEEEEEEEeC-C
Confidence 012246778889999999999999999999999999876 5444322 1 233455556543 4
Q ss_pred hHHHHHHHHHHHhhcCce
Q 014547 387 EVRAQNALAEVQEFTSFL 404 (423)
Q Consensus 387 d~~v~~aL~eL~~~~~~v 404 (423)
.+.++++++.|++..-.+
T Consensus 382 ~~~~~~~~~~l~~~g~~~ 399 (403)
T PRK08526 382 KEHQEEIRKILTEKGFNF 399 (403)
T ss_pred HHHHHHHHHHHHHCCCCe
Confidence 567888888888765444
No 46
>PRK04435 hypothetical protein; Provisional
Probab=95.79 E-value=0.1 Score=47.43 Aligned_cols=77 Identities=14% Similarity=0.144 Sum_probs=55.6
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e 396 (423)
.+++|.+.+.|+||.|.++++.++..|+|+..|...-..+. .....|=||... .+..+.++++.
T Consensus 68 r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g--------------~a~vs~tVevs~--~~~~L~~Li~~ 131 (147)
T PRK04435 68 KIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQG--------------RANVTISIDTSS--MEGDIDELLEK 131 (147)
T ss_pred cEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCC--------------EEEEEEEEEeCC--hHHHHHHHHHH
Confidence 47889999999999999999999999999999986422110 134556666632 33478888888
Q ss_pred HHhh--cCceEEEcc
Q 014547 397 VQEF--TSFLRVLGS 409 (423)
Q Consensus 397 L~~~--~~~vrvLGs 409 (423)
|++. ...++++|.
T Consensus 132 L~~i~gV~~V~i~~~ 146 (147)
T PRK04435 132 LRNLDGVEKVELIGM 146 (147)
T ss_pred HHcCCCcEEEEEEec
Confidence 8743 345777774
No 47
>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=95.77 E-value=0.054 Score=44.18 Aligned_cols=63 Identities=11% Similarity=0.181 Sum_probs=42.7
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceee--eeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCc-ChH-HHHHHHHH
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLT--KIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASM-AEV-RAQNALAE 396 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLt--kIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~-~d~-~v~~aL~e 396 (423)
|-+..+|+||-|+++.++|++.|+++. ||.|--... .-.=.||||.+|.. .++ +.+.+-+.
T Consensus 3 lev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Ge---------------rv~D~Fyv~~~g~kl~d~~~~~~L~~~ 67 (75)
T cd04896 3 LQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGY---------------REVDLFIVQSDGKKIMDPKKQAALCAR 67 (75)
T ss_pred EEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccC---------------EEEEEEEEeCCCCccCCHHHHHHHHHH
Confidence 446678999999999999999999997 566432222 12458999887743 443 33444444
Q ss_pred HH
Q 014547 397 VQ 398 (423)
Q Consensus 397 L~ 398 (423)
|.
T Consensus 68 L~ 69 (75)
T cd04896 68 LR 69 (75)
T ss_pred HH
Confidence 44
No 48
>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=95.71 E-value=0.09 Score=40.85 Aligned_cols=69 Identities=16% Similarity=0.128 Sum_probs=48.8
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
|.+...++||.|.++.+.++..|+|+.+++++..+.. .....|-|++. +.+.++.+++.|++.
T Consensus 2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~--------------~~~~~~~vev~---~~~~l~~i~~~L~~i 64 (74)
T cd04887 2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRD--------------YTVRDITVDAP---SEEHAETIVAAVRAL 64 (74)
T ss_pred EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCC--------------EEEEEEEEEcC---CHHHHHHHHHHHhcC
Confidence 5677889999999999999999999999998764321 12334444443 346778888888754
Q ss_pred cCceEEE
Q 014547 401 TSFLRVL 407 (423)
Q Consensus 401 ~~~vrvL 407 (423)
- .|.++
T Consensus 65 ~-gV~~~ 70 (74)
T cd04887 65 P-EVKVL 70 (74)
T ss_pred C-CeEEE
Confidence 3 35443
No 49
>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=95.63 E-value=0.042 Score=42.92 Aligned_cols=62 Identities=10% Similarity=0.081 Sum_probs=44.3
Q ss_pred EEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhc
Q 014547 322 VFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFT 401 (423)
Q Consensus 322 vf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~ 401 (423)
.+.++++||+|.++++.++. +.|++.|.=|-... +.....+=|++.+ ...++++++.|++..
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~--------------~~~~v~v~ie~~~---~~~~~~i~~~L~~~G 63 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGG--------------DEARVLVGIQVPD---REDLAELKERLEALG 63 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCC--------------CceEEEEEEEeCC---HHHHHHHHHHHHHcC
Confidence 46789999999999999999 99999997765431 1123444445433 356777788887654
No 50
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=95.43 E-value=0.15 Score=43.68 Aligned_cols=72 Identities=14% Similarity=0.241 Sum_probs=53.7
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHH
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEV 397 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL 397 (423)
+..|.+-+.|+||.|.++-..|+.||.|+..|-.-|.... .-..+.|-+. ++..+.+++++|
T Consensus 8 ~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~~---------------~iSRmtivv~---~~~~i~Qi~kQL 69 (96)
T PRK08178 8 NVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQDG---------------DKSRIWLLVN---DDQRLEQMISQI 69 (96)
T ss_pred CEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCCC---------------CceEEEEEEc---CchHHHHHHHHH
Confidence 4567777789999999999999999999999987776532 1234444443 357899999999
Q ss_pred HhhcCceEEE
Q 014547 398 QEFTSFLRVL 407 (423)
Q Consensus 398 ~~~~~~vrvL 407 (423)
++.-.-+++.
T Consensus 70 ~KLidVikV~ 79 (96)
T PRK08178 70 EKLEDVLKVR 79 (96)
T ss_pred hCCcCEEEEE
Confidence 9876555543
No 51
>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=95.43 E-value=0.13 Score=39.37 Aligned_cols=64 Identities=17% Similarity=0.197 Sum_probs=45.9
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
|.+...|++|.|.++++.|+++++|+.++..++.... | .....|-++. .+...++++++.|++.
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~----------~---~~~~~i~~~~---~~~~~l~~~i~~L~~~ 66 (79)
T cd04881 3 LRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGG----------E---TAPVVIVTHE---TSEAALNAALAEIEAL 66 (79)
T ss_pred EEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCC----------C---ceeEEEEEcc---CCHHHHHHHHHHHHcC
Confidence 4566779999999999999999999999988664321 0 1223333332 3568889999999864
No 52
>PRK00194 hypothetical protein; Validated
Probab=95.26 E-value=0.11 Score=42.36 Aligned_cols=36 Identities=17% Similarity=0.181 Sum_probs=31.1
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeee
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRP 353 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP 353 (423)
+-.+.+.-+|+||.+.++.+.|+.+|+|+..+++.-
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~ 38 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTI 38 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHh
Confidence 345666778999999999999999999999998874
No 53
>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=95.24 E-value=0.16 Score=40.37 Aligned_cols=62 Identities=5% Similarity=0.014 Sum_probs=46.2
Q ss_pred EEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 323 FAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 323 f~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
+.-+|+||-+.++-+.|+.+|+|+..++++-..+ .+...|.+++....+-..++++|+.+.+
T Consensus 4 v~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~---------------~f~~~~~v~~p~~~~~~~l~~~l~~l~~ 65 (75)
T cd04870 4 VTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHG---------------RLSLGILVQIPDSADSEALLKDLLFKAH 65 (75)
T ss_pred EEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcC---------------eeEEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence 3457899999999999999999999998665432 2556677776544445777777777763
No 54
>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=95.08 E-value=0.13 Score=41.97 Aligned_cols=67 Identities=15% Similarity=0.202 Sum_probs=48.0
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEec-CcChHHHHHHHHHH
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEA-SMAEVRAQNALAEV 397 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg-~~~d~~v~~aL~eL 397 (423)
-.+.+.-+|+||.+.++.+.|+.+|+|+..++..-..+ .+...+-+++.+ ..+-..+++.|++|
T Consensus 2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~---------------~f~~~~~v~~~~~~~~~~~L~~~l~~l 66 (88)
T cd04872 2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDG---------------YFTMIMIVDISESNLDFAELQEELEEL 66 (88)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCC---------------ccEEEEEEEeCCCCCCHHHHHHHHHHH
Confidence 34666778999999999999999999999998764321 234455566654 33456777777777
Q ss_pred Hhh
Q 014547 398 QEF 400 (423)
Q Consensus 398 ~~~ 400 (423)
.+.
T Consensus 67 ~~~ 69 (88)
T cd04872 67 GKE 69 (88)
T ss_pred HHH
Confidence 643
No 55
>PRK08639 threonine dehydratase; Validated
Probab=94.92 E-value=1.6 Score=45.97 Aligned_cols=74 Identities=12% Similarity=0.156 Sum_probs=50.5
Q ss_pred CeEEEEEEeCCCccHHHHHHH-HHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLS-AFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALA 395 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~-~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~ 395 (423)
.+..+.|.+|++||+|.++|+ .+.... |++.|+-|.....+ .. ...|.+|.. +.+.+++.++
T Consensus 335 r~~~~~v~ipdrPGaL~~~l~~i~~~~~-NI~~~~~~~~~~~~-------------~~--~v~v~iE~~-~~~h~~~i~~ 397 (420)
T PRK08639 335 LKHYFIVNFPQRPGALREFLDDVLGPND-DITRFEYLKKNNRE-------------TG--PVLVGIELK-DAEDYDGLIE 397 (420)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCC-cEEEEEEeecCCCC-------------ce--EEEEEEEeC-CHHHHHHHHH
Confidence 477899999999999999999 555555 99999766533221 12 344555542 3356777888
Q ss_pred HHHhhcCceEEE
Q 014547 396 EVQEFTSFLRVL 407 (423)
Q Consensus 396 eL~~~~~~vrvL 407 (423)
.|++....++.+
T Consensus 398 ~L~~~Gy~~~~~ 409 (420)
T PRK08639 398 RMEAFGPSYIDI 409 (420)
T ss_pred HHHHCCCceEEC
Confidence 888776555544
No 56
>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=94.91 E-value=0.34 Score=34.89 Aligned_cols=63 Identities=8% Similarity=0.125 Sum_probs=44.4
Q ss_pred EEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhc
Q 014547 322 VFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFT 401 (423)
Q Consensus 322 vf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~ 401 (423)
.+..+++||.|.++++.|+++++|+.+++....... ...+.+.++. .+...+..+++.|+..-
T Consensus 2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~----------------~~~~~~~~~~-~~~~~~~~~~~~l~~~~ 64 (71)
T cd04876 2 RVEAIDRPGLLADITTVIAEEKINILSVNTRTDDDG----------------LATIRLTLEV-RDLEHLARIMRKLRQIP 64 (71)
T ss_pred EEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCCC----------------EEEEEEEEEE-CCHHHHHHHHHHHhCCC
Confidence 355778999999999999999999999988764311 1233444442 23467788888887653
No 57
>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=94.82 E-value=0.19 Score=39.76 Aligned_cols=59 Identities=20% Similarity=0.347 Sum_probs=46.6
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
|.+...|++|.|.++++.++..|+|+..+++++. + + .+++++.. +-..+..+++.|++.
T Consensus 3 l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~------------------~-i~l~i~v~-~~~~L~~li~~L~~i 61 (74)
T cd04877 3 LEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-G------------------R-IYLNFPTI-EFEKLQTLMPEIRRI 61 (74)
T ss_pred EEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-C------------------e-EEEEeEec-CHHHHHHHHHHHhCC
Confidence 5566678999999999999999999999999753 2 2 66677643 456788888888754
No 58
>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=94.77 E-value=1.2 Score=48.19 Aligned_cols=213 Identities=16% Similarity=0.191 Sum_probs=114.4
Q ss_pred HHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhc--CCcEEEEEEEEeeeeeeee--cCC--CCcCcc---------cE
Q 014547 161 VAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLR--HRLHIVGEVQLPVHHCLLA--LPG--VRKEYL---------TR 225 (423)
Q Consensus 161 ~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~--~~L~IvgEi~lpI~h~Lla--~~g--~~l~dI---------k~ 225 (423)
|+++.+. +..|+-|+|+= .+|.+.-+.-.|.. .+.+|+|--... .-++.. ..| ..++.+ ++
T Consensus 158 EI~~q~~-~~~D~vvvpvG--gGGliaGia~~lk~~~p~~kVIgVep~~-~~~~~~s~~~g~~~~~~~~~t~adgiav~~ 233 (499)
T TIGR01124 158 EILRQVA-NPLDAVFVPVG--GGGLAAGVAALIKQLMPEIKVIGVEPTD-SDCMKQALDAGEPVDLDQVGLFADGVAVKR 233 (499)
T ss_pred HHHHhCC-CCCCEEEEccC--ccHHHHHHHHHHHHhCCCCEEEEEEECC-ChHHHHHHhcCCceeCCCCCCccCcccCCC
Confidence 4444442 36899999976 57777766655542 467888833311 111110 011 111111 12
Q ss_pred EEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCceeecCccCCCCCeeEEEEEe
Q 014547 226 VISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQVLEDGIQDDSSNVTRFVMLA 305 (423)
Q Consensus 226 VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~ILa~nIqD~~~N~TRFlVLs 305 (423)
+ =+..+.-|++++.. +..+..+....|.+.+.+.. -.-+.+.-|+-+.+|.-+.+... . .+.|=-+|++
T Consensus 234 ~--g~~~~~~~~~~vd~----vv~V~d~ei~~ai~~l~~~~---gii~EpagA~~lAal~~~~~~~~-~-~~~~vv~i~s 302 (499)
T TIGR01124 234 V--GDETFRLCQQYLDD----IVTVDTDEVCAAIKDLFEDT---RAVAEPAGALALAGLKKYVALHG-I-RGQTLVAILS 302 (499)
T ss_pred c--cHHHHHHHHHhCCE----EEEECHHHHHHHHHHHHHhc---CcEEechHHHHHHHHHHhhhhcC-C-CCCeEEEEEC
Confidence 2 13566666665443 33333333455666666542 22234445555556554433221 1 1333333333
Q ss_pred eCCCCC--------C--CCCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceE
Q 014547 306 REPIIP--------R--TDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEY 375 (423)
Q Consensus 306 r~~~~~--------~--~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY 375 (423)
--.... + -.......+.+.+|++||+|.++++.+..+ |+|.++=|-.... +=
T Consensus 303 G~n~~~~~l~~~~~r~~~~~~re~~l~V~iPerPGal~~f~~~i~~~--nItef~yr~~~~~----------------~a 364 (499)
T TIGR01124 303 GANMNFHRLRYVSERCELGEQREALLAVTIPEQPGSFLKFCELLGNR--NITEFNYRYADRK----------------DA 364 (499)
T ss_pred CCCCCHHHHHHHHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhhc--ceEEEEEEecCCC----------------eE
Confidence 322211 0 012247788899999999999999999974 8888888753221 22
Q ss_pred EEEEEEecCcChHHHHHHHHHHHhhcCceEEE
Q 014547 376 MFYIDFEASMAEVRAQNALAEVQEFTSFLRVL 407 (423)
Q Consensus 376 ~FfID~eg~~~d~~v~~aL~eL~~~~~~vrvL 407 (423)
..||.++.. +.+.++++++.|++..-.+..|
T Consensus 365 ~v~vgie~~-~~~~~~~l~~~L~~~Gy~~~dl 395 (499)
T TIGR01124 365 HIFVGVQLS-NPQERQEILARLNDGGYSVVDL 395 (499)
T ss_pred EEEEEEEeC-CHHHHHHHHHHHHHcCCCeEEC
Confidence 345666543 4567888888888776666555
No 59
>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=94.72 E-value=0.23 Score=40.57 Aligned_cols=69 Identities=10% Similarity=0.074 Sum_probs=44.3
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
+.+.++++||+|.++|+.++..||+ .+.=+-.... .....+-+++.+. ...++.+++.|++.
T Consensus 4 l~v~ipD~PG~L~~ll~~l~~anI~--~~~y~~~~~~--------------~~~v~i~ie~~~~--~~~~~~i~~~L~~~ 65 (85)
T cd04906 4 LAVTIPERPGSFKKFCELIGPRNIT--EFNYRYADEK--------------DAHIFVGVSVANG--AEELAELLEDLKSA 65 (85)
T ss_pred EEEecCCCCcHHHHHHHHhCCCcee--EEEEEccCCC--------------eeEEEEEEEeCCc--HHHHHHHHHHHHHC
Confidence 5678999999999999999955555 4443322211 1244555566431 35677888888877
Q ss_pred cCceEEE
Q 014547 401 TSFLRVL 407 (423)
Q Consensus 401 ~~~vrvL 407 (423)
.-.+..+
T Consensus 66 G~~~~~~ 72 (85)
T cd04906 66 GYEVVDL 72 (85)
T ss_pred CCCeEEC
Confidence 6555544
No 60
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=94.63 E-value=0.21 Score=39.98 Aligned_cols=59 Identities=12% Similarity=0.180 Sum_probs=38.4
Q ss_pred EeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHH
Q 014547 324 AHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQ 398 (423)
Q Consensus 324 ~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~ 398 (423)
.=+|+||.+..+.+.++++|.|+..++-.-..+ .+...+.|++... .-++++++|+++.
T Consensus 8 ~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~---------------~f~~~~~v~~~~~-~~~~l~~~L~~l~ 66 (76)
T PF13740_consen 8 VGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGG---------------RFTLIMLVSIPED-SLERLESALEELA 66 (76)
T ss_dssp EEE--TTHHHHHHHHHHCTT-EEEEEEEEEETT---------------EEEEEEEEEESHH-HHHHHHHHHHHHH
T ss_pred EecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcC---------------eEEEEEEEEeCcc-cHHHHHHHHHHHH
Confidence 347999999999999999999998777665543 2445555555422 2356666777663
No 61
>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=94.62 E-value=0.31 Score=37.30 Aligned_cols=36 Identities=8% Similarity=0.038 Sum_probs=31.6
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCC
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHR 355 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~ 355 (423)
-|.+..+|+||.|.++.+.|+.+++|+.++..++..
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~ 37 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLG 37 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecC
Confidence 355677899999999999999999999999988764
No 62
>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=94.56 E-value=0.23 Score=39.26 Aligned_cols=36 Identities=14% Similarity=0.247 Sum_probs=30.9
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeC
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPH 354 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~ 354 (423)
|-|.+..+|+||.|+++.++|+.+|+|+......+.
T Consensus 2 tri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~ 37 (72)
T cd04926 2 VRLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQ 37 (72)
T ss_pred eEEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecC
Confidence 456778889999999999999999999988766554
No 63
>PRK08577 hypothetical protein; Provisional
Probab=94.55 E-value=0.44 Score=42.36 Aligned_cols=69 Identities=14% Similarity=0.227 Sum_probs=48.9
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHH
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEV 397 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL 397 (423)
...|.+...|+||.|.++++.|+.+++|+..+.++...... .+.-.|-+|+... +..+.+++++|
T Consensus 56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~-------------~~~i~l~vev~~~--~~~l~~l~~~L 120 (136)
T PRK08577 56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGE-------------LAECVIIVDLSKS--DIDLEELEEEL 120 (136)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCC-------------EEEEEEEEEeCCc--hhhHHHHHHHH
Confidence 45677888999999999999999999999999887764211 0122333455432 24677888888
Q ss_pred Hhhc
Q 014547 398 QEFT 401 (423)
Q Consensus 398 ~~~~ 401 (423)
++.-
T Consensus 121 ~~l~ 124 (136)
T PRK08577 121 KKLE 124 (136)
T ss_pred HcCC
Confidence 7654
No 64
>PRK07334 threonine dehydratase; Provisional
Probab=94.47 E-value=1 Score=46.92 Aligned_cols=219 Identities=15% Similarity=0.106 Sum_probs=113.4
Q ss_pred HHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhh--cCCcEEEEEEEEeeeeeeee-cCCCC--c---CcccEEEechhH
Q 014547 161 VAFQAVELWIADRAVLPVENSLGGSIHRNYDLLL--RHRLHIVGEVQLPVHHCLLA-LPGVR--K---EYLTRVISHPQA 232 (423)
Q Consensus 161 ~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~--~~~L~IvgEi~lpI~h~Lla-~~g~~--l---~dIk~VySHPqA 232 (423)
|+++.+ ++.|+-|+|+- ..|.+.-+...|. ..+.+|++--.-. .-++.. ..+.. . .-+.-+- =+++
T Consensus 164 Ei~~q~--~~~d~vv~~vG--~GG~~~Gi~~~lk~~~~~~~vi~ve~~~-~~~~~~~~~~~~~~~~~~~~~~gi~-~~~~ 237 (403)
T PRK07334 164 EMLEDA--PDLDTLVVPIG--GGGLISGMATAAKALKPDIEIIGVQTEL-YPSMYAAIKGVALPCGGSTIAEGIA-VKQP 237 (403)
T ss_pred HHHhcC--CCCCEEEEecC--HHHHHHHHHHHHHHhCCCCEEEEEEECC-CchHHHHHhCCCccCCCCCccceec-CCCc
Confidence 444443 35899999987 4666666666553 3467777733211 111111 01100 0 0011111 1112
Q ss_pred HHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCceeecCccCCCCCeeEEEEEeeCCCCCC
Q 014547 233 LSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQVLEDGIQDDSSNVTRFVMLAREPIIPR 312 (423)
Q Consensus 233 L~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~~ 312 (423)
-.....|+.++.-.+..+.-.....|++.+++.. +. .+.+.-|+-+-++.-+.+.. .+.+=-+++.--...+.
T Consensus 238 ~~~~~~~~~~~~d~~v~V~d~e~~~a~~~l~~~~--gi-~v~~s~a~~~aa~~~~~~~~----~~~~vv~i~~ggn~d~~ 310 (403)
T PRK07334 238 GQLTLEIVRRLVDDILLVSEADIEQAVSLLLEIE--KT-VVEGAGAAGLAALLAYPERF----RGRKVGLVLSGGNIDTR 310 (403)
T ss_pred cHHHHHHHHHhCCeEEEECHHHHHHHHHHHHHhc--CC-EEechHHHHHHHHHhCchhc----CCCeEEEEECCCCCCHH
Confidence 2345556665543333332222446677776542 22 33333333333332222212 22222233322211110
Q ss_pred ----------CCCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeC-CCCCcccccccCCCCCCcceEEEEEEE
Q 014547 313 ----------TDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPH-RNRPIRLVDDANVGTAKHFEYMFYIDF 381 (423)
Q Consensus 313 ----------~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~-~~~p~~~~~~~~~G~~~~~eY~FfID~ 381 (423)
....+.+.|.+...|++|.|.++++.+++.++|+.++.++.. ...+ - ..+...|-|++
T Consensus 311 ~l~~il~~~l~~~~y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~--------~---~~~~i~l~i~V 379 (403)
T PRK07334 311 LLANVLLRGLVRAGRLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLP--------A---KGAELELVIET 379 (403)
T ss_pred HHHHHHHHHHHhCCCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCC--------C---CeEEEEEEEEe
Confidence 123467899999999999999999999999999999998854 1100 0 01233444444
Q ss_pred ecCcChHHHHHHHHHHHhhcCceEE
Q 014547 382 EASMAEVRAQNALAEVQEFTSFLRV 406 (423)
Q Consensus 382 eg~~~d~~v~~aL~eL~~~~~~vrv 406 (423)
. +.+.+.++++.|++..-.+.+
T Consensus 380 ~---d~~~L~~vi~~Lr~~g~~~~~ 401 (403)
T PRK07334 380 R---DAAHLQEVIAALRAAGFEARL 401 (403)
T ss_pred C---CHHHHHHHHHHHHHcCCeeEe
Confidence 2 457899999999987655543
No 65
>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=94.43 E-value=0.4 Score=36.24 Aligned_cols=36 Identities=6% Similarity=0.035 Sum_probs=31.4
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCC
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHR 355 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~ 355 (423)
-+.+..+++||.|.++.+.|+.+|+|+..+......
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~ 37 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTG 37 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecC
Confidence 356778899999999999999999999999887654
No 66
>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=94.16 E-value=2.7 Score=44.09 Aligned_cols=75 Identities=15% Similarity=0.085 Sum_probs=49.3
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e 396 (423)
.+..+.|.+|++||+|.++|+.....+-|+++++-|..... ..-...|.+|.. +.+.++++++.
T Consensus 324 r~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~y~~~~~~---------------~~~~v~v~iE~~-~~~h~~~i~~~ 387 (409)
T TIGR02079 324 LKHYFIVRFPQRPGALREFLNDVLGPNDDITRFEYTKKSNR---------------ETGPALIGIELN-DKEDFAGLLER 387 (409)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeecCCC---------------CeEEEEEEEEeC-CHHHHHHHHHH
Confidence 36788899999999999999944444559998887752211 122344455442 23566777888
Q ss_pred HHhhcCceEEE
Q 014547 397 VQEFTSFLRVL 407 (423)
Q Consensus 397 L~~~~~~vrvL 407 (423)
|++....++++
T Consensus 388 L~~~Gy~~~~~ 398 (409)
T TIGR02079 388 MAAADIHYEDI 398 (409)
T ss_pred HHHCCCCeEEC
Confidence 88776555443
No 67
>PRK09224 threonine dehydratase; Reviewed
Probab=94.06 E-value=2.9 Score=45.23 Aligned_cols=73 Identities=10% Similarity=0.123 Sum_probs=50.7
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e 396 (423)
.+..+.+.+|++||+|.++++.+. +-|+|.++=|-.... +=..+|.++..-.+..++++++.
T Consensus 327 re~~l~v~iPerPGaL~~f~~~l~--~~nItef~yr~~~~~----------------~a~V~vgie~~~~~~~~~~i~~~ 388 (504)
T PRK09224 327 REALLAVTIPEEPGSFLKFCELLG--GRNVTEFNYRYADAK----------------EAHIFVGVQLSRGQEERAEIIAQ 388 (504)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhc--cCcEEEEEEEecCCC----------------eEEEEEEEEeCChhhHHHHHHHH
Confidence 467888999999999999999998 688888887764321 22345555543223347778888
Q ss_pred HHhhcCceEEE
Q 014547 397 VQEFTSFLRVL 407 (423)
Q Consensus 397 L~~~~~~vrvL 407 (423)
|++..-.++.|
T Consensus 389 L~~~gy~~~~l 399 (504)
T PRK09224 389 LRAHGYPVVDL 399 (504)
T ss_pred HHHcCCCeEEC
Confidence 87766555544
No 68
>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=94.03 E-value=0.37 Score=39.03 Aligned_cols=33 Identities=15% Similarity=0.267 Sum_probs=27.4
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceee--eeee
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLT--KIES 351 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLt--kIES 351 (423)
|-|-+..+|+||-|+++.++|++.|+++. ||.+
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT 36 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCITKAYISS 36 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEee
Confidence 44556778999999999999999999997 4544
No 69
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=94.03 E-value=0.26 Score=44.69 Aligned_cols=76 Identities=17% Similarity=0.263 Sum_probs=59.0
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeee-eeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIE-SRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALA 395 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIE-SRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~ 395 (423)
...++.+.+.|+.|.|.++|.+.++..+|+.-|. +-|..++ ..-..-||..+ -+..+.++++
T Consensus 71 ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~---------------Anvtlsi~~ss--m~~~V~~ii~ 133 (150)
T COG4492 71 RIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGR---------------ANVTLSIDTSS--MEKDVDKIIE 133 (150)
T ss_pred eEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCce---------------eeEEEEEEchh--hhhhHHHHHH
Confidence 4778999999999999999999999999998875 4566543 24566667653 4578888998
Q ss_pred HHHh--hcCceEEEcc
Q 014547 396 EVQE--FTSFLRVLGS 409 (423)
Q Consensus 396 eL~~--~~~~vrvLGs 409 (423)
+|++ ....|.++|+
T Consensus 134 kl~k~e~V~kVeivgs 149 (150)
T COG4492 134 KLRKVEGVEKVEIVGS 149 (150)
T ss_pred HHhcccceeEEEEeec
Confidence 8874 4556888875
No 70
>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=93.94 E-value=0.31 Score=36.07 Aligned_cols=34 Identities=18% Similarity=0.134 Sum_probs=30.0
Q ss_pred EEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCC
Q 014547 322 VFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHR 355 (423)
Q Consensus 322 vf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~ 355 (423)
.+.++|+||.|.++++.|.++|+|+..+...+..
T Consensus 2 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~ 35 (56)
T cd04889 2 SVFVENKPGRLAEVTEILAEAGINIKAISIAETR 35 (56)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEcc
Confidence 3567899999999999999999999999877764
No 71
>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=93.91 E-value=0.64 Score=36.53 Aligned_cols=62 Identities=11% Similarity=0.146 Sum_probs=43.2
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCc-----ChHHHHHHHH
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASM-----AEVRAQNALA 395 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~-----~d~~v~~aL~ 395 (423)
|.+.-+|+||-+.++.+.|+++|+|+..+++.-.... -.|++.++... +-..++++|+
T Consensus 2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~-----------------~~f~~~~~~~~~~~~~~~~~l~~~l~ 64 (74)
T cd04875 2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVDPDS-----------------GRFFMRVEFELEGFDLSREALEAAFA 64 (74)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeecCCC-----------------CeEEEEEEEEeCCCCCCHHHHHHHHH
Confidence 3455689999999999999999999999988743221 13555444332 2366667777
Q ss_pred HHHh
Q 014547 396 EVQE 399 (423)
Q Consensus 396 eL~~ 399 (423)
.|.+
T Consensus 65 ~l~~ 68 (74)
T cd04875 65 PVAA 68 (74)
T ss_pred HHHH
Confidence 6654
No 72
>PRK12483 threonine dehydratase; Reviewed
Probab=93.89 E-value=3.6 Score=44.82 Aligned_cols=216 Identities=14% Similarity=0.119 Sum_probs=110.6
Q ss_pred HHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhh--cCCcEEEEEEEEeeeeeee----ecCCCCcCcccEEEe-----c
Q 014547 161 VAFQAVELWIADRAVLPVENSLGGSIHRNYDLLL--RHRLHIVGEVQLPVHHCLL----ALPGVRKEYLTRVIS-----H 229 (423)
Q Consensus 161 ~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~--~~~L~IvgEi~lpI~h~Ll----a~~g~~l~dIk~VyS-----H 229 (423)
|+++.+. +..|+-|+|+- .+|.+.-+.-.+. ..+++|+|--.-. .-++. ..+-..+..+.++.. .
T Consensus 178 EI~eQ~~-~~~D~VvvpvG--gGGliaGia~~~K~~~p~vkVIGVep~~-a~~~~~sl~~g~~~~~~~~~t~adGiav~~ 253 (521)
T PRK12483 178 EILRQHP-GPLDAIFVPVG--GGGLIAGIAAYVKYVRPEIKVIGVEPDD-SNCLQAALAAGERVVLGQVGLFADGVAVAQ 253 (521)
T ss_pred HHHHHhC-CCCCEEEEecC--ccHHHHHHHHHHHHhCCCCEEEEEEeCC-CchhhHHHhcCCcccCCCCCceeceeccCC
Confidence 4444442 25899999986 5676666665543 3568888833211 11111 111111122211111 1
Q ss_pred --hhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCceeecCccCCCCCeeEEEEEeeC
Q 014547 230 --PQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQVLEDGIQDDSSNVTRFVMLARE 307 (423)
Q Consensus 230 --PqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~ 307 (423)
+..+.-|++++. .+..+.-+....|.+.+.+.. ..-+.+.-|+-+.+|.-+..... . .+.+=-+|++-.
T Consensus 254 ~g~~~~~~~~~~vd----~vv~Vse~ei~~ai~~l~~~~---~i~vEpagAaalAal~~~~~~~~-~-~g~~VV~IlsGg 324 (521)
T PRK12483 254 IGEHTFELCRHYVD----EVVTVSTDELCAAIKDIYDDT---RSITEPAGALAVAGIKKYAEREG-I-EGQTLVAIDSGA 324 (521)
T ss_pred CCHHHHHHHHHhCC----EEEEECHHHHHHHHHHHHHhC---CcEEeHHHHHHHHHHHHHHHhcC-C-CCCEEEEEeCCC
Confidence 234444444332 233332223445666666532 22233334444555433221111 0 133333444443
Q ss_pred CCCCC----------CCCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEE
Q 014547 308 PIIPR----------TDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMF 377 (423)
Q Consensus 308 ~~~~~----------~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~F 377 (423)
..... -....+..|.+.++++||+|.++++.+... |++.|+=|-... .+=..
T Consensus 325 Nid~~~l~~i~~r~l~~~~r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v 386 (521)
T PRK12483 325 NVNFDRLRHVAERAELGEQREAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYRYADA----------------REAHL 386 (521)
T ss_pred CCCHHHHHHHHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEEecCC----------------CeeEE
Confidence 32110 012247788899999999999999999988 999988774221 12345
Q ss_pred EEEEecCcChHHH-HHHHHHHHhhcCceEEEc
Q 014547 378 YIDFEASMAEVRA-QNALAEVQEFTSFLRVLG 408 (423)
Q Consensus 378 fID~eg~~~d~~v-~~aL~eL~~~~~~vrvLG 408 (423)
+|.+|.. +.+.+ +++++.|++..-.++.+.
T Consensus 387 ~v~ie~~-~~~~~~~~i~~~l~~~g~~~~dls 417 (521)
T PRK12483 387 FVGVQTH-PRHDPRAQLLASLRAQGFPVLDLT 417 (521)
T ss_pred EEEEEeC-ChhhhHHHHHHHHHHCCCCeEECC
Confidence 5566543 22444 788888887776666553
No 73
>PRK06382 threonine dehydratase; Provisional
Probab=93.72 E-value=0.42 Score=49.96 Aligned_cols=35 Identities=14% Similarity=0.088 Sum_probs=32.5
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
.++.|.+.++|+||.|.++++.|+..++|+++|+-
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 47788889999999999999999999999999986
No 74
>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=93.19 E-value=0.71 Score=36.46 Aligned_cols=35 Identities=14% Similarity=0.280 Sum_probs=29.6
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCC
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHR 355 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~ 355 (423)
+.+.-+|+||-+.++-+.|+.+|+|+..+++.-..
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~ 36 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYS 36 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence 34566789999999999999999999999885543
No 75
>PLN02550 threonine dehydratase
Probab=92.96 E-value=2.7 Score=46.54 Aligned_cols=209 Identities=12% Similarity=0.055 Sum_probs=111.0
Q ss_pred CcCeEEEeeccCCCCchHHHHHHhh--cCCcEEEEEEEEe---eeeeeeecCCCCcCcccE----EEe---chhHHHHHH
Q 014547 170 IADRAVLPVENSLGGSIHRNYDLLL--RHRLHIVGEVQLP---VHHCLLALPGVRKEYLTR----VIS---HPQALSQCE 237 (423)
Q Consensus 170 ~~d~gVVPIENS~~G~V~~tlDlL~--~~~L~IvgEi~lp---I~h~Lla~~g~~l~dIk~----VyS---HPqAL~QC~ 237 (423)
..|+-|+|+- .+|.+.-+.-.+. ..+++|+|--.-. +...+-+.+-+.++.+.+ +.. =++.+.-|+
T Consensus 258 ~~D~VvvpVG--gGGLiaGia~~lK~l~p~vkVIGVEp~~a~~~~~s~~~G~~v~~~~~~tiAdGiav~~~G~~t~~i~~ 335 (591)
T PLN02550 258 PLHAIFVPVG--GGGLIAGIAAYVKRVRPEVKIIGVEPSDANAMALSLHHGERVMLDQVGGFADGVAVKEVGEETFRLCR 335 (591)
T ss_pred CCCEEEEEeC--hhHHHHHHHHHHHHhCCCCEEEEEEECCChHHHHHHhcCCccccCCCCCccceeecCCCCHHHHHHHH
Confidence 5899999986 5666666665554 3568888833211 101111111111222211 111 144555555
Q ss_pred HHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCceeecCccCCCCCeeEEEEEeeCCCCCC-----
Q 014547 238 HTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELYGMQVLEDGIQDDSSNVTRFVMLAREPIIPR----- 312 (423)
Q Consensus 238 ~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~~----- 312 (423)
+++. .+..+..+...+|.+.+.+.. ..-+-+.-|+-+.+|.-..+... .+ +.+=-+|++--.....
T Consensus 336 ~~vD----~vV~Vsd~eI~~Ai~~l~e~~---givvEpAGA~alAall~~~~~~~-~~-g~~Vv~vlsGgNid~~~l~~v 406 (591)
T PLN02550 336 ELVD----GVVLVSRDAICASIKDMFEEK---RSILEPAGALALAGAEAYCKYYG-LK-DENVVAITSGANMNFDRLRIV 406 (591)
T ss_pred hhCC----EEEEECHHHHHHHHHHHHHHC---CCEEeHHHHHHHHHHHHHHHhcC-CC-CCeEEEEecCCCCCHHHHHHH
Confidence 5443 333443344566777777642 12233334444555443332111 11 2222233333222110
Q ss_pred -----CCCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcCh
Q 014547 313 -----TDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAE 387 (423)
Q Consensus 313 -----~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d 387 (423)
.....+..|.+.++++||+|.++++.+... |+++|+=|-... .+-..+|.+|.. +.
T Consensus 407 ~~~~~~~~~r~~~~~v~ipd~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v~v~ie~~-~~ 467 (591)
T PLN02550 407 TELADVGRQQEAVLATFMPEEPGSFKRFCELVGPM--NITEFKYRYSSE----------------KEALVLYSVGVH-TE 467 (591)
T ss_pred HHHHHhccCCEEEEEEEcCCCCCHHHHHHHHhhhh--cceEEEEEecCC----------------CceEEEEEEEeC-CH
Confidence 012235678889999999999999999986 999998776321 123455556543 45
Q ss_pred HHHHHHHHHHHhhcCceEEEc
Q 014547 388 VRAQNALAEVQEFTSFLRVLG 408 (423)
Q Consensus 388 ~~v~~aL~eL~~~~~~vrvLG 408 (423)
+.++++++.|++..-.++.|-
T Consensus 468 ~~~~~i~~~l~~~g~~~~~l~ 488 (591)
T PLN02550 468 QELQALKKRMESAQLRTVNLT 488 (591)
T ss_pred HHHHHHHHHHHHCCCCeEeCC
Confidence 788889999988765555443
No 76
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=91.66 E-value=1.2 Score=41.45 Aligned_cols=75 Identities=17% Similarity=0.238 Sum_probs=51.4
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeee-eeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTK-IESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALA 395 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtk-IESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~ 395 (423)
.+.++.+.++|+||-|.++|+.++..|.|+.. |+||-.+..| .--.-|-|++. .++..++.++
T Consensus 4 mritldIEL~D~PGQLl~vLqPls~~g~NiItIiH~r~kk~g~---------------r~pV~i~~~~d-~~~~~~~i~~ 67 (170)
T COG2061 4 MRITLDIELKDKPGQLLKVLQPLSKTGANIITIIHSRDKKYGP---------------RVPVQIVFEGD-REDKDAKIIR 67 (170)
T ss_pred eEEEEEEEecCCCcchhhhhcchhhcCccEEEEEeecCcccCC---------------ceeEEEEEEec-ccHHHHHHHH
Confidence 36788899999999999999999999999875 6788765433 12222333432 2356667777
Q ss_pred HHHhhcCceEEE
Q 014547 396 EVQEFTSFLRVL 407 (423)
Q Consensus 396 eL~~~~~~vrvL 407 (423)
.+++.+..++-.
T Consensus 68 ~~e~~Gi~I~~~ 79 (170)
T COG2061 68 LLEEEGIIIIRF 79 (170)
T ss_pred HHHhCCcEEEEe
Confidence 776665544433
No 77
>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=91.62 E-value=1.5 Score=34.54 Aligned_cols=34 Identities=9% Similarity=0.169 Sum_probs=28.3
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeee--eeee
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTK--IESR 352 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtk--IESR 352 (423)
+-+.+..+|+||-|+++-++|+.+|+|+.. |.+.
T Consensus 2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~ 37 (73)
T cd04900 2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTT 37 (73)
T ss_pred EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEe
Confidence 346667789999999999999999999995 5444
No 78
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=91.06 E-value=1.1 Score=40.21 Aligned_cols=65 Identities=9% Similarity=0.177 Sum_probs=46.6
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
+.+..+|+||.|.+++.+|.+++|||-.|.---+++. .-..++-. +.+..+++.|++.
T Consensus 72 laVEmeD~PG~l~~I~~vl~d~diNldYiYAFv~ek~----------------KAlli~r~------ed~d~~~~aLed~ 129 (142)
T COG4747 72 LAVEMEDVPGGLSRIAEVLGDADINLDYIYAFVTEKQ----------------KALLIVRV------EDIDRAIKALEDA 129 (142)
T ss_pred EEEEecCCCCcHHHHHHHHhhcCcCceeeeeeeecCc----------------eEEEEEEh------hHHHHHHHHHHHc
Confidence 4567899999999999999999999998877665542 23444444 3455666777665
Q ss_pred cCceEEEcc
Q 014547 401 TSFLRVLGS 409 (423)
Q Consensus 401 ~~~vrvLGs 409 (423)
.++++|+
T Consensus 130 --gi~~~~~ 136 (142)
T COG4747 130 --GIKLIGM 136 (142)
T ss_pred --CCeecCh
Confidence 3667764
No 79
>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=90.91 E-value=1.6 Score=35.12 Aligned_cols=63 Identities=10% Similarity=0.186 Sum_probs=47.0
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecC-cChHHHHHHHHHHHhhcCc
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEAS-MAEVRAQNALAEVQEFTSF 403 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~-~~d~~v~~aL~eL~~~~~~ 403 (423)
.++.+|.+.++++.|++++||+-.|-+ +. ..+.|-|+-... ..++.+++++++|++.+ .
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~vDmI~~-s~------------------~~isftv~~~~~~~~~~~~~~l~~el~~~~-~ 70 (75)
T cd04935 11 MWQQVGFLADVFAPFKKHGVSVDLVST-SE------------------TNVTVSLDPDPNGLDPDVLDALLDDLNQIC-R 70 (75)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe-CC------------------CEEEEEEeCcccccchHHHHHHHHHHHhce-E
Confidence 356799999999999999999999965 11 257777765431 33458999999999854 5
Q ss_pred eEEE
Q 014547 404 LRVL 407 (423)
Q Consensus 404 vrvL 407 (423)
|.++
T Consensus 71 v~~~ 74 (75)
T cd04935 71 VKII 74 (75)
T ss_pred EEEe
Confidence 6554
No 80
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=90.13 E-value=1.5 Score=41.76 Aligned_cols=35 Identities=9% Similarity=0.232 Sum_probs=29.8
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCC
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHR 355 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~ 355 (423)
+.+.-.|+||-++++-+.|+.+|||+..++++-..
T Consensus 98 v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~ 132 (190)
T PRK11589 98 VQVEVADSPHLIERFTALFDSHHMNIAELVSRTQP 132 (190)
T ss_pred EEEEECCCCCHHHHHHHHHHHcCCChhheEEeeec
Confidence 33455789999999999999999999999998543
No 81
>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=89.78 E-value=3.6 Score=32.86 Aligned_cols=64 Identities=11% Similarity=0.038 Sum_probs=44.0
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
+.+.-+|+||-.+++-+.++++|.|++.+...-..+ .|-++.-++++. .+.+.+++.++++.+.
T Consensus 4 ltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~---------------~F~m~~~~~~~~-~~~~~l~~~l~~~~~~ 67 (77)
T cd04893 4 ISALGTDRPGILNELTRAVSESGCNILDSRMAILGT---------------EFALTMLVEGSW-DAIAKLEAALPGLARR 67 (77)
T ss_pred EEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcC---------------EEEEEEEEEecc-ccHHHHHHHHHHHHHH
Confidence 345568999999999999999999999776654221 233444445542 2346777778877644
No 82
>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=88.37 E-value=4 Score=32.83 Aligned_cols=62 Identities=21% Similarity=0.227 Sum_probs=44.3
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHH-HHHHHHHhhcCc
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQ-NALAEVQEFTSF 403 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~-~aL~eL~~~~~~ 403 (423)
.++.||.+.++++.|+++|||+-.|-+ +. ..+.|-|+-.....+..++ .++++|++.+ .
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~VDmI~~-s~------------------~~iSftv~~~d~~~~~~~~~~l~~~l~~~~-~ 70 (75)
T cd04932 11 MLHAQGFLAKVFGILAKHNISVDLITT-SE------------------ISVALTLDNTGSTSDQLLTQALLKELSQIC-D 70 (75)
T ss_pred CCCCcCHHHHHHHHHHHcCCcEEEEee-cC------------------CEEEEEEeccccchhHHHHHHHHHHHHhcc-E
Confidence 466899999999999999999999965 11 2577777753322235565 7888888744 4
Q ss_pred eEE
Q 014547 404 LRV 406 (423)
Q Consensus 404 vrv 406 (423)
|.+
T Consensus 71 v~~ 73 (75)
T cd04932 71 VKV 73 (75)
T ss_pred EEe
Confidence 443
No 83
>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=88.37 E-value=3.6 Score=33.60 Aligned_cols=33 Identities=12% Similarity=0.260 Sum_probs=27.1
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceee--eeee
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLT--KIES 351 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLt--kIES 351 (423)
|-|-+..+|+||-|+++...|.+.|+++. ||.+
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T 36 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDT 36 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEee
Confidence 34456778999999999999999999997 3544
No 84
>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=88.15 E-value=3.9 Score=32.39 Aligned_cols=56 Identities=14% Similarity=0.204 Sum_probs=43.3
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcC-hHHHHHHHHHHHh
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMA-EVRAQNALAEVQE 399 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~-d~~v~~aL~eL~~ 399 (423)
+.+.+|.+.++++.|+++|||+..|-+.+ ....|.|+-+.... +..++.++++|++
T Consensus 11 l~~~~g~~~~if~~L~~~~I~v~~i~~s~-------------------~~is~~v~~~~~~~~~~~~~~~~~~l~~ 67 (75)
T cd04912 11 MLGAHGFLAKVFEIFAKHGLSVDLISTSE-------------------VSVSLTLDPTKNLSDQLLLDALVKDLSQ 67 (75)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEcCC-------------------cEEEEEEEchhhccchHHHHHHHHHHHh
Confidence 45679999999999999999998886421 25788887654222 3588899999988
No 85
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=87.41 E-value=2.3 Score=40.10 Aligned_cols=74 Identities=16% Similarity=0.230 Sum_probs=51.1
Q ss_pred EEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcCh-HHHHHHHHHHHhhc
Q 014547 323 FAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAE-VRAQNALAEVQEFT 401 (423)
Q Consensus 323 f~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d-~~v~~aL~eL~~~~ 401 (423)
+.-.|+||-+.++-..|..+||||-.++||-..- | |+ ..-+|.+++..+..- -++..+.++++.+|
T Consensus 97 v~a~DrpgIv~~~T~lf~~~~inie~L~~~~~~a-~---------~s---~~~lfha~it~~lPa~~~i~~l~~~f~al~ 163 (176)
T COG2716 97 VDANDRPGIVEEFTALFDGHGINIENLVSRTYPA-P---------GS---SAPLFHAQITARLPANLSISALRDAFEALC 163 (176)
T ss_pred EEecCCccHHHHHHHHHHhcCCchhhceeeeeec-C---------CC---CccceehhhhccCCCcCcHHHHHHHHHHHH
Confidence 3456899999999999999999999999985432 1 11 246899998755432 34445555566666
Q ss_pred CceEEEcc
Q 014547 402 SFLRVLGS 409 (423)
Q Consensus 402 ~~vrvLGs 409 (423)
..+.+=|+
T Consensus 164 ~~L~v~~~ 171 (176)
T COG2716 164 DELNVDGS 171 (176)
T ss_pred Hhhcceee
Confidence 66665554
No 86
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=87.21 E-value=3.2 Score=38.82 Aligned_cols=74 Identities=15% Similarity=0.217 Sum_probs=53.5
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHH
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEV 397 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL 397 (423)
+-.+.+-+.|+||.|.++.+.|+.||.|+-.|---|.... ..=.--+-..| ++..++++.+.|
T Consensus 4 ~rilsvlv~ne~GvLsRv~glfsrRG~NIeSltv~~tE~~---------------~~SRiTivv~g--~~~~~EQi~kQL 66 (163)
T COG0440 4 RRILSLLVENEPGVLSRVTGLFSRRGYNIESLTVGPTETP---------------GLSRITIVVSG--DEQVLEQIIKQL 66 (163)
T ss_pred eEEEEEEEECCCCeeehhhHHHHhcCcccceEEEEecCCC---------------CceEEEEEEcC--CcchHHHHHHHH
Confidence 3455566778999999999999999999998888777542 11222233334 557788888888
Q ss_pred HhhcCceEEEc
Q 014547 398 QEFTSFLRVLG 408 (423)
Q Consensus 398 ~~~~~~vrvLG 408 (423)
.+.-.-++|+-
T Consensus 67 ~kLidV~kV~d 77 (163)
T COG0440 67 NKLIDVLKVLD 77 (163)
T ss_pred HhhccceeEEE
Confidence 88877777664
No 87
>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=87.01 E-value=4.5 Score=32.42 Aligned_cols=26 Identities=8% Similarity=0.153 Sum_probs=23.4
Q ss_pred EEeCCCccHHHHHHHHHHhCCceeee
Q 014547 323 FAHDKGTSVLFKVLSAFAFRNISLTK 348 (423)
Q Consensus 323 f~l~~~pGaL~~vL~~Fa~~~INLtk 348 (423)
+..+|+||-|+++.++|+.+|+|+..
T Consensus 5 i~~~Dr~gLfa~i~~~l~~~~l~I~~ 30 (76)
T cd04927 5 LFCSDRKGLLHDVTEVLYELELTIER 30 (76)
T ss_pred EEECCCCCHHHHHHHHHHHCCCeEEE
Confidence 45678999999999999999999984
No 88
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=86.98 E-value=1.7 Score=41.30 Aligned_cols=83 Identities=16% Similarity=0.147 Sum_probs=57.0
Q ss_pred ccEEEEeCCCccHHHHHHhhhC-C--C------CceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhh---
Q 014547 127 QLRVAYQGVPGAYSEAAAGKAY-P--N------CEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLL--- 194 (423)
Q Consensus 127 ~~~VayLGP~GTfSh~AA~~~f-~--~------~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~--- 194 (423)
..+|++-.|..+.++.+....+ . + .+.++..+.+.++.+|.+|++|.|+++- .+++.+.
T Consensus 105 Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~~Da~~~~~---------~~~~~~~~~~ 175 (243)
T PF12974_consen 105 GKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGKADAAAIPS---------DAFERLEAEG 175 (243)
T ss_dssp GSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTSSSEEEEEH---------HHHHHHHHH-
T ss_pred CCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCCccEEEEec---------hhHHHHHHcc
Confidence 3589987776555577766544 2 1 3456788999999999999999999883 4555443
Q ss_pred ---cCCcEEEEEEEEeeeeeeeecCCC
Q 014547 195 ---RHRLHIVGEVQLPVHHCLLALPGV 218 (423)
Q Consensus 195 ---~~~L~IvgEi~lpI~h~Lla~~g~ 218 (423)
..+++|+++-..-..+.+++.++.
T Consensus 176 ~~~~~~~rvl~~s~~~p~~~~~~~~~~ 202 (243)
T PF12974_consen 176 PDIPSQLRVLWTSPPYPNWPLVASPDL 202 (243)
T ss_dssp HHHHTTEEEEEEEEEEE--EEEEETTS
T ss_pred CcccccEEEEEEeCCCCCcEEEEeCCC
Confidence 357999998876667778887764
No 89
>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=86.88 E-value=9.4 Score=36.09 Aligned_cols=138 Identities=17% Similarity=0.067 Sum_probs=74.8
Q ss_pred cEEEEeCCCccHHH-HHHh-hhCC------CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhh-cCCc
Q 014547 128 LRVAYQGVPGAYSE-AAAG-KAYP------NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLL-RHRL 198 (423)
Q Consensus 128 ~~VayLGP~GTfSh-~AA~-~~f~------~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~-~~~L 198 (423)
+||||+.. +.... .|.. .+|. ++++++..+..+++++|.+|++|+|++... ..+ .... ..++
T Consensus 1 l~vg~~~~-~~~~~~~a~~~g~f~~~g~~l~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~----~~~----~~~~~g~~~ 71 (288)
T TIGR01728 1 VRIGYQKN-GHSALALAKEKGLLEKELGKTKVEWVEFPAGPPALEALGAGSLDFGYIGPG----PAL----FAYAAGADI 71 (288)
T ss_pred CeEEecCC-CchHHHHHHHhCHHHHhhCCceEEEEecCCCcHHHHHHhcCCccccccCCc----HHH----HHHhcCCCE
Confidence 47899875 33332 3332 2442 356778888889999999999999976432 111 1112 2367
Q ss_pred EEEEEEEEeeeeeeeecCCCCc---Cccc--EEEechh--HHHHHHHHHHHcCCc---eeEEeccCHHHHHHHHHhcCCC
Q 014547 199 HIVGEVQLPVHHCLLALPGVRK---EYLT--RVISHPQ--ALSQCEHTLTKLGLN---VAREAVDDTAGAAEYIAANDLR 268 (423)
Q Consensus 199 ~IvgEi~lpI~h~Lla~~g~~l---~dIk--~VySHPq--AL~QC~~fL~~~~p~---~~~v~~~STA~AA~~va~~~~~ 268 (423)
.+++-..-.-..+++++++..+ +|++ +|...+- .......+|++++.. +..+. .+.+.+.+.+..++
T Consensus 72 ~~i~~~~~~~~~~~v~~~~~~i~s~~dL~Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~-~~~~~~~~al~~g~-- 148 (288)
T TIGR01728 72 KAVGLVSDNKATAIVVIKGSPIRTVADLKGKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILY-LGPSDARAAFAAGQ-- 148 (288)
T ss_pred EEEEEecCCCceEEEECCCCCCCCHHHcCCCEEEecCCccHHHHHHHHHHHcCCCccceeEEe-cCcHHHHHHHHCCC--
Confidence 7766444322466666654322 3332 5543211 223445567665432 22332 35566777777653
Q ss_pred CeeEEccHH
Q 014547 269 DTAAIASAR 277 (423)
Q Consensus 269 ~~AAIaS~~ 277 (423)
-.|++....
T Consensus 149 vda~~~~~p 157 (288)
T TIGR01728 149 VDAWAIWEP 157 (288)
T ss_pred CCEEEeccc
Confidence 345555543
No 90
>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=84.78 E-value=7.7 Score=31.06 Aligned_cols=55 Identities=11% Similarity=0.231 Sum_probs=43.2
Q ss_pred CCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhc
Q 014547 327 KGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFT 401 (423)
Q Consensus 327 ~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~ 401 (423)
..+|.+.++++.|+++|||+-.|-+ .. ..+.|-++-. +..++.+++++++|++.+
T Consensus 13 ~~~g~~~~If~~la~~~I~vd~I~~---s~----------------~~isftv~~~-~~~~~~l~~l~~el~~~~ 67 (73)
T cd04934 13 LSHGFLARIFAILDKYRLSVDLIST---SE----------------VHVSMALHME-NAEDTNLDAAVKDLQKLG 67 (73)
T ss_pred cccCHHHHHHHHHHHcCCcEEEEEe---CC----------------CEEEEEEehh-hcChHHHHHHHHHHHHhe
Confidence 4689999999999999999999976 11 2578888764 333458999999998844
No 91
>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=84.45 E-value=45 Score=33.03 Aligned_cols=149 Identities=15% Similarity=0.081 Sum_probs=82.1
Q ss_pred ccEEEEe-CCCccHHHHHHhhhCC----CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhc--CCcE
Q 014547 127 QLRVAYQ-GVPGAYSEAAAGKAYP----NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLR--HRLH 199 (423)
Q Consensus 127 ~~~VayL-GP~GTfSh~AA~~~f~----~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~--~~L~ 199 (423)
..|||++ ||....=+.+...++. +++++.+.+..+..+|+..|++|.+.. +........... .++.
T Consensus 19 ~l~vG~~~~~~~~~~~~~~~~~~~~~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~-------q~~~~l~~~~~~~g~~lv 91 (258)
T TIGR00363 19 HIKVGVISGAEQQVAEVAAKVAKEKYGLDVELVEFNDYALPNEAVSKGDLDANAF-------QHKPYLDQDAKAKGYKLV 91 (258)
T ss_pred cEEEEeCCCChHHHHHHHHHHHHHhcCCEEEEEEeCCcHHHHHHHHcCCCCeEec-------CCHHHHHHHHHhCCCcEE
Confidence 5899998 4444443444544443 468889999999999999999998632 222222222233 3455
Q ss_pred EEEEEEEeeeeeeeecCCCCcCccc---EEEec--hhHHHHHHHHHHHc---------------------CCceeEEecc
Q 014547 200 IVGEVQLPVHHCLLALPGVRKEYLT---RVISH--PQALSQCEHTLTKL---------------------GLNVAREAVD 253 (423)
Q Consensus 200 IvgEi~lpI~h~Lla~~g~~l~dIk---~VySH--PqAL~QC~~fL~~~---------------------~p~~~~v~~~ 253 (423)
+++...+- ...+...+=.+++|++ +|.-. |.-.++.-..|++. .-+++++...
T Consensus 92 ~v~~~~~~-p~~~ys~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel~ 170 (258)
T TIGR00363 92 AVGNTFVY-PLAGYSKKIKNVNELQDGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITELE 170 (258)
T ss_pred EEeeeEEe-cccccCcCCCCHHHcCCCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEcC
Confidence 56533221 1233333334566764 55433 44444444566663 2235666654
Q ss_pred CHHHHHHHHHhcCCCCeeEEccHHHHHHcCCce
Q 014547 254 DTAGAAEYIAANDLRDTAAIASARAAELYGMQV 286 (423)
Q Consensus 254 STA~AA~~va~~~~~~~AAIaS~~AAelYgL~I 286 (423)
. +..++.+.++ .-.||+...--+...||..
T Consensus 171 ~-~~~~~al~~g--~vDaa~v~~~~~~~agl~~ 200 (258)
T TIGR00363 171 T-SQLPRALDDP--KVDLAVINTTYAGQVGLNP 200 (258)
T ss_pred H-HHHHHHhhcc--cccEEEEChHHHHHcCCCc
Confidence 3 3444444432 2356666665666777764
No 92
>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=84.41 E-value=9.7 Score=34.04 Aligned_cols=48 Identities=21% Similarity=0.216 Sum_probs=38.5
Q ss_pred cEEEEeCCCccHHHHHHhhhCC-CCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYP-NCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~-~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|++. .|++......+.++ +.+++.+.+.++++++|.+|++|+.++.
T Consensus 111 ~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~ 159 (225)
T PF00497_consen 111 KRIGVV--RGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVD 159 (225)
T ss_dssp SEEEEE--TTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEE
T ss_pred cccccc--cchhHHHHhhhhccchhhhcccccHHHHHHHHhcCCeeeeecc
Confidence 478865 55666655555565 7888999999999999999999999886
No 93
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=84.38 E-value=7.7 Score=39.07 Aligned_cols=67 Identities=12% Similarity=0.194 Sum_probs=46.8
Q ss_pred EEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEe--cCcChHHHHHHHHH
Q 014547 319 TSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFE--ASMAEVRAQNALAE 396 (423)
Q Consensus 319 TSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~e--g~~~d~~v~~aL~e 396 (423)
..+.+.-+|+||-..++-+.|+.+|+|+..+.+.-....+ .|...++++ ...+...++++|++
T Consensus 8 ~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~---------------~F~m~~~~~~p~~~~~~~L~~~L~~ 72 (286)
T PRK13011 8 FVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLSG---------------RFFMRVEFHSEEGLDEDALRAGFAP 72 (286)
T ss_pred EEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCC---------------eEEEEEEEecCCCCCHHHHHHHHHH
Confidence 3455556899999999999999999999999997333221 233334443 33445788888888
Q ss_pred HHhh
Q 014547 397 VQEF 400 (423)
Q Consensus 397 L~~~ 400 (423)
|.+.
T Consensus 73 l~~~ 76 (286)
T PRK13011 73 IAAR 76 (286)
T ss_pred HHHH
Confidence 7543
No 94
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=83.55 E-value=21 Score=30.78 Aligned_cols=113 Identities=19% Similarity=0.125 Sum_probs=64.3
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCC---cCcc--c
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVR---KEYL--T 224 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~---l~dI--k 224 (423)
+.++++. +..++++++.+|++|+++.......+ ....+ ..........+.++.+++.. ++|+ +
T Consensus 40 ~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~-----~~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~dL~g~ 107 (219)
T smart00062 40 KVEFVEV-SFDNLLTALKSGKIDVVAAGMTITPE-----RAKQV------DFSDPYYKSGQVILVRKDSPIKSLEDLKGK 107 (219)
T ss_pred eEEEEec-cHHHHHHHHHCCcccEEeccccCCHH-----HHhhe------eeccceeeceeEEEEecCCCCCChHHhCCC
Confidence 4577888 88999999999999999876432111 00111 11111222335666665532 2333 2
Q ss_pred EEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHH
Q 014547 225 RVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARA 278 (423)
Q Consensus 225 ~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~A 278 (423)
+|..-. . .-...++....++...+.+.+..++.+++..+ +..|++.....
T Consensus 108 ~i~~~~-g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~~ 157 (219)
T smart00062 108 KVAVVA-G-TTGEELLKKLYPEAKIVSYDSQAEALAALKAG--RADAAVADAPA 157 (219)
T ss_pred EEEEec-C-ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcC--cccEEEeccHH
Confidence 333332 1 22345566555566777788888888888765 34566655543
No 95
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=83.14 E-value=4.1 Score=42.89 Aligned_cols=63 Identities=22% Similarity=0.311 Sum_probs=44.9
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceE-EEEEEEecCcChHHHHHHHHH
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEY-MFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY-~FfID~eg~~~d~~v~~aL~e 396 (423)
.-.|++..+|+||.+.++++.+++++||+-.+..+... ++ +..||+++...+ +++++
T Consensus 338 ~~rlii~h~d~pG~ia~it~~l~~~~iNI~~m~~~~~~------------------~~A~~iie~D~~~~~----~~~~~ 395 (409)
T PRK11790 338 GHRLLHIHENRPGVLAAINQIFAEQGINIAAQYLQTDG------------------EIGYVVIDVDADYAE----EALDA 395 (409)
T ss_pred CceEEEEeCCCCCHHHHHHHHHHhcCCCHHHheeccCC------------------CEEEEEEEeCCCCcH----HHHHH
Confidence 45678888999999999999999999999877663322 23 334499886543 45566
Q ss_pred HHhhcC
Q 014547 397 VQEFTS 402 (423)
Q Consensus 397 L~~~~~ 402 (423)
|++.-.
T Consensus 396 i~~i~~ 401 (409)
T PRK11790 396 LKAIPG 401 (409)
T ss_pred HHcCCC
Confidence 665433
No 96
>PRK06349 homoserine dehydrogenase; Provisional
Probab=82.62 E-value=5.1 Score=42.29 Aligned_cols=64 Identities=20% Similarity=0.212 Sum_probs=46.3
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
-|.|.+.|+||.|.++-+.|.+++||+..|...+.... ..+..+.++. ..+..+++++++|++
T Consensus 350 ylRl~v~d~pGvLa~I~~~f~~~~vsI~si~q~~~~~~--------------~~~ivivT~~---~~e~~l~~~i~~L~~ 412 (426)
T PRK06349 350 YLRLLVADKPGVLAKIAAIFAENGISIESILQKGAGGE--------------GAEIVIVTHE---TSEAALRAALAAIEA 412 (426)
T ss_pred EEEEEecCCcchHHHHHHHHhhcCccEEEEEeccCCCC--------------ceeEEEEEEe---CCHHHHHHHHHHHhc
Confidence 44456779999999999999999999998877654321 1234444332 346889999999986
Q ss_pred h
Q 014547 400 F 400 (423)
Q Consensus 400 ~ 400 (423)
.
T Consensus 413 l 413 (426)
T PRK06349 413 L 413 (426)
T ss_pred C
Confidence 4
No 97
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=82.30 E-value=6.1 Score=33.53 Aligned_cols=78 Identities=14% Similarity=0.039 Sum_probs=52.5
Q ss_pred cEEEEeCCCccHHHHHHhhhCCC-----------CceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhh--
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYPN-----------CEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLL-- 194 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~~-----------~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~-- 194 (423)
.+|+++ .||+.+..+++..+. .++..+++..+++.+|..|+ |..+.. ++ ++..+.
T Consensus 14 ~~vgv~--~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d--~~-------~~~~~~~~ 81 (134)
T smart00079 14 IEYGTI--RGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLME--ST-------YLDYELSQ 81 (134)
T ss_pred ccceEe--cCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEee--hH-------hHHHHHhC
Confidence 578886 899999988776543 25678999999999999999 855554 11 122222
Q ss_pred cCCcEEEEEEEEeeeeeeeecCC
Q 014547 195 RHRLHIVGEVQLPVHHCLLALPG 217 (423)
Q Consensus 195 ~~~L~IvgEi~lpI~h~Lla~~g 217 (423)
..++.++++..-+-.++++.+++
T Consensus 82 ~~~~~~~~~~~~~~~~~ia~~k~ 104 (134)
T smart00079 82 NCDLMTVGENFGRKGYGIAFPKG 104 (134)
T ss_pred CCCeEEcCcccCCCceEEEecCC
Confidence 23467777655455566666655
No 98
>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=82.19 E-value=31 Score=29.98 Aligned_cols=32 Identities=13% Similarity=-0.022 Sum_probs=24.7
Q ss_pred hhCCCCceeec-CCHHHHHHHHHcCCcCeEEEe
Q 014547 146 KAYPNCEAIPC-DQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 146 ~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
+.||+.++.-. .+..++.+.|.+|++|+|++.
T Consensus 24 ~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08452 24 KKFPSVKVELRELSSPDQVEELLKGRIDIGFLH 56 (197)
T ss_pred HHCCCcEEEEEecChHHHHHHHHCCCccEEEee
Confidence 34687765443 467889999999999999975
No 99
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=81.76 E-value=30 Score=33.01 Aligned_cols=139 Identities=16% Similarity=0.122 Sum_probs=78.7
Q ss_pred CccEEEEeCCCccHHHHHHhh--hCC----CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhh---cC
Q 014547 126 SQLRVAYQGVPGAYSEAAAGK--AYP----NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLL---RH 196 (423)
Q Consensus 126 ~~~~VayLGP~GTfSh~AA~~--~f~----~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~---~~ 196 (423)
...+|||+...+.+.-..|.+ +|. ++++..+.+-.++.+++..|++|++.+ ....+.+ ++.=. ..
T Consensus 6 ~~l~ig~~~~~~~~p~~~a~~~g~f~~~G~~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~-----~~~g~~~~~~ 79 (252)
T PF13379_consen 6 TTLRIGYLPGPDYAPLYVAQEKGLFEKEGLDVEWVQFASGADILEALAAGEIDIAFV-LAPALIA-----IAKGAGGPDV 79 (252)
T ss_dssp SEEEEEETSSGGGHHHHHHHHTTHHHHTTSCEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHH-----HHTTTTT---
T ss_pred cEEEEEeecchHHHHHHHHHHcChHHHcCCEEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHH-----HHcCCCCccc
Confidence 468999986555554444432 442 467899999999999999999999988 4322111 11100 11
Q ss_pred CcEEEEEEEEeeeeeeeecCC-------CCcCcc---------cEEEe-chhH--HHHHHHHHHHcCC----ceeEEecc
Q 014547 197 RLHIVGEVQLPVHHCLLALPG-------VRKEYL---------TRVIS-HPQA--LSQCEHTLTKLGL----NVAREAVD 253 (423)
Q Consensus 197 ~L~IvgEi~lpI~h~Lla~~g-------~~l~dI---------k~VyS-HPqA--L~QC~~fL~~~~p----~~~~v~~~ 253 (423)
++.+++-...- ..+|+++.+ .+++|+ ++|.. ++-. ....+.+|++++. +++++.+.
T Consensus 80 ~~~~~~~~~~~-g~~lvv~~~~~~~~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~ 158 (252)
T PF13379_consen 80 DIVVLAGLSQN-GNALVVRNDLKDASDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVP 158 (252)
T ss_dssp -EEEEEECSBS-SEEEEECGGGTTCSTTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--
T ss_pred ceEEeeccCCC-ceEEEEcCccccCCCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecC
Confidence 34444432221 245666532 234555 46665 5533 3446788988753 34666665
Q ss_pred CHHHHHHHHHhcCCCCeeEE
Q 014547 254 DTAGAAEYIAANDLRDTAAI 273 (423)
Q Consensus 254 STA~AA~~va~~~~~~~AAI 273 (423)
. .++.+.++.++ -+.+++
T Consensus 159 ~-~~~~~al~~g~-iDa~~~ 176 (252)
T PF13379_consen 159 P-PEMVAALRAGE-IDAAVL 176 (252)
T ss_dssp G-HHHHHHHHTTS--SEEEE
T ss_pred H-HHHHHHHhCCC-cCEEEe
Confidence 5 77777777653 334444
No 100
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=81.47 E-value=5 Score=38.06 Aligned_cols=60 Identities=12% Similarity=0.154 Sum_probs=44.1
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHH
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQ 398 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~ 398 (423)
|.+...++||+|.++-...+.+|.|+|.++..-.+.. ..-..|.++||-.+ .+.++++|+
T Consensus 5 lsi~~enk~GvL~~ltgiiae~ggNIt~~q~~~~~~g---------------~~~~iYmEiEgi~d---~e~l~~~lk 64 (218)
T COG1707 5 LSIIAENKPGVLRDLTGIIAEEGGNITYAQQFLEKDG---------------EKALIYMEIEGIDD---FEKLLERLK 64 (218)
T ss_pred eEEEeecCccHHHHHHHHHHhcCCceEeeehhhhccC---------------ceEEEEEEeeCCCC---HHHHHHHhh
Confidence 4455668999999999999999999999887655431 13478889998432 345666665
No 101
>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=81.35 E-value=27 Score=30.44 Aligned_cols=123 Identities=15% Similarity=0.071 Sum_probs=60.2
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecC-CCCcCcc-
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALP-GVRKEYL- 223 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~-g~~l~dI- 223 (423)
.+|+.++.... +-+++.+.+.+|++|+|+........+.. ...|.+..+.++. +-.|-|.... ..+++++
T Consensus 26 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~v~----~~~hpl~~~~~~i~~~dL~ 98 (203)
T cd08445 26 AAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIR---RIVLREEPLVVAL----PAGHPLAQEKAPLTLAQLA 98 (203)
T ss_pred HCCCeEEEEEeCChHHHHHHHHcCCCcEEEecCCCCCCCce---eEEEEeccEEEEe----eCCCCCccCCCCcCHHHhc
Confidence 36776665443 46899999999999999964321111111 0111222222221 2233333222 2233332
Q ss_pred --cEEEechh---H-HHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 224 --TRVISHPQ---A-LSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 224 --k~VySHPq---A-L~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
.-|.-... . ..+..+|+.+.+.... ...++|...+.++++.+ ...+|.+...+
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 158 (203)
T cd08445 99 DEPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAG---EGVTLVPASVQ 158 (203)
T ss_pred CCCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcC---CCeEEehHHhh
Confidence 23331111 1 2345566666543322 33456666777777764 45677776543
No 102
>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=80.23 E-value=37 Score=29.15 Aligned_cols=124 Identities=21% Similarity=0.114 Sum_probs=67.7
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcccE
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLTR 225 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk~ 225 (423)
.+|+.++... .+-.++.+.+.+|++|+|++.-.+...+.. ...|.+.++.++.- -.|-+.. +..+++++..
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v~~----~~~~~~~-~~~~~~~L~~ 96 (200)
T cd08417 25 EAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLR---SQPLFEDRFVCVAR----KDHPLAG-GPLTLEDYLA 96 (200)
T ss_pred hCCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccCCCccc---hhhhhcCceEEEec----CCCcccc-cccCHHHHhC
Confidence 3577665443 456789999999999999987544322222 23344555555443 3343332 2233444432
Q ss_pred ---E-Eechh-HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 226 ---V-ISHPQ-ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 226 ---V-ySHPq-AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
| +.+.. .......|+++++.... ...+++...+.+.+..+ ...+|.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08417 97 APHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGT---DLIATVPRRLAEA 155 (200)
T ss_pred CCeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcC---CeeeeccHHHHHh
Confidence 2 33322 23345667766543222 23455666666777664 4577777766543
No 103
>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=80.17 E-value=18 Score=29.59 Aligned_cols=64 Identities=9% Similarity=0.106 Sum_probs=44.9
Q ss_pred EEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 320 SIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 320 Sivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
-+.|++|.+||+|.+.|+.+. -+-|+|.++=|-.... .=.-||-++-. +..+..+++.|++
T Consensus 3 ~~~v~iPErpGal~~Fl~~l~-p~~~ITeF~YR~~~~~----------------~a~vlvGi~~~--~~~~~~l~~~l~~ 63 (81)
T cd04907 3 LFRFEFPERPGALKKFLNELL-PKWNITLFHYRNQGSD----------------YGRVLVGIQVP--DADLDELKERLDA 63 (81)
T ss_pred EEEEEcCCCCCHHHHHHHHhC-CCCeEeEEEEecCCCC----------------ceeEEEEEEeC--hHHHHHHHHHHHH
Confidence 467889999999999999993 3789999998876431 11345555432 2367777888877
Q ss_pred hcC
Q 014547 400 FTS 402 (423)
Q Consensus 400 ~~~ 402 (423)
..-
T Consensus 64 ~g~ 66 (81)
T cd04907 64 LGY 66 (81)
T ss_pred cCC
Confidence 543
No 104
>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=79.97 E-value=16 Score=28.92 Aligned_cols=30 Identities=13% Similarity=0.173 Sum_probs=25.4
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeee
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIE 350 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIE 350 (423)
|-+..+|+||-|+++-.+|+.+|+|+..-.
T Consensus 3 ~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~ 32 (74)
T cd04925 3 IELTGTDRPGLLSEVFAVLADLHCNVVEAR 32 (74)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCCcEEEEE
Confidence 445567999999999999999999998533
No 105
>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=79.73 E-value=32 Score=29.72 Aligned_cols=125 Identities=14% Similarity=0.094 Sum_probs=62.0
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccC--CCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENS--LGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL 223 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS--~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI 223 (423)
.+|+.++.... +..+..+.+.+|++|+|++.-... ....+ ....|.+.++.++ .+-.|-+...+..+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~--~~~~l~~~~~~~v----~~~~hp~~~~~~i~~~~L 98 (200)
T cd08453 25 AYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAPPAL--AYRPLLSEPLVLA----VPAAWAAEGGAPLALAAV 98 (200)
T ss_pred hCCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCcccCCCcce--eEEEeeeCceEEE----EECCCccccCCCCCHHHh
Confidence 36777665443 467889999999999999743211 01000 1122233333322 222333332222333333
Q ss_pred ---cEEEec-h---hHHHHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 224 ---TRVISH-P---QALSQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 224 ---k~VySH-P---qAL~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
.-|... . .....+..|+++++...+. ..+++...+.++++.+ ...++.+...++
T Consensus 99 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08453 99 AAEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAG---MGVALVPASLRN 160 (200)
T ss_pred ccCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcC---CcEEEeEhHHhh
Confidence 333322 1 1234567778776533232 2345555566666654 456666665543
No 106
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=79.52 E-value=24 Score=34.32 Aligned_cols=144 Identities=14% Similarity=0.090 Sum_probs=74.9
Q ss_pred CccEEEEeCCCccH--HHH--HHhhhCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEE
Q 014547 126 SQLRVAYQGVPGAY--SEA--AAGKAYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHI 200 (423)
Q Consensus 126 ~~~~VayLGP~GTf--Sh~--AA~~~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 200 (423)
+..+|+....-+.+ .+. ...+.+|+.++.... +.+++++++++|++|+||++......+.. ...|.+.++.+
T Consensus 91 g~l~i~~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~---~~~l~~~~~~~ 167 (305)
T PRK11151 91 GPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFI---EVPLFDEPMLL 167 (305)
T ss_pred ceEEEEecchhHHHHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCeE---EEEeccCcEEE
Confidence 35677776544421 111 123446887765544 58999999999999999987654433311 12222333333
Q ss_pred EEEEEEeeeeeeeecCCCCcCccc--EEEechhH---HHHHHHHHHHcC--CceeEEeccCHHHHHHHHHhcCCCCeeEE
Q 014547 201 VGEVQLPVHHCLLALPGVRKEYLT--RVISHPQA---LSQCEHTLTKLG--LNVAREAVDDTAGAAEYIAANDLRDTAAI 273 (423)
Q Consensus 201 vgEi~lpI~h~Lla~~g~~l~dIk--~VySHPqA---L~QC~~fL~~~~--p~~~~v~~~STA~AA~~va~~~~~~~AAI 273 (423)
+. +-.|-|...+..+++++. ..++++.. ..+..+|+..++ ++. ...++|...+.+.++.+ ...+|
T Consensus 168 ~~----~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g---~gi~i 239 (305)
T PRK11151 168 AV----YEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDT-HFRATSLETLRNMVAAG---SGITL 239 (305)
T ss_pred Ee----cCCCCcccCCccCHHHhcCCCeEeecCCccHHHHHHHHHHHCCCCCCc-eEEeccHHHHHHHHHcC---CCEEE
Confidence 22 223333322222333322 12222221 234445555543 333 33467777777887764 56777
Q ss_pred ccHHHHH
Q 014547 274 ASARAAE 280 (423)
Q Consensus 274 aS~~AAe 280 (423)
.+...+.
T Consensus 240 lp~~~~~ 246 (305)
T PRK11151 240 LPALAVP 246 (305)
T ss_pred eeHHhhh
Confidence 7776553
No 107
>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=79.40 E-value=13 Score=26.52 Aligned_cols=30 Identities=23% Similarity=0.184 Sum_probs=25.5
Q ss_pred EeCCCccHHHHHHHHHHhCCceeeeeeeee
Q 014547 324 AHDKGTSVLFKVLSAFAFRNISLTKIESRP 353 (423)
Q Consensus 324 ~l~~~pGaL~~vL~~Fa~~~INLtkIESRP 353 (423)
..++.+|.+.++++.|++++||+..|..-+
T Consensus 7 ~~~~~~~~~~~i~~~L~~~~i~i~~i~~~~ 36 (61)
T cd04891 7 GVPDKPGVAAKIFSALAEAGINVDMIVQSV 36 (61)
T ss_pred cCCCCCcHHHHHHHHHHHcCCcEEEEEEcC
Confidence 356789999999999999999998876544
No 108
>PRK06545 prephenate dehydrogenase; Validated
Probab=78.80 E-value=5.5 Score=40.86 Aligned_cols=40 Identities=13% Similarity=0.132 Sum_probs=34.7
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCC
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNR 357 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~ 357 (423)
-..+.+.++|+||.|.+++..+...|||+..|+-.-.+..
T Consensus 290 ~~~~~v~v~d~pg~~~~~~~~~~~~~i~i~~~~i~~~~~~ 329 (359)
T PRK06545 290 FYDLYVDVPDEPGVIARVTAILGEEGISIENLRILEARED 329 (359)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHcCCCeecceeeeccCC
Confidence 4567788999999999999999999999999887766653
No 109
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=78.21 E-value=76 Score=31.55 Aligned_cols=146 Identities=17% Similarity=0.172 Sum_probs=81.4
Q ss_pred ccEEEEe-CCCccHHHHHHhhhC---C-CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHH-Hhh--cCCc
Q 014547 127 QLRVAYQ-GVPGAYSEAAAGKAY---P-NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYD-LLL--RHRL 198 (423)
Q Consensus 127 ~~~VayL-GP~GTfSh~AA~~~f---~-~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlD-lL~--~~~L 198 (423)
.++|||. +|.....+.+...++ + +++++.+.+..+.++++.+|++|..+ .+... .++ .+. ..++
T Consensus 32 ~I~IG~~~~~~~~~~~~~~~~l~~~~G~~Vel~~f~~~~~~~~ALa~GdID~~~-------~qh~~-~l~~~~~~~g~~l 103 (271)
T PRK11063 32 HIKVGVIVGAEQQVAEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANA-------FQHKP-YLDQQIKDRGYKL 103 (271)
T ss_pred cEEEEeCCCChHHHHHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHcCCcceec-------ccCHH-HHHHHHHHcCCcE
Confidence 4899998 565544444444333 2 57889999999999999999999865 12211 112 222 2456
Q ss_pred EEEEEEEE-eeeeeeeecCCCCcCccc---EEEec--hhHHHHHHHHHHHcCC---------------------ceeEEe
Q 014547 199 HIVGEVQL-PVHHCLLALPGVRKEYLT---RVISH--PQALSQCEHTLTKLGL---------------------NVAREA 251 (423)
Q Consensus 199 ~IvgEi~l-pI~h~Lla~~g~~l~dIk---~VySH--PqAL~QC~~fL~~~~p---------------------~~~~v~ 251 (423)
.+++-..+ |+ .+....=.+++|++ +|.-. |.-.+.+-.+|++.+. ++++++
T Consensus 104 ~~~~~~~vvp~--~~ys~~i~si~DL~~Gk~IAip~d~~n~~r~L~lL~~~Gli~l~~~~~~~~t~~di~~n~~~v~~v~ 181 (271)
T PRK11063 104 VAVGNTFVYPI--AGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVGLIKLKDGVGLLPTVLDIVENPKNLKIVE 181 (271)
T ss_pred EEEeEEEEEEe--eccccCCCCHHHhcCCCEEEecCCCccHHHHHHHHHHCCCEEecCCCCCCCCHHHHhcCCCCCEEEE
Confidence 66665433 43 22222223456664 56544 6666666667777433 466666
Q ss_pred ccCHHHHHHHHHhcCCCCeeEEccHHHHHHcCCc
Q 014547 252 VDDTAGAAEYIAANDLRDTAAIASARAAELYGMQ 285 (423)
Q Consensus 252 ~~STA~AA~~va~~~~~~~AAIaS~~AAelYgL~ 285 (423)
+ +.+..++.+.++ .-.||+...--+..-|+.
T Consensus 182 ~-~~~~~~~al~~g--~vDaa~i~~~~a~~a~~~ 212 (271)
T PRK11063 182 L-EAPQLPRSLDDA--QIALAVINTTYASQIGLT 212 (271)
T ss_pred C-cHHHHHHhcccc--cccEEEEChHHHHHcCCC
Confidence 5 333333433322 234666555555555553
No 110
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=78.11 E-value=7.1 Score=45.67 Aligned_cols=48 Identities=15% Similarity=0.173 Sum_probs=41.8
Q ss_pred cEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+. +.|++.+...++.||+.+++.++|..+++++|..|++|..|..
T Consensus 165 ~~i~~--~~g~~~~~~~~~~~p~~~i~~~~s~~~al~av~~G~~Da~i~~ 212 (1197)
T PRK09959 165 VNIAR--VANYPPDEVIHQSFPKATIISFTNLYQALASVSAGQNDYFIGS 212 (1197)
T ss_pred eEEEE--eCCCCCHHHHHHhCCCCEEEeCCCHHHHHHHHHcCCCCEEEcc
Confidence 46776 4588888888889999999999999999999999999988764
No 111
>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=78.07 E-value=23 Score=33.44 Aligned_cols=126 Identities=21% Similarity=0.133 Sum_probs=74.0
Q ss_pred HHHHHHHHHcCCcCeEEEeeccC--CCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCC-----CCcCcc---cEEEe
Q 014547 159 FEVAFQAVELWIADRAVLPVENS--LGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPG-----VRKEYL---TRVIS 228 (423)
Q Consensus 159 f~~Vf~aV~~g~~d~gVVPIENS--~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g-----~~l~dI---k~VyS 228 (423)
-...+.++.+|.+|.|.+-+-.. -+-.+....++|...++.++.-..- +.-|+.++| ..++|+ ...+-
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 SRAGLSALARGEADIAGIHLPDPESGEYNIPFVRRLLPGIEVVLVRLARR--EQGLIVRPGNPKGITSLEDLADPGLRFV 97 (193)
T ss_pred CHHHHHHHHCCCceEEEecCCCCcccccchHHHHHhcCCCcEEEEeeeEE--eeeEEEeCCCCccCCCHHHhccCCcEEE
Confidence 34567899999999998855433 2222333444555555655543222 456777777 234444 22233
Q ss_pred chhHHHHHHHHHHHcC----------CceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH-cCCceeec
Q 014547 229 HPQALSQCEHTLTKLG----------LNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAEL-YGMQVLED 289 (423)
Q Consensus 229 HPqAL~QC~~fL~~~~----------p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel-YgL~ILa~ 289 (423)
-.|.=.=.+.+|++.. ++.. ..+.+..+.|..|+.+ ...++|+.+.+|+. |||..+.=
T Consensus 98 nR~~GSGtR~l~d~~l~~~gi~~~~i~gy~-~~~~th~~vA~aVa~G--~AD~G~g~~~~A~~~~gL~Fvpl 166 (193)
T PF12727_consen 98 NRQPGSGTRILFDQLLAEEGIDPEDIPGYA-QEANTHLAVAAAVASG--KADAGIGIRAAAEEFYGLDFVPL 166 (193)
T ss_pred ECCCCCHHHHHHHHHHHHcCCChhhCCCcc-ccccChHHHHHHHHcC--CCCEEeehHHHHHhhcCCCcEEc
Confidence 3333333555554432 1212 2345566778888876 57899999999974 89988653
No 112
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=77.64 E-value=8 Score=32.90 Aligned_cols=69 Identities=13% Similarity=0.184 Sum_probs=47.8
Q ss_pred EEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecC-cChHHHHH-HHHHHHhh
Q 014547 323 FAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEAS-MAEVRAQN-ALAEVQEF 400 (423)
Q Consensus 323 f~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~-~~d~~v~~-aL~eL~~~ 400 (423)
+.=+|+||.-..+-++++++|+|+..|+---.++ .|...+++|+... .+-..+++ +-++.++.
T Consensus 8 V~GkDr~GIva~is~vLAe~~vNIldisQtvm~~---------------~ftm~~lV~~~~~~~d~~~lr~~l~~~~~~l 72 (90)
T COG3830 8 VIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDG---------------FFTMIMLVDISKEVVDFAALRDELAAEGKKL 72 (90)
T ss_pred EEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhh---------------hceeeeEEcCChHhccHHHHHHHHHHHHHhc
Confidence 3447899999999999999999999998765543 3678899999532 22244444 33344555
Q ss_pred cCceEE
Q 014547 401 TSFLRV 406 (423)
Q Consensus 401 ~~~vrv 406 (423)
...+++
T Consensus 73 gv~V~v 78 (90)
T COG3830 73 GVDVRV 78 (90)
T ss_pred CcEEEE
Confidence 555553
No 113
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=77.27 E-value=7.1 Score=36.43 Aligned_cols=48 Identities=17% Similarity=0.142 Sum_probs=39.8
Q ss_pred cEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+||+. .|++.+....+.+++.+.+++++.++++.+|..|++|..+.+
T Consensus 127 ~~Igv~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~grvDa~i~~ 174 (243)
T PRK15007 127 KKVGVQ--NGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGD 174 (243)
T ss_pred CeEEEe--cCcHHHHHHHHhCCCCeEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 478885 677776666666778888999999999999999999999865
No 114
>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=76.51 E-value=49 Score=28.48 Aligned_cols=125 Identities=18% Similarity=0.096 Sum_probs=62.2
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc--
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL-- 223 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI-- 223 (423)
.+|+.++... .+..++++.+.+|++|+|+..-.....+. ....|.+..+.++. +-.|-|......+++++
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 4677765544 46788999999999999997533211110 01112222222221 11222211111222222
Q ss_pred -cEEE-ech-hHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 224 -TRVI-SHP-QALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 224 -k~Vy-SHP-qAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
.-|. ... ....+..+|+.+++.... ...+++...+.+++..+ ...|+.+...++.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 157 (200)
T cd08411 99 ERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAG---LGITLLPELAVPS 157 (200)
T ss_pred CceEecCCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CCEEEeCHHHhcc
Confidence 2222 111 123345556665543222 34566777777777764 4678888776653
No 115
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=76.42 E-value=9.4 Score=38.36 Aligned_cols=75 Identities=13% Similarity=0.162 Sum_probs=54.7
Q ss_pred CCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEE--EEEEecCcChHHHHH
Q 014547 315 RPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMF--YIDFEASMAEVRAQN 392 (423)
Q Consensus 315 ~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~F--fID~eg~~~d~~v~~ 392 (423)
+..|..|-.-+.|+||.|.++-.+|+.||.|+-.+----... +-.| -|=+.| .|.-+++
T Consensus 74 r~krHvinclVqnEpGvlsRisGvlAaRGfNIdSLvVc~tev-----------------k~LsrmTIVl~G--td~VveQ 134 (309)
T KOG2663|consen 74 RVKRHVINCLVQNEPGVLSRISGVLAARGFNIDSLVVCLTEV-----------------KALSRMTIVLQG--TDGVVEQ 134 (309)
T ss_pred cccceeEEEEecCCchHHHHHHHHHHhccCCchheeeechhh-----------------hhhhhceEEEec--cHHHHHH
Confidence 334666666677999999999999999999976544332221 2234 455667 6789999
Q ss_pred HHHHHHhhcCceEEEc
Q 014547 393 ALAEVQEFTSFLRVLG 408 (423)
Q Consensus 393 aL~eL~~~~~~vrvLG 408 (423)
+.++|++...-++||.
T Consensus 135 a~rQiedlVnV~aVlD 150 (309)
T KOG2663|consen 135 ARRQIEDLVNVYAVLD 150 (309)
T ss_pred HHHHHHHhhhhheeee
Confidence 9999999887777764
No 116
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=76.07 E-value=6.8 Score=36.58 Aligned_cols=48 Identities=15% Similarity=0.142 Sum_probs=40.2
Q ss_pred cEEEEeCCCccHHHHHHhhhCC-CCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYP-NCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~-~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|++. .|+..+....+.++ +.+++.+.+.++++++|.+|++|+.++.
T Consensus 132 ~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~ 180 (250)
T TIGR01096 132 KTVGVQ--SGTTHEQYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTD 180 (250)
T ss_pred CEEEEe--cCchHHHHHHHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 478874 67777776666777 7788999999999999999999999874
No 117
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=75.28 E-value=15 Score=37.22 Aligned_cols=65 Identities=9% Similarity=0.147 Sum_probs=46.6
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEe----cCcChHHHHHHHHH
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFE----ASMAEVRAQNALAE 396 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~e----g~~~d~~v~~aL~e 396 (423)
|.+.-+|+||-.+++=+.++++|+|+..+... ... .. ..|+..++++ ...+...++++|++
T Consensus 12 itv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~-~d~---------~~-----~~ffm~i~~~~~~~~~~~~~~l~~~l~~ 76 (289)
T PRK13010 12 LTLACPSAPGIVAAVSGFLAEKGCYIVELTQF-DDD---------ES-----GRFFMRVSFHAQSAEAASVDTFRQEFQP 76 (289)
T ss_pred EEEECCCCCCcHHHHHHHHHHCCCCEEecccc-ccc---------cc-----CcEEEEEEEEcCCCCCCCHHHHHHHHHH
Confidence 44455899999999999999999999998875 211 11 2566666666 22345788888888
Q ss_pred HHhh
Q 014547 397 VQEF 400 (423)
Q Consensus 397 L~~~ 400 (423)
+.+.
T Consensus 77 l~~~ 80 (289)
T PRK13010 77 VAEK 80 (289)
T ss_pred HHHH
Confidence 7543
No 118
>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=75.23 E-value=51 Score=28.10 Aligned_cols=123 Identities=14% Similarity=0.061 Sum_probs=60.4
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccC--CCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENS--LGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL 223 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS--~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI 223 (423)
.+|+.++... .+..++.+.+.+|++|+|++..... ..|.. ...|.+.++.++. +-+|-|...+..+++++
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~~~l~~~~~~~~~----~~~~~l~~~~~~~~~dL 97 (201)
T cd08435 25 RHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLA---SEELADEPLVVVA----RPGHPLARRARLTLADL 97 (201)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCCCCcE---EEEcccCcEEEEE----eCCCcCcccCCcCHHHH
Confidence 4677665443 4678899999999999999753211 11111 1122233333222 22333322222233332
Q ss_pred c---EEEe-chh-HHHHHHHHHHHcC---CceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 224 T---RVIS-HPQ-ALSQCEHTLTKLG---LNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 224 k---~VyS-HPq-AL~QC~~fL~~~~---p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
. -|.. ... -.....+++++.+ ++. ...+++...+.+++..+ ...|+.+...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08435 98 ADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRN-VVETASISALLALLARS---DMLAVLPRSVAE 158 (201)
T ss_pred hcCCEEecCCCCcHHHHHHHHHHHcCCCCCCc-eEEEccHHHHHHHHhcC---CeEEEeEHHHhh
Confidence 2 2221 111 1123455566543 222 23355666666777664 457788877665
No 119
>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=74.92 E-value=9.8 Score=37.63 Aligned_cols=128 Identities=16% Similarity=0.145 Sum_probs=71.6
Q ss_pred CccEEEEeCCCccHHHHHHhhhC---C-CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEE
Q 014547 126 SQLRVAYQGVPGAYSEAAAGKAY---P-NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIV 201 (423)
Q Consensus 126 ~~~~VayLGP~GTfSh~AA~~~f---~-~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Iv 201 (423)
...++|..|+ |+.+|.++..+. + +.+.+|+++-.+++.+|..|++|.++...- ...+++...++++.
T Consensus 105 ~~~~~g~~g~-g~~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~~--------~~~~~~~~G~~k~L 175 (274)
T PF03401_consen 105 GKLTFGSSGP-GSSDHLAAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSPG--------EALPYVEAGDLKPL 175 (274)
T ss_dssp CC-EEEESST-TSHHHHHHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEHH--------HHHHHHHTTSEEEE
T ss_pred CCeEEEecCC-CchHHHHHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecHH--------HHHHHHhCCCceEE
Confidence 3578898885 888998876554 2 567899999999999999999999977533 22233322222222
Q ss_pred E----------------------EEEEeeeeeeeecCCCCcCcccEEEechh---HHHHHHHHHHHcCCceeEEeccCHH
Q 014547 202 G----------------------EVQLPVHHCLLALPGVRKEYLTRVISHPQ---ALSQCEHTLTKLGLNVAREAVDDTA 256 (423)
Q Consensus 202 g----------------------Ei~lpI~h~Lla~~g~~l~dIk~VySHPq---AL~QC~~fL~~~~p~~~~v~~~STA 256 (423)
+ ++.+...+.+++++|++.+-++++..--+ .....++|+++.+ .... ..+..
T Consensus 176 av~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~~g--~~~~-~~~~~ 252 (274)
T PF03401_consen 176 AVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEKMG--LEPV-YMDGE 252 (274)
T ss_dssp EECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHHHT--EEEE-CESHH
T ss_pred EEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHHCC--CcCC-CCCHH
Confidence 1 12344556777888775332222221111 1223355666654 2222 45666
Q ss_pred HHHHHHHhc
Q 014547 257 GAAEYIAAN 265 (423)
Q Consensus 257 ~AA~~va~~ 265 (423)
+..+.+.++
T Consensus 253 ~~~~~l~~~ 261 (274)
T PF03401_consen 253 EFDAFLAEE 261 (274)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 666666653
No 120
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=74.40 E-value=11 Score=41.05 Aligned_cols=104 Identities=17% Similarity=0.205 Sum_probs=68.4
Q ss_pred HHHHHHcCCceeec--CccCCCCCeeEEEEEeeCCCCC-----CCC---------------CCCeEEEEEEeCCCccHHH
Q 014547 276 ARAAELYGMQVLED--GIQDDSSNVTRFVMLAREPIIP-----RTD---------------RPFKTSIVFAHDKGTSVLF 333 (423)
Q Consensus 276 ~~AAelYgL~ILa~--nIqD~~~N~TRFlVLsr~~~~~-----~~~---------------~~~KTSivf~l~~~pGaL~ 333 (423)
...|+..|+++-.. +..+...|.-++.+-+...... ..+ .+...++++...|+||.+.
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 36688888886543 3344467777776655331100 000 1235667778889999999
Q ss_pred HHHHHHHhCCceeeeee-eeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 334 KVLSAFAFRNISLTKIE-SRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 334 ~vL~~Fa~~~INLtkIE-SRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
++.+.|.+++||+.... +|-.++ .+.+..|+++....++ +|++|++
T Consensus 468 ~v~~~L~~~~iNIa~m~~~r~~~g----------------~~al~~i~~D~~v~~~----~l~~i~~ 514 (526)
T PRK13581 468 KVGTLLGEAGINIAGMQLGRREAG----------------GEALMVLSVDDPVPEE----VLEELRA 514 (526)
T ss_pred HHHHHHhhcCCCchhcEeccCCCC----------------CeEEEEEECCCCCCHH----HHHHHhc
Confidence 99999999999998765 453322 3678889998877644 5555554
No 121
>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=74.07 E-value=50 Score=28.99 Aligned_cols=142 Identities=13% Similarity=0.022 Sum_probs=70.2
Q ss_pred ccEEEEeCCCccHH-HHH---HhhhCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEE
Q 014547 127 QLRVAYQGVPGAYS-EAA---AGKAYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIV 201 (423)
Q Consensus 127 ~~~VayLGP~GTfS-h~A---A~~~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Iv 201 (423)
..+||+....+.+- -.+ -++.+|+.++.- ..+..++.+.+.+|++|+|++.-..-..|. ....|.+.++.+
T Consensus 2 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~~~~~---~~~~l~~~~~~l- 77 (198)
T cd08486 2 ELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGI---EIVNIAQEDLYL- 77 (198)
T ss_pred eEEEEEechhhHHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCCCCce---EEEEEeeccEEE-
Confidence 35677766554321 111 123467776543 356789999999999999997422111110 001112222221
Q ss_pred EEEEEeeeeeeeecCCCCcCcc---cEEEech----hHHHHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEE
Q 014547 202 GEVQLPVHHCLLALPGVRKEYL---TRVISHP----QALSQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAI 273 (423)
Q Consensus 202 gEi~lpI~h~Lla~~g~~l~dI---k~VySHP----qAL~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAI 273 (423)
.++-+|-|......+++++ .-|.-.+ ....+..+++++.+...+. ..+++......+++.+ ...+|
T Consensus 78 ---v~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~ 151 (198)
T cd08486 78 ---AVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG---AASSI 151 (198)
T ss_pred ---EecCCCccccCCcccHHHHcCCCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---ceEEE
Confidence 1233343332223334444 3343222 2345677777776544333 2345555555566553 45666
Q ss_pred ccHHH
Q 014547 274 ASARA 278 (423)
Q Consensus 274 aS~~A 278 (423)
.+..+
T Consensus 152 lp~~~ 156 (198)
T cd08486 152 VPASV 156 (198)
T ss_pred cchhh
Confidence 66643
No 122
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=73.68 E-value=21 Score=40.52 Aligned_cols=69 Identities=10% Similarity=0.174 Sum_probs=51.1
Q ss_pred CCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHH
Q 014547 316 PFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALA 395 (423)
Q Consensus 316 ~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~ 395 (423)
.+.+.|.+...|++|.|.++...++..++|+.++.++..+.. .+.-.|-|++. +-..+..+|.
T Consensus 624 ~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~--------------~~~~~~~ieV~---~~~~L~~i~~ 686 (702)
T PRK11092 624 EFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGR--------------VYSAFIRLTAR---DRVHLANIMR 686 (702)
T ss_pred eeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCC--------------EEEEEEEEEEC---CHHHHHHHHH
Confidence 367788888899999999999999999999999998754321 12223444442 3378888999
Q ss_pred HHHhhc
Q 014547 396 EVQEFT 401 (423)
Q Consensus 396 eL~~~~ 401 (423)
.|+..-
T Consensus 687 ~Lr~i~ 692 (702)
T PRK11092 687 KIRVMP 692 (702)
T ss_pred HHhCCC
Confidence 988654
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=73.40 E-value=19 Score=32.18 Aligned_cols=133 Identities=17% Similarity=0.096 Sum_probs=77.9
Q ss_pred eCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeee
Q 014547 133 QGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCL 212 (423)
Q Consensus 133 LGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~L 212 (423)
.|...-+-.+++.+.--+.++++. ++..+++++++|++|.++-++.. +.+. ...+.... -+....+.+
T Consensus 22 ~G~~~dl~~~i~~~~g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~--------~~~r--~~~~~~s~-p~~~~~~~~ 89 (225)
T PF00497_consen 22 SGIDVDLLRAIAKRLGIKIEFVPM-PWSRLLEMLENGKADIIIGGLSI--------TPER--AKKFDFSD-PYYSSPYVL 89 (225)
T ss_dssp ESHHHHHHHHHHHHHTCEEEEEEE-EGGGHHHHHHTTSSSEEESSEB---------BHHH--HTTEEEES-ESEEEEEEE
T ss_pred EEEhHHHHHHHHhhcccccceeec-ccccccccccccccccccccccc--------cccc--cccccccc-cccchhhee
Confidence 444444555555554225678888 99999999999999987644432 2222 11222232 233445667
Q ss_pred eecCCC-----Cc---Ccc--cEEEechhHHHHHHHHHHHcCC-ceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 213 LALPGV-----RK---EYL--TRVISHPQALSQCEHTLTKLGL-NVAREAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 213 la~~g~-----~l---~dI--k~VySHPqAL~QC~~fL~~~~p-~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
+.+++. .+ +++ ++|..-.-.. -.++|.+..+ +++++.+.|..++.+++..+ +-.|+|.....++.
T Consensus 90 ~~~~~~~~~~~~~~~~~dl~~~~i~~~~g~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~i~~~~~~~~ 165 (225)
T PF00497_consen 90 VVRKGDAPPIKTIKSLDDLKGKRIGVVRGSS--YADYLKQQYPSNINIVEVDSPEEALEALLSG--RIDAFIVDESTAEY 165 (225)
T ss_dssp EEETTSTCSTSSHSSGGGGTTSEEEEETTSH--HHHHHHHHTHHTSEEEEESSHHHHHHHHHTT--SSSEEEEEHHHHHH
T ss_pred eeccccccccccccchhhhcCcccccccchh--HHHHhhhhccchhhhcccccHHHHHHHHhcC--Ceeeeeccchhhhh
Confidence 766542 22 244 2344333322 2234444333 56777889999999998876 46688877765543
No 124
>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=73.15 E-value=17 Score=41.77 Aligned_cols=66 Identities=14% Similarity=0.116 Sum_probs=45.9
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEe-cC-cChHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFE-AS-MAEVRAQNAL 394 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~e-g~-~~d~~v~~aL 394 (423)
..|.|-+...|+||-|+++.++|+.+|||+......-...+ -.-+|||... |. ..++..+++-
T Consensus 778 ~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~---------------~~d~F~v~~~~g~~~~~~~~~~l~ 842 (850)
T TIGR01693 778 KATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEK---------------AEDVFYVTDLFGLKLTDEEEQRLL 842 (850)
T ss_pred CeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCcc---------------ceeEEEEECCCCCCCCHHHHHHHH
Confidence 46777788899999999999999999999997665544322 3579999653 33 3333333333
Q ss_pred HHH
Q 014547 395 AEV 397 (423)
Q Consensus 395 ~eL 397 (423)
+.|
T Consensus 843 ~~L 845 (850)
T TIGR01693 843 EVL 845 (850)
T ss_pred HHH
Confidence 333
No 125
>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=73.08 E-value=26 Score=26.15 Aligned_cols=27 Identities=26% Similarity=0.246 Sum_probs=23.7
Q ss_pred EeCCCccHHHHHHHHHHhCCceeeeee
Q 014547 324 AHDKGTSVLFKVLSAFAFRNISLTKIE 350 (423)
Q Consensus 324 ~l~~~pGaL~~vL~~Fa~~~INLtkIE 350 (423)
.+++.+|.+.++++.+++.|||+.-|-
T Consensus 8 ~~~~~~g~~~~i~~~L~~~~I~i~~i~ 34 (75)
T cd04913 8 GVPDKPGVAAKIFGALAEANINVDMIV 34 (75)
T ss_pred CCCCCCcHHHHHHHHHHHcCCeEEEEE
Confidence 457789999999999999999998664
No 126
>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=72.89 E-value=11 Score=32.79 Aligned_cols=48 Identities=29% Similarity=0.320 Sum_probs=38.3
Q ss_pred cEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|++. .|+..+....+.++..+++++.+.++++++|.+|++|.+++.
T Consensus 106 ~~i~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 153 (218)
T cd00134 106 KKVAVQ--KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVD 153 (218)
T ss_pred CEEEEE--cCchHHHHHHHhCCcccEEEeCCHHHHHHHHHcCCccEEEec
Confidence 478877 565556666666666778899999999999999999988775
No 127
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=72.23 E-value=5.6 Score=46.53 Aligned_cols=49 Identities=24% Similarity=0.176 Sum_probs=42.8
Q ss_pred ccEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 127 QLRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 127 ~~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
..+||. +.|++.+....+.+++.+++.+++.++++++|.+|++|.+|..
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 358888 5788888888888899999999999999999999999998764
No 128
>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=72.15 E-value=24 Score=39.77 Aligned_cols=69 Identities=13% Similarity=0.129 Sum_probs=50.9
Q ss_pred CCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHH
Q 014547 316 PFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALA 395 (423)
Q Consensus 316 ~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~ 395 (423)
.+.+.|.+...|++|.|.++++.++..++|+..+..+-... ..+.+-++++- .+-..+..++.
T Consensus 608 ~f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~----------------~~~~~~~~ieV-~~~~~L~~ii~ 670 (683)
T TIGR00691 608 RFIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGK----------------REAILNITVEI-KNYKHLLKIML 670 (683)
T ss_pred eeEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCC----------------CEEEEEEEEEE-CCHHHHHHHHH
Confidence 46788889999999999999999999999999999864321 12233333432 13478888898
Q ss_pred HHHhhc
Q 014547 396 EVQEFT 401 (423)
Q Consensus 396 eL~~~~ 401 (423)
.|+..-
T Consensus 671 ~L~~i~ 676 (683)
T TIGR00691 671 KIKTKN 676 (683)
T ss_pred HHhCCC
Confidence 887653
No 129
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=72.09 E-value=1e+02 Score=30.63 Aligned_cols=151 Identities=13% Similarity=0.056 Sum_probs=79.3
Q ss_pred ccccccCCCCCCCCCccEEEEeCCCccHHHHHH-hhhC-C----CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCc
Q 014547 112 PLTITDLSPAPMHGSQLRVAYQGVPGAYSEAAA-GKAY-P----NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGS 185 (423)
Q Consensus 112 ~~~~~~~~~~~~~~~~~~VayLGP~GTfSh~AA-~~~f-~----~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~ 185 (423)
.|-++.++. +-...||+|+...+-+ ..|- +.+| . +++++.+.+-.++++++..|++|+|++...
T Consensus 12 ~~~~~~~~~---~~~~v~~~y~~~~~~~-~vA~~~g~f~~~~Gl~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~------ 81 (320)
T PRK11480 12 ALAFIAFQA---QAVNVTVAYQTSAEPA-KVAQADNTFAKESGATVDWRKFDSGASIVRALASGDVQIGNLGSS------ 81 (320)
T ss_pred HHHhhhccc---CCCeEEEEecCCCcHH-HHHHHcCchHHHcCCeeEEEEeCCHHHHHHHHHCCCCCEECcCch------
Confidence 344555552 3347899998532222 2222 2234 2 478899999999999999999999966432
Q ss_pred hHHHHHHhhcCCcEEEEEEEE-eeeeeeeecCCC-CcCcc--cEEEechhH--HHHHHHHHHHcCC---ceeEEeccCHH
Q 014547 186 IHRNYDLLLRHRLHIVGEVQL-PVHHCLLALPGV-RKEYL--TRVISHPQA--LSQCEHTLTKLGL---NVAREAVDDTA 256 (423)
Q Consensus 186 V~~tlDlL~~~~L~IvgEi~l-pI~h~Lla~~g~-~l~dI--k~VySHPqA--L~QC~~fL~~~~p---~~~~v~~~STA 256 (423)
....-.....++.+++-... .....|+++++. +++|+ |+|...+-. ...-..+|++.+. +++.+... .+
T Consensus 82 -~~~~a~~~g~~~~~v~~~~~~~~~~~lv~~~~I~s~~DLkGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~-~~ 159 (320)
T PRK11480 82 -PLAVAASQQVPIEVFLLASKLGNSEALVVKKTISKPEDLIGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQ-PP 159 (320)
T ss_pred -HHHHHHHCCCCeEEEEeeccCCcceEEEecCCCCChHHcCCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECC-cH
Confidence 11111122345655543222 223467776543 33344 356543221 1234567877653 34444433 34
Q ss_pred HHHHHHHhcCCCCeeEEcc
Q 014547 257 GAAEYIAANDLRDTAAIAS 275 (423)
Q Consensus 257 ~AA~~va~~~~~~~AAIaS 275 (423)
.++..+..++ -+.+++..
T Consensus 160 ~~~~Al~~G~-VDAa~~~~ 177 (320)
T PRK11480 160 AIIAAWQRGD-IDGAYVWA 177 (320)
T ss_pred HHHHHHHcCC-cCEEEEcc
Confidence 4555555542 33344433
No 130
>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=71.94 E-value=62 Score=27.59 Aligned_cols=124 Identities=15% Similarity=0.078 Sum_probs=61.3
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCc---Cc
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRK---EY 222 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l---~d 222 (423)
.+|+.++... .+-.++++.+.+|++|+|++.-.....|.. ...|.+..+.+ ..+-.|-|...+..++ .+
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 4677665433 457889999999999999985332211111 01122222221 1222333332222222 23
Q ss_pred ccEEE-echhHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 223 LTRVI-SHPQALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 223 Ik~Vy-SHPqAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
..-|. .......+-.+|+.+++.... ...+++...+.+++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (198)
T cd08412 98 EPLILLDLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANG---LGYSLLNDRPYR 154 (198)
T ss_pred CcEEecCchhHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CCEEEeeccccc
Confidence 33333 222222334556666542222 23356667777777654 456777766554
No 131
>PRK11260 cystine transporter subunit; Provisional
Probab=71.91 E-value=9.6 Score=36.54 Aligned_cols=48 Identities=13% Similarity=0.074 Sum_probs=40.3
Q ss_pred cEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+. ..|+..+....+.+++.++..+++..+++++|.+|++|+.+.+
T Consensus 150 ~~Igv--~~G~~~~~~l~~~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d 197 (266)
T PRK11260 150 KKVGV--GLGTNYEQWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVD 197 (266)
T ss_pred CEEEE--ecCCcHHHHHHHhCCCCceEecCCHHHHHHHHHcCCCCEEEec
Confidence 47776 6777777767677888889999999999999999999998874
No 132
>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=70.55 E-value=16 Score=27.26 Aligned_cols=51 Identities=20% Similarity=0.252 Sum_probs=37.5
Q ss_pred CCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHH
Q 014547 326 DKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEV 397 (423)
Q Consensus 326 ~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL 397 (423)
.+.+|...++++.|++++||+-.|.+ .. ....|+|+-.- .+..++.++++|
T Consensus 11 ~~~~~~~~~if~~l~~~~i~v~~i~t---~~----------------~~is~~v~~~~--~~~~~~~l~~~l 61 (62)
T cd04890 11 NGEVGFLRKIFEILEKHGISVDLIPT---SE----------------NSVTLYLDDSL--LPKKLKRLLAEL 61 (62)
T ss_pred CcccCHHHHHHHHHHHcCCeEEEEec---CC----------------CEEEEEEehhh--hhHHHHHHHHhh
Confidence 45789999999999999999999965 11 26888887632 135666666655
No 133
>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=70.38 E-value=52 Score=28.42 Aligned_cols=124 Identities=18% Similarity=0.133 Sum_probs=60.7
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc--
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL-- 223 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI-- 223 (423)
.+|+.++.... +..++.+.+.+|++|+|+.+......+ + ....|.+..+.++ .+-+|-|...+ .+++++
T Consensus 25 ~~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~-l--~~~~l~~~~~~~v----~~~~~~l~~~~-i~~~~L~~ 96 (201)
T cd08459 25 VAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAG-F--FQQRLFRERYVCL----VRKDHPRIGST-LTLEQFLA 96 (201)
T ss_pred HCCCCeEEEEecCccCHHHHhhCCCceEEEEcCCCCccc-c--eEEEeecCceEEE----EcCCCccccCC-cCHHHHhh
Confidence 46776655443 446888999999999999864321100 0 0111222222221 22233332211 233322
Q ss_pred -cEEEech--hHHHHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 224 -TRVISHP--QALSQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 224 -k~VySHP--qAL~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
+-|...+ ....+.++|+.+++..... ..++|.....+.++.+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (201)
T cd08459 97 ARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQT---DLVATVPERLARL 155 (201)
T ss_pred CCcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcC---CEEEecHHHHHHH
Confidence 2233222 1223456677666433332 3344555555666653 4688888876654
No 134
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=70.06 E-value=23 Score=34.76 Aligned_cols=124 Identities=14% Similarity=0.016 Sum_probs=67.3
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcccE
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLTR 225 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk~ 225 (423)
.+|+.++.... +-.++++.|.+|++|+|+++.+-...+.. ...|.+.++.++ .+-.|-|. ....+++++..
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 46777665443 46888999999999999997542211111 112223333332 23344432 22234444431
Q ss_pred ----EEechhHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 226 ----VISHPQALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 226 ----VySHPqAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
++.++....+...|+.+.+.+.. ...++|.....+.++.+ ...++.+...++.
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 266 (314)
T PRK09508 209 EQHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQT---HLVAIAPRWLAEE 266 (314)
T ss_pred CCCEEecCCCCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhC---ChHHHHHHHHHHH
Confidence 23333333445667776543222 33466777777777764 3567777766653
No 135
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=69.72 E-value=36 Score=32.34 Aligned_cols=110 Identities=19% Similarity=0.225 Sum_probs=67.7
Q ss_pred HHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeee---eeecCCCCcCcc-----cEEEe-c
Q 014547 159 FEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHC---LLALPGVRKEYL-----TRVIS-H 229 (423)
Q Consensus 159 f~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~---Lla~~g~~l~dI-----k~VyS-H 229 (423)
-.|+-.-|+.|.+|+|++= .|.|.+++-.+.--..|...+| ++++++.+...+ ++|.+ .
T Consensus 49 ~~Dip~yV~~G~aDlGI~G------------~D~l~E~~~~v~~~~dL~fg~crl~vA~p~~~~~~~~~~l~~~rIATky 116 (182)
T TIGR00070 49 PQDIPTYVEHGAADLGITG------------YDVLLESGADVYELLDLGFGKCRLVLAVPQESDISSVEDLKGKRIATKY 116 (182)
T ss_pred cchhHHHHhCCCccEEEec------------chhhhhCCCCEEEEeecCcCceEEEEEEECCCCCCChHHhCCCEEEECC
Confidence 3467789999999999762 3566665544444345666666 445554332221 46777 5
Q ss_pred hhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEE----ccHHHHHHcCCceee
Q 014547 230 PQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAI----ASARAAELYGMQVLE 288 (423)
Q Consensus 230 PqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAI----aS~~AAelYgL~ILa 288 (423)
|. -.++|+++++.+++++..+-.-|+|-. - .-+-|| .+-..-+.+||++++
T Consensus 117 p~---i~~~~f~~~Gi~v~ii~l~GsvE~aP~---~--GlaD~IvDiv~TG~TL~~NgL~~ie 171 (182)
T TIGR00070 117 PN---LARRYFEKKGIDVEIIKLNGSVELAPL---L--GLADAIVDIVSTGTTLRENGLRIIE 171 (182)
T ss_pred HH---HHHHHHHHcCCeEEEEECcceeecccC---C--CceeEEEEEeCCHHHHHHCCCEEee
Confidence 55 567799999888888776554443321 1 122244 245566779999985
No 136
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=69.68 E-value=28 Score=39.50 Aligned_cols=70 Identities=13% Similarity=0.189 Sum_probs=53.9
Q ss_pred CCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHH
Q 014547 316 PFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALA 395 (423)
Q Consensus 316 ~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~ 395 (423)
.+.+.|.+...|++|.|.+++++++..++|+.++.++...++ .+.+.++++-+ +-..+..++.
T Consensus 625 ~f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~~----------------~~~~~~~i~v~-n~~~L~~i~~ 687 (701)
T COG0317 625 VYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQ----------------FATMQFTIEVK-NLNHLGRVLA 687 (701)
T ss_pred ceEEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCCc----------------eEEEEEEEEEC-cHHHHHHHHH
Confidence 367888888899999999999999999999999999987332 34455555432 3467888888
Q ss_pred HHHhhcC
Q 014547 396 EVQEFTS 402 (423)
Q Consensus 396 eL~~~~~ 402 (423)
.|++...
T Consensus 688 ~l~~~~~ 694 (701)
T COG0317 688 RLKQLPD 694 (701)
T ss_pred HHhcCCC
Confidence 8876543
No 137
>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=68.95 E-value=18 Score=34.06 Aligned_cols=87 Identities=11% Similarity=0.010 Sum_probs=49.8
Q ss_pred cEEEEeCCCccHHHHHH----hhhCC------CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCC
Q 014547 128 LRVAYQGVPGAYSEAAA----GKAYP------NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHR 197 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA----~~~f~------~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~ 197 (423)
.+|++.+|.++..+... .+..+ ..+++...+..+++++|..|++|.++++-. ...+...+..+ ...+
T Consensus 142 k~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~~Da~~~~~~-~~~~~~~~~~~--~~~~ 218 (254)
T TIGR01098 142 KTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGKVDAATNNSS-AIGRLKKRGPS--DMKK 218 (254)
T ss_pred CEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCCCCeEEecHH-HHHHHHHhCcc--chhh
Confidence 58999987654433322 22222 145677788999999999999999998732 11111111000 0125
Q ss_pred cEEEEEEEEeeeeeeeecCC
Q 014547 198 LHIVGEVQLPVHHCLLALPG 217 (423)
Q Consensus 198 L~IvgEi~lpI~h~Lla~~g 217 (423)
+.+.++-.....+.++.+++
T Consensus 219 ~~~~~~~~~~~~~~~~~~~~ 238 (254)
T TIGR01098 219 VRVIWKSPLIPNDPIAVRKD 238 (254)
T ss_pred eEEEEecCCCCCCCEEEECC
Confidence 77887644433455655554
No 138
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=68.62 E-value=27 Score=39.88 Aligned_cols=70 Identities=9% Similarity=0.138 Sum_probs=51.5
Q ss_pred CCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHH
Q 014547 316 PFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALA 395 (423)
Q Consensus 316 ~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~ 395 (423)
.+.+.|.+...|++|.|.++.++++..++|+..+.++..++.. ...-.|-|++. +-..+..++.
T Consensus 664 ~~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~~-------------~~~~~~~ieV~---~~~~L~~l~~ 727 (743)
T PRK10872 664 GYSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQQ-------------LATIDMTIEIY---NLQVLGRVLG 727 (743)
T ss_pred eeEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCC-------------EEEEEEEEEEC---CHHHHHHHHH
Confidence 3677888888999999999999999999999999987654210 12334445553 3367888888
Q ss_pred HHHhhc
Q 014547 396 EVQEFT 401 (423)
Q Consensus 396 eL~~~~ 401 (423)
.|+..-
T Consensus 728 ~L~~i~ 733 (743)
T PRK10872 728 KLNQVP 733 (743)
T ss_pred HHhcCC
Confidence 887543
No 139
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=67.87 E-value=63 Score=31.76 Aligned_cols=138 Identities=17% Similarity=0.108 Sum_probs=70.7
Q ss_pred ccEEEEeCCCccHHHHHHh-----hhCCC--CceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcE
Q 014547 127 QLRVAYQGVPGAYSEAAAG-----KAYPN--CEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLH 199 (423)
Q Consensus 127 ~~~VayLGP~GTfSh~AA~-----~~f~~--~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~ 199 (423)
..+|||+.. ......+-. +.+++ .+++...+-.++++++.+|++|+|+.. ........-...++.
T Consensus 28 ~lrIg~~~~-~~~~~l~~~~~~~~~~~p~v~ie~~~~~~~~~~~~aL~~G~iDia~~~-------~~~~~~~~~~g~~~~ 99 (314)
T PRK11553 28 ALRIGYQKG-SIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGSTG-------DIPPIFAQAAGADLV 99 (314)
T ss_pred eEEEEeCCC-chHHHHHHhhCHHHHhCCCCeeEEEECCCcHHHHHHHHcCCCCEEccC-------CHHHHHHHhCCCCEE
Confidence 678999742 222222221 12344 456677667899999999999999742 211111111123556
Q ss_pred EEEEEEE-eeeeeeeecCCCC---cCcc--cEEEech--hHHHHHHHHHHHcCC---ceeEEeccCHHHHHHHHHhcCCC
Q 014547 200 IVGEVQL-PVHHCLLALPGVR---KEYL--TRVISHP--QALSQCEHTLTKLGL---NVAREAVDDTAGAAEYIAANDLR 268 (423)
Q Consensus 200 IvgEi~l-pI~h~Lla~~g~~---l~dI--k~VySHP--qAL~QC~~fL~~~~p---~~~~v~~~STA~AA~~va~~~~~ 268 (423)
+++.... +-..+++++++.. ++|+ ++|...+ .....+.++|++.+. .++.+.. +..++.+.+..+ .
T Consensus 100 ~v~~~~~~~~~~~lvv~~~s~i~s~~dL~Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~-~~~~~~~al~~G--~ 176 (314)
T PRK11553 100 YVGVEPPKPKAEVILVAENSPIKTVADLKGHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYL-TPADARAAFQQG--N 176 (314)
T ss_pred EEEEecCCCcceEEEEeCCCCCCCHHHhCCCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEec-ChHHHHHHHHcC--C
Confidence 6654322 2235677776643 2333 2344321 133456667776643 2233333 445566666654 2
Q ss_pred CeeEEcc
Q 014547 269 DTAAIAS 275 (423)
Q Consensus 269 ~~AAIaS 275 (423)
-.|+++.
T Consensus 177 vDa~~~~ 183 (314)
T PRK11553 177 VDAWAIW 183 (314)
T ss_pred CCEEEEc
Confidence 4455543
No 140
>PRK05092 PII uridylyl-transferase; Provisional
Probab=66.98 E-value=25 Score=40.92 Aligned_cols=35 Identities=14% Similarity=0.165 Sum_probs=29.6
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeee
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESR 352 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESR 352 (423)
.|.|.+..+|+||-|+++.++|+..|||+..-...
T Consensus 843 ~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~ 877 (931)
T PRK05092 843 FTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIA 877 (931)
T ss_pred eEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEE
Confidence 46666778899999999999999999999965444
No 141
>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=66.93 E-value=79 Score=26.82 Aligned_cols=31 Identities=26% Similarity=-0.002 Sum_probs=23.9
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEe
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+.++... .+-+++++.+.+|++|+|++.
T Consensus 25 ~~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~ 56 (197)
T cd08438 25 RYPNIELELVEYGGKKVEQAVLNGELDVGITV 56 (197)
T ss_pred HCcCeEEEEEEcCcHHHHHHHHcCCCCEEEEe
Confidence 3577665433 467889999999999999975
No 142
>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=66.73 E-value=13 Score=31.03 Aligned_cols=67 Identities=12% Similarity=0.185 Sum_probs=43.5
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e 396 (423)
.+..+.|.+|.+||+|.+.|+.+..++ |+|.++=|-.... .| .-+|-++-. +.+..+.+++.
T Consensus 9 ~E~~~~v~~PE~pGal~~F~~~l~~~~-nITeF~YR~~~~~---------~a-------~vlvgi~v~-~~~~~~~l~~~ 70 (91)
T PF00585_consen 9 REALFAVEFPERPGALKRFLDALGPRN-NITEFHYRYSGDD---------FA-------RVLVGIEVP-DAEDLEELIER 70 (91)
T ss_dssp -EEEEEEE--BSTTHCHHHHHCCSSSE--EEEEEEE-TTTS---------CS-------EEEEEEE-S-STHHHHHHHHH
T ss_pred CEEEEEEECCCCccHHHHHHHHhCCCc-eEEEEEEcCCCCC---------ee-------eEEEEEEeC-CHHHHHHHHHH
Confidence 467788999999999999999987665 5888888876542 11 344445432 23457788888
Q ss_pred HHhhc
Q 014547 397 VQEFT 401 (423)
Q Consensus 397 L~~~~ 401 (423)
|++..
T Consensus 71 L~~~g 75 (91)
T PF00585_consen 71 LKALG 75 (91)
T ss_dssp HTSSS
T ss_pred HHHcC
Confidence 87665
No 143
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=66.69 E-value=15 Score=34.61 Aligned_cols=47 Identities=17% Similarity=0.044 Sum_probs=37.7
Q ss_pred cEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEE
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVL 176 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVV 176 (423)
.+|++. .|+..+.-..+.+++.+++.+++.++++++|.+|++|..+.
T Consensus 132 ~~I~v~--~g~~~~~~l~~~~~~~~i~~~~~~~~~~~~L~~grvDa~i~ 178 (247)
T PRK09495 132 KVVAVK--SGTGSVDYAKANIKTKDLRQFPNIDNAYLELGTGRADAVLH 178 (247)
T ss_pred CEEEEe--cCchHHHHHHhcCCCCceEEcCCHHHHHHHHHcCceeEEEe
Confidence 378864 47766666666677778888999999999999999998875
No 144
>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=66.68 E-value=78 Score=26.68 Aligned_cols=31 Identities=16% Similarity=-0.038 Sum_probs=23.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEe
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+.++.-. .+..++.+.+++|++|+|+..
T Consensus 25 ~~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~ 56 (197)
T cd08440 25 RHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGS 56 (197)
T ss_pred hCCCcEEEEEeCChHHHHHHHHcCCccEEEEe
Confidence 3677665443 356889999999999999985
No 145
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=66.53 E-value=78 Score=31.02 Aligned_cols=116 Identities=16% Similarity=0.113 Sum_probs=60.3
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCC------C
Q 014547 147 AYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGV------R 219 (423)
Q Consensus 147 ~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~------~ 219 (423)
.+|+.++.. ..+-++++++|.+|++|+|+++..+... ..+ +..+.....+.++++.++. +
T Consensus 122 ~~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~-----------~~~--l~~~~l~~~~~~lv~~~~~pl~~~i~ 188 (312)
T PRK10341 122 VFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMK-----------LQD--LHVEPLFESEFVLVASKSRTCTGTTT 188 (312)
T ss_pred hCCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCcccc-----------cCC--eeEEEEecccEEEEEcCCCchhccCC
Confidence 357766543 3456899999999999999987543210 011 2222223334444443332 2
Q ss_pred cCcc---cEEEec--hhHHHHHHHHHHHcC--CceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 220 KEYL---TRVISH--PQALSQCEHTLTKLG--LNVAREAVDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 220 l~dI---k~VySH--PqAL~QC~~fL~~~~--p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
++|+ .-|.-- .....+..+|+.+++ ++. ...++|.....+.+..+ ...++.+...+
T Consensus 189 ~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 251 (312)
T PRK10341 189 LESLKNEQWVLPQTNMGYYSELLTTLQRNGISIEN-IVKTDSVVTIYNLVLNA---DFLTVIPCDMT 251 (312)
T ss_pred HHHHhCCCeEccCCCCcHHHHHHHHHHHcCcCCCc-eEEecCHHHHHHHHHhC---CcEEEeeHHhc
Confidence 2221 222211 112334455666653 332 34466677777777764 45677776654
No 146
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=65.73 E-value=17 Score=31.33 Aligned_cols=49 Identities=29% Similarity=0.309 Sum_probs=37.7
Q ss_pred cEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEee
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
.+|++.. |+..+......+++.+.+.+.+..+++.+|.+|++|+++++-
T Consensus 107 ~~i~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 155 (219)
T smart00062 107 KKVAVVA--GTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADA 155 (219)
T ss_pred CEEEEec--CccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEecc
Confidence 4787763 555555554455667888999999999999999999998863
No 147
>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=65.29 E-value=26 Score=28.65 Aligned_cols=58 Identities=16% Similarity=0.136 Sum_probs=41.1
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCc----ChHHHHHHHHHHHhh
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASM----AEVRAQNALAEVQEF 400 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~----~d~~v~~aL~eL~~~ 400 (423)
.++.||.+.++++.|+++|||+-.|-+ +. ..+.|-|+-..-. -+..++++..+|++.
T Consensus 11 ~~~~~g~~a~IF~~La~~~InVDmI~q-s~------------------~sISftV~~sd~~~~~~~~~~l~~~~~~~~~~ 71 (78)
T cd04933 11 MLGQYGFLAKVFSIFETLGISVDVVAT-SE------------------VSISLTLDPSKLWSRELIQQELDHVVEELEKD 71 (78)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe-cC------------------CEEEEEEEhhhhhhhhhHHHHHHHHHHHHHHc
Confidence 456799999999999999999999965 11 2577877653210 013566777777765
Q ss_pred c
Q 014547 401 T 401 (423)
Q Consensus 401 ~ 401 (423)
+
T Consensus 72 ~ 72 (78)
T cd04933 72 A 72 (78)
T ss_pred C
Confidence 5
No 148
>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=65.26 E-value=27 Score=33.44 Aligned_cols=57 Identities=12% Similarity=0.211 Sum_probs=43.9
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeee-eeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHH
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIE-SRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRA 390 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIE-SRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v 390 (423)
-..|++...|+||.+.++-+.|.+++||+..+. +|-.++ .+=+-.|.++....++-+
T Consensus 148 g~~L~~~~~D~PG~Ig~vg~~Lg~~~iNIa~m~v~r~~~g----------------~~Ai~vl~vD~~v~~~vl 205 (208)
T TIGR00719 148 HPAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIG----------------NIALLTIEIDKNIDDHIK 205 (208)
T ss_pred ccEEEEEeCCCCChHHHHHHHHHhCCccEEEEEEEecCCC----------------CEEEEEEEeCCCCCHHHH
Confidence 456788889999999999999999999997764 443332 356788899887776543
No 149
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=64.84 E-value=41 Score=33.82 Aligned_cols=63 Identities=8% Similarity=0.050 Sum_probs=42.8
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCc-----ChHHHHHHHH
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASM-----AEVRAQNALA 395 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~-----~d~~v~~aL~ 395 (423)
+.+.-+|+||-..++-+.|+.+|+|+..+.+.=... + . .|++-++.+. +-..++++|+
T Consensus 9 itv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~-----------~-----g-~F~m~i~v~~~~~~~~~~~L~~~L~ 71 (286)
T PRK06027 9 LTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPE-----------T-----G-RFFMRVEFEGDGLIFNLETLRADFA 71 (286)
T ss_pred EEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCC-----------C-----C-eEEEEEEEEeCCCCCCHHHHHHHHH
Confidence 334457999999999999999999999888764221 1 1 2444333322 3367888888
Q ss_pred HHHhh
Q 014547 396 EVQEF 400 (423)
Q Consensus 396 eL~~~ 400 (423)
+|.+.
T Consensus 72 ~l~~~ 76 (286)
T PRK06027 72 ALAEE 76 (286)
T ss_pred HHHHH
Confidence 87644
No 150
>PRK05007 PII uridylyl-transferase; Provisional
Probab=64.71 E-value=18 Score=41.95 Aligned_cols=35 Identities=23% Similarity=0.208 Sum_probs=29.5
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceee--eeee
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLT--KIES 351 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLt--kIES 351 (423)
..|.|=+..+|+||-|+++.++|.+.||++. ||-+
T Consensus 807 ~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T 843 (884)
T PRK05007 807 RRSYMELIALDQPGLLARVGKIFADLGISLHGARITT 843 (884)
T ss_pred CeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEec
Confidence 3566667788999999999999999999997 4554
No 151
>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=64.53 E-value=17 Score=39.55 Aligned_cols=104 Identities=15% Similarity=0.217 Sum_probs=66.9
Q ss_pred HHHHHHcCCceeecCcc--CCCCCeeEEEEEeeCCCC-C----CCC---------------CCCeEEEEEEeCCCccHHH
Q 014547 276 ARAAELYGMQVLEDGIQ--DDSSNVTRFVMLAREPII-P----RTD---------------RPFKTSIVFAHDKGTSVLF 333 (423)
Q Consensus 276 ~~AAelYgL~ILa~nIq--D~~~N~TRFlVLsr~~~~-~----~~~---------------~~~KTSivf~l~~~pGaL~ 333 (423)
...|+..|+++...... +...|.-++-+-+..... - ..+ .+.-..+++...|+||.+.
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 46789999998665433 235576666554332110 0 000 0123456777789999999
Q ss_pred HHHHHHHhCCceeeeee-eeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 334 KVLSAFAFRNISLTKIE-SRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 334 ~vL~~Fa~~~INLtkIE-SRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
++.+.+..++||+..+. +|-.++ .+.+..++++....++ ++++|++
T Consensus 467 ~v~~~L~~~~iNIa~m~~~R~~~g----------------~~al~~i~~D~~v~~~----~l~~i~~ 513 (525)
T TIGR01327 467 KVGTLLGTAGINIASMQLGRKEKG----------------GEALMLLSLDQPVPDE----VLEEIKA 513 (525)
T ss_pred HHHhHHhhcCCChHHcEeecCCCC----------------CeEEEEEEcCCCCCHH----HHHHHhc
Confidence 99999999999998764 554432 3678889998877644 4555543
No 152
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=64.08 E-value=75 Score=30.41 Aligned_cols=145 Identities=16% Similarity=0.058 Sum_probs=68.6
Q ss_pred CccEEEEeCCCccH-HHHHHh---hhCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEE
Q 014547 126 SQLRVAYQGVPGAY-SEAAAG---KAYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHI 200 (423)
Q Consensus 126 ~~~~VayLGP~GTf-Sh~AA~---~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 200 (423)
+..+|+.....+.+ --.+.. +.||+..+... .+..++.+.+.+|++|+|+++......+... ..|.+.++.+
T Consensus 91 ~~i~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~ 167 (296)
T PRK11242 91 GSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA---QPLFTETLAL 167 (296)
T ss_pred eEEEEEeccchhhhhhHHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCCCCcceeE---EEeeeccEEE
Confidence 45777764333322 111111 23577766554 4568899999999999999865432222110 1122222222
Q ss_pred EEEEEEeeeeeeeecCC-CCcCc---ccEEEechhHH--HHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEE
Q 014547 201 VGEVQLPVHHCLLALPG-VRKEY---LTRVISHPQAL--SQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAI 273 (423)
Q Consensus 201 vgEi~lpI~h~Lla~~g-~~l~d---Ik~VySHPqAL--~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAI 273 (423)
+. +-.|-|...+. .++++ -.-|.-.+... ..-.+|+.+++...+. ..+++-..+.+.+..+ ...++
T Consensus 168 ~~----~~~~pl~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~ 240 (296)
T PRK11242 168 VV----GRHHPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG---RLATL 240 (296)
T ss_pred EE----cCCCcccccCCCcCHHHHhCCCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhC---CeEEE
Confidence 21 11222221111 12222 22343333321 2334566665433332 3355556666777764 34667
Q ss_pred ccHHHHH
Q 014547 274 ASARAAE 280 (423)
Q Consensus 274 aS~~AAe 280 (423)
.++..++
T Consensus 241 ~p~~~~~ 247 (296)
T PRK11242 241 LPAAIAR 247 (296)
T ss_pred eehhhcc
Confidence 7766544
No 153
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=63.87 E-value=43 Score=32.30 Aligned_cols=94 Identities=12% Similarity=0.068 Sum_probs=54.1
Q ss_pred cEEEEeCCCccHHHHHHhhh----CCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEE
Q 014547 128 LRVAYQGVPGAYSEAAAGKA----YPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGE 203 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~----f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgE 203 (423)
.+||+ ..||..+....++ ..+.+++.+++..+++++|..|++|..+.. ..+ +..+.+....++++
T Consensus 149 ~~V~v--~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~d------~~~---~~~~~~~~~~~~~~ 217 (259)
T PRK11917 149 ANIGV--AQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVD------KSI---LLGYVDDKSEILPD 217 (259)
T ss_pred CeEEE--ecCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEec------HHH---HHHhhhcCCeecCC
Confidence 47888 4556555433222 223567788999999999999999977552 111 11112223344444
Q ss_pred EEEeeeeeeeecCCCCcCcccEEEechhHHHHHHHHHHHc
Q 014547 204 VQLPVHHCLLALPGVRKEYLTRVISHPQALSQCEHTLTKL 243 (423)
Q Consensus 204 i~lpI~h~Lla~~g~~l~dIk~VySHPqAL~QC~~fL~~~ 243 (423)
..-+..++++.+++ +++-..+..++|.++
T Consensus 218 ~~~~~~~~~a~~k~-----------~~~l~~~ln~~l~~~ 246 (259)
T PRK11917 218 SFEPQSYGIVTKKD-----------DPAFAKYVDDFVKEH 246 (259)
T ss_pred cCCCCceEEEEeCC-----------CHHHHHHHHHHHHHH
Confidence 33344455555543 245567777777664
No 154
>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=62.60 E-value=95 Score=26.24 Aligned_cols=34 Identities=15% Similarity=0.017 Sum_probs=25.2
Q ss_pred hhCCCCceeec-CCHHHHHHHHHcCCcCeEEEeec
Q 014547 146 KAYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVE 179 (423)
Q Consensus 146 ~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIE 179 (423)
+.+|+.++... .+-.++.+.+.+|++|+|+..-.
T Consensus 24 ~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (194)
T cd08436 24 RRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLP 58 (194)
T ss_pred HHCCCcEEEEecCCHHHHHHHHHcCCccEEEEecC
Confidence 34677665443 35678999999999999998643
No 155
>TIGR00655 PurU formyltetrahydrofolate deformylase. This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.
Probab=62.59 E-value=44 Score=33.64 Aligned_cols=65 Identities=8% Similarity=0.128 Sum_probs=44.2
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEE--EEEecC-cChHHHHHHHHH-
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFY--IDFEAS-MAEVRAQNALAE- 396 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~Ff--ID~eg~-~~d~~v~~aL~e- 396 (423)
|.+.-+|+||-.+++=+.++++|+|++.+...-.... ..|.-. +|+.+. .+.+.++++|++
T Consensus 3 itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~---------------~~F~mr~~v~~~~~~~~~~~l~~~l~~~ 67 (280)
T TIGR00655 3 LLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPET---------------GRFFMRVEFQLEGFRLEESSLLAAFKSA 67 (280)
T ss_pred EEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCC---------------CeEEEEEEEEeCCCCCCHHHHHHHHHHH
Confidence 4455689999999999999999999998877643211 122222 344332 345788888888
Q ss_pred HHhh
Q 014547 397 VQEF 400 (423)
Q Consensus 397 L~~~ 400 (423)
+.+.
T Consensus 68 ~~~~ 71 (280)
T TIGR00655 68 LAEK 71 (280)
T ss_pred HHHH
Confidence 6543
No 156
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=62.47 E-value=94 Score=28.85 Aligned_cols=116 Identities=14% Similarity=0.097 Sum_probs=63.0
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCC----CcCccc-
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGV----RKEYLT- 224 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~----~l~dIk- 224 (423)
+.++++. +..++++++++|++|+++.++..+.+- . + .+.... -.......++.+.+. .+++++
T Consensus 64 ~~~~~~~-~~~~~~~~l~~G~~D~~~~~~~~~~~r----~-~-----~~~~s~-p~~~~~~~~~~~~~~~~~~~~~dl~g 131 (250)
T TIGR01096 64 KCKFVEQ-NFDGLIPSLKAKKVDAIMATMSITPKR----Q-K-----QIDFSD-PYYATGQGFVVKKGSDLAKTLEDLDG 131 (250)
T ss_pred eEEEEeC-CHHHHHHHHhCCCcCEEEecCccCHHH----h-h-----cccccc-chhcCCeEEEEECCCCcCCChHHcCC
Confidence 5678884 689999999999999886543211110 0 0 011111 111112333333322 122221
Q ss_pred -EEEechhHHHHHHHHHHHcCC-ceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 225 -RVISHPQALSQCEHTLTKLGL-NVAREAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 225 -~VySHPqAL~QC~~fL~~~~p-~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
+|-. .....+ ..++.+.++ ++.++.+.|..++.+++..+ +-.++|.....+..
T Consensus 132 ~~i~~-~~g~~~-~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g--~vD~~v~~~~~~~~ 186 (250)
T TIGR01096 132 KTVGV-QSGTTH-EQYLKDYFKPGVDIVEYDSYDNANMDLKAG--RIDAVFTDASVLAE 186 (250)
T ss_pred CEEEE-ecCchH-HHHHHHhccCCcEEEEcCCHHHHHHHHHcC--CCCEEEeCHHHHHH
Confidence 3322 222222 245666555 66777888999999998876 46777777665544
No 157
>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=60.77 E-value=1.1e+02 Score=26.31 Aligned_cols=32 Identities=9% Similarity=-0.198 Sum_probs=24.9
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEee
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
.+|+.++... .+-+++.+.+.+|++|+|++.-
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (198)
T cd08437 25 TGLMIQIDTYEGGSAELLEQLLQGDLDIALLGS 57 (198)
T ss_pred hCCceEEEEEEcCHHHHHHHHHcCCCCEEEecC
Confidence 4677766544 3578899999999999999853
No 158
>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=59.65 E-value=1.1e+02 Score=26.13 Aligned_cols=123 Identities=15% Similarity=0.109 Sum_probs=59.2
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcC---c
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKE---Y 222 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~---d 222 (423)
.+|+.++... .+.+++.+.+.+|++|+|+.+-.....+.. ...|.+..+.++ .+-+|-|...+..+++ +
T Consensus 26 ~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~ 98 (198)
T cd08446 26 ARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIA---VENVAQERLYLA----VPKSHPLAARPAVSLADLRN 98 (198)
T ss_pred HCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecCCCCCCce---eEEeeeccEEEE----EeCCCCcccCCccCHHHHcC
Confidence 4677665443 356778899999999999975321111110 011222222222 2223333221112222 2
Q ss_pred ccEEE-ech---hHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 223 LTRVI-SHP---QALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 223 Ik~Vy-SHP---qAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
..-|. ... ....+...|+++.+.... ...++|...+.+.++.+ ...++.++..+
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 157 (198)
T cd08446 99 EPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAG---FGVCIVPESVA 157 (198)
T ss_pred CCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcC---CcEEEchhhhh
Confidence 33343 111 112334556666543222 23466777777777764 45777776544
No 159
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form 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 bin
Probab=59.36 E-value=1e+02 Score=25.52 Aligned_cols=116 Identities=16% Similarity=0.108 Sum_probs=60.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCC------
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVR------ 219 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~------ 219 (423)
.+|+.++... .+-+++++.+.+|++|+|+........ + +..+.......++++.++..
T Consensus 25 ~~p~i~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~-------------~--~~~~~l~~~~~~~~~~~~~~~~~~~~ 89 (197)
T cd05466 25 RYPGVELSLVEGGSSELLEALLEGELDLAIVALPVDDP-------------G--LESEPLFEEPLVLVVPPDHPLAKRKS 89 (197)
T ss_pred HCCCCEEEEEECChHHHHHHHHcCCceEEEEcCCCCCC-------------c--ceEeeeeccceEEEecCCCCcccCcE
Confidence 3566554332 234689999999999999986442111 1 12222333445555544321
Q ss_pred --cCccc--EEEechh---HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 220 --KEYLT--RVISHPQ---ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 220 --l~dIk--~VySHPq---AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
++++. .++.+.. ...+..+|+.++..... ...+++...+.+.+..+ ...++.+...+.
T Consensus 90 ~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~---~g~~~~p~~~~~ 155 (197)
T cd05466 90 VTLADLADEPLILFERGSGLRRLLDRAFAEAGFTPNIALEVDSLEAIKALVAAG---LGIALLPESAVE 155 (197)
T ss_pred ecHHHHcCCCEEEecCCchHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHhC---CCEEEehHHHHh
Confidence 22221 1222221 23445567776654333 33456666677777764 356666665554
No 160
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=59.20 E-value=1.2e+02 Score=30.13 Aligned_cols=144 Identities=19% Similarity=0.146 Sum_probs=72.8
Q ss_pred CccEEEEeCCCccHHHH----HHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEE
Q 014547 126 SQLRVAYQGVPGAYSEA----AAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIV 201 (423)
Q Consensus 126 ~~~~VayLGP~GTfSh~----AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Iv 201 (423)
...+||+...-+.+-=. +..+.+|+.++... ...++++.|.+|++|+|+.+-.....+... ..|.+..+.++
T Consensus 117 ~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~lv 192 (317)
T PRK11482 117 RTITIATTPSVGALVMPVIYQAIKTHYPQLLLRNI-PISDAENQLSQFQTDLIIDTHSCSNRTIQH---HVLFTDNVVLV 192 (317)
T ss_pred ceEEEEecHHHHHHHHHHHHHHHHHHCCCCEEEEe-cchhHHHHHHCCCcCEEEeccCCCCCceEE---EEEecCcEEEE
Confidence 35677776554432111 12234677765432 446789999999999999865432222211 12223333322
Q ss_pred EEEEEeeeeeeeecCCCCcCcccE----E-EechhHHHHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEEcc
Q 014547 202 GEVQLPVHHCLLALPGVRKEYLTR----V-ISHPQALSQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAIAS 275 (423)
Q Consensus 202 gEi~lpI~h~Lla~~g~~l~dIk~----V-ySHPqAL~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAIaS 275 (423)
.+-.|-|... ..+++++.. + ..........++++.+.+..... ..+.+.......++.+ ...+|.+
T Consensus 193 ----~~~~hpl~~~-~~~~~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~ilp 264 (317)
T PRK11482 193 ----CRQGHPLLSL-EDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASS---DMLGIMP 264 (317)
T ss_pred ----EeCCCCccCC-CCCHHHHhhCCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcC---CeeEEeH
Confidence 3344544332 344555542 2 22222222345556554433332 2345555566666654 5677877
Q ss_pred HHHHHH
Q 014547 276 ARAAEL 281 (423)
Q Consensus 276 ~~AAel 281 (423)
...+..
T Consensus 265 ~~~~~~ 270 (317)
T PRK11482 265 SRFYNL 270 (317)
T ss_pred HHHHHH
Confidence 776654
No 161
>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=58.83 E-value=61 Score=27.81 Aligned_cols=125 Identities=20% Similarity=0.169 Sum_probs=63.0
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCccc-
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLT- 224 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk- 224 (423)
.||+.++.... +-+++.+.+.+|++|+|++.......+.. ...|.+.++.++..- .|-+.. +..+++++.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~---~~~l~~~~~~lv~~~----~~p~~~-~~~~~~~L~~ 96 (198)
T cd08461 25 EAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLR---SRPLFEERYVCVTRR----GHPLLQ-GPLSLDQFCA 96 (198)
T ss_pred HCCCcEEEEeeCCcccHHHHHhcCCCcEEEecCccCCccce---eeeeecCcEEEEEcC----CChhhc-CCCCHHHHhh
Confidence 46777665543 45678899999999999985332111111 112223333333222 222221 112222222
Q ss_pred --EEEechhH---HHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHc
Q 014547 225 --RVISHPQA---LSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAELY 282 (423)
Q Consensus 225 --~VySHPqA---L~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelY 282 (423)
-|.-++.. -.+-.+|+.+++...+ ...++|...+...+..+ ...||.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~ 157 (198)
T cd08461 97 LDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAAT---DMVAFVPSRLVPNL 157 (198)
T ss_pred CCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcC---CeEEEchHHHHHhh
Confidence 23322211 1235566766543222 23456666666777664 57888888776654
No 162
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=58.27 E-value=1.4e+02 Score=29.26 Aligned_cols=122 Identities=13% Similarity=0.036 Sum_probs=60.3
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccC-CCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc-
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENS-LGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL- 223 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS-~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI- 223 (423)
.+|+.++... .+..++.+.|.+|++|+|+.+-... ..+ + ....|.+.++. +..+..|-|...+..+++++
T Consensus 118 ~~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~-l--~~~~l~~~~~~----~v~~~~hpl~~~~~~~~~~L~ 190 (309)
T PRK12683 118 VFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPD-L--VSFPYYSWHHV----VVVPKGHPLTGRENLTLEAIA 190 (309)
T ss_pred HCCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCC-c--eEEEcccCeEE----EEecCCCCcccCCccCHHHHh
Confidence 3677765433 4678999999999999999752211 111 1 11122222322 22344444433322333333
Q ss_pred --cEEEech--hHHHHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEEccHHH
Q 014547 224 --TRVISHP--QALSQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAIASARA 278 (423)
Q Consensus 224 --k~VySHP--qAL~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAIaS~~A 278 (423)
.-|.-.+ .--.+...|+.+.+..... ..++|.....+.+..+ ...++.+...
T Consensus 191 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~ 247 (309)
T PRK12683 191 EYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELG---MGVGIVAAMA 247 (309)
T ss_pred cCCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhC---CCeEEeehhh
Confidence 3333211 1234567777776533332 3345555555666654 2344445433
No 163
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=58.26 E-value=1.1e+02 Score=28.76 Aligned_cols=116 Identities=17% Similarity=0.149 Sum_probs=66.1
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhh-cCCcEEEEEEEE-----eeeeeeeecCCCC---c
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLL-RHRLHIVGEVQL-----PVHHCLLALPGVR---K 220 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~-~~~L~IvgEi~l-----pI~h~Lla~~g~~---l 220 (423)
.+++++..++.+..+++.+|++|+++++ ...+-.+. +.++..++...- ..+-.++++++.. +
T Consensus 30 ~v~~~~~~~~~~~~~~l~~g~~D~~~~~---------~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds~i~~l 100 (243)
T PF12974_consen 30 PVELVPADDYAEFIEALRSGEIDLAFMG---------PLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADSPITSL 100 (243)
T ss_dssp EEEEE--SSHHHHHHHHHTTS-SEEE-----------HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTSS--SH
T ss_pred CEEEEEcCCHHHHHHHHHcCCccEEEEC---------cHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCCCCCCh
Confidence 3678999999999999999999999886 22333333 457777776665 3344466776653 3
Q ss_pred Ccc---cEEEechhH---HHHHHHHH-HHcCCc----eeEEeccCHHHHHHHHHhcCCCCeeEEcc
Q 014547 221 EYL---TRVISHPQA---LSQCEHTL-TKLGLN----VAREAVDDTAGAAEYIAANDLRDTAAIAS 275 (423)
Q Consensus 221 ~dI---k~VySHPqA---L~QC~~fL-~~~~p~----~~~v~~~STA~AA~~va~~~~~~~AAIaS 275 (423)
+|+ +-.+..|.. .--.+.+| ++++.. .+.+++.+-..+++.|..+. -+.|++.+
T Consensus 101 ~dL~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~-~Da~~~~~ 165 (243)
T PF12974_consen 101 ADLKGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGK-ADAAAIPS 165 (243)
T ss_dssp HHHGGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTS-SSEEEEEH
T ss_pred hhcCCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCC-ccEEEEec
Confidence 344 234445553 33455666 565533 24456667778888888753 34455444
No 164
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=58.22 E-value=31 Score=39.93 Aligned_cols=31 Identities=19% Similarity=0.164 Sum_probs=27.9
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceee
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLT 347 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLt 347 (423)
..|.|=+..+|+||-|+++.++|.+.||++.
T Consensus 782 ~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~ 812 (854)
T PRK01759 782 EQTEMELFALDRAGLLAQVSQVFSELNLNLL 812 (854)
T ss_pred CeEEEEEEeCCchHHHHHHHHHHHHCCCEEE
Confidence 4677778889999999999999999999987
No 165
>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=57.11 E-value=1.3e+02 Score=25.92 Aligned_cols=121 Identities=17% Similarity=0.041 Sum_probs=58.8
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc--
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL-- 223 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI-- 223 (423)
.+|+.++.... +-+++++.+.+|++|+|++.......+.. ...|.+..+.++ .+-.|.|...+..+++++
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08457 25 LRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGF---LIETRSLPAVVA----VPMGHPLAQLDVVSPQDLAG 97 (196)
T ss_pred HCCCeEEEEEecCcHHHHHHHHcCCccEEEeccCCCCCCcE---EEEeccCCeEEE----eeCCCccccCCccCHHHhCC
Confidence 46776655443 34788999999999999986432211111 011222222221 223344433222333333
Q ss_pred -cEEE-echh-HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHH
Q 014547 224 -TRVI-SHPQ-ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASAR 277 (423)
Q Consensus 224 -k~Vy-SHPq-AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~ 277 (423)
.-|. ++.. ......+++.+++.... ...+++...+.+.++.+ ...++.+..
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~ 152 (196)
T cd08457 98 ERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREG---LGIAIIDPA 152 (196)
T ss_pred CceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcC---CeEEEEChH
Confidence 3333 2222 23446667776543222 33455555666666654 345565544
No 166
>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=56.53 E-value=56 Score=28.20 Aligned_cols=116 Identities=16% Similarity=0.121 Sum_probs=64.2
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCc---Cccc--
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRK---EYLT-- 224 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l---~dIk-- 224 (423)
+.++++.. ..++++++.+|++|+++.+....- .-.+.+ .+. +......+.++++++..+ +|++
T Consensus 39 ~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~-----~~~~~~-----~~~-~~~~~~~~~~~~~~~~~~~~~~dl~g~ 106 (218)
T cd00134 39 KVKFVEVD-WDGLITALKSGKVDLIAAGMTITP-----ERAKQV-----DFS-DPYYKSGQVILVKKGSPIKSVKDLKGK 106 (218)
T ss_pred eEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCH-----HHHhhc-----cCc-ccceeccEEEEEECCCCCCChHHhCCC
Confidence 45677777 789999999999999988752111 111111 111 122223455666655432 2322
Q ss_pred EEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 225 RVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 225 ~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
+|..- .. .-...++.+.........+.+..++.+++..+ ...|++.....+..
T Consensus 107 ~i~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~~~~~ 159 (218)
T cd00134 107 KVAVQ-KG-STAEKYLKKALPEAKVVSYDDNAEALAALENG--RADAVIVDEIALAA 159 (218)
T ss_pred EEEEE-cC-chHHHHHHHhCCcccEEEeCCHHHHHHHHHcC--CccEEEeccHHHHH
Confidence 22221 11 11234555544345567788888899998876 35677766654443
No 167
>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=56.20 E-value=1.3e+02 Score=26.22 Aligned_cols=124 Identities=17% Similarity=0.039 Sum_probs=59.5
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc--
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL-- 223 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI-- 223 (423)
.+|+.++.... +-.++.+.+.+|++|+|+.+-.....+.+ ....|.+.++. +..+..|-|......+++++
T Consensus 25 ~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~--~~~~l~~~~~~----~v~~~~hpl~~~~~i~~~~l~~ 98 (198)
T cd08413 25 RYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDL--VTLPCYRWNHC----VIVPPGHPLADLGPLTLEDLAQ 98 (198)
T ss_pred hCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCc--EEEEeeeeeEE----EEecCCCcccccCCCCHHHHhc
Confidence 46776665444 45788999999999999985211000100 00111111111 11233343432222333332
Q ss_pred -cEEEech-h-HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 224 -TRVISHP-Q-ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 224 -k~VySHP-q-AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
+-|.-.. . -..+.+.|+++.+.... ...++|......+++.+ ...|+.++..+
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~ 155 (198)
T cd08413 99 YPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLG---LGVGIIAEMAY 155 (198)
T ss_pred CCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhC---CCEEEcccccc
Confidence 2333111 1 23445566666543222 33456777777777765 34566666443
No 168
>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=56.19 E-value=1.4e+02 Score=26.05 Aligned_cols=50 Identities=18% Similarity=0.055 Sum_probs=32.7
Q ss_pred cEEEEeCCCccH--HHH--HHhhhCCCCceeecC-CHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAY--SEA--AAGKAYPNCEAIPCD-QFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTf--Sh~--AA~~~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|++....+.+ ... +-++.+|+.++.... +.+++++++.+|++|+|+++
T Consensus 3 l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~ 57 (198)
T cd08485 3 LRVAYFGTVVLHTLPLLLRQLLSVAPSATVSLTQMSKNRQIEALDAGTIDIGFGR 57 (198)
T ss_pred EEEEEeccchhHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHcCCccEEEec
Confidence 566666544432 221 122346887765543 67789999999999999985
No 169
>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=55.95 E-value=1.3e+02 Score=25.54 Aligned_cols=115 Identities=13% Similarity=0.011 Sum_probs=59.3
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCC--------
Q 014547 148 YPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGV-------- 218 (423)
Q Consensus 148 f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~-------- 218 (423)
+|+.++... .+.+++.+.+.+|++|+|++.-+.- ..+ +..+.......++++.++-
T Consensus 26 ~p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~-------------~~~--~~~~~l~~~~~~~v~~~~~~l~~~~~~ 90 (197)
T cd08414 26 YPDVELELREMTTAEQLEALRAGRLDVGFVRPPPD-------------PPG--LASRPLLREPLVVALPADHPLAARESV 90 (197)
T ss_pred CCCcEEEEecCChHHHHHHHHcCCccEEEEcCCCC-------------CCC--eeEEEEeeccEEEEecCCCccccCCcc
Confidence 576665443 3568899999999999999864321 111 1222222334444443332
Q ss_pred C---cCcccEEEech----hHHHHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 219 R---KEYLTRVISHP----QALSQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 219 ~---l~dIk~VySHP----qAL~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
+ +.+..-|.-.. .-..+...|+.+++..... ..++|...+.+++..+ ...++.+...++
T Consensus 91 ~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08414 91 SLADLADEPFVLFPREPGPGLYDQILALCRRAGFTPRIVQEASDLQTLLALVAAG---LGVALVPASVAR 157 (197)
T ss_pred CHHHhccCCEEEecCCcchhHHHHHHHHHHHcCCCcccceecccHHHHHHHHHcC---CcEEEccChhhh
Confidence 1 22222333221 1224566677766433222 3355566666666654 356666665443
No 170
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=55.95 E-value=1.3e+02 Score=32.13 Aligned_cols=114 Identities=18% Similarity=0.120 Sum_probs=60.3
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCC----CcCccc-
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGV----RKEYLT- 224 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~----~l~dIk- 224 (423)
+.+++...+++++++++++|++|+++..+-- |-+- +..+. ...-++.+...|+.+++. ++++++
T Consensus 81 ~~e~v~~~~~~~ll~aL~~G~iDi~~~~lt~--------T~eR--~~~~~-FS~Py~~~~~~lv~r~~~~~i~~l~dL~G 149 (482)
T PRK10859 81 KLEIKVRDNISQLFDALDKGKADLAAAGLTY--------TPER--LKQFR-FGPPYYSVSQQLVYRKGQPRPRSLGDLKG 149 (482)
T ss_pred cEEEEecCCHHHHHHHHhCCCCCEEeccCcC--------Chhh--hccCc-ccCCceeeeEEEEEeCCCCCCCCHHHhCC
Confidence 4677778999999999999999976433211 1110 01111 111223345556655542 223332
Q ss_pred -EEEe-----chhHHHHHHHHHHHcCCceeE--EeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 225 -RVIS-----HPQALSQCEHTLTKLGLNVAR--EAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 225 -~VyS-----HPqAL~QC~~fL~~~~p~~~~--v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
+|.. +.+.+ +++ .+.+|++.+ +...++.++.+.|..+ .-.++|+....+.
T Consensus 150 k~I~V~~gS~~~~~L---~~l-~~~~p~i~~~~~~~~s~~e~l~aL~~G--~iDa~v~d~~~~~ 207 (482)
T PRK10859 150 GTLTVAAGSSHVETL---QEL-KKKYPELSWEESDDKDSEELLEQVAEG--KIDYTIADSVEIS 207 (482)
T ss_pred CeEEEECCCcHHHHH---HHH-HHhCCCceEEecCCCCHHHHHHHHHCC--CCCEEEECcHHHH
Confidence 3322 22222 122 223455443 3346788899998876 3567777655443
No 171
>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=55.93 E-value=1.4e+02 Score=25.95 Aligned_cols=32 Identities=13% Similarity=-0.004 Sum_probs=23.9
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCcCeEEEee
Q 014547 147 AYPNCEAIPCDQFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 147 ~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
.+|+.++.....-.+.++.|++|++|+|+++-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~l~~g~~D~~i~~~ 56 (200)
T cd08462 25 EAPGVRFELLPPDDQPHELLERGEVDLLIAPE 56 (200)
T ss_pred HCCCCEEEEecCChhHHHHHhcCCeeEEEecC
Confidence 46776654443223999999999999999863
No 172
>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=55.60 E-value=1.6e+02 Score=26.75 Aligned_cols=108 Identities=12% Similarity=0.021 Sum_probs=69.1
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc-----c
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL-----T 224 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI-----k 224 (423)
+++++...+-.++++++..|++|+|+.... ......-...++++++...-.-...|+++++..+.++ |
T Consensus 22 ~ve~~~~~~~~~~~~~l~~G~~D~~~~~~~-------~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DLkGK 94 (216)
T PF09084_consen 22 DVEIVFFGGGGDVLEALASGKADIAVAGPD-------AVLFARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADLKGK 94 (216)
T ss_dssp EEEEEEESSHHHHHHHHHTTSHSEEEEECH-------HHHHHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGGTTS
T ss_pred EEEEEEecChhHHHHHHhcCCceEEeccch-------HHHHHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHhCCC
Confidence 468899999999999999999999987644 1111111235788888776555577888877544444 3
Q ss_pred EEEech--hHHHHHHHHHHHcCC---ceeEEeccCHHHHHHHHHhc
Q 014547 225 RVISHP--QALSQCEHTLTKLGL---NVAREAVDDTAGAAEYIAAN 265 (423)
Q Consensus 225 ~VySHP--qAL~QC~~fL~~~~p---~~~~v~~~STA~AA~~va~~ 265 (423)
+|...+ .....-+.+|++++. +++.+.. +....+..+..+
T Consensus 95 ~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~-~~~~~~~al~~g 139 (216)
T PF09084_consen 95 KIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNL-GPPELAQALLSG 139 (216)
T ss_dssp EEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTT
T ss_pred EEEEecCcchhHHHHHHHHHhccccccceeeee-ehhhhhhhhhcC
Confidence 666555 345556678887753 3444443 345555566654
No 173
>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=55.58 E-value=1.4e+02 Score=25.98 Aligned_cols=125 Identities=13% Similarity=0.063 Sum_probs=60.2
Q ss_pred hhCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCccc
Q 014547 146 KAYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLT 224 (423)
Q Consensus 146 ~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk 224 (423)
+.+|+.++... .+.+++.+.+.+|++|+|+..-.-.....+. ...|.+.++.++ .+-+|.+......+++++.
T Consensus 24 ~~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~~~v----~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08443 24 ERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLI--TLPCYHWNRCVV----VKRDHPLADKQSISIEELA 97 (198)
T ss_pred HHCCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccccccCCce--EeeeeeceEEEE----EcCCCccccCCCCCHHHHh
Confidence 34677765444 4678899999999999999742100001110 111222222222 2223333322222333332
Q ss_pred --EEEechh--H-HHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 225 --RVISHPQ--A-LSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 225 --~VySHPq--A-L~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
.+.+++. . ......++++++.... ...+++.....++++.+ ...|+.+...+
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~~p~~~~ 155 (198)
T cd08443 98 TYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLG---LGVGVIASMAY 155 (198)
T ss_pred cCCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CcEEEeecccc
Confidence 1223332 2 2234456665543322 33456777777777764 34556565443
No 174
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=55.38 E-value=33 Score=36.59 Aligned_cols=70 Identities=23% Similarity=0.416 Sum_probs=52.0
Q ss_pred EeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcCc
Q 014547 324 AHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTSF 403 (423)
Q Consensus 324 ~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~~ 403 (423)
...|+.|-.-++|..+..++|||..||=-|.. ..|++|- .++-..++.++.+|+..
T Consensus 6 ~cedRlGltrelLdlLv~r~idl~~iEid~~~--------------------~IYln~p-~l~~~~fs~L~aei~~I--- 61 (511)
T COG3283 6 FCEDRLGLTRELLDLLVLRGIDLRGIEIDPIG--------------------RIYLNFP-ELEFESFSSLMAEIRRI--- 61 (511)
T ss_pred EehhhhchHHHHHHHHHhcccCccceeecCCC--------------------eEEEecc-ccCHHHHHHHHHHHhcC---
Confidence 34578999999999999999999999985543 4677774 35667788888888743
Q ss_pred eEEEccccCCCCCCCCC
Q 014547 404 LRVLGSYPMDMTPWSPS 420 (423)
Q Consensus 404 vrvLGsYp~~~~pw~p~ 420 (423)
=|..-+...+|-|+
T Consensus 62 ---~GV~~vr~V~~mPs 75 (511)
T COG3283 62 ---PGVTDVRTVPWMPS 75 (511)
T ss_pred ---CCccceeeecCCcc
Confidence 34444455677775
No 175
>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=55.30 E-value=60 Score=23.51 Aligned_cols=27 Identities=22% Similarity=0.236 Sum_probs=23.8
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
+.+.++.+.++++.+++++|++-.|..
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04923 10 MRSHPGVAAKMFKALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEc
Confidence 556789999999999999999988864
No 176
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=54.89 E-value=32 Score=37.27 Aligned_cols=58 Identities=19% Similarity=0.316 Sum_probs=43.9
Q ss_pred EEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 322 VFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 322 vf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
-+...|+.|.-.++|..|..++|||.-||=-|.. ..|++|. .++....+.+++++++.
T Consensus 4 ~~~~~dr~g~~~~~l~~~~~~~~~~~~~e~~~~~--------------------~~~~~~~-~~~~~~~~~~~~~~~~~ 61 (520)
T PRK10820 4 EVFCEDRLGLTRELLDLLVLRSIDLRGIEIDPIG--------------------RIYLNFA-ELEFESFSSLMAEIRRI 61 (520)
T ss_pred EEEeeccccHHHHHHHHHHhcCCCccEEEEcCCC--------------------eEEEeCC-CcChhhHHHHHHHHhcC
Confidence 3455689999999999999999999999964432 3677886 35555667778887543
No 177
>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=54.52 E-value=1.4e+02 Score=25.73 Aligned_cols=116 Identities=17% Similarity=0.049 Sum_probs=70.0
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCC-------
Q 014547 147 AYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGV------- 218 (423)
Q Consensus 147 ~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~------- 218 (423)
.+|+.++.. ..+..++++.+.+|++|+|+..... ...+ +..+.....++++++.++-
T Consensus 31 ~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~-------------~~~~--~~~~~l~~~~~~~~~~~~~pl~~~~~ 95 (209)
T PF03466_consen 31 RHPNIRIEIREGDSDELIEALRSGELDLAITFGPP-------------PPPG--LESEPLGEEPLVLVVSPDHPLAQKKP 95 (209)
T ss_dssp HSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSS-------------SSTT--EEEEEEEEEEEEEEEETTSGGGTTSS
T ss_pred HCCCcEEEEEeccchhhhHHHhcccccEEEEEeec-------------cccc--cccccccceeeeeeeecccccccccc
Confidence 467766533 3555899999999999999997653 1112 3334444555666655442
Q ss_pred -CcCcc---cEEEe--chhHHHHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 219 -RKEYL---TRVIS--HPQALSQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 219 -~l~dI---k~VyS--HPqAL~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
+++++ ..|.- ...-..+..+++.+++..... ..++|...+..+++.+ ...+|.+...++
T Consensus 96 i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 161 (209)
T PF03466_consen 96 ITLEDLADYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASG---DGIAILPDSLAQ 161 (209)
T ss_dssp SSGGGGTTSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTT---SEBEEEEHHHHH
T ss_pred chhhhhhhccccccccccccccccccccccccccccccccccchhhhccccccc---cceeecCccccc
Confidence 23333 33332 223556677777776543333 4466777777777764 577888877764
No 178
>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=54.39 E-value=1.1e+02 Score=25.94 Aligned_cols=31 Identities=10% Similarity=-0.030 Sum_probs=23.0
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEe
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+.++.... +-.++.+.+.+|++|+|+..
T Consensus 25 ~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08456 25 RHPDVTISIHTRDSPTVEQWLSAQQCDLGLVS 56 (196)
T ss_pred HCCCcEEEEEeCCHHHHHHHHHcCCccEEEEe
Confidence 46776654433 45678899999999999975
No 179
>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=54.26 E-value=2.1e+02 Score=27.54 Aligned_cols=124 Identities=17% Similarity=0.155 Sum_probs=61.3
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCC--CCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSL--GGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL 223 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~--~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI 223 (423)
.||+.++.... +-.++++++.+|++|+|++...+.. .+. .+.-|.+.++.++. +-.|-|...+..+++|+
T Consensus 118 ~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~~~l~~~~~~~~~----~~~hpl~~~~~i~~~dL 190 (300)
T TIGR02424 118 RAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGL---SFEHLYNEPVVFVV----RAGHPLLAAPSLPVASL 190 (300)
T ss_pred hCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCcccccce---eeeeecCCceEEEE----cCCCccccCCCCCHHHH
Confidence 46777665443 6678999999999999997543221 110 01112222222221 22233332222233333
Q ss_pred cE--EEechhH---HHHHHHHHHHcCCc--eeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 224 TR--VISHPQA---LSQCEHTLTKLGLN--VAREAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 224 k~--VySHPqA---L~QC~~fL~~~~p~--~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
.. .+..+.. -.....|+.+++.. -....+.+......++..+ ...++.+...++
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 13345677665422 1234566666677777664 346677766664
No 180
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=54.12 E-value=1.9e+02 Score=26.97 Aligned_cols=146 Identities=12% Similarity=0.089 Sum_probs=69.5
Q ss_pred CccEEEEeCCCccH--HHH--HHhhhCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEE
Q 014547 126 SQLRVAYQGVPGAY--SEA--AAGKAYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHI 200 (423)
Q Consensus 126 ~~~~VayLGP~GTf--Sh~--AA~~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 200 (423)
...+||.-...+.. ... ...+.+|+.++... .+.+++.+.+.+|++|+|++...+...+.+ ....|...++.+
T Consensus 67 ~~l~I~~~~~~~~~~~~~~l~~~~~~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~--~~~~l~~~~~~~ 144 (269)
T PRK11716 67 GELSLFCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASV--AFSPIDEIPLVL 144 (269)
T ss_pred ceEEEEecchHHHHHHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcce--EEEEcccceEEE
Confidence 35677654433321 221 12234677665443 577899999999999999985433222111 112223333333
Q ss_pred EEEEEEeeeeeeeecC-C---CCcCcccEEEe-chhHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEc
Q 014547 201 VGEVQLPVHHCLLALP-G---VRKEYLTRVIS-HPQALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIA 274 (423)
Q Consensus 201 vgEi~lpI~h~Lla~~-g---~~l~dIk~VyS-HPqAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIa 274 (423)
+. +-+|.+.... . .++.+..-|.. .......-..|+..++...+ ...++|.....+.+..+ ...++.
T Consensus 145 v~----~~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~ 217 (269)
T PRK11716 145 IA----PALPCPVRQQLSQEKPDWSRIPFILPEHGPARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALG---CGVGLL 217 (269)
T ss_pred EE----cCCcchhhhccccchhhHhhCCeeecCCCchHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcC---CCeEec
Confidence 32 2222222111 0 12223333331 11112223456665542222 23456666666667654 457777
Q ss_pred cHHHHH
Q 014547 275 SARAAE 280 (423)
Q Consensus 275 S~~AAe 280 (423)
+...++
T Consensus 218 p~~~~~ 223 (269)
T PRK11716 218 PEVVLE 223 (269)
T ss_pred cHHHhh
Confidence 776654
No 181
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=53.89 E-value=1.1e+02 Score=32.79 Aligned_cols=78 Identities=12% Similarity=0.030 Sum_probs=48.3
Q ss_pred cEEEEeCCCccHHHHHHhh---hCCCCc--eeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhh--cCCcEE
Q 014547 128 LRVAYQGVPGAYSEAAAGK---AYPNCE--AIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLL--RHRLHI 200 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~---~f~~~e--~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~--~~~L~I 200 (423)
.+|++. .||..++...+ .+++.. .+.+.+.++++++|.+|++|+.|+.-. ++.++. ..++.+
T Consensus 150 k~I~V~--~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d~~---------~~~~~~~~~p~l~v 218 (482)
T PRK10859 150 GTLTVA--AGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIADSV---------EISLNQRYHPELAV 218 (482)
T ss_pred CeEEEE--CCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEECcH---------HHHHHHHhCCCcee
Confidence 478874 67776665543 345543 356789999999999999999987421 122221 235666
Q ss_pred EEEEEEeeeeeeeecC
Q 014547 201 VGEVQLPVHHCLLALP 216 (423)
Q Consensus 201 vgEi~lpI~h~Lla~~ 216 (423)
...+.-+...+++.++
T Consensus 219 ~~~l~~~~~~~~av~k 234 (482)
T PRK10859 219 AFDLTDEQPVAWALPP 234 (482)
T ss_pred eeecCCCceeEEEEeC
Confidence 5544444445555554
No 182
>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=53.24 E-value=73 Score=24.63 Aligned_cols=33 Identities=30% Similarity=0.199 Sum_probs=25.6
Q ss_pred eEEEEEE-eCC-CccHHHHHHHHHHhCCceeeeee
Q 014547 318 KTSIVFA-HDK-GTSVLFKVLSAFAFRNISLTKIE 350 (423)
Q Consensus 318 KTSivf~-l~~-~pGaL~~vL~~Fa~~~INLtkIE 350 (423)
+.++.-. +.. .||.+.++.+.+++.|||+..|-
T Consensus 8 ~i~v~g~g~~~~~~Gv~a~i~~~La~~~I~i~~is 42 (65)
T PF13840_consen 8 KISVVGPGLRFDVPGVAAKIFSALAEAGINIFMIS 42 (65)
T ss_dssp EEEEEEECGTTTSHHHHHHHHHHHHHTTS-ECEEE
T ss_pred EEEEEccccCCCcccHHHHHHHHHHHCCCCEEEEE
Confidence 3444444 544 89999999999999999998887
No 183
>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=52.97 E-value=85 Score=27.19 Aligned_cols=123 Identities=20% Similarity=0.123 Sum_probs=62.5
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCccc--
Q 014547 147 AYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLT-- 224 (423)
Q Consensus 147 ~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk-- 224 (423)
.||+.++.......++.+.+.+|++|+|++.... ....+ ....|.+..+.++. +-.|-|... ..+++|+.
T Consensus 25 ~~P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~-~~~~~--~~~~l~~~~~~~v~----~~~hpl~~~-~~~l~dl~~~ 96 (200)
T cd08460 25 EAPGVRLRFVPESDKDVDALREGRIDLEIGVLGP-TGPEI--RVQTLFRDRFVGVV----RAGHPLARG-PITPERYAAA 96 (200)
T ss_pred HCCCCEEEEecCchhHHHHHHCCCccEEEecCCC-CCcch--heeeeeccceEEEE----eCCCCCCCC-CCCHHHHhcC
Confidence 4677766554433388899999999999984321 11111 11222233333222 333433322 12333333
Q ss_pred -EEE-echh-HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 225 -RVI-SHPQ-ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 225 -~Vy-SHPq-AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
-|. +... .-.+..+++++.+.... ...++|...+..+++.+ ...++.+...++
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 153 (200)
T cd08460 97 PHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGS---DLIALVPERVTA 153 (200)
T ss_pred CCEEEecCCCCcchHHHHHHhcCCceeEEEEcCcHHHHHHHHhcC---CHHHHHHHHHHH
Confidence 222 1111 12446777777653322 33466777777777764 356677766554
No 184
>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=52.93 E-value=58 Score=22.68 Aligned_cols=27 Identities=26% Similarity=0.253 Sum_probs=23.3
Q ss_pred CCccHHHHHHHHHHhCCceeeeeeeee
Q 014547 327 KGTSVLFKVLSAFAFRNISLTKIESRP 353 (423)
Q Consensus 327 ~~pGaL~~vL~~Fa~~~INLtkIESRP 353 (423)
+.+|.+.++++.+++++|++..|..-.
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~~~~ 38 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMISQSE 38 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEEcCC
Confidence 478999999999999999998876543
No 185
>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=52.28 E-value=71 Score=23.09 Aligned_cols=27 Identities=22% Similarity=0.237 Sum_probs=23.8
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
+.+.+|.+.++++.+++++|++--|..
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04936 10 MRSHPGVAAKMFEALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 556789999999999999999988864
No 186
>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=51.47 E-value=1.6e+02 Score=25.50 Aligned_cols=124 Identities=15% Similarity=0.100 Sum_probs=61.5
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeec-cCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCc---C
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVE-NSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRK---E 221 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIE-NS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l---~ 221 (423)
.||+.++... .+-+++++.+.+|++|+|+..-. +...+.. ...|.+.++. +..+..|-|...+..++ .
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 4677665443 35678899999999999997411 0011100 0111111211 22333444432222222 3
Q ss_pred cccEEEechh-H-HHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 222 YLTRVISHPQ-A-LSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 222 dIk~VySHPq-A-L~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
+..-|.-++. . -.++..|+.+++.... ...+++...+.+++..+ ...+|.+...++
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08444 98 KWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLG---MGIGIVAEMAFE 156 (198)
T ss_pred CCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcC---CcEEeccHHHHh
Confidence 3334443332 1 2346677776543222 33456666777777764 356666665443
No 187
>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=51.44 E-value=1.5e+02 Score=25.21 Aligned_cols=125 Identities=12% Similarity=0.089 Sum_probs=59.9
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCC-CCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcC---
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSL-GGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKE--- 221 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~-~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~--- 221 (423)
.+|+.++... .+-.++.+.+.+|++|+|+....... ...+ ....|.+.++.+ ..+-.|-+.......++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~l--~~~~l~~~~~~~----v~~~~hp~~~~~~~~~~~L~ 98 (199)
T cd08416 25 RRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDF--EVVPLFEDDIFL----AVPATSPLAASSEIDLRDLK 98 (199)
T ss_pred hCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCCCCCe--EEEEeecceEEE----EECCCCcccccCccCHHHhc
Confidence 4677665444 35567889999999999998643210 1100 001111222221 22333433322222222
Q ss_pred cccEEE-echh-HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 222 YLTRVI-SHPQ-ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 222 dIk~Vy-SHPq-AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
+...|. +... ......+++.+.+.... ...++|...+.+++..+ ...++.+...++
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (199)
T cd08416 99 DEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGG---VGYALLPGRIAD 157 (199)
T ss_pred CCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcC---CcEEEechhhhh
Confidence 333333 2221 12235556665542222 23456666677777754 356677765544
No 188
>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=51.27 E-value=1.6e+02 Score=25.26 Aligned_cols=124 Identities=19% Similarity=0.082 Sum_probs=61.5
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc--
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL-- 223 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI-- 223 (423)
.+|+.++.... +..++.+.+.+|++|+|++--.....+. ....|.+.++.++.. -.|-+.. ...+++++
T Consensus 25 ~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~lv~~----~~~~~~~-~~~~~~~L~~ 96 (200)
T cd08466 25 LAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSF---KSELLFEDELVCVAR----KDHPRIQ-GSLSLEQYLA 96 (200)
T ss_pred HCCCCEEEEecCchHhHHHHHHcCCccEEEecccCCCCCc---eeeeecccceEEEEe----CCCCCCC-CCcCHHHHhh
Confidence 46777765544 5678999999999999997421111111 111223333333322 2232321 12334444
Q ss_pred -cEEEechhH-HHHHHHHHHHcCC-cee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 224 -TRVISHPQA-LSQCEHTLTKLGL-NVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 224 -k~VySHPqA-L~QC~~fL~~~~p-~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
..+.-.+.. ..+-.+|+.+.+. ..+ ...++|.....++++.+ ...|+.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08466 97 EKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQT---DLIAIAPRWLADQ 155 (200)
T ss_pred CCcEEecCCCCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCC---CeehhhHHHHHHH
Confidence 223322221 1234555555432 222 33455666666666654 4677777766654
No 189
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=50.80 E-value=2.5e+02 Score=27.53 Aligned_cols=53 Identities=23% Similarity=0.134 Sum_probs=34.0
Q ss_pred CCccEEEEeCCCccH-HHHHHh---hhCCCCceeec-CCHHHHHHHHHcCCcCeEEEe
Q 014547 125 GSQLRVAYQGVPGAY-SEAAAG---KAYPNCEAIPC-DQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 125 ~~~~~VayLGP~GTf-Sh~AA~---~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
....+|+.....+.+ -..+.. +.+|+.++... .+..++++.+.+|++|+++.+
T Consensus 92 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 92 QGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred CCeEEEEechHHHHHHhHHHHHHHHHHCCCceEEEEeCChHHHHHHHHCCCcCEEEee
Confidence 346788875444432 112222 23577665443 467899999999999999986
No 190
>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=50.50 E-value=1.6e+02 Score=25.13 Aligned_cols=32 Identities=16% Similarity=-0.100 Sum_probs=24.2
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEee
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
.+|+.++... .+..++++.|.+|++|+|+..-
T Consensus 26 ~~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~ 58 (197)
T cd08425 26 RYPGIALSLREMPQERIEAALADDRLDLGIAFA 58 (197)
T ss_pred HCCCcEEEEEECcHHHHHHHHHcCCccEEEEec
Confidence 3577665443 3567899999999999999753
No 191
>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=50.32 E-value=1.6e+02 Score=25.07 Aligned_cols=123 Identities=15% Similarity=0.109 Sum_probs=61.2
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCC--CCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSL--GGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL 223 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~--~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI 223 (423)
.+|+.++... .+..++++.+.+|++|+|+....... .+. ....|.+.++.++..- +|-+. .. .+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~~~l~~~~~~~v~~~----~~~~~-~~-~~~~~l 95 (201)
T cd08418 25 QFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKEL---ISEPLFESDFVVVARK----DHPLQ-GA-RSLEEL 95 (201)
T ss_pred HCCCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCCCCcce---eEEeecCCceEEEeCC----CCccc-cC-CCHHHH
Confidence 3577665443 35678999999999999998532111 110 0111222233322211 22111 11 122332
Q ss_pred c---EEEec--hhHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 224 T---RVISH--PQALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 224 k---~VySH--PqAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
. .|... ........+++.+.+.... ...++|...+.++++.+ ...||.+...++.
T Consensus 96 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 156 (201)
T cd08418 96 LDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKA---DFLTILSRDMGRG 156 (201)
T ss_pred cCCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhC---CEEEEeEHHHhhh
Confidence 2 23321 1223445666766543322 23456667777777764 5678888766553
No 192
>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=50.27 E-value=1.6e+02 Score=25.04 Aligned_cols=33 Identities=21% Similarity=0.198 Sum_probs=24.9
Q ss_pred hhCCCCceeecC-CHHHHHHHHHcCCcCeEEEee
Q 014547 146 KAYPNCEAIPCD-QFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 146 ~~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
+.+|+.++.... +-+++++.+.+|++|+|++..
T Consensus 25 ~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~ 58 (199)
T cd08451 25 EAYPDVELTLEEANTAELLEALREGRLDAAFVRP 58 (199)
T ss_pred HHCCCcEEEEecCChHHHHHHHHCCCccEEEEec
Confidence 346776655443 467889999999999999863
No 193
>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=50.11 E-value=85 Score=22.33 Aligned_cols=53 Identities=21% Similarity=0.226 Sum_probs=36.3
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhh
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEF 400 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~ 400 (423)
..+.++.+.++++.|++++|++.-|..-.. . ..+.|.|+- ..+..+++.|.+.
T Consensus 10 ~~~~~~~~~~i~~~l~~~~i~v~~i~~~~~-~----------------~~i~~~v~~------~~~~~~~~~l~~~ 62 (65)
T cd04892 10 MRGTPGVAARIFSALAEAGINIIMISQGSS-E----------------VNISFVVDE------DDADKAVKALHEE 62 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEcCCC-c----------------eeEEEEEeH------HHHHHHHHHHHHH
Confidence 346789999999999999999987754211 1 256777765 3445566666543
No 194
>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=50.08 E-value=31 Score=33.34 Aligned_cols=48 Identities=21% Similarity=0.097 Sum_probs=37.8
Q ss_pred cEEEEeCCCccHHHHHHhhh-CCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKA-YPNCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~-f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+. +.|++.+....+. ++..+++.+++.++++++|.+|++|+.+..
T Consensus 145 ~~Igv--~~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d 193 (275)
T TIGR02995 145 AKIAA--PGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGRADAYSLT 193 (275)
T ss_pred ceEEE--eCCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCCCCEEecC
Confidence 57885 5677777666543 455678899999999999999999988764
No 195
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=49.77 E-value=65 Score=30.29 Aligned_cols=131 Identities=10% Similarity=-0.032 Sum_probs=70.9
Q ss_pred CCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeee
Q 014547 134 GVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLL 213 (423)
Q Consensus 134 GP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Ll 213 (423)
|..--+-++.+.+.--..++++. ++..+++++++|++|.++..+. -+. +-.+.+. . ..-++.....|+
T Consensus 48 G~~vdl~~~ia~~lg~~~~~~~~-~~~~~~~~l~~G~vDi~~~~~~-~t~----~R~~~~~-f-----s~p~~~~~~~~~ 115 (247)
T PRK09495 48 GFDIDLWAAIAKELKLDYTLKPM-DFSGIIPALQTKNVDLALAGIT-ITD----ERKKAID-F-----SDGYYKSGLLVM 115 (247)
T ss_pred EEeHHHHHHHHHHhCCceEEEeC-CHHHHHHHHhCCCcCEEEecCc-cCH----HHHhhcc-c-----cchheecceEEE
Confidence 44444555555543225677776 6899999999999998765432 011 1111110 0 011122233444
Q ss_pred ecCCC----CcCccc--EEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 214 ALPGV----RKEYLT--RVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 214 a~~g~----~l~dIk--~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
.+++. ++++++ +|..-... .. ..|+.+..|+.+++.+.+...+.+.+..+ +-.|+|+....+.
T Consensus 116 ~~~~~~~~~~~~dL~g~~I~v~~g~-~~-~~~l~~~~~~~~i~~~~~~~~~~~~L~~g--rvDa~i~~~~~~~ 184 (247)
T PRK09495 116 VKANNNDIKSVKDLDGKVVAVKSGT-GS-VDYAKANIKTKDLRQFPNIDNAYLELGTG--RADAVLHDTPNIL 184 (247)
T ss_pred EECCCCCCCChHHhCCCEEEEecCc-hH-HHHHHhcCCCCceEEcCCHHHHHHHHHcC--ceeEEEeChHHHH
Confidence 44332 233443 44332221 11 35777777777777788888888887765 4567777665443
No 196
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=49.75 E-value=20 Score=32.36 Aligned_cols=29 Identities=14% Similarity=0.116 Sum_probs=24.1
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeee
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKI 349 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkI 349 (423)
|.+-+.|+||-|.++++.++.+|||+..+
T Consensus 6 ISvFlENk~GRL~~~~~~L~eagINiRA~ 34 (142)
T COG4747 6 ISVFLENKPGRLASVANKLKEAGINIRAF 34 (142)
T ss_pred EEEEecCCcchHHHHHHHHHHcCCceEEE
Confidence 33445689999999999999999999644
No 197
>PRK04374 PII uridylyl-transferase; Provisional
Probab=49.60 E-value=72 Score=37.14 Aligned_cols=36 Identities=14% Similarity=0.245 Sum_probs=29.9
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceee--eeeee
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLT--KIESR 352 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLt--kIESR 352 (423)
..|.|.+...|+||-|+++-.+|+..|+|+. ||.+.
T Consensus 795 ~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~ 832 (869)
T PRK04374 795 RRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATF 832 (869)
T ss_pred CeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEec
Confidence 3566667778999999999999999999998 45554
No 198
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=49.08 E-value=1.9e+02 Score=28.84 Aligned_cols=144 Identities=17% Similarity=0.124 Sum_probs=74.4
Q ss_pred CccEEEEeCCCccHH-HHHH---hhhCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEE
Q 014547 126 SQLRVAYQGVPGAYS-EAAA---GKAYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHI 200 (423)
Q Consensus 126 ~~~~VayLGP~GTfS-h~AA---~~~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 200 (423)
+..+||+....+.+- -.+. .+.+|+.++.... +.++++++|.+|++|+|+++-..-..+... ...|.+..+.
T Consensus 93 g~lrIg~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~~- 169 (327)
T PRK12680 93 GQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGI--AVPLYRWRRL- 169 (327)
T ss_pred eEEEEEecchhHHHhhHHHHHHHHHHCCCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCCcce--EEEeeccceE-
Confidence 357888876655442 1111 2346777765544 568999999999999999863211111110 1112222322
Q ss_pred EEEEEEeeeeeeeec-CCCCcCcc---cEEEech-hHH-HHHHHHHHHcC--CceeEEeccCHHHHHHHHHhcCCCCeeE
Q 014547 201 VGEVQLPVHHCLLAL-PGVRKEYL---TRVISHP-QAL-SQCEHTLTKLG--LNVAREAVDDTAGAAEYIAANDLRDTAA 272 (423)
Q Consensus 201 vgEi~lpI~h~Lla~-~g~~l~dI---k~VySHP-qAL-~QC~~fL~~~~--p~~~~v~~~STA~AA~~va~~~~~~~AA 272 (423)
+.++..|-|... ...+++|+ .-|..-+ ... ....+|++.++ ++. ...+++.....++|..+ ...|
T Consensus 170 ---l~~~~~hpl~~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~G---~Gia 242 (327)
T PRK12680 170 ---VVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSI-ALTALDADLIKTYVRAG---LGVG 242 (327)
T ss_pred ---EEEeCCChhhccCCCCCHHHHhcCCEEEecCCCchHHHHHHHHHHCCCCCcE-EEEECCHHHHHHHHHcC---CCEE
Confidence 223445555432 12333333 3333222 122 44666777664 333 23456677777777765 3456
Q ss_pred EccHHHH
Q 014547 273 IASARAA 279 (423)
Q Consensus 273 IaS~~AA 279 (423)
+.+..++
T Consensus 243 ~lp~~~~ 249 (327)
T PRK12680 243 LLAEMAV 249 (327)
T ss_pred Eeechhc
Confidence 6665544
No 199
>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=48.98 E-value=1.7e+02 Score=24.90 Aligned_cols=127 Identities=14% Similarity=0.088 Sum_probs=62.7
Q ss_pred hhCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecC-CC---Cc
Q 014547 146 KAYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALP-GV---RK 220 (423)
Q Consensus 146 ~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~-g~---~l 220 (423)
+.+|+.++.-. .+..++++.+.+|++|+|++.-.......+ ....|.+..+.+ ..+-+|-+...+ .. ++
T Consensus 24 ~~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l--~~~~l~~~~~~~----~~~~~~~~~~~~~~~~~~~l 97 (199)
T cd08430 24 AQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARL--AFLPLATSPLVF----IAPNIACAVTQQLSQGEIDW 97 (199)
T ss_pred HHCCCceEEEEeCCHHHHHHHHHCCCCCEEEEecCCCCCccc--EEEeeccceEEE----EEeCCchhhhhhcccccccc
Confidence 34687766544 467789999999999999985321111111 011222223222 223344333221 11 22
Q ss_pred CcccEEEechh-HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 221 EYLTRVISHPQ-ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 221 ~dIk~VySHPq-AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
.+..-|...+. ......+|+.+++...+ ...+++.....+.+..+ ...|+.+...++.
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~lp~~~~~~ 157 (199)
T cd08430 98 SRLPFILPERGLARERLDQWFRRRGIKPNIYAQVAGHEAIVSMVALG---CGVGIVPELVLDN 157 (199)
T ss_pred ccCCeEEccCChHHHHHHHHHHHcCCCCCeeEEEccHHHHHHHHHhC---CeEEEccHHHhhh
Confidence 33333432111 12334567766543222 23355555566666654 4577777766553
No 200
>PRK11260 cystine transporter subunit; Provisional
Probab=48.93 E-value=1.7e+02 Score=27.89 Aligned_cols=117 Identities=15% Similarity=0.038 Sum_probs=64.1
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCC-----CcCccc
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGV-----RKEYLT 224 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~-----~l~dIk 224 (423)
+.++++. ...++++++++|++|.++-++.-+ .+... .+....- ++.....++.+++. .+++++
T Consensus 81 ~~e~~~~-~~~~~~~~l~~G~~D~~~~~~~~~-----~~r~~-----~~~fs~p-~~~~~~~~~~~~~~~~~~~~~~dL~ 148 (266)
T PRK11260 81 KASLKPT-KWDGMLASLDSKRIDVVINQVTIS-----DERKK-----KYDFSTP-YTVSGIQALVKKGNEGTIKTAADLK 148 (266)
T ss_pred eEEEEeC-CHHHHHHHHhcCCCCEEEeccccC-----HHHHh-----ccccCCc-eeecceEEEEEcCCcCCCCCHHHcC
Confidence 5678886 578999999999999876433100 00001 1111111 11122234443321 122221
Q ss_pred --EEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHc
Q 014547 225 --RVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELY 282 (423)
Q Consensus 225 --~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelY 282 (423)
+|-.- ..... .+|+.+..|+.++..+.+..++.+.+..+ +-.++|+....+..+
T Consensus 149 g~~Igv~-~G~~~-~~~l~~~~~~~~i~~~~~~~~~l~~L~~G--rvD~~i~d~~~~~~~ 204 (266)
T PRK11260 149 GKKVGVG-LGTNY-EQWLRQNVQGVDVRTYDDDPTKYQDLRVG--RIDAILVDRLAALDL 204 (266)
T ss_pred CCEEEEe-cCCcH-HHHHHHhCCCCceEecCCHHHHHHHHHcC--CCCEEEechHHHHHH
Confidence 23221 11111 46787788888888888999988888876 456888776654443
No 201
>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=48.59 E-value=1.7e+02 Score=24.83 Aligned_cols=32 Identities=19% Similarity=0.019 Sum_probs=23.9
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEee
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
.+|+.++.... +-+++.+.+.+|++|+|++.-
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (200)
T cd08423 25 RHPGLEVRLREAEPPESLDALRAGELDLAVVFD 57 (200)
T ss_pred hCCCCeEEEEeCCHHHHHHHHhcCCccEEEEec
Confidence 35776654433 467889999999999999863
No 202
>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=48.18 E-value=1.7e+02 Score=24.87 Aligned_cols=124 Identities=15% Similarity=0.096 Sum_probs=60.2
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc--
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL-- 223 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI-- 223 (423)
.+|+.++... .+.+++.+.+.+|++|+|+..-.....+.. ...|.+.++.++ .+-+|-+...+..+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~hpl~~~~~~~~~~l~~ 97 (199)
T cd08426 25 RYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIR---VHSRQPAPIGAV----VPPGHPLARQPSVTLAQLAG 97 (199)
T ss_pred hCCCeEEEEEeCCcHHHHHHHHCCCccEEEecCCCCCCCeE---EEeeccCcEEEE----ecCCCCcccCCccCHHHHhC
Confidence 3576665443 356889999999999999975332211110 111222222211 122222222211222222
Q ss_pred -cEEEechh--HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 224 -TRVISHPQ--ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 224 -k~VySHPq--AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
..|.-.+. .......|+.+++.... ...+++...+.+++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (199)
T cd08426 98 YPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAG---GGISLLTELAVR 155 (199)
T ss_pred CCeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcC---CCEEEEchHhhh
Confidence 23332211 12345566666543322 33466677777777764 456777766443
No 203
>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=47.68 E-value=80 Score=23.90 Aligned_cols=33 Identities=15% Similarity=0.193 Sum_probs=25.6
Q ss_pred EEEEE-EeCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 319 TSIVF-AHDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 319 TSivf-~l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
.+++= .+.+.||.+.++++.+++.|||+..+-.
T Consensus 4 isvvG~~~~~~~gi~~~if~aL~~~~I~v~~~~~ 37 (64)
T cd04937 4 VTIIGSRIRGVPGVMAKIVGALSKEGIEILQTAD 37 (64)
T ss_pred EEEECCCccCCcCHHHHHHHHHHHCCCCEEEEEc
Confidence 34443 3456899999999999999999975554
No 204
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=47.65 E-value=2.4e+02 Score=26.88 Aligned_cols=53 Identities=17% Similarity=0.167 Sum_probs=34.2
Q ss_pred CccEEEEeCCCccHH--HH--HHhhhCCCCceee-cCCHHHHHHHHHcCCcCeEEEee
Q 014547 126 SQLRVAYQGVPGAYS--EA--AAGKAYPNCEAIP-CDQFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 126 ~~~~VayLGP~GTfS--h~--AA~~~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
+..+|+.....+.+= .. ..++.+|+.++.. ..+-.++++.+.+|++|+|+++-
T Consensus 89 g~l~i~~~~~~~~~~~~~~l~~~~~~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~~ 146 (290)
T PRK10837 89 GALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEG 146 (290)
T ss_pred CeEEEEecchhHhhhhHHHHHHHHHHCCCceEEEEECCHHHHHHHHHhCCceEEEecC
Confidence 456777765544321 11 1223467766543 35778899999999999999853
No 205
>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=47.53 E-value=97 Score=22.74 Aligned_cols=27 Identities=19% Similarity=0.159 Sum_probs=23.5
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
+++.++.+.++++.+++.+||+--|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~q 37 (66)
T cd04924 11 MRGTPGVAGRVFGALGKAGINVIMISQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 556799999999999999999987753
No 206
>PRK09034 aspartate kinase; Reviewed
Probab=47.49 E-value=2.1e+02 Score=30.54 Aligned_cols=128 Identities=16% Similarity=0.061 Sum_probs=73.3
Q ss_pred CceeEEeccCHHHHHHHHHhcCCCCeeEEccHH---HHHHcCCceeecCccCCCCCeeEEEEEeeCCCCC-C-----CCC
Q 014547 245 LNVAREAVDDTAGAAEYIAANDLRDTAAIASAR---AAELYGMQVLEDGIQDDSSNVTRFVMLAREPIIP-R-----TDR 315 (423)
Q Consensus 245 p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~---AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~-~-----~~~ 315 (423)
|+++.+..-|-.+|.++...+ |-+-... -|..++++|.-.|..+....-|..- ....... . ...
T Consensus 233 ~~A~~l~~lsy~Ea~ela~~G-----akvlhp~ai~~a~~~~Ipi~v~~~~~p~~~GT~I~--~~~~~~~~~~Vk~It~~ 305 (454)
T PRK09034 233 KNPKSIKEITYREMRELSYAG-----FSVFHDEALIPAYRGGIPINIKNTNNPEDPGTLIV--PDRDNKNKNPITGIAGD 305 (454)
T ss_pred CCCeECCccCHHHHHHHHhCC-----cccCCHHHHHHHHHcCCCEEEEcCCCCCCCccEEE--eccccCccccceEEEec
Confidence 556666667788888876532 2232222 2456899999998876544445442 2211100 0 001
Q ss_pred CCeEEEEEE---eCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHH
Q 014547 316 PFKTSIVFA---HDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQN 392 (423)
Q Consensus 316 ~~KTSivf~---l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~ 392 (423)
.+-+.|-+. ....+|.+.++++.|+++|||+-.| +... ....|+|+=+ ..+...+..
T Consensus 306 ~~i~~Itv~~~~~~~~~g~~a~if~~la~~~I~Vd~i---~ss~----------------~sis~~v~~~-~~~~a~~~~ 365 (454)
T PRK09034 306 KGFTSIYISKYLMNREVGFGRKVLQILEDHGISYEHM---PSGI----------------DDLSIIIRER-QLTPKKEDE 365 (454)
T ss_pred CCEEEEEEccCCCCCCccHHHHHHHHHHHcCCeEEEE---cCCC----------------cEEEEEEeHH-HhhHHHHHH
Confidence 112233232 3447899999999999999999988 2211 3578888742 222222256
Q ss_pred HHHHHHh
Q 014547 393 ALAEVQE 399 (423)
Q Consensus 393 aL~eL~~ 399 (423)
++++|++
T Consensus 366 l~~el~~ 372 (454)
T PRK09034 366 ILAEIKQ 372 (454)
T ss_pred HHHHHHH
Confidence 6667653
No 207
>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=46.83 E-value=2.5e+02 Score=26.26 Aligned_cols=143 Identities=11% Similarity=0.019 Sum_probs=72.7
Q ss_pred ccEEEEeCCCccHHHH----HHhhhC----C-CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCC
Q 014547 127 QLRVAYQGVPGAYSEA----AAGKAY----P-NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHR 197 (423)
Q Consensus 127 ~~~VayLGP~GTfSh~----AA~~~f----~-~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~ 197 (423)
.++||+.+....+... ...+++ + ++++++..++.+.++++..|++|+++...+- +.....+.+
T Consensus 33 ~l~vg~~~~~~~~~~~~~~~~l~~~l~~~~g~~v~~~~~~~~~~~~~~l~~g~~Di~~~~~~~--------~~~~~~~~~ 104 (254)
T TIGR01098 33 ELNFGILPGENASNLTRRWEPLADYLEKKLGIKVQLFVATDYSAVIEAMRFGRVDIAWFGPSS--------YVLAHYRAN 104 (254)
T ss_pred ceEEEECCCCCHHHHHHHHHHHHHHHHHHhCCcEEEEeCCCHHHHHHHHHcCCccEEEECcHH--------HHHHHHhcC
Confidence 5788888754433221 111222 1 4667788899999999999999999765331 111112222
Q ss_pred cEEEEEEEEe------eeeeeeecCCCCcCccc-----EEEec-hhHH---HHHHHHHHHc-C--C---ceeEEeccCHH
Q 014547 198 LHIVGEVQLP------VHHCLLALPGVRKEYLT-----RVISH-PQAL---SQCEHTLTKL-G--L---NVAREAVDDTA 256 (423)
Q Consensus 198 L~IvgEi~lp------I~h~Lla~~g~~l~dIk-----~VySH-PqAL---~QC~~fL~~~-~--p---~~~~v~~~STA 256 (423)
...+...+.. -...|+++++..+.+++ +|... +.+. .--..+|.+. + + ...++...+..
T Consensus 105 ~~~~~~~~~~~~~~~~~~~~lvv~~d~~i~~~~dL~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~ 184 (254)
T TIGR01098 105 AEVFALTAVSTDGSPGYYSVIIVKADSPIKSLKDLKGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHD 184 (254)
T ss_pred CceEEeeccccCCCCceEEEEEEECCCCCCChHHhcCCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchH
Confidence 2211111110 11256666654333332 44433 2211 1112334332 2 1 13455555667
Q ss_pred HHHHHHHhcCCCCeeEEccHHHH
Q 014547 257 GAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 257 ~AA~~va~~~~~~~AAIaS~~AA 279 (423)
++.+.+..+ .-.|++.....+
T Consensus 185 ~~~~al~~G--~~Da~~~~~~~~ 205 (254)
T TIGR01098 185 ASALAVANG--KVDAATNNSSAI 205 (254)
T ss_pred HHHHHHHcC--CCCeEEecHHHH
Confidence 788888865 356777665444
No 208
>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=46.16 E-value=1.8e+02 Score=24.57 Aligned_cols=124 Identities=16% Similarity=0.035 Sum_probs=60.0
Q ss_pred hhCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCc---C
Q 014547 146 KAYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRK---E 221 (423)
Q Consensus 146 ~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l---~ 221 (423)
+.+|+.++... .+..+..+.+.+|++|+|++.-.....+ .....|.+..+.++. +-.|-|...+..++ .
T Consensus 24 ~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~---~~~~~l~~~~~~~v~----~~~~~l~~~~~~~~~~l~ 96 (196)
T cd08415 24 ARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPG---LESEPLASGRAVCVL----PPGHPLARKDVVTPADLA 96 (196)
T ss_pred HHCCCcEEEEEecchHHHHHHHHcCCccEEEEeCCCCCCc---ceeeeecccceEEEE----cCCCChHhcCccCHHHhc
Confidence 34677665433 3567899999999999999864321111 011122222222221 11222221111222 2
Q ss_pred cccEEE-ech-hHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 222 YLTRVI-SHP-QALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 222 dIk~Vy-SHP-qAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
+..-|. .+. ....+..+|+.+++...+ ...++|.....+.+..+ ...++.+...+
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~ 154 (196)
T cd08415 97 GEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAG---LGVAIVDPLTA 154 (196)
T ss_pred CCcEEEeCCCccHHHHHHHHHHHcCCCceEEEEEeHHHHHHHHHHcC---CCeEEechhhh
Confidence 223333 222 223456667776653322 23355666666666654 45666666544
No 209
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=45.98 E-value=93 Score=29.61 Aligned_cols=65 Identities=12% Similarity=0.193 Sum_probs=43.0
Q ss_pred eEEEEEEe--CCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCc-ChHHHHHHH
Q 014547 318 KTSIVFAH--DKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASM-AEVRAQNAL 394 (423)
Q Consensus 318 KTSivf~l--~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~-~d~~v~~aL 394 (423)
++.+++++ +|+||-..++-+.++++|.|+. +||-..- | ..|.-++.| ++.. .-..++.+|
T Consensus 6 ~~~lviTviG~DrpGIVa~vs~~l~~~g~NI~--ds~~t~l-----------g--g~Fa~i~lv--s~~~~~~~~le~~L 68 (190)
T PRK11589 6 QHYLVITALGADRPGIVNTITRHVSSCGCNIE--DSRLAML-----------G--EEFTFIMLL--SGSWNAITLIESTL 68 (190)
T ss_pred ccEEEEEEEcCCCChHHHHHHHHHHHcCCCee--ehhhHhh-----------C--CceEEEEEE--eCChhHHHHHHHHH
Confidence 45566654 7899999999999999999997 6776652 2 123334444 4432 225666677
Q ss_pred HHHHh
Q 014547 395 AEVQE 399 (423)
Q Consensus 395 ~eL~~ 399 (423)
..+.+
T Consensus 69 ~~l~~ 73 (190)
T PRK11589 69 PLKGA 73 (190)
T ss_pred Hhhhh
Confidence 66653
No 210
>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=45.92 E-value=70 Score=26.27 Aligned_cols=57 Identities=21% Similarity=0.221 Sum_probs=40.4
Q ss_pred CCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcC
Q 014547 326 DKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTS 402 (423)
Q Consensus 326 ~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~ 402 (423)
..+.|-+.++|++|.++||+.-++ |+.- ......|+=. ...++.++.++++|++.+.
T Consensus 12 n~evGF~rk~L~I~E~~~is~Eh~---PSGI----------------D~~Siii~~~-~~~~~~~~~i~~~i~~~~~ 68 (76)
T cd04911 12 NREVGFGRKLLSILEDNGISYEHM---PSGI----------------DDISIIIRDN-QLTDEKEQKILAEIKEELH 68 (76)
T ss_pred cchhcHHHHHHHHHHHcCCCEeee---cCCC----------------ccEEEEEEcc-ccchhhHHHHHHHHHHhcC
Confidence 347899999999999999998765 5432 1344444432 2444588999999998654
No 211
>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=45.55 E-value=1.9e+02 Score=24.68 Aligned_cols=124 Identities=13% Similarity=0.004 Sum_probs=60.4
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCccc-
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLT- 224 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk- 224 (423)
.+|+.++.... +-.++.+.+.+|++|+|++.-.....+ .....|.+.++.++. +-+|-+. ....+++++.
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~---~~~~~l~~~~~~~v~----~~~~~~~-~~~~~~~~l~~ 96 (200)
T cd08464 25 EAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAW---LKREVLYTEGYACLF----DPQQLSL-SAPLTLEDYVA 96 (200)
T ss_pred HCCCcEEEEecCCcccHHHHHhcCcccEEEecCCCCccc---ceeeeecccceEEEE----eCCCccc-cCCCCHHHHhc
Confidence 46777665443 345778999999999999753211111 011122233333222 2223221 1112333322
Q ss_pred --EE-EechhH-HHHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 225 --RV-ISHPQA-LSQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 225 --~V-ySHPqA-L~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
.| +.+... .....+|+.+++..... ..+++.......++.+ ...||.+...++.
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 23345677665432222 2355555555556553 4688888877763
No 212
>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=45.41 E-value=1.6e+02 Score=23.61 Aligned_cols=32 Identities=16% Similarity=0.205 Sum_probs=26.6
Q ss_pred EEEEeCCCccHHHHHHHHHHhCCceeeeeeee
Q 014547 321 IVFAHDKGTSVLFKVLSAFAFRNISLTKIESR 352 (423)
Q Consensus 321 ivf~l~~~pGaL~~vL~~Fa~~~INLtkIESR 352 (423)
|++..+++||.+.++-++|+.+|+|+..=...
T Consensus 4 I~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~ 35 (68)
T cd04928 4 ITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAF 35 (68)
T ss_pred EEEEECCCcchHHHHHHHHHHCCCceEEEEEE
Confidence 55667799999999999999999999954333
No 213
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=45.38 E-value=3e+02 Score=26.80 Aligned_cols=137 Identities=15% Similarity=0.085 Sum_probs=69.2
Q ss_pred CccEEEEeCCCccH-HHHHHh---hhCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEE
Q 014547 126 SQLRVAYQGVPGAY-SEAAAG---KAYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHI 200 (423)
Q Consensus 126 ~~~~VayLGP~GTf-Sh~AA~---~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 200 (423)
+..+||.....+++ --.... +.+|+.++... .+.+++++.+.+|++|+|+.+-.... ..+ +
T Consensus 93 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~------------~~~--l 158 (309)
T PRK12682 93 GTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLAD------------DPD--L 158 (309)
T ss_pred CeEEEeeCchHHHHHHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHcCCccEEEecCcccC------------CCc--c
Confidence 46788777554432 111111 33677766543 45789999999999999997522100 011 1
Q ss_pred EEEEEEeeeeeeeecCC--------CCcCcc---cEEEe-chhH-HHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcC
Q 014547 201 VGEVQLPVHHCLLALPG--------VRKEYL---TRVIS-HPQA-LSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAAND 266 (423)
Q Consensus 201 vgEi~lpI~h~Lla~~g--------~~l~dI---k~VyS-HPqA-L~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~ 266 (423)
..+......+++++.++ .+++++ .-|.- .... ..+-..|+.+++...+ ...++|.....+++..+
T Consensus 159 ~~~~l~~~~~~~~~~~~~pl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g- 237 (309)
T PRK12682 159 ATLPCYDWQHAVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLG- 237 (309)
T ss_pred eEEEeeeeeEEEEecCCCccccCCCcCHHHHhcCCceeeCCCccHHHHHHHHHHHcCCCCcEEEEeCCHHHHHHHHHhC-
Confidence 22223333444444332 222222 22321 1111 1234455655543222 34467788888888875
Q ss_pred CCCeeEEccHHHH
Q 014547 267 LRDTAAIASARAA 279 (423)
Q Consensus 267 ~~~~AAIaS~~AA 279 (423)
...++.+...+
T Consensus 238 --~Gi~~lp~~~~ 248 (309)
T PRK12682 238 --LGVGIVAEMAY 248 (309)
T ss_pred --CceEEehhhhh
Confidence 34566565444
No 214
>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=45.28 E-value=1.9e+02 Score=24.56 Aligned_cols=31 Identities=19% Similarity=0.012 Sum_probs=24.2
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEe
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+.++... .+-.++.+.+.+|++|+|++.
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~ 56 (198)
T cd08421 25 AHPDVRIDLEERLSADIVRAVAEGRADLGIVA 56 (198)
T ss_pred HCCCceEEEEecCcHHHHHHHhcCCceEEEEe
Confidence 4677665443 456889999999999999985
No 215
>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=45.05 E-value=47 Score=30.67 Aligned_cols=48 Identities=15% Similarity=0.077 Sum_probs=32.8
Q ss_pred cEEEEeCCCccHHHHHHhhhC--CCCce--e-----ecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAY--PNCEA--I-----PCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f--~~~e~--v-----p~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+||. +.|+..+....+.. .+... . ...+..+++.+|..|++|.+++.
T Consensus 105 ~~V~v--~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~ 161 (232)
T TIGR03871 105 LRIGV--FAGTPPAHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVW 161 (232)
T ss_pred CeEEE--EcCChHHHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEec
Confidence 47887 45888777654432 22111 1 13478999999999999999885
No 216
>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=45.03 E-value=2.1e+02 Score=24.85 Aligned_cols=120 Identities=13% Similarity=0.028 Sum_probs=60.9
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCC------CC
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPG------VR 219 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g------~~ 219 (423)
.+|+.++... .+-.++.+.|.+|++|+|++.-.+. .....+ +..+.......++++.++ .+
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~----------~~~~~~--~~~~~l~~~~~~~~~~~~hpl~~~~~ 92 (202)
T cd08468 25 LAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDD----------GAEPRL--IEERDWWEDTYVVIASRDHPRLSRLT 92 (202)
T ss_pred hCCCCEEEEEECChHhHHHHHHCCCccEEEeccccc----------ccCCCC--EEEEEEecCcEEEEEeCCCCCcCCCC
Confidence 4677766544 3578999999999999999753211 000011 122222222334443332 22
Q ss_pred cCccc---EEEec--hhHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 220 KEYLT---RVISH--PQALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 220 l~dIk---~VySH--PqAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
++++. .|.-. -..-.+..+++++.+...+ ...++|.....+.++. .+..++.++.+++.
T Consensus 93 ~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~---~~~~~~~p~~~~~~ 157 (202)
T cd08468 93 LDAFLAERHLVVTPWNEDRGVVDQVLEKQGLEREIALQLPNVLNAPFIVAS---SDLLMTLPRQAARA 157 (202)
T ss_pred HHHHhhCCCeEEecCCCCCchHHHHHHHcCCCceEEEEcChhHhHHHHHhc---CCeeeecHHHHHHH
Confidence 33321 12111 1122345666666543322 2345566556666654 35677888877654
No 217
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=44.84 E-value=2e+02 Score=28.37 Aligned_cols=143 Identities=13% Similarity=0.092 Sum_probs=67.2
Q ss_pred CccEEEEeCCCccH-HHHHH---hhhCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEE
Q 014547 126 SQLRVAYQGVPGAY-SEAAA---GKAYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHI 200 (423)
Q Consensus 126 ~~~~VayLGP~GTf-Sh~AA---~~~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 200 (423)
+..+||+...-+.+ --... .+.+|+.++.. ..+-.++++.+.+|++|+|+..-.......+ ....|.+..+.
T Consensus 93 g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l--~~~~l~~~~~~- 169 (316)
T PRK12679 93 GVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQL--VAFPWFRWHHS- 169 (316)
T ss_pred ceEEEEechHhhhcchHHHHHHHHHHCCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCCCCc--eEEEccCCcEE-
Confidence 46788875433322 11111 22357766544 3456789999999999999974221000000 01112222222
Q ss_pred EEEEEEeeeeeeeecCCCCcCcc---cEEEechh--HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEc
Q 014547 201 VGEVQLPVHHCLLALPGVRKEYL---TRVISHPQ--ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIA 274 (423)
Q Consensus 201 vgEi~lpI~h~Lla~~g~~l~dI---k~VySHPq--AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIa 274 (423)
+..+..|-|......+++++ +-|.-++. .-.....|+..++.... ...++|+....+++..+ ...|+.
T Consensus 170 ---~v~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g---~Gi~~l 243 (316)
T PRK12679 170 ---LLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALG---LGIGLV 243 (316)
T ss_pred ---EEecCCCccccCCCCCHHHHhCCCeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcC---CcEEEe
Confidence 22344444433222233332 23332221 22235566666543222 33455666666666654 345666
Q ss_pred cHH
Q 014547 275 SAR 277 (423)
Q Consensus 275 S~~ 277 (423)
+..
T Consensus 244 p~~ 246 (316)
T PRK12679 244 AEQ 246 (316)
T ss_pred ccc
Confidence 654
No 218
>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=44.60 E-value=1.2e+02 Score=22.35 Aligned_cols=27 Identities=22% Similarity=0.225 Sum_probs=23.7
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
+.+.+|.+.++++.|++.|||+--|..
T Consensus 11 ~~~~~~~~~~i~~~l~~~~I~v~~i~~ 37 (66)
T cd04922 11 MAGTPGVAATFFSALAKANVNIRAIAQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 556799999999999999999988753
No 219
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=43.93 E-value=97 Score=36.17 Aligned_cols=35 Identities=20% Similarity=0.189 Sum_probs=29.6
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceee--eeeee
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLT--KIESR 352 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLt--kIESR 352 (423)
-|-|.+..+|+||-|+++-++|+..|+|+. ||.+.
T Consensus 814 ~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~ 850 (895)
T PRK00275 814 VTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATL 850 (895)
T ss_pred eEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEec
Confidence 466667788999999999999999999998 56555
No 220
>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=43.49 E-value=70 Score=26.14 Aligned_cols=64 Identities=16% Similarity=0.116 Sum_probs=40.6
Q ss_pred CccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecC-cChHHHHHHHHHHHh
Q 014547 328 GTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEAS-MAEVRAQNALAEVQE 399 (423)
Q Consensus 328 ~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~-~~d~~v~~aL~eL~~ 399 (423)
.+|.++++=+.++.+|+|+.+|...-.+ .+ . .++..+..|..-+++++. .+...++.+|.++.+
T Consensus 10 ~a~~ia~Vs~~lA~~~~NI~~I~~l~~~-~~--~-----~~~~~~~~~~~e~~v~~~~~~~~~lr~~L~~la~ 74 (84)
T cd04871 10 TAEQLAAVTRVVADQGLNIDRIRRLSGR-VP--L-----EEQDDSPKACVEFSVRGQPADLEALRAALLELAS 74 (84)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHhhcc-cc--c-----cccCCCCcEEEEEEEeCCCCCHHHHHHHHHHHhc
Confidence 6899999999999999999998764111 00 0 011112345555555543 344678888887754
No 221
>PRK03381 PII uridylyl-transferase; Provisional
Probab=43.44 E-value=85 Score=35.97 Aligned_cols=34 Identities=9% Similarity=0.084 Sum_probs=28.6
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
.|-|.+..+|+||.|+++-.+|+.+|+|+..-..
T Consensus 707 ~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI 740 (774)
T PRK03381 707 ATVLEVRAADRPGLLARLARALERAGVDVRWARV 740 (774)
T ss_pred eEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEE
Confidence 4666677789999999999999999999995443
No 222
>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=42.91 E-value=68 Score=31.10 Aligned_cols=72 Identities=22% Similarity=0.171 Sum_probs=43.5
Q ss_pred ccEEEEeCCCccHHHHHHhhhC---C-CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEE
Q 014547 127 QLRVAYQGVPGAYSEAAAGKAY---P-NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVG 202 (423)
Q Consensus 127 ~~~VayLGP~GTfSh~AA~~~f---~-~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Ivg 202 (423)
..|||+.= +||=.+.-++.+. + ..|++..++..++++++++|++|-|||+.|=+. |.-. -|+|.+.++++=|
T Consensus 68 ~~rI~vwR-kGsaADvl~Ral~d~~~~~~EvVytdD~~~i~~Ml~~g~vdsAVv~~~~~~-G~~f--Edl~~~~g~~~Pg 143 (201)
T PF12916_consen 68 KPRIAVWR-KGSAADVLTRALLDLKGIKAEVVYTDDMSEIVKMLNEGEVDSAVVGSEFSK-GETF--EDLLGSLGLYAPG 143 (201)
T ss_dssp SSEEEESS-TTSHHHHHHHHHHHHH--T-EEEE---HHHHHHHHHTT-E--EEEETTT----EEH--HHHHHHTT-----
T ss_pred CceEEEEe-cccHHHHHHHHHHhhccccceeEEecCHHHHHHHHhcCceeeeeecchhcc-chhH--HHHHhhcCCCCCh
Confidence 45899996 8998887666543 3 589999999999999999999999999955333 3222 2677778877665
No 223
>PF07485 DUF1529: Domain of Unknown Function (DUF1259); InterPro: IPR011094 This family is the lppY/lpqO homologue family. They are related to 'probable conserved lipoproteins' LppY and LpqO from Mycobacterium bovis.
Probab=42.66 E-value=1e+02 Score=27.51 Aligned_cols=51 Identities=16% Similarity=0.212 Sum_probs=40.8
Q ss_pred cHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH
Q 014547 330 SVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE 396 (423)
Q Consensus 330 GaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e 396 (423)
..+..+++.+.++||.+|-|..--...+| -.||+-++++-+...+...+++
T Consensus 68 ~EV~pvi~aL~~~GI~vtAlHNH~l~e~P----------------rl~ymH~~~~gdp~~lA~~vr~ 118 (123)
T PF07485_consen 68 DEVNPVISALRKNGIEVTALHNHWLFEQP----------------RLFYMHIWGVGDPAKLARKVRA 118 (123)
T ss_pred HHHHHHHHHHHHCCceEEEEecccccCCC----------------CEEEEEEEecCCHHHHHHHHHH
Confidence 45778999999999999999998887766 4899999987655566555554
No 224
>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=42.15 E-value=3.2e+02 Score=28.23 Aligned_cols=98 Identities=18% Similarity=0.077 Sum_probs=57.6
Q ss_pred CceeEEeccCHHHHHHHHHhcCCCCeeEEccH---HHHHHcCCceeecCccCCCCCeeEEEEEeeCCC-CCC----CCCC
Q 014547 245 LNVAREAVDDTAGAAEYIAANDLRDTAAIASA---RAAELYGMQVLEDGIQDDSSNVTRFVMLAREPI-IPR----TDRP 316 (423)
Q Consensus 245 p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~---~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~-~~~----~~~~ 316 (423)
|+++.+..-|..+|.++...+ |-+-.. ..|..++.+|.-.|..+.. --|.. .+... .+. ....
T Consensus 188 ~~a~~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~a~~~~i~i~i~~~~~~~-~gT~I---~~~~~~~~~v~~I~~~~ 258 (401)
T TIGR00656 188 EAAKRIDKISYEEALELATFG-----AKVLHPRTVEPAMRSGVPIEVRSSFDPE-EGTLI---TNSMENPPLVKGIALRK 258 (401)
T ss_pred CCcEECCccCHHHHHHHHHcC-----CcccCHHHHHHHHHCCCeEEEEECCCCC-CCeEE---EeCcccCCceEEEEEEC
Confidence 455666666777887776642 223333 3345688988888775533 23333 22211 000 0011
Q ss_pred CeEEEEEE---eCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 317 FKTSIVFA---HDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 317 ~KTSivf~---l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
+.+-+.+. +.+++|.+.++++.|++++||+..|..
T Consensus 259 ~va~vsv~g~~~~~~~g~~~~if~~L~~~~I~i~~i~~ 296 (401)
T TIGR00656 259 NVTRVTVHGLGMLGKRGFLARIFGALAERNINVDLISQ 296 (401)
T ss_pred CEEEEEEecCCCCCCccHHHHHHHHHHHcCCcEEEEEc
Confidence 22333333 567899999999999999999987754
No 225
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=41.35 E-value=3.2e+02 Score=26.00 Aligned_cols=146 Identities=12% Similarity=0.047 Sum_probs=71.3
Q ss_pred CccEEEEeCCCccH-HHH---HHhhhCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEE
Q 014547 126 SQLRVAYQGVPGAY-SEA---AAGKAYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHI 200 (423)
Q Consensus 126 ~~~~VayLGP~GTf-Sh~---AA~~~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 200 (423)
+..+||+....+.+ -.. +..+.+|+.++.- ..+-+++++.+.+|++|+|++.-....... .-....|.+.++.+
T Consensus 97 ~~l~I~~~~~~~~~~l~~~l~~f~~~~p~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~-~l~~~~l~~~~~~~ 175 (294)
T PRK09986 97 GRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNP-GFTSRRLHESAFAV 175 (294)
T ss_pred ceEEEEEehHHhHHHHHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHcCCCCEEEecCCccCCCC-CeEEEEeecccEEE
Confidence 46788886554421 111 1223467765543 345688999999999999997311000000 00001111122221
Q ss_pred EEEEEEeeeeeeeecCCCCcCccc---EEEech--hHHH-HHHHHHHHcC--CceeEEeccCHHHHHHHHHhcCCCCeeE
Q 014547 201 VGEVQLPVHHCLLALPGVRKEYLT---RVISHP--QALS-QCEHTLTKLG--LNVAREAVDDTAGAAEYIAANDLRDTAA 272 (423)
Q Consensus 201 vgEi~lpI~h~Lla~~g~~l~dIk---~VySHP--qAL~-QC~~fL~~~~--p~~~~v~~~STA~AA~~va~~~~~~~AA 272 (423)
..+-.|-|...+..+++++. -|...+ .... +..+++.+++ ++. ...++|.....+.|+.+ ...+
T Consensus 176 ----v~~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g---~gi~ 247 (294)
T PRK09986 176 ----AVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVCQQAGFSPQI-IRQVNEPQTVLAMVSMG---IGIT 247 (294)
T ss_pred ----EEcCCCCcccCCccCHHHHcCCCEEecCCCchhHHHHHHHHHHHCCCCCce-eeecCCHHHHHHHHHcC---CeEE
Confidence 12223333332223344443 344322 1233 5556665553 332 23466677777777764 5677
Q ss_pred EccHHHHH
Q 014547 273 IASARAAE 280 (423)
Q Consensus 273 IaS~~AAe 280 (423)
+.++..++
T Consensus 248 ~l~~~~~~ 255 (294)
T PRK09986 248 LLPDSYAQ 255 (294)
T ss_pred EccHHHhh
Confidence 77776554
No 226
>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=41.30 E-value=2.2e+02 Score=24.09 Aligned_cols=32 Identities=19% Similarity=0.009 Sum_probs=24.3
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEee
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
.+|+.++... .+..+..+.+.+|++|+|++..
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08449 25 QYPNVTVRFHELSPEAQKAALLSKRIDLGFVRF 57 (197)
T ss_pred HCCCeEEEEEECCHHHHHHHHhCCCccEEEecc
Confidence 4677665443 3578899999999999999754
No 227
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=41.28 E-value=3.3e+02 Score=26.09 Aligned_cols=124 Identities=11% Similarity=0.018 Sum_probs=61.7
Q ss_pred hhCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCc---C
Q 014547 146 KAYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRK---E 221 (423)
Q Consensus 146 ~~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l---~ 221 (423)
+.+|+.++.... +.+++++.+.+|++|+|++.-.....+ + ....|.+.++.++. +-.|-|......++ .
T Consensus 114 ~~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~-l--~~~~l~~~~~~~v~----~~~~pl~~~~~i~~~~L~ 186 (296)
T PRK09906 114 LRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDE-I--DYLELLDEPLVVVL----PVDHPLAHEKEITAAQLD 186 (296)
T ss_pred HHCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecCCCCCCC-c--eEEEEecccEEEEe----cCCCccccCCCcCHHHHc
Confidence 346777665433 568899999999999999854321111 0 11222233333322 22232322222222 2
Q ss_pred cccEEEech---h-HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 222 YLTRVISHP---Q-ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 222 dIk~VySHP---q-AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
+..-|.--+ . ...+..+|++..+...+ ...++|.......++.+ ...++.+...+
T Consensus 187 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g~~~~p~~~~ 246 (296)
T PRK09906 187 GVNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG---LGCTIIPGYMN 246 (296)
T ss_pred CCCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcEEEeeHHHh
Confidence 333343211 1 13445667766542222 33456666677777754 34555665544
No 228
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=40.89 E-value=63 Score=32.68 Aligned_cols=50 Identities=30% Similarity=0.242 Sum_probs=37.7
Q ss_pred cEEEEeCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeec
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVE 179 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIE 179 (423)
.|||.-|+--| ++.-.+-++|+.++++. -|+++..||.+|++|-|++=.|
T Consensus 96 ~rvavpG~~TT-A~lL~rl~~p~~~~V~m-~fdeI~~Avl~G~VDaGvlIHE 145 (272)
T COG2107 96 KRVAVPGEMTT-AALLFRLAYPKAEIVYM-PFDEIIPAVLEGKVDAGVLIHE 145 (272)
T ss_pred ceEecCCcccH-HHHHHHHhCCCceEEEe-eHHHHHHHHHcCCCccceEEee
Confidence 47887776533 34444556788777764 5999999999999999999766
No 229
>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=40.77 E-value=2.2e+02 Score=23.94 Aligned_cols=123 Identities=20% Similarity=0.153 Sum_probs=59.9
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCc---
Q 014547 147 AYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEY--- 222 (423)
Q Consensus 147 ~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~d--- 222 (423)
.+|+.++.. ..+..++.+++.+|++|+|++.......+.. ...|.+..+.++. +-.|-+......++++
T Consensus 25 ~~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v~----~~~~~~~~~~~i~~~~l~~ 97 (201)
T cd08420 25 RYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLI---VEPFAEDELVLVV----PPDHPLAGRKEVTAEELAA 97 (201)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEecCCCCCcceE---EEeecCccEEEEe----cCCCCccccCccCHHHHhc
Confidence 367765533 3466789999999999999985432211111 0112222222221 1222222221222222
Q ss_pred ccEEEechh--HHHHHHHHHHHcC-----CceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 223 LTRVISHPQ--ALSQCEHTLTKLG-----LNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 223 Ik~VySHPq--AL~QC~~fL~~~~-----p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
..-|.-.+. -..+..+|+.+++ ++. ...+++...+.+.++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08420 98 EPWILREPGSGTREVFERALAEAGLDGLDLNI-VMELGSTEAIKEAVEAG---LGISILSRLAVR 158 (201)
T ss_pred CCEEEecCCCCHHHHHHHHHHHcCcccccCce-EEEECCHHHHHHHHHcC---CCEEEeeHHHHH
Confidence 233332211 1234556666432 222 33456666777777754 467777776554
No 230
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=40.23 E-value=3.5e+02 Score=26.71 Aligned_cols=144 Identities=20% Similarity=0.139 Sum_probs=68.2
Q ss_pred CccEEEEeCCCccH-HHHHH---hhhCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEE
Q 014547 126 SQLRVAYQGVPGAY-SEAAA---GKAYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHI 200 (423)
Q Consensus 126 ~~~~VayLGP~GTf-Sh~AA---~~~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 200 (423)
+..+|+.....+.+ =.... .+.+|+.++.. ...-.++.+.|.+|++|+|+++-.--..+.. +..|.+..+.+
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 35788876443332 11111 12357766543 3456788999999999999985210001100 11122222222
Q ss_pred EEEEEEeeeeeeeecCCCCcCccc---EEE--echhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEcc
Q 014547 201 VGEVQLPVHHCLLALPGVRKEYLT---RVI--SHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIAS 275 (423)
Q Consensus 201 vgEi~lpI~h~Lla~~g~~l~dIk---~Vy--SHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS 275 (423)
+ ++-.|-|......+++++. -|. .+.........|+++.+...+...++|.....+.+..+ ...+|.+
T Consensus 166 v----~~~~hpl~~~~~i~~~~L~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~i~p 238 (317)
T PRK15421 166 V----LAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAAR---MGIAALP 238 (317)
T ss_pred E----EcCCCCccccCcCCHHHhCCCcEEecCCchhhHHHHHHHHHHhCCCCceeecCCHHHHHHHHHhC---CcEEEec
Confidence 1 2333333322223333332 222 11122344555666654333333466777677777764 3455666
Q ss_pred HHHH
Q 014547 276 ARAA 279 (423)
Q Consensus 276 ~~AA 279 (423)
...+
T Consensus 239 ~~~~ 242 (317)
T PRK15421 239 HWVV 242 (317)
T ss_pred chhc
Confidence 5533
No 231
>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=39.94 E-value=1.7e+02 Score=22.30 Aligned_cols=33 Identities=9% Similarity=0.189 Sum_probs=26.2
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeee
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIE 350 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIE 350 (423)
+.|++=.+...+|.+.++++.|++.|||+.-|-
T Consensus 3 ~VsvVG~~~~~~~~~~~i~~aL~~~~I~v~~i~ 35 (65)
T cd04918 3 IISLIGNVQRSSLILERAFHVLYTKGVNVQMIS 35 (65)
T ss_pred EEEEECCCCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 445555555578999999999999999997665
No 232
>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=39.88 E-value=1.5e+02 Score=21.88 Aligned_cols=27 Identities=11% Similarity=0.160 Sum_probs=23.4
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
+.+.+|.+.++++.|++.|||+--|..
T Consensus 11 ~~~~~~~~~~if~~L~~~~I~v~~i~q 37 (66)
T cd04919 11 MKNMIGIAGRMFTTLADHRINIEMISQ 37 (66)
T ss_pred CCCCcCHHHHHHHHHHHCCCCEEEEEe
Confidence 446799999999999999999987754
No 233
>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=39.64 E-value=2.7e+02 Score=24.55 Aligned_cols=32 Identities=9% Similarity=-0.159 Sum_probs=23.4
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCcCeEEEee
Q 014547 147 AYPNCEAIP-CDQFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 147 ~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
.+|+.++.- ..+-.++.+.+.+|++|+|+...
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 25 EAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred HCCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 357765533 23566889999999999999853
No 234
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=39.57 E-value=3.5e+02 Score=25.93 Aligned_cols=116 Identities=11% Similarity=-0.010 Sum_probs=60.7
Q ss_pred hhCCCCcee-ecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCccc
Q 014547 146 KAYPNCEAI-PCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLT 224 (423)
Q Consensus 146 ~~f~~~e~v-p~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk 224 (423)
+.||+.++. -.....++++.|++|++|+|+....... + . +..+......+++++.++-.+..-.
T Consensus 113 ~~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~--------~-----~--l~~~~l~~~~~~~v~~~~~~~~~~~ 177 (275)
T PRK03601 113 QNQEALQFEARIAQRQSLVKQLHERQLDLLITTEAPKM--------D-----E--FSSQLLGHFTLALYTSAPSKKKSEL 177 (275)
T ss_pred HhCCCcEEEEEECChHHHHHHHHcCCCCEEEEcCCCcc--------C-----C--ccEEEecceeEEEEecCchhhcccC
Confidence 346777664 3566778999999999999997533211 1 1 1222222334455555442211111
Q ss_pred EEE--echhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 225 RVI--SHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 225 ~Vy--SHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
..+ ..+..+.+-..++....+.. ...++|.....++++.+ ...++.+...++
T Consensus 178 ~~i~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g---~gv~~~p~~~~~ 231 (275)
T PRK03601 178 NYIRLEWGADFQQHEAGLIGADEVP-ILTTSSAELARQLLATL---NGCAFLPVHWAK 231 (275)
T ss_pred CeEEccCCccHhHHHHHhcccCCcc-eEEeCcHHHHHHHHHhC---CCEEEEcHHHHh
Confidence 111 12222333222222222222 34567777777787764 457787776654
No 235
>PRK03059 PII uridylyl-transferase; Provisional
Probab=39.07 E-value=1.4e+02 Score=34.71 Aligned_cols=36 Identities=11% Similarity=0.194 Sum_probs=29.9
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeee--eeee
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTK--IESR 352 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtk--IESR 352 (423)
..|-|.+..+|+||-|+++-++|+..|+|+.. |.+.
T Consensus 785 ~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~ 822 (856)
T PRK03059 785 QYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTL 822 (856)
T ss_pred CEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeec
Confidence 35666677789999999999999999999984 5554
No 236
>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=39.05 E-value=2.2e+02 Score=27.46 Aligned_cols=131 Identities=10% Similarity=0.015 Sum_probs=70.1
Q ss_pred CCCccHHHHHHhhhCC-CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeee
Q 014547 134 GVPGAYSEAAAGKAYP-NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCL 212 (423)
Q Consensus 134 GP~GTfSh~AA~~~f~-~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~L 212 (423)
|..--+-++++.. .+ +.......++.+++.++++|++|..+..+. +.+.-. ..+.... -++.....+
T Consensus 56 G~~~dl~~~i~~~-lg~~~~~~~~~~w~~~~~~l~~G~~Di~~~~~~------~t~eR~----~~~~fs~-py~~~~~~~ 123 (275)
T TIGR02995 56 GAAPDVARAIFKR-LGIADVNASITEYGALIPGLQAGRFDAIAAGLF------IKPERC----KQVAFTQ-PILCDAEAL 123 (275)
T ss_pred cchHHHHHHHHHH-hCCCceeeccCCHHHHHHHHHCCCcCEEeeccc------CCHHHH----hcccccc-ceeecceeE
Confidence 4444444444443 22 112345567899999999999997544221 111111 1111111 112233456
Q ss_pred eecCCC-----CcCcc-----cEEEechhHHHHHHHHHHHc-CCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 213 LALPGV-----RKEYL-----TRVISHPQALSQCEHTLTKL-GLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 213 la~~g~-----~l~dI-----k~VySHPqAL~QC~~fL~~~-~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
+.+++. .++++ ++|-....... .++|++. .++.+++.+.|..++.+.+..+ +-.++|.....+.
T Consensus 124 ~~~~~~~~~i~~~~dl~~~~g~~Igv~~g~~~--~~~l~~~~~~~~~i~~~~~~~~~i~~L~~g--rvDa~i~d~~~~~ 198 (275)
T TIGR02995 124 LVKKGNPKGLKSYKDIAKNPDAKIAAPGGGTE--EKLAREAGVKREQIIVVPDGQSGLKMVQDG--RADAYSLTVLTIN 198 (275)
T ss_pred EEECCCCCCCCCHHHhccCCCceEEEeCCcHH--HHHHHHcCCChhhEEEeCCHHHHHHHHHcC--CCCEEecChHHHH
Confidence 665543 23344 24443333322 4567654 3555677788999999999976 4678888776544
No 237
>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=38.90 E-value=2.4e+02 Score=23.82 Aligned_cols=118 Identities=14% Similarity=0.013 Sum_probs=60.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCC------
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVR------ 219 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~------ 219 (423)
.+|+.++... .+.+++.+.+.+|++|+|+..-..... ..+ +..+......+++++.++-.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~-----------~~~--~~~~~l~~~~~~~v~~~~~p~~~~~~ 91 (195)
T cd08427 25 RHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPL-----------PKD--LVWTPLVREPLVLIAPAELAGDDPRE 91 (195)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCCCEEEEcCCCCcc-----------ccC--ceEEEcccCcEEEEECCCCCcchHHH
Confidence 4677766543 356889999999999999985321110 001 12222223334444433221
Q ss_pred -cCcccEEEe-chhH-HHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 220 -KEYLTRVIS-HPQA-LSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 220 -l~dIk~VyS-HPqA-L~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
+.+-.-|.. +... -.+..+|+.++..... ...+++...+.+++..+ ...||.+...++
T Consensus 92 ~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 153 (195)
T cd08427 92 LLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQG---LGVAIVPDIAVP 153 (195)
T ss_pred HhcCCCeEEecCCchHHHHHHHHHHHcCCCCCeEEEeccHHHHHHHHHhC---CcEEEccHHHHh
Confidence 222222221 1111 2334566666543222 23455666666677664 467777776554
No 238
>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=38.54 E-value=3.7e+02 Score=25.96 Aligned_cols=55 Identities=15% Similarity=0.062 Sum_probs=38.8
Q ss_pred CCCccEEEEeCCCccHHHHH---Hhhh---CCCC--ceeecCCHHHHHHHHHcCCcCeEEEee
Q 014547 124 HGSQLRVAYQGVPGAYSEAA---AGKA---YPNC--EAIPCDQFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 124 ~~~~~~VayLGP~GTfSh~A---A~~~---f~~~--e~vp~~Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
....++|++..+.|+|--.+ ++.+ +++. ++++..+-.+.+++|.+|++|++++..
T Consensus 28 ~~~~l~Ig~~~~~~~~~~~~~~la~~~~~~~~~i~v~~~~~~~~~~~~~~l~~G~~D~~~~~~ 90 (320)
T TIGR02122 28 EPTFVTIGTGGTGGVYYPIGGAIAQLINKKSGKLRVRVQSTGGSVENVNLLEAGEADLAIVQS 90 (320)
T ss_pred CCceEEEEeCCCCCChHHHHHHHHHHHhccCCCeeEEEEeCcchHHHHHHHhCCCCcEEEEcc
Confidence 34478999999999865432 2222 3433 455556677899999999999999863
No 239
>PRK06635 aspartate kinase; Reviewed
Probab=38.29 E-value=4.2e+02 Score=27.39 Aligned_cols=28 Identities=18% Similarity=0.214 Sum_probs=24.9
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeeee
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIESR 352 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIESR 352 (423)
..++||.|.++++.|+++|||+..|.+-
T Consensus 270 ~~~~~g~l~~i~~~L~~~~I~i~~is~s 297 (404)
T PRK06635 270 VPDKPGIAAQIFGALAEANINVDMIVQN 297 (404)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEec
Confidence 5678999999999999999999988554
No 240
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=38.16 E-value=89 Score=29.73 Aligned_cols=48 Identities=15% Similarity=0.231 Sum_probs=36.4
Q ss_pred cEEEEeCCCccHHHHHHhhhCC--CCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYP--NCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~--~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+||+ +.|+..+.-..+.+. +.+.+..++.++++++|..|++|+.+..
T Consensus 134 ~~Igv--~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 134 KHVGV--LQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred CEEEE--ecCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeC
Confidence 47888 478776554444333 4677889999999999999999998764
No 241
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=38.02 E-value=55 Score=32.46 Aligned_cols=46 Identities=20% Similarity=0.137 Sum_probs=37.4
Q ss_pred CCCccHHHHHHhhh--CC--CCceeecCCHHHHHHHHHcCCcCeEEEeec
Q 014547 134 GVPGAYSEAAAGKA--YP--NCEAIPCDQFEVAFQAVELWIADRAVLPVE 179 (423)
Q Consensus 134 GP~GTfSh~AA~~~--f~--~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIE 179 (423)
-|.|-|+.++-.+. +. ...++.-.+.++++..|+.|++|+|+|=.-
T Consensus 146 ~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~s 195 (258)
T COG0725 146 VPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYVS 195 (258)
T ss_pred CCchHHHHHHHHHhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEEE
Confidence 48999999987653 22 246788899999999999999999999643
No 242
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=37.99 E-value=52 Score=30.80 Aligned_cols=48 Identities=29% Similarity=0.247 Sum_probs=37.1
Q ss_pred cEEEEeCCCccH--HHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAY--SEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTf--Sh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+.+ .||. .+.......+..+++.+++..+++.++.+|++|..+..
T Consensus 147 k~v~v~--~gt~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d 196 (275)
T COG0834 147 KKVGVQ--LGTTDEAEEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSD 196 (275)
T ss_pred CEEEEE--cCcchhHHHHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcc
Confidence 466665 5666 45445444567889999999999999999999998774
No 243
>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=36.69 E-value=2.6e+02 Score=23.57 Aligned_cols=31 Identities=16% Similarity=0.028 Sum_probs=23.9
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCcCeEEEe
Q 014547 147 AYPNCEAIP-CDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 147 ~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+.++.. ..+-.++.+.+.+|++|+|+..
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~ 56 (197)
T cd08448 25 EYPGIEVALHEMSSAEQIEALLRGELDLGFVH 56 (197)
T ss_pred HCCCCeEEEEeCCHHHHHHHHHcCCcceEEEe
Confidence 467776543 3357889999999999999974
No 244
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=36.31 E-value=68 Score=29.91 Aligned_cols=72 Identities=21% Similarity=0.368 Sum_probs=45.6
Q ss_pred HHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHH--HHhh--cCceEEEc
Q 014547 333 FKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAE--VQEF--TSFLRVLG 408 (423)
Q Consensus 333 ~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~e--L~~~--~~~vrvLG 408 (423)
.+.|++.++|||.+.|. .|+..... + ..|+|.| .|++.+++++++. .+.. -..|..||
T Consensus 58 ~R~~s~lK~hGI~~~H~-aRqit~~D--------F---~~FDYI~------~MDesN~~dL~~~a~~~~~~~kakV~Llg 119 (159)
T KOG3217|consen 58 PRTLSILKKHGIKIDHL-ARQITTSD--------F---REFDYIL------AMDESNLRDLLRKASNQPKGSKAKVLLLG 119 (159)
T ss_pred hHHHHHHHHcCCcchhh-cccccHhH--------h---hhcceeE------EecHHHHHHHHHHhccCCCCcceEEEEee
Confidence 58899999999997765 57766431 0 1233332 3677888777764 3322 23588999
Q ss_pred cccCC-----CCCCCCCCC
Q 014547 409 SYPMD-----MTPWSPSRG 422 (423)
Q Consensus 409 sYp~~-----~~pw~p~~~ 422 (423)
+|-.. .+||.-+.+
T Consensus 120 sy~~~~~~~I~DPyYg~~~ 138 (159)
T KOG3217|consen 120 SYDKNGQKIIEDPYYGGDS 138 (159)
T ss_pred ccCCCCCeecCCCCCCccc
Confidence 99632 378876543
No 245
>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=35.52 E-value=2.7e+02 Score=23.44 Aligned_cols=116 Identities=15% Similarity=0.025 Sum_probs=62.1
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCC-------
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGV------- 218 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~------- 218 (423)
.+|+.++... .+-+++.+.+.+|++|+|++....-.. .+..+.......++++.++-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~---------------~~~~~~l~~~~~~~v~~~~~~~~~~~~ 89 (193)
T cd08442 25 RYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHP---------------RLEQEPVFQEELVLVSPKGHPPVSRAE 89 (193)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEEeCCCCCC---------------CcEEEEeecCcEEEEecCCCcccccHH
Confidence 4677765443 356788999999999999975221101 12222233333444443322
Q ss_pred CcCcccEEEec-h-hHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 219 RKEYLTRVISH-P-QALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 219 ~l~dIk~VySH-P-qAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
++.+..-|.-. . ....+...|+.+++.... ...+++...+.+++.++ ...++.+...++
T Consensus 90 ~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 151 (193)
T cd08442 90 DLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAG---MGIALLPRSVLD 151 (193)
T ss_pred HhCCCceEEecCCCcHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHhC---CcEEEcCHHHHh
Confidence 12223333211 1 123446677776643222 33466666777777764 457777777665
No 246
>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=35.11 E-value=4.3e+02 Score=25.66 Aligned_cols=127 Identities=13% Similarity=-0.043 Sum_probs=67.7
Q ss_pred EEEEeCCCccHHHHHHhh-hC----C-CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHh-hcCCcEEE
Q 014547 129 RVAYQGVPGAYSEAAAGK-AY----P-NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLL-LRHRLHIV 201 (423)
Q Consensus 129 ~VayLGP~GTfSh~AA~~-~f----~-~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL-~~~~L~Iv 201 (423)
+|+|+=.. +--..|-.+ +| + +++++++.+-.++++++..|++|++++... . ++... ...++.++
T Consensus 2 ~~~~~~~~-~p~~va~~~G~~~k~~Gl~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~-------~-~~~a~~~g~~~~~v 72 (300)
T TIGR01729 2 TVGYQTIV-EPFKVAQADGAAAKEAGATIDWRKFDSGADISTALASGNVPIGVIGSS-------P-LAAAASRGVPIELF 72 (300)
T ss_pred EEEecCCC-CHHHHHHHcCchHHhcCCeeEEEecCcHHHHHHHHHcCCCCEeccCCC-------H-HHHHHHCCCCeEEE
Confidence 68886433 323344333 23 2 468889999899999999999999865311 1 11111 22355554
Q ss_pred EEEE-EeeeeeeeecCCCCc---Cccc--EEEechhH--HHHHHHHHHHcCCc---eeEEeccCHHHHHHHHHhc
Q 014547 202 GEVQ-LPVHHCLLALPGVRK---EYLT--RVISHPQA--LSQCEHTLTKLGLN---VAREAVDDTAGAAEYIAAN 265 (423)
Q Consensus 202 gEi~-lpI~h~Lla~~g~~l---~dIk--~VySHPqA--L~QC~~fL~~~~p~---~~~v~~~STA~AA~~va~~ 265 (423)
.-.. ..-.+.|+++++..+ +|++ +|..++-. ...-..||++++.. ++.+.. +..+++..+..+
T Consensus 73 ~~~~~~~~~~~lv~~~~s~I~s~~DLkGK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~G 146 (300)
T TIGR01729 73 WILDNIGKSEALVAREGSGIEKPEDLKGKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQRG 146 (300)
T ss_pred EEeccCCccceEEecCCCCCCChhHcCCCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHcC
Confidence 4221 112357888776433 3333 56544321 22234577766532 444444 345566666654
No 247
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=34.84 E-value=6.2e+02 Score=29.47 Aligned_cols=129 Identities=12% Similarity=0.058 Sum_probs=74.4
Q ss_pred CceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHH---HHcCCceeecCccCCCCCeeEEEEEeeCCCCCC----CCCCC
Q 014547 245 LNVAREAVDDTAGAAEYIAANDLRDTAAIASARAA---ELYGMQVLEDGIQDDSSNVTRFVMLAREPIIPR----TDRPF 317 (423)
Q Consensus 245 p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AA---elYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~~----~~~~~ 317 (423)
|+++.+..-|..+|.++...+ |.+-...|+ ..+|.+|.-.+..+....-|..- ......+. ....+
T Consensus 249 ~~a~~i~~ls~~e~~el~~~g-----~~v~~~~a~~~a~~~~i~i~v~~~~~~~~~gT~I~--~~~~~~~~v~~It~~~~ 321 (861)
T PRK08961 249 PDARLLTRLDYDEAQEIATTG-----AKVLHPRSIKPCRDAGIPMAILDTERPDLSGTSID--GDAEPVPGVKAISRKNG 321 (861)
T ss_pred CCceEecccCHHHHHHHHHCC-----CeEECHHHHHHHHHCCCCEEEEeCCCCCCCccEEe--CCCCCCCcceeEEEECC
Confidence 455666666777777765532 455555554 45799998888765443444432 11111010 01112
Q ss_pred eEEEEEE---eCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCc-ChHHHHHH
Q 014547 318 KTSIVFA---HDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASM-AEVRAQNA 393 (423)
Q Consensus 318 KTSivf~---l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~-~d~~v~~a 393 (423)
-+-|-+. ..+.+|.+.++++.|++++||+-.|.+-. ....|.|+-.... .+..++.+
T Consensus 322 v~lItv~~~~~~~~~g~~a~if~~la~~~I~Vd~I~sse-------------------~sis~~i~~~~~~~~~~~~~~l 382 (861)
T PRK08961 322 IVLVSMETIGMWQQVGFLADVFTLFKKHGLSVDLISSSE-------------------TNVTVSLDPSENLVNTDVLAAL 382 (861)
T ss_pred EEEEEEecCCccccccHHHHHHHHHHHcCCeEEEEEcCC-------------------CEEEEEEccccccchHHHHHHH
Confidence 2333332 23578999999999999999999995421 2467777654321 23456666
Q ss_pred HHHHHh
Q 014547 394 LAEVQE 399 (423)
Q Consensus 394 L~eL~~ 399 (423)
+++|++
T Consensus 383 ~~~l~~ 388 (861)
T PRK08961 383 SADLSQ 388 (861)
T ss_pred HHHHhh
Confidence 666653
No 248
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=33.54 E-value=2.7e+02 Score=26.43 Aligned_cols=131 Identities=13% Similarity=0.088 Sum_probs=67.6
Q ss_pred eCCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeee
Q 014547 133 QGVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCL 212 (423)
Q Consensus 133 LGP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~L 212 (423)
.|..--.-++++.+.--+.++++. .+..+++++++|++|.++-++--+-+= ...++. ...+ +.....+
T Consensus 49 ~G~~vdi~~~ia~~lg~~i~~~~~-pw~~~~~~l~~g~~D~~~~~~~~t~eR--~~~~~f--s~p~-------~~~~~~~ 116 (259)
T PRK15437 49 VGFDIDLAKELCKRINTQCTFVEN-PLDALIPSLKAKKIDAIMSSLSITEKR--QQEIAF--TDKL-------YAADSRL 116 (259)
T ss_pred EeeeHHHHHHHHHHcCCceEEEeC-CHHHHHHHHHCCCCCEEEecCCCCHHH--hhhccc--cchh-------hcCceEE
Confidence 455555666666654346778875 599999999999999765554322110 000110 0011 1112233
Q ss_pred eecCCC----CcCccc--EEEechhHHHHHHHHHHHcC--CceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 213 LALPGV----RKEYLT--RVISHPQALSQCEHTLTKLG--LNVAREAVDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 213 la~~g~----~l~dIk--~VySHPqAL~QC~~fL~~~~--p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
+++++. +++|++ +|-.-.-. .+ .+|+.++. .++.++...+..++.+++..+ +-.++|.+...+
T Consensus 117 ~~~~~~~~~~~~~dl~g~~Igv~~g~-~~-~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~g--rvD~~v~~~~~~ 187 (259)
T PRK15437 117 VVAKNSDIQPTVESLKGKRVGVLQGT-TQ-ETFGNEHWAPKGIEIVSYQGQDNIYSDLTAG--RIDAAFQDEVAA 187 (259)
T ss_pred EEECCCCCCCChHHhCCCEEEEecCc-HH-HHHHHhhccccCceEEecCCHHHHHHHHHcC--CccEEEechHHH
Confidence 333332 122222 22211111 11 23554432 245667778888888888765 456778777654
No 249
>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=33.42 E-value=2.5e+02 Score=24.37 Aligned_cols=33 Identities=15% Similarity=-0.053 Sum_probs=25.4
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCcCeEEEeec
Q 014547 147 AYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVE 179 (423)
Q Consensus 147 ~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIE 179 (423)
.+|+.++.. ..+..++++.+.+|++|+|+...+
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~ 58 (200)
T cd08465 25 EAPGIDLAVSQASREAMLAQVADGEIDLALGVFP 58 (200)
T ss_pred HCCCcEEEEecCChHhHHHHHHCCCccEEEeccc
Confidence 367776543 356789999999999999997543
No 250
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=33.15 E-value=1.5e+02 Score=22.89 Aligned_cols=63 Identities=16% Similarity=0.228 Sum_probs=46.2
Q ss_pred EEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcCh-HHHHHHHHHHHhh
Q 014547 322 VFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAE-VRAQNALAEVQEF 400 (423)
Q Consensus 322 vf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d-~~v~~aL~eL~~~ 400 (423)
-|.+.+..-+|...|.-.-..++.-..|...|.. .++.|.|+-.|+++. .-+.+|++.|.+.
T Consensus 2 ~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~~~~~-----------------~~~~~~IeT~g~~~p~~~l~~A~~~l~~~ 64 (66)
T PF01193_consen 2 EFLLKGEDHTLGNALRRILLSEVPGVAIDGHPNE-----------------DKFVFRIETDGSLTPKEALLKAIKILKEK 64 (66)
T ss_dssp EEEEESHHHHHHHHHHHHHHSSSEEEEEEESSEE-----------------EEEEEEEEEBSSS-HHHHHHHHHHHHHHH
T ss_pred EeEEcCCchHHHHHHHHHHHhcCCCceEEecCCC-----------------CEEEEEEEECCCCCHHHHHHHHHHHHHHh
Confidence 3555555667888999888889888888884432 478999999998653 5668888888765
Q ss_pred c
Q 014547 401 T 401 (423)
Q Consensus 401 ~ 401 (423)
+
T Consensus 65 ~ 65 (66)
T PF01193_consen 65 L 65 (66)
T ss_dssp H
T ss_pred c
Confidence 3
No 251
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=33.13 E-value=4.6e+02 Score=25.41 Aligned_cols=52 Identities=13% Similarity=0.027 Sum_probs=36.0
Q ss_pred CccEEEEeCCCcc-HHHHHH---hhhCCCCceeecC-CHHHHHHHHHcCCcCeEEEe
Q 014547 126 SQLRVAYQGVPGA-YSEAAA---GKAYPNCEAIPCD-QFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 126 ~~~~VayLGP~GT-fSh~AA---~~~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVP 177 (423)
+..+|+.....+. +-.... .+.+|+.++.... +..++.+.|.+|++|+|+..
T Consensus 95 g~l~ig~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 95 GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred ceEEEEEcCcchHhHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEEc
Confidence 4688998877664 322222 2346777665443 56888999999999999984
No 252
>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=33.03 E-value=2.2e+02 Score=21.98 Aligned_cols=27 Identities=19% Similarity=0.166 Sum_probs=23.4
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
+.+.+|.+.++++.|++.+|++..|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~~ 37 (80)
T cd04921 11 MVGVPGIAARIFSALARAGINVILISQ 37 (80)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEe
Confidence 456789999999999999999987754
No 253
>PRK05007 PII uridylyl-transferase; Provisional
Probab=32.53 E-value=1.5e+02 Score=34.55 Aligned_cols=35 Identities=20% Similarity=0.187 Sum_probs=29.5
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeee--eeee
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTK--IESR 352 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtk--IESR 352 (423)
-|.|.+..+|+||-|+++.++|+.+|+|+.. |.+.
T Consensus 701 ~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~ 737 (884)
T PRK05007 701 GTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTS 737 (884)
T ss_pred eEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEc
Confidence 5677778889999999999999999999985 4444
No 254
>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=32.00 E-value=67 Score=24.96 Aligned_cols=27 Identities=26% Similarity=0.303 Sum_probs=23.7
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeeeee
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIESR 352 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIESR 352 (423)
.++.+|.+.++++.+++++||+-.| ++
T Consensus 9 ~~~~~~~~a~if~~La~~~InvDmI-~~ 35 (67)
T cd04914 9 KDNENDLQQRVFKALANAGISVDLI-NV 35 (67)
T ss_pred CCCCccHHHHHHHHHHHcCCcEEEE-Ee
Confidence 3467999999999999999999999 44
No 255
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=31.71 E-value=83 Score=31.29 Aligned_cols=47 Identities=21% Similarity=0.162 Sum_probs=37.2
Q ss_pred cEEEEeCCCccHHHHHHhhhCC----CCceeecCCHHHHHHHHHcCCcCeEEE
Q 014547 128 LRVAYQGVPGAYSEAAAGKAYP----NCEAIPCDQFEVAFQAVELWIADRAVL 176 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f~----~~e~vp~~Sf~~Vf~aV~~g~~d~gVV 176 (423)
.+||. ..||..++...++.+ +.+++.+.+.++++++|..|++|..+.
T Consensus 154 k~V~v--~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~ 204 (302)
T PRK10797 154 KAVVV--TSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMM 204 (302)
T ss_pred CEEEE--eCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEc
Confidence 47776 478777776655432 467899999999999999999998865
No 256
>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=31.71 E-value=3.2e+02 Score=23.21 Aligned_cols=123 Identities=20% Similarity=0.129 Sum_probs=59.6
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcC---c
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKE---Y 222 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~---d 222 (423)
.+|+.++... .+-.++.+.+.+|++|+|+..-.+...+. ....|.+..+.++ .+-.|-+...+..+++ +
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 4677665444 35678899999999999997533221111 0111122222211 2223332221222222 2
Q ss_pred ccEEE-echhH-HHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 223 LTRVI-SHPQA-LSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 223 Ik~Vy-SHPqA-L~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
..-|. .+... .....+|++++....+ ...+++...+.+.++.+ ...||.+...+
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~ 154 (198)
T cd08433 98 LPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAG---LGYTILPASAV 154 (198)
T ss_pred CceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcC---CcEEEcchhhh
Confidence 22332 22222 2345666666543222 33466677777777764 45666666544
No 257
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=31.69 E-value=5e+02 Score=25.40 Aligned_cols=147 Identities=12% Similarity=-0.006 Sum_probs=69.5
Q ss_pred ccEEEEeCCCcc-HHHHHH---hhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCC----CchH----HHHHHhh
Q 014547 127 QLRVAYQGVPGA-YSEAAA---GKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLG----GSIH----RNYDLLL 194 (423)
Q Consensus 127 ~~~VayLGP~GT-fSh~AA---~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~----G~V~----~tlDlL~ 194 (423)
..+|+...+.+. +--... .+.+|+.++.....-.++.+.+.+|++|+|++. .+... |... .....|.
T Consensus 98 ~l~I~~~~~~~~~~~~~~l~~f~~~~P~v~v~i~~~~~~~~~~l~~g~~D~~i~~-~~~~~~~~~~~~~~~~~~~~~~l~ 176 (319)
T PRK10216 98 KFELAAESPLMMIMLNALSKRIYQRYPQATIKLRNWDYDSLDAITRGEVDIGFTG-RESHPRSRELLSLLPLAIDFEVLF 176 (319)
T ss_pred EEEEEecchhHHHHHHHHHHHHHHHCCCCEEEEEeCCcchHHHHhcCCccEEEec-CCCCccccccccccccccceeeee
Confidence 467776544332 222221 234677655433332357899999999999984 21111 1100 0111112
Q ss_pred cCCcEEEEEEEEeeeeeeeecCCCCcCcc---cEEEech--hHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCC
Q 014547 195 RHRLHIVGEVQLPVHHCLLALPGVRKEYL---TRVISHP--QALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLR 268 (423)
Q Consensus 195 ~~~L~IvgEi~lpI~h~Lla~~g~~l~dI---k~VySHP--qAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~ 268 (423)
+..+.+ .++-+|-+. .....++++ .-|..-+ ....+...++.+.+.... ...++|.....+.++.++ .
T Consensus 177 ~~~~~~----v~~~~hp~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~-~ 250 (319)
T PRK10216 177 SDLPCV----WLRKDHPAL-HEEWNLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPEFEQSLFMAAQPD-H 250 (319)
T ss_pred ecceEE----EEeCCCCcc-CCCCCHHHHhhCCCeEecCCCCCcchHHHHHHHhCCccceEEECCcHHHHHHHHHcCC-c
Confidence 222222 233344432 222223332 2333211 123356777776543222 245667777788887531 2
Q ss_pred CeeEEccHHHHH
Q 014547 269 DTAAIASARAAE 280 (423)
Q Consensus 269 ~~AAIaS~~AAe 280 (423)
...+|.++.+++
T Consensus 251 ~gi~ilp~~~~~ 262 (319)
T PRK10216 251 LLLATAPRYCQY 262 (319)
T ss_pred ceEeccHHHHHH
Confidence 357888876543
No 258
>PRK09224 threonine dehydratase; Reviewed
Probab=30.93 E-value=1.3e+02 Score=32.56 Aligned_cols=35 Identities=17% Similarity=0.263 Sum_probs=30.2
Q ss_pred eEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeee
Q 014547 318 KTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRP 353 (423)
Q Consensus 318 KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP 353 (423)
..-+.|.+|.+||+|.+.|+.+. -+-|+|.+|=|-
T Consensus 423 e~~~~~~fPerpGal~~Fl~~l~-~~~~It~f~Yr~ 457 (504)
T PRK09224 423 ERLYRFEFPERPGALLKFLSTLG-THWNISLFHYRN 457 (504)
T ss_pred eEEEEEeCCCCCCHHHHHHHhcC-CCCeeEEEEEcc
Confidence 44677899999999999999887 789999999983
No 259
>PRK00489 hisG ATP phosphoribosyltransferase; Reviewed
Probab=30.42 E-value=5.4e+02 Score=25.44 Aligned_cols=121 Identities=11% Similarity=0.045 Sum_probs=0.0
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEE-EEeeeeeeeecCCCCcCcccEE--
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEV-QLPVHHCLLALPGVRKEYLTRV-- 226 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi-~lpI~h~Lla~~g~~l~dIk~V-- 226 (423)
+.++++..+ .++...|.+|++|+|+. ..+.-.-....+.....+ +..-..+++++++..+.++..+
T Consensus 45 ~ie~~~~~~-~~i~~~L~sG~vDlgi~----------g~~~~~er~~~v~~~~~l~~~~~~lvvvvp~~~~i~sl~DL~G 113 (287)
T PRK00489 45 PIEVLFLRP-DDIPGYVADGVVDLGIT----------GEDLLEESGADVEELLDLGFGKCRLVLAVPEDSDWQGVEDLAG 113 (287)
T ss_pred CEEEEEECc-HHHHHHHHcCCCCEEEc----------chHHHHHCCCCceEeeeccCCceEEEEEEECCCCCCChHHhCC
Q ss_pred ----EechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHc--CCcee
Q 014547 227 ----ISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELY--GMQVL 287 (423)
Q Consensus 227 ----ySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelY--gL~IL 287 (423)
.+.+ ..-++|+++++.+++++...+..+++-.. +.-+..+--......+- ||.++
T Consensus 114 k~ia~~~~---~~~~~~l~~~gi~~~iv~~~gs~eaa~~~---G~aDaivd~~~~~~~l~~~~L~~v 174 (287)
T PRK00489 114 KRIATSYP---NLTRRYLAEKGIDAEVVELSGAVEVAPRL---GLADAIVDVVSTGTTLRANGLKIV 174 (287)
T ss_pred CEEEEcCc---HHHHHHHHHcCCceEEEECCCchhhhhcC---CcccEEEeeHHHHHHHHHCCCEEE
No 260
>PRK08210 aspartate kinase I; Reviewed
Probab=30.23 E-value=2.1e+02 Score=29.71 Aligned_cols=96 Identities=17% Similarity=0.047 Sum_probs=51.7
Q ss_pred ceeEEeccCHHHHHHHHHhcCCCCeeEEccHH---HHHHcCCceeecCccCCCCCeeEEEEEeeCCC-------CC--C-
Q 014547 246 NVAREAVDDTAGAAEYIAANDLRDTAAIASAR---AAELYGMQVLEDGIQDDSSNVTRFVMLAREPI-------IP--R- 312 (423)
Q Consensus 246 ~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~---AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~-------~~--~- 312 (423)
+++.+..-|..+|.++...+ +-+-... .|..++.+|.-.|..+... -|..- ...+. .+ +
T Consensus 193 ~a~~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~~~~~~i~i~i~~~~~~~~-gT~I~--~~~~~~~~~~~~~~~v~~ 264 (403)
T PRK08210 193 DARLLDVVSYNEVFQMAYQG-----AKVIHPRAVEIAMQANIPLRIRSTYSDSP-GTLIT--SLGDAKGGIDVEERLITG 264 (403)
T ss_pred CCeECCccCHHHHHHHHHCC-----ccccCHHHHHHHHHCCCeEEEEecCCCcC-CcEEE--ecCccccccccccCceEE
Confidence 44555555556666655432 2233333 3456788888877765322 34331 11110 00 0
Q ss_pred -CCCCCeEEEEE-EeCCCccHHHHHHHHHHhCCceeeee
Q 014547 313 -TDRPFKTSIVF-AHDKGTSVLFKVLSAFAFRNISLTKI 349 (423)
Q Consensus 313 -~~~~~KTSivf-~l~~~pGaL~~vL~~Fa~~~INLtkI 349 (423)
....+-+.+.+ ..++.+|.|.++++.|+++|||+-.|
T Consensus 265 It~~~~i~~isv~~~~~~~g~la~If~~L~~~~I~i~~i 303 (403)
T PRK08210 265 IAHVSNVTQIKVKAKENAYDLQQEVFKALAEAGISVDFI 303 (403)
T ss_pred EEEcCCcEEEEEecCCCcchHHHHHHHHHHHcCCeEEEE
Confidence 00112233333 23445999999999999999999988
No 261
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=30.21 E-value=5.1e+02 Score=25.03 Aligned_cols=168 Identities=11% Similarity=-0.028 Sum_probs=79.8
Q ss_pred ccEEEEeCCCccH--HHHHH--hhhCCCCceeec-CCHHHHHHHHHcCCcCeEEEeecc--CCCCchHHHHHHhhcCCcE
Q 014547 127 QLRVAYQGVPGAY--SEAAA--GKAYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVEN--SLGGSIHRNYDLLLRHRLH 199 (423)
Q Consensus 127 ~~~VayLGP~GTf--Sh~AA--~~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIEN--S~~G~V~~tlDlL~~~~L~ 199 (423)
..+|+..-..+.+ ....+ .+.+|+.++... .+-+++.+.+.+|++|+|++.... .....+ ....|.+.++.
T Consensus 94 ~l~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l--~~~~l~~~~~~ 171 (296)
T PRK11062 94 LFDVGVADALSKRLVSRVLLTAVPEDESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEGL--FSKKLGECGVS 171 (296)
T ss_pred EEEEEecchhhHhhHHHHHHHHHhcCCceEEEEEeCCHHHHHHHHHcCCCCEEEecCCCccccccch--hhhhhhccCcc
Confidence 5677764433322 11111 123577665443 467899999999999999974221 111111 11233344443
Q ss_pred EEEEEEEeeeeeeeecCCCCcCcccEEEec-hhH-HHHHHHHHHHcCCceeE-EeccCHHHHHHHHHhcCCCCeeEEccH
Q 014547 200 IVGEVQLPVHHCLLALPGVRKEYLTRVISH-PQA-LSQCEHTLTKLGLNVAR-EAVDDTAGAAEYIAANDLRDTAAIASA 276 (423)
Q Consensus 200 IvgEi~lpI~h~Lla~~g~~l~dIk~VySH-PqA-L~QC~~fL~~~~p~~~~-v~~~STA~AA~~va~~~~~~~AAIaS~ 276 (423)
++.- -.|-+.. .-.++.+..-|... ... ..+-..|+..++...+. ..++|.....+.+.++ ...++.+.
T Consensus 172 ~~~~----~~~~~~~-~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~ 243 (296)
T PRK11062 172 FFCT----NPLPEKP-FPACLEERRLLIPGRRTMLGRKLLNWFNSQGLNVEILGEFDDAALMKAFGAYH---DAIFVAPS 243 (296)
T ss_pred eEec----CCCcccc-ChHHHhcCCeeecCCCchHHHHHHHHHHHcCCCceeeeeeCcHHHHHHHHHcC---CceEECCH
Confidence 3221 1221111 01122333333321 111 22345566665432222 2456666666666654 56788888
Q ss_pred HHHHHc----CCceeecCccCCCCCeeEEEEEeeCC
Q 014547 277 RAAELY----GMQVLEDGIQDDSSNVTRFVMLAREP 308 (423)
Q Consensus 277 ~AAelY----gL~ILa~nIqD~~~N~TRFlVLsr~~ 308 (423)
..++.+ +|..+.. ...-...|+++.++.
T Consensus 244 ~~~~~~~~~~~l~~l~~----~~~~~~~~~lv~~~~ 275 (296)
T PRK11062 244 LYAQDFYADHSVVEIGR----VDNVKEEYHVIFAER 275 (296)
T ss_pred HHHHHHHHcCCeEEcCC----ccccceEEEEEEecC
Confidence 777643 2444321 122244666666543
No 262
>PF02566 OsmC: OsmC-like protein; InterPro: IPR003718 Osmotically inducible protein C (OsmC) is a stress-induced protein found in Escherichia coli. The transcription of the osmC gene of E. coli is regulated as a function of the phase of growth and is induced during the late exponential phase when the growth rate slows before entry into stationary phase. The transcription is initiated by two overlapping promoters, osmCp1 and osmCp2 []. An organic hydroperoxide detoxification protein (OHR) from Xanthomonas campestris pv. phaseoli is highly induced by organic hydroperoxides, weakly induced by H2O2, and not induced at all by a superoxide generator. Ohr may be a new type of organic hydroperoxide detoxification protein [, ].; GO: 0006950 response to stress; PDB: 2D7V_A 2BJO_A 1USP_A 2PN2_A 2QL8_A 1N2F_A 1UKK_A 1VLA_D 3CJE_A 2ONF_B ....
Probab=29.85 E-value=1.5e+02 Score=23.93 Aligned_cols=65 Identities=11% Similarity=0.110 Sum_probs=38.9
Q ss_pred HHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHhhcC
Q 014547 333 FKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQEFTS 402 (423)
Q Consensus 333 ~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~ 402 (423)
..+...++.+||++..++-+-... .|+.....-....+.++|++.+..+++.++++++...+.|.
T Consensus 22 ~~~~~~a~~~gi~~~~~~v~v~~~-----~~~~~~~~~~~i~~~~~v~~~~~~~~~~~~~~~~~a~~~C~ 86 (100)
T PF02566_consen 22 MTLRMVAEKRGIDLEDLEVEVEGE-----LDPEGPRRFESIHLRITVKSDGDDDEEELEELLERAEKRCP 86 (100)
T ss_dssp HHHHHHHHHTT-EEEEEEEEEEEE-----EETTTCECEEEEEEEEEEEETTSHHHHHHHHHHHHHHHHSH
T ss_pred HHHHHHHHHcCCCcceEEEEEEEE-----EeecCCccceEEEEEEEEEcCCCCcHHHHHHHHHHHHhhCc
Confidence 445667789999998876654421 11111100112457778877765445888888888877764
No 263
>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=29.22 E-value=2.3e+02 Score=20.71 Aligned_cols=26 Identities=19% Similarity=0.197 Sum_probs=23.0
Q ss_pred eCCCccHHHHHHHHHHhCCceeeeee
Q 014547 325 HDKGTSVLFKVLSAFAFRNISLTKIE 350 (423)
Q Consensus 325 l~~~pGaL~~vL~~Fa~~~INLtkIE 350 (423)
+.+.++.+.++++.+++.|||+--|.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~i~v~~i~ 36 (66)
T cd04916 11 MKNTVGVSARATAALAKAGINIRMIN 36 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 45679999999999999999998774
No 264
>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=29.03 E-value=6.4e+02 Score=25.76 Aligned_cols=131 Identities=11% Similarity=0.059 Sum_probs=71.1
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHh--hcCCcEEEEEEE-EeeeeeeeecCCCCcCcc--c
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLL--LRHRLHIVGEVQ-LPVHHCLLALPGVRKEYL--T 224 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL--~~~~L~IvgEi~-lpI~h~Lla~~g~~l~dI--k 224 (423)
+++++.+.+-.++++++..|++|+|.+ |.... +-+. ...+++|+.-.. -.-...|++++..+++|+ |
T Consensus 36 ~Ve~~~f~~~~~~l~Al~aG~iD~~~~-------g~~~~-~~~~~a~g~~~~iv~v~~~~~g~~~ivv~~i~svaDLKGK 107 (328)
T TIGR03427 36 TIEVVQINDYVESINQYTAGKFDGCTM-------TNMDA-LTIPAAGGVDTTALIVGDFSNGNDGIVLKGGKSLADLKGQ 107 (328)
T ss_pred eEEEEECCChHHHHHHHHcCCCCEEee-------cCHHH-HHHHHhCCCCeEEEEEEccCCCceEEEECCCCCHHHcCCC
Confidence 478889999999999999999999855 22111 1111 123444443221 122245667655556666 4
Q ss_pred EEEechhHHHH--HHHHHHHcCC---ceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHH---HHcCCceeecC
Q 014547 225 RVISHPQALSQ--CEHTLTKLGL---NVAREAVDDTAGAAEYIAANDLRDTAAIASARAA---ELYGMQVLEDG 290 (423)
Q Consensus 225 ~VySHPqAL~Q--C~~fL~~~~p---~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AA---elYgL~ILa~n 290 (423)
+|..+.-...+ ....|++.+. .++++.... +.+...+..++ -+.+++-....+ +..|.++|...
T Consensus 108 kIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~~-~d~~aAl~~G~-VDAa~~~eP~~s~~~~~~g~~~l~~~ 179 (328)
T TIGR03427 108 KVNLVELSVSHYLLARALESVGLSEKDVKVVNTSD-ADIVAAFITKD-VTAVVTWNPQLSEIKAQPGANEVFDS 179 (328)
T ss_pred EEeccCCChHHHHHHHHHHHcCCCHHHeEEEeCCh-HHHHHHHhcCC-CcEEEEcCchHHHHHhCCCcEEeccc
Confidence 77655443332 4455666654 366666643 55555555442 344444333322 23466666543
No 265
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=28.00 E-value=5.5e+02 Score=24.71 Aligned_cols=32 Identities=9% Similarity=-0.039 Sum_probs=24.6
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCcCeEEEee
Q 014547 147 AYPNCEAIP-CDQFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 147 ~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
.+|+.++.. ..+..++.+++.+|++|+|+++.
T Consensus 120 ~~p~i~~~~~~~~~~~~~~~l~~g~~Di~i~~~ 152 (302)
T PRK09791 120 QHPQVKVRIMEGQLVSMINELRQGELDFTINTY 152 (302)
T ss_pred HCCCeEEEEEeCChHHHHHHHHCCCccEEEEec
Confidence 357665432 45778999999999999999853
No 266
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=27.70 E-value=91 Score=24.50 Aligned_cols=70 Identities=11% Similarity=0.334 Sum_probs=41.4
Q ss_pred EEEEEeCC-CccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHH
Q 014547 320 SIVFAHDK-GTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQ 398 (423)
Q Consensus 320 Sivf~l~~-~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~ 398 (423)
.+.|.=.. .-..|.++...| |+..+=+...-.. +.+..+| .+++++.| ++..++++++.|+
T Consensus 6 ~l~f~g~~~~~piis~l~~~~---~v~~nIl~g~i~~------i~~~~~G-------~l~l~l~g--~~~~~~~a~~~L~ 67 (76)
T PF09383_consen 6 RLTFTGNSAQEPIISQLIREF---GVDVNILHGNIEE------IQGTPFG-------ILILELPG--DDEEIEKAIAYLR 67 (76)
T ss_dssp EEEEESCSSSSCHHHHHHHHH---T-EEEEEEEEEEE------ETTEEEE-------EEEEEEES---HHHHHHHHHHHH
T ss_pred EEEEcCCCcCchHHHHHHHHh---CCCEEEEEEEeEE------cCCeeEE-------EEEEEEEC--CHHHHHHHHHHHH
Confidence 34454333 345778887777 5554433333211 1111233 68889988 4577999999999
Q ss_pred hhcCceEEE
Q 014547 399 EFTSFLRVL 407 (423)
Q Consensus 399 ~~~~~vrvL 407 (423)
+....+.+|
T Consensus 68 ~~~v~vEvl 76 (76)
T PF09383_consen 68 EQGVEVEVL 76 (76)
T ss_dssp HTTEEEEEE
T ss_pred HCCCeEEEC
Confidence 887666654
No 267
>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=27.69 E-value=3.7e+02 Score=22.59 Aligned_cols=116 Identities=15% Similarity=0.092 Sum_probs=60.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCC-------
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGV------- 218 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~------- 218 (423)
.+|+.++... .+..++++.+.+|++|+|+........ + +..+.......++++.++-
T Consensus 24 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~-------------~--~~~~~l~~~~~~~~~~~~~~l~~~~~ 88 (197)
T cd08419 24 RHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDL-------------D--LVAEPFLDNPLVVIAPPDHPLAGQKR 88 (197)
T ss_pred HCCCceEEEEECCHHHHHHHHhcCCccEEEecCCCCCC-------------C--eEEEEeccCCEEEEecCCCCCcCCCC
Confidence 3677665443 467788999999999999974321111 1 2222333334444443322
Q ss_pred -CcCc---ccEEEech-h-HHHHHHHHHHHcCCce-eEEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 219 -RKEY---LTRVISHP-Q-ALSQCEHTLTKLGLNV-AREAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 219 -~l~d---Ik~VySHP-q-AL~QC~~fL~~~~p~~-~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
++++ ..-|.-.+ . ...+-..|+.+++... ....+++...+.++++.+ ...++.+...++
T Consensus 89 ~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (197)
T cd08419 89 IPLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAG---LGLSVLSLHTLA 154 (197)
T ss_pred cCHHHHhCCCcEEecCCCcHHHHHHHHHHHCCCCcceEEEECCHHHHHHHHHhC---CceEeecHHHHH
Confidence 2222 22232111 1 1234556666654322 234466777777788765 346777766554
No 268
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=27.36 E-value=6.2e+02 Score=25.07 Aligned_cols=115 Identities=13% Similarity=0.068 Sum_probs=62.9
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCC---cCccc--
Q 014547 150 NCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVR---KEYLT-- 224 (423)
Q Consensus 150 ~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~---l~dIk-- 224 (423)
++++++.. ++..+.+|..|++|+++-.+.-+- +. ...+.-.. -++.....|+++++.. ++|++
T Consensus 87 ~~~~v~~~-~~~~i~~L~~G~~Di~~~~~~~t~--------eR--~~~~~fS~-Py~~~~~~lv~r~~~~i~sl~dL~Gk 154 (302)
T PRK10797 87 QVKLIPIT-SQNRIPLLQNGTFDFECGSTTNNL--------ER--QKQAAFSD-TIFVVGTRLLTKKGGDIKDFADLKGK 154 (302)
T ss_pred eEEEEEcC-hHhHHHHHHCCCccEEecCCccCc--------ch--hhcceecc-cEeeccEEEEEECCCCCCChHHcCCC
Confidence 35667764 667899999999999754432111 10 01111111 1122234555555432 23333
Q ss_pred EEEechh--HHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHH
Q 014547 225 RVISHPQ--ALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARA 278 (423)
Q Consensus 225 ~VySHPq--AL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~A 278 (423)
+|....- ....-+++..+..+++.++.+.++.++.+.+..+ +-.|.|.....
T Consensus 155 ~V~v~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~G--rvDa~i~d~~~ 208 (302)
T PRK10797 155 AVVVTSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESG--RAVAFMMDDAL 208 (302)
T ss_pred EEEEeCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcC--CceEEEccHHH
Confidence 3433332 2222334444444567888889999999999876 45777776543
No 269
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=27.10 E-value=1.7e+02 Score=27.85 Aligned_cols=48 Identities=15% Similarity=0.144 Sum_probs=35.2
Q ss_pred cEEEEeCCCccHHHHHHhhhC--CCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAY--PNCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f--~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+||+. .|++.++-..+++ .+.+++...+.++++++|..|++|+.+..
T Consensus 134 ~~Igv~--~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~ 183 (259)
T PRK15437 134 KRVGVL--QGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQD 183 (259)
T ss_pred CEEEEe--cCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEec
Confidence 478884 5776554443333 24678889999999999999999988653
No 270
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=25.69 E-value=5.2e+02 Score=24.09 Aligned_cols=114 Identities=18% Similarity=0.175 Sum_probs=69.0
Q ss_pred HHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCC---cEEEEEEEEeeeee---eeecCCCC---cCccc---EEE
Q 014547 160 EVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHR---LHIVGEVQLPVHHC---LLALPGVR---KEYLT---RVI 227 (423)
Q Consensus 160 ~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~---L~IvgEi~lpI~h~---Lla~~g~~---l~dIk---~Vy 227 (423)
.|+-.-|+.|.+|+||+= .|.|.++. -.+.--..|+..+| ++++.+.. +++++ +|.
T Consensus 4 ~DIp~yV~~G~~DlGI~G------------~D~l~E~~~~~~~v~~~~dL~fg~crl~vAvp~~~~~~~~~~l~~~~rIA 71 (163)
T PF01634_consen 4 QDIPTYVEDGIADLGITG------------KDVLLESGLGRADVEELLDLGFGKCRLVVAVPEDWPYKSVEDLKAGLRIA 71 (163)
T ss_dssp GHHHHHHHTTSSSEEEEE------------HHHHHHHTHH-SSEEEEEEESCSEEEEEEEEETTSCGCCGGGGSSTEEEE
T ss_pred HHHHHHHHCCCCcEEEee------------hheeccCCCCccceEEEeecccccEEEEEEEECCcCCCCHHHhccCCEEE
Confidence 467778999999999873 46555444 23555556777766 44444432 34444 777
Q ss_pred echhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEE-ccHHHHHHcCCceeec
Q 014547 228 SHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAI-ASARAAELYGMQVLED 289 (423)
Q Consensus 228 SHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAI-aS~~AAelYgL~ILa~ 289 (423)
+-..-+ .++|+++++.+++++..+-..|+|=.+ +-..-..=| .+-...+.+||++++.
T Consensus 72 Tkyp~l--~~~yf~~~g~~~~ii~l~GsvE~ap~~--glAD~IvDiv~TG~TLr~NgL~~i~~ 130 (163)
T PF01634_consen 72 TKYPNL--TRRYFAEKGINVEIIKLSGSVELAPPL--GLADAIVDIVETGTTLRANGLKEIET 130 (163)
T ss_dssp ES-HHH--HHHHHHHCT-EEEEEE-SS-TTHHHHT--TSSSEEEEEESSSHHHHHTTEEEEEE
T ss_pred ECCHHH--HHHHHHHcCCcEEEEEccCCccccCCC--CCCCEEEEeccCcHHHHHCCCEEeEE
Confidence 776655 578999999888888776665555432 100112222 4556678899999843
No 271
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=25.15 E-value=4e+02 Score=25.63 Aligned_cols=120 Identities=16% Similarity=-0.002 Sum_probs=57.2
Q ss_pred CCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc---c
Q 014547 148 YPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL---T 224 (423)
Q Consensus 148 f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI---k 224 (423)
+|+.++....+ +..+.+.+|++|+|++..+....+... ..|.+..+.++ .+-.|.+......+++++ .
T Consensus 120 ~p~i~i~l~~~--~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~~----~~~~~~~~~~~~i~~~dL~~~p 190 (297)
T PRK11139 120 HPDIDVRLKAV--DRLEDFLRDDVDVAIRYGRGNWPGLRV---EKLLDEYLLPV----CSPALLNGGKPLKTPEDLARHT 190 (297)
T ss_pred CCCceEEEEeC--CChhhhccCCCCEEEEeCCCCCCCceE---EEeccceeEEE----eCHHHhcccCCCCCHHHhhcCc
Confidence 57655433322 334678889999999876533222111 11222233222 223343332222333333 3
Q ss_pred EEEechhHHHHHHHHHHHcCC---cee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 225 RVISHPQALSQCEHTLTKLGL---NVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 225 ~VySHPqAL~QC~~fL~~~~p---~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
-|...+ ......|+...+. ... ...+++...+.+.+..+ ...||.+...++.
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 2345667766433 111 23355565555666654 4567777765543
No 272
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=25.10 E-value=2.4e+02 Score=32.79 Aligned_cols=36 Identities=19% Similarity=0.281 Sum_probs=30.2
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeee--eeee
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTK--IESR 352 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtk--IESR 352 (423)
.-|.|.+..+|+||-|+++-++|+.+|+|+.. |.+.
T Consensus 676 ~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~ 713 (854)
T PRK01759 676 GGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITS 713 (854)
T ss_pred CeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEc
Confidence 35777778889999999999999999999974 5443
No 273
>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=25.02 E-value=3.1e+02 Score=21.01 Aligned_cols=49 Identities=20% Similarity=0.183 Sum_probs=35.1
Q ss_pred CccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHHHh
Q 014547 328 GTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEVQE 399 (423)
Q Consensus 328 ~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL~~ 399 (423)
.+|.+.++++.+++.|||+..|-.=++.. .-.|.|+- .+..++++.|.+
T Consensus 14 ~~gv~~ki~~~L~~~~I~v~~i~~~~s~~-----------------~is~~V~~------~~~~~av~~Lh~ 62 (66)
T cd04915 14 TPGVLARGLAALAEAGIEPIAAHQSMRNV-----------------DVQFVVDR------DDYDNAIKALHA 62 (66)
T ss_pred cchHHHHHHHHHHHCCCCEEEEEecCCee-----------------EEEEEEEH------HHHHHHHHHHHH
Confidence 78999999999999999997776544421 34566553 556677777654
No 274
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. 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, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. 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=24.89 E-value=4.5e+02 Score=22.57 Aligned_cols=31 Identities=13% Similarity=0.025 Sum_probs=24.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCcCeEEEe
Q 014547 147 AYPNCEAIPC-DQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 147 ~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.+|+.++... .+..++.+.+.+|++|+|++.
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08458 25 DRPDVSVYLDTVPSQTVLELVSLQHYDLGISI 56 (196)
T ss_pred HCCCcEEEEeccChHHHHHHHHcCCCCEEEEe
Confidence 4677766544 456789999999999999984
No 275
>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=24.84 E-value=5.8e+02 Score=23.85 Aligned_cols=140 Identities=20% Similarity=0.149 Sum_probs=69.1
Q ss_pred CccEEEEeCCCccHHHHHHh---hhCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEE
Q 014547 126 SQLRVAYQGVPGAYSEAAAG---KAYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIV 201 (423)
Q Consensus 126 ~~~~VayLGP~GTfSh~AA~---~~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Iv 201 (423)
+..+|++.++ + +--.+.. +.+|+.++.. ..+..++++.+.+|++|+|++.......+. ....|.+..+.++
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 3578887643 1 2112221 2357766544 457889999999999999998533221111 0111222222221
Q ss_pred EEEEEeeeeeeeecCCCCcCcc---cEEEech--hHHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEcc
Q 014547 202 GEVQLPVHHCLLALPGVRKEYL---TRVISHP--QALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIAS 275 (423)
Q Consensus 202 gEi~lpI~h~Lla~~g~~l~dI---k~VySHP--qAL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS 275 (423)
. +-.|-|...+..+++++ ..|...+ .......+|+.+++.... ...++|...+.+.+..+ ...++.+
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 11222222222233333 3343222 123456777777643222 33467777777777754 3456666
Q ss_pred HH
Q 014547 276 AR 277 (423)
Q Consensus 276 ~~ 277 (423)
..
T Consensus 235 ~~ 236 (279)
T TIGR03339 235 AA 236 (279)
T ss_pred hh
Confidence 54
No 276
>PHA03169 hypothetical protein; Provisional
Probab=24.81 E-value=3.5e+02 Score=28.86 Aligned_cols=69 Identities=9% Similarity=0.123 Sum_probs=48.6
Q ss_pred CCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHH
Q 014547 315 RPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNAL 394 (423)
Q Consensus 315 ~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL 394 (423)
..+|--++|.- .|-+||++-.+|.+.||--+-+.--|..... .-.|.|..||=|.-.-..+.|+.|-
T Consensus 320 ~~W~~~v~fWg--dP~~LyrLsraLqfpG~~ssgvq~lP~~p~~-----------p~~~~y~ItVyCqsk~TaK~V~kaq 386 (413)
T PHA03169 320 GPWCWVVFCWG--DPYSLYRLSRCLQFPGAVSSGVQTFPDAPGS-----------PVIWAYCITVFCQSRGTAKAVIKAQ 386 (413)
T ss_pred CceeEEEEecC--CcHHHHHHHHHhccCCeeccceeecCCCCCC-----------CCCceeEEEEEecCcccHHHHHHHH
Confidence 45788777765 5899999999999999988888888875421 1247787777776544445555444
Q ss_pred HH
Q 014547 395 AE 396 (423)
Q Consensus 395 ~e 396 (423)
+.
T Consensus 387 ~~ 388 (413)
T PHA03169 387 KK 388 (413)
T ss_pred HH
Confidence 43
No 277
>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=24.58 E-value=4.6e+02 Score=22.64 Aligned_cols=124 Identities=22% Similarity=0.141 Sum_probs=60.5
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCccc-
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLT- 224 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk- 224 (423)
.+|+.++.... +-.++.+.|.+|++|+|+..... ..+.+. ...|.+.++.++ .+-+|-|... ..+++++.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~-~~~~~~--~~~l~~~~~~~v----~~~~h~l~~~-~~~~~dL~~ 96 (200)
T cd08467 25 RAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAV-PPDGLV--VRRLYDDGFACL----VRHGHPALAQ-EWTLDDFAT 96 (200)
T ss_pred hCCCCEEEEecCCcccHHHHhhCCCcCEEEecCCC-CCccce--eEEeeeccEEEE----EcCCCccccC-CCCHHHHhC
Confidence 46887776554 34578999999999999974221 011110 111222233222 2233333322 13333322
Q ss_pred --EEEech-h-HHHHHHHHHHHcCCcee-EEeccCHHHHHHHHHhcCCCCeeEEccHHHHHH
Q 014547 225 --RVISHP-Q-ALSQCEHTLTKLGLNVA-REAVDDTAGAAEYIAANDLRDTAAIASARAAEL 281 (423)
Q Consensus 225 --~VySHP-q-AL~QC~~fL~~~~p~~~-~v~~~STA~AA~~va~~~~~~~AAIaS~~AAel 281 (423)
.|.-.. . ......+++++.+.... ...+++.....++++.+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08467 97 LRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAAT---DLIATVPRRVATQ 155 (200)
T ss_pred CCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcC---CeEEeeHHHHHHH
Confidence 222111 1 11234455555543222 23456666777777764 4577777766553
No 278
>PRK06635 aspartate kinase; Reviewed
Probab=23.83 E-value=2.2e+02 Score=29.45 Aligned_cols=28 Identities=21% Similarity=0.248 Sum_probs=24.9
Q ss_pred EeCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 324 AHDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 324 ~l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
.+++.||.+.++++.|+++|||+..|.+
T Consensus 349 ~~~~~~g~~a~i~~~La~~~Ini~~i~s 376 (404)
T PRK06635 349 GMRSHPGVAAKMFEALAEEGINIQMIST 376 (404)
T ss_pred CCCCCchHHHHHHHHHHHCCCCEEEEEe
Confidence 3567899999999999999999998864
No 279
>PF11966 SSURE: Fibronectin-binding repeat; InterPro: IPR021021 Streptococcal surface repeat domain - SSURE - is a protein fragment found to bind to extracellular matrix protein fibronectin but not to collagen or submaxillary mucin in Streptococci. Anti-SSURE antibodies recognised the corresponding protein on the surface of streptococcal cells. The full-length proteins are thus fibronectin-binding surface adhesins []. The proteins are further characterised by having an N-terminal motif resembling [YF]SIRKxxxGxxS[VIA] IPR005877 from INTERPRO and a C-terminal LPXTG motif-containing region which is a characteristic of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall (see IPR019931 from INTERPRO).
Probab=23.52 E-value=1.6e+02 Score=24.45 Aligned_cols=38 Identities=18% Similarity=0.382 Sum_probs=30.4
Q ss_pred cceEEEEEEEecCcChHHHHHHHHHHHhhcC-----ceEEEcc
Q 014547 372 HFEYMFYIDFEASMAEVRAQNALAEVQEFTS-----FLRVLGS 409 (423)
Q Consensus 372 ~~eY~FfID~eg~~~d~~v~~aL~eL~~~~~-----~vrvLGs 409 (423)
...|+|=||+.|+..-..=|++|+.|+.... .|+|-|.
T Consensus 18 kGkYFYqV~L~Gnt~Gk~~q~LLDqlraNGt~tY~ATv~VYga 60 (81)
T PF11966_consen 18 KGKYFYQVDLNGNTAGKQGQALLDQLRANGTHTYQATVKVYGA 60 (81)
T ss_pred CccEEEEEecCCcccCcchHHHHHHHHhCCceeeEEEEEEEec
Confidence 3589999999998777778899999986554 3777776
No 280
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=23.44 E-value=6.4e+02 Score=23.85 Aligned_cols=131 Identities=15% Similarity=0.113 Sum_probs=67.9
Q ss_pred CCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeee
Q 014547 134 GVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLL 213 (423)
Q Consensus 134 GP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Ll 213 (423)
|..--.-.+.|++.--+.++++. ++++++++++.|++|.++-++.-+ -+. +..+.....+ +.....++
T Consensus 50 G~~vdl~~~ia~~lg~~~~~~~~-~~~~~~~~l~~g~~Di~~~~~~~t--------~eR--~~~~~fs~p~-~~~~~~~~ 117 (260)
T PRK15010 50 GFDIDLGNEMCKRMQVKCTWVAS-DFDALIPSLKAKKIDAIISSLSIT--------DKR--QQEIAFSDKL-YAADSRLI 117 (260)
T ss_pred eeeHHHHHHHHHHhCCceEEEeC-CHHHHHHHHHCCCCCEEEecCcCC--------HHH--Hhhcccccce-EeccEEEE
Confidence 43333444445443224667764 689999999999999776433211 111 0111112222 22345666
Q ss_pred ecCCCC----cCccc--EEEechhHHHHHHHHHHHcC--CceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 214 ALPGVR----KEYLT--RVISHPQALSQCEHTLTKLG--LNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 214 a~~g~~----l~dIk--~VySHPqAL~QC~~fL~~~~--p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
++++.. +++++ +|--..-... ..|+.+.. .++..+.+.+..++.+++..+ +-.|.|+....+.
T Consensus 118 ~~~~~~~~~~~~dl~g~~Igv~~gs~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--riDa~i~d~~~~~ 188 (260)
T PRK15010 118 AAKGSPIQPTLDSLKGKHVGVLQGSTQ--EAYANETWRSKGVDVVAYANQDLVYSDLAAG--RLDAALQDEVAAS 188 (260)
T ss_pred EECCCCCCCChhHcCCCEEEEecCchH--HHHHHHhcccCCceEEecCCHHHHHHHHHcC--CccEEEeCcHHHH
Confidence 665432 22332 3333222211 23444322 235566677777788888876 4667787766543
No 281
>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=23.44 E-value=3.3e+02 Score=20.61 Aligned_cols=56 Identities=18% Similarity=0.108 Sum_probs=36.6
Q ss_pred EEEEE-EeCCCccHHHHHHHHHHhCCceeeeeeeeeCCCCCcccccccCCCCCCcceEEEEEEEecCcChHHHHHHHHHH
Q 014547 319 TSIVF-AHDKGTSVLFKVLSAFAFRNISLTKIESRPHRNRPIRLVDDANVGTAKHFEYMFYIDFEASMAEVRAQNALAEV 397 (423)
Q Consensus 319 TSivf-~l~~~pGaL~~vL~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~G~~~~~eY~FfID~eg~~~d~~v~~aL~eL 397 (423)
.|++= .+.+.+|.+.++++.|++.+|++...-.... .-.|+||- .+..+++..|
T Consensus 3 VsvVG~g~~~~~gv~~~~~~~L~~~~i~~i~~~~s~~-------------------~is~vv~~------~d~~~av~~L 57 (63)
T cd04920 3 VSLVGRGIRSLLHKLGPALEVFGKKPVHLVSQAANDL-------------------NLTFVVDE------DQADGLCARL 57 (63)
T ss_pred EEEECCCcccCccHHHHHHHHHhcCCceEEEEeCCCC-------------------eEEEEEeH------HHHHHHHHHH
Confidence 34443 3456799999999999998888854443321 34577765 4556666666
Q ss_pred Hh
Q 014547 398 QE 399 (423)
Q Consensus 398 ~~ 399 (423)
-+
T Consensus 58 H~ 59 (63)
T cd04920 58 HF 59 (63)
T ss_pred HH
Confidence 43
No 282
>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=23.36 E-value=4.6e+02 Score=22.15 Aligned_cols=32 Identities=13% Similarity=-0.067 Sum_probs=24.7
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCcCeEEEee
Q 014547 147 AYPNCEAIPCD-QFEVAFQAVELWIADRAVLPV 178 (423)
Q Consensus 147 ~f~~~e~vp~~-Sf~~Vf~aV~~g~~d~gVVPI 178 (423)
.+|+.++.... +-.++++.+++|++|+|++..
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08450 25 EHPDLDVELSSLFSPQLAEALMRGKLDVAFMRP 57 (196)
T ss_pred hCCCcEEEEEecChHHHHHHHhcCCccEEEEeC
Confidence 46777765544 467899999999999999753
No 283
>PF05576 Peptidase_S37: PS-10 peptidase S37; InterPro: IPR008761 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. These group of serine peptidases belong to MEROPS peptidase family S37 (clan SC). The members of this group of secreted peptidases are restricted to bacteria. In Streptomyces lividans the peptidase removes tripeptides from the N terminus of extracellular proteins (tripeptidyl aminopeptidase,Tap) [, ].
Probab=22.98 E-value=1.2e+02 Score=32.65 Aligned_cols=103 Identities=18% Similarity=0.339 Sum_probs=56.8
Q ss_pred HHHHcCCceeecCccCCCCCeeEEEEEeeCCCCCC---CCCCCeEEEEEEeCC--CccHHHHHHHHHHhCCceeeeeeee
Q 014547 278 AAELYGMQVLEDGIQDDSSNVTRFVMLAREPIIPR---TDRPFKTSIVFAHDK--GTSVLFKVLSAFAFRNISLTKIESR 352 (423)
Q Consensus 278 AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~~---~~~~~KTSivf~l~~--~pGaL~~vL~~Fa~~~INLtkIESR 352 (423)
...+-||.++++. +..-.||++|.-+.+..- ..+.++--|.+.+++ +|.+| ...|-|+. .+
T Consensus 12 L~aIpG~s~iee~----p~~gyRffvl~y~QPvDH~~P~~gtF~QRvtLlHk~~drPtV~-------~T~GY~~~---~~ 77 (448)
T PF05576_consen 12 LLAIPGMSLIEEK----PYDGYRFFVLRYTQPVDHRHPEKGTFQQRVTLLHKDFDRPTVL-------YTEGYNVS---TS 77 (448)
T ss_pred HhcCCCceeeecc----CCCceEEEEEeeecCCCCCCCCCCceEEEEEEEEcCCCCCeEE-------EecCcccc---cC
Confidence 3456688887764 345669999987654321 223344455555543 56544 34455543 24
Q ss_pred eCCCCCcccccccCCCCCCcceEEEEE------------EEecCc-ChHHHHHHHHHHH
Q 014547 353 PHRNRPIRLVDDANVGTAKHFEYMFYI------------DFEASM-AEVRAQNALAEVQ 398 (423)
Q Consensus 353 P~~~~p~~~~~~~~~G~~~~~eY~FfI------------D~eg~~-~d~~v~~aL~eL~ 398 (423)
|.+.+|-+++|...+. -||.||- +++-.. +.-++-++|+.|-
T Consensus 78 p~r~Ept~Lld~NQl~----vEhRfF~~SrP~p~DW~~Lti~QAA~D~Hri~~A~K~iY 132 (448)
T PF05576_consen 78 PRRSEPTQLLDGNQLS----VEHRFFGPSRPEPADWSYLTIWQAASDQHRIVQAFKPIY 132 (448)
T ss_pred ccccchhHhhccceEE----EEEeeccCCCCCCCCcccccHhHhhHHHHHHHHHHHhhc
Confidence 5555666666666554 4666664 343222 2246666776664
No 284
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=22.79 E-value=3e+02 Score=32.21 Aligned_cols=32 Identities=22% Similarity=0.116 Sum_probs=28.7
Q ss_pred CCeEEEEEEeCCCccHHHHHHHHHHhCCceee
Q 014547 316 PFKTSIVFAHDKGTSVLFKVLSAFAFRNISLT 347 (423)
Q Consensus 316 ~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLt 347 (423)
+.+|.|=+.-.|+||.|+.+.++|++.+++|.
T Consensus 789 ~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~ 820 (867)
T COG2844 789 NDKTVLEVRALDRPGLLAALAGVFADLGLSLH 820 (867)
T ss_pred CCceEEEEEeCCcccHHHHHHHHHHhccccee
Confidence 35788888888999999999999999999987
No 285
>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=22.75 E-value=7.1e+02 Score=24.14 Aligned_cols=116 Identities=19% Similarity=0.221 Sum_probs=58.6
Q ss_pred hhHHHHHHHHHHH-cCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHH--HHHHcCCce--eecCccCCCCCeeEEEEE
Q 014547 230 PQALSQCEHTLTK-LGLNVAREAVDDTAGAAEYIAANDLRDTAAIASAR--AAELYGMQV--LEDGIQDDSSNVTRFVML 304 (423)
Q Consensus 230 PqAL~QC~~fL~~-~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~--AAelYgL~I--La~nIqD~~~N~TRFlVL 304 (423)
|-.+++-+.|+.+ ++.+++++...+.....+.+..+. -+.+..+... .+...|..+ +. +.+...+. ..++
T Consensus 11 p~~va~~~G~~~k~~Gl~Ve~~~~~~~~~~~~al~~G~-iD~~~~~~~~~~~a~~~g~~~~~v~--~~~~~~~~--~~lv 85 (300)
T TIGR01729 11 PFKVAQADGAAAKEAGATIDWRKFDSGADISTALASGN-VPIGVIGSSPLAAAASRGVPIELFW--ILDNIGKS--EALV 85 (300)
T ss_pred HHHHHHHcCchHHhcCCeeEEEecCcHHHHHHHHHcCC-CCEeccCCCHHHHHHHCCCCeEEEE--EeccCCcc--ceEE
Confidence 5667888888875 677888888877666667777653 3444433222 233345543 32 22222222 3444
Q ss_pred eeCC--CCCCCCCCCeEEEEEEeCCCccHHHHHHHHHHhCCceeeeeeeee
Q 014547 305 AREP--IIPRTDRPFKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKIESRP 353 (423)
Q Consensus 305 sr~~--~~~~~~~~~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkIESRP 353 (423)
.++. +....+-..|+ |-+ ......=+.++..++..|++...++-.+
T Consensus 86 ~~~~s~I~s~~DLkGK~-Igv--~~~s~~~~~l~~~L~~~Gl~~~dv~~v~ 133 (300)
T TIGR01729 86 AREGSGIEKPEDLKGKN-VAV--PFVSTTHYSLLAALKHWKTDPREVNILN 133 (300)
T ss_pred ecCCCCCCChhHcCCCE-EEe--CCCCcHHHHHHHHHHHcCCChhheEEEe
Confidence 4432 21111222354 332 2222222334455677788766666554
No 286
>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=22.49 E-value=2.8e+02 Score=28.71 Aligned_cols=27 Identities=22% Similarity=0.240 Sum_probs=23.8
Q ss_pred EeCCCccHHHHHHHHHHhCCceeeeee
Q 014547 324 AHDKGTSVLFKVLSAFAFRNISLTKIE 350 (423)
Q Consensus 324 ~l~~~pGaL~~vL~~Fa~~~INLtkIE 350 (423)
.+.+.||.+.++++.++..|||+..|-
T Consensus 346 ~~~~~~g~~a~i~~~L~~~gIni~~i~ 372 (401)
T TIGR00656 346 GMVGAPGVASEIFSALEEKNINILMIG 372 (401)
T ss_pred CcccCccHHHHHHHHHHHCCCcEEEEE
Confidence 356789999999999999999998765
No 287
>PRK05925 aspartate kinase; Provisional
Probab=22.24 E-value=9.9e+02 Score=25.64 Aligned_cols=100 Identities=12% Similarity=0.021 Sum_probs=54.6
Q ss_pred CceeEEeccCHHHHHHHHHhcCCCCeeEEcc---HHHHHHcCCceeecCccCCCCCeeEEEEEeeC-CCCCC----CCCC
Q 014547 245 LNVAREAVDDTAGAAEYIAANDLRDTAAIAS---ARAAELYGMQVLEDGIQDDSSNVTRFVMLARE-PIIPR----TDRP 316 (423)
Q Consensus 245 p~~~~v~~~STA~AA~~va~~~~~~~AAIaS---~~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~-~~~~~----~~~~ 316 (423)
|+++.+..-+..+|.++...+ +-+.. ..-|..+|.++.-.|--|..+--|.|.--.+. ...+. ....
T Consensus 224 ~~A~~i~~is~~ea~ela~~G-----a~vl~~~~~~~a~~~~Ipi~I~~~~~p~~~GT~i~~~~~~~~~~~~ik~It~~~ 298 (440)
T PRK05925 224 KDAQLIPELSFEEMQNLASFG-----AKVLHPPMLKPCVRAGIPIFVTSTFDVTKGGTWIYASDKEVSYEPRIKALSLKQ 298 (440)
T ss_pred CCCeEeeEECHHHHHHHHhCC-----CCcCCHHHHHHHHHCCCcEEEecCCCCCCCccEEecCCccccCCCceEEEEEeC
Confidence 456666666677776654321 11111 24456789999887765544345666321100 00000 0111
Q ss_pred CeEEEEEEe-CCCccHHHHHHHHHHhCCceeeee
Q 014547 317 FKTSIVFAH-DKGTSVLFKVLSAFAFRNISLTKI 349 (423)
Q Consensus 317 ~KTSivf~l-~~~pGaL~~vL~~Fa~~~INLtkI 349 (423)
+-+.+.+.. ....|.+.++++.|+++|||+-.|
T Consensus 299 ~~~~i~v~~~~~~~~~~~~if~~l~~~~I~vd~i 332 (440)
T PRK05925 299 NQALWSVDYNSLGLVRLEDVLGILRSLGIVPGLV 332 (440)
T ss_pred CEEEEEEecCCcchhHHHHHHHHHHHcCCcEEEE
Confidence 222233321 235788999999999999999766
No 288
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=22.09 E-value=7.4e+02 Score=24.09 Aligned_cols=122 Identities=13% Similarity=0.049 Sum_probs=58.2
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeccCC-CCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCc---C
Q 014547 147 AYPNCEAIP-CDQFEVAFQAVELWIADRAVLPVENSL-GGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRK---E 221 (423)
Q Consensus 147 ~f~~~e~vp-~~Sf~~Vf~aV~~g~~d~gVVPIENS~-~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l---~ 221 (423)
.+|+.++.- ..+..++.+.+.+|++|+|+..-. .. .|.. ...|....+ -..+|..|-+...+...+ .
T Consensus 119 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~-~~~~~~~---~~~l~~~~~----~~~~~~~~pl~~~~~i~~~dL~ 190 (309)
T PRK11013 119 RYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETL-HTPAGTE---RTELLTLDE----VCVLPAGHPLAAKKVLTPDDFA 190 (309)
T ss_pred HCCCCeEEEEeCCHHHHHHHHHcCCCCEEEEcCC-CCCCCce---eeeecceeE----EEEEcCCCccccCCccCHHHHC
Confidence 357766533 345677889999999999997421 11 1110 111111111 123455555543322233 3
Q ss_pred cccEEEechh-HH-HHHHHHHHHcCCceeEEe-ccCHHHHHHHHHhcCCCCeeEEccHHHH
Q 014547 222 YLTRVISHPQ-AL-SQCEHTLTKLGLNVAREA-VDDTAGAAEYIAANDLRDTAAIASARAA 279 (423)
Q Consensus 222 dIk~VySHPq-AL-~QC~~fL~~~~p~~~~v~-~~STA~AA~~va~~~~~~~AAIaS~~AA 279 (423)
+.+-|.-.+. .. ..+..|+..++....+.. +++...+.+++..+ ...++.+...+
T Consensus 191 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gv~~~p~~~~ 248 (309)
T PRK11013 191 GENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAG---VGVSIVNPLTA 248 (309)
T ss_pred CCcEEeecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEeChhhh
Confidence 3344543322 22 235667777653323233 44444555556543 34555555443
No 289
>PRK09084 aspartate kinase III; Validated
Probab=21.80 E-value=9.9e+02 Score=25.50 Aligned_cols=101 Identities=18% Similarity=0.091 Sum_probs=59.8
Q ss_pred CceeEEeccCHHHHHHHHHhcCCCCeeEEccH--HHHHHcCCceeecCccCCCCCeeEEEEEeeCCCCCC----CCCCCe
Q 014547 245 LNVAREAVDDTAGAAEYIAANDLRDTAAIASA--RAAELYGMQVLEDGIQDDSSNVTRFVMLAREPIIPR----TDRPFK 318 (423)
Q Consensus 245 p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~--~AAelYgL~ILa~nIqD~~~N~TRFlVLsr~~~~~~----~~~~~K 318 (423)
|+++.+..-|-.+|.++...+ .-.+-++ ..|..+|.++.-.|..|...--|.+- ......+. ....+-
T Consensus 233 ~~a~~i~~is~~ea~ela~~G----a~vlh~~~~~~~~~~~i~i~i~~~~~~~~~GT~I~--~~~~~~~~v~~it~~~~i 306 (448)
T PRK09084 233 PAAKRIDEISFEEAAEMATFG----AKVLHPATLLPAVRSNIPVFVGSSKDPEAGGTWIC--NDTENPPLFRAIALRRNQ 306 (448)
T ss_pred CCCeEcccCCHHHHHHHHhCC----CcccCHHHHHHHHHcCCcEEEEeCCCCCCCceEEe--cCCCCCCeeEEEEeeCCE
Confidence 556677677777888765532 2223222 23567899999888766443445542 11111000 011122
Q ss_pred EEEEEE---eCCCccHHHHHHHHHHhCCceeeeeee
Q 014547 319 TSIVFA---HDKGTSVLFKVLSAFAFRNISLTKIES 351 (423)
Q Consensus 319 TSivf~---l~~~pGaL~~vL~~Fa~~~INLtkIES 351 (423)
+-+-+. ..+.+|.+.++++.|++++||+-.|.+
T Consensus 307 ~lItv~~~~~~~~~g~~a~if~~l~~~~I~Vd~I~s 342 (448)
T PRK09084 307 TLLTLHSLNMLHARGFLAEVFGILARHKISVDLITT 342 (448)
T ss_pred EEEEEecCCCCccccHHHHHHHHHHHcCCeEEEEec
Confidence 223332 135789999999999999999999975
No 290
>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=21.63 E-value=4.1e+02 Score=30.76 Aligned_cols=35 Identities=17% Similarity=0.228 Sum_probs=29.7
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeee--eee
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTK--IES 351 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtk--IES 351 (423)
.-|-|.+..+|+||-|+++.++|+.+|+|+.. |-+
T Consensus 667 ~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~t 703 (850)
T TIGR01693 667 GGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNT 703 (850)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEE
Confidence 35677778889999999999999999999984 543
No 291
>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=21.55 E-value=1.4e+02 Score=25.33 Aligned_cols=119 Identities=13% Similarity=-0.060 Sum_probs=57.7
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCcc---
Q 014547 147 AYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYL--- 223 (423)
Q Consensus 147 ~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dI--- 223 (423)
.+|+.++.... .+..+.+.+|++|+|++...-...|. ....|.+.++.++. +-+| +......+++++
T Consensus 25 ~~P~i~l~~~~--~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~-~~~~~~~~~~~L~~~ 94 (190)
T cd08483 25 KHPEIELSLLP--SADLVDLRPDGIDVAIRYGNGDWPGL---ESEPLTAAPFVVVA----APGL-LGDRKVDSLADLAGL 94 (190)
T ss_pred HCCCceEEEEe--cCCcCCCCCCCcCEEEEecCCCCCCc---EEEeecccceEeee----CHHH-HhhCCCCCHHHHhcC
Confidence 36776554432 23457789999999998532111221 11233344444332 2233 322222333333
Q ss_pred cEEEechhHHHHHHHHHHHcCCcee---EEeccCHHHHHHHHHhcCCCCeeEEccHHHHH
Q 014547 224 TRVISHPQALSQCEHTLTKLGLNVA---REAVDDTAGAAEYIAANDLRDTAAIASARAAE 280 (423)
Q Consensus 224 k~VySHPqAL~QC~~fL~~~~p~~~---~v~~~STA~AA~~va~~~~~~~AAIaS~~AAe 280 (423)
+-|. +.. ......|+.+++.... ...+++.....++++.+ ...++.++..++
T Consensus 95 ~~i~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~~ 149 (190)
T cd08483 95 PWLQ-ERG-TNEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAG---LGLSIQARALVE 149 (190)
T ss_pred ceec-cCC-chHHHHHHHHcCCCcccccCceeCcHHHHHHHHHcC---CcEEeecHHhhH
Confidence 3333 221 1234567776542211 23356666677777664 456677665444
No 292
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=21.17 E-value=90 Score=27.40 Aligned_cols=27 Identities=22% Similarity=0.281 Sum_probs=22.4
Q ss_pred EEEEEEecCcChHHHHHHHHHHHhhcC
Q 014547 376 MFYIDFEASMAEVRAQNALAEVQEFTS 402 (423)
Q Consensus 376 ~FfID~eg~~~d~~v~~aL~eL~~~~~ 402 (423)
.+.||..|+++++.+.+.+.|+.....
T Consensus 2 ~vaiDtSGSis~~~l~~fl~ev~~i~~ 28 (126)
T PF09967_consen 2 VVAIDTSGSISDEELRRFLSEVAGILR 28 (126)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHH
Confidence 478999999999999999998865443
No 293
>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=21.06 E-value=5.2e+02 Score=21.97 Aligned_cols=143 Identities=21% Similarity=0.174 Sum_probs=67.7
Q ss_pred cEEEEeCCCccH--HHHH--HhhhCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEE
Q 014547 128 LRVAYQGVPGAY--SEAA--AGKAYPNCEAIPC-DQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVG 202 (423)
Q Consensus 128 ~~VayLGP~GTf--Sh~A--A~~~f~~~e~vp~-~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Ivg 202 (423)
.+||+-..-+.+ .... -.+.+|+.++... .+-.++.+.+.+|++|+|+..-.-...+ + ....|.+.++.++
T Consensus 2 l~Ig~~~~~~~~~~~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~-~--~~~~l~~~~~~~~- 77 (198)
T cd08441 2 LRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPG-I--AYEPLFDYEVVLV- 77 (198)
T ss_pred EEEEeeccchhhhhHHHHHHHHHhCCCeEEEEEeCCchhHHHHHHcCCceEEEecCCcCCCC-c--EEEEccCCcEEEE-
Confidence 466666555432 1111 1234677666544 3557889999999999999742110000 0 0111222222222
Q ss_pred EEEEeeeeeeeecCCCCcCccc--EEEech--h-HHHHHHHHHHHcCCce-eEEeccCHHHHHHHHHhcCCCCeeEEccH
Q 014547 203 EVQLPVHHCLLALPGVRKEYLT--RVISHP--Q-ALSQCEHTLTKLGLNV-AREAVDDTAGAAEYIAANDLRDTAAIASA 276 (423)
Q Consensus 203 Ei~lpI~h~Lla~~g~~l~dIk--~VySHP--q-AL~QC~~fL~~~~p~~-~~v~~~STA~AA~~va~~~~~~~AAIaS~ 276 (423)
.+-.|-|......+++++. ..+.++ . .......|+.+++... ....++|...+.+.++.+ ...++.+.
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 2223333222122233332 122222 1 1233556666654222 233466777777777764 34566666
Q ss_pred HHHH
Q 014547 277 RAAE 280 (423)
Q Consensus 277 ~AAe 280 (423)
..++
T Consensus 152 ~~~~ 155 (198)
T cd08441 152 WAVR 155 (198)
T ss_pred HHHH
Confidence 5544
No 294
>PRK05092 PII uridylyl-transferase; Provisional
Probab=20.59 E-value=4.8e+02 Score=30.67 Aligned_cols=33 Identities=9% Similarity=0.067 Sum_probs=28.7
Q ss_pred CeEEEEEEeCCCccHHHHHHHHHHhCCceeeee
Q 014547 317 FKTSIVFAHDKGTSVLFKVLSAFAFRNISLTKI 349 (423)
Q Consensus 317 ~KTSivf~l~~~pGaL~~vL~~Fa~~~INLtkI 349 (423)
.-|.|.+..+|+||.|.++.++|+.+|+|+..-
T Consensus 731 ~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A 763 (931)
T PRK05092 731 GVTEVTVLAADHPGLFSRIAGACAAAGANIVDA 763 (931)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEE
Confidence 357777888899999999999999999999843
No 295
>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=20.29 E-value=1.2e+02 Score=31.01 Aligned_cols=47 Identities=13% Similarity=-0.061 Sum_probs=35.7
Q ss_pred cEEEEeCCCccHHHHHHhhhC-------CCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 014547 128 LRVAYQGVPGAYSEAAAGKAY-------PNCEAIPCDQFEVAFQAVELWIADRAVLP 177 (423)
Q Consensus 128 ~~VayLGP~GTfSh~AA~~~f-------~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVP 177 (423)
.|||+ +.||.+|....+.. .++++++.. ..+...|+.+|++|.++++
T Consensus 107 KkIav--~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~-~~d~~aAl~~G~VDAa~~~ 160 (328)
T TIGR03427 107 QKVNL--VELSVSHYLLARALESVGLSEKDVKVVNTS-DADIVAAFITKDVTAVVTW 160 (328)
T ss_pred CEEec--cCCChHHHHHHHHHHHcCCCHHHeEEEeCC-hHHHHHHHhcCCCcEEEEc
Confidence 48998 67999986654432 147788875 4788999999999998863
No 296
>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=20.29 E-value=2.9e+02 Score=23.26 Aligned_cols=122 Identities=13% Similarity=-0.020 Sum_probs=55.8
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeeeecCCCCcCccc--
Q 014547 147 AYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEYLT-- 224 (423)
Q Consensus 147 ~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~dIk-- 224 (423)
.+|+.++.....-. .+.+.+|++|+|++...+...+.. ...|.+.++.++ .+-+| +...+..+++|+.
T Consensus 25 ~~P~i~i~i~~~~~--~~~l~~~~~Dl~l~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~-~~~~~~~~~~dl~~~ 94 (194)
T cd08481 25 RHPDITVNLVTRDE--PFDFSQGSFDAAIHFGDPVWPGAE---SEYLMDEEVVPV----CSPAL-LAGRALAAPADLAHL 94 (194)
T ss_pred HCCCceEEEEeccc--ccCcccCCCCEEEEcCCCCCCCcc---ceecccCeeeec----CCHHH-HhcCCCCcHHHHhhC
Confidence 35766554332211 236889999999986543322211 122333333322 22223 2222222333332
Q ss_pred -EEEechhHHHHHHHHHHHcCCce----eEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHc
Q 014547 225 -RVISHPQALSQCEHTLTKLGLNV----AREAVDDTAGAAEYIAANDLRDTAAIASARAAELY 282 (423)
Q Consensus 225 -~VySHPqAL~QC~~fL~~~~p~~----~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelY 282 (423)
-|. .......-..|+.+++... ....+++...+.+.+..+ ...|+.++..++.+
T Consensus 95 ~~i~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~~~~ 153 (194)
T cd08481 95 PLLQ-QTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAG---LGVALLPRFLIEEE 153 (194)
T ss_pred ceEe-cCCCCcCHHHHHHHcCCCCCCccCceEeccHHHHHHHHHhC---CCeEEecHHHHHHH
Confidence 221 1100112345666554211 112345666667777764 45777787766543
No 297
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=20.01 E-value=6.9e+02 Score=22.98 Aligned_cols=133 Identities=8% Similarity=0.099 Sum_probs=68.4
Q ss_pred CCCccHHHHHHhhhCCCCceeecCCHHHHHHHHHcCCcCeEEEeeccCCCCchHHHHHHhhcCCcEEEEEEEEeeeeeee
Q 014547 134 GVPGAYSEAAAGKAYPNCEAIPCDQFEVAFQAVELWIADRAVLPVENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLL 213 (423)
Q Consensus 134 GP~GTfSh~AA~~~f~~~e~vp~~Sf~~Vf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Ll 213 (423)
|-.--+-+..+++.--..++++ .++.+++++++.|++|..+..+..+-+ -.+ .+.....+ ......++
T Consensus 45 G~~~dl~~~i~~~lg~~~~~~~-~~~~~~~~~l~~g~~D~~~~~~~~~~~-----r~~-----~~~fs~p~-~~~~~~~v 112 (243)
T PRK15007 45 GFDVDLAQALCKEIDATCTFSN-QAFDSLIPSLKFRRVEAVMAGMDITPE-----REK-----QVLFTTPY-YDNSALFV 112 (243)
T ss_pred eeeHHHHHHHHHHhCCcEEEEe-CCHHHHhHHHhCCCcCEEEEcCccCHH-----Hhc-----ccceecCc-cccceEEE
Confidence 3333444445544322456665 468999999999999976543321111 001 11111111 11112233
Q ss_pred ecCC--CCcCccc--EEEechhHHHHHHHHHHHcCCceeEEeccCHHHHHHHHHhcCCCCeeEEccHHHHHHc
Q 014547 214 ALPG--VRKEYLT--RVISHPQALSQCEHTLTKLGLNVAREAVDDTAGAAEYIAANDLRDTAAIASARAAELY 282 (423)
Q Consensus 214 a~~g--~~l~dIk--~VySHPqAL~QC~~fL~~~~p~~~~v~~~STA~AA~~va~~~~~~~AAIaS~~AAelY 282 (423)
.+.+ .++++++ +|-. ...... .+||.+..|++..+.+.+...+.+.+..+ +-.|+++....+..|
T Consensus 113 ~~~~~~~~~~dL~g~~Igv-~~g~~~-~~~l~~~~~~~~~~~~~~~~~~~~~L~~g--rvDa~i~~~~~~~~~ 181 (243)
T PRK15007 113 GQQGKYTSVDQLKGKKVGV-QNGTTH-QKFIMDKHPEITTVPYDSYQNAKLDLQNG--RIDAVFGDTAVVTEW 181 (243)
T ss_pred EeCCCCCCHHHhCCCeEEE-ecCcHH-HHHHHHhCCCCeEEEcCCHHHHHHHHHcC--CCCEEEeCHHHHHHH
Confidence 3322 1223332 3322 222233 36777777788888777888888777765 457788777654433
Done!