Query 015945
Match_columns 398
No_of_seqs 306 out of 1295
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 02:22:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015945.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015945hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10622 pheA bifunctional cho 100.0 2.4E-94 5.2E-99 729.4 31.5 348 26-396 5-379 (386)
2 COG0077 PheA Prephenate dehydr 100.0 6.2E-86 1.3E-90 635.3 32.1 271 111-396 2-276 (279)
3 PLN02317 arogenate dehydratase 100.0 1.2E-84 2.6E-89 651.4 36.0 312 86-397 69-380 (382)
4 PRK11899 prephenate dehydratas 100.0 5.6E-84 1.2E-88 627.8 34.2 273 110-396 3-276 (279)
5 PRK11898 prephenate dehydratas 100.0 3.1E-77 6.7E-82 583.0 34.2 270 112-396 2-279 (283)
6 KOG2797 Prephenate dehydratase 100.0 9.4E-72 2E-76 531.8 23.0 291 102-397 81-373 (377)
7 PF00800 PDT: Prephenate dehyd 100.0 1.6E-51 3.5E-56 377.8 18.0 177 114-290 1-181 (181)
8 PRK06034 hypothetical protein; 100.0 6.3E-32 1.4E-36 260.9 8.2 160 18-189 1-171 (279)
9 cd04904 ACT_AAAH ACT domain of 99.8 3.5E-21 7.6E-26 152.0 9.5 73 301-389 1-73 (74)
10 cd04931 ACT_PAH ACT domain of 99.8 3.7E-20 8.1E-25 151.7 10.1 72 296-382 10-81 (90)
11 cd04930 ACT_TH ACT domain of t 99.8 7.6E-20 1.7E-24 156.4 9.1 76 298-389 39-114 (115)
12 cd04905 ACT_CM-PDT C-terminal 99.8 2.4E-19 5.1E-24 143.1 11.2 80 300-393 1-80 (80)
13 cd04929 ACT_TPH ACT domain of 99.8 8.1E-20 1.8E-24 144.5 8.1 71 301-387 1-71 (74)
14 cd04880 ACT_AAAH-PDT-like ACT 99.8 1E-18 2.2E-23 137.5 9.9 75 302-390 1-75 (75)
15 TIGR01268 Phe4hydrox_tetr phen 99.7 6.6E-17 1.4E-21 164.9 10.4 79 299-392 15-94 (436)
16 TIGR01270 Trp_5_monoox tryptop 99.6 1E-14 2.2E-19 149.5 9.9 77 296-388 27-104 (464)
17 TIGR01801 CM_A chorismate muta 99.5 4.7E-15 1E-19 124.3 -1.7 76 26-110 4-87 (102)
18 TIGR01797 CM_P_1 chorismate mu 99.4 2.3E-14 5E-19 115.8 -0.7 73 28-109 1-82 (83)
19 PRK07248 hypothetical protein; 99.4 2.7E-14 5.9E-19 116.2 -1.7 75 27-110 2-84 (87)
20 PRK11199 tyrA bifunctional cho 99.4 1.2E-13 2.6E-18 140.3 2.0 128 27-165 4-153 (374)
21 TIGR01805 CM_mono_grmpos monof 99.4 7.5E-14 1.6E-18 112.2 -0.4 73 28-109 1-81 (81)
22 TIGR01807 CM_P2 chorismate mut 99.3 2.8E-13 6.1E-18 107.6 0.8 66 28-102 1-76 (76)
23 TIGR01799 CM_T chorismate muta 99.3 1.9E-13 4E-18 110.5 -0.7 73 28-109 1-82 (83)
24 TIGR01803 CM-like chorismate m 99.3 2.1E-13 4.5E-18 109.9 -0.8 72 28-108 1-81 (82)
25 PRK06443 chorismate mutase; Va 99.3 2.1E-12 4.5E-17 116.7 2.7 81 16-123 3-95 (177)
26 PRK06285 chorismate mutase; Pr 99.2 3.2E-13 6.9E-18 112.1 -2.7 76 26-110 7-91 (96)
27 TIGR01791 CM_archaeal chorisma 99.2 6E-13 1.3E-17 107.3 -1.2 73 28-109 1-82 (83)
28 PRK07075 isochorismate-pyruvat 99.2 4.5E-13 9.7E-18 112.2 -3.0 75 26-109 8-90 (101)
29 COG1605 PheA Chorismate mutase 99.2 5.2E-13 1.1E-17 111.8 -3.6 78 26-112 8-95 (101)
30 PRK12595 bifunctional 3-deoxy- 99.1 4.2E-12 9E-17 128.4 -2.1 74 27-109 5-86 (360)
31 TIGR01795 CM_mono_cladeE monof 99.1 3.3E-12 7.2E-17 105.6 -2.4 74 26-109 3-86 (94)
32 PRK09239 chorismate mutase; Pr 99.1 1.5E-12 3.3E-17 109.5 -4.7 82 21-111 5-95 (104)
33 PF01817 CM_2: Chorismate muta 99.0 3.8E-12 8.2E-17 101.9 -5.2 70 32-110 1-79 (81)
34 TIGR01808 CM_M_hiGC-arch monof 98.9 2.3E-10 4.9E-15 90.6 0.9 65 27-106 1-73 (74)
35 PRK07857 hypothetical protein; 98.9 3.9E-10 8.5E-15 94.7 2.1 60 15-80 17-84 (106)
36 smart00830 CM_2 Chorismate mut 98.8 6.7E-10 1.5E-14 88.2 -1.4 69 32-109 1-78 (79)
37 TIGR01269 Tyr_3_monoox tyrosin 98.7 4.8E-08 1E-12 99.9 8.6 74 298-384 35-109 (457)
38 PRK08818 prephenate dehydrogen 98.7 5.1E-08 1.1E-12 99.2 8.0 65 299-379 294-359 (370)
39 KOG3820 Aromatic amino acid hy 98.5 4.7E-07 1E-11 90.9 8.7 76 298-389 34-109 (461)
40 TIGR01806 CM_mono2 chorismate 98.2 1.1E-07 2.4E-12 81.4 -3.2 60 45-110 9-77 (114)
41 cd04886 ACT_ThrD-II-like C-ter 98.1 3.6E-05 7.8E-10 58.2 9.1 69 304-385 2-70 (73)
42 PF01842 ACT: ACT domain; Int 98.0 3.2E-05 7E-10 57.9 8.0 38 301-338 1-38 (66)
43 PRK09269 chorismate mutase; Pr 97.8 2E-06 4.3E-11 80.1 -2.8 60 45-110 37-105 (193)
44 PRK08055 chorismate mutase; Pr 97.7 2.8E-06 6.1E-11 78.3 -2.8 60 45-110 30-98 (181)
45 cd04882 ACT_Bt0572_2 C-termina 97.4 0.0011 2.3E-08 49.6 7.9 59 303-382 2-60 (65)
46 cd04884 ACT_CBS C-terminal ACT 97.3 0.0017 3.8E-08 50.2 8.7 65 303-382 2-66 (72)
47 PRK06737 acetolactate synthase 97.2 0.0038 8.2E-08 49.8 9.3 70 301-387 3-72 (76)
48 cd04883 ACT_AcuB C-terminal AC 97.1 0.0033 7.1E-08 48.1 8.5 66 301-385 2-67 (72)
49 cd04878 ACT_AHAS N-terminal AC 97.1 0.0062 1.3E-07 45.6 9.5 66 302-384 2-67 (72)
50 cd04874 ACT_Af1403 N-terminal 97.1 0.0049 1.1E-07 46.4 8.9 63 302-383 2-64 (72)
51 PF13710 ACT_5: ACT domain; PD 96.9 0.0059 1.3E-07 46.7 7.8 61 309-386 1-61 (63)
52 cd04888 ACT_PheB-BS C-terminal 96.8 0.013 2.7E-07 45.3 9.1 73 302-390 2-76 (76)
53 cd02116 ACT ACT domains are co 96.7 0.0095 2.1E-07 40.9 7.3 58 304-379 2-59 (60)
54 PF13291 ACT_4: ACT domain; PD 96.7 0.015 3.3E-07 45.7 8.8 71 297-383 3-73 (80)
55 cd04909 ACT_PDH-BS C-terminal 96.6 0.0069 1.5E-07 46.1 6.1 36 302-337 3-38 (69)
56 cd04908 ACT_Bt0572_1 N-termina 96.5 0.017 3.7E-07 43.9 8.0 35 302-336 3-37 (66)
57 cd04902 ACT_3PGDH-xct C-termin 96.5 0.01 2.2E-07 45.2 6.7 60 303-378 2-61 (73)
58 TIGR00119 acolac_sm acetolacta 96.5 0.022 4.9E-07 51.5 9.9 70 302-388 3-72 (157)
59 PRK11895 ilvH acetolactate syn 96.5 0.025 5.3E-07 51.4 10.1 71 301-388 3-73 (161)
60 cd04885 ACT_ThrD-I Tandem C-te 96.5 0.014 3E-07 44.8 7.2 62 304-383 2-63 (68)
61 cd04903 ACT_LSD C-terminal ACT 96.4 0.017 3.7E-07 43.1 7.5 62 303-383 2-63 (71)
62 PRK11152 ilvM acetolactate syn 96.4 0.036 7.8E-07 44.2 9.1 67 300-384 3-69 (76)
63 CHL00100 ilvH acetohydroxyacid 96.3 0.024 5.3E-07 52.1 9.3 71 301-388 3-73 (174)
64 cd04879 ACT_3PGDH-like ACT_3PG 96.2 0.026 5.6E-07 42.0 7.5 62 303-383 2-63 (71)
65 PRK08178 acetolactate synthase 96.2 0.053 1.1E-06 45.1 9.5 72 299-388 7-78 (96)
66 cd04887 ACT_MalLac-Enz ACT_Mal 96.2 0.041 8.8E-07 42.3 8.4 63 303-382 2-64 (74)
67 PRK04435 hypothetical protein; 96.1 0.058 1.2E-06 48.2 10.3 78 298-391 67-146 (147)
68 PRK13562 acetolactate synthase 96.1 0.056 1.2E-06 43.9 9.0 71 301-388 3-74 (84)
69 cd04896 ACT_ACR-like_3 ACT dom 95.9 0.039 8.4E-07 43.9 7.4 63 303-380 3-69 (75)
70 cd04926 ACT_ACR_4 C-terminal 95.8 0.056 1.2E-06 42.0 7.9 36 301-336 2-37 (72)
71 cd04906 ACT_ThrD-I_1 First of 95.8 0.057 1.2E-06 43.4 8.0 69 303-389 4-72 (85)
72 cd04901 ACT_3PGDH C-terminal A 95.7 0.026 5.7E-07 42.6 5.4 60 303-383 2-61 (69)
73 cd04881 ACT_HSDH-Hom ACT_HSDH_ 95.5 0.1 2.2E-06 39.6 8.3 64 303-382 3-66 (79)
74 PRK08198 threonine dehydratase 95.5 0.11 2.3E-06 53.5 10.7 77 299-389 326-403 (404)
75 PRK00194 hypothetical protein; 95.2 0.11 2.3E-06 41.8 7.7 36 300-335 3-38 (90)
76 cd04872 ACT_1ZPV ACT domain pr 95.0 0.12 2.6E-06 41.6 7.5 67 301-382 2-69 (88)
77 cd04873 ACT_UUR-ACR-like ACT d 95.0 0.21 4.6E-06 37.3 8.4 36 302-337 2-37 (70)
78 cd04876 ACT_RelA-SpoT ACT dom 94.9 0.28 6E-06 35.2 8.7 63 304-383 2-64 (71)
79 cd04877 ACT_TyrR N-terminal AC 94.9 0.17 3.7E-06 39.3 7.7 59 303-382 3-61 (74)
80 PRK08577 hypothetical protein; 94.8 0.38 8.3E-06 42.0 10.7 70 299-383 55-124 (136)
81 TIGR01127 ilvA_1Cterm threonin 94.8 0.15 3.3E-06 51.9 9.3 73 300-386 305-378 (380)
82 cd04889 ACT_PDH-BS-like C-term 94.7 0.095 2.1E-06 38.2 5.6 34 304-337 2-35 (56)
83 cd04899 ACT_ACR-UUR-like_2 C-t 94.6 0.28 6.1E-06 37.0 8.2 36 302-337 2-37 (70)
84 PRK06382 threonine dehydratase 94.5 0.2 4.2E-06 51.9 9.5 36 299-334 329-364 (406)
85 COG4492 PheB ACT domain-contai 94.5 0.19 4.2E-06 44.1 7.7 77 298-391 70-149 (150)
86 cd04875 ACT_F4HF-DF N-terminal 94.4 0.16 3.5E-06 39.3 6.7 33 303-335 2-34 (74)
87 cd04870 ACT_PSP_1 CT domains f 94.4 0.24 5.3E-06 38.6 7.7 61 305-380 4-64 (75)
88 PRK08526 threonine dehydratase 94.4 0.83 1.8E-05 47.3 13.7 212 153-387 167-400 (403)
89 PF13740 ACT_6: ACT domain; PD 94.4 0.22 4.8E-06 39.0 7.4 35 303-337 3-39 (76)
90 cd04895 ACT_ACR_1 ACT domain-c 94.3 0.28 6.1E-06 38.6 7.8 29 301-329 2-30 (72)
91 PRK08639 threonine dehydratase 93.3 1.1 2.4E-05 46.5 12.4 74 299-389 335-409 (420)
92 cd04869 ACT_GcvR_2 ACT domains 93.1 0.68 1.5E-05 36.1 8.2 35 303-337 2-36 (81)
93 COG2061 ACT-domain-containing 92.9 0.8 1.7E-05 41.2 8.9 74 300-389 5-79 (170)
94 TIGR01124 ilvA_2Cterm threonin 92.2 2.5 5.4E-05 45.1 13.4 150 214-389 236-395 (499)
95 PRK07334 threonine dehydratase 92.1 0.96 2.1E-05 46.7 9.9 77 298-388 324-401 (403)
96 cd04900 ACT_UUR-like_1 ACT dom 91.6 1.3 2.9E-05 34.1 8.0 32 301-332 2-33 (73)
97 TIGR02079 THD1 threonine dehyd 91.3 1.4 3.1E-05 45.7 10.1 75 299-389 324-398 (409)
98 cd04893 ACT_GcvR_1 ACT domains 90.7 2.1 4.6E-05 33.5 8.4 64 303-382 4-67 (77)
99 COG1707 ACT domain-containing 90.2 0.85 1.8E-05 41.7 6.3 61 303-381 5-65 (218)
100 cd04897 ACT_ACR_3 ACT domain-c 89.9 2.1 4.5E-05 34.0 7.7 29 301-329 2-30 (75)
101 PLN02550 threonine dehydratase 89.9 3 6.5E-05 45.4 11.4 209 154-389 258-487 (591)
102 COG4747 ACT domain-containing 89.9 2.1 4.5E-05 37.1 8.1 38 301-338 70-107 (142)
103 COG0440 IlvH Acetolactate synt 89.0 2.2 4.7E-05 38.9 8.1 73 300-389 4-76 (163)
104 cd04935 ACT_AKiii-DAPDC_1 ACT 88.6 3.2 7E-05 32.6 7.9 62 308-389 12-74 (75)
105 cd04932 ACT_AKiii-LysC-EC_1 AC 88.1 4.2 9.1E-05 31.9 8.3 58 307-383 11-69 (75)
106 PRK11589 gcvR glycine cleavage 88.1 2.4 5.1E-05 39.6 7.9 35 303-337 98-132 (190)
107 COG2716 GcvR Glycine cleavage 88.0 2.4 5.2E-05 38.9 7.7 74 305-391 97-171 (176)
108 PRK09224 threonine dehydratase 86.9 4.1 8.8E-05 43.5 10.0 73 299-389 327-399 (504)
109 COG3830 ACT domain-containing 86.4 1.9 4.1E-05 35.5 5.5 66 308-388 11-78 (90)
110 cd04927 ACT_ACR-like_2 Second 86.3 6 0.00013 31.0 8.3 28 304-331 4-31 (76)
111 cd04907 ACT_ThrD-I_2 Second of 86.1 6.9 0.00015 31.3 8.6 65 302-385 3-67 (81)
112 PRK12483 threonine dehydratase 85.7 4.8 0.0001 43.3 9.7 72 299-389 344-416 (521)
113 cd04912 ACT_AKiii-LysC-EC-like 85.6 6.2 0.00013 30.6 8.0 56 307-381 11-67 (75)
114 cd08417 PBP2_Nitroaromatics_li 84.6 25 0.00054 30.2 12.7 121 132-263 26-155 (200)
115 PRK13011 formyltetrahydrofolat 83.5 7.1 0.00015 38.7 9.2 67 301-382 8-76 (286)
116 PF12974 Phosphonate-bd: ABC t 83.4 2.1 4.5E-05 40.3 5.3 84 110-202 104-202 (243)
117 cd04934 ACT_AK-Hom3_1 CT domai 83.1 5.6 0.00012 31.1 6.7 55 309-383 13-67 (73)
118 PRK06349 homoserine dehydrogen 81.0 5.9 0.00013 41.3 8.0 64 302-382 350-413 (426)
119 PRK06545 prephenate dehydrogen 80.3 4 8.7E-05 41.4 6.3 40 300-339 290-329 (359)
120 cd04891 ACT_AK-LysC-DapG-like_ 80.1 7.6 0.00017 27.4 6.2 30 306-335 7-36 (61)
121 cd04925 ACT_ACR_2 ACT domain-c 79.9 15 0.00032 28.5 8.1 32 303-334 3-34 (74)
122 PRK13010 purU formyltetrahydro 78.2 11 0.00025 37.3 8.6 66 302-382 11-80 (289)
123 PF12727 PBP_like: PBP superfa 78.0 32 0.00069 31.9 11.1 132 135-271 13-166 (193)
124 TIGR01728 SsuA_fam ABC transpo 77.6 18 0.00039 34.0 9.6 137 113-259 2-157 (288)
125 PF03401 TctC: Tripartite tric 77.3 4.8 0.0001 39.3 5.6 64 99-163 94-161 (274)
126 PRK11092 bifunctional (p)ppGpp 76.9 25 0.00055 39.2 11.7 69 298-383 624-692 (702)
127 PF00585 Thr_dehydrat_C: C-ter 76.4 4.6 0.0001 33.0 4.4 69 298-384 8-76 (91)
128 TIGR00691 spoT_relA (p)ppGpp s 75.7 18 0.00039 40.2 10.2 68 299-383 609-676 (683)
129 PRK11790 D-3-phosphoglycerate 75.1 9.4 0.0002 39.7 7.4 63 299-383 337-400 (409)
130 cd04913 ACT_AKii-LysC-BS-like_ 75.1 14 0.0003 27.3 6.6 28 306-333 8-35 (75)
131 COG0317 SpoT Guanosine polypho 75.0 18 0.0004 40.2 9.8 70 298-384 625-694 (701)
132 PF00497 SBP_bac_3: Bacterial 75.0 48 0.001 29.3 11.3 49 111-161 110-159 (225)
133 PRK09959 hybrid sensory histid 73.6 10 0.00022 44.1 8.1 50 110-161 163-212 (1197)
134 cd08411 PBP2_OxyR The C-termin 73.5 56 0.0012 28.0 11.0 123 131-263 26-157 (200)
135 TIGR01693 UTase_glnD [Protein- 71.8 21 0.00046 40.6 9.7 51 298-363 777-827 (850)
136 TIGR00363 lipoprotein, YaeC fa 71.6 1E+02 0.0022 29.9 14.4 147 110-268 18-200 (258)
137 PRK06027 purU formyltetrahydro 70.4 27 0.00058 34.6 9.0 33 303-335 9-41 (286)
138 TIGR00719 sda_beta L-serine de 70.1 18 0.00038 34.1 7.4 55 301-371 149-204 (208)
139 PRK05092 PII uridylyl-transfer 70.1 20 0.00043 41.2 9.1 53 299-366 842-895 (931)
140 PRK11151 DNA-binding transcrip 69.6 60 0.0013 31.3 11.3 144 109-262 90-246 (305)
141 PRK10872 relA (p)ppGpp synthet 69.3 24 0.00051 39.7 9.2 68 299-382 665-732 (743)
142 COG4747 ACT domain-containing 68.7 6 0.00013 34.4 3.4 29 303-331 6-34 (142)
143 cd04890 ACT_AK-like_1 ACT doma 68.7 17 0.00038 26.5 5.7 51 308-379 11-61 (62)
144 cd04933 ACT_AK1-AT_1 ACT domai 67.8 27 0.00058 27.8 6.9 58 307-383 11-72 (78)
145 PRK05007 PII uridylyl-transfer 67.2 16 0.00035 41.8 7.5 36 298-333 806-843 (884)
146 cd08445 PBP2_BenM_CatM_CatR Th 66.8 85 0.0018 27.1 10.8 120 132-261 27-158 (203)
147 PRK11063 metQ DL-methionine tr 65.3 1.4E+02 0.0031 29.1 14.6 107 110-226 31-151 (271)
148 PF00497 SBP_bac_3: Bacterial 65.0 37 0.0008 30.1 8.2 124 123-263 28-165 (225)
149 PRK13581 D-3-phosphoglycerate 64.1 16 0.00035 39.2 6.5 105 257-381 387-514 (526)
150 cd08452 PBP2_AlsR The C-termin 64.1 95 0.0021 26.7 12.4 122 131-262 25-157 (197)
151 PRK15007 putative ABC transpor 63.7 17 0.00036 33.7 5.9 50 110-161 125-174 (243)
152 TIGR00655 PurU formyltetrahydr 62.9 40 0.00087 33.3 8.5 34 303-336 3-36 (280)
153 cd08435 PBP2_GbpR The C-termin 62.7 96 0.0021 26.3 11.2 122 131-262 25-158 (201)
154 cd04928 ACT_TyrKc Uncharacteri 61.5 50 0.0011 25.7 7.1 35 303-337 4-38 (68)
155 cd00134 PBPb Bacterial peripla 61.3 22 0.00048 30.8 5.9 49 111-161 105-153 (218)
156 TIGR01096 3A0103s03R lysine-ar 60.3 20 0.00044 33.1 5.8 49 111-161 131-180 (250)
157 cd08440 PBP2_LTTR_like_4 TThe 58.9 1.1E+02 0.0024 25.7 11.1 122 131-262 25-155 (197)
158 cd08486 PBP2_CbnR The C-termin 58.8 1.1E+02 0.0025 26.5 10.1 140 112-261 3-157 (198)
159 KOG2663 Acetolactate synthase, 58.7 27 0.00059 34.2 6.2 73 299-390 76-150 (309)
160 PF13379 NMT1_2: NMT1-like fam 58.4 1.6E+02 0.0035 27.6 12.6 145 110-260 6-181 (252)
161 PRK09034 aspartate kinase; Rev 58.0 2E+02 0.0043 30.3 13.2 127 228-381 234-372 (454)
162 PRK09508 leuO leucine transcri 57.4 36 0.00077 33.2 7.2 122 131-263 137-266 (314)
163 cd08412 PBP2_PAO1_like The C-t 57.2 1.2E+02 0.0026 25.7 12.1 122 131-262 25-154 (198)
164 PRK01759 glnD PII uridylyl-tra 56.9 31 0.00066 39.4 7.4 32 298-329 781-812 (854)
165 cd04911 ACT_AKiii-YclM-BS_1 AC 56.6 50 0.0011 26.3 6.5 57 308-384 12-68 (76)
166 PRK11260 cystine transporter s 56.2 24 0.00052 33.5 5.6 49 111-161 149-197 (266)
167 KOG3217 Protein tyrosine phosp 55.2 8.4 0.00018 34.6 2.0 62 315-394 58-123 (159)
168 PRK09495 glnH glutamine ABC tr 54.5 26 0.00057 32.7 5.5 49 111-161 131-179 (247)
169 TIGR01327 PGDH D-3-phosphoglyc 53.7 24 0.00052 37.9 5.6 104 258-381 387-513 (525)
170 cd08450 PBP2_HcaR The C-termin 53.7 1.4E+02 0.003 25.3 10.0 32 131-162 25-57 (196)
171 PRK09959 hybrid sensory histid 53.3 19 0.00041 42.0 5.1 50 110-161 406-455 (1197)
172 PRK03381 PII uridylyl-transfer 52.7 53 0.0012 37.1 8.3 38 299-336 706-743 (774)
173 cd04923 ACT_AK-LysC-DapG-like_ 52.6 67 0.0015 22.8 6.4 27 307-333 10-36 (63)
174 smart00062 PBPb Bacterial peri 52.5 34 0.00074 29.4 5.6 51 111-163 106-156 (219)
175 cd08446 PBP2_Chlorocatechol Th 52.5 1.5E+02 0.0032 25.3 12.0 122 131-262 26-158 (198)
176 TIGR00656 asp_kin_monofn aspar 51.9 1.7E+02 0.0038 29.8 11.4 98 228-334 189-297 (401)
177 PRK10820 DNA-binding transcrip 51.8 38 0.00083 36.2 6.8 58 303-381 3-60 (520)
178 cd04868 ACT_AK-like ACT domain 51.8 35 0.00075 23.5 4.6 27 309-335 12-38 (60)
179 PRK04374 PII uridylyl-transfer 51.8 70 0.0015 36.7 9.2 52 298-366 794-848 (869)
180 cd08421 PBP2_LTTR_like_1 The C 51.7 1.5E+02 0.0032 25.1 10.1 122 131-262 25-155 (198)
181 PF03466 LysR_substrate: LysR 51.7 1.6E+02 0.0034 25.3 11.7 137 109-263 5-162 (209)
182 PF12916 DUF3834: Protein of u 51.5 34 0.00073 32.2 5.5 82 99-185 57-142 (201)
183 PRK11553 alkanesulfonate trans 51.1 1.2E+02 0.0027 29.4 9.9 137 108-256 25-182 (314)
184 PRK12680 transcriptional regul 51.0 2.5E+02 0.0055 27.6 12.4 145 109-262 92-250 (327)
185 smart00079 PBPe Eukaryotic hom 51.0 37 0.00081 28.3 5.4 47 112-161 14-71 (134)
186 cd04936 ACT_AKii-LysC-BS-like_ 50.9 75 0.0016 22.6 6.4 27 307-333 10-36 (63)
187 PRK12683 transcriptional regul 50.4 2.5E+02 0.0054 27.3 12.0 143 109-261 92-248 (309)
188 PF07485 DUF1529: Domain of Un 50.0 87 0.0019 27.2 7.5 62 300-377 56-117 (123)
189 cd08420 PBP2_CysL_like C-termi 50.0 95 0.002 26.2 7.9 122 131-262 25-158 (201)
190 cd04924 ACT_AK-Arch_2 ACT doma 49.8 83 0.0018 22.7 6.6 27 307-333 11-37 (66)
191 cd04892 ACT_AK-like_2 ACT doma 49.7 83 0.0018 22.0 6.4 27 307-333 10-36 (65)
192 PRK11242 DNA-binding transcrip 48.9 1.3E+02 0.0029 28.4 9.5 121 132-262 117-247 (296)
193 cd04918 ACT_AK1-AT_2 ACT domai 48.5 1.1E+02 0.0024 22.7 7.5 36 300-335 3-38 (65)
194 smart00062 PBPb Bacterial peri 47.3 1.8E+02 0.0039 24.8 9.5 111 134-260 40-157 (219)
195 cd08453 PBP2_IlvR The C-termin 47.1 1.8E+02 0.0039 24.8 11.2 123 131-262 25-160 (200)
196 PRK10341 DNA-binding transcrip 46.2 2.4E+02 0.0053 27.2 11.1 115 132-262 123-252 (312)
197 COG2107 Predicted periplasmic 46.1 30 0.00065 34.0 4.4 54 110-165 94-147 (272)
198 PRK03059 PII uridylyl-transfer 45.6 93 0.002 35.6 8.9 37 298-334 784-822 (856)
199 PRK00275 glnD PII uridylyl-tra 44.9 88 0.0019 36.0 8.6 36 299-334 813-850 (895)
200 cd08459 PBP2_DntR_NahR_LinR_li 44.6 1.8E+02 0.0039 24.8 9.0 122 131-263 25-155 (201)
201 cd04914 ACT_AKi-DapG-BS_1 ACT 44.5 33 0.00071 26.0 3.6 28 307-335 9-36 (67)
202 cd08462 PBP2_NodD The C-termin 44.5 1.6E+02 0.0034 25.4 8.6 121 131-263 25-155 (200)
203 PRK05007 PII uridylyl-transfer 44.0 1.1E+02 0.0024 35.2 9.2 34 299-332 700-733 (884)
204 cd04922 ACT_AKi-HSDH-ThrA_2 AC 43.6 60 0.0013 23.5 4.9 27 307-333 11-37 (66)
205 PRK06635 aspartate kinase; Rev 43.2 3.4E+02 0.0074 27.7 12.0 29 307-335 270-298 (404)
206 cd08466 PBP2_LeuO The C-termin 42.2 2.2E+02 0.0047 24.2 9.7 123 131-264 25-156 (200)
207 cd08413 PBP2_CysB_like The C-t 41.8 2.3E+02 0.0049 24.4 11.4 121 131-261 25-155 (198)
208 TIGR01098 3A0109s03R phosphate 41.7 45 0.00097 31.1 4.9 53 110-162 140-202 (254)
209 PRK11917 bifunctional adhesin/ 41.5 1.2E+02 0.0027 28.8 8.0 49 110-160 147-199 (259)
210 cd04919 ACT_AK-Hom3_2 ACT doma 41.1 72 0.0016 23.2 5.0 26 308-333 12-37 (66)
211 PRK09906 DNA-binding transcrip 40.8 3.2E+02 0.007 25.9 12.0 122 131-262 115-247 (296)
212 cd08465 PBP2_ToxR The C-termin 39.8 2.1E+02 0.0045 24.7 8.7 31 132-162 26-57 (200)
213 cd08441 PBP2_MetR The C-termin 39.6 1.6E+02 0.0035 25.1 7.8 122 131-262 25-155 (198)
214 PRK15010 ABC transporter lysin 39.4 3.3E+02 0.0071 25.5 11.2 113 134-262 66-188 (260)
215 TIGR02424 TF_pcaQ pca operon t 39.3 3.4E+02 0.0075 25.7 11.7 145 108-262 91-251 (300)
216 TIGR03339 phn_lysR aminoethylp 38.9 3.2E+02 0.007 25.3 11.0 139 110-259 87-236 (279)
217 cd04937 ACT_AKi-DapG-BS_2 ACT 38.8 1.4E+02 0.0031 22.0 6.3 33 301-333 4-37 (64)
218 TIGR02995 ectoine_ehuB ectoine 38.5 60 0.0013 31.0 5.3 49 111-161 144-193 (275)
219 PRK10859 membrane-bound lytic 38.2 93 0.002 32.8 7.1 113 134-262 81-207 (482)
220 PRK12684 transcriptional regul 38.2 2.9E+02 0.0063 26.8 10.2 143 109-262 92-249 (313)
221 PRK11480 tauA taurine transpor 38.2 39 0.00085 33.3 4.1 144 108-260 21-180 (320)
222 PRK08210 aspartate kinase I; R 38.1 4.6E+02 0.01 26.9 13.0 96 228-331 193-303 (403)
223 PRK09224 threonine dehydratase 37.6 81 0.0018 33.7 6.6 35 299-334 422-456 (504)
224 cd08461 PBP2_DntR_like_3 The C 37.4 1.7E+02 0.0036 24.9 7.6 123 131-264 25-157 (198)
225 cd00460 RNAP_RPB11_RPB3 RPB11 37.3 1.5E+02 0.0032 23.8 6.6 76 300-384 8-84 (86)
226 cd08438 PBP2_CidR The C-termin 37.0 2.5E+02 0.0055 23.5 11.4 32 131-162 25-57 (197)
227 PRK11589 gcvR glycine cleavage 36.7 1.4E+02 0.0029 27.9 7.1 36 300-337 6-43 (190)
228 PF13840 ACT_7: ACT domain ; P 36.7 72 0.0016 24.0 4.4 33 300-332 8-42 (65)
229 PRK11260 cystine transporter s 36.0 2.5E+02 0.0054 26.4 9.1 117 132-264 78-204 (266)
230 PRK08961 bifunctional aspartat 35.7 5.2E+02 0.011 29.6 12.9 127 228-380 250-387 (861)
231 PF11966 SSURE: Fibronectin-bi 35.7 85 0.0018 25.1 4.6 38 354-391 18-60 (81)
232 cd04921 ACT_AKi-HSDH-ThrA-like 35.2 1.9E+02 0.004 21.9 6.8 27 307-333 11-37 (80)
233 cd04871 ACT_PSP_2 ACT domains 35.1 1E+02 0.0023 24.5 5.3 64 310-381 10-74 (84)
234 COG3265 GntK Gluconate kinase 35.1 82 0.0018 28.7 5.1 78 96-178 79-158 (161)
235 PRK11482 putative DNA-binding 34.2 4.5E+02 0.0098 25.6 11.2 143 110-264 117-271 (317)
236 cd08456 PBP2_LysR The C-termin 34.1 2.8E+02 0.0062 23.3 9.6 32 131-162 25-57 (196)
237 cd00134 PBPb Bacterial peripla 34.0 1.4E+02 0.003 25.6 6.6 114 134-263 39-159 (218)
238 PRK03601 transcriptional regul 33.9 4.1E+02 0.009 25.1 11.6 114 131-262 114-231 (275)
239 TIGR02995 ectoine_ehuB ectoine 33.6 3.8E+02 0.0082 25.4 10.0 110 138-262 76-198 (275)
240 PRK12679 cbl transcriptional r 33.5 4.2E+02 0.009 25.7 10.5 144 109-261 92-248 (316)
241 cd04916 ACT_AKiii-YclM-BS_2 AC 33.4 1.8E+02 0.0039 20.8 6.5 27 307-333 11-37 (66)
242 COG2844 GlnD UTP:GlnB (protein 33.0 1.6E+02 0.0035 33.6 8.0 33 298-330 789-821 (867)
243 cd08468 PBP2_Pa0477 The C-term 32.9 1E+02 0.0022 26.7 5.5 32 131-162 25-57 (202)
244 COG0834 HisJ ABC-type amino ac 32.8 85 0.0018 29.1 5.3 49 111-161 146-196 (275)
245 PF01193 RNA_pol_L: RNA polyme 32.7 1.3E+02 0.0028 22.7 5.3 62 304-382 2-64 (66)
246 PRK10859 membrane-bound lytic 31.7 3.4E+02 0.0074 28.6 10.1 49 111-161 149-202 (482)
247 cd08464 PBP2_DntR_like_2 The C 31.7 2.4E+02 0.0052 23.9 7.6 122 131-263 25-155 (200)
248 cd08425 PBP2_CynR The C-termin 30.9 3.3E+02 0.0071 23.0 9.1 121 132-262 27-157 (197)
249 PF12974 Phosphonate-bd: ABC t 30.5 4.4E+02 0.0096 24.4 10.2 118 134-260 30-168 (243)
250 cd08437 PBP2_MleR The substrat 28.9 3.6E+02 0.0078 22.8 10.9 122 131-261 25-156 (198)
251 TIGR00070 hisG ATP phosphoribo 28.9 2.5E+02 0.0055 26.0 7.5 108 143-270 49-171 (182)
252 COG0725 ModA ABC-type molybdat 28.8 80 0.0017 30.7 4.4 53 110-163 134-195 (258)
253 PRK15437 histidine ABC transpo 28.7 3.3E+02 0.0071 25.5 8.6 40 122-163 54-94 (259)
254 cd08418 PBP2_TdcA The C-termin 28.0 3.7E+02 0.0079 22.6 9.2 120 132-263 26-156 (201)
255 cd08436 PBP2_LTTR_like_3 The C 27.5 3.6E+02 0.0079 22.4 11.1 33 131-163 25-58 (194)
256 PRK15010 ABC transporter lysin 27.3 1.5E+02 0.0032 27.9 5.9 50 110-161 132-183 (260)
257 PRK09495 glnH glutamine ABC tr 26.7 1.8E+02 0.0038 27.0 6.3 123 123-262 53-184 (247)
258 PRK09181 aspartate kinase; Val 26.5 8E+02 0.017 26.1 13.0 125 228-382 256-391 (475)
259 PLN02550 threonine dehydratase 26.4 2.5E+02 0.0053 30.9 8.0 70 300-388 510-579 (591)
260 cd08460 PBP2_DntR_like_1 The C 26.2 1.1E+02 0.0023 26.4 4.4 121 131-262 25-153 (200)
261 PF08946 Osmo_CC: Osmosensory 25.9 32 0.00069 24.8 0.7 27 29-60 15-41 (46)
262 PRK08055 chorismate mutase; Pr 25.7 49 0.0011 30.7 2.2 26 27-57 116-141 (181)
263 TIGR01693 UTase_glnD [Protein- 25.6 2.8E+02 0.0062 31.6 8.7 34 299-332 667-700 (850)
264 COG4472 Uncharacterized protei 25.6 73 0.0016 25.8 2.8 25 17-41 46-70 (88)
265 PLN02551 aspartokinase 25.3 4.5E+02 0.0098 28.4 9.7 99 228-332 293-401 (521)
266 PRK05092 PII uridylyl-transfer 25.3 3.3E+02 0.0071 31.5 9.2 34 299-332 731-764 (931)
267 PF06153 DUF970: Protein of un 24.8 2.2E+02 0.0047 24.4 5.7 53 316-386 15-67 (109)
268 cd08451 PBP2_BudR The C-termin 24.7 4.2E+02 0.0091 22.2 12.6 33 131-163 26-59 (199)
269 PRK10797 glutamate and asparta 24.5 1.2E+02 0.0027 29.7 4.9 50 110-161 152-205 (302)
270 COG2150 Predicted regulator of 24.1 4.3E+02 0.0092 24.3 7.7 63 300-381 95-157 (167)
271 cd08443 PBP2_CysB The C-termin 24.0 4.6E+02 0.01 22.4 11.1 122 131-261 25-155 (198)
272 cd08467 PBP2_SyrM The C-termin 23.9 4.4E+02 0.0095 22.6 8.0 122 131-263 25-155 (200)
273 COG3283 TyrR Transcriptional r 23.8 2.4E+02 0.0052 29.6 6.8 70 304-394 4-75 (511)
274 PRK02228 V-type ATP synthase s 23.5 4.2E+02 0.0091 21.8 7.5 63 112-178 1-66 (100)
275 PRK01759 glnD PII uridylyl-tra 23.3 2.5E+02 0.0055 32.1 7.7 32 299-330 676-707 (854)
276 PRK02047 hypothetical protein; 23.2 4.1E+02 0.0089 21.6 7.6 59 308-383 24-85 (91)
277 PRK06291 aspartate kinase; Pro 23.1 8.9E+02 0.019 25.4 14.1 98 228-332 248-356 (465)
278 cd08469 PBP2_PnbR The C-termin 23.0 5E+02 0.011 22.5 8.3 32 131-162 25-57 (221)
279 cd08429 PBP2_NhaR The C-termin 22.6 5.2E+02 0.011 22.6 8.8 122 131-262 25-157 (204)
280 TIGR01096 3A0103s03R lysine-ar 22.4 5.9E+02 0.013 23.2 10.8 114 134-263 64-186 (250)
281 PRK15437 histidine ABC transpo 22.4 1.9E+02 0.0042 27.1 5.7 50 110-161 132-183 (259)
282 PF00072 Response_reg: Respons 22.3 62 0.0014 25.5 2.0 77 210-290 4-81 (112)
283 PRK09269 chorismate mutase; Pr 22.0 60 0.0013 30.4 2.0 24 25-51 122-145 (193)
284 TIGR03871 ABC_peri_MoxJ_2 quin 22.0 1.9E+02 0.0041 26.3 5.4 22 140-161 140-161 (232)
285 PRK09466 metL bifunctional asp 21.8 1.2E+03 0.027 26.6 13.4 99 228-333 245-353 (810)
286 PF01250 Ribosomal_S6: Ribosom 21.6 4.1E+02 0.009 21.0 7.9 66 300-381 4-80 (92)
287 PRK01686 hisG ATP phosphoribos 21.6 2.8E+02 0.0062 26.4 6.5 109 143-270 54-177 (215)
288 PF09084 NMT1: NMT1/THI5 like; 21.6 5.9E+02 0.013 22.7 15.9 105 134-247 22-139 (216)
289 cd08416 PBP2_MdcR The C-termin 21.2 5E+02 0.011 21.8 11.4 123 131-263 25-158 (199)
290 PRK12682 transcriptional regul 21.1 7.4E+02 0.016 23.7 13.3 53 109-161 92-149 (309)
291 PRK05473 hypothetical protein; 21.1 82 0.0018 25.8 2.3 25 17-41 46-70 (86)
292 PRK06635 aspartate kinase; Rev 21.0 2.9E+02 0.0062 28.3 7.0 28 306-333 349-376 (404)
293 cd08449 PBP2_XapR The C-termin 21.0 5E+02 0.011 21.7 11.2 33 131-163 25-58 (197)
294 PRK07431 aspartate kinase; Pro 20.9 3.1E+02 0.0067 29.8 7.5 128 228-380 190-334 (587)
295 PRK11716 DNA-binding transcrip 20.9 6.5E+02 0.014 23.0 11.3 145 109-262 66-223 (269)
296 PF03180 Lipoprotein_9: NLPA l 20.8 6.1E+02 0.013 24.3 8.8 87 112-208 1-95 (237)
297 PRK13584 hisG ATP phosphoribos 20.8 2.3E+02 0.0049 26.9 5.6 110 143-271 52-168 (204)
298 cd08457 PBP2_OccR The C-termin 20.4 5.3E+02 0.011 21.8 10.7 120 131-260 25-153 (196)
299 cd08442 PBP2_YofA_SoxR_like Th 20.4 5.1E+02 0.011 21.6 11.2 115 131-263 25-152 (193)
300 PF13379 NMT1_2: NMT1-like fam 20.3 2.2E+02 0.0047 26.7 5.6 50 110-161 120-177 (252)
301 COG0788 PurU Formyltetrahydrof 20.2 4.2E+02 0.0091 26.4 7.4 36 299-334 6-41 (287)
No 1
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=100.00 E-value=2.4e-94 Score=729.36 Aligned_cols=348 Identities=31% Similarity=0.476 Sum_probs=323.1
Q ss_pred CCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhcc-CCCCccccccCCCc
Q 015945 26 PNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQ-SSGFHKDLNLLPKP 96 (398)
Q Consensus 26 ~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~-~G~lp~~~i~~~~~ 96 (398)
.+|+++|.+||+||++ |++||+| |++++.+|| | | |+|+|| +++++++.+.. .++++++.++ .
T Consensus 5 ~~L~~lR~~ID~ID~~---ii~Ll~~--R~~~~~~I~~~K~~~~~pi~dp~RE-~~vl~~~~~~a~~~~l~~~~i~---~ 75 (386)
T PRK10622 5 NPLLALREKISALDEK---LLALLAE--RRELAVEVAKAKLLSHRPVRDIDRE-RDLLERLITLGKAHHLDAHYIT---R 75 (386)
T ss_pred hHHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCcChHHH-HHHHHHHHHhcccCCCCHHHHH---H
Confidence 4799999999999999 9999999 999999999 4 6 999999 99999988754 4779999999 5
Q ss_pred cchhhcccCCCCCce-------------eEEEEEcCCCcHHHHHHHHhCCC--Cc--cccCCCHHHHHHHHHcCCccEEE
Q 015945 97 LSIMELSSSPDDGTK-------------VRVAYQGLPGAYSEAAARKAYPK--CE--TVPCDQFEAAFKAVELWLVDKAV 159 (398)
Q Consensus 97 I~R~iis~s~~~q~~-------------~kVa~lGp~Gs~s~~AA~~~fg~--~~--~~~~~s~~~v~~aV~~g~~d~gv 159 (398)
||+.||.+|+..|.. .+||||||+|||||+||+.+|+. .+ .++|.||++||++|++|++||||
T Consensus 76 if~~ii~~S~~~Q~~~~~~~~~~~~~~~~~va~lGp~GtfSh~Aa~~~~~~~~~~~~~~~~~s~~~v~~av~~g~~d~gV 155 (386)
T PRK10622 76 LFQLIIEDSVLTQQALLQQHLNKTNPHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAV 155 (386)
T ss_pred HHHHHHHHHHHHhhhhhhccccccccccceEEEECCCCcHHHHHHHHhhccccccccccCCCCHHHHHHHHHCCCCCEEE
Confidence 999999999887744 78999999999999999988863 22 34899999999999999999999
Q ss_pred EeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCccEEEecHHHHHHHHHHHhh-cCCeEEecCCHH
Q 015945 160 LPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSN-LGIVRISADDTA 238 (398)
Q Consensus 160 VPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~~V~SHpqal~QC~~fl~~-~~~~~v~~~STA 238 (398)
||||||++|.|.+|||+|.+++++|+||+.+||+|||++.+|.++++|++||||||||+||++||++ ++++.++++|||
T Consensus 156 vPiENS~~G~V~~t~DlL~~~~l~I~~E~~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~p~~~~~~~~sTa 235 (386)
T PRK10622 156 LPIENTSSGAINDVYDLLQHTSLSIVGEMTLPIDHCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRYPHWKIEYTESTA 235 (386)
T ss_pred EEEecCCceehHHHHHHHhcCCCEEEEEEEEEEEEEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHCCCceEEEcCChH
Confidence 9999999999999999999999999999999999999999999999999999999999999999999 589999999999
Q ss_pred HHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecccccCCCCceEEEEEecCCCCCCCCCCceEEEEEEeCCCcchHHHHH
Q 015945 239 GAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLFKAL 318 (398)
Q Consensus 239 ~Aa~~v~~~~~~~~AAI~s~~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~L 318 (398)
+||++|++.+.++.|||||+.||++|||+||+++|||.++|+|||+||++.+..+...+.+||||+|+++|+||+|+++|
T Consensus 236 ~Aa~~v~~~~~~~~AAI~s~~aa~~ygL~vl~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~~L 315 (386)
T PRK10622 236 AAMEKVAQANSPHVAALGSEAGGALYGLQVLERNLANQQQNITRFIVLARKAINVSDQVPAKTTLLMATGQQAGALVEAL 315 (386)
T ss_pred HHHHHHHhcCCCCEEEECCHHHHHHcCCcChhhcCcCCccccceEEEEecCCCCCCCCCCCcEEEEEEcCCCCcHHHHHH
Confidence 99999998777788999999999999999999999999999999999999863222234579999999999999999999
Q ss_pred HHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCC
Q 015945 319 AVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDT 396 (398)
Q Consensus 319 ~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~~vkiLGsYp~~~ 396 (398)
++|+.+|||||+|||||+++++ |+|.||||++||.+|+.++++|++|++.|.++|+|||||+..
T Consensus 316 ~~Fa~~giNLtkIeSRP~~~~~--------------~~Y~Ffid~eg~~~d~~~~~aL~~l~~~~~~~kvLGsYp~~~ 379 (386)
T PRK10622 316 LVLRNHNLIMTKLESRPIHGNP--------------WEEMFYLDVQANLRSAEMQKALKELGEITRSLKVLGCYPSEN 379 (386)
T ss_pred HHHHHcCCCeeEEEeeecCCCC--------------ceEEEEEEEeCCCCCHHHHHHHHHHHHhcCcEEEeeeecCCc
Confidence 9999999999999999999865 999999999999999999999999999999999999999763
No 2
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=6.2e-86 Score=635.35 Aligned_cols=271 Identities=48% Similarity=0.744 Sum_probs=257.4
Q ss_pred eeEEEEEcCCCcHHHHHHHHhCCC-CccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEE
Q 015945 111 KVRVAYQGLPGAYSEAAARKAYPK-CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQ 189 (398)
Q Consensus 111 ~~kVa~lGp~Gs~s~~AA~~~fg~-~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~ 189 (398)
+++|+||||+|||||+||+++|++ .+..+|+|+++||++|++|++||||||||||++|+|++|+|+|...+++|+||+.
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 EeeeEeeecCCCCCccCccEEEecHHHHHHHHHHHhhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCc
Q 015945 190 LVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLD 267 (398)
Q Consensus 190 l~I~h~Ll~~~g~~l~~I~~V~SHpqal~QC~~fl~~~--~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ygL~ 267 (398)
+||+|||+++.+.++++|++|||||||++||++||+++ ++++++++|||+||+++++.++...|||||+.||++|||+
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 99999999998889999999999999999999999994 7999999999999999999877899999999999999999
Q ss_pred eeecccccCCCCceEEEEEecC-CCCCCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccC
Q 015945 268 ILAEKIQDDDDNVTRFLILARE-PIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDD 346 (398)
Q Consensus 268 il~~~I~D~~~N~TRF~vi~~~-~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~ 346 (398)
||++||||.++|+|||+||+|. +....+ +..||||+|+++|+||+|+++|++|+.||||||||||||+++.+
T Consensus 162 il~~~I~D~~~N~TRF~vl~r~~~~~~~~-~~~kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~~~------ 234 (279)
T COG0077 162 ILAENIEDEPNNRTRFLVLSRRKPPSVSD-GPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTGL------ 234 (279)
T ss_pred hHhhcccCCCCCeEEEEEEeccCCCCcCC-CCceEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCCCC------
Confidence 9999999999999999999985 321122 55799999999999999999999999999999999999999864
Q ss_pred CCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCC
Q 015945 347 SNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDT 396 (398)
Q Consensus 347 ~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~~vkiLGsYp~~~ 396 (398)
|+|+||||++||.+|+.++++|++|+..+.++|+|||||...
T Consensus 235 --------~~Y~F~iD~eg~~~~~~v~~AL~el~~~t~~~kilGsYp~~~ 276 (279)
T COG0077 235 --------GEYLFFIDIEGHIDDPLVKEALEELKEITEFVKILGSYPSAR 276 (279)
T ss_pred --------eeEEEEEEEecCcCcHhHHHHHHHHHhheeEEEEEeeccccc
Confidence 999999999999999999999999999999999999999864
No 3
>PLN02317 arogenate dehydratase
Probab=100.00 E-value=1.2e-84 Score=651.44 Aligned_cols=312 Identities=83% Similarity=1.269 Sum_probs=287.0
Q ss_pred CccccccCCCccchhhcccCCCCCceeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEeeccc
Q 015945 86 FHKDLNLLPKPLSIMELSSSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENS 165 (398)
Q Consensus 86 lp~~~i~~~~~I~R~iis~s~~~q~~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS 165 (398)
+.++....|+++-...++.+-......+|+||||+|||||+||+++|++.++++|++|++||++|++|++||||||||||
T Consensus 69 ~~~~~~~~~~~~~~~~~~~~~~~~~~~rVaylGp~GtfSe~AA~~~f~~~e~vp~~sf~~vf~AVe~g~ad~gVvPIENS 148 (382)
T PLN02317 69 FHRDLSGLPRPLSITDLSPSPMHGSKLRVAYQGVPGAYSEAAARKAYPNCEAVPCEQFEAAFQAVELWLADRAVLPIENS 148 (382)
T ss_pred cccccccccccccHhhhcccccCCCCcEEEEECCCcCHHHHHHHHhhCcCceeecCCHHHHHHHHHCCCCCEEEEEEecc
Confidence 44444333444433344444444557899999999999999999999988999999999999999999999999999999
Q ss_pred cccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCccEEEecHHHHHHHHHHHhhcCCeEEecCCHHHHHHHHH
Q 015945 166 VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLGIVRISADDTAGAAQMVA 245 (398)
Q Consensus 166 ~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~~V~SHpqal~QC~~fl~~~~~~~v~~~STA~Aa~~v~ 245 (398)
++|.|.+|||+|.+++++|+||+.+||+|||++++|.++++|++||||||||+||++||++++++++++.|||+||++|+
T Consensus 149 ~~GsV~~t~DlL~~~~l~IvgEv~l~I~h~Ll~~~g~~l~~Ik~VySHPQALaQC~~~L~~~~~~~~~~~sTA~AA~~Va 228 (382)
T PLN02317 149 LGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEELKRVISHPQALAQCENTLTKLGVVREAVDDTAGAAKMVA 228 (382)
T ss_pred CccchHHHHHHHhcCCCEEEEEEEEEeeeEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHcCCeEEEcCCHHHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCCeEEEcCHHhHHHcCCceeecccccCCCCceEEEEEecCCCCCCCCCCceEEEEEEeCCCcchHHHHHHHHHhCC
Q 015945 246 SIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRD 325 (398)
Q Consensus 246 ~~~~~~~AAI~s~~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~ 325 (398)
+.+..+.|||||+.||++|||+||+++|||.++|+|||+||+|++..+.+.+.+||||+|+++++||+|+++|++|+.+|
T Consensus 229 ~~~~~~~AAIaS~~aA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KTSivfsl~~~pG~L~k~L~~Fa~~~ 308 (382)
T PLN02317 229 ANGLRDTAAIASARAAELYGLDILAEGIQDDSDNVTRFLMLAREPIIPRTDRPFKTSIVFSLEEGPGVLFKALAVFALRD 308 (382)
T ss_pred hcCCCCceeecCHHHHHHcCCcchhhhhcCCCCCeeeEEEEecCCcCCCCCCCccEEEEEEcCCCCchHHHHHHHHHHCC
Confidence 87777889999999999999999999999999999999999998754444556799999999999999999999999999
Q ss_pred ceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCCC
Q 015945 326 INLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDTT 397 (398)
Q Consensus 326 INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~~vkiLGsYp~~~~ 397 (398)
||||||||||.++.|++|+||++.|.++.|+|.|||||+|++.|++++++|++|++++.++|+|||||+..+
T Consensus 309 INLtkIESRP~~~~~~~~~~~~~~~~~~~~eY~FyVD~eg~~~d~~~~~aL~~L~~~~~~lrvLGsYp~~~~ 380 (382)
T PLN02317 309 INLTKIESRPQRKRPLRVVDDSNSGTAKYFDYLFYVDFEASMADPRAQNALAHLQEFATFLRVLGSYPMDMT 380 (382)
T ss_pred CCEEEEEeeecCCCCccccccccccccccccEEEEEEEEcCcCCHHHHHHHHHHHHhcCeEEEEeeeecCCC
Confidence 999999999999999999999999999999999999999999999999999999999999999999998765
No 4
>PRK11899 prephenate dehydratase; Provisional
Probab=100.00 E-value=5.6e-84 Score=627.85 Aligned_cols=273 Identities=45% Similarity=0.668 Sum_probs=258.8
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEE
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQ 189 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~ 189 (398)
++++|+||||+|||||+||+++|++.++++|.||++||++|++|++||||||||||++|.|.+|+|+|.+++++|+||+.
T Consensus 3 ~~~kvaylGp~GsfS~~Aa~~~~~~~~~v~~~s~~~vf~av~~g~~d~gVvPiENS~~G~V~~~~Dll~~~~l~Iv~E~~ 82 (279)
T PRK11899 3 KTNRIAFQGEPGANSHLACRDAFPDMEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVADIHHLLPESGLHIVGEYF 82 (279)
T ss_pred CCCEEEEECCCCCHHHHHHHHhcCcCceeecCCHHHHHHHHHCCCCCEEEEEeeccCCccHHHHHHHHhcCCCEEEEEEE
Confidence 56789999999999999999999988899999999999999999999999999999999999999999999999999999
Q ss_pred EeeeEeeecCCCCCccCccEEEecHHHHHHHHHHHhhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCcee
Q 015945 190 LVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDIL 269 (398)
Q Consensus 190 l~I~h~Ll~~~g~~l~~I~~V~SHpqal~QC~~fl~~~~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ygL~il 269 (398)
+||+|||++.+|.++++|++||||||||+||++||++++++.+++.|||+||++|++.+.++.|||||+.||++|||+||
T Consensus 83 l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAIas~~aa~~YgL~il 162 (279)
T PRK11899 83 LPIRHQLMALPGATLEEIKTVHSHPHALGQCRKIIRALGLKPVVAADTAGAARLVAERGDPSMAALASRLAAELYGLDIL 162 (279)
T ss_pred EEeeEEEecCCCCCHHHCeEEEEeHHHHHHHHHHHHHcCCeEEEcCChHHHHHHHHhcCCCCeeEeCCHHHHHHcCCcch
Confidence 99999999999999999999999999999999999998999999999999999999877778999999999999999999
Q ss_pred ecccccCCCCceEEEEEecCCCC-CCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCC
Q 015945 270 AEKIQDDDDNVTRFLILAREPII-AGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSN 348 (398)
Q Consensus 270 ~~~I~D~~~N~TRF~vi~~~~~~-~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~ 348 (398)
+++|||.++|+|||+||++++.. +.+.+.+||||+|+++|+||+|+++|++|+.+|||||+|||||+++++
T Consensus 163 ~~~IqD~~~N~TRF~vi~~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~-------- 234 (279)
T PRK11899 163 AENIEDADHNTTRFVVLSREADWAARGDGPIVTTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSF-------- 234 (279)
T ss_pred hhcccCCcccceeEEEEecCCCCCCCCCCCceEEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCC--------
Confidence 99999999999999999998632 223345699999999999999999999999999999999999999865
Q ss_pred CCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCC
Q 015945 349 KGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDT 396 (398)
Q Consensus 349 ~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~~vkiLGsYp~~~ 396 (398)
|+|.||||++||.+|++++++|++|++.+.++|+|||||+..
T Consensus 235 ------~~Y~F~id~eg~~~d~~v~~aL~~l~~~~~~~kvLGsYp~~~ 276 (279)
T PRK11899 235 ------TATQFYADIEGHPEDRNVALALEELRFFSEEVRILGVYPAHP 276 (279)
T ss_pred ------ceEEEEEEEECCCCCHHHHHHHHHHHHhcCcEEEeeeecCcc
Confidence 999999999999999999999999999999999999999764
No 5
>PRK11898 prephenate dehydratase; Provisional
Probab=100.00 E-value=3.1e-77 Score=582.99 Aligned_cols=270 Identities=44% Similarity=0.618 Sum_probs=252.3
Q ss_pred eEEEEEcCCCcHHHHHHHHhCCC---CccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcC-CeEEEEE
Q 015945 112 VRVAYQGLPGAYSEAAARKAYPK---CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRH-RLHIVGE 187 (398)
Q Consensus 112 ~kVa~lGp~Gs~s~~AA~~~fg~---~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~-~l~I~~E 187 (398)
++|+||||+|||||+||+.+|+. .++++|+|+++||++|++|++||||||||||++|.|.+|+|+|.++ +++|+||
T Consensus 2 ~~va~lGp~Gs~s~~Aa~~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~v~~~~d~L~~~~~~~iv~E 81 (283)
T PRK11898 2 MKIAYLGPEGTFTEAAALKFFPADGEAELVPYDSIPDVLDAVEAGEVDYAVVPIENSIEGSVNPTLDYLAHGSPLQIVAE 81 (283)
T ss_pred cEEEEECCCCCHHHHHHHHhhccccccceEecCCHHHHHHHHHcCCCCEEEEEecccCceecHHHHHHhccCCCcEEEEE
Confidence 57999999999999999999975 6899999999999999999999999999999999999999999765 8999999
Q ss_pred EEEeeeEeeecCCCCCccCccEEEecHHHHHHHHHHHhhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHcC
Q 015945 188 VQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYG 265 (398)
Q Consensus 188 i~l~I~h~Ll~~~g~~l~~I~~V~SHpqal~QC~~fl~~~--~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~yg 265 (398)
+.+||+|||+++++.. ++|++||||||||+||++||+++ +++.+.++|||+||+++++++..+.|||+|+.||++||
T Consensus 82 ~~l~I~~~L~~~~~~~-~~i~~V~SHpqal~QC~~~l~~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~yg 160 (283)
T PRK11898 82 IVLPIAQHLLVHPGHA-AKIRTVYSHPQALAQCRKWLAEHLPGAELEPANSTAAAAQYVAEHPDEPIAAIASELAAELYG 160 (283)
T ss_pred EEeeeeEEEeCCCCCh-hcCeEEEEeHHHHHHHHHHHHhcCCCCEEEEcCchHHHHHHHhcCCCCCeEEECCHHHHHHcC
Confidence 9999999999998865 99999999999999999999984 89999999999999999987666779999999999999
Q ss_pred CceeecccccCCCCceEEEEEecCCC-CCCCCCCceEEEEEEeCCC-cchHHHHHHHHHhCCceeeeeeeeeCCCCCCcc
Q 015945 266 LDILAEKIQDDDDNVTRFLILAREPI-IAGTDRPYKTSIVFTLEEG-PGMLFKALAVFALRDINLTKIESRPQRKRPLRV 343 (398)
Q Consensus 266 L~il~~~I~D~~~N~TRF~vi~~~~~-~~~~~~~~ktsi~f~~~~~-pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~ 343 (398)
|+||++||||.++|+|||+||++++. .+...+.+||||+|+++++ ||+|+++|++|+.+|||||||||||+++.+
T Consensus 161 L~il~~~I~d~~~N~TRF~vi~~~~~~~~~~~~~~ktslif~l~~~~pGsL~~~L~~F~~~~INLt~IeSRP~~~~~--- 237 (283)
T PRK11898 161 LEILAEDIQDYPNNRTRFWLLGRKKPPPPLRTGGDKTSLVLTLPNNLPGALYKALSEFAWRGINLTRIESRPTKTGL--- 237 (283)
T ss_pred CcEehhcCCCCCccceEEEEEEcCcccCCCCCCCCeEEEEEEeCCCCccHHHHHHHHHHHCCCCeeeEecccCCCCC---
Confidence 99999999999999999999999853 2234567799999999875 999999999999999999999999999864
Q ss_pred ccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCC
Q 015945 344 VDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDT 396 (398)
Q Consensus 344 ~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~~vkiLGsYp~~~ 396 (398)
|+|.|||||+|+.+|++++++|++|++.+.++|+|||||...
T Consensus 238 -----------~~y~F~vd~eg~~~~~~~~~al~~L~~~~~~~k~LGsY~~~~ 279 (283)
T PRK11898 238 -----------GTYFFFIDVEGHIDDVLVAEALKELEALGEDVKVLGSYPVYW 279 (283)
T ss_pred -----------ccEEEEEEEEccCCCHHHHHHHHHHHHhcCcEEEEEeecccc
Confidence 999999999999999999999999999999999999999754
No 6
>KOG2797 consensus Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=9.4e-72 Score=531.80 Aligned_cols=291 Identities=71% Similarity=1.120 Sum_probs=277.2
Q ss_pred cccCCCCCceeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCC
Q 015945 102 LSSSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHR 181 (398)
Q Consensus 102 is~s~~~q~~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~ 181 (398)
++.+..-....+|+|||++|+||+.||.+.|+...-++|..|+.+|++|+.-.+|++|||||||+.|+|...||+|.+++
T Consensus 81 l~psp~~~s~lRva~qg~pgaysesaa~ka~pn~~avpc~~f~~afqave~w~vD~AVLPiENS~gGsIhrnYDLLlrh~ 160 (377)
T KOG2797|consen 81 LSPSPMHGSTLRVAYQGVPGAYSESAALKAYPNCEAVPCDQFEAAFQAVELWIVDYAVLPIENSTGGSIHRNYDLLLRHR 160 (377)
T ss_pred cccCCCCCceEEEEeecCCchhhhhhhhhhcCCcccccHhHHHHHHHHHHHhhccceeeeeeccCCceeeechHHHhhcc
Confidence 44444455678999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEEEEeeeEeeecCCCCCccCccEEEecHHHHHHHHHHHhh--cCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHH
Q 015945 182 LHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSN--LGIVRISADDTAGAAQMVASIGERDTGAVASAQ 259 (398)
Q Consensus 182 l~I~~Ei~l~I~h~Ll~~~g~~l~~I~~V~SHpqal~QC~~fl~~--~~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~ 259 (398)
+.|+||+.+||+|||++.+|...+++++|.||||||+||..||.+ +++.++.++|||+||+.++.++..+++||+|+.
T Consensus 161 lhiVgEv~vPvhHCLi~~~gv~~e~~~~VlSHPQal~Qce~~L~~l~~~~~r~a~~dTa~Aa~~~s~~~~~d~~AIASe~ 240 (377)
T KOG2797|consen 161 LHIVGEVQVPVHHCLIALPGVRKEEVVRVLSHPQALGQCECSLTKLGPNAAREAVSDTAGAAEQISASNTADTAAIASER 240 (377)
T ss_pred hheeeEEecceeeeEecCCCCChhheeeeecCcHHHHHHHHHHHhcccceeeeeccchHHHHHHHHhcccccHHHHHHHH
Confidence 999999999999999999999999999999999999999999999 468999999999999999998888999999999
Q ss_pred hHHHcCCceeecccccCCCCceEEEEEecCCCCCCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCC
Q 015945 260 AAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 339 (398)
Q Consensus 260 aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~ 339 (398)
||++|||.||++||||+.+|+|||+++.|++.+|..++..||||+|...+.||.|+++|++|+-|+||||+|||||.+..
T Consensus 241 aA~ly~l~Il~~~IqDd~~NvTRFLmLar~p~ip~t~rl~ktsivf~~~~gp~vLfkvl~vfa~r~inltkIesRP~h~~ 320 (377)
T KOG2797|consen 241 AAELYGLNILEKNIQDDLGNVTRFLMLAREPIIPDTDRLFKTSIVFFREKGPGVLFKVLSVFAFRSINLTKIESRPFHNR 320 (377)
T ss_pred HHHHhcchhhhhhcccccCCeeEEEEEeccCCCCCCCccceeeEEEEeecCCchHHHHHHHHHhhhceeeeeecccccCC
Confidence 99999999999999999999999999999998888888899999999999999999999999999999999999999999
Q ss_pred CCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCCC
Q 015945 340 PLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDTT 397 (398)
Q Consensus 340 ~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~~vkiLGsYp~~~~ 397 (398)
|+||+|| .+.|+|.||||++..+.+++.++++.+++++++++++|||||.+.+
T Consensus 321 p~r~v~~-----~k~f~ylFyidfeasmae~~aq~al~~~~e~~sflrvlGsyp~d~t 373 (377)
T KOG2797|consen 321 PLRVVDD-----SKNFEYLFYIDFEASMAEPRAQNALGEVQEFTSFLRVLGSYPMDMT 373 (377)
T ss_pred Ccccccc-----cccccEEEEEEEEeccCcHHHHHHHHHHHHHHHHHHHhcCCccccc
Confidence 9999998 3679999999999999999999999999999999999999998764
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=1.6e-51 Score=377.79 Aligned_cols=177 Identities=48% Similarity=0.768 Sum_probs=163.7
Q ss_pred EEEEcCCCcHHHHHHHHhC--CCCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEe
Q 015945 114 VAYQGLPGAYSEAAARKAY--PKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLV 191 (398)
Q Consensus 114 Va~lGp~Gs~s~~AA~~~f--g~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~ 191 (398)
|+||||+|||||+||++|| .+.++++++||++||++|.++++||||||||||++|.|.+|+|+|.+.+++|+||+.+|
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 46899999999999999999999999999999999999999999999999999999999
Q ss_pred eeEeeecCCCCCccCccEEEecHHHHHHHHHHHhhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCcee
Q 015945 192 VNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDIL 269 (398)
Q Consensus 192 I~h~Ll~~~g~~l~~I~~V~SHpqal~QC~~fl~~~--~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ygL~il 269 (398)
|+|||+++++.++++|++|||||||++||++||+++ +++++.+.||++||++++..+.++.|||+|+.||++|||+||
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 999999999988999999999999999999999994 899999999999999987777788999999999999999999
Q ss_pred ecccccCCCCceEEEEEecCC
Q 015945 270 AEKIQDDDDNVTRFLILAREP 290 (398)
Q Consensus 270 ~~~I~D~~~N~TRF~vi~~~~ 290 (398)
+++|||.++|+|||+||++++
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 999999999999999999873
No 8
>PRK06034 hypothetical protein; Provisional
Probab=99.97 E-value=6.3e-32 Score=260.85 Aligned_cols=160 Identities=13% Similarity=0.062 Sum_probs=145.5
Q ss_pred CCCCCCCCCCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C------C-CCCchhhHHHHHhhhhccCCCCcc
Q 015945 18 HKGLPDLVPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R------P-YTPDVQSSEANERSQDSQSSGFHK 88 (398)
Q Consensus 18 ~~~~~~~~~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k------~-~~P~rE~~~il~rl~~~~~G~lp~ 88 (398)
|+..|+..++|+++|.+||+||++ |++||+| |++++.+|+ | + |+|+|| ++|++++.+.+.|+|++
T Consensus 1 ~~~~p~~~~~L~eLR~eID~ID~e---Ll~LL~e--R~~lv~~Va~~K~~~~~~pv~dP~RE-~evl~rl~~~~~g~L~~ 74 (279)
T PRK06034 1 GSTAPPAPPSLAELRWEIDAIDEE---LHQLLME--RGDIIDRLIAVKRTQEVGSAFRPGRE-ADMMRRLVSRHRGILPL 74 (279)
T ss_pred CCCCccccccHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHhhccCCCCccChHHH-HHHHHHHHHhccCCCCH
Confidence 678899999999999999999999 9999999 999999999 4 5 999999 99999999989999999
Q ss_pred ccccCCCccchhhcccCCCCCceeEE-EEEcCCCcHHHHHHHHhCC-CCccccCCCHHHHHHHHHcCCccEEEEeecccc
Q 015945 89 DLNLLPKPLSIMELSSSPDDGTKVRV-AYQGLPGAYSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSV 166 (398)
Q Consensus 89 ~~i~~~~~I~R~iis~s~~~q~~~kV-a~lGp~Gs~s~~AA~~~fg-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~ 166 (398)
+.++ +|||+||+.|+.+|.+.+| +|+||+|+|+|+||++||| ..+++++.||++||++|++|++|||||||+++
T Consensus 75 ~~ie---~Ifr~Iis~Sr~lQ~~~~V~a~lG~~gs~s~~AA~~~FG~s~~~~~~~s~~dVf~AV~~g~adyGVVPI~~~- 150 (279)
T PRK06034 75 DTVE---SIWRVIIATFTYVQAPFSVHADGSGGEAAMRDSARFHFGFTVPYVPHFSAQAVVEAVARSKGDLGLVSLTSS- 150 (279)
T ss_pred HHHH---HHHHHHHHHHHHhcCCceEEEEeCCccHHHHHHHHHHhccccCCccCCCHHHHHHHHHcCCCCEEEEECCCC-
Confidence 9999 5999999999999999999 9999999999999999999 57889999999999999999999999999544
Q ss_pred ccchHHhHHhhhcCCeEEEEEEE
Q 015945 167 GGSIHRNYDLLLRHRLHIVGEVQ 189 (398)
Q Consensus 167 ~G~V~~tld~L~~~~l~I~~Ei~ 189 (398)
.+.+|..|.. +...+|++...
T Consensus 151 ~~~WW~~L~~--~~~~~iiarlP 171 (279)
T PRK06034 151 DTPWWGRLEA--EGAPKIIARLP 171 (279)
T ss_pred CCcHHHHhcc--CCCCeEEEeCC
Confidence 5788877653 55677776544
No 9
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=99.85 E-value=3.5e-21 Score=152.04 Aligned_cols=73 Identities=34% Similarity=0.559 Sum_probs=68.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 380 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~ 380 (398)
||++|+++|+||+|+++|+.|+.+|||||||||||++..+ |+|.|||||+| ++++++++|++|+
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 6899999999999999999999999999999999999864 99999999999 5678999999999
Q ss_pred HhcCceEEE
Q 015945 381 EFATFLRVL 389 (398)
Q Consensus 381 ~~~~~vkiL 389 (398)
+.+..++++
T Consensus 65 ~~~~~~~~~ 73 (74)
T cd04904 65 RVVADVNIL 73 (74)
T ss_pred HhcCeEEEc
Confidence 999999985
No 10
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.82 E-value=3.7e-20 Score=151.73 Aligned_cols=72 Identities=35% Similarity=0.556 Sum_probs=66.3
Q ss_pred CCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHH
Q 015945 296 DRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFA 375 (398)
Q Consensus 296 ~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~a 375 (398)
++.+||||+|+++|+||+|+++|+.|+.+||||+||||||+++.+ |+|.|||||+|+ .+++++++
T Consensus 10 ~~~~ktslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~--------------~~Y~FfVDieg~-~~~~~~~~ 74 (90)
T cd04931 10 NKNGVISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNK--------------DEYEFFINLDKK-SAPALDPI 74 (90)
T ss_pred CCCCcEEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCC--------------ceEEEEEEEEcC-CCHHHHHH
Confidence 345689999999999999999999999999999999999998754 999999999998 78999999
Q ss_pred HHHHHHh
Q 015945 376 LGHLQEF 382 (398)
Q Consensus 376 l~~L~~~ 382 (398)
|++|++.
T Consensus 75 l~~L~~~ 81 (90)
T cd04931 75 IKSLRND 81 (90)
T ss_pred HHHHHHH
Confidence 9999863
No 11
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.81 E-value=7.6e-20 Score=156.38 Aligned_cols=76 Identities=28% Similarity=0.400 Sum_probs=69.8
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
.+||||+|+++|+||+|+++|+.|+.+|||||||||||++..+ |+|.|||||+|+.+ .++++|+
T Consensus 39 ~~ktSlifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~~~~--------------~eY~FfIdieg~~~--~~~~aL~ 102 (115)
T cd04930 39 PQKATLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSRKEG--------------GDLEVLVRCEVHRS--DLLQLIS 102 (115)
T ss_pred cccEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCCCCC--------------ceEEEEEEEEeCHH--HHHHHHH
Confidence 3589999999999999999999999999999999999998764 99999999999863 6999999
Q ss_pred HHHHhcCceEEE
Q 015945 378 HLQEFATFLRVL 389 (398)
Q Consensus 378 ~L~~~~~~vkiL 389 (398)
+|+..+.++++-
T Consensus 103 ~L~~~~~~~kv~ 114 (115)
T cd04930 103 SLRQVAEDVRLT 114 (115)
T ss_pred HHHHhcCeeEec
Confidence 999999988763
No 12
>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=99.81 E-value=2.4e-19 Score=143.11 Aligned_cols=80 Identities=54% Similarity=0.937 Sum_probs=75.4
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHH
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 379 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L 379 (398)
|+|++|.++|+||+|.++|+.|+++||||++|+|||.+.. .|+|.||||++|+.++++++++++.|
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 5899999999999999999999999999999999999764 38999999999987789999999999
Q ss_pred HHhcCceEEEcccc
Q 015945 380 QEFATFLRVLGCYP 393 (398)
Q Consensus 380 ~~~~~~vkiLGsYp 393 (398)
+..+.++|+|||||
T Consensus 67 ~~~~~~~~~lG~y~ 80 (80)
T cd04905 67 KRLTEFVKVLGSYP 80 (80)
T ss_pred HHhCCeEEEeeeeC
Confidence 99999999999997
No 13
>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=99.81 E-value=8.1e-20 Score=144.53 Aligned_cols=71 Identities=30% Similarity=0.440 Sum_probs=65.1
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 380 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~ 380 (398)
||++|+++|+||+|+++|+.|+.+||||+||||||++..+ |+|.|||||+||. .+++.++++|+
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 5899999999999999999999999999999999998764 9999999999986 48999999999
Q ss_pred HhcCceE
Q 015945 381 EFATFLR 387 (398)
Q Consensus 381 ~~~~~vk 387 (398)
+.+...+
T Consensus 65 ~~~~~~~ 71 (74)
T cd04929 65 REVASVN 71 (74)
T ss_pred Hhccccc
Confidence 8877544
No 14
>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=99.78 E-value=1e-18 Score=137.54 Aligned_cols=75 Identities=52% Similarity=0.826 Sum_probs=71.0
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
|++|+++|+||+|+++|+.|+.+|+||++|||||.++.+ |+|.||||++|+.++.++++++++|++
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 015945 382 FATFLRVLG 390 (398)
Q Consensus 382 ~~~~vkiLG 390 (398)
.+.++++||
T Consensus 67 ~~~~~~~lG 75 (75)
T cd04880 67 VTEDVKVLG 75 (75)
T ss_pred hCCeeEECC
Confidence 999999998
No 15
>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=99.69 E-value=6.6e-17 Score=164.88 Aligned_cols=79 Identities=35% Similarity=0.632 Sum_probs=74.3
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
+||||+|+++|+||+|+++|++|+.+|||||||||||+++.+ |+|.|||||+|+. +++++++|++
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 489999999999999999999999999999999999998864 9999999999986 5899999999
Q ss_pred HHHhc-CceEEEccc
Q 015945 379 LQEFA-TFLRVLGCY 392 (398)
Q Consensus 379 L~~~~-~~vkiLGsY 392 (398)
|++.+ ..+++||+-
T Consensus 80 Lk~~~~~~vkiLGs~ 94 (436)
T TIGR01268 80 LRQKAEVTVNILSRD 94 (436)
T ss_pred HHHhccceEEEeCCC
Confidence 99999 899999983
No 16
>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=99.56 E-value=1e-14 Score=149.46 Aligned_cols=77 Identities=29% Similarity=0.292 Sum_probs=69.9
Q ss_pred CCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccc-eEEEEEeecCCCcHHHHH
Q 015945 296 DRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFD-YLFYIDFEASMADPRAQF 374 (398)
Q Consensus 296 ~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~-y~Ffvd~~g~~~d~~v~~ 374 (398)
++.+||||+|+++|+||+|+++|+.|+.+|||||||||||+++.+ |+ |.|||||+|+. .++++
T Consensus 27 ~~~~ktSLIFsL~d~pGaL~~vL~vFa~~gINLThIESRPsk~~~--------------~e~Y~FfVD~Eg~~--~~l~~ 90 (464)
T TIGR01270 27 EGVQRLSIIFSLSNVVGDLSKAIAIFQDRHINILHLESRDSKDGT--------------SKTMDVLVDVELFH--YGLQE 90 (464)
T ss_pred CCCceEEEEEECCCCchHHHHHHHHHHHCCCCEEEEECCcCCCCC--------------CccEEEEEEEEcCH--HHHHH
Confidence 456799999999999999999999999999999999999998754 89 99999999975 68999
Q ss_pred HHHHHHHhcCceEE
Q 015945 375 ALGHLQEFATFLRV 388 (398)
Q Consensus 375 al~~L~~~~~~vki 388 (398)
+|++|++.+..+.+
T Consensus 91 aL~~Lk~~~~~~~~ 104 (464)
T TIGR01270 91 AMDLLKSGLDVHEV 104 (464)
T ss_pred HHHHHHHhccccee
Confidence 99999998887555
No 17
>TIGR01801 CM_A chorismate mutase domain of gram positive AroA protein. This model represents a small clade of chorismate mutase domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some gram positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other trusted CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44% identity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the gram positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role.
Probab=99.45 E-value=4.7e-15 Score=124.28 Aligned_cols=76 Identities=9% Similarity=0.058 Sum_probs=70.8
Q ss_pred CCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccCCCcc
Q 015945 26 PNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPKPL 97 (398)
Q Consensus 26 ~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~~G~lp~~~i~~~~~I 97 (398)
.+|+++|.+||+||++ |++||++ |+.++.+|| | | |+|+|| .++++++.+.+.|++|++.++ .|
T Consensus 4 ~~L~~lR~~ID~ID~e---Il~LL~e--R~~~~~~Ig~~K~~~~~~i~dp~RE-~~vl~~~~~~~~g~l~~~~i~---~I 74 (102)
T TIGR01801 4 QSLEDLRAEVDQLNRQ---ILALISR--RGEVVAQIGHAKSAQGPNHYDPARE-EQMLNELIKINPGPFPTATIK---GI 74 (102)
T ss_pred chHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHCCCCCCChHHH-HHHHHHHHHhcCCCCCHHHHH---HH
Confidence 4699999999999999 9999999 999999999 4 6 999999 999999999888999999999 59
Q ss_pred chhhcccCCCCCc
Q 015945 98 SIMELSSSPDDGT 110 (398)
Q Consensus 98 ~R~iis~s~~~q~ 110 (398)
|+.||+.|+..|.
T Consensus 75 f~~I~~~Sr~~Q~ 87 (102)
T TIGR01801 75 FKEIFKASLALQE 87 (102)
T ss_pred HHHHHHHHHHHHH
Confidence 9999999988773
No 18
>TIGR01797 CM_P_1 chorismate mutase domain of proteobacterial P-protein, clade 1. This model represents the chorismate mutase domain of the gamma and beta proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain.
Probab=99.41 E-value=2.3e-14 Score=115.77 Aligned_cols=73 Identities=11% Similarity=0.051 Sum_probs=66.6
Q ss_pred cchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhcc-CCCCccccccCCCccc
Q 015945 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQ-SSGFHKDLNLLPKPLS 98 (398)
Q Consensus 28 l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~-~G~lp~~~i~~~~~I~ 98 (398)
|.++|.+||+||++ |++||++ |+.++.+|| | | |+|+|| +++++++.+.. .|+|+++.++ .||
T Consensus 1 ~~~lR~~ID~ID~~---lv~Ll~~--R~~~~~~i~~~K~~~~~~v~dp~RE-~~vl~~~~~~~~~~~l~~~~i~---~if 71 (83)
T TIGR01797 1 LLALREKISAIDEK---LLKLLAE--RRELAFEVGKSKLLSHRPVRDIERE-RDLLQRLITLGKAYHLDAHYIT---RLF 71 (83)
T ss_pred CHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHcCCCCCChHHH-HHHHHHHHHHhhhCCCCHHHHH---HHH
Confidence 57899999999999 9999999 999999999 4 6 999999 99999988855 4889999999 599
Q ss_pred hhhcccCCCCC
Q 015945 99 IMELSSSPDDG 109 (398)
Q Consensus 99 R~iis~s~~~q 109 (398)
+.||+.|...|
T Consensus 72 ~~ii~~S~~~Q 82 (83)
T TIGR01797 72 QLIIEDSVLTQ 82 (83)
T ss_pred HHHHHHHHHhc
Confidence 99999998766
No 19
>PRK07248 hypothetical protein; Provisional
Probab=99.38 E-value=2.7e-14 Score=116.24 Aligned_cols=75 Identities=9% Similarity=0.023 Sum_probs=68.7
Q ss_pred CcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccCCCccc
Q 015945 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPKPLS 98 (398)
Q Consensus 27 ~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~~G~lp~~~i~~~~~I~ 98 (398)
+|.++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| +++++++.+...|+++++.++ .||
T Consensus 2 ~L~~lR~~ID~iD~~---i~~Ll~~--R~~l~~~I~~~K~~~~~~v~d~~RE-~~vl~~~~~~~~~~~~~~~i~---~if 72 (87)
T PRK07248 2 DLEEIRQEIDQIDDQ---LVALLEK--RMALVEQVVAYKKATGKPVLDTKRE-QVILDKVSSLVENKAYQETIV---ATF 72 (87)
T ss_pred CHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHcCCCCCChHHH-HHHHHHHHHHcccCCCHHHHH---HHH
Confidence 789999999999999 9999999 999999999 4 6 999999 999999999877888888888 499
Q ss_pred hhhcccCCCCCc
Q 015945 99 IMELSSSPDDGT 110 (398)
Q Consensus 99 R~iis~s~~~q~ 110 (398)
+.||+.|+..|.
T Consensus 73 ~~I~~~S~~~Q~ 84 (87)
T PRK07248 73 KDIMKRSRDYQT 84 (87)
T ss_pred HHHHHHHHHHHH
Confidence 999999987664
No 20
>PRK11199 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
Probab=99.37 E-value=1.2e-13 Score=140.33 Aligned_cols=128 Identities=13% Similarity=0.127 Sum_probs=98.4
Q ss_pred CcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhcc-CCCCccccccCCCcc
Q 015945 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQ-SSGFHKDLNLLPKPL 97 (398)
Q Consensus 27 ~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~-~G~lp~~~i~~~~~I 97 (398)
+|.++|.+||+||++ |++||++ |++++.+|| | | |+|+|| +++++++.+.. .++++++.++ .|
T Consensus 4 ~L~~lR~~ID~iD~~---iv~Ll~~--R~~~~~~ia~~K~~~~~~v~d~~Re-~~vl~~~~~~~~~~~l~~~~~~---~i 74 (374)
T PRK11199 4 ELTALRDQIDEVDKQ---LLELLAK--RLELVAQVGEVKSRHGLPIYVPERE-AAMLASRRAEAEALGVPPDLIE---DV 74 (374)
T ss_pred HHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCCChHHH-HHHHHHHHHHHHhCCCCHHHHH---HH
Confidence 589999999999999 9999999 999999999 4 6 999999 99999977743 3679999998 49
Q ss_pred chhhcccCCCCC----------ceeEEEEEcCCCcHHHHHHHHhC--C-CCccccCCCHHHHHHHHHcCCccEEEEeecc
Q 015945 98 SIMELSSSPDDG----------TKVRVAYQGLPGAYSEAAARKAY--P-KCETVPCDQFEAAFKAVELWLVDKAVLPIEN 164 (398)
Q Consensus 98 ~R~iis~s~~~q----------~~~kVa~lGp~Gs~s~~AA~~~f--g-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIEN 164 (398)
|+.||+.|+..| ...+|+++|+.|.++...|+.+. | .+.....+++.+.-+.+. ++|+.++.++.
T Consensus 75 ~~~i~~~s~~~q~~~~~~~~~~~~~~I~IiGG~GlmG~slA~~l~~~G~~V~~~d~~~~~~~~~~~~--~aDlVilavP~ 152 (374)
T PRK11199 75 LRRVMRESYSSENDKGFKTLNPDLRPVVIVGGKGQLGRLFAKMLTLSGYQVRILEQDDWDRAEDILA--DAGMVIVSVPI 152 (374)
T ss_pred HHHHHHHHHHHhHHhcccccCcccceEEEEcCCChhhHHHHHHHHHCCCeEEEeCCCcchhHHHHHh--cCCEEEEeCcH
Confidence 999999998765 23789999988999877776543 2 233344344444444444 35666665553
Q ss_pred c
Q 015945 165 S 165 (398)
Q Consensus 165 S 165 (398)
+
T Consensus 153 ~ 153 (374)
T PRK11199 153 H 153 (374)
T ss_pred H
Confidence 3
No 21
>TIGR01805 CM_mono_grmpos monofunctional chorismate mutase, gram positive-type, clade 2. This model represents a clade of chorismate mutase proteins/domains from gram positive species. The sequence from Enterococcus is fused to the C-terminus of an aparrent acetyltransferase, and the seuence from Clostridium acetobutylicum (but not perfringens) is fused to the N-terminus of shikimate-5-dehydrogenase, another enzyme of the chorismate pathway. All the other members of this clade are mono-functional. Members of this clade from Streptococcus and Lactococcus have been found which represent the sole chorismate mutase domain in their respective genomes which also exhibit evidence of the enzymes of both the upstream and downstream branches of the chorismate pathways.
Probab=99.36 E-value=7.5e-14 Score=112.22 Aligned_cols=73 Identities=8% Similarity=0.003 Sum_probs=66.8
Q ss_pred cchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccCCCccch
Q 015945 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPKPLSI 99 (398)
Q Consensus 28 l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~~G~lp~~~i~~~~~I~R 99 (398)
|.++|.+||.||.+ |++||++ |+.++.+|| | | |+|+|| .++++++.+...|+++++.++ .||+
T Consensus 1 L~~lR~~Id~iD~~---i~~Ll~~--R~~~~~~i~~~K~~~~~~i~d~~RE-~~vl~~~~~~~~~~~~~~~i~---~if~ 71 (81)
T TIGR01805 1 LELIRKKIDEIDDK---LVVLFEE--RMEVVKEIAAYKKKNGIPIFDSKRE-QEIIDKCTKNVENKEYRETIE---EFFR 71 (81)
T ss_pred CHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHcCCCCCChHHH-HHHHHHHHHHcccCCCHHHHH---HHHH
Confidence 57899999999999 9999999 999999999 4 6 999999 999999999888888888888 4999
Q ss_pred hhcccCCCCC
Q 015945 100 MELSSSPDDG 109 (398)
Q Consensus 100 ~iis~s~~~q 109 (398)
.||+.|+..|
T Consensus 72 ~I~~~Sr~~Q 81 (81)
T TIGR01805 72 NIMDISKEVQ 81 (81)
T ss_pred HHHHHHHhcC
Confidence 9999998765
No 22
>TIGR01807 CM_P2 chorismate mutase domain of proteobacterial P-protein, clade 2. This model represents one of two separate clades of the chorismate mutase domain of the gamma and beta and epsilon proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. It is also found in Aquifex aolicus.
Probab=99.32 E-value=2.8e-13 Score=107.61 Aligned_cols=66 Identities=11% Similarity=0.161 Sum_probs=61.4
Q ss_pred cchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-------C-CCCchhhHHHHHhhhhccCCCCccccccCCCcc
Q 015945 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-------P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPKPL 97 (398)
Q Consensus 28 l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-------~-~~P~rE~~~il~rl~~~~~G~lp~~~i~~~~~I 97 (398)
|.++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| +++++++.+.+.|++|++.++ .|
T Consensus 1 L~~lR~~ID~iD~~---iv~Ll~~--R~~~~~~i~~~K~~~~~~~~i~d~~Re-~~vl~~~~~~~~~~l~~~~i~---~i 71 (76)
T TIGR01807 1 LEELRNKIDAIDDR---ILDLLSE--RATYAQAVGELKGSGASGASFYRPERE-AQVIRRLQNLNKGPLDQEAIA---RI 71 (76)
T ss_pred CHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhccCCCCcCChHHH-HHHHHHHHHhccCCCCHHHHH---HH
Confidence 57899999999999 9999999 999999999 4 5 999999 999999988888999999999 49
Q ss_pred chhhc
Q 015945 98 SIMEL 102 (398)
Q Consensus 98 ~R~ii 102 (398)
|+.||
T Consensus 72 f~~I~ 76 (76)
T TIGR01807 72 FREIM 76 (76)
T ss_pred HHHHC
Confidence 99886
No 23
>TIGR01799 CM_T chorismate mutase domain of T-protein. This model represents the chorismate mutase domain of the gamma proteobacterial "T-protein" which consists of an N-terminal chorismate mutase domain and a C-terminal prephenate dehydrogenase domain.
Probab=99.31 E-value=1.9e-13 Score=110.46 Aligned_cols=73 Identities=14% Similarity=0.165 Sum_probs=64.8
Q ss_pred cchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhc-cCCCCccccccCCCccc
Q 015945 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDS-QSSGFHKDLNLLPKPLS 98 (398)
Q Consensus 28 l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~-~~G~lp~~~i~~~~~I~ 98 (398)
|.++|.+||+||++ |++||++ |+.++.+|| | | |+|+|| +++++++.+. ..++++++.++ .||
T Consensus 1 L~~lR~~ID~ID~~---il~Ll~~--R~~~~~~ia~~K~~~~~~v~d~~RE-~~vl~~~~~~a~~~gl~~~~i~---~if 71 (83)
T TIGR01799 1 LEDLRGEIDGVDQE---LLHLLAK--RLELVAQVGKVKHAAGLPIYAPERE-AAMLAARREEAEKAGIAPDLIE---DVL 71 (83)
T ss_pred CHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCCCHHHH-HHHHHHHHHHhhcCCCCHHHHH---HHH
Confidence 57899999999999 9999999 999999999 4 6 999999 9999997773 33669999999 499
Q ss_pred hhhcccCCCCC
Q 015945 99 IMELSSSPDDG 109 (398)
Q Consensus 99 R~iis~s~~~q 109 (398)
+.||+.|...|
T Consensus 72 ~~i~~~s~~~~ 82 (83)
T TIGR01799 72 RRFMRESYANE 82 (83)
T ss_pred HHHHHHHHHcc
Confidence 99999987654
No 24
>TIGR01803 CM-like chorismate mutase related enzymes. This subfamily includes two enzymes which are variants on the mechanism of chorismate mutase and are likely to have evolved from an ancestral chorismate mutase enzyme. 4-amino-4-deoxy-chorismate mutase produces amino-deoxy-prephenate which is subsequently converted to para-dimethylamino-phenylalanine, a component of the natural product pristinamycin. Isochorismate-pyruvate lyase presumably catalyzes the same type of 2+2+2 cyclo-rearrangement as chorismate mutase, but acting on isochorismate, this results in two broken bonds instead of one broken and one made. The product of this reaction is salicylate (2-hydroxy-benzoate) which is also incorporated into various natural products.
Probab=99.31 E-value=2.1e-13 Score=109.93 Aligned_cols=72 Identities=8% Similarity=-0.007 Sum_probs=64.5
Q ss_pred cchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhcc-CCCCccccccCCCccc
Q 015945 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQ-SSGFHKDLNLLPKPLS 98 (398)
Q Consensus 28 l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~-~G~lp~~~i~~~~~I~ 98 (398)
|.++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| +++++++.+.. .++++++.++ .||
T Consensus 1 L~~lR~~ID~ID~~---lv~Ll~~--R~~~~~~ia~~K~~~~~~v~d~~Re-~~vl~~~~~~a~~~gl~~~~~~---~if 71 (82)
T TIGR01803 1 LADIREAIDRIDLA---LVQALGR--RMDYVKRASEFKRSHEAAIPAPERV-AAVLPNAARWAEENGLDPPFVE---GLF 71 (82)
T ss_pred CHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHhhcCCCCCCChHHH-HHHHHHHHHHHHHcCCCHHHHH---HHH
Confidence 57899999999999 9999999 999999999 4 6 999999 99999987744 4779999999 499
Q ss_pred hhhcccCCCC
Q 015945 99 IMELSSSPDD 108 (398)
Q Consensus 99 R~iis~s~~~ 108 (398)
+.||++|...
T Consensus 72 ~~ii~~si~~ 81 (82)
T TIGR01803 72 AQIIHWYIAE 81 (82)
T ss_pred HHHHHHHHhc
Confidence 9999988653
No 25
>PRK06443 chorismate mutase; Validated
Probab=99.26 E-value=2.1e-12 Score=116.67 Aligned_cols=81 Identities=7% Similarity=0.047 Sum_probs=69.6
Q ss_pred CcCCCCCCCCCCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCc
Q 015945 16 HFHKGLPDLVPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFH 87 (398)
Q Consensus 16 ~~~~~~~~~~~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~~G~lp 87 (398)
||| +|.++|.+||+||++ |++||+| |++++.+|| | | |+|.|| +++++++.+.+.
T Consensus 3 ~~~--------dLeeLR~eID~ID~e---IL~LL~k--Rm~la~eIg~~K~~~g~pI~Dp~RE-~eVLerl~~~n~---- 64 (177)
T PRK06443 3 HFI--------DMEDLRSEILENTMD---IIELIEK--RRELARMIGIIKMRNGLSIRDSERE-NYVKNNLKSDNP---- 64 (177)
T ss_pred ccc--------cHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHhcCCCCCCChHHH-HHHHHHHHHhCH----
Confidence 888 899999999999999 9999999 999999999 4 6 999999 999999887552
Q ss_pred cccccCCCccchhhcccCCCCC----ceeEEEEEcCCCcH
Q 015945 88 KDLNLLPKPLSIMELSSSPDDG----TKVRVAYQGLPGAY 123 (398)
Q Consensus 88 ~~~i~~~~~I~R~iis~s~~~q----~~~kVa~lGp~Gs~ 123 (398)
||++||+.|+..| ....|...|-.|++
T Consensus 65 ---------If~eIms~Sr~~Q~~~~~~~~i~~sg~y~~~ 95 (177)
T PRK06443 65 ---------LLNMIFEATIHYQKNISLNINIEVSGDYDSL 95 (177)
T ss_pred ---------HHHHHHHHHHHHHhcccccceeeeecchHHH
Confidence 8899999998887 34556666655554
No 26
>PRK06285 chorismate mutase; Provisional
Probab=99.25 E-value=3.2e-13 Score=112.05 Aligned_cols=76 Identities=11% Similarity=0.223 Sum_probs=68.3
Q ss_pred CCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhc-cCCCCccccccCCCc
Q 015945 26 PNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDS-QSSGFHKDLNLLPKP 96 (398)
Q Consensus 26 ~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~-~~G~lp~~~i~~~~~ 96 (398)
.+|.++|.+||+||++ |++||++ |+.++.+|| | | |+|.|| ++++.++.+. ..++++++.++ .
T Consensus 7 ~~L~elR~~ID~ID~~---iv~Ll~~--R~~l~~~I~~~K~~~~~~v~dp~RE-~~vl~~~~~~a~~~~l~~~~i~---~ 77 (96)
T PRK06285 7 KRLNEIRKRIDEIDEQ---IIDLIAE--RTSLAKEIAELKKSLGMPIFDPERE-DYIHEKIRKLCEEHNIDENIGL---K 77 (96)
T ss_pred HHHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHcCCCCCChHHH-HHHHHHHHHHhhhCCCCHHHHH---H
Confidence 5799999999999999 9999999 999999999 4 6 999999 9999998874 44779999998 4
Q ss_pred cchhhcccCCCCCc
Q 015945 97 LSIMELSSSPDDGT 110 (398)
Q Consensus 97 I~R~iis~s~~~q~ 110 (398)
||+.||+.|...|.
T Consensus 78 if~~Ii~~s~~~Q~ 91 (96)
T PRK06285 78 IMKILMEHSKELQK 91 (96)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999999987663
No 27
>TIGR01791 CM_archaeal chorismate mutase, archaeal type. This model represents a clade of archaeal chorismate mutases. Chorismate mutase catalyzes the conversion of chorismate into prephenate which is subsequently converted into either phenylalanine or tyrosine. In Sulfolobus this gene is found as a fusion with prephenate dehydrogenase (although the non-TIGR annotation contains a typographical error indicating it as a dehydratase) which is the next enzyme in the tyrosine biosynthesis pathway. The Archaeoglobus gene contains an N-terminal prephenate dehydrogenase domain and a C-terminal prephenate dehydratase domain followed by a regulatory amino acid-binding ACT domain. The Thermoplasma volcanium gene is adjacent to prephenate dehydratase.
Probab=99.25 E-value=6e-13 Score=107.33 Aligned_cols=73 Identities=11% Similarity=0.125 Sum_probs=64.4
Q ss_pred cchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccCCCccc
Q 015945 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPKPLS 98 (398)
Q Consensus 28 l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~-~~~G~lp~~~i~~~~~I~ 98 (398)
|.++|.+||+||++ |++||++ |+.++.+|| | | |+|+|| +++++++.+ ...++++++.++ .||
T Consensus 1 L~~lR~~Id~iD~~---i~~Ll~~--R~~l~~~i~~~K~~~g~~i~d~~RE-~~v~~~~~~~~~~~~l~~~~i~---~if 71 (83)
T TIGR01791 1 IEELRQEIEEIDKS---ILDLIEK--RIKIARKIGEIKHNNGLPITDEERE-ERVIERLRNTARNLGLDVLKLK---EIF 71 (83)
T ss_pred CHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHcCCCCCChHHH-HHHHHHHHHHHHhcCCCHHHHH---HHH
Confidence 57899999999999 9999999 999999999 4 6 999999 999999776 232449999988 499
Q ss_pred hhhcccCCCCC
Q 015945 99 IMELSSSPDDG 109 (398)
Q Consensus 99 R~iis~s~~~q 109 (398)
+.||+.|...|
T Consensus 72 ~~i~~~s~~~Q 82 (83)
T TIGR01791 72 EILMSLSKEEQ 82 (83)
T ss_pred HHHHHHHHHhh
Confidence 99999998766
No 28
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=99.23 E-value=4.5e-13 Score=112.20 Aligned_cols=75 Identities=9% Similarity=0.038 Sum_probs=67.2
Q ss_pred CCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C----C-CCCchhhHHHHHhhhhc-cCCCCccccccCCCcc
Q 015945 26 PNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R----P-YTPDVQSSEANERSQDS-QSSGFHKDLNLLPKPL 97 (398)
Q Consensus 26 ~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k----~-~~P~rE~~~il~rl~~~-~~G~lp~~~i~~~~~I 97 (398)
.+|+++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| .++++++... ..++++++.++ .|
T Consensus 8 ~~L~~lR~~ID~ID~~---iv~LL~e--R~~~~~~ia~~K~~~~~i~d~~Re-~~vl~~~~~~a~~~gl~~~~i~---~i 78 (101)
T PRK07075 8 TGLDDIREAIDRLDRD---IIAALGR--RMQYVKAASRFKPSEASIPAPERV-AAMLPERRRWAEQAGLDADFVE---KL 78 (101)
T ss_pred hhHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHhcCcCCCCCChHHH-HHHHHHHHHHhhcCCCCHHHHH---HH
Confidence 4799999999999999 9999999 999999999 5 5 999999 9999998774 34779999999 49
Q ss_pred chhhcccCCCCC
Q 015945 98 SIMELSSSPDDG 109 (398)
Q Consensus 98 ~R~iis~s~~~q 109 (398)
|+.||+.|...|
T Consensus 79 f~~Ii~~~i~~q 90 (101)
T PRK07075 79 FAQLIHWYIAQQ 90 (101)
T ss_pred HHHHHHHHHHHH
Confidence 999999886654
No 29
>COG1605 PheA Chorismate mutase [Amino acid transport and metabolism]
Probab=99.21 E-value=5.2e-13 Score=111.79 Aligned_cols=78 Identities=18% Similarity=0.231 Sum_probs=70.5
Q ss_pred CCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C------C-CCCchhhHHHHHhhhh-ccCCCCccccccCCC
Q 015945 26 PNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R------P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPK 95 (398)
Q Consensus 26 ~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k------~-~~P~rE~~~il~rl~~-~~~G~lp~~~i~~~~ 95 (398)
..|.++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| ++|++++.. .+.++++++.++
T Consensus 8 ~~L~~lR~~Id~iD~~---ll~Ll~e--R~~l~~~Va~~K~~~g~~pi~d~~RE-~~vl~~~~~~~~~~~l~~~~i~--- 78 (101)
T COG1605 8 EELEELREEIDEIDRE---LLDLLAE--RLELAKEVGEAKAASGKLPIYDPERE-EQVLERLRAEAEKGGLDPELIE--- 78 (101)
T ss_pred hHHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHcCCCCCCChHHH-HHHHHHHHHHHHhCCCCHHHHH---
Confidence 4799999999999999 9999999 999999999 3 6 999999 999999884 788889999999
Q ss_pred ccchhhcccCCCCCcee
Q 015945 96 PLSIMELSSSPDDGTKV 112 (398)
Q Consensus 96 ~I~R~iis~s~~~q~~~ 112 (398)
++|+++|+.|...|...
T Consensus 79 ~~f~~i~~~~~~~q~~~ 95 (101)
T COG1605 79 RLFREIMEASKAVQYKL 95 (101)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 49999999998777543
No 30
>PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed
Probab=99.13 E-value=4.2e-12 Score=128.43 Aligned_cols=74 Identities=14% Similarity=0.081 Sum_probs=69.8
Q ss_pred CcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccCCCccc
Q 015945 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPKPLS 98 (398)
Q Consensus 27 ~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~~G~lp~~~i~~~~~I~ 98 (398)
+|.++|.+||+||++ |++||+| |++++.+|| | | |+|+|| +++++++.+.+.|+|+++.++ .||
T Consensus 5 ~L~~lR~~ID~ID~e---Il~LL~~--R~~~~~~I~~~K~~~g~pi~dp~RE-~~vl~~~~~~~~g~l~~~~i~---~If 75 (360)
T PRK12595 5 ELEQLRKEIDEINLQ---LLELLSK--RGELVQEIGEEKTKQGTKRYDPVRE-REMLDMIAENNEGPFEDSTIQ---HLF 75 (360)
T ss_pred HHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCCChHHH-HHHHHHHHHhccCCCCHHHHH---HHH
Confidence 599999999999999 9999999 999999999 4 6 999999 999999999888999999999 499
Q ss_pred hhhcccCCCCC
Q 015945 99 IMELSSSPDDG 109 (398)
Q Consensus 99 R~iis~s~~~q 109 (398)
|.||+.|+..|
T Consensus 76 ~~I~~~Sr~~Q 86 (360)
T PRK12595 76 KEIFKASLELQ 86 (360)
T ss_pred HHHHHHHHHHH
Confidence 99999998876
No 31
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=99.13 E-value=3.3e-12 Score=105.58 Aligned_cols=74 Identities=7% Similarity=0.051 Sum_probs=66.5
Q ss_pred CCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh--ccCCCCccccccCCC
Q 015945 26 PNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD--SQSSGFHKDLNLLPK 95 (398)
Q Consensus 26 ~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~--~~~G~lp~~~i~~~~ 95 (398)
..|.++|.+||+||++ |++||++ |+.++.+|| | | |+|+|| +++++++.. ...| ++++.++.
T Consensus 3 ~~L~~lR~~ID~ID~q---Lv~LL~~--R~~~~~~ia~~K~~~~~~v~dp~Re-~~vl~~~~~~a~~~g-l~p~~~e~-- 73 (94)
T TIGR01795 3 AELKALRQSIDNIDAA---VIHMLAE--RFKCTSQVGVLKANAGLAPADPARE-DYQIARLRRLAIDAG-LDPEFAEK-- 73 (94)
T ss_pred hhHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCCCHHHH-HHHHHHHHHHHHHCC-CCHHHHHH--
Confidence 3899999999999999 9999999 999999999 5 5 999999 999999776 4567 99999984
Q ss_pred ccchhhcccCCCCC
Q 015945 96 PLSIMELSSSPDDG 109 (398)
Q Consensus 96 ~I~R~iis~s~~~q 109 (398)
||+.|+.+|...|
T Consensus 74 -i~~~i~~esir~q 86 (94)
T TIGR01795 74 -FLNFIVTEVIKHH 86 (94)
T ss_pred -HHHHHHHHHHHHH
Confidence 9999999887665
No 32
>PRK09239 chorismate mutase; Provisional
Probab=99.12 E-value=1.5e-12 Score=109.48 Aligned_cols=82 Identities=10% Similarity=0.101 Sum_probs=70.3
Q ss_pred CCCCCCCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhc-cCCCCccccc
Q 015945 21 LPDLVPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDS-QSSGFHKDLN 91 (398)
Q Consensus 21 ~~~~~~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~-~~G~lp~~~i 91 (398)
.|-+-.+|.++|.+||+||++ |++||++ |+.++.+|| | | |+|.|| +++++++... ...+++++.+
T Consensus 5 ~~~~~~~L~~lR~~ID~ID~e---Iv~LLa~--R~~l~~~Ia~~K~~~~~~i~dp~RE-~~vl~~~~~~a~~~gl~p~~~ 78 (104)
T PRK09239 5 QARAPAELAALRQSIDNIDAA---LIHMLAE--RFKCTQAVGVLKAEHGLPPADPARE-AYQIERLRQLAKDANLDPDFA 78 (104)
T ss_pred cHHHHHHHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHCCCCCCCHHHH-HHHHHHHHHHHHHCCCCHHHH
Confidence 344556899999999999999 9999999 999999999 4 6 999999 9999998773 3345999999
Q ss_pred cCCCccchhhcccCCCCCce
Q 015945 92 LLPKPLSIMELSSSPDDGTK 111 (398)
Q Consensus 92 ~~~~~I~R~iis~s~~~q~~ 111 (398)
+ .||+.||.+|.+.|..
T Consensus 79 ~---~i~~~ii~esir~q~~ 95 (104)
T PRK09239 79 E---KFLNFIIKEVIRHHER 95 (104)
T ss_pred H---HHHHHHHHHHHHHHHH
Confidence 8 4999999998776643
No 33
>PF01817 CM_2: Chorismate mutase type II; InterPro: IPR020822 Chorismate mutase, 5.4.99.5 from EC, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [, ]. Prephenate dehydratase (IPR001086 from INTERPRO, 4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [].; GO: 0046417 chorismate metabolic process; PDB: 1YBZ_A 2GTV_X 2FP1_B 2F6L_B 2FP2_B 2AO2_A 3HGW_C 3HGX_B 2H9C_A 3RET_B ....
Probab=99.05 E-value=3.8e-12 Score=101.92 Aligned_cols=70 Identities=17% Similarity=0.209 Sum_probs=62.5
Q ss_pred hhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccC-CCCccccccCCCccchhhc
Q 015945 32 GLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQS-SGFHKDLNLLPKPLSIMEL 102 (398)
Q Consensus 32 R~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~~-G~lp~~~i~~~~~I~R~ii 102 (398)
|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| +++++++.+... ++++++.++ .||+.+|
T Consensus 1 R~~Id~iD~~---i~~Ll~~--R~~l~~~i~~~K~~~~~~i~d~~RE-~~v~~~~~~~~~~~~l~~~~i~---~if~~ii 71 (81)
T PF01817_consen 1 RKEIDEIDRE---IVDLLAE--RMDLVRKIAEYKKENGLPIFDPDRE-EEVLERLRELAEEGGLDPEFIE---RIFRAII 71 (81)
T ss_dssp HHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHTTCCSSTHHHH-HHHHHHHHHHHHHTTSEHHHHH---HHHHHHH
T ss_pred ChHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCCCcHHH-HHHHHHHHHHhHhCCCCHHHHH---HHHHHHH
Confidence 8899999999 9999999 999999999 4 6 999999 999999888544 779999999 4999999
Q ss_pred ccCCCCCc
Q 015945 103 SSSPDDGT 110 (398)
Q Consensus 103 s~s~~~q~ 110 (398)
+.|...|.
T Consensus 72 ~~s~~~Q~ 79 (81)
T PF01817_consen 72 EESRAIQY 79 (81)
T ss_dssp HHHHHHHH
T ss_pred HHHHHHHc
Confidence 98876553
No 34
>TIGR01808 CM_M_hiGC-arch monofunctional chorismate mutase, high GC gram positive type. This model represents the monofunctional chorismate mutase from high GC gram-positive bacteria and archaea. Trusted annotations from Corynebacterium and Pyrococcus are aparrently the sole chorismate mutase enzymes in their respective genomes. This is coupled with the presence in those genomes of the enzymes of the chorismate pathways both up- and downstream of chorismate mutase.
Probab=98.93 E-value=2.3e-10 Score=90.62 Aligned_cols=65 Identities=15% Similarity=0.064 Sum_probs=53.0
Q ss_pred CcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccCCCccc
Q 015945 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPKPLS 98 (398)
Q Consensus 27 ~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~~G~lp~~~i~~~~~I~ 98 (398)
.|.++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| .++++++.+.+ +-++ .+|
T Consensus 1 ~l~~lR~~ID~ID~~---ii~LL~~--R~~~~~~i~~~K~~~~~~i~d~~RE-~~vl~~~~~~~--~~~~-------~i~ 65 (74)
T TIGR01808 1 EIDTLREEIDRLDAE---ILALVKR--RAEISQAIGKARMASGGTRLVHSRE-MKVIERYSELG--PEGK-------DLA 65 (74)
T ss_pred CHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCCChHHH-HHHHHHHHHhC--CCCH-------HHH
Confidence 378899999999999 9999999 999999999 4 6 999999 99999987644 2122 366
Q ss_pred hhhcccCC
Q 015945 99 IMELSSSP 106 (398)
Q Consensus 99 R~iis~s~ 106 (398)
..++..|+
T Consensus 66 e~i~~~~r 73 (74)
T TIGR01808 66 IKLLRVGR 73 (74)
T ss_pred HHHHHhhc
Confidence 66665553
No 35
>PRK07857 hypothetical protein; Provisional
Probab=98.92 E-value=3.9e-10 Score=94.71 Aligned_cols=60 Identities=10% Similarity=0.006 Sum_probs=53.4
Q ss_pred CCcCCCCCCCCCCcchhhhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh
Q 015945 15 PHFHKGLPDLVPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD 80 (398)
Q Consensus 15 ~~~~~~~~~~~~~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~ 80 (398)
+..-++-|....+|.++|.+||+||++ |++||++ |+.++.+|| | + |+|+|| .++++++.+
T Consensus 17 ~~~~~~~p~~~~~L~~lR~eID~ID~e---Il~LL~e--R~~la~eIg~~K~~~g~pI~dp~RE-~eVl~rl~~ 84 (106)
T PRK07857 17 MPTGTDDPLSDAEIDELREEIDRLDAE---ILALVKR--RTEVSQAIGKARMASGGTRLVHSRE-MKVIERYRE 84 (106)
T ss_pred CCCCCCCCcchhhHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHhccCCCccChHHH-HHHHHHHHH
Confidence 344455677778999999999999999 9999999 999999999 4 5 999999 999999776
No 36
>smart00830 CM_2 Chorismate mutase type II. Chorismate mutase, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine PUBMED:9642265, PUBMED:9497350.
Probab=98.77 E-value=6.7e-10 Score=88.16 Aligned_cols=69 Identities=20% Similarity=0.286 Sum_probs=59.7
Q ss_pred hhHHHhhhchhhHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccC-CCCccccccCCCccchhhc
Q 015945 32 GLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQS-SGFHKDLNLLPKPLSIMEL 102 (398)
Q Consensus 32 R~~Id~iD~~~~~i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~~-G~lp~~~i~~~~~I~R~ii 102 (398)
|.+||.||.+ |++||++ |+.++.+|| | | |+|+|| .+++.++.+... -.++++.++ .||+.+|
T Consensus 1 R~~Id~iD~~---ii~Ll~~--R~~l~~~i~~~K~~~~~~i~d~~Re-~~vl~~~~~~a~~~~l~~~~~~---~if~~ii 71 (79)
T smart00830 1 RAEIDAIDDQ---ILALLAE--RAALAREVARLKAKNGLPIYDPERE-AEVLERLRALAEGPGLDPELVE---RIFREII 71 (79)
T ss_pred CchHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHCCCCCCChHHH-HHHHHHHHHHcccCCcCHHHHH---HHHHHHH
Confidence 6899999999 9999999 999999999 4 6 999999 999999777433 237888988 4999999
Q ss_pred ccCCCCC
Q 015945 103 SSSPDDG 109 (398)
Q Consensus 103 s~s~~~q 109 (398)
.+|...|
T Consensus 72 ~~s~~~q 78 (79)
T smart00830 72 EASKALQ 78 (79)
T ss_pred HHHHHhc
Confidence 9887655
No 37
>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=98.69 E-value=4.8e-08 Score=99.86 Aligned_cols=74 Identities=20% Similarity=0.262 Sum_probs=61.1
Q ss_pred CceEEEEEEeCCC-cchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHH
Q 015945 298 PYKTSIVFTLEEG-PGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFAL 376 (398)
Q Consensus 298 ~~ktsi~f~~~~~-pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al 376 (398)
...++++|+++++ +|+|.++|++|+.++|||+||||||++... . ...+|.|||||+++ +.++.+++
T Consensus 35 ~~~~~~~~~~~~~~~g~L~~~l~~f~~~~inl~hiEsr~~~~~~--------~---~~~~~~~~v~~~~~--~~~~~~~~ 101 (457)
T TIGR01269 35 AAMQNNQFYIRTKEISSLHRILKYIETFKLNLVHFETRPTRTLS--------N---ADVDYSCLITLEAN--EINMSLLI 101 (457)
T ss_pred ccceeEEEEeccCcchhHHHHHHHHHHcCCcEEEeecCCccccC--------C---CCCceEEEEEEecc--HhhHHHHH
Confidence 3457888888754 999999999999999999999999987542 0 12479999999986 47799999
Q ss_pred HHHHHhcC
Q 015945 377 GHLQEFAT 384 (398)
Q Consensus 377 ~~L~~~~~ 384 (398)
+.|++.+.
T Consensus 102 ~~l~~~~~ 109 (457)
T TIGR01269 102 ESLRGNSF 109 (457)
T ss_pred HHHHhhhc
Confidence 99998765
No 38
>PRK08818 prephenate dehydrogenase; Provisional
Probab=98.66 E-value=5.1e-08 Score=99.18 Aligned_cols=65 Identities=26% Similarity=0.335 Sum_probs=52.7
Q ss_pred ceEEEEEEeC-CCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 299 YKTSIVFTLE-EGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 299 ~ktsi~f~~~-~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
.-++|+|.++ |+||+|+++|++|+.+|||||+||| .+.++ |+|.|||||++..+-..+..+-.
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 55543 99999999998643344444444
Q ss_pred HH
Q 015945 378 HL 379 (398)
Q Consensus 378 ~L 379 (398)
++
T Consensus 358 ~~ 359 (370)
T PRK08818 358 EI 359 (370)
T ss_pred hh
Confidence 44
No 39
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=98.47 E-value=4.7e-07 Score=90.87 Aligned_cols=76 Identities=28% Similarity=0.410 Sum_probs=64.9
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
...++++|++++++|+|.++|+.|..+++|+.||||||++... .+|.|||+++... .++.++++
T Consensus 34 ~~~~~~if~~r~~~~~l~~~Lk~f~~~~vnl~HiEsR~s~~~~--------------~~~evlv~~~~~~--~~l~~~i~ 97 (461)
T KOG3820|consen 34 GARISLIFSLRNKVGALARALKAFEEFHVNLLHIESRPSERRS--------------SGYEVLVELDATR--GQLIQAIE 97 (461)
T ss_pred cceEEEEEEecccchHHHHHHHHhhhcCceEEEeecccccccC--------------CCceEEEeeccch--hhHHHHHH
Confidence 4578999999999999999999999999999999999997642 4699999999864 48888999
Q ss_pred HHHHhcCceEEE
Q 015945 378 HLQEFATFLRVL 389 (398)
Q Consensus 378 ~L~~~~~~vkiL 389 (398)
.|+..+..+...
T Consensus 98 ~lrq~~~~~~~~ 109 (461)
T KOG3820|consen 98 LLRQNHVALSYF 109 (461)
T ss_pred HHHHhcccceec
Confidence 999887554433
No 40
>TIGR01806 CM_mono2 chorismate mutase, putative. This model represents a clade of probable chorismate mutases from alpha, beta and gamma proteobacteria as well as Mycobacterium tuberculosis and a clade of nematodes. Although the most likely function for the enzymes represented by this model is as a chorismate mutase, in no species are these enzymes the sole chorismate mutase in the genome. Also, in no case are these enzymes located in a region of the genome proximal to any other enzymes involved in chorismate pathways. Although the Pantoea enzyme has been shown to complement a CM-free mutant of E. coli, this was also shown to be the case with isochorismate-pyruvate lyase which only has a secondary (non-physiologically relevant) chorismate mutase activity. This enzyme is believed to be a homodimer and be localized to the periplasm.
Probab=98.17 E-value=1.1e-07 Score=81.42 Aligned_cols=60 Identities=10% Similarity=0.088 Sum_probs=53.1
Q ss_pred HHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhcc-CCCCccccccCCCccchhhcccCCCCCc
Q 015945 45 CVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQ-SSGFHKDLNLLPKPLSIMELSSSPDDGT 110 (398)
Q Consensus 45 i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~-~G~lp~~~i~~~~~I~R~iis~s~~~q~ 110 (398)
|++||++ |+.++.+|| | | |+|+|| +++++++.+.. .++++++.++ .||+.||+.|+..|.
T Consensus 9 Lv~Ll~e--R~~la~eVa~~K~~~~~pI~Dp~RE-~~Vl~~~~~~a~~~gL~~~~i~---~if~~Ii~~Sk~~Q~ 77 (114)
T TIGR01806 9 LVDAANE--RLQLADDVAGYKARNNLPIEDSPRE-EQVLDSLRAQAQSAGLDPDYVT---RFFQAQINANKAIQY 77 (114)
T ss_pred HHHHHHH--HHHHHHHHHHHHHHCCCCCCChHHH-HHHHHHHHHHhHcCCCCHHHHH---HHHHHHHHHHHHHHH
Confidence 9999999 999999999 4 6 999999 99999987744 3779999998 499999999988663
No 41
>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=98.06 E-value=3.6e-05 Score=58.23 Aligned_cols=69 Identities=20% Similarity=0.170 Sum_probs=54.9
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhc
Q 015945 304 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFA 383 (398)
Q Consensus 304 ~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~ 383 (398)
.+.++|+||.|.++++.|+..|+|++.|.+++....- ..+.+.+++.++.. +...++.+++.|+..+
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 4678999999999999999999999999999865310 02567888888874 4577889999998765
Q ss_pred Cc
Q 015945 384 TF 385 (398)
Q Consensus 384 ~~ 385 (398)
..
T Consensus 69 ~~ 70 (73)
T cd04886 69 YD 70 (73)
T ss_pred CE
Confidence 43
No 42
>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=98.01 E-value=3.2e-05 Score=57.93 Aligned_cols=38 Identities=18% Similarity=0.377 Sum_probs=35.0
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 338 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~ 338 (398)
+.+.+.++|+||.|.++++.|+++|||+..+.+++...
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 45778889999999999999999999999999999875
No 43
>PRK09269 chorismate mutase; Provisional
Probab=97.77 E-value=2e-06 Score=80.06 Aligned_cols=60 Identities=13% Similarity=0.083 Sum_probs=53.3
Q ss_pred HHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhcc-CCCCccccccCCCccchhhcccCCCCCc
Q 015945 45 CVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQ-SSGFHKDLNLLPKPLSIMELSSSPDDGT 110 (398)
Q Consensus 45 i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~-~G~lp~~~i~~~~~I~R~iis~s~~~q~ 110 (398)
|++||+| |+.++.+|+ | | |+|.|| +++++++.+.. .++++++.++ .||+.+|++|...|.
T Consensus 37 Lv~Li~e--Rl~la~~VA~~K~~~~~pI~Dp~RE-~~VL~~v~~~A~~~gLdp~~v~---~iF~~~I~aSk~iQ~ 105 (193)
T PRK09269 37 LVDLAAQ--RLALADPVALSKWDSGKPIEDPPRE-AQVLANVEAQAPAHGVDPDYVR---RFFRDQIEANKLVQY 105 (193)
T ss_pred HHHHHHH--HHHHHHHHHHHHHhCCCCCCChHHH-HHHHHHHHHHhhcCCCCHHHHH---HHHHHHHHHHHHHHH
Confidence 9999999 999999999 5 6 999999 99999987744 3779999998 499999999988764
No 44
>PRK08055 chorismate mutase; Provisional
Probab=97.71 E-value=2.8e-06 Score=78.27 Aligned_cols=60 Identities=7% Similarity=0.138 Sum_probs=52.4
Q ss_pred HHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccC-CCCccccccCCCccchhhcccCCCCCc
Q 015945 45 CVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQS-SGFHKDLNLLPKPLSIMELSSSPDDGT 110 (398)
Q Consensus 45 i~~ll~~~~R~~~~~~v~--k-----~-~~P~rE~~~il~rl~~~~~-G~lp~~~i~~~~~I~R~iis~s~~~q~ 110 (398)
|++||+| |+.++.+|+ | | |+|.|| +++++++.+... ++++++.++ +||+.+|++|...|.
T Consensus 30 Lv~Li~e--Rl~la~~VA~~K~~~~~PI~Dp~RE-~~VL~~v~~~A~~~GLdp~~i~---~~F~~~I~asK~iQ~ 98 (181)
T PRK08055 30 LATLINE--RLSYMKDVAGYKAEHHLPIEDLTQE-QKVLAEAEEEAASNGLDPESIK---PFIVAQMDAAKAIQY 98 (181)
T ss_pred HHHHHHH--HHHHHHHHHHHHHhCCCCCCChHHH-HHHHHHHHHHhhhCCCCHHHHH---HHHHHHHHHHHHHHH
Confidence 9999999 999999999 4 6 999999 999999877543 339999998 499999999988763
No 45
>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=97.38 E-value=0.0011 Score=49.57 Aligned_cols=59 Identities=22% Similarity=0.265 Sum_probs=43.3
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
+.+.++|+||.|.++++.|+++|+|+..+...+.... ....+++.+++ ...+++.|++.
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 4568899999999999999999999999987665421 23456666654 33556666654
No 46
>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=97.32 E-value=0.0017 Score=50.19 Aligned_cols=65 Identities=14% Similarity=0.125 Sum_probs=45.0
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
+.+.++|+||+|.++++.++++|+|+..+...+..... +....+|.+++.. +..++.+++.|++.
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~--------------~~~~~~v~v~~e~-~~~~~~i~~~L~~~ 66 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPD--------------GMRRVFIRVTPMD-RSKENELIEELKAK 66 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCC--------------CccEEEEEEEEec-chHHHHHHHHHhCc
Confidence 55788999999999999999999999999766653221 2233455554422 23466777777655
No 47
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=97.18 E-value=0.0038 Score=49.77 Aligned_cols=70 Identities=11% Similarity=0.251 Sum_probs=54.6
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 380 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~ 380 (398)
-+|.+-+.|+||.|.++++.|+.||.|+..|..-|+... .-+.+-|-+.| ++..+..+.++|+
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 456777889999999999999999999999998887642 34566666666 4577888888888
Q ss_pred HhcCceE
Q 015945 381 EFATFLR 387 (398)
Q Consensus 381 ~~~~~vk 387 (398)
+.-.=++
T Consensus 66 KLidV~~ 72 (76)
T PRK06737 66 KLINVLQ 72 (76)
T ss_pred CCcCEEE
Confidence 7655443
No 48
>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=97.14 E-value=0.0033 Score=48.13 Aligned_cols=66 Identities=15% Similarity=0.242 Sum_probs=46.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 380 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~ 380 (398)
+.+.+.++|+||.|.++++.|+++|+|+.++...+.... ....++|.+++. +.. ++++.|+
T Consensus 2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~---------------~~~~v~i~v~~~-~~~---~~~~~L~ 62 (72)
T cd04883 2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEE---------------DNKILVFRVQTM-NPR---PIIEDLR 62 (72)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCC---------------CeEEEEEEEecC-CHH---HHHHHHH
Confidence 457788999999999999999999999999976554321 234566666652 222 5666666
Q ss_pred HhcCc
Q 015945 381 EFATF 385 (398)
Q Consensus 381 ~~~~~ 385 (398)
+..-.
T Consensus 63 ~~G~~ 67 (72)
T cd04883 63 RAGYE 67 (72)
T ss_pred HCCCe
Confidence 65433
No 49
>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=97.10 E-value=0.0062 Score=45.61 Aligned_cols=66 Identities=18% Similarity=0.239 Sum_probs=50.8
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
+|.+...|+||.|.++++.|+.+|+|+..+.+.+.+.. ....+++.++. .+ ..+..+++.|++
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 46778899999999999999999999999998765221 12345556654 34 788999999987
Q ss_pred hcC
Q 015945 382 FAT 384 (398)
Q Consensus 382 ~~~ 384 (398)
...
T Consensus 65 ~~~ 67 (72)
T cd04878 65 LVD 67 (72)
T ss_pred Ccc
Confidence 654
No 50
>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=97.09 E-value=0.0049 Score=46.39 Aligned_cols=63 Identities=19% Similarity=0.245 Sum_probs=47.7
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
++.+..+|+||.|.++++.|+++++|+.++...+... +.+.+++++++. ..+..+++.|++
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 4667789999999999999999999999998765432 245667888764 345566777765
Q ss_pred hc
Q 015945 382 FA 383 (398)
Q Consensus 382 ~~ 383 (398)
..
T Consensus 63 ~~ 64 (72)
T cd04874 63 LP 64 (72)
T ss_pred CC
Confidence 44
No 51
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=96.90 E-value=0.0059 Score=46.68 Aligned_cols=61 Identities=18% Similarity=0.263 Sum_probs=47.8
Q ss_pred CCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhcCce
Q 015945 309 EGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFL 386 (398)
Q Consensus 309 ~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~~v 386 (398)
|+||.|.++++.|..+|+|+..|..-|+... .-+.+-+.++|. +..+..+.+.|++...-+
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~---------------~~~riti~v~~~--~~~i~~l~~Ql~KlidV~ 61 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDP---------------GISRITIVVSGD--DREIEQLVKQLEKLIDVV 61 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-SST---------------TEEEEEEEEES---CCHHHHHHHHHHCSTTEE
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecCCC---------------CEEEEEEEEeeC--chhHHHHHHHHhccCCeE
Confidence 6899999999999999999999999995432 458888888884 467788888888765533
No 52
>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=96.80 E-value=0.013 Score=45.26 Aligned_cols=73 Identities=23% Similarity=0.250 Sum_probs=49.9
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
+|.+..+|+||.|.++++.+++.|+|+..+.+..... +.+...|-++. +..+..+..+++.|++
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~--------------~~~~i~~~v~v--~~~~~~l~~l~~~L~~ 65 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIH--------------GRANVTISIDT--STMNGDIDELLEELRE 65 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCC--------------CeEEEEEEEEc--CchHHHHHHHHHHHhc
Confidence 5778889999999999999999999999998743211 01334444444 3233377788888875
Q ss_pred h--cCceEEEc
Q 015945 382 F--ATFLRVLG 390 (398)
Q Consensus 382 ~--~~~vkiLG 390 (398)
. ...|+++|
T Consensus 66 i~~V~~v~~~~ 76 (76)
T cd04888 66 IDGVEKVELVG 76 (76)
T ss_pred CCCeEEEEEeC
Confidence 4 33466655
No 53
>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=96.72 E-value=0.0095 Score=40.91 Aligned_cols=58 Identities=28% Similarity=0.320 Sum_probs=43.4
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHH
Q 015945 304 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 379 (398)
Q Consensus 304 ~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L 379 (398)
.+..++++|.+.++++.|+.+|+|+.++.+++.... +...|++.++... ....+++.|
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 466788999999999999999999999998876421 3567777776531 455555544
No 54
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=96.66 E-value=0.015 Score=45.71 Aligned_cols=71 Identities=14% Similarity=0.272 Sum_probs=52.2
Q ss_pred CCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHH
Q 015945 297 RPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFAL 376 (398)
Q Consensus 297 ~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al 376 (398)
+...+.|.+...|+||.|.++.+.++..|+|+..++....+.. ..+.+.++++-. +-..+..++
T Consensus 3 ~~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~---------------~~~~~~l~v~V~-d~~~L~~ii 66 (80)
T PF13291_consen 3 KSFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDD---------------GTARITLTVEVK-DLEHLNQII 66 (80)
T ss_dssp --EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ET---------------TEEEEEEEEEES-SHHHHHHHH
T ss_pred cEEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccC---------------CEEEEEEEEEEC-CHHHHHHHH
Confidence 3567889999999999999999999999999999999997521 245666666553 457888899
Q ss_pred HHHHHhc
Q 015945 377 GHLQEFA 383 (398)
Q Consensus 377 ~~L~~~~ 383 (398)
+.|++.-
T Consensus 67 ~~L~~i~ 73 (80)
T PF13291_consen 67 RKLRQIP 73 (80)
T ss_dssp HHHCTST
T ss_pred HHHHCCC
Confidence 9887553
No 55
>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=96.57 E-value=0.0069 Score=46.13 Aligned_cols=36 Identities=17% Similarity=0.346 Sum_probs=31.6
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 337 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~ 337 (398)
.+.+.++|+||.|.++++.|+.+|+|+..+...+.+
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~ 38 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIR 38 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEee
Confidence 466788999999999999999999999999876653
No 56
>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=96.52 E-value=0.017 Score=43.87 Aligned_cols=35 Identities=20% Similarity=0.313 Sum_probs=31.2
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 336 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~ 336 (398)
-|.+.++|+||.|.++++.|+++|+|+..+..-+.
T Consensus 3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~ 37 (66)
T cd04908 3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADT 37 (66)
T ss_pred EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEec
Confidence 36678899999999999999999999999987664
No 57
>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=96.50 E-value=0.01 Score=45.21 Aligned_cols=60 Identities=13% Similarity=0.186 Sum_probs=42.8
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
+++..+|+||.|.++++.|+++|+|+..+.+.+.... ......+++++. ....+.+.|++
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~---------------~~~~~~i~v~~~-~~~~~~~~l~~ 61 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPG---------------GEALMVLSVDEP-VPDEVLEELRA 61 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCC---------------CEEEEEEEeCCC-CCHHHHHHHHc
Confidence 4668899999999999999999999999987665321 244566688773 23344333433
No 58
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=96.50 E-value=0.022 Score=51.49 Aligned_cols=70 Identities=17% Similarity=0.254 Sum_probs=54.6
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
.|.+.+.|+||.|.++.+.|+.+|+|+..+-.-|.... +.+.+.+-+++ ++..+..+.++|++
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 56678899999999999999999999999988887421 34566667776 46788888888887
Q ss_pred hcCceEE
Q 015945 382 FATFLRV 388 (398)
Q Consensus 382 ~~~~vki 388 (398)
...=+++
T Consensus 66 li~V~~V 72 (157)
T TIGR00119 66 LVDVIKV 72 (157)
T ss_pred CccEEEE
Confidence 6554433
No 59
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=96.49 E-value=0.025 Score=51.44 Aligned_cols=71 Identities=17% Similarity=0.250 Sum_probs=55.2
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 380 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~ 380 (398)
-+|.+.++|+||.|.++.+.|+.+|+|+..+-.-|.... +.+.+.+-++| ++..+..+.++|+
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 457778899999999999999999999999988887421 34566677776 4678888899988
Q ss_pred HhcCceEE
Q 015945 381 EFATFLRV 388 (398)
Q Consensus 381 ~~~~~vki 388 (398)
+...-+++
T Consensus 66 KLidV~~V 73 (161)
T PRK11895 66 KLIDVLKV 73 (161)
T ss_pred ccccEEEE
Confidence 77554443
No 60
>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=96.46 E-value=0.014 Score=44.84 Aligned_cols=62 Identities=23% Similarity=0.189 Sum_probs=44.5
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhc
Q 015945 304 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFA 383 (398)
Q Consensus 304 ~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~ 383 (398)
.+.+|++||+|.++++.++. |.|++.+.=|-.... .....+=+++.+ ...++++++.|++..
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~~--------------~~~v~v~ie~~~---~~~~~~i~~~L~~~G 63 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGGD--------------EARVLVGIQVPD---REDLAELKERLEALG 63 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCCC--------------ceEEEEEEEeCC---HHHHHHHHHHHHHcC
Confidence 57889999999999999999 999999977654321 133444444433 356777888887654
No 61
>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=96.45 E-value=0.017 Score=43.13 Aligned_cols=62 Identities=16% Similarity=0.306 Sum_probs=44.0
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
+.+..+|+||.|.++++.|+++|+|+..+...+.... ......++++.. .+.++++.|++.
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 5667889999999999999999999999988764221 122344666553 344667777654
Q ss_pred c
Q 015945 383 A 383 (398)
Q Consensus 383 ~ 383 (398)
-
T Consensus 63 ~ 63 (71)
T cd04903 63 P 63 (71)
T ss_pred C
Confidence 3
No 62
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=96.35 E-value=0.036 Score=44.17 Aligned_cols=67 Identities=9% Similarity=0.165 Sum_probs=49.2
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHH
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 379 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L 379 (398)
|-+|.+.+.|+||.|.++++.|+.||.|+..|..-|+... .-...-+-+. ++..+..+.++|
T Consensus 3 ~~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~---------------~~sriti~v~---~~~~i~ql~kQL 64 (76)
T PRK11152 3 QHQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDA---------------QNINIELTVA---SERPIDLLSSQL 64 (76)
T ss_pred eEEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCC---------------CEEEEEEEEC---CCchHHHHHHHH
Confidence 4567777889999999999999999999999999886532 1223333332 456777788888
Q ss_pred HHhcC
Q 015945 380 QEFAT 384 (398)
Q Consensus 380 ~~~~~ 384 (398)
.+.-.
T Consensus 65 ~KL~d 69 (76)
T PRK11152 65 NKLVD 69 (76)
T ss_pred hcCcC
Confidence 76543
No 63
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=96.35 E-value=0.024 Score=52.10 Aligned_cols=71 Identities=17% Similarity=0.273 Sum_probs=54.0
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 380 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~ 380 (398)
-.|.+...|+||.|.++.+.|+.||+|+..+.+.|.... +...+-+.+.+. +..+..+.++|+
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 456677789999999999999999999999999886542 234677777764 233677777888
Q ss_pred HhcCceEE
Q 015945 381 EFATFLRV 388 (398)
Q Consensus 381 ~~~~~vki 388 (398)
+.+.-+++
T Consensus 66 KLidVl~V 73 (174)
T CHL00100 66 KLVNILKV 73 (174)
T ss_pred HHhHhhEE
Confidence 77665544
No 64
>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=96.24 E-value=0.026 Score=41.96 Aligned_cols=62 Identities=15% Similarity=0.247 Sum_probs=44.5
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
+.+..+|+||.|.++++.|+++|+|+.++++.+.... ..+...++++.. ...+++++|++.
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 5677889999999999999999999999999875421 134455566442 244566666654
Q ss_pred c
Q 015945 383 A 383 (398)
Q Consensus 383 ~ 383 (398)
.
T Consensus 63 ~ 63 (71)
T cd04879 63 P 63 (71)
T ss_pred C
Confidence 3
No 65
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=96.18 E-value=0.053 Score=45.11 Aligned_cols=72 Identities=18% Similarity=0.319 Sum_probs=54.3
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
.+-.|.+-+.|+||.|.++-+.|+.||.|+..|-.-|+... .-..+.|-+. +|..+.++.++
T Consensus 7 ~~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~~---------------~iSRmtivv~---~~~~i~Qi~kQ 68 (96)
T PRK08178 7 DNVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQDG---------------DKSRIWLLVN---DDQRLEQMISQ 68 (96)
T ss_pred CCEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCCC---------------CceEEEEEEc---CchHHHHHHHH
Confidence 34567777889999999999999999999999988887542 2245555453 35788899999
Q ss_pred HHHhcCceEE
Q 015945 379 LQEFATFLRV 388 (398)
Q Consensus 379 L~~~~~~vki 388 (398)
|++.-.-+++
T Consensus 69 L~KLidVikV 78 (96)
T PRK08178 69 IEKLEDVLKV 78 (96)
T ss_pred HhCCcCEEEE
Confidence 9887654443
No 66
>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=96.15 E-value=0.041 Score=42.26 Aligned_cols=63 Identities=16% Similarity=0.223 Sum_probs=45.9
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
|.+...|+||.|.++.+.++..|+|+..++++..... .....|-+++. +...+..+++.|+..
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 5678899999999999999999999999999864321 12233444443 346777788887643
No 67
>PRK04435 hypothetical protein; Provisional
Probab=96.12 E-value=0.058 Score=48.17 Aligned_cols=78 Identities=19% Similarity=0.195 Sum_probs=56.7
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
..+++|.+.+.|+||.|.++++.++..|+|+..|....... +.....|=||... .+..+.++++
T Consensus 67 ~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~--------------g~a~vs~tVevs~--~~~~L~~Li~ 130 (147)
T PRK04435 67 GKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQ--------------GRANVTISIDTSS--MEGDIDELLE 130 (147)
T ss_pred CcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCC--------------CEEEEEEEEEeCC--hHHHHHHHHH
Confidence 44788999999999999999999999999999998642211 0134555566532 2347888888
Q ss_pred HHHHh--cCceEEEcc
Q 015945 378 HLQEF--ATFLRVLGC 391 (398)
Q Consensus 378 ~L~~~--~~~vkiLGs 391 (398)
.|+.. ...++++|.
T Consensus 131 ~L~~i~gV~~V~i~~~ 146 (147)
T PRK04435 131 KLRNLDGVEKVELIGM 146 (147)
T ss_pred HHHcCCCcEEEEEEec
Confidence 88754 446777774
No 68
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=96.10 E-value=0.056 Score=43.91 Aligned_cols=71 Identities=11% Similarity=0.131 Sum_probs=52.4
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEee-cCCCcHHHHHHHHHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFE-ASMADPRAQFALGHL 379 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~-g~~~d~~v~~al~~L 379 (398)
-.|.+-+.|+||.|.++-+.|+.||+|+..|..-|+... +=..+=|-++ | ++..+.++.++|
T Consensus 3 ~~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~---------------~iSRmtivv~~~--d~~~ieqI~kQL 65 (84)
T PRK13562 3 RILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQP---------------GISNMEIQVDIQ--DDTSLHILIKKL 65 (84)
T ss_pred EEEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCCC---------------CceEEEEEEeCC--CHHHHHHHHHHH
Confidence 356667789999999999999999999999998887642 1234444444 4 456778888888
Q ss_pred HHhcCceEE
Q 015945 380 QEFATFLRV 388 (398)
Q Consensus 380 ~~~~~~vki 388 (398)
++.-.-+++
T Consensus 66 ~KlidVikV 74 (84)
T PRK13562 66 KQQINVLTV 74 (84)
T ss_pred hCCccEEEE
Confidence 877554443
No 69
>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=95.95 E-value=0.039 Score=43.89 Aligned_cols=63 Identities=16% Similarity=0.246 Sum_probs=42.9
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceee--eeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCC-CcHH-HHHHHHH
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLT--KIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASM-ADPR-AQFALGH 378 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt--~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~-~d~~-v~~al~~ 378 (398)
|-+..+|+||-|+++.+.|++.|+++. ||.|--... .-.-.||||.+|.. .|+. .+.+-+.
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 446678999999999999999999987 666332221 23458999988854 4543 3333334
Q ss_pred HH
Q 015945 379 LQ 380 (398)
Q Consensus 379 L~ 380 (398)
|.
T Consensus 68 L~ 69 (75)
T cd04896 68 LR 69 (75)
T ss_pred HH
Confidence 43
No 70
>cd04926 ACT_ACR_4 C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.83 E-value=0.056 Score=42.00 Aligned_cols=36 Identities=22% Similarity=0.328 Sum_probs=31.4
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 336 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~ 336 (398)
|.+.+..+|+||.|+++.+.|+.+|+|+......+.
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 457778899999999999999999999998876654
No 71
>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=95.80 E-value=0.057 Score=43.43 Aligned_cols=69 Identities=16% Similarity=0.157 Sum_probs=44.6
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
+.+.+|++||+|.++|+.++..||| .+.=+-.... .....+-+++.+. ...++++++.|++.
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 6788899999999999999955555 4443332211 1344555666541 35677788888877
Q ss_pred cCceEEE
Q 015945 383 ATFLRVL 389 (398)
Q Consensus 383 ~~~vkiL 389 (398)
.-.+.++
T Consensus 66 G~~~~~~ 72 (85)
T cd04906 66 GYEVVDL 72 (85)
T ss_pred CCCeEEC
Confidence 6666554
No 72
>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=95.69 E-value=0.026 Score=42.58 Aligned_cols=60 Identities=18% Similarity=0.222 Sum_probs=43.4
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
+++...|+||.|.++++.|+++|+|+..+.+++..+ .-...++++.. ...++++.|++.
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 566778999999999999999999999987765321 22344566654 445677777754
Q ss_pred c
Q 015945 383 A 383 (398)
Q Consensus 383 ~ 383 (398)
-
T Consensus 61 ~ 61 (69)
T cd04901 61 P 61 (69)
T ss_pred C
Confidence 3
No 73
>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=95.53 E-value=0.1 Score=39.59 Aligned_cols=64 Identities=16% Similarity=0.242 Sum_probs=45.9
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
|.+...|+||.|.++++.|+.+|+|+.++.+.+.... ....+.+.++- .+...+.++++.|++.
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~---------------~~~~~~i~~~~-~~~~~l~~~i~~L~~~ 66 (79)
T cd04881 3 LRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGG---------------ETAPVVIVTHE-TSEAALNAALAEIEAL 66 (79)
T ss_pred EEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCC---------------CceeEEEEEcc-CCHHHHHHHHHHHHcC
Confidence 4567789999999999999999999999988764321 11223333332 3567888889988854
No 74
>PRK08198 threonine dehydratase; Provisional
Probab=95.48 E-value=0.11 Score=53.54 Aligned_cols=77 Identities=16% Similarity=0.174 Sum_probs=57.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeee-CCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP-QRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP-~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
...++.+.++|+||.|.++|+.++..|+|++.|.-.. ..+.+ .+...+.|.++.. +....+++++
T Consensus 326 r~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~~~~~~~-------------~~~~~v~v~ie~~-~~~~~~~l~~ 391 (404)
T PRK08198 326 RYLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDRFSPDLR-------------LGEVEVELTLETR-GPEHIEEILD 391 (404)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEEccCCCC-------------CceEEEEEEEEeC-CHHHHHHHHH
Confidence 3568889999999999999999999999999987654 33222 1345666666663 3346778899
Q ss_pred HHHHhcCceEEE
Q 015945 378 HLQEFATFLRVL 389 (398)
Q Consensus 378 ~L~~~~~~vkiL 389 (398)
.|++..-.++++
T Consensus 392 ~L~~~G~~v~~~ 403 (404)
T PRK08198 392 ALRDAGYEVKVV 403 (404)
T ss_pred HHHHCCCeEEEc
Confidence 998877666543
No 75
>PRK00194 hypothetical protein; Validated
Probab=95.18 E-value=0.11 Score=41.84 Aligned_cols=36 Identities=19% Similarity=0.230 Sum_probs=31.6
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeee
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 335 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP 335 (398)
+-.+.+.-+|+||-+.++.+.|+.+|+|+..+++.-
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~ 38 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTI 38 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHh
Confidence 445667778999999999999999999999998874
No 76
>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=95.04 E-value=0.12 Score=41.56 Aligned_cols=67 Identities=16% Similarity=0.215 Sum_probs=46.1
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeec-CCCcHHHHHHHHHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEA-SMADPRAQFALGHL 379 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g-~~~d~~v~~al~~L 379 (398)
-.+.+.-+|+||-++++.+.|+.+|+|+..+++.-..+ .+...+-+++.+ ..+-..+.+.|+.|
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 45677789999999999999999999999998775221 233445555543 22335666666666
Q ss_pred HHh
Q 015945 380 QEF 382 (398)
Q Consensus 380 ~~~ 382 (398)
...
T Consensus 67 ~~~ 69 (88)
T cd04872 67 GKE 69 (88)
T ss_pred HHH
Confidence 533
No 77
>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=94.98 E-value=0.21 Score=37.31 Aligned_cols=36 Identities=17% Similarity=0.214 Sum_probs=31.8
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 337 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~ 337 (398)
-+.+..+|+||.|.++.+.|+.+|+|+..+......
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~ 37 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTG 37 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecC
Confidence 356788999999999999999999999999887654
No 78
>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=94.95 E-value=0.28 Score=35.20 Aligned_cols=63 Identities=16% Similarity=0.189 Sum_probs=44.5
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhc
Q 015945 304 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFA 383 (398)
Q Consensus 304 ~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~ 383 (398)
.+..+++||.+.++++.|+++++|+..++...... ....+.+.++.. +...+..+++.|+..-
T Consensus 2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~----------------~~~~~~~~~~~~-~~~~~~~~~~~l~~~~ 64 (71)
T cd04876 2 RVEAIDRPGLLADITTVIAEEKINILSVNTRTDDD----------------GLATIRLTLEVR-DLEHLARIMRKLRQIP 64 (71)
T ss_pred EEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCC----------------CEEEEEEEEEEC-CHHHHHHHHHHHhCCC
Confidence 45678999999999999999999999998876431 112344445432 3456777788777543
No 79
>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=94.86 E-value=0.17 Score=39.29 Aligned_cols=59 Identities=20% Similarity=0.356 Sum_probs=47.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
|.+...|++|-|.++++.++..|+|+..+++++. + + .+++++.. +-..+..+++.|++.
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 5566789999999999999999999999999763 2 2 66777654 456788888888754
No 80
>PRK08577 hypothetical protein; Provisional
Probab=94.81 E-value=0.38 Score=42.04 Aligned_cols=70 Identities=17% Similarity=0.281 Sum_probs=49.6
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
....|.+...|+||.|.++++.|+.+|+|+..+.++...... .+.-.|-+|+... +..+.++++.
T Consensus 55 ~~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~-------------~~~i~l~vev~~~--~~~l~~l~~~ 119 (136)
T PRK08577 55 KLVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGE-------------LAECVIIVDLSKS--DIDLEELEEE 119 (136)
T ss_pred cEEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCC-------------EEEEEEEEEeCCc--hhhHHHHHHH
Confidence 356788888999999999999999999999999988764311 1112333455432 2467788888
Q ss_pred HHHhc
Q 015945 379 LQEFA 383 (398)
Q Consensus 379 L~~~~ 383 (398)
|++..
T Consensus 120 L~~l~ 124 (136)
T PRK08577 120 LKKLE 124 (136)
T ss_pred HHcCC
Confidence 87653
No 81
>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=94.77 E-value=0.15 Score=51.93 Aligned_cols=73 Identities=22% Similarity=0.250 Sum_probs=50.5
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeee-eCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR-PQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESR-P~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
..+|.+.++|+||.|.++++.++.+|.|++.|.-+ ..+..+ .......|.++.. +....+++++.
T Consensus 305 ~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~r~~~~~~-------------~~~~~v~v~vet~-~~~~~~~i~~~ 370 (380)
T TIGR01127 305 KVRIETVLPDRPGALYHLLESIAEARANIVKIDHDRLSKEIP-------------PGFAMVEITLETR-GKEHLDEILKI 370 (380)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeccccCCC-------------CceEEEEEEEEeC-CHHHHHHHHHH
Confidence 44788899999999999999999999999999654 222221 1233444555543 23566678888
Q ss_pred HHHhcCce
Q 015945 379 LQEFATFL 386 (398)
Q Consensus 379 L~~~~~~v 386 (398)
|++....+
T Consensus 371 L~~~G~~v 378 (380)
T TIGR01127 371 LRDMGYNF 378 (380)
T ss_pred HHHcCCcc
Confidence 87765444
No 82
>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=94.67 E-value=0.095 Score=38.21 Aligned_cols=34 Identities=26% Similarity=0.362 Sum_probs=30.4
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 015945 304 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 337 (398)
Q Consensus 304 ~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~ 337 (398)
.+.++|+||.|.++++.|.++|+|+..+...+..
T Consensus 2 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~ 35 (56)
T cd04889 2 SVFVENKPGRLAEVTEILAEAGINIKAISIAETR 35 (56)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEcc
Confidence 4577899999999999999999999999877765
No 83
>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=94.58 E-value=0.28 Score=37.02 Aligned_cols=36 Identities=19% Similarity=0.253 Sum_probs=31.9
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 337 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~ 337 (398)
-+.+..+|+||.|.++.+.|+.+|+|+.++...+..
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~ 37 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLG 37 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecC
Confidence 456677899999999999999999999999988754
No 84
>PRK06382 threonine dehydratase; Provisional
Probab=94.54 E-value=0.2 Score=51.85 Aligned_cols=36 Identities=19% Similarity=0.255 Sum_probs=33.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeee
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 334 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESR 334 (398)
.++.|.+.++|+||+|.++++.|+.+|+|+++|+-.
T Consensus 329 ~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~~ 364 (406)
T PRK06382 329 QLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEVD 364 (406)
T ss_pred CEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEEe
Confidence 477888999999999999999999999999999973
No 85
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=94.49 E-value=0.19 Score=44.11 Aligned_cols=77 Identities=21% Similarity=0.339 Sum_probs=60.3
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHH
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIE-SRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFAL 376 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IE-SRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al 376 (398)
....++.+.+.|+.|.|.++|...++.++|+..|. +-|..+. .+-..-+|..+ -...+.+++
T Consensus 70 ~ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~---------------Anvtlsi~~ss--m~~~V~~ii 132 (150)
T COG4492 70 ERIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGR---------------ANVTLSIDTSS--MEKDVDKII 132 (150)
T ss_pred ceEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCce---------------eeEEEEEEchh--hhhhHHHHH
Confidence 45779999999999999999999999999998885 4565543 34566777764 347888899
Q ss_pred HHHHHh--cCceEEEcc
Q 015945 377 GHLQEF--ATFLRVLGC 391 (398)
Q Consensus 377 ~~L~~~--~~~vkiLGs 391 (398)
++|++. ...|.++|+
T Consensus 133 ~kl~k~e~V~kVeivgs 149 (150)
T COG4492 133 EKLRKVEGVEKVEIVGS 149 (150)
T ss_pred HHHhcccceeEEEEeec
Confidence 998853 556888876
No 86
>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=94.44 E-value=0.16 Score=39.29 Aligned_cols=33 Identities=12% Similarity=0.225 Sum_probs=29.6
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeee
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRP 335 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP 335 (398)
|.+.-+|+||-+.++.+.|+++|+|+..+++.-
T Consensus 2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~ 34 (74)
T cd04875 2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFV 34 (74)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeee
Confidence 345668999999999999999999999999885
No 87
>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=94.40 E-value=0.24 Score=38.56 Aligned_cols=61 Identities=11% Similarity=0.072 Sum_probs=42.4
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHH
Q 015945 305 FTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 380 (398)
Q Consensus 305 f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~ 380 (398)
+.=+|+||-++++-+.|+++|+|+..++++=..+ .+...|.+++....+-..+++.|+.+.
T Consensus 4 v~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~---------------~f~~~~~v~~p~~~~~~~l~~~l~~l~ 64 (75)
T cd04870 4 VTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHG---------------RLSLGILVQIPDSADSEALLKDLLFKA 64 (75)
T ss_pred EEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcC---------------eeEEEEEEEcCCCCCHHHHHHHHHHHH
Confidence 3447999999999999999999999998665432 244455555533223456666666665
No 88
>PRK08526 threonine dehydratase; Provisional
Probab=94.39 E-value=0.83 Score=47.31 Aligned_cols=212 Identities=17% Similarity=0.144 Sum_probs=109.4
Q ss_pred CCccEEEEeeccccccchHHhHHhhh--cCCeEEEEEEEEeee---EeeecCCCCCccCccEEE----e---cHHHHHHH
Q 015945 153 WLVDKAVLPIENSVGGSIHRNYDLLL--RHRLHIVGEVQLVVN---HCLLGLPGVLKEELKRVF----S---HPQALAQC 220 (398)
Q Consensus 153 g~~d~gvVPIENS~~G~V~~tld~L~--~~~l~I~~Ei~l~I~---h~Ll~~~g~~l~~I~~V~----S---Hpqal~QC 220 (398)
++.|+.|+|+- ..|.+.-....|. ..+.+|+|--.-.-. ..+-..+......+.++. . -|..+..|
T Consensus 167 ~~~D~vvvpvG--gGGl~aGia~~~k~~~p~~kvigVep~~~~~~~~s~~~g~~~~~~~~~tiadgiav~~~~~~~~~~~ 244 (403)
T PRK08526 167 SDLDMVVVPVG--GGGLISGIASAAKQINPNIKIIGVGAKGAPAMYESFHAKKIINSKSVRTIADGIAVRDASPINLAII 244 (403)
T ss_pred CCCCEEEEecC--hHHHHHHHHHHHHHhCCCCEEEEEEECCCChHHHHHHcCCcccCCCCCceeccccCCCCCHHHHHHH
Confidence 35899999985 3455544444443 345666654331110 001110001112222221 1 16666767
Q ss_pred HHHHhhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecccccCCCCceEEEEEecCCCCCC------
Q 015945 221 EMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAG------ 294 (398)
Q Consensus 221 ~~fl~~~~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~------ 294 (398)
+++++. +..++-....+|.+.+++.. + -.+.+..|+-+.+|.--...+. ++-+.=+++-|-+-....
T Consensus 245 ~~~vd~--~v~V~d~ei~~A~~~l~~~~--g-i~ve~aga~~lAall~~~~~~~--~~~~Vv~ilsGGnid~~~~~~i~~ 317 (403)
T PRK08526 245 LECVDD--FVQVDDEEIANAILFLLEKQ--K-IVVEGAGAASVAALLHQKIDLK--KGKKIGVVLSGGNIDVQMLNIIIE 317 (403)
T ss_pred HHhCCE--EEEECHHHHHHHHHHHHHhc--C-cEeeHHHHHHHHHHHhCccccc--cCCeEEEEECCCCCCHHHHHHHHH
Confidence 665542 22233333456666666542 2 2234444444444431111111 122233333332211000
Q ss_pred ---CCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeee-eeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcH
Q 015945 295 ---TDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIES-RPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADP 370 (398)
Q Consensus 295 ---~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IES-RP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~ 370 (398)
-....+..+.+.++++||+|.++++.+...+.|++.|+= |.....+ .++-...|.++.. +..
T Consensus 318 ~~l~~~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~~~~~-------------~~~~~~~~~~e~~-~~~ 383 (403)
T PRK08526 318 KGLIKSYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFSTKLD-------------YGDAMISITLETK-GKE 383 (403)
T ss_pred HHHHhcCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEeccCCCC-------------CccEEEEEEEEeC-CHH
Confidence 012346788899999999999999999999999999976 5544322 1234555666654 446
Q ss_pred HHHHHHHHHHHhcCceE
Q 015945 371 RAQFALGHLQEFATFLR 387 (398)
Q Consensus 371 ~v~~al~~L~~~~~~vk 387 (398)
.++++++.|++....++
T Consensus 384 ~~~~~~~~l~~~g~~~~ 400 (403)
T PRK08526 384 HQEEIRKILTEKGFNFY 400 (403)
T ss_pred HHHHHHHHHHHCCCCeE
Confidence 78888888877655443
No 89
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=94.36 E-value=0.22 Score=39.03 Aligned_cols=35 Identities=20% Similarity=0.318 Sum_probs=25.8
Q ss_pred EEEEe--CCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 015945 303 IVFTL--EEGPGMLFKALAVFALRDINLTKIESRPQR 337 (398)
Q Consensus 303 i~f~~--~~~pGaL~~~L~~F~~~~INLt~IESRP~~ 337 (398)
+++++ +|+||-++.+.+.++++|.|+..++-.-..
T Consensus 3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~ 39 (76)
T PF13740_consen 3 LVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLG 39 (76)
T ss_dssp EEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEET
T ss_pred EEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEc
Confidence 44444 799999999999999999999877766544
No 90
>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=94.31 E-value=0.28 Score=38.63 Aligned_cols=29 Identities=28% Similarity=0.436 Sum_probs=25.7
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceee
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLT 329 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt 329 (398)
|-|-+..+|+||-|+++.++|++.|+++.
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~ 30 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCIT 30 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEE
Confidence 44557778999999999999999999988
No 91
>PRK08639 threonine dehydratase; Validated
Probab=93.29 E-value=1.1 Score=46.52 Aligned_cols=74 Identities=16% Similarity=0.218 Sum_probs=51.2
Q ss_pred ceEEEEEEeCCCcchHHHHHH-HHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALA-VFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~-~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
.+..+.|.+|++||+|.++|+ .+.... |++.|+-|.....+ .+ ..+|.++.. +.+.++++++
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 555444 99999777543221 12 344555543 3357778888
Q ss_pred HHHHhcCceEEE
Q 015945 378 HLQEFATFLRVL 389 (398)
Q Consensus 378 ~L~~~~~~vkiL 389 (398)
.|++....++.+
T Consensus 398 ~L~~~Gy~~~~~ 409 (420)
T PRK08639 398 RMEAFGPSYIDI 409 (420)
T ss_pred HHHHCCCceEEC
Confidence 888776666554
No 92
>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=93.12 E-value=0.68 Score=36.06 Aligned_cols=35 Identities=17% Similarity=0.397 Sum_probs=30.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 337 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~ 337 (398)
+.+..+|+||-+.++-+.|+.+|+|+..+++.-..
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~ 36 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYS 36 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence 44667899999999999999999999999886543
No 93
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=92.88 E-value=0.8 Score=41.24 Aligned_cols=74 Identities=22% Similarity=0.328 Sum_probs=52.4
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceee-eeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLT-KIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt-~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
+.++.+.++|+||.|.++|+.++..|.|+. =|+||--+..| .--.-|-|++. ..+..++.++.
T Consensus 5 ritldIEL~D~PGQLl~vLqPls~~g~NiItIiH~r~kk~g~---------------r~pV~i~~~~d-~~~~~~~i~~~ 68 (170)
T COG2061 5 RITLDIELKDKPGQLLKVLQPLSKTGANIITIIHSRDKKYGP---------------RVPVQIVFEGD-REDKDAKIIRL 68 (170)
T ss_pred EEEEEEEecCCCcchhhhhcchhhcCccEEEEEeecCcccCC---------------ceeEEEEEEec-ccHHHHHHHHH
Confidence 567889999999999999999999999986 46788655433 22233344443 24667778888
Q ss_pred HHHhcCceEEE
Q 015945 379 LQEFATFLRVL 389 (398)
Q Consensus 379 L~~~~~~vkiL 389 (398)
+++....++-.
T Consensus 69 ~e~~Gi~I~~~ 79 (170)
T COG2061 69 LEEEGIIIIRF 79 (170)
T ss_pred HHhCCcEEEEe
Confidence 87666655444
No 94
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic, long form. Forms scoring between the trusted and noise cutoff tend to branch with this subgroup of threonine ammonia-lyase phylogenetically but have only a single copy of the C-terminal domain.
Probab=92.20 E-value=2.5 Score=45.11 Aligned_cols=150 Identities=18% Similarity=0.203 Sum_probs=83.5
Q ss_pred HHHHHHHHHHHhhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecccccCCCCceEEEEEecCCCCC
Q 015945 214 PQALAQCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIA 293 (398)
Q Consensus 214 pqal~QC~~fl~~~~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~ 293 (398)
+..+.-|++++.. +-.+......+|.+.+.+.. + .-+.+..|+.+.+|.-+.+... .+ +.|=-+|++-.....
T Consensus 236 ~~~~~~~~~~vd~--vv~V~d~ei~~ai~~l~~~~--g-ii~EpagA~~lAal~~~~~~~~-~~-~~~vv~i~sG~n~~~ 308 (499)
T TIGR01124 236 DETFRLCQQYLDD--IVTVDTDEVCAAIKDLFEDT--R-AVAEPAGALALAGLKKYVALHG-IR-GQTLVAILSGANMNF 308 (499)
T ss_pred HHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhc--C-cEEechHHHHHHHHHHhhhhcC-CC-CCeEEEEECCCCCCH
Confidence 4566666665432 22222333445666666542 1 2234445555556554432211 11 223222332221110
Q ss_pred C----------CCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEe
Q 015945 294 G----------TDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDF 363 (398)
Q Consensus 294 ~----------~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~ 363 (398)
. -.......+.+++|++||+|.++++.+.. -|+|.++=|-.... .=..||.+
T Consensus 309 ~~l~~~~~r~~~~~~re~~l~V~iPerPGal~~f~~~i~~--~nItef~yr~~~~~----------------~a~v~vgi 370 (499)
T TIGR01124 309 HRLRYVSERCELGEQREALLAVTIPEQPGSFLKFCELLGN--RNITEFNYRYADRK----------------DAHIFVGV 370 (499)
T ss_pred HHHHHHHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhh--cceEEEEEEecCCC----------------eEEEEEEE
Confidence 0 01234778889999999999999999997 48898888864321 22345666
Q ss_pred ecCCCcHHHHHHHHHHHHhcCceEEE
Q 015945 364 EASMADPRAQFALGHLQEFATFLRVL 389 (398)
Q Consensus 364 ~g~~~d~~v~~al~~L~~~~~~vkiL 389 (398)
+.. +...+.++++.|++..-.+..+
T Consensus 371 e~~-~~~~~~~l~~~L~~~Gy~~~dl 395 (499)
T TIGR01124 371 QLS-NPQERQEILARLNDGGYSVVDL 395 (499)
T ss_pred EeC-CHHHHHHHHHHHHHcCCCeEEC
Confidence 654 4467888888888776666554
No 95
>PRK07334 threonine dehydratase; Provisional
Probab=92.05 E-value=0.96 Score=46.67 Aligned_cols=77 Identities=14% Similarity=0.160 Sum_probs=55.7
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC-CCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHH
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR-KRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFAL 376 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~-~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al 376 (398)
...+.|.+...|++|.|.++++.+++.++|+.++.++... ..+ . ..+...|-|++. +...+.+++
T Consensus 324 ~y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~--------~---~~~~i~l~i~V~---d~~~L~~vi 389 (403)
T PRK07334 324 GRLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLP--------A---KGAELELVIETR---DAAHLQEVI 389 (403)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCC--------C---CeEEEEEEEEeC---CHHHHHHHH
Confidence 3468999999999999999999999999999999988641 101 0 112333444442 457889999
Q ss_pred HHHHHhcCceEE
Q 015945 377 GHLQEFATFLRV 388 (398)
Q Consensus 377 ~~L~~~~~~vki 388 (398)
+.|++....+.+
T Consensus 390 ~~Lr~~g~~~~~ 401 (403)
T PRK07334 390 AALRAAGFEARL 401 (403)
T ss_pred HHHHHcCCeeEe
Confidence 999887655543
No 96
>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=91.60 E-value=1.3 Score=34.14 Aligned_cols=32 Identities=13% Similarity=0.305 Sum_probs=27.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeee
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIE 332 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IE 332 (398)
+.+.+..+|+||-|+++-++|+.+|+|+..-.
T Consensus 2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~ 33 (73)
T cd04900 2 TEVFIYTPDRPGLFARIAGALDQLGLNILDAR 33 (73)
T ss_pred EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeE
Confidence 35677778999999999999999999999543
No 97
>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=91.30 E-value=1.4 Score=45.66 Aligned_cols=75 Identities=15% Similarity=0.099 Sum_probs=50.6
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
....+.|.+|++||+|.++++.....+-|+++++-|..... ..-...|.++.. +...++++++.
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 36788999999999999999944445559999888763211 122344555543 23567778888
Q ss_pred HHHhcCceEEE
Q 015945 379 LQEFATFLRVL 389 (398)
Q Consensus 379 L~~~~~~vkiL 389 (398)
|++....++++
T Consensus 388 L~~~Gy~~~~~ 398 (409)
T TIGR02079 388 MAAADIHYEDI 398 (409)
T ss_pred HHHCCCCeEEC
Confidence 88776555543
No 98
>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=90.65 E-value=2.1 Score=33.53 Aligned_cols=64 Identities=16% Similarity=0.052 Sum_probs=42.9
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 382 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~ 382 (398)
+.+.-+|+||-.+++-+.++++|.|+..+...-..+ .+-+..-++++. ..-..+.+.++.+.+.
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 456668999999999999999999999877665221 133334445442 2335666667766643
No 99
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=90.21 E-value=0.85 Score=41.75 Aligned_cols=61 Identities=21% Similarity=0.276 Sum_probs=46.0
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
+.+...|+||.|.++-.+++++|.|+|..+..-.+.. ..-..|.+++|- +| .+.++++|+.
T Consensus 5 lsi~~enk~GvL~~ltgiiae~ggNIt~~q~~~~~~g---------------~~~~iYmEiEgi-~d--~e~l~~~lks 65 (218)
T COG1707 5 LSIIAENKPGVLRDLTGIIAEEGGNITYAQQFLEKDG---------------EKALIYMEIEGI-DD--FEKLLERLKS 65 (218)
T ss_pred eEEEeecCccHHHHHHHHHHhcCCceEeeehhhhccC---------------ceEEEEEEeeCC-CC--HHHHHHHhhc
Confidence 4455679999999999999999999999988765542 134778899995 33 3456666654
No 100
>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=89.92 E-value=2.1 Score=34.01 Aligned_cols=29 Identities=14% Similarity=0.298 Sum_probs=25.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceee
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLT 329 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt 329 (398)
|-|-+..+|+||-|+++...|.+.|+++.
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~ 30 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVF 30 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEE
Confidence 34557779999999999999999999987
No 101
>PLN02550 threonine dehydratase
Probab=89.91 E-value=3 Score=45.43 Aligned_cols=209 Identities=14% Similarity=0.126 Sum_probs=106.7
Q ss_pred CccEEEEeeccccccchHHhHHhhh--cCCeEEEEEEEEeee---EeeecCCCCCccCccE----EE---ecHHHHHHHH
Q 015945 154 LVDKAVLPIENSVGGSIHRNYDLLL--RHRLHIVGEVQLVVN---HCLLGLPGVLKEELKR----VF---SHPQALAQCE 221 (398)
Q Consensus 154 ~~d~gvVPIENS~~G~V~~tld~L~--~~~l~I~~Ei~l~I~---h~Ll~~~g~~l~~I~~----V~---SHpqal~QC~ 221 (398)
..|+.|||+- ..|.+.-....+. ..+++|+|--.-.-. ..+-..+...++.+.+ +. .-+..+.-|+
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 4899999986 3444444444333 346777664442110 0111100011111111 11 1145556565
Q ss_pred HHHhhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecccccCCCCceEEEEEecCCCCC--------
Q 015945 222 MTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIA-------- 293 (398)
Q Consensus 222 ~fl~~~~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~-------- 293 (398)
+++.. +-.|......+|.+.+.+.. + .-+-+..|+.+.+|.-..+... ..+-..=+++-|.+-...
T Consensus 336 ~~vD~--vV~Vsd~eI~~Ai~~l~e~~--g-ivvEpAGA~alAall~~~~~~~-~~g~~Vv~vlsGgNid~~~l~~v~~~ 409 (591)
T PLN02550 336 ELVDG--VVLVSRDAICASIKDMFEEK--R-SILEPAGALALAGAEAYCKYYG-LKDENVVAITSGANMNFDRLRIVTEL 409 (591)
T ss_pred hhCCE--EEEECHHHHHHHHHHHHHHC--C-CEEeHHHHHHHHHHHHHHHhcC-CCCCeEEEEecCCCCCHHHHHHHHHH
Confidence 55432 22233334556666666642 1 2233334444444433322111 122223333333332110
Q ss_pred -CCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHH
Q 015945 294 -GTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRA 372 (398)
Q Consensus 294 -~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v 372 (398)
.-....+..+.+.++++||+|.++++.+... |++.|+=|-... .+-..+|.++.. ....+
T Consensus 410 ~~~~~~r~~~~~v~ipd~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v~v~ie~~-~~~~~ 470 (591)
T PLN02550 410 ADVGRQQEAVLATFMPEEPGSFKRFCELVGPM--NITEFKYRYSSE----------------KEALVLYSVGVH-TEQEL 470 (591)
T ss_pred HHhccCCEEEEEEEcCCCCCHHHHHHHHhhhh--cceEEEEEecCC----------------CceEEEEEEEeC-CHHHH
Confidence 0012235678899999999999999999986 999998876321 233555666654 45688
Q ss_pred HHHHHHHHHhcCceEEE
Q 015945 373 QFALGHLQEFATFLRVL 389 (398)
Q Consensus 373 ~~al~~L~~~~~~vkiL 389 (398)
+++++.|++..-.++.|
T Consensus 471 ~~i~~~l~~~g~~~~~l 487 (591)
T PLN02550 471 QALKKRMESAQLRTVNL 487 (591)
T ss_pred HHHHHHHHHCCCCeEeC
Confidence 88999998876655544
No 102
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=89.87 E-value=2.1 Score=37.11 Aligned_cols=38 Identities=29% Similarity=0.326 Sum_probs=33.2
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 338 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~ 338 (398)
.-+.+..+|+||+|.+++.+|.+++||+-.|.-.-.++
T Consensus 70 dVlaVEmeD~PG~l~~I~~vl~d~diNldYiYAFv~ek 107 (142)
T COG4747 70 DVLAVEMEDVPGGLSRIAEVLGDADINLDYIYAFVTEK 107 (142)
T ss_pred eEEEEEecCCCCcHHHHHHHHhhcCcCceeeeeeeecC
Confidence 34567889999999999999999999999998877665
No 103
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=89.02 E-value=2.2 Score=38.88 Aligned_cols=73 Identities=18% Similarity=0.290 Sum_probs=53.1
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHH
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 379 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L 379 (398)
+-.+.+-+.|+||.|.++.+.|+.+|.|+-.|---|+-.. ..=.--+-..| ++..++++.+.|
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 3456667789999999999999999999999988887542 12233333444 456778888888
Q ss_pred HHhcCceEEE
Q 015945 380 QEFATFLRVL 389 (398)
Q Consensus 380 ~~~~~~vkiL 389 (398)
.+.-.-+|++
T Consensus 67 ~kLidV~kV~ 76 (163)
T COG0440 67 NKLIDVLKVL 76 (163)
T ss_pred HhhccceeEE
Confidence 8776666655
No 104
>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=88.56 E-value=3.2 Score=32.55 Aligned_cols=62 Identities=11% Similarity=0.227 Sum_probs=45.7
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecC-CCcHHHHHHHHHHHHhcCce
Q 015945 308 EEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEAS-MADPRAQFALGHLQEFATFL 386 (398)
Q Consensus 308 ~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~-~~d~~v~~al~~L~~~~~~v 386 (398)
++.||.+.++++.|+++|||+-.|-+ +. ..+.|-|+-... ..+..+++++++|++.+ .+
T Consensus 12 ~~~~g~~~~IF~~La~~~I~vDmI~~-s~------------------~~isftv~~~~~~~~~~~~~~l~~el~~~~-~v 71 (75)
T cd04935 12 WQQVGFLADVFAPFKKHGVSVDLVST-SE------------------TNVTVSLDPDPNGLDPDVLDALLDDLNQIC-RV 71 (75)
T ss_pred CCccCHHHHHHHHHHHcCCcEEEEEe-CC------------------CEEEEEEeCcccccchHHHHHHHHHHHhce-EE
Confidence 56799999999999999999999965 11 257777775431 23348889999998854 35
Q ss_pred EEE
Q 015945 387 RVL 389 (398)
Q Consensus 387 kiL 389 (398)
.++
T Consensus 72 ~~~ 74 (75)
T cd04935 72 KII 74 (75)
T ss_pred EEe
Confidence 443
No 105
>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=88.10 E-value=4.2 Score=31.94 Aligned_cols=58 Identities=19% Similarity=0.299 Sum_probs=42.1
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHH-HHHHHHHHhc
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQ-FALGHLQEFA 383 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~-~al~~L~~~~ 383 (398)
.++.||.+.++++.|+++|||+-.|-+ +. .++.|-|+-.-...+..++ +++++|++.+
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~VDmI~~-s~------------------~~iSftv~~~d~~~~~~~~~~l~~~l~~~~ 69 (75)
T cd04932 11 MLHAQGFLAKVFGILAKHNISVDLITT-SE------------------ISVALTLDNTGSTSDQLLTQALLKELSQIC 69 (75)
T ss_pred CCCCcCHHHHHHHHHHHcCCcEEEEee-cC------------------CEEEEEEeccccchhHHHHHHHHHHHHhcc
Confidence 467899999999999999999999965 11 2577777753222234565 6888888744
No 106
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=88.06 E-value=2.4 Score=39.60 Aligned_cols=35 Identities=20% Similarity=0.419 Sum_probs=29.9
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 337 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~ 337 (398)
+.+.=+|+||-++++-+.|+.+|||+..+.|+-..
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 44444799999999999999999999999998543
No 107
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=87.98 E-value=2.4 Score=38.91 Aligned_cols=74 Identities=20% Similarity=0.250 Sum_probs=52.4
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCC-cHHHHHHHHHHHHhc
Q 015945 305 FTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMA-DPRAQFALGHLQEFA 383 (398)
Q Consensus 305 f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~-d~~v~~al~~L~~~~ 383 (398)
+...|+||-+.++-+.|..|||||-.++||-.... | ...-.|.+++.-+.. .-.+..+.++++..|
T Consensus 97 v~a~DrpgIv~~~T~lf~~~~inie~L~~~~~~a~----------~---s~~~lfha~it~~lPa~~~i~~l~~~f~al~ 163 (176)
T COG2716 97 VDANDRPGIVEEFTALFDGHGINIENLVSRTYPAP----------G---SSAPLFHAQITARLPANLSISALRDAFEALC 163 (176)
T ss_pred EEecCCccHHHHHHHHHHhcCCchhhceeeeeecC----------C---CCccceehhhhccCCCcCcHHHHHHHHHHHH
Confidence 44479999999999999999999999999854321 1 135689999865532 224555566677777
Q ss_pred CceEEEcc
Q 015945 384 TFLRVLGC 391 (398)
Q Consensus 384 ~~vkiLGs 391 (398)
..+.+=|+
T Consensus 164 ~~L~v~~~ 171 (176)
T COG2716 164 DELNVDGS 171 (176)
T ss_pred Hhhcceee
Confidence 76666554
No 108
>PRK09224 threonine dehydratase; Reviewed
Probab=86.90 E-value=4.1 Score=43.51 Aligned_cols=73 Identities=15% Similarity=0.229 Sum_probs=50.9
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
....+.+++|++||+|.++++.+. +-|+|.++=|-.... .=..+|.++....+..++++++.
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 467889999999999999999999 688998887774321 22345555543222236778888
Q ss_pred HHHhcCceEEE
Q 015945 379 LQEFATFLRVL 389 (398)
Q Consensus 379 L~~~~~~vkiL 389 (398)
|++..-.++.+
T Consensus 389 L~~~gy~~~~l 399 (504)
T PRK09224 389 LRAHGYPVVDL 399 (504)
T ss_pred HHHcCCCeEEC
Confidence 87765555544
No 109
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=86.36 E-value=1.9 Score=35.48 Aligned_cols=66 Identities=14% Similarity=0.221 Sum_probs=45.5
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecC-CCcHHHHH-HHHHHHHhcCc
Q 015945 308 EEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEAS-MADPRAQF-ALGHLQEFATF 385 (398)
Q Consensus 308 ~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~-~~d~~v~~-al~~L~~~~~~ 385 (398)
+|+||-.+.+-++++++|+|+..|+---..+ .+...++||+.-. .+-..+++ +-++.++....
T Consensus 11 kDr~GIva~is~vLAe~~vNIldisQtvm~~---------------~ftm~~lV~~~~~~~d~~~lr~~l~~~~~~lgv~ 75 (90)
T COG3830 11 KDRVGIVAAVSRVLAEHGVNILDISQTVMDG---------------FFTMIMLVDISKEVVDFAALRDELAAEGKKLGVD 75 (90)
T ss_pred CCCCchhHHHHHHHHHcCCcEEEHHHHHHhh---------------hceeeeEEcCChHhccHHHHHHHHHHHHHhcCcE
Confidence 7999999999999999999999997655443 3678899999532 22234443 33344555555
Q ss_pred eEE
Q 015945 386 LRV 388 (398)
Q Consensus 386 vki 388 (398)
+++
T Consensus 76 V~v 78 (90)
T COG3830 76 VRV 78 (90)
T ss_pred EEE
Confidence 553
No 110
>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=86.32 E-value=6 Score=30.97 Aligned_cols=28 Identities=11% Similarity=0.278 Sum_probs=24.3
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeee
Q 015945 304 VFTLEEGPGMLFKALAVFALRDINLTKI 331 (398)
Q Consensus 304 ~f~~~~~pGaL~~~L~~F~~~~INLt~I 331 (398)
-+..+|+||-|+++.+.|+.+|+|+..=
T Consensus 4 ei~~~Dr~gLfa~i~~~l~~~~l~I~~A 31 (76)
T cd04927 4 KLFCSDRKGLLHDVTEVLYELELTIERV 31 (76)
T ss_pred EEEECCCCCHHHHHHHHHHHCCCeEEEE
Confidence 3456799999999999999999999843
No 111
>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=86.11 E-value=6.9 Score=31.27 Aligned_cols=65 Identities=22% Similarity=0.211 Sum_probs=45.3
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
-+.|++|.+||||.+.|+.+. -+-|+|.++=|-.... .+ .-||-++-. ++.+..+++.|++
T Consensus 3 ~~~v~iPErpGal~~Fl~~l~-p~~~ITeF~YR~~~~~--------------~a--~vlvGi~~~--~~~~~~l~~~l~~ 63 (81)
T cd04907 3 LFRFEFPERPGALKKFLNELL-PKWNITLFHYRNQGSD--------------YG--RVLVGIQVP--DADLDELKERLDA 63 (81)
T ss_pred EEEEEcCCCCCHHHHHHHHhC-CCCeEeEEEEecCCCC--------------ce--eEEEEEEeC--hHHHHHHHHHHHH
Confidence 467899999999999999994 3889999998875432 12 344555432 2366777777776
Q ss_pred hcCc
Q 015945 382 FATF 385 (398)
Q Consensus 382 ~~~~ 385 (398)
..-.
T Consensus 64 ~g~~ 67 (81)
T cd04907 64 LGYP 67 (81)
T ss_pred cCCC
Confidence 5443
No 112
>PRK12483 threonine dehydratase; Reviewed
Probab=85.71 E-value=4.8 Score=43.26 Aligned_cols=72 Identities=17% Similarity=0.177 Sum_probs=52.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHH-HHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRA-QFALG 377 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v-~~al~ 377 (398)
.+..+.+.++++||+|.++++.+... |++.++=+-... .+-..+|.++.. +.... +++++
T Consensus 344 r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v~v~ie~~-~~~~~~~~i~~ 404 (521)
T PRK12483 344 REAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYRYADA----------------REAHLFVGVQTH-PRHDPRAQLLA 404 (521)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEEecCC----------------CeeEEEEEEEeC-ChhhhHHHHHH
Confidence 47788999999999999999999987 999988875221 123455666654 22444 78888
Q ss_pred HHHHhcCceEEE
Q 015945 378 HLQEFATFLRVL 389 (398)
Q Consensus 378 ~L~~~~~~vkiL 389 (398)
.|++..-.++.+
T Consensus 405 ~l~~~g~~~~dl 416 (521)
T PRK12483 405 SLRAQGFPVLDL 416 (521)
T ss_pred HHHHCCCCeEEC
Confidence 888776666554
No 113
>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=85.60 E-value=6.2 Score=30.60 Aligned_cols=56 Identities=14% Similarity=0.230 Sum_probs=42.9
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCC-cHHHHHHHHHHHH
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMA-DPRAQFALGHLQE 381 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~-d~~v~~al~~L~~ 381 (398)
+.+.||.+.++++.|+++|||+-.+-+.+ -...|.|+-+.... +..++.++++|++
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 45679999999999999999999886421 25788887644322 3578888999987
No 114
>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=84.55 E-value=25 Score=30.18 Aligned_cols=121 Identities=21% Similarity=0.140 Sum_probs=65.9
Q ss_pred CCCCccc-cCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc--
Q 015945 132 YPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK-- 208 (398)
Q Consensus 132 fg~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~-- 208 (398)
++++++. ...+..++.+.+.+|++|+|++.-.....+... ..|.+..+.++. +-.|-+.. +..+++++.
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~v~----~~~~~~~~-~~~~~~~L~~~ 97 (200)
T cd08417 26 APGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRS---QPLFEDRFVCVA----RKDHPLAG-GPLTLEDYLAA 97 (200)
T ss_pred CCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccCCCccch---hhhhcCceEEEe----cCCCcccc-cccCHHHHhCC
Confidence 4555543 234667899999999999999875543332222 223344444432 33343433 223344443
Q ss_pred -EE-EecHH-HHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 209 -RV-FSHPQ-ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 209 -~V-~SHpq-al~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
-| +.+.. .......|+...+. . ...++|...+.+++..+ ...|+.+...++.
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08417 98 PHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGT---DLIATVPRRLAEA 155 (200)
T ss_pred CeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcC---CeeeeccHHHHHh
Confidence 22 33322 22345666666443 2 34566677777777764 3577888776654
No 115
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=83.54 E-value=7.1 Score=38.69 Aligned_cols=67 Identities=9% Similarity=0.196 Sum_probs=46.2
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEee--cCCCcHHHHHHHHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFE--ASMADPRAQFALGH 378 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~--g~~~d~~v~~al~~ 378 (398)
..+.+.-+|+||-..++-+.|+++|+|+..+.+.-.... ..|...++++ ...+-..++++|+.
T Consensus 8 ~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~---------------~~F~m~~~~~~p~~~~~~~L~~~L~~ 72 (286)
T PRK13011 8 FVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLS---------------GRFFMRVEFHSEEGLDEDALRAGFAP 72 (286)
T ss_pred EEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCC---------------CeEEEEEEEecCCCCCHHHHHHHHHH
Confidence 345556689999999999999999999999999833222 2233344554 22334677777777
Q ss_pred HHHh
Q 015945 379 LQEF 382 (398)
Q Consensus 379 L~~~ 382 (398)
+.+.
T Consensus 73 l~~~ 76 (286)
T PRK13011 73 IAAR 76 (286)
T ss_pred HHHH
Confidence 7543
No 116
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=83.38 E-value=2.1 Score=40.33 Aligned_cols=84 Identities=18% Similarity=0.176 Sum_probs=56.0
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhC-C----C----CccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhh--
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAY-P----K----CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL-- 178 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~f-g----~----~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~-- 178 (398)
+..+|++-.|..+.+.++.+.++ . + ...+...+.++++.+|.+|++|.|+++- .+++.+.
T Consensus 104 ~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~~Da~~~~~---------~~~~~~~~~ 174 (243)
T PF12974_consen 104 KGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGKADAAAIPS---------DAFERLEAE 174 (243)
T ss_dssp GGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTSSSEEEEEH---------HHHHHHHHH
T ss_pred CCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCCccEEEEec---------hhHHHHHHc
Confidence 56789987665444466666555 2 1 2345777999999999999999999873 3444332
Q ss_pred ----cCCeEEEEEEEEeeeEeeecCCCC
Q 015945 179 ----RHRLHIVGEVQLVVNHCLLGLPGV 202 (398)
Q Consensus 179 ----~~~l~I~~Ei~l~I~h~Ll~~~g~ 202 (398)
..+++|.++...-..+.++++++.
T Consensus 175 ~~~~~~~~rvl~~s~~~p~~~~~~~~~~ 202 (243)
T PF12974_consen 175 GPDIPSQLRVLWTSPPYPNWPLVASPDL 202 (243)
T ss_dssp -HHHHTTEEEEEEEEEEE--EEEEETTS
T ss_pred cCcccccEEEEEEeCCCCCcEEEEeCCC
Confidence 357999999887777788887663
No 117
>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=83.05 E-value=5.6 Score=31.08 Aligned_cols=55 Identities=16% Similarity=0.268 Sum_probs=43.1
Q ss_pred CCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhc
Q 015945 309 EGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFA 383 (398)
Q Consensus 309 ~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~ 383 (398)
..||.+.++++.|+++|||+-.|-+ .. .++.|-++-.. ..++.+++++++|++.+
T Consensus 13 ~~~g~~~~If~~la~~~I~vd~I~~---s~----------------~~isftv~~~~-~~~~~l~~l~~el~~~~ 67 (73)
T cd04934 13 LSHGFLARIFAILDKYRLSVDLIST---SE----------------VHVSMALHMEN-AEDTNLDAAVKDLQKLG 67 (73)
T ss_pred cccCHHHHHHHHHHHcCCcEEEEEe---CC----------------CEEEEEEehhh-cChHHHHHHHHHHHHhe
Confidence 4699999999999999999999966 11 25788887643 33458889999998743
No 118
>PRK06349 homoserine dehydrogenase; Provisional
Probab=80.98 E-value=5.9 Score=41.30 Aligned_cols=64 Identities=17% Similarity=0.258 Sum_probs=45.8
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
-|.+.+.|+||.|.++-+.|.+++||+..+...+.... ..+..+.++. ..+..+++++++|++
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 34556679999999999999999999998887764321 1233433332 245788889998875
Q ss_pred h
Q 015945 382 F 382 (398)
Q Consensus 382 ~ 382 (398)
.
T Consensus 413 l 413 (426)
T PRK06349 413 L 413 (426)
T ss_pred C
Confidence 4
No 119
>PRK06545 prephenate dehydrogenase; Validated
Probab=80.28 E-value=4 Score=41.42 Aligned_cols=40 Identities=13% Similarity=0.304 Sum_probs=35.4
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCC
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 339 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~ 339 (398)
-..+.+.++|+||.|.+++..+...|||+..|+-.-++..
T Consensus 290 ~~~~~v~v~d~pg~~~~~~~~~~~~~i~i~~~~i~~~~~~ 329 (359)
T PRK06545 290 FYDLYVDVPDEPGVIARVTAILGEEGISIENLRILEARED 329 (359)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHcCCCeecceeeeccCC
Confidence 4568889999999999999999999999999988777654
No 120
>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=80.12 E-value=7.6 Score=27.43 Aligned_cols=30 Identities=23% Similarity=0.327 Sum_probs=25.9
Q ss_pred EeCCCcchHHHHHHHHHhCCceeeeeeeee
Q 015945 306 TLEEGPGMLFKALAVFALRDINLTKIESRP 335 (398)
Q Consensus 306 ~~~~~pGaL~~~L~~F~~~~INLt~IESRP 335 (398)
..++.||.+.++++.|+++|||+..|..-+
T Consensus 7 ~~~~~~~~~~~i~~~L~~~~i~i~~i~~~~ 36 (61)
T cd04891 7 GVPDKPGVAAKIFSALAEAGINVDMIVQSV 36 (61)
T ss_pred cCCCCCcHHHHHHHHHHHcCCcEEEEEEcC
Confidence 357889999999999999999998886644
No 121
>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=79.93 E-value=15 Score=28.48 Aligned_cols=32 Identities=28% Similarity=0.361 Sum_probs=26.6
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeee
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESR 334 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESR 334 (398)
|-+..+|+||-|+++-+.|+.+|+|+..-...
T Consensus 3 ~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~ 34 (74)
T cd04925 3 IELTGTDRPGLLSEVFAVLADLHCNVVEARAW 34 (74)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCCcEEEEEEE
Confidence 44566899999999999999999999854444
No 122
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=78.16 E-value=11 Score=37.30 Aligned_cols=66 Identities=9% Similarity=0.172 Sum_probs=46.8
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeec----CCCcHHHHHHHH
Q 015945 302 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEA----SMADPRAQFALG 377 (398)
Q Consensus 302 si~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g----~~~d~~v~~al~ 377 (398)
-|.+.-+|+||-.+++-+.++++|+|+..+... .... .+.|+..++++. ..+...++++++
T Consensus 11 iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~-~d~~--------------~~~ffm~i~~~~~~~~~~~~~~l~~~l~ 75 (289)
T PRK13010 11 VLTLACPSAPGIVAAVSGFLAEKGCYIVELTQF-DDDE--------------SGRFFMRVSFHAQSAEAASVDTFRQEFQ 75 (289)
T ss_pred EEEEECCCCCCcHHHHHHHHHHCCCCEEecccc-cccc--------------cCcEEEEEEEEcCCCCCCCHHHHHHHHH
Confidence 345555899999999999999999999999886 2111 145666666652 233467777777
Q ss_pred HHHHh
Q 015945 378 HLQEF 382 (398)
Q Consensus 378 ~L~~~ 382 (398)
++.+.
T Consensus 76 ~l~~~ 80 (289)
T PRK13010 76 PVAEK 80 (289)
T ss_pred HHHHH
Confidence 76543
No 123
>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=78.02 E-value=32 Score=31.88 Aligned_cols=132 Identities=23% Similarity=0.181 Sum_probs=75.5
Q ss_pred CccccCCCHHHHHHHHHcCCccEEEEeecccccc--chHHhHHhhhcCCeEEEEEEEEeeeEeeecCCC-----CCccCc
Q 015945 135 CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGG--SIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG-----VLKEEL 207 (398)
Q Consensus 135 ~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G--~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g-----~~l~~I 207 (398)
+......|. +.+.++.+|.+|++.+=+...-.| .+...-+.|...++.++.-. .=...|+.+++ .+++|+
T Consensus 13 v~~~~~gS~-~gl~~L~~g~~~iAg~h~~~~~~~~~n~~~~~~~l~g~~~v~v~~~--~r~~Gl~v~~~np~~i~~~~dL 89 (193)
T PF12727_consen 13 VAVQYTGSR-AGLSALARGEADIAGIHLPDPESGEYNIPFVRRLLPGIEVVLVRLA--RREQGLIVRPGNPKGITSLEDL 89 (193)
T ss_pred EEEEecCCH-HHHHHHHCCCceEEEecCCCCcccccchHHHHHhcCCCcEEEEeee--EEeeeEEEeCCCCccCCCHHHh
Confidence 344444454 667888899999999865433222 23333344444444443222 22346676666 334444
Q ss_pred ---cEEEecHHHHHHHHHHHhh----cCC-----e--EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH-cCCceeec
Q 015945 208 ---KRVFSHPQALAQCEMTLSN----LGI-----V--RISADDTAGAAQMVASIGERDTGAVASAQAAEI-YGLDILAE 271 (398)
Q Consensus 208 ---~~V~SHpqal~QC~~fl~~----~~~-----~--~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~-ygL~il~~ 271 (398)
...+--.+.=.=.|.+|++ .++ . ..++.|..+.|..|+.+. ..++++.+.+|+. |||.++-=
T Consensus 90 ~~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G~--AD~G~g~~~~A~~~~gL~Fvpl 166 (193)
T PF12727_consen 90 ADPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASGK--ADAGIGIRAAAEEFYGLDFVPL 166 (193)
T ss_pred ccCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcCC--CCEEeehHHHHHhhcCCCcEEc
Confidence 2223333333345555555 222 1 235667778888888763 5689999999975 79998763
No 124
>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=77.57 E-value=18 Score=34.00 Aligned_cols=137 Identities=18% Similarity=0.083 Sum_probs=70.6
Q ss_pred EEEEEcCCCcHHHHHH--HHhCC------CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEE
Q 015945 113 RVAYQGLPGAYSEAAA--RKAYP------KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHI 184 (398)
Q Consensus 113 kVa~lGp~Gs~s~~AA--~~~fg------~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I 184 (398)
+|+|+.. +......| +.+|. ++++....+..++++++.+|++|+|++.... .+.. .-...++.+
T Consensus 2 ~vg~~~~-~~~~~~~a~~~g~f~~~g~~l~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~----~~~~---~~~g~~~~~ 73 (288)
T TIGR01728 2 RIGYQKN-GHSALALAKEKGLLEKELGKTKVEWVEFPAGPPALEALGAGSLDFGYIGPGP----ALFA---YAAGADIKA 73 (288)
T ss_pred eEEecCC-CchHHHHHHHhCHHHHhhCCceEEEEecCCCcHHHHHHhcCCccccccCCcH----HHHH---HhcCCCEEE
Confidence 6888864 43332222 22442 3567777788899999999999999764321 1111 011235666
Q ss_pred EEEEEEeeeEeeecCCCC---CccCc--cEEEecHH--HHHHHHHHHhhcCCe---E-EecCCHHHHHHHHHhcCCCCeE
Q 015945 185 VGEVQLVVNHCLLGLPGV---LKEEL--KRVFSHPQ--ALAQCEMTLSNLGIV---R-ISADDTAGAAQMVASIGERDTG 253 (398)
Q Consensus 185 ~~Ei~l~I~h~Ll~~~g~---~l~~I--~~V~SHpq--al~QC~~fl~~~~~~---~-v~~~STA~Aa~~v~~~~~~~~A 253 (398)
++-..-.-..+++++++. +++|+ ++|...+- .......+|.+.++. . ....+.+++.+.+..+. -+ |
T Consensus 74 i~~~~~~~~~~~v~~~~~~i~s~~dL~Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~-vd-a 151 (288)
T TIGR01728 74 VGLVSDNKATAIVVIKGSPIRTVADLKGKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQ-VD-A 151 (288)
T ss_pred EEEecCCCceEEEECCCCCCCCHHHcCCCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCC-CC-E
Confidence 654432124556655432 23333 25543221 123344466654331 1 22345667777777653 23 5
Q ss_pred EEcCHH
Q 015945 254 AVASAQ 259 (398)
Q Consensus 254 AI~s~~ 259 (398)
++.++.
T Consensus 152 ~~~~~p 157 (288)
T TIGR01728 152 WAIWEP 157 (288)
T ss_pred EEeccc
Confidence 555443
No 125
>PF03401 TctC: Tripartite tricarboxylate transporter family receptor; InterPro: IPR005064 Bordetella pertussis, the causative agent of human whooping cough (pertussis), is an obligate human pathogen with diverse high-affinity transport systems for the assimilation of iron, a biometal that is essential for growth []. Periplasmic binding proteins of a new family, particularly well represented in this organism (and more generally in beta-proteobacteria), have been called Bug receptors []. They adopt a characteristic Venus flytrap fold with two globular domains bisected by a ligand-binding cleft. The family is specific for carboxylated solutes, with a characteristic mode of binding involving two highly conserved beta strand-beta turn-alpha helix motifs originating from each domain. These two motifs form hydrogen bonds with a carboxylate group of the ligand, both directly and via conserved water molecules, and have thus been termed the carboxylate pincers. Domain 1 recognises the ligand and the carboxylate group serves as an initial anchoring point. Domain 2 discriminates between productively and non-productively bound ligands as proper interactions with this domain is needed for the of the closed conformation []. BugE has a glutamate bound ligand. No charged residues are involved in glutamate binding by BugE, unlike what has been described for all glutamate receptors reported so far. The Bug architecture is highly conserved despite limited sequence identity [].; GO: 0030288 outer membrane-bounded periplasmic space; PDB: 2QPQ_C 2DVZ_A 2F5X_A.
Probab=77.27 E-value=4.8 Score=39.30 Aligned_cols=64 Identities=23% Similarity=0.123 Sum_probs=44.9
Q ss_pred hhhcccCCCCCceeEEEEEcCCCcHHHHHHHHhC---C-CCccccCCCHHHHHHHHHcCCccEEEEeec
Q 015945 99 IMELSSSPDDGTKVRVAYQGLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIE 163 (398)
Q Consensus 99 R~iis~s~~~q~~~kVa~lGp~Gs~s~~AA~~~f---g-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIE 163 (398)
.+++..........+++..| .|+.+|+++..++ | +.+.+++++-.++..++..|++|+++....
T Consensus 94 ~eli~~ak~~p~~~~~g~~g-~g~~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~~ 161 (274)
T PF03401_consen 94 EELIEYAKANPGKLTFGSSG-PGSSDHLAAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSPG 161 (274)
T ss_dssp HHHHHHHHCSCCC-EEEESS-TTSHHHHHHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEHH
T ss_pred HHHHHHHHhCCCCeEEEecC-CCchHHHHHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecHH
Confidence 44555555555667788766 5788887765443 3 567899999999999999999999987543
No 126
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=76.85 E-value=25 Score=39.22 Aligned_cols=69 Identities=12% Similarity=0.154 Sum_probs=50.6
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
...+.|.+...|++|.|.++.+.++..++|+..+.++..+. ..+...++++-. +-..+..++.
T Consensus 624 ~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~----------------~~~~~~~~ieV~-~~~~L~~i~~ 686 (702)
T PRK11092 624 EFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDG----------------RVYSAFIRLTAR-DRVHLANIMR 686 (702)
T ss_pred eeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCC----------------CEEEEEEEEEEC-CHHHHHHHHH
Confidence 45677888889999999999999999999999999875432 122333344332 3368888888
Q ss_pred HHHHhc
Q 015945 378 HLQEFA 383 (398)
Q Consensus 378 ~L~~~~ 383 (398)
.|+..-
T Consensus 687 ~Lr~i~ 692 (702)
T PRK11092 687 KIRVMP 692 (702)
T ss_pred HHhCCC
Confidence 887543
No 127
>PF00585 Thr_dehydrat_C: C-terminal regulatory domain of Threonine dehydratase; InterPro: IPR001721 Threonine dehydratases including Serine/threonine dehydratase (see IPR001926 from INTERPRO) contain a common C-terminal region that may have a regulatory role. Some members contain two copies of this region [].; GO: 0004794 L-threonine ammonia-lyase activity, 0009097 isoleucine biosynthetic process; PDB: 1TDJ_A 3IAU_A.
Probab=76.45 E-value=4.6 Score=33.00 Aligned_cols=69 Identities=16% Similarity=0.198 Sum_probs=43.5
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
..+..+.|++|++||+|.+.|+.+..++ |+|.++=|-..... . .-+|-++-. +....+.+++
T Consensus 8 ~~E~~~~v~~PE~pGal~~F~~~l~~~~-nITeF~YR~~~~~~--------------a--~vlvgi~v~-~~~~~~~l~~ 69 (91)
T PF00585_consen 8 GREALFAVEFPERPGALKRFLDALGPRN-NITEFHYRYSGDDF--------------A--RVLVGIEVP-DAEDLEELIE 69 (91)
T ss_dssp --EEEEEEE--BSTTHCHHHHHCCSSSE--EEEEEEE-TTTSC--------------S--EEEEEEE-S-STHHHHHHHH
T ss_pred CCEEEEEEECCCCccHHHHHHHHhCCCc-eEEEEEEcCCCCCe--------------e--eEEEEEEeC-CHHHHHHHHH
Confidence 3467788999999999999999987655 59999988765421 2 344455443 3345777888
Q ss_pred HHHHhcC
Q 015945 378 HLQEFAT 384 (398)
Q Consensus 378 ~L~~~~~ 384 (398)
.|++..-
T Consensus 70 ~L~~~gy 76 (91)
T PF00585_consen 70 RLKALGY 76 (91)
T ss_dssp HHTSSS-
T ss_pred HHHHcCC
Confidence 8876543
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=75.71 E-value=18 Score=40.19 Aligned_cols=68 Identities=13% Similarity=0.138 Sum_probs=50.0
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
..+.|.+...|++|.|.++.+.++..++|+..+.++-... ..+.+.++++-. +-..+..++..
T Consensus 609 f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~----------------~~~~~~~~ieV~-~~~~L~~ii~~ 671 (683)
T TIGR00691 609 FIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGK----------------REAILNITVEIK-NYKHLLKIMLK 671 (683)
T ss_pred eEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCC----------------CEEEEEEEEEEC-CHHHHHHHHHH
Confidence 4667788889999999999999999999999999864321 123344444432 34678888888
Q ss_pred HHHhc
Q 015945 379 LQEFA 383 (398)
Q Consensus 379 L~~~~ 383 (398)
|+..-
T Consensus 672 L~~i~ 676 (683)
T TIGR00691 672 IKTKN 676 (683)
T ss_pred HhCCC
Confidence 87553
No 129
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=75.11 E-value=9.4 Score=39.68 Aligned_cols=63 Identities=24% Similarity=0.296 Sum_probs=45.2
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccce-EEEEEeecCCCcHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDY-LFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y-~Ffvd~~g~~~d~~v~~al~ 377 (398)
..-.|++..+|+||.+.++++.++++|||+-.+..+... ++ +..||+++... + ++++
T Consensus 337 ~~~rlii~h~d~pG~ia~it~~l~~~~iNI~~m~~~~~~------------------~~A~~iie~D~~~~-~---~~~~ 394 (409)
T PRK11790 337 GGHRLLHIHENRPGVLAAINQIFAEQGINIAAQYLQTDG------------------EIGYVVIDVDADYA-E---EALD 394 (409)
T ss_pred CCceEEEEeCCCCCHHHHHHHHHHhcCCCHHHheeccCC------------------CEEEEEEEeCCCCc-H---HHHH
Confidence 345678888999999999999999999999877764322 33 33449988653 3 4566
Q ss_pred HHHHhc
Q 015945 378 HLQEFA 383 (398)
Q Consensus 378 ~L~~~~ 383 (398)
+|++.-
T Consensus 395 ~i~~i~ 400 (409)
T PRK11790 395 ALKAIP 400 (409)
T ss_pred HHHcCC
Confidence 666543
No 130
>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=75.08 E-value=14 Score=27.34 Aligned_cols=28 Identities=25% Similarity=0.392 Sum_probs=24.3
Q ss_pred EeCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 306 TLEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 306 ~~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
.+++.||.+.++++.+++.|||+.-|-.
T Consensus 8 ~~~~~~g~~~~i~~~L~~~~I~i~~i~~ 35 (75)
T cd04913 8 GVPDKPGVAAKIFGALAEANINVDMIVQ 35 (75)
T ss_pred CCCCCCcHHHHHHHHHHHcCCeEEEEEe
Confidence 4578899999999999999999986643
No 131
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=75.02 E-value=18 Score=40.18 Aligned_cols=70 Identities=17% Similarity=0.206 Sum_probs=54.0
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
...+.|.+...|++|.|.++++.++..++|++++.++...+ ..+.+.++++-+ +-..+..++.
T Consensus 625 ~f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~----------------~~~~~~~~i~v~-n~~~L~~i~~ 687 (701)
T COG0317 625 VYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKD----------------QFATMQFTIEVK-NLNHLGRVLA 687 (701)
T ss_pred ceEEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCC----------------ceEEEEEEEEEC-cHHHHHHHHH
Confidence 45677888889999999999999999999999999998733 235566666554 3467778888
Q ss_pred HHHHhcC
Q 015945 378 HLQEFAT 384 (398)
Q Consensus 378 ~L~~~~~ 384 (398)
.|+....
T Consensus 688 ~l~~~~~ 694 (701)
T COG0317 688 RLKQLPD 694 (701)
T ss_pred HHhcCCC
Confidence 8876543
No 132
>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=74.96 E-value=48 Score=29.35 Aligned_cols=49 Identities=20% Similarity=0.255 Sum_probs=37.9
Q ss_pred eeEEEEEcCCCcHHHHHHHHhCC-CCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 111 KVRVAYQGLPGAYSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 111 ~~kVa~lGp~Gs~s~~AA~~~fg-~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
..+|++. .|++........+. ..+++.+.|.++++++|.+|++|+.+++
T Consensus 110 ~~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~ 159 (225)
T PF00497_consen 110 GKRIGVV--RGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVD 159 (225)
T ss_dssp TSEEEEE--TTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEE
T ss_pred Ccccccc--cchhHHHHhhhhccchhhhcccccHHHHHHHHhcCCeeeeecc
Confidence 3688876 45555544444554 6778889999999999999999999886
No 133
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=73.65 E-value=10 Score=44.14 Aligned_cols=50 Identities=14% Similarity=0.160 Sum_probs=41.6
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
...+|++. .|+..+...+.+|++.+++.++|..+++++|.+|++|..+..
T Consensus 163 ~~~~i~~~--~g~~~~~~~~~~~p~~~i~~~~s~~~al~av~~G~~Da~i~~ 212 (1197)
T PRK09959 163 KPVNIARV--ANYPPDEVIHQSFPKATIISFTNLYQALASVSAGQNDYFIGS 212 (1197)
T ss_pred cCeEEEEe--CCCCCHHHHHHhCCCCEEEeCCCHHHHHHHHHcCCCCEEEcc
Confidence 34567775 466666667778999999999999999999999999998875
No 134
>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=73.46 E-value=56 Score=28.00 Aligned_cols=123 Identities=20% Similarity=0.121 Sum_probs=61.2
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCc--
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 207 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I-- 207 (398)
.|+++++... .+..++.+.+.+|++|+|+..-.....+.. ...|.+..+.++ .+-.|-+......+++++
T Consensus 26 ~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~ 98 (200)
T cd08411 26 AYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLE---EEPLFDEPFLLA----VPKDHPLAKRKSVTPEDLAG 98 (200)
T ss_pred HCCCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCCCCCce---EEEeeccceEEE----ecCCCCccccCccCHHHHcC
Confidence 3566655433 467889999999999999975432211110 111122222221 122222221111222222
Q ss_pred -cEEE-ecH-HHHHHHHHHHhhcCC---eEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 208 -KRVF-SHP-QALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 208 -~~V~-SHp-qal~QC~~fl~~~~~---~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
.-|. +.. ....+...|+.+.+. ....++|...+.+++..+ ...|+.+...++.
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 122344455555332 245677778888888865 3578888887764
No 135
>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=71.78 E-value=21 Score=40.57 Aligned_cols=51 Identities=12% Similarity=0.180 Sum_probs=41.4
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEe
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDF 363 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~ 363 (398)
.+.|.+-+..+|+||-|+++.+.|+++|||+......-.... ..-.|||..
T Consensus 777 ~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~---------------~~d~F~v~~ 827 (850)
T TIGR01693 777 RKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEK---------------AEDVFYVTD 827 (850)
T ss_pred CCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCcc---------------ceeEEEEEC
Confidence 457888899999999999999999999999997666654322 356899965
No 136
>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=71.57 E-value=1e+02 Score=29.95 Aligned_cols=147 Identities=18% Similarity=0.129 Sum_probs=80.8
Q ss_pred ceeEEEEE-cCCCcHHHHHHHHhCC----CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhh-hcC--C
Q 015945 110 TKVRVAYQ-GLPGAYSEAAARKAYP----KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLL-LRH--R 181 (398)
Q Consensus 110 ~~~kVa~l-Gp~Gs~s~~AA~~~fg----~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L-~~~--~ 181 (398)
+..||+++ ||....-+.+...+|. +++++.++++.+..+++.+|++|.+..- .. ..+... ... +
T Consensus 18 ~~l~vG~~~~~~~~~~~~~~~~~~~~~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~q-------~~-~~l~~~~~~~g~~ 89 (258)
T TIGR00363 18 LHIKVGVISGAEQQVAEVAAKVAKEKYGLDVELVEFNDYALPNEAVSKGDLDANAFQ-------HK-PYLDQDAKAKGYK 89 (258)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCEEEEEEeCCcHHHHHHHHcCCCCeEecC-------CH-HHHHHHHHhCCCc
Confidence 46899998 4444455566665553 4788999999999999999999987532 11 222222 223 4
Q ss_pred eEEEEEEEEeeeEeeecCCCCCccCcc---EEEec--HHHHHHHHHHHhhc-----------------------CCeEEe
Q 015945 182 LHIVGEVQLVVNHCLLGLPGVLKEELK---RVFSH--PQALAQCEMTLSNL-----------------------GIVRIS 233 (398)
Q Consensus 182 l~I~~Ei~l~I~h~Ll~~~g~~l~~I~---~V~SH--pqal~QC~~fl~~~-----------------------~~~~v~ 233 (398)
+.+++...+- ...+.+.+-.++++++ +|.-. |.-.++.-..|++. ++++++
T Consensus 90 lv~v~~~~~~-p~~~ys~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~ve 168 (258)
T TIGR00363 90 LVAVGNTFVY-PLAGYSKKIKNVNELQDGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITE 168 (258)
T ss_pred EEEEeeeEEe-cccccCcCCCCHHHcCCCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEE
Confidence 5555533221 1234444434667774 55432 33233333345542 245555
Q ss_pred cCCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCce
Q 015945 234 ADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDI 268 (398)
Q Consensus 234 ~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ygL~i 268 (398)
... ++.++.+.++ .-+ ||+....-+...||..
T Consensus 169 l~~-~~~~~al~~g-~vD-aa~v~~~~~~~agl~~ 200 (258)
T TIGR00363 169 LET-SQLPRALDDP-KVD-LAVINTTYAGQVGLNP 200 (258)
T ss_pred cCH-HHHHHHhhcc-ccc-EEEEChHHHHHcCCCc
Confidence 544 3344444432 233 5666555666677763
No 137
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=70.37 E-value=27 Score=34.56 Aligned_cols=33 Identities=9% Similarity=0.174 Sum_probs=28.4
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeee
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRP 335 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP 335 (398)
+.+.-+|+||-..++-+.|+++|+|+..+.+.=
T Consensus 9 itv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~ 41 (286)
T PRK06027 9 LTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFV 41 (286)
T ss_pred EEEECCCCCcHHHHHHHHHHHCCCCEEEceeEE
Confidence 444448999999999999999999999888765
No 138
>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=70.10 E-value=18 Score=34.06 Aligned_cols=55 Identities=16% Similarity=0.234 Sum_probs=42.7
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHH
Q 015945 301 TSIVFTLEEGPGMLFKALAVFALRDINLTKIE-SRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPR 371 (398)
Q Consensus 301 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IE-SRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~ 371 (398)
..+++.-.|+||.+.++-+.+.++|||+.... +|-.++ ++-.-.+.++....++-
T Consensus 149 ~~L~~~~~D~PG~Ig~vg~~Lg~~~iNIa~m~v~r~~~g----------------~~Ai~vl~vD~~v~~~v 204 (208)
T TIGR00719 149 PAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIG----------------NIALLTIEIDKNIDDHI 204 (208)
T ss_pred cEEEEEeCCCCChHHHHHHHHHhCCccEEEEEEEecCCC----------------CEEEEEEEeCCCCCHHH
Confidence 46788889999999999999999999998765 343222 35678889988776543
No 139
>PRK05092 PII uridylyl-transferase; Provisional
Probab=70.08 E-value=20 Score=41.25 Aligned_cols=53 Identities=17% Similarity=0.231 Sum_probs=40.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEE-EeecC
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYI-DFEAS 366 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffv-d~~g~ 366 (398)
..|.|.+..+|+||-|+++.++|+.+|||+..-...-... ...-.||| |-+|.
T Consensus 842 ~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~---------------~~~D~F~v~d~~g~ 895 (931)
T PRK05092 842 RFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGE---------------RAVDVFYVTDLFGL 895 (931)
T ss_pred CeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCC---------------EEEEEEEEeCCCCC
Confidence 3577788889999999999999999999999665553222 23568999 44554
No 140
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=69.62 E-value=60 Score=31.28 Aligned_cols=144 Identities=15% Similarity=0.101 Sum_probs=75.0
Q ss_pred CceeEEEEEcCCCc--HHHHH--HHHhCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeE
Q 015945 109 GTKVRVAYQGLPGA--YSEAA--ARKAYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLH 183 (398)
Q Consensus 109 q~~~kVa~lGp~Gs--~s~~A--A~~~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~ 183 (398)
.+..+|++...-+. +.... .++.++++++... .+.+++++.+.+|++|+|+++......+... ..|.+.++.
T Consensus 90 ~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~ 166 (305)
T PRK11151 90 SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIE---VPLFDEPML 166 (305)
T ss_pred CceEEEEecchhHHHHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCeEE---EEeccCcEE
Confidence 35677777543332 12221 1234566665443 3578999999999999999876544333211 122222333
Q ss_pred EEEEEEEeeeEeeecCCCCCccCcc--EEEecHHH---HHHHHHHHhhcC--C-eEEecCCHHHHHHHHHhcCCCCeEEE
Q 015945 184 IVGEVQLVVNHCLLGLPGVLKEELK--RVFSHPQA---LAQCEMTLSNLG--I-VRISADDTAGAAQMVASIGERDTGAV 255 (398)
Q Consensus 184 I~~Ei~l~I~h~Ll~~~g~~l~~I~--~V~SHpqa---l~QC~~fl~~~~--~-~~v~~~STA~Aa~~v~~~~~~~~AAI 255 (398)
++ .+-+|-+...+..+++++. ..++++.. ..+...|+...+ . ....++|...++++++.+ ...+|
T Consensus 167 ~~----~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~i 239 (305)
T PRK11151 167 LA----VYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAG---SGITL 239 (305)
T ss_pred EE----ecCCCCcccCCccCHHHhcCCCeEeecCCccHHHHHHHHHHHCCCCCCceEEeccHHHHHHHHHcC---CCEEE
Confidence 32 2333434332222333322 12222221 234445554432 2 235678888888888764 45788
Q ss_pred cCHHhHH
Q 015945 256 ASAQAAE 262 (398)
Q Consensus 256 ~s~~aA~ 262 (398)
.+...+.
T Consensus 240 lp~~~~~ 246 (305)
T PRK11151 240 LPALAVP 246 (305)
T ss_pred eeHHhhh
Confidence 8887664
No 141
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=69.32 E-value=24 Score=39.68 Aligned_cols=68 Identities=19% Similarity=0.261 Sum_probs=48.8
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 378 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~ 378 (398)
..+.|.+...|++|.|.++.+.++..++|+..+.++..++. ....-.|-|++. +-..+..++..
T Consensus 665 ~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~-------------~~~~~~~~ieV~---~~~~L~~l~~~ 728 (743)
T PRK10872 665 YSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQ-------------QLATIDMTIEIY---NLQVLGRVLGK 728 (743)
T ss_pred eEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCC-------------CEEEEEEEEEEC---CHHHHHHHHHH
Confidence 35567778889999999999999999999999998765421 012233444443 33678888888
Q ss_pred HHHh
Q 015945 379 LQEF 382 (398)
Q Consensus 379 L~~~ 382 (398)
|+..
T Consensus 729 L~~i 732 (743)
T PRK10872 729 LNQV 732 (743)
T ss_pred HhcC
Confidence 8754
No 142
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=68.74 E-value=6 Score=34.38 Aligned_cols=29 Identities=28% Similarity=0.332 Sum_probs=24.4
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeee
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKI 331 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~I 331 (398)
|.+-+.|+||-|..+++.++.+|||+.-+
T Consensus 6 ISvFlENk~GRL~~~~~~L~eagINiRA~ 34 (142)
T COG4747 6 ISVFLENKPGRLASVANKLKEAGINIRAF 34 (142)
T ss_pred EEEEecCCcchHHHHHHHHHHcCCceEEE
Confidence 34446799999999999999999998643
No 143
>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=68.68 E-value=17 Score=26.51 Aligned_cols=51 Identities=18% Similarity=0.234 Sum_probs=37.2
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHH
Q 015945 308 EEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 379 (398)
Q Consensus 308 ~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L 379 (398)
.+.+|...++++.|+++|||+-.|.+ +. ....|+++-.-. +..+++++++|
T Consensus 11 ~~~~~~~~~if~~l~~~~i~v~~i~t----~~---------------~~is~~v~~~~~--~~~~~~l~~~l 61 (62)
T cd04890 11 NGEVGFLRKIFEILEKHGISVDLIPT----SE---------------NSVTLYLDDSLL--PKKLKRLLAEL 61 (62)
T ss_pred CcccCHHHHHHHHHHHcCCeEEEEec----CC---------------CEEEEEEehhhh--hHHHHHHHHhh
Confidence 46799999999999999999999965 11 258888876321 24566666554
No 144
>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=67.82 E-value=27 Score=27.78 Aligned_cols=58 Identities=14% Similarity=0.192 Sum_probs=39.7
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCC----CcHHHHHHHHHHHHh
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASM----ADPRAQFALGHLQEF 382 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~----~d~~v~~al~~L~~~ 382 (398)
.++.||.+.++++.|+++|||+-.|-+ + . ..+.|-|+-.... -+..+++++.+|++.
T Consensus 11 ~~~~~g~~a~IF~~La~~~InVDmI~q-s-~-----------------~sISftV~~sd~~~~~~~~~~l~~~~~~~~~~ 71 (78)
T cd04933 11 MLGQYGFLAKVFSIFETLGISVDVVAT-S-E-----------------VSISLTLDPSKLWSRELIQQELDHVVEELEKD 71 (78)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe-c-C-----------------CEEEEEEEhhhhhhhhhHHHHHHHHHHHHHHc
Confidence 357899999999999999999999965 1 1 2577777653210 013455666666655
Q ss_pred c
Q 015945 383 A 383 (398)
Q Consensus 383 ~ 383 (398)
+
T Consensus 72 ~ 72 (78)
T cd04933 72 A 72 (78)
T ss_pred C
Confidence 4
No 145
>PRK05007 PII uridylyl-transferase; Provisional
Probab=67.16 E-value=16 Score=41.80 Aligned_cols=36 Identities=22% Similarity=0.365 Sum_probs=30.9
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeee
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLT--KIES 333 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt--~IES 333 (398)
.+.|.|=+..+|+||-|+++.++|.+.||++. ||-+
T Consensus 806 ~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T 843 (884)
T PRK05007 806 DRRSYMELIALDQPGLLARVGKIFADLGISLHGARITT 843 (884)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEec
Confidence 45677778889999999999999999999998 5544
No 146
>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=66.78 E-value=85 Score=27.14 Aligned_cols=120 Identities=13% Similarity=0.037 Sum_probs=59.2
Q ss_pred CCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCC-CCCccCc--
Q 015945 132 YPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLP-GVLKEEL-- 207 (398)
Q Consensus 132 fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~-g~~l~~I-- 207 (398)
++++++... .+..++.+.+.+|++|+|+........|.... .|.+..+.+ ..+-+|-|.... ..+++++
T Consensus 27 ~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~l~~~~~~~----v~~~~hpl~~~~~~i~~~dL~~ 99 (203)
T cd08445 27 APDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRRI---VLREEPLVV----ALPAGHPLAQEKAPLTLAQLAD 99 (203)
T ss_pred CCCeEEEEEeCChHHHHHHHHcCCCcEEEecCCCCCCCceeE---EEEeccEEE----EeeCCCCCccCCCCcCHHHhcC
Confidence 455554332 35789999999999999996432111221110 111112222 123334343322 2233332
Q ss_pred -cEEEecHH---H-HHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015945 208 -KRVFSHPQ---A-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAA 261 (398)
Q Consensus 208 -~~V~SHpq---a-l~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA 261 (398)
.-|.-... . ..+..+|+.+.+. . ...++|...+.++++.+ ...++.+...+
T Consensus 100 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 158 (203)
T cd08445 100 EPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAG---EGVTLVPASVQ 158 (203)
T ss_pred CCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcC---CCeEEehHHhh
Confidence 23331111 1 2344556665432 3 34567777777888765 34777777644
No 147
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=65.28 E-value=1.4e+02 Score=29.13 Aligned_cols=107 Identities=18% Similarity=0.164 Sum_probs=61.4
Q ss_pred ceeEEEEE-cCCCcHHHHHHHHhC---C-CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHH-hhh--cCC
Q 015945 110 TKVRVAYQ-GLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD-LLL--RHR 181 (398)
Q Consensus 110 ~~~kVa~l-Gp~Gs~s~~AA~~~f---g-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld-~L~--~~~ 181 (398)
+..+|++. ++.....+.+...++ | +++++.++++.+..+++.+|++|.... ..+ ..+. .+. ..+
T Consensus 31 ~~I~IG~~~~~~~~~~~~~~~~l~~~~G~~Vel~~f~~~~~~~~ALa~GdID~~~~-----qh~---~~l~~~~~~~g~~ 102 (271)
T PRK11063 31 NHIKVGVIVGAEQQVAEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAF-----QHK---PYLDQQIKDRGYK 102 (271)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHcCCcceecc-----cCH---HHHHHHHHHcCCc
Confidence 35899997 454444454444333 4 688999999999999999999998751 111 1222 122 235
Q ss_pred eEEEEEEEE-eeeEeeecCCCCCccCcc---EEEec--HHHHHHHHHHHhh
Q 015945 182 LHIVGEVQL-VVNHCLLGLPGVLKEELK---RVFSH--PQALAQCEMTLSN 226 (398)
Q Consensus 182 l~I~~Ei~l-~I~h~Ll~~~g~~l~~I~---~V~SH--pqal~QC~~fl~~ 226 (398)
+.+++-... |+ .+.+..=.+++|++ +|... |.-.+.+-.+|++
T Consensus 103 l~~~~~~~vvp~--~~ys~~i~si~DL~~Gk~IAip~d~~n~~r~L~lL~~ 151 (271)
T PRK11063 103 LVAVGNTFVYPI--AGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQK 151 (271)
T ss_pred EEEEeEEEEEEe--eccccCCCCHHHhcCCCEEEecCCCccHHHHHHHHHH
Confidence 666655433 33 22232223456654 56544 5445555555655
No 148
>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=65.00 E-value=37 Score=30.12 Aligned_cols=124 Identities=16% Similarity=0.081 Sum_probs=70.9
Q ss_pred HHHHHHHHhCC-CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCC
Q 015945 123 YSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG 201 (398)
Q Consensus 123 ~s~~AA~~~fg-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g 201 (398)
+-.+++++. | +.+++.. +|.++++.+.+|++|+++-++..+.+ . ...+.... -+....+.++.+++
T Consensus 28 l~~~i~~~~-g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~--------r--~~~~~~s~-p~~~~~~~~~~~~~ 94 (225)
T PF00497_consen 28 LLRAIAKRL-GIKIEFVPM-PWSRLLEMLENGKADIIIGGLSITPE--------R--AKKFDFSD-PYYSSPYVLVVRKG 94 (225)
T ss_dssp HHHHHHHHH-TCEEEEEEE-EGGGHHHHHHTTSSSEEESSEB-BHH--------H--HTTEEEES-ESEEEEEEEEEETT
T ss_pred HHHHHHhhc-ccccceeec-cccccccccccccccccccccccccc--------c--cccccccc-cccchhheeeeccc
Confidence 334444433 4 5677777 99999999999999998756553322 1 11122221 22333455555543
Q ss_pred C-----C---ccCc--cEEEecHHHHHHHHHHHhh--c-CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 202 V-----L---KEEL--KRVFSHPQALAQCEMTLSN--L-GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 202 ~-----~---l~~I--~~V~SHpqal~QC~~fl~~--~-~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
. . ++++ ++|..-.-.. -.++|.+ . +++++.+.|..++.+++..+. ..|+|+....+..
T Consensus 95 ~~~~~~~~~~~~dl~~~~i~~~~g~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~--~d~~i~~~~~~~~ 165 (225)
T PF00497_consen 95 DAPPIKTIKSLDDLKGKRIGVVRGSS--YADYLKQQYPSNINIVEVDSPEEALEALLSGR--IDAFIVDESTAEY 165 (225)
T ss_dssp STCSTSSHSSGGGGTTSEEEEETTSH--HHHHHHHHTHHTSEEEEESSHHHHHHHHHTTS--SSEEEEEHHHHHH
T ss_pred cccccccccchhhhcCcccccccchh--HHHHhhhhccchhhhcccccHHHHHHHHhcCC--eeeeeccchhhhh
Confidence 1 1 2244 2343333211 1223333 1 678888999999999998763 4478877776654
No 149
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=64.09 E-value=16 Score=39.22 Aligned_cols=105 Identities=15% Similarity=0.233 Sum_probs=66.8
Q ss_pred CHHhHHHcCCceeeccc--ccCCCCceEEEEEecCCCC-----CCCC---------------CCceEEEEEEeCCCcchH
Q 015945 257 SAQAAEIYGLDILAEKI--QDDDDNVTRFLILAREPII-----AGTD---------------RPYKTSIVFTLEEGPGML 314 (398)
Q Consensus 257 s~~aA~~ygL~il~~~I--~D~~~N~TRF~vi~~~~~~-----~~~~---------------~~~ktsi~f~~~~~pGaL 314 (398)
+...|+..|+++-.... .+.-.|.-++.+-+..... .-.. ..+-.++++...|+||.+
T Consensus 387 A~~iA~e~GI~~~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~ggg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I 466 (526)
T PRK13581 387 APLLAKERGIEVEESKSEESPDYSNLITVTVTTDDGERSVAGTVFGDGEPRIVEIDGYRVDAKPEGHMLIIRNRDRPGVI 466 (526)
T ss_pred HHHHHHHcCCEEEEEEecCCCCCCCEEEEEEEeCCeEEEEEEEEecCCceEEEEECCEEEEeeCCceEEEEEeCCcCChh
Confidence 34568888888755433 3335676677665433110 0000 112456777778999999
Q ss_pred HHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 315 FKALAVFALRDINLTKIE-SRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 315 ~~~L~~F~~~~INLt~IE-SRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
.++.+.|.+++||+.... +|-.++ .+....++++....+ +++++|++
T Consensus 467 ~~v~~~L~~~~iNIa~m~~~r~~~g----------------~~al~~i~~D~~v~~----~~l~~i~~ 514 (526)
T PRK13581 467 GKVGTLLGEAGINIAGMQLGRREAG----------------GEALMVLSVDDPVPE----EVLEELRA 514 (526)
T ss_pred HHHHHHHhhcCCCchhcEeccCCCC----------------CeEEEEEECCCCCCH----HHHHHHhc
Confidence 999999999999998775 453222 467888999887653 34555553
No 150
>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=64.09 E-value=95 Score=26.74 Aligned_cols=122 Identities=10% Similarity=-0.023 Sum_probs=59.7
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCc--
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 207 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I-- 207 (398)
.|+++++.- ..+..++.+.+.+|++|+|++.-.....|... ..|.+..+. +..+-.|-+......+++++
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----lv~~~~hpl~~~~~~~~~~L~~ 97 (197)
T cd08452 25 KFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHI---ETVQSSPCV----LALPKQHPLASKEEITIEDLRD 97 (197)
T ss_pred HCCCcEEEEEecChHHHHHHHHCCCccEEEeeCCCCCCCeeE---EEeeeccEE----EEEeCCCccccCCCCCHHHhcC
Confidence 456665433 34677899999999999999853221111111 111111221 12233444432222222222
Q ss_pred -cEEEecHH----HHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 208 -KRVFSHPQ----ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 208 -~~V~SHpq----al~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
.-|...+. ...+..+|+.+.+. . ...++|...+.++++.+ ...|+.+...+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 157 (197)
T cd08452 98 EPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAG---IGVTFVPSSAKK 157 (197)
T ss_pred CCEEeccCCcchhHHHHHHHHHHHcCCCccceeecccHHHHHHHHHcC---CCEEEchHHHhh
Confidence 23332111 12334456665432 2 23566777777777764 346777776543
No 151
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=63.71 E-value=17 Score=33.69 Aligned_cols=50 Identities=20% Similarity=0.199 Sum_probs=38.5
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
...+|++. .|+.......+.++....+..++..+++.+|.+|++|+.+.+
T Consensus 125 ~g~~Igv~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~grvDa~i~~ 174 (243)
T PRK15007 125 KGKKVGVQ--NGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGD 174 (243)
T ss_pred CCCeEEEe--cCcHHHHHHHHhCCCCeEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 34688885 565555444445667778888999999999999999999875
No 152
>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=62.86 E-value=40 Score=33.30 Aligned_cols=34 Identities=9% Similarity=0.204 Sum_probs=29.7
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 336 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~ 336 (398)
|.+.-+|+||-.+++-+.++++|+|++.+...=.
T Consensus 3 itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~ 36 (280)
T TIGR00655 3 LLVSCPDQKGLVAAISTFIAKHGANIISNDQHTD 36 (280)
T ss_pred EEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEc
Confidence 4566799999999999999999999999887653
No 153
>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=62.69 E-value=96 Score=26.31 Aligned_cols=122 Identities=15% Similarity=0.100 Sum_probs=59.9
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccc--cccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCc
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENS--VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 207 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS--~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I 207 (398)
.|+++++.. ..+..++.+.+.+|++|+|++..... ..|... ..|.+..+.++ .+-+|-+...+..+++++
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~---~~l~~~~~~~~----~~~~~~l~~~~~~~~~dL 97 (201)
T cd08435 25 RHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLAS---EELADEPLVVV----ARPGHPLARRARLTLADL 97 (201)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCCCCcEE---EEcccCcEEEE----EeCCCcCcccCCcCHHHH
Confidence 356655433 34678899999999999999753322 122111 11222233222 223333332222233332
Q ss_pred c---EEEe-cHH-HHHHHHHHHhhcCC---e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 208 K---RVFS-HPQ-ALAQCEMTLSNLGI---V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 208 ~---~V~S-Hpq-al~QC~~fl~~~~~---~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
. -|.. ... -......|+...+. . ...+++...+.+++..+ ...|+.+...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08435 98 ADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARS---DMLAVLPRSVAE 158 (201)
T ss_pred hcCCEEecCCCCcHHHHHHHHHHHcCCCCCCceEEEccHHHHHHHHhcC---CeEEEeEHHHhh
Confidence 2 2221 111 11234455554332 2 23456666666777764 357888887765
No 154
>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=61.49 E-value=50 Score=25.66 Aligned_cols=35 Identities=14% Similarity=0.268 Sum_probs=28.7
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 337 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~ 337 (398)
|++..+|+||-+.++-++|+.+|+|+..=....++
T Consensus 4 I~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~ 38 (68)
T cd04928 4 ITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTD 38 (68)
T ss_pred EEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcC
Confidence 56677899999999999999999999965544443
No 155
>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=61.26 E-value=22 Score=30.76 Aligned_cols=49 Identities=29% Similarity=0.337 Sum_probs=37.4
Q ss_pred eeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 111 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 111 ~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
..+|++. .|+..+......++...+..+.+.+++++.|.+|++|++++.
T Consensus 105 g~~i~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 153 (218)
T cd00134 105 GKKVAVQ--KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVD 153 (218)
T ss_pred CCEEEEE--cCchHHHHHHHhCCcccEEEeCCHHHHHHHHHcCCccEEEec
Confidence 4678876 454444445556666677889999999999999999998876
No 156
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=60.27 E-value=20 Score=33.13 Aligned_cols=49 Identities=16% Similarity=0.193 Sum_probs=38.4
Q ss_pred eeEEEEEcCCCcHHHHHHHHhCC-CCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 111 KVRVAYQGLPGAYSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 111 ~~kVa~lGp~Gs~s~~AA~~~fg-~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
..+|++. .|+........++. +.++..+.+.++++++|.+|++|+.++.
T Consensus 131 g~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~ 180 (250)
T TIGR01096 131 GKTVGVQ--SGTTHEQYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTD 180 (250)
T ss_pred CCEEEEe--cCchHHHHHHHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 4578874 56655555555666 6778889999999999999999999884
No 157
>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=58.85 E-value=1.1e+02 Score=25.70 Aligned_cols=122 Identities=21% Similarity=0.080 Sum_probs=58.4
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCc--
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 207 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I-- 207 (398)
.++++++.- ..+..++.+.+.+|++|+|+..-+....|... ..|.+.++.++ .+-+|-+...+..+++++
T Consensus 25 ~~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~~----~~~~~pl~~~~~~~~~~l~~ 97 (197)
T cd08440 25 RHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEF---EPLLRDPFVLV----CPKDHPLARRRSVTWAELAG 97 (197)
T ss_pred hCCCcEEEEEeCChHHHHHHHHcCCccEEEEeCCCCCCCeeE---EEeecccEEEE----ecCCCCcccCCccCHHHHcc
Confidence 356655433 23567899999999999999853321111100 01111122211 222232222212222332
Q ss_pred -cEE-EecHHH-HHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 208 -KRV-FSHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 208 -~~V-~SHpqa-l~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
.-| +++... .....+|+.+.+. + ...++|...+.+++..+ ...|+.+...+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (197)
T cd08440 98 YPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAG---LGVAVLPALALP 155 (197)
T ss_pred CCEEecCCCccHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEcchhHHH
Confidence 222 222211 1233445555332 2 34567777777777764 457788876654
No 158
>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=58.77 E-value=1.1e+02 Score=26.47 Aligned_cols=140 Identities=10% Similarity=-0.019 Sum_probs=69.0
Q ss_pred eEEEEEcCCCcH--HHHHH--HHhCCCCccc-cCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEE
Q 015945 112 VRVAYQGLPGAY--SEAAA--RKAYPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVG 186 (398)
Q Consensus 112 ~kVa~lGp~Gs~--s~~AA--~~~fg~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~ 186 (398)
.+|++...-+.+ ....+ ++.++++++. ...+..++.+.+.+|++|+|++.-.....|.. ...+.+.++.+
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~~~~~~---~~~l~~~~~~l-- 77 (198)
T cd08486 3 LSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIE---IVNIAQEDLYL-- 77 (198)
T ss_pred EEEEEechhhHHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCCCCceE---EEEEeeccEEE--
Confidence 567766444332 11111 2235665543 33577899999999999999974321111110 00111222221
Q ss_pred EEEEeeeEeeecCCCCCccCc---cEEEecH----HHHHHHHHHHhhcC--Ce-EEecCCHHHHHHHHHhcCCCCeEEEc
Q 015945 187 EVQLVVNHCLLGLPGVLKEEL---KRVFSHP----QALAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDTGAVA 256 (398)
Q Consensus 187 Ei~l~I~h~Ll~~~g~~l~~I---~~V~SHp----qal~QC~~fl~~~~--~~-~v~~~STA~Aa~~v~~~~~~~~AAI~ 256 (398)
.++-+|-+......+++++ .-|.-.+ .-..+..+++.+.+ .+ ...+++......+++.+ ...+|.
T Consensus 78 --v~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~l 152 (198)
T cd08486 78 --AVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG---AASSIV 152 (198)
T ss_pred --EecCCCccccCCcccHHHHcCCCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---ceEEEc
Confidence 2233444433223334433 3332111 23456667777644 23 33566666666677654 457777
Q ss_pred CHHhH
Q 015945 257 SAQAA 261 (398)
Q Consensus 257 s~~aA 261 (398)
+..++
T Consensus 153 p~~~~ 157 (198)
T cd08486 153 PASVA 157 (198)
T ss_pred chhhc
Confidence 76543
No 159
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=58.75 E-value=27 Score=34.19 Aligned_cols=73 Identities=19% Similarity=0.259 Sum_probs=52.9
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEE--EEEeecCCCcHHHHHHH
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLF--YIDFEASMADPRAQFAL 376 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~F--fvd~~g~~~d~~v~~al 376 (398)
.+-.|-+-+.|+||.|.++=++|+.+|.|+-.+----...+ -.| -|=+.| .|.-++++.
T Consensus 76 krHvinclVqnEpGvlsRisGvlAaRGfNIdSLvVc~tevk-----------------~LsrmTIVl~G--td~VveQa~ 136 (309)
T KOG2663|consen 76 KRHVINCLVQNEPGVLSRISGVLAARGFNIDSLVVCLTEVK-----------------ALSRMTIVLQG--TDGVVEQAR 136 (309)
T ss_pred cceeEEEEecCCchHHHHHHHHHHhccCCchheeeechhhh-----------------hhhhceEEEec--cHHHHHHHH
Confidence 35566666789999999999999999999765554433322 233 455566 578889999
Q ss_pred HHHHHhcCceEEEc
Q 015945 377 GHLQEFATFLRVLG 390 (398)
Q Consensus 377 ~~L~~~~~~vkiLG 390 (398)
++|++...-++++.
T Consensus 137 rQiedlVnV~aVlD 150 (309)
T KOG2663|consen 137 RQIEDLVNVYAVLD 150 (309)
T ss_pred HHHHHhhhhheeee
Confidence 99998877666653
No 160
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=58.41 E-value=1.6e+02 Score=27.61 Aligned_cols=145 Identities=12% Similarity=0.049 Sum_probs=77.9
Q ss_pred ceeEEEEEcCCCcHHHHHHH--HhC---C-CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeE
Q 015945 110 TKVRVAYQGLPGAYSEAAAR--KAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLH 183 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~--~~f---g-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~ 183 (398)
...+|+|+...+.+.-..|. .+| | ++++....+..++.+++.+|++|++.+ ......+.-... .-...++.
T Consensus 6 ~~l~ig~~~~~~~~p~~~a~~~g~f~~~G~~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~--~~~~~~~~ 82 (252)
T PF13379_consen 6 TTLRIGYLPGPDYAPLYVAQEKGLFEKEGLDVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGA--GGPDVDIV 82 (252)
T ss_dssp SEEEEEETSSGGGHHHHHHHHTTHHHHTTSCEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTT--TT----EE
T ss_pred cEEEEEeecchHHHHHHHHHHcChHHHcCCEEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCC--CCcccceE
Confidence 56789997544433333332 244 2 478899999999999999999999999 442221110000 00011344
Q ss_pred EEEEEEEeeeEeeecCC------C-CCccCc---------cEEEe-cHH--HHHHHHHHHhhc------CCeEEecCCHH
Q 015945 184 IVGEVQLVVNHCLLGLP------G-VLKEEL---------KRVFS-HPQ--ALAQCEMTLSNL------GIVRISADDTA 238 (398)
Q Consensus 184 I~~Ei~l~I~h~Ll~~~------g-~~l~~I---------~~V~S-Hpq--al~QC~~fl~~~------~~~~v~~~STA 238 (398)
+.+-...-- .+++.+. + .+++|+ ++|.. ++- ..-..+.+|++. .++++.+.. .
T Consensus 83 ~~~~~~~~g-~~lvv~~~~~~~~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~ 160 (252)
T PF13379_consen 83 VLAGLSQNG-NALVVRNDLKDASDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-P 160 (252)
T ss_dssp EEEECSBSS-EEEEECGGGTTCSTTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-H
T ss_pred EeeccCCCc-eEEEEcCccccCCCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-H
Confidence 443322221 3444442 2 244555 46665 553 334567888873 245666666 7
Q ss_pred HHHHHHHhcCCCCeEEEcCHHh
Q 015945 239 GAAQMVASIGERDTGAVASAQA 260 (398)
Q Consensus 239 ~Aa~~v~~~~~~~~AAI~s~~a 260 (398)
++.+.+..+ .-+.+++..+.+
T Consensus 161 ~~~~al~~g-~iDa~~~~eP~~ 181 (252)
T PF13379_consen 161 EMVAALRAG-EIDAAVLWEPFA 181 (252)
T ss_dssp HHHHHHHTT-S-SEEEEETTHH
T ss_pred HHHHHHhCC-CcCEEEecCCHH
Confidence 777777765 345555555543
No 161
>PRK09034 aspartate kinase; Reviewed
Probab=58.01 E-value=2e+02 Score=30.32 Aligned_cols=127 Identities=15% Similarity=0.091 Sum_probs=75.1
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecccccCCCCceEEEEEecCCCCC-C-----CCCC
Q 015945 228 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPIIA-G-----TDRP 298 (398)
Q Consensus 228 ~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a---A~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~-~-----~~~~ 298 (398)
+++.+..-|-.+|.+++..+ |-+-.+.| |..++++|.-.|..+....-|..- ....... . ....
T Consensus 234 ~A~~l~~lsy~Ea~ela~~G-----akvlhp~ai~~a~~~~Ipi~v~~~~~p~~~GT~I~--~~~~~~~~~~Vk~It~~~ 306 (454)
T PRK09034 234 NPKSIKEITYREMRELSYAG-----FSVFHDEALIPAYRGGIPINIKNTNNPEDPGTLIV--PDRDNKNKNPITGIAGDK 306 (454)
T ss_pred CCeECCccCHHHHHHHHhCC-----cccCCHHHHHHHHHcCCCEEEEcCCCCCCCccEEE--eccccCccccceEEEecC
Confidence 56677778888999986532 44444444 456899999998876554555542 2211000 0 0012
Q ss_pred ceEEEEEE---eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHH
Q 015945 299 YKTSIVFT---LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFA 375 (398)
Q Consensus 299 ~ktsi~f~---~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~a 375 (398)
+-+.|.+. ..+.+|.+.++++.|+++|||+-.| ++.. ....|+|+=. ..+......+
T Consensus 307 ~i~~Itv~~~~~~~~~g~~a~if~~la~~~I~Vd~i---~ss~----------------~sis~~v~~~-~~~~a~~~~l 366 (454)
T PRK09034 307 GFTSIYISKYLMNREVGFGRKVLQILEDHGISYEHM---PSGI----------------DDLSIIIRER-QLTPKKEDEI 366 (454)
T ss_pred CEEEEEEccCCCCCCccHHHHHHHHHHHcCCeEEEE---cCCC----------------cEEEEEEeHH-HhhHHHHHHH
Confidence 22333232 3457899999999999999999988 2211 3577888742 2221122556
Q ss_pred HHHHHH
Q 015945 376 LGHLQE 381 (398)
Q Consensus 376 l~~L~~ 381 (398)
+++|+.
T Consensus 367 ~~el~~ 372 (454)
T PRK09034 367 LAEIKQ 372 (454)
T ss_pred HHHHHH
Confidence 666653
No 162
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=57.45 E-value=36 Score=33.18 Aligned_cols=122 Identities=14% Similarity=0.012 Sum_probs=65.8
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCccE
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR 209 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~~ 209 (398)
.++++.+... .+..++++.+.+|++|+|+++-+....+.... .|.+..+.++ .+..|-+. ....+++++..
T Consensus 137 ~~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~l~~~---~l~~~~~~lv----~~~~hpl~-~~~~~~~~L~~ 208 (314)
T PRK09508 137 IAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFTSV---PLFKDELVLV----ASKNHPRI-KGPITEEQLYN 208 (314)
T ss_pred hCCCcEEEEEeCcchhHHHHHhcCCccEEEecCCCCcccccee---eeecCceEEE----EcCCCCcc-CCCCCHHHHhh
Confidence 3556554332 34678899999999999999754322221111 1222233222 23344443 22233444431
Q ss_pred ----EEecHHHHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 210 ----VFSHPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 210 ----V~SHpqal~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
+++++....+...|+.+.+. . ...++|.....++|+.+ ...++.+...++.
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 266 (314)
T PRK09508 209 EQHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQT---HLVAIAPRWLAEE 266 (314)
T ss_pred CCCEEecCCCCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhC---ChHHHHHHHHHHH
Confidence 23333333344667766433 2 34677777788888764 3477888877754
No 163
>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=57.18 E-value=1.2e+02 Score=25.68 Aligned_cols=122 Identities=15% Similarity=0.041 Sum_probs=60.5
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCcc---C
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKE---E 206 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~---~ 206 (398)
.++++++.. ..+..++++.+.+|++|+|++.-+....|... ..|.+..+.+ ..+-.|-|...+..+++ +
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~---~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08412 25 AYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAF---EPLARLPPYV----WLPADHPLAGKDEVSLADLAA 97 (198)
T ss_pred HCCCcEEEEEECCHHHHHHHHHcCCCcEEEEcCCCCCcccce---eeeeccceEE----EecCCCCCCCCCcCCHHHHcC
Confidence 456555432 34678899999999999999854322222111 1111112111 12233434322222222 2
Q ss_pred ccEEE-ecHHHHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 207 LKRVF-SHPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 207 I~~V~-SHpqal~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
..-|. .......+-.+|+.+.+. . ...++|...+.+++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (198)
T cd08412 98 EPLILLDLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANG---LGYSLLNDRPYR 154 (198)
T ss_pred CcEEecCchhHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CCEEEeeccccc
Confidence 33333 222222333455555433 2 33567777777777764 347788776654
No 164
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=56.86 E-value=31 Score=39.42 Aligned_cols=32 Identities=22% Similarity=0.294 Sum_probs=29.0
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLT 329 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt 329 (398)
.+.|.|=+..+|+||-|+++-++|.+.|+++.
T Consensus 781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~ 812 (854)
T PRK01759 781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLL 812 (854)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEE
Confidence 45677888899999999999999999999987
No 165
>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=56.65 E-value=50 Score=26.30 Aligned_cols=57 Identities=19% Similarity=0.203 Sum_probs=40.7
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhcC
Q 015945 308 EEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFAT 384 (398)
Q Consensus 308 ~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~ 384 (398)
....|-+.++|++|.++||+.-++ |+.- ......|+=.. ..++..++++++|++.+.
T Consensus 12 n~evGF~rk~L~I~E~~~is~Eh~---PSGI----------------D~~Siii~~~~-~~~~~~~~i~~~i~~~~~ 68 (76)
T cd04911 12 NREVGFGRKLLSILEDNGISYEHM---PSGI----------------DDISIIIRDNQ-LTDEKEQKILAEIKEELH 68 (76)
T ss_pred cchhcHHHHHHHHHHHcCCCEeee---cCCC----------------ccEEEEEEccc-cchhhHHHHHHHHHHhcC
Confidence 457899999999999999987765 6543 23455554332 334488899999988654
No 166
>PRK11260 cystine transporter subunit; Provisional
Probab=56.18 E-value=24 Score=33.52 Aligned_cols=49 Identities=12% Similarity=0.116 Sum_probs=38.2
Q ss_pred eeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 111 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 111 ~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
..+|++ ..|+......+..+...++..+++..+++++|.+|++|+.+.+
T Consensus 149 g~~Igv--~~G~~~~~~l~~~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d 197 (266)
T PRK11260 149 GKKVGV--GLGTNYEQWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVD 197 (266)
T ss_pred CCEEEE--ecCCcHHHHHHHhCCCCceEecCCHHHHHHHHHcCCCCEEEec
Confidence 357777 4666555555556767778889999999999999999999885
No 167
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=55.23 E-value=8.4 Score=34.61 Aligned_cols=62 Identities=18% Similarity=0.277 Sum_probs=39.7
Q ss_pred HHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHH--HHH--hcCceEEEc
Q 015945 315 FKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH--LQE--FATFLRVLG 390 (398)
Q Consensus 315 ~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~--L~~--~~~~vkiLG 390 (398)
.+.+++.++|||.++|. +|+.+... |.++ |..-.+++.+++++++. ... .-..|..||
T Consensus 58 ~R~~s~lK~hGI~~~H~-aRqit~~D--------------F~~F---DYI~~MDesN~~dL~~~a~~~~~~~kakV~Llg 119 (159)
T KOG3217|consen 58 PRTLSILKKHGIKIDHL-ARQITTSD--------------FREF---DYILAMDESNLRDLLRKASNQPKGSKAKVLLLG 119 (159)
T ss_pred hHHHHHHHHcCCcchhh-cccccHhH--------------hhhc---ceeEEecHHHHHHHHHHhccCCCCcceEEEEee
Confidence 58899999999997776 67776531 2221 33334677777777663 221 223499999
Q ss_pred cccC
Q 015945 391 CYPM 394 (398)
Q Consensus 391 sYp~ 394 (398)
||-.
T Consensus 120 sy~~ 123 (159)
T KOG3217|consen 120 SYDK 123 (159)
T ss_pred ccCC
Confidence 9954
No 168
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=54.46 E-value=26 Score=32.69 Aligned_cols=49 Identities=14% Similarity=0.054 Sum_probs=37.0
Q ss_pred eeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 111 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 111 ~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
..+|++. .|+......+..+++.++..+++.++++.+|.+|++|+.+.-
T Consensus 131 g~~I~v~--~g~~~~~~l~~~~~~~~i~~~~~~~~~~~~L~~grvDa~i~~ 179 (247)
T PRK09495 131 GKVVAVK--SGTGSVDYAKANIKTKDLRQFPNIDNAYLELGTGRADAVLHD 179 (247)
T ss_pred CCEEEEe--cCchHHHHHHhcCCCCceEEcCCHHHHHHHHHcCceeEEEeC
Confidence 4578875 466555545555666677788899999999999999998864
No 169
>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=53.70 E-value=24 Score=37.87 Aligned_cols=104 Identities=14% Similarity=0.254 Sum_probs=64.8
Q ss_pred HHhHHHcCCceeeccccc--CCCCceEEEEEecCCCC-----CCCC---------------CCceEEEEEEeCCCcchHH
Q 015945 258 AQAAEIYGLDILAEKIQD--DDDNVTRFLILAREPII-----AGTD---------------RPYKTSIVFTLEEGPGMLF 315 (398)
Q Consensus 258 ~~aA~~ygL~il~~~I~D--~~~N~TRF~vi~~~~~~-----~~~~---------------~~~ktsi~f~~~~~pGaL~ 315 (398)
...|+..|+++....... .-.|.-++-+-+..... .-.. ..+-..+++...|+||.+.
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 456888999986654432 23465565544332110 0000 0112356777789999999
Q ss_pred HHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 316 KALAVFALRDINLTKIE-SRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 316 ~~L~~F~~~~INLt~IE-SRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
++.+.+.+++||+.... +|-.++ .+....++++....++ ++++|++
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 554332 4678888998876533 4455543
No 170
>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=53.70 E-value=1.4e+02 Score=25.32 Aligned_cols=32 Identities=13% Similarity=-0.090 Sum_probs=23.5
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEee
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPI 162 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPI 162 (398)
.++++++... .+..++++.+.+|++|+|++.-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08450 25 EHPDLDVELSSLFSPQLAEALMRGKLDVAFMRP 57 (196)
T ss_pred hCCCcEEEEEecChHHHHHHHhcCCccEEEEeC
Confidence 3566655433 3567889999999999999754
No 171
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=53.32 E-value=19 Score=42.04 Aligned_cols=50 Identities=24% Similarity=0.229 Sum_probs=41.4
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
+..+||+. .|+..+...+..+++.+++.++|..+++.+|.+|++|+++..
T Consensus 406 ~g~~vav~--~g~~~~~~~~~~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~ 455 (1197)
T PRK09959 406 KGMKVAIP--YYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDALVAT 455 (1197)
T ss_pred cCCEEEEe--CCcchHHHHHHHCCCcEEEEcCCHHHHHHHHHcCCCCEEehh
Confidence 35688884 576666666667888899999999999999999999998865
No 172
>PRK03381 PII uridylyl-transferase; Provisional
Probab=52.65 E-value=53 Score=37.08 Aligned_cols=38 Identities=11% Similarity=0.154 Sum_probs=31.4
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 336 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~ 336 (398)
+-|-|.+..+|+||-|+++-++|+.+|+|+..-...-.
T Consensus 706 ~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~ 743 (774)
T PRK03381 706 DATVLEVRAADRPGLLARLARALERAGVDVRWARVATL 743 (774)
T ss_pred CeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeec
Confidence 35677788899999999999999999999996554443
No 173
>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=52.62 E-value=67 Score=22.81 Aligned_cols=27 Identities=26% Similarity=0.426 Sum_probs=23.9
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
+.+.||.+.++++.++++|||+-.|-+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04923 10 MRSHPGVAAKMFKALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEc
Confidence 456799999999999999999998864
No 174
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=52.49 E-value=34 Score=29.41 Aligned_cols=51 Identities=27% Similarity=0.312 Sum_probs=36.5
Q ss_pred eeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEeec
Q 015945 111 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIE 163 (398)
Q Consensus 111 ~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVPIE 163 (398)
..+|++.. |+........++....+....+..+++.+|.+|++|+++++-.
T Consensus 106 g~~i~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~ 156 (219)
T smart00062 106 GKKVAVVA--GTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADAP 156 (219)
T ss_pred CCEEEEec--CccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEeccH
Confidence 46788753 5443333333445567788889999999999999999998643
No 175
>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=52.45 E-value=1.5e+02 Score=25.26 Aligned_cols=122 Identities=12% Similarity=0.037 Sum_probs=59.6
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCcc---C
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKE---E 206 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~---~ 206 (398)
.++++++.. ..+..+..+.+.+|++|+|+.+-.....+.... .|.+..+.+ ..+-+|-+...+..+++ +
T Consensus 26 ~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~l~~~~~~~----v~~~~~pl~~~~~~~~~~l~~ 98 (198)
T cd08446 26 ARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAVE---NVAQERLYL----AVPKSHPLAARPAVSLADLRN 98 (198)
T ss_pred HCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecCCCCCCceeE---EeeeccEEE----EEeCCCCcccCCccCHHHHcC
Confidence 456655433 346778889999999999997533221111110 111222222 22233333322112222 2
Q ss_pred ccEEE-ecH---HHHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 207 LKRVF-SHP---QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 207 I~~V~-SHp---qal~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
..-|. ... ....+...|+.+.+. . ...++|...+.++++.+ ...++.+...+.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (198)
T cd08446 99 EPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAG---FGVCIVPESVAA 158 (198)
T ss_pred CCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcC---CcEEEchhhhhc
Confidence 33332 111 112334456655332 2 24567777777777764 357777776553
No 176
>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=51.90 E-value=1.7e+02 Score=29.84 Aligned_cols=98 Identities=18% Similarity=0.121 Sum_probs=61.0
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecccccCCCCceEEEEEecCCCCC-C----CCCCc
Q 015945 228 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPIIA-G----TDRPY 299 (398)
Q Consensus 228 ~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a---A~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~-~----~~~~~ 299 (398)
+++.+..-|..+|.++...+ |-+-...| |..++.++.-.|..+.. --|.. ......+ . ....+
T Consensus 189 ~a~~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~a~~~~i~i~i~~~~~~~-~gT~I---~~~~~~~~~v~~I~~~~~ 259 (401)
T TIGR00656 189 AAKRIDKISYEEALELATFG-----AKVLHPRTVEPAMRSGVPIEVRSSFDPE-EGTLI---TNSMENPPLVKGIALRKN 259 (401)
T ss_pred CcEECCccCHHHHHHHHHcC-----CcccCHHHHHHHHHCCCeEEEEECCCCC-CCeEE---EeCcccCCceEEEEEECC
Confidence 45677777888888887642 33444444 45689999888866543 23433 2221111 0 01122
Q ss_pred eEEEEEE---eCCCcchHHHHHHHHHhCCceeeeeeee
Q 015945 300 KTSIVFT---LEEGPGMLFKALAVFALRDINLTKIESR 334 (398)
Q Consensus 300 ktsi~f~---~~~~pGaL~~~L~~F~~~~INLt~IESR 334 (398)
.+-+.+. +.++||.+.++++.|+++|||+-.|..-
T Consensus 260 va~vsv~g~~~~~~~g~~~~if~~L~~~~I~i~~i~~~ 297 (401)
T TIGR00656 260 VTRVTVHGLGMLGKRGFLARIFGALAERNINVDLISQT 297 (401)
T ss_pred EEEEEEecCCCCCCccHHHHHHHHHHHcCCcEEEEEcC
Confidence 3333333 5688999999999999999999888543
No 177
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=51.81 E-value=38 Score=36.22 Aligned_cols=58 Identities=21% Similarity=0.344 Sum_probs=43.8
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHH
Q 015945 303 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 381 (398)
Q Consensus 303 i~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~ 381 (398)
+-+...|+.|-..++|..|..++|||..||--|.. ..|++|.. .+....+.+++++++
T Consensus 3 l~~~~~dr~g~~~~~l~~~~~~~~~~~~~e~~~~~--------------------~~~~~~~~-~~~~~~~~~~~~~~~ 60 (520)
T PRK10820 3 LEVFCEDRLGLTRELLDLLVLRSIDLRGIEIDPIG--------------------RIYLNFAE-LEFESFSSLMAEIRR 60 (520)
T ss_pred EEEEeeccccHHHHHHHHHHhcCCCccEEEEcCCC--------------------eEEEeCCC-cChhhHHHHHHHHhc
Confidence 44566799999999999999999999999975531 46778863 444556667777654
No 178
>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=51.81 E-value=35 Score=23.50 Aligned_cols=27 Identities=26% Similarity=0.359 Sum_probs=23.7
Q ss_pred CCcchHHHHHHHHHhCCceeeeeeeee
Q 015945 309 EGPGMLFKALAVFALRDINLTKIESRP 335 (398)
Q Consensus 309 ~~pGaL~~~L~~F~~~~INLt~IESRP 335 (398)
+.+|.+.++++.+++++||+..+..-.
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~~~~ 38 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMISQSE 38 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEEcCC
Confidence 578999999999999999999886654
No 179
>PRK04374 PII uridylyl-transferase; Provisional
Probab=51.77 E-value=70 Score=36.67 Aligned_cols=52 Identities=19% Similarity=0.305 Sum_probs=39.4
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeeeeeCCCCCCccccCCCCCCCcccceEEEE-EeecC
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLT--KIESRPQRKRPLRVVDDSNKGSAKYFDYLFYI-DFEAS 366 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt--~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffv-d~~g~ 366 (398)
.+.|.|.+...|+||-|+++-++|+.+|+|+. +|.+. .+ ...-.||| |-+|.
T Consensus 794 ~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~--g~---------------~a~D~F~V~d~~g~ 848 (869)
T PRK04374 794 GRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATF--GE---------------RAEDQFQITDEHDR 848 (869)
T ss_pred CCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEec--CC---------------EEEEEEEEECCCCC
Confidence 34677778889999999999999999999998 45444 22 23457888 55665
No 180
>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=51.70 E-value=1.5e+02 Score=25.14 Aligned_cols=122 Identities=19% Similarity=0.072 Sum_probs=59.0
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc-
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 208 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~- 208 (398)
.++++++.. ..+..++.+.+.+|++|+|++.-.-...+.. ...|.+..+.++ .+-.|-+...+..+++++.
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~ 97 (198)
T cd08421 25 AHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLE---TRPYRTDRLVVV----VPRDHPLAGRASVAFADTLD 97 (198)
T ss_pred HCCCceEEEEecCcHHHHHHHhcCCceEEEEecCCCCCCcE---EEEeecCcEEEE----eCCCCCccccCCCCHHHhcC
Confidence 456555433 3456789999999999999986332111111 111122222221 1222323222222233332
Q ss_pred --EEEecH-HH-HHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 209 --RVFSHP-QA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 209 --~V~SHp-qa-l~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
-|.-.+ .. ..++..++...+. . ...++|...+..+++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08421 98 HDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAG---LGIGIVPESAAR 155 (198)
T ss_pred CceEeecCCcchHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CCeEEccchhhh
Confidence 222111 11 1234444444333 2 34567777777777764 347787777665
No 181
>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=51.68 E-value=1.6e+02 Score=25.35 Aligned_cols=137 Identities=18% Similarity=0.092 Sum_probs=76.2
Q ss_pred CceeEEEEEcCCCcH--HHHHH--HHhCCCCcc-ccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeE
Q 015945 109 GTKVRVAYQGLPGAY--SEAAA--RKAYPKCET-VPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLH 183 (398)
Q Consensus 109 q~~~kVa~lGp~Gs~--s~~AA--~~~fg~~~~-~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~ 183 (398)
++..+|++...-+.+ ..... ++.++++++ +...+..++.+.+.+|++|+|+........|
T Consensus 5 ~~~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~--------------- 69 (209)
T PF03466_consen 5 RGTLRIGASPSFASSLLPPLLAEFRERHPNIRIEIREGDSDELIEALRSGELDLAITFGPPPPPG--------------- 69 (209)
T ss_dssp EEEEEEEEEHHHHHHTHHHHHHHHHHHSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSSSSTT---------------
T ss_pred ceEEEEEEEhHHHHHHHHHHHHHHHHHCCCcEEEEEeccchhhhHHHhcccccEEEEEeeccccc---------------
Confidence 345677776332221 12211 224566654 3345668999999999999999986642221
Q ss_pred EEEEEEEeeeEeeecCCC--------CCccCc---cEEEec--HHHHHHHHHHHhhcCC---eEEecCCHHHHHHHHHhc
Q 015945 184 IVGEVQLVVNHCLLGLPG--------VLKEEL---KRVFSH--PQALAQCEMTLSNLGI---VRISADDTAGAAQMVASI 247 (398)
Q Consensus 184 I~~Ei~l~I~h~Ll~~~g--------~~l~~I---~~V~SH--pqal~QC~~fl~~~~~---~~v~~~STA~Aa~~v~~~ 247 (398)
+..+.......++++.++ .+++++ .-|.-. ..-..+..+|+.+.+. ....++|...+..+++.+
T Consensus 70 ~~~~~l~~~~~~~~~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g 149 (209)
T PF03466_consen 70 LESEPLGEEPLVLVVSPDHPLAQKKPITLEDLADYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASG 149 (209)
T ss_dssp EEEEEEEEEEEEEEEETTSGGGTTSSSSGGGGTTSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTT
T ss_pred cccccccceeeeeeeeccccccccccchhhhhhhccccccccccccccccccccccccccccccccccchhhhccccccc
Confidence 222223333344443333 233333 333322 1234556666666544 234677888888888764
Q ss_pred CCCCeEEEcCHHhHHH
Q 015945 248 GERDTGAVASAQAAEI 263 (398)
Q Consensus 248 ~~~~~AAI~s~~aA~~ 263 (398)
...++.+...+..
T Consensus 150 ---~gi~~~p~~~~~~ 162 (209)
T PF03466_consen 150 ---DGIAILPDSLAQD 162 (209)
T ss_dssp ---SEBEEEEHHHHHH
T ss_pred ---cceeecCcccccc
Confidence 4678888887743
No 182
>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=51.46 E-value=34 Score=32.21 Aligned_cols=82 Identities=28% Similarity=0.196 Sum_probs=44.6
Q ss_pred hhhcccCCCCCceeEEEEEcCCCcHHHHHHHHhC---C-CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhH
Q 015945 99 IMELSSSPDDGTKVRVAYQGLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNY 174 (398)
Q Consensus 99 R~iis~s~~~q~~~kVa~lGp~Gs~s~~AA~~~f---g-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tl 174 (398)
+++|+-+-.. ...||+++= +|+-.+.-+|.+. + .++++..+++.++++.+.+|++|-+||+.+-+. |.-- -
T Consensus 57 ~~l~~v~p~~-~~~rI~vwR-kGsaADvl~Ral~d~~~~~~EvVytdD~~~i~~Ml~~g~vdsAVv~~~~~~-G~~f--E 131 (201)
T PF12916_consen 57 KKLMSVYPNI-GKPRIAVWR-KGSAADVLTRALLDLKGIKAEVVYTDDMSEIVKMLNEGEVDSAVVGSEFSK-GETF--E 131 (201)
T ss_dssp ---EEEEE-T-TSSEEEESS-TTSHHHHHHHHHHHHH--T-EEEE---HHHHHHHHHTT-E--EEEETTT----EEH--H
T ss_pred EeeEEEecCC-CCceEEEEe-cccHHHHHHHHHHhhccccceeEEecCHHHHHHHHhcCceeeeeecchhcc-chhH--H
Confidence 4455444443 345899885 7887665555433 4 588999999999999999999999999944333 3322 3
Q ss_pred HhhhcCCeEEE
Q 015945 175 DLLLRHRLHIV 185 (398)
Q Consensus 175 d~L~~~~l~I~ 185 (398)
|+|.+.++++=
T Consensus 132 dl~~~~g~~~P 142 (201)
T PF12916_consen 132 DLLGSLGLYAP 142 (201)
T ss_dssp HHHHHTT----
T ss_pred HHHhhcCCCCC
Confidence 56677787763
No 183
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=51.15 E-value=1.2e+02 Score=29.39 Aligned_cols=137 Identities=15% Similarity=0.084 Sum_probs=66.9
Q ss_pred CCceeEEEEEcCCCcHHHHHHH------HhCCC--CccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhc
Q 015945 108 DGTKVRVAYQGLPGAYSEAAAR------KAYPK--CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLR 179 (398)
Q Consensus 108 ~q~~~kVa~lGp~Gs~s~~AA~------~~fg~--~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~ 179 (398)
.....+|++... ..+...+. +.+++ +++....+..++.+++.+|++|+|+.. ........-..
T Consensus 25 ~~~~lrIg~~~~--~~~~~l~~~~~~~~~~~p~v~ie~~~~~~~~~~~~aL~~G~iDia~~~-------~~~~~~~~~~g 95 (314)
T PRK11553 25 SPEALRIGYQKG--SIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGSTG-------DIPPIFAQAAG 95 (314)
T ss_pred CCCeEEEEeCCC--chHHHHHHhhCHHHHhCCCCeeEEEECCCcHHHHHHHHcCCCCEEccC-------CHHHHHHHhCC
Confidence 346788998632 22222121 12333 456666677899999999999999852 11111100012
Q ss_pred CCeEEEEEEEE-eeeEeeecCCCC---CccCc--cEEEecH--HHHHHHHHHHhhcCC-----eEEecCCHHHHHHHHHh
Q 015945 180 HRLHIVGEVQL-VVNHCLLGLPGV---LKEEL--KRVFSHP--QALAQCEMTLSNLGI-----VRISADDTAGAAQMVAS 246 (398)
Q Consensus 180 ~~l~I~~Ei~l-~I~h~Ll~~~g~---~l~~I--~~V~SHp--qal~QC~~fl~~~~~-----~~v~~~STA~Aa~~v~~ 246 (398)
.++.+++.... +-..+++.+++. +++|+ ++|...+ .....+..+|++.+. +.+.. +..++...+..
T Consensus 96 ~~~~~v~~~~~~~~~~~lvv~~~s~i~s~~dL~Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~-~~~~~~~al~~ 174 (314)
T PRK11553 96 ADLVYVGVEPPKPKAEVILVAENSPIKTVADLKGHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYL-TPADARAAFQQ 174 (314)
T ss_pred CCEEEEEEecCCCcceEEEEeCCCCCCCHHHhCCCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEec-ChHHHHHHHHc
Confidence 34555544322 222456665543 23333 2344322 123455666766443 23333 45555665555
Q ss_pred cCCCCeEEEc
Q 015945 247 IGERDTGAVA 256 (398)
Q Consensus 247 ~~~~~~AAI~ 256 (398)
+ .-+ |+++
T Consensus 175 G-~vD-a~~~ 182 (314)
T PRK11553 175 G-NVD-AWAI 182 (314)
T ss_pred C-CCC-EEEE
Confidence 4 334 4444
No 184
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=51.04 E-value=2.5e+02 Score=27.61 Aligned_cols=145 Identities=15% Similarity=0.065 Sum_probs=74.7
Q ss_pred CceeEEEEEcCCCcHH--HHHH--HHhCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeE
Q 015945 109 GTKVRVAYQGLPGAYS--EAAA--RKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLH 183 (398)
Q Consensus 109 q~~~kVa~lGp~Gs~s--~~AA--~~~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~ 183 (398)
.+..+|++...-+.+- .... ...++++++.. ..+.+++.+.+.+|++|+|+++-.....+... ...|.+..+.
T Consensus 92 ~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~~ 169 (327)
T PRK12680 92 QGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGI--AVPLYRWRRL 169 (327)
T ss_pred ceEEEEEecchhHHHhhHHHHHHHHHHCCCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCCcce--EEEeeccceE
Confidence 4567888765544421 1111 22356666544 34568999999999999999864321111110 0112222222
Q ss_pred EEEEEEEeeeEeeecC-CCCCccCc---cEEEecH-HHH-HHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEE
Q 015945 184 IVGEVQLVVNHCLLGL-PGVLKEEL---KRVFSHP-QAL-AQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGA 254 (398)
Q Consensus 184 I~~Ei~l~I~h~Ll~~-~g~~l~~I---~~V~SHp-qal-~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AA 254 (398)
+.++..|-|... ....++++ .-|..-+ ... ....+|+...+. . ...++|.....++|+.+ ...|
T Consensus 170 ----l~~~~~hpl~~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G---~Gia 242 (327)
T PRK12680 170 ----VVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAG---LGVG 242 (327)
T ss_pred ----EEEeCCChhhccCCCCCHHHHhcCCEEEecCCCchHHHHHHHHHHCCCCCcEEEEECCHHHHHHHHHcC---CCEE
Confidence 234555655432 12233333 3332222 222 445667766443 2 34667777777777764 3366
Q ss_pred EcCHHhHH
Q 015945 255 VASAQAAE 262 (398)
Q Consensus 255 I~s~~aA~ 262 (398)
+.+..++.
T Consensus 243 ~lp~~~~~ 250 (327)
T PRK12680 243 LLAEMAVN 250 (327)
T ss_pred Eeechhcc
Confidence 76666554
No 185
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=50.97 E-value=37 Score=28.31 Aligned_cols=47 Identities=9% Similarity=0.055 Sum_probs=36.6
Q ss_pred eEEEEEcCCCcHHHHHHHHhCCC-----------CccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 112 VRVAYQGLPGAYSEAAARKAYPK-----------CETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 112 ~kVa~lGp~Gs~s~~AA~~~fg~-----------~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
.+|+++ .||..+..++.+.+. .++..+++..+++.+|.+|+ |..+..
T Consensus 14 ~~vgv~--~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d 71 (134)
T smart00079 14 IEYGTI--RGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLME 71 (134)
T ss_pred ccceEe--cCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEee
Confidence 678885 788888877765543 15667899999999999999 977665
No 186
>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=50.85 E-value=75 Score=22.56 Aligned_cols=27 Identities=26% Similarity=0.431 Sum_probs=24.0
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
+++.+|.+.++++.++++|||+-.|.+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04936 10 MRSHPGVAAKMFEALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 557799999999999999999988864
No 187
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=50.43 E-value=2.5e+02 Score=27.28 Aligned_cols=143 Identities=12% Similarity=0.042 Sum_probs=69.2
Q ss_pred CceeEEEEEcCCCcH--HHHHH--HHhCCCCccc-cCCCHHHHHHHHHcCCccEEEEeeccc-cccchHHhHHhhhcCCe
Q 015945 109 GTKVRVAYQGLPGAY--SEAAA--RKAYPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENS-VGGSIHRNYDLLLRHRL 182 (398)
Q Consensus 109 q~~~kVa~lGp~Gs~--s~~AA--~~~fg~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIENS-~~G~V~~tld~L~~~~l 182 (398)
.+..+|++...-+.+ ..... +..++++++. ...+..++.+.|.+|++|+|+.+-... ..+.. ...|.+..+
T Consensus 92 ~g~l~Ig~~~~~~~~~l~~~i~~f~~~~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~l~---~~~l~~~~~ 168 (309)
T PRK12683 92 SGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDLV---SFPYYSWHH 168 (309)
T ss_pred CceEEEEeccchHHHHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCCce---EEEcccCeE
Confidence 356777774322221 11111 2235665543 345788999999999999999753211 11111 111222222
Q ss_pred EEEEEEEEeeeEeeecCCCCCccCc---cEEEecH--HHHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEE
Q 015945 183 HIVGEVQLVVNHCLLGLPGVLKEEL---KRVFSHP--QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGA 254 (398)
Q Consensus 183 ~I~~Ei~l~I~h~Ll~~~g~~l~~I---~~V~SHp--qal~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AA 254 (398)
. ++.+..|-|...+..+++++ .-|.-.+ .--.+...|+.+.+. . ...++|......+|..+. + .+
T Consensus 169 ~----~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~--G-i~ 241 (309)
T PRK12683 169 V----VVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGM--G-VG 241 (309)
T ss_pred E----EEecCCCCcccCCccCHHHHhcCCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhCC--C-eE
Confidence 2 23444455443333333333 3332211 123456677776443 3 234556666666676542 3 55
Q ss_pred EcCHHhH
Q 015945 255 VASAQAA 261 (398)
Q Consensus 255 I~s~~aA 261 (398)
+.+...+
T Consensus 242 ~lp~~~~ 248 (309)
T PRK12683 242 IVAAMAY 248 (309)
T ss_pred Eeehhhc
Confidence 5555443
No 188
>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=50.05 E-value=87 Score=27.24 Aligned_cols=62 Identities=11% Similarity=0.103 Sum_probs=42.8
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHH
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 377 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~ 377 (398)
++.++-.+-=-+..+..+++.+.++||.+|-|..--...+| -.||+-+.|+-+...+.+.++
T Consensus 56 ~A~~~Gd~vll~~EV~pvi~aL~~~GI~vtAlHNH~l~e~P----------------rl~ymH~~~~gdp~~lA~~vr 117 (123)
T PF07485_consen 56 KAMVMGDFVLLEDEVNPVISALRKNGIEVTALHNHWLFEQP----------------RLFYMHIWGVGDPAKLARKVR 117 (123)
T ss_pred cEEEeecEEecHHHHHHHHHHHHHCCceEEEEecccccCCC----------------CEEEEEEEecCCHHHHHHHHH
Confidence 44444332222445777888889999999999999887765 489999999754444444443
No 189
>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=50.00 E-value=95 Score=26.19 Aligned_cols=122 Identities=18% Similarity=0.127 Sum_probs=60.1
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccC---
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEE--- 206 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~--- 206 (398)
.++++++.. ..+..++.+.+.+|++|+|+........+... ..|.+..+.++ .+-.|-+......++++
T Consensus 25 ~~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~~~~~~~~i~~~~l~~ 97 (201)
T cd08420 25 RYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIV---EPFAEDELVLV----VPPDHPLAGRKEVTAEELAA 97 (201)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEecCCCCCcceEE---EeecCccEEEE----ecCCCCccccCccCHHHHhc
Confidence 355554422 34567889999999999999864432222111 11122222222 22223332222222222
Q ss_pred ccEEEecHH--HHHHHHHHHhhcC-----Ce-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 207 LKRVFSHPQ--ALAQCEMTLSNLG-----IV-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 207 I~~V~SHpq--al~QC~~fl~~~~-----~~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
..-|...+. -..+...|+...+ .. ...+.+...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08420 98 EPWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAG---LGISILSRLAVR 158 (201)
T ss_pred CCEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcC---CCEEEeeHHHHH
Confidence 233332211 1234555665321 22 34567777777788764 457888877654
No 190
>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=49.82 E-value=83 Score=22.66 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=23.5
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
+++.+|.+.++++.++++|||+-.|-.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~q 37 (66)
T cd04924 11 MRGTPGVAGRVFGALGKAGINVIMISQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 457799999999999999999988754
No 191
>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=49.68 E-value=83 Score=22.04 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=23.3
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
..+.+|.+.++++.|++++|++-.+..
T Consensus 10 ~~~~~~~~~~i~~~l~~~~i~v~~i~~ 36 (65)
T cd04892 10 MRGTPGVAARIFSALAEAGINIIMISQ 36 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 346789999999999999999988854
No 192
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=48.86 E-value=1.3e+02 Score=28.44 Aligned_cols=121 Identities=15% Similarity=0.051 Sum_probs=59.8
Q ss_pred CCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCC-CCccC---
Q 015945 132 YPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG-VLKEE--- 206 (398)
Q Consensus 132 fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g-~~l~~--- 206 (398)
|++..+.. ..+..++.+.+.+|++|+|+++.+...++.... .|.+..+.++ .+-+|-|...+. .++++
T Consensus 117 ~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~~---~l~~~~~~~~----~~~~~pl~~~~~~i~~~~L~~ 189 (296)
T PRK11242 117 YPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEAQ---PLFTETLALV----VGRHHPLAARRKALTLDELAD 189 (296)
T ss_pred CCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCCCCcceeEE---EeeeccEEEE----EcCCCcccccCCCcCHHHHhC
Confidence 45555544 346688999999999999998654333222111 1112222221 122222322111 12222
Q ss_pred ccEEEecHHHH--HHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 207 LKRVFSHPQAL--AQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 207 I~~V~SHpqal--~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
-.-|.-.+... ..-..|+.+.+. + ...++|-..+.++++.+ ...++.++..+.
T Consensus 190 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 247 (296)
T PRK11242 190 EPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG---RLATLLPAAIAR 247 (296)
T ss_pred CCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhC---CeEEEeehhhcc
Confidence 22333333321 233455655433 2 34566666777777765 346777776554
No 193
>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=48.52 E-value=1.1e+02 Score=22.72 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=28.5
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeee
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 335 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP 335 (398)
+.|++-.+...+|.+.++++.|++.|||+..|-.=+
T Consensus 3 ~VsvVG~~~~~~~~~~~i~~aL~~~~I~v~~i~~g~ 38 (65)
T cd04918 3 IISLIGNVQRSSLILERAFHVLYTKGVNVQMISQGA 38 (65)
T ss_pred EEEEECCCCCCccHHHHHHHHHHHCCCCEEEEEecC
Confidence 456666666678999999999999999997776333
No 194
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=47.27 E-value=1.8e+02 Score=24.75 Aligned_cols=111 Identities=21% Similarity=0.141 Sum_probs=60.2
Q ss_pred CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCC---CccCc--c
Q 015945 134 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV---LKEEL--K 208 (398)
Q Consensus 134 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~---~l~~I--~ 208 (398)
.+++.+. ++.++.+++.+|++|+++.....+.+.. ..+. .........+.++.+++. +++|+ +
T Consensus 40 ~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~~-----~~~~------~~~~~~~~~~~~~~~~~~~~~~~~dL~g~ 107 (219)
T smart00062 40 KVEFVEV-SFDNLLTALKSGKIDVVAAGMTITPERA-----KQVD------FSDPYYKSGQVILVRKDSPIKSLEDLKGK 107 (219)
T ss_pred eEEEEec-cHHHHHHHHHCCcccEEeccccCCHHHH-----hhee------eccceeeceeEEEEecCCCCCChHHhCCC
Confidence 3567777 8999999999999999987643221110 0010 011111222455554442 22333 2
Q ss_pred EEEecHHHHHHHHHHHhhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHh
Q 015945 209 RVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQA 260 (398)
Q Consensus 209 ~V~SHpqal~QC~~fl~~~--~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a 260 (398)
+|..-+ . .-...++... +...+.+.+..++.+++..+. ..|++.....
T Consensus 108 ~i~~~~-g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~--~d~~~~~~~~ 157 (219)
T smart00062 108 KVAVVA-G-TTGEELLKKLYPEAKIVSYDSQAEALAALKAGR--ADAAVADAPA 157 (219)
T ss_pred EEEEec-C-ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCc--ccEEEeccHH
Confidence 333322 1 1233455443 567778888888888887653 3355555443
No 195
>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=47.13 E-value=1.8e+02 Score=24.79 Aligned_cols=123 Identities=14% Similarity=0.020 Sum_probs=60.7
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhH--HhhhcCCeEEEEEEEEeeeEeeecCCCCCccCc
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNY--DLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 207 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tl--d~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I 207 (398)
.++++++... .+..+..+.+.+|++|+|+..-.... .....+ ..|.+..+.+ ..+-.|-+...+..+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~--~~~~~~~~~~l~~~~~~~----v~~~~hp~~~~~~i~~~~L 98 (200)
T cd08453 25 AYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGA--SAPPALAYRPLLSEPLVL----AVPAAWAAEGGAPLALAAV 98 (200)
T ss_pred hCCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCccc--CCCcceeEEEeeeCceEE----EEECCCccccCCCCCHHHh
Confidence 3566555333 35678899999999999997532110 001111 1122223322 2233343333222233333
Q ss_pred ---cEEEe-cH---HHHHHHHHHHhhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 208 ---KRVFS-HP---QALAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 208 ---~~V~S-Hp---qal~QC~~fl~~~~~--~~-v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
.-|.. .. .....+..|+.+.+. +. ..++|...+.++++.+ ...++.+...++
T Consensus 99 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08453 99 AAEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAG---MGVALVPASLRN 160 (200)
T ss_pred ccCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcC---CcEEEeEhHHhh
Confidence 33332 21 123456777777543 22 3456666666677764 346777776543
No 196
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=46.22 E-value=2.4e+02 Score=27.22 Aligned_cols=115 Identities=17% Similarity=0.155 Sum_probs=58.3
Q ss_pred CCCCccc-cCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCC------Cc
Q 015945 132 YPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV------LK 204 (398)
Q Consensus 132 fg~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~------~l 204 (398)
++++++. ...+..++++.|.+|++|+|+++..+... .. + +..+.......++++.++- ++
T Consensus 123 ~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~~--------~--l~~~~l~~~~~~lv~~~~~pl~~~i~~ 189 (312)
T PRK10341 123 FPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMK---LQ--------D--LHVEPLFESEFVLVASKSRTCTGTTTL 189 (312)
T ss_pred CCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCcccc---cC--------C--eeEEEEecccEEEEEcCCCchhccCCH
Confidence 4555543 33456899999999999999987543211 00 0 1112222222333333221 22
Q ss_pred cCc---cEEEecH--HHHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 205 EEL---KRVFSHP--QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 205 ~~I---~~V~SHp--qal~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
+++ .-|.--+ ....+...|+.+.+. . ...++|.....+++..+ ...++.+...++
T Consensus 190 ~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 252 (312)
T PRK10341 190 ESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA---DFLTVIPCDMTS 252 (312)
T ss_pred HHHhCCCeEccCCCCcHHHHHHHHHHHcCcCCCceEEecCHHHHHHHHHhC---CcEEEeeHHhcC
Confidence 222 2221111 122344456655432 2 35677777777777764 346777776553
No 197
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=46.11 E-value=30 Score=33.99 Aligned_cols=54 Identities=35% Similarity=0.304 Sum_probs=40.5
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEeeccc
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENS 165 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS 165 (398)
+..+||+-|+.-| .++..|.+.++.+++.. -|+++..||.+|++|.|++--|..
T Consensus 94 ~~~rvavpG~~TT-A~lL~rl~~p~~~~V~m-~fdeI~~Avl~G~VDaGvlIHE~~ 147 (272)
T COG2107 94 KGKRVAVPGEMTT-AALLFRLAYPKAEIVYM-PFDEIIPAVLEGKVDAGVLIHEEQ 147 (272)
T ss_pred ccceEecCCcccH-HHHHHHHhCCCceEEEe-eHHHHHHHHHcCCCccceEEeehh
Confidence 5678998665444 46666766677665554 589999999999999999987743
No 198
>PRK03059 PII uridylyl-transferase; Provisional
Probab=45.63 E-value=93 Score=35.63 Aligned_cols=37 Identities=16% Similarity=0.307 Sum_probs=31.1
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeee--eeee
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTK--IESR 334 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~--IESR 334 (398)
.+.|.|.+..+|+||-|+++-++|+.+|+|+.. |.+.
T Consensus 784 ~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~ 822 (856)
T PRK03059 784 GQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTL 822 (856)
T ss_pred CCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeec
Confidence 346778888899999999999999999999984 5444
No 199
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=44.87 E-value=88 Score=35.99 Aligned_cols=36 Identities=25% Similarity=0.329 Sum_probs=30.6
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeeee
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLT--KIESR 334 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt--~IESR 334 (398)
+-|-|.+..+|+||-|+++-++|+..|+|+. +|.+.
T Consensus 813 ~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~ 850 (895)
T PRK00275 813 PVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATL 850 (895)
T ss_pred CeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEec
Confidence 4577778889999999999999999999998 55544
No 200
>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=44.61 E-value=1.8e+02 Score=24.80 Aligned_cols=122 Identities=18% Similarity=0.156 Sum_probs=59.8
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCc--
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 207 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I-- 207 (398)
.|+++++... .+..++.+.+.+|++|+|+.+......+.. ...|.+..+.+ ..+-+|-+...+ .+++++
T Consensus 25 ~~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~l~---~~~l~~~~~~~----v~~~~~~l~~~~-i~~~~L~~ 96 (201)
T cd08459 25 VAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFF---QQRLFRERYVC----LVRKDHPRIGST-LTLEQFLA 96 (201)
T ss_pred HCCCCeEEEEecCccCHHHHhhCCCceEEEEcCCCCcccce---EEEeecCceEE----EEcCCCccccCC-cCHHHHhh
Confidence 3555554333 345588899999999999986432111100 01111222221 223333333221 233332
Q ss_pred -cEEEecH--HHHHHHHHHHhhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 208 -KRVFSHP--QALAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 208 -~~V~SHp--qal~QC~~fl~~~~~--~~-v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
.-|...+ ....+..+|+.+.+. .. ..++|.....++++.+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (201)
T cd08459 97 ARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQT---DLVATVPERLARL 155 (201)
T ss_pred CCcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcC---CEEEecHHHHHHH
Confidence 2233222 112345667766443 33 3455555566666654 4588888877664
No 201
>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=44.50 E-value=33 Score=26.04 Aligned_cols=28 Identities=11% Similarity=0.143 Sum_probs=24.2
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeee
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIESRP 335 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IESRP 335 (398)
+++.||.+.++++.++++|||+-.| ++-
T Consensus 9 ~~~~~~~~a~if~~La~~~InvDmI-~~~ 36 (67)
T cd04914 9 KDNENDLQQRVFKALANAGISVDLI-NVS 36 (67)
T ss_pred CCCCccHHHHHHHHHHHcCCcEEEE-Eec
Confidence 3567999999999999999999999 443
No 202
>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=44.45 E-value=1.6e+02 Score=25.39 Aligned_cols=121 Identities=14% Similarity=0.103 Sum_probs=57.5
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc-
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 208 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~- 208 (398)
.++++++... .+. +..+.+.+|++|+|+++-+....+... ..|.+..+.+ ..+-+|-+.. ...+++++.
T Consensus 25 ~~P~i~l~i~~~~~-~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~----v~~~~hpl~~-~~~~~~~l~~ 95 (200)
T cd08462 25 EAPGVRFELLPPDD-QPHELLERGEVDLLIAPERFMSDGHPS---EPLFEEEFVC----VVWADNPLVG-GELTAEQYFS 95 (200)
T ss_pred HCCCCEEEEecCCh-hHHHHHhcCCeeEEEecCCCCCCCcee---eeeeccceEE----EEcCCCCccC-CCCCHHHHhh
Confidence 4565554333 244 999999999999999863322121110 0111112111 1233343332 223334333
Q ss_pred --EEE-ecHHHH-HHHHH-HHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 209 --RVF-SHPQAL-AQCEM-TLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 209 --~V~-SHpqal-~QC~~-fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
-|. +..... ....+ ++.+.+. . ...++|.....++++.+ ...||.+...++.
T Consensus 96 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~giailp~~~~~~ 155 (200)
T cd08462 96 AGHVVVRFGRNRRPSFEDWFLNEYGLKRRVEVVTPSFSSIPPLLVGT---NRIATLHRRLAEQ 155 (200)
T ss_pred CCCEEEecCCCCCccHHHHHHHHcCCcceEEEEeChHHHHHHHHHcC---chhhhhHHHHHHh
Confidence 111 111111 11222 2344333 2 34566667777777764 4578888877653
No 203
>PRK05007 PII uridylyl-transferase; Provisional
Probab=43.98 E-value=1.1e+02 Score=35.16 Aligned_cols=34 Identities=15% Similarity=0.160 Sum_probs=29.5
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeee
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIE 332 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IE 332 (398)
+-|.|.+..+|+||-|+++.++|+.+|+|+..-.
T Consensus 700 ~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~ 733 (884)
T PRK05007 700 GGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQ 733 (884)
T ss_pred CeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEE
Confidence 3577888889999999999999999999998543
No 204
>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=43.55 E-value=60 Score=23.51 Aligned_cols=27 Identities=19% Similarity=0.389 Sum_probs=23.7
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
+++.||.+.++++.+++.|||+-.|-.
T Consensus 11 ~~~~~~~~~~i~~~l~~~~I~v~~i~~ 37 (66)
T cd04922 11 MAGTPGVAATFFSALAKANVNIRAIAQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 457899999999999999999988853
No 205
>PRK06635 aspartate kinase; Reviewed
Probab=43.16 E-value=3.4e+02 Score=27.73 Aligned_cols=29 Identities=21% Similarity=0.364 Sum_probs=25.6
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeee
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIESRP 335 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IESRP 335 (398)
..++||.|.++++.|+++|||+-.|.+-.
T Consensus 270 ~~~~~g~l~~i~~~L~~~~I~i~~is~s~ 298 (404)
T PRK06635 270 VPDKPGIAAQIFGALAEANINVDMIVQNV 298 (404)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEecC
Confidence 57899999999999999999999886544
No 206
>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=42.18 E-value=2.2e+02 Score=24.23 Aligned_cols=123 Identities=17% Similarity=0.069 Sum_probs=61.3
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCc--
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 207 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I-- 207 (398)
.++++++.. ..+..++.+.+.+|++|+|++--.....+... ..|.+..+.++. +-.|-+... ..+++++
T Consensus 25 ~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~lv~----~~~~~~~~~-~~~~~~L~~ 96 (200)
T cd08466 25 LAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKS---ELLFEDELVCVA----RKDHPRIQG-SLSLEQYLA 96 (200)
T ss_pred HCCCCEEEEecCchHhHHHHHHcCCccEEEecccCCCCCcee---eeecccceEEEE----eCCCCCCCC-CcCHHHHhh
Confidence 356665533 34677899999999999999742211111111 112223333322 223333221 2234444
Q ss_pred -cEEEecHHH-HHHHHHHHhhcCC---e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHc
Q 015945 208 -KRVFSHPQA-LAQCEMTLSNLGI---V-RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 264 (398)
Q Consensus 208 -~~V~SHpqa-l~QC~~fl~~~~~---~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~y 264 (398)
..+.-.+.. ..+...|+.+.+. . ...++|.....++++.+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~~ 156 (200)
T cd08466 97 EKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQT---DLIAIAPRWLADQY 156 (200)
T ss_pred CCcEEecCCCCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCC---CeehhhHHHHHHHh
Confidence 222222221 1233455554332 2 34566666667777654 45788887776543
No 207
>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=41.80 E-value=2.3e+02 Score=24.38 Aligned_cols=121 Identities=15% Similarity=0.015 Sum_probs=59.4
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccc-cccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCc-
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENS-VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL- 207 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS-~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I- 207 (398)
.|+++++.. ..+..++.+.+.+|++|+|+.+-... ..+... ..|.+..+. ++.+.+|-|......+++++
T Consensus 25 ~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~---~~l~~~~~~----~v~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08413 25 RYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLVT---LPCYRWNHC----VIVPPGHPLADLGPLTLEDLA 97 (198)
T ss_pred hCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCcEE---EEeeeeeEE----EEecCCCcccccCCCCHHHHh
Confidence 356555433 33567899999999999999852211 111100 011111111 12233444433322333332
Q ss_pred --cEEEec-HH-HHHHHHHHHhhcCC---eEEecCCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015945 208 --KRVFSH-PQ-ALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAA 261 (398)
Q Consensus 208 --~~V~SH-pq-al~QC~~fl~~~~~---~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA 261 (398)
.-|.-. .. -..+.+.|+.+.+. ....++|......+++.+ ...|+.+...+
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~ 155 (198)
T cd08413 98 QYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLG---LGVGIIAEMAY 155 (198)
T ss_pred cCCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhC---CCEEEcccccc
Confidence 223211 11 22345566666443 234567777777888765 23677776544
No 208
>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=41.67 E-value=45 Score=31.08 Aligned_cols=53 Identities=19% Similarity=0.025 Sum_probs=35.6
Q ss_pred ceeEEEEEcCCCcHHHHH----HHHhCC-C-----CccccCCCHHHHHHHHHcCCccEEEEee
Q 015945 110 TKVRVAYQGLPGAYSEAA----ARKAYP-K-----CETVPCDQFEAAFKAVELWLVDKAVLPI 162 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~A----A~~~fg-~-----~~~~~~~s~~~v~~aV~~g~~d~gvVPI 162 (398)
...+|++.++.++..+.. ..+..+ . ..+....++.+++++|.+|++|.++.+-
T Consensus 140 ~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~~Da~~~~~ 202 (254)
T TIGR01098 140 KGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGKVDAATNNS 202 (254)
T ss_pred cCCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCCCCeEEecH
Confidence 357899887654432222 222333 1 3556667789999999999999999873
No 209
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=41.52 E-value=1.2e+02 Score=28.78 Aligned_cols=49 Identities=12% Similarity=0.070 Sum_probs=32.5
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhC---C-CCccccCCCHHHHHHHHHcCCccEEEE
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVL 160 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~f---g-~~~~~~~~s~~~v~~aV~~g~~d~gvV 160 (398)
...+|++. .|+..+.....+. + ...+...++..+++++|.+|++|..+.
T Consensus 147 ~g~~V~v~--~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~ 199 (259)
T PRK11917 147 KGANIGVA--QAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSV 199 (259)
T ss_pred CCCeEEEe--cCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEe
Confidence 45688885 4443332211221 2 345677889999999999999998865
No 210
>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=41.07 E-value=72 Score=23.24 Aligned_cols=26 Identities=19% Similarity=0.226 Sum_probs=23.0
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeee
Q 015945 308 EEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 308 ~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
.+.||.+.++++.|+++|||+-.|-.
T Consensus 12 ~~~~~~~~~if~~L~~~~I~v~~i~q 37 (66)
T cd04919 12 KNMIGIAGRMFTTLADHRINIEMISQ 37 (66)
T ss_pred CCCcCHHHHHHHHHHHCCCCEEEEEe
Confidence 46799999999999999999988854
No 211
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=40.76 E-value=3.2e+02 Score=25.87 Aligned_cols=122 Identities=11% Similarity=-0.012 Sum_probs=61.2
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCcc---C
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKE---E 206 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~---~ 206 (398)
.++++.+.. ..+.+++++.+.+|++|+|++.-+....+. ....|.+..+.++ .+-.|-|......+++ +
T Consensus 115 ~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~l---~~~~l~~~~~~~v----~~~~~pl~~~~~i~~~~L~~ 187 (296)
T PRK09906 115 RHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEI---DYLELLDEPLVVV----LPVDHPLAHEKEITAAQLDG 187 (296)
T ss_pred HCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecCCCCCCCc---eEEEEecccEEEE----ecCCCccccCCCcCHHHHcC
Confidence 456666543 335678999999999999998644211111 1112222233222 2223333322222222 3
Q ss_pred ccEEEecH---HH-HHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 207 LKRVFSHP---QA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 207 I~~V~SHp---qa-l~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
..-|.--+ .. ..+...|+...++ . ...++|...+..+|+.+ ...++.+...++
T Consensus 188 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g~~~~p~~~~~ 247 (296)
T PRK09906 188 VNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG---LGCTIIPGYMNN 247 (296)
T ss_pred CCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcEEEeeHHHhh
Confidence 33332211 11 2445667766443 2 34567777777788764 336666665543
No 212
>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=39.77 E-value=2.1e+02 Score=24.73 Aligned_cols=31 Identities=19% Similarity=0.039 Sum_probs=23.7
Q ss_pred CCCCccc-cCCCHHHHHHHHHcCCccEEEEee
Q 015945 132 YPKCETV-PCDQFEAAFKAVELWLVDKAVLPI 162 (398)
Q Consensus 132 fg~~~~~-~~~s~~~v~~aV~~g~~d~gvVPI 162 (398)
++++++. ...+..++.+.+.+|++|+|+...
T Consensus 26 ~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~ 57 (200)
T cd08465 26 APGIDLAVSQASREAMLAQVADGEIDLALGVF 57 (200)
T ss_pred CCCcEEEEecCChHhHHHHHHCCCccEEEecc
Confidence 5566543 335678999999999999999743
No 213
>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=39.59 E-value=1.6e+02 Score=25.09 Aligned_cols=122 Identities=20% Similarity=0.137 Sum_probs=59.8
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc-
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 208 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~- 208 (398)
.++++++.-. .+..++.+.+.+|++|+|+..-.....+.. ...|.+..+.+ ..+..|-+......+++++.
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08441 25 RWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIA---YEPLFDYEVVL----VVAPDHPLAAKEFITPEDLAD 97 (198)
T ss_pred hCCCeEEEEEeCCchhHHHHHHcCCceEEEecCCcCCCCcE---EEEccCCcEEE----EEcCCCChHHcccCCHHHhcC
Confidence 4566554333 355788999999999999974221111110 01112222222 22333333322222233332
Q ss_pred -EEEecH--HH-HHHHHHHHhhcCC---eEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 209 -RVFSHP--QA-LAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 209 -~V~SHp--qa-l~QC~~fl~~~~~---~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
....++ .. ......|+.+.+. ....++|...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 155 (198)
T cd08441 98 ETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASG---RGVAALPNWAVR 155 (198)
T ss_pred CceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhC---CcEEEeeHHHHH
Confidence 122222 11 2334556665432 234677777777777765 346777776554
No 214
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=39.36 E-value=3.3e+02 Score=25.52 Aligned_cols=113 Identities=15% Similarity=0.147 Sum_probs=59.4
Q ss_pred CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCC----CccCcc-
Q 015945 134 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV----LKEELK- 208 (398)
Q Consensus 134 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~----~l~~I~- 208 (398)
.++++. .+|.+++.++..|++|+++-++.-+.+- -+ .+....-+ +.....++++++. +++++.
T Consensus 66 ~~~~~~-~~~~~~~~~l~~g~~Di~~~~~~~t~eR-----~~-----~~~fs~p~-~~~~~~~~~~~~~~~~~~~~dl~g 133 (260)
T PRK15010 66 KCTWVA-SDFDALIPSLKAKKIDAIISSLSITDKR-----QQ-----EIAFSDKL-YAADSRLIAAKGSPIQPTLDSLKG 133 (260)
T ss_pred ceEEEe-CCHHHHHHHHHCCCCCEEEecCcCCHHH-----Hh-----hcccccce-EeccEEEEEECCCCCCCChhHcCC
Confidence 456665 4799999999999999877554422110 00 01111111 1223445554432 122332
Q ss_pred -EEEecHHHHHHHHHHHh----hcCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 209 -RVFSHPQALAQCEMTLS----NLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 209 -~V~SHpqal~QC~~fl~----~~~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
+|--..-... ..|+. ..++..+.+.+..++.+++..+. -.|.|++...+.
T Consensus 134 ~~Igv~~gs~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~gr--iDa~i~d~~~~~ 188 (260)
T PRK15010 134 KHVGVLQGSTQ--EAYANETWRSKGVDVVAYANQDLVYSDLAAGR--LDAALQDEVAAS 188 (260)
T ss_pred CEEEEecCchH--HHHHHHhcccCCceEEecCCHHHHHHHHHcCC--ccEEEeCcHHHH
Confidence 3333221111 12333 23567777888888888888753 346777765543
No 215
>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=39.27 E-value=3.4e+02 Score=25.74 Aligned_cols=145 Identities=18% Similarity=0.150 Sum_probs=70.0
Q ss_pred CCceeEEEEEcCCCc-H-HHHHH--HHhCCCCccccC-CCHHHHHHHHHcCCccEEEEeecccc--ccchHHhHHhhhcC
Q 015945 108 DGTKVRVAYQGLPGA-Y-SEAAA--RKAYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSV--GGSIHRNYDLLLRH 180 (398)
Q Consensus 108 ~q~~~kVa~lGp~Gs-~-s~~AA--~~~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~--~G~V~~tld~L~~~ 180 (398)
..+..+|++..+-+. + ..... +..|+++.+... .+..++.+.+.+|++|+|++...+.. .+.... -|.+.
T Consensus 91 ~~~~l~I~~~~~~~~~~~~~~l~~~~~~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~---~l~~~ 167 (300)
T TIGR02424 91 EGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGLSFE---HLYNE 167 (300)
T ss_pred CCceEEEecccHHHHhhhHHHHHHHHHhCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCcccccceeee---eecCC
Confidence 345677876533221 1 12111 224566655433 36678899999999999997543221 111111 11222
Q ss_pred CeEEEEEEEEeeeEeeecCCCCCccCcc--EEEecHHH---HHHHHHHHhhcCC----eEEecCCHHHHHHHHHhcCCCC
Q 015945 181 RLHIVGEVQLVVNHCLLGLPGVLKEELK--RVFSHPQA---LAQCEMTLSNLGI----VRISADDTAGAAQMVASIGERD 251 (398)
Q Consensus 181 ~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~--~V~SHpqa---l~QC~~fl~~~~~----~~v~~~STA~Aa~~v~~~~~~~ 251 (398)
.+.++ .+-.|-|...+..+++++. ..+..+.. ......|+.+.+. ....+.|......++..+ .
T Consensus 168 ~~~~~----~~~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~ 240 (300)
T TIGR02424 168 PVVFV----VRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQES---D 240 (300)
T ss_pred ceEEE----EcCCCccccCCCCCHHHHhCCCEEecCCCCchHHHHHHHHHHCCCCCCCceEEeccHHHHHHHHHhC---C
Confidence 22222 1223333332222333332 12222221 1334566665332 235677777777777764 3
Q ss_pred eEEEcCHHhHH
Q 015945 252 TGAVASAQAAE 262 (398)
Q Consensus 252 ~AAI~s~~aA~ 262 (398)
..++.+...++
T Consensus 241 gi~~lp~~~~~ 251 (300)
T TIGR02424 241 AIWIISRGVVA 251 (300)
T ss_pred ceEeCcHHHHh
Confidence 46777777664
No 216
>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=38.91 E-value=3.2e+02 Score=25.33 Aligned_cols=139 Identities=21% Similarity=0.140 Sum_probs=69.0
Q ss_pred ceeEEEEEcCCCcHHHHHHH--HhCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEE
Q 015945 110 TKVRVAYQGLPGAYSEAAAR--KAYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVG 186 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~--~~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~ 186 (398)
+..+|++.++ +-+....+. ..++++++.- ..+..++++.+.+|++|+|++....+..+... ..|.+..+.++
T Consensus 87 ~~l~ig~~~~-~~~~~~l~~~~~~~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~lv- 161 (279)
T TIGR03339 87 GSLRIAATAP-YYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDR---VVLGNDPLVAV- 161 (279)
T ss_pred eEEEEeCchH-HHHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEecccCCCceEE---EEcCCceEEEE-
Confidence 5677887543 112222121 1345555433 35778999999999999999854332221111 11112222221
Q ss_pred EEEEeeeEeeecCCCCCccCc---cEEEecH--HHHHHHHHHHhhcCC---eEEecCCHHHHHHHHHhcCCCCeEEEcCH
Q 015945 187 EVQLVVNHCLLGLPGVLKEEL---KRVFSHP--QALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASA 258 (398)
Q Consensus 187 Ei~l~I~h~Ll~~~g~~l~~I---~~V~SHp--qal~QC~~fl~~~~~---~~v~~~STA~Aa~~v~~~~~~~~AAI~s~ 258 (398)
.+-+|-|...+..+++++ .-|...+ ........|+.+.+. ....++|...+.+++..+ ...++.+.
T Consensus 162 ---~s~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~ 235 (279)
T TIGR03339 162 ---VHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAG---LGVSVVSA 235 (279)
T ss_pred ---ECCCCccccCCCcCHHHHhCCCeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcC---CCEEEcch
Confidence 122232322222233333 3333222 123456777776432 234577877777788764 33567766
Q ss_pred H
Q 015945 259 Q 259 (398)
Q Consensus 259 ~ 259 (398)
.
T Consensus 236 ~ 236 (279)
T TIGR03339 236 A 236 (279)
T ss_pred h
Confidence 4
No 217
>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=38.83 E-value=1.4e+02 Score=21.96 Aligned_cols=33 Identities=15% Similarity=0.332 Sum_probs=25.5
Q ss_pred EEEEE-EeCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 301 TSIVF-TLEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 301 tsi~f-~~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
.+++- .+.+.||-+.++++.+++.|||+..+-+
T Consensus 4 isvvG~~~~~~~gi~~~if~aL~~~~I~v~~~~~ 37 (64)
T cd04937 4 VTIIGSRIRGVPGVMAKIVGALSKEGIEILQTAD 37 (64)
T ss_pred EEEECCCccCCcCHHHHHHHHHHHCCCCEEEEEc
Confidence 34443 3457899999999999999999975554
No 218
>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=38.53 E-value=60 Score=31.01 Aligned_cols=49 Identities=20% Similarity=0.181 Sum_probs=36.2
Q ss_pred eeEEEEEcCCCcHHHHHHHHh-CCCCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 111 KVRVAYQGLPGAYSEAAARKA-YPKCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 111 ~~kVa~lGp~Gs~s~~AA~~~-fg~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
..+|+++ .|+....+.+.. +...+++.+++.++++++|.+|++|+.+..
T Consensus 144 g~~Igv~--~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d 193 (275)
T TIGR02995 144 DAKIAAP--GGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGRADAYSLT 193 (275)
T ss_pred CceEEEe--CCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCCCCEEecC
Confidence 4688874 566655544432 344567788999999999999999988875
No 219
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=38.24 E-value=93 Score=32.82 Aligned_cols=113 Identities=17% Similarity=0.084 Sum_probs=58.7
Q ss_pred CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCC----CccCcc-
Q 015945 134 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV----LKEELK- 208 (398)
Q Consensus 134 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~----~l~~I~- 208 (398)
.++++...+|++++.++.+|++|+++..+.-+-+ -...+. . ..-++.+...|+.+++. ++++++
T Consensus 81 ~~e~v~~~~~~~ll~aL~~G~iDi~~~~lt~T~e-----R~~~~~-F-----S~Py~~~~~~lv~r~~~~~i~~l~dL~G 149 (482)
T PRK10859 81 KLEIKVRDNISQLFDALDKGKADLAAAGLTYTPE-----RLKQFR-F-----GPPYYSVSQQLVYRKGQPRPRSLGDLKG 149 (482)
T ss_pred cEEEEecCCHHHHHHHHhCCCCCEEeccCcCChh-----hhccCc-c-----cCCceeeeEEEEEeCCCCCCCCHHHhCC
Confidence 4677778899999999999999987544432211 001110 0 11122334445544432 223332
Q ss_pred -EEEe-----cHHHHHHHHHHHhh-cCCeE--EecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 209 -RVFS-----HPQALAQCEMTLSN-LGIVR--ISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 209 -~V~S-----Hpqal~QC~~fl~~-~~~~~--v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
+|.. +.+.+. ++... +++.. +...|+.++.++|..+. -.++|+....+.
T Consensus 150 k~I~V~~gS~~~~~L~---~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~--iDa~v~d~~~~~ 207 (482)
T PRK10859 150 GTLTVAAGSSHVETLQ---ELKKKYPELSWEESDDKDSEELLEQVAEGK--IDYTIADSVEIS 207 (482)
T ss_pred CeEEEECCCcHHHHHH---HHHHhCCCceEEecCCCCHHHHHHHHHCCC--CCEEEECcHHHH
Confidence 3322 222222 22222 34433 34568889999998763 336666655443
No 220
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=38.21 E-value=2.9e+02 Score=26.77 Aligned_cols=143 Identities=14% Similarity=0.004 Sum_probs=68.6
Q ss_pred CceeEEEEEcCCCcH-H-HHHH--HHhCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHH--hhhcCC
Q 015945 109 GTKVRVAYQGLPGAY-S-EAAA--RKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHR 181 (398)
Q Consensus 109 q~~~kVa~lGp~Gs~-s-~~AA--~~~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld--~L~~~~ 181 (398)
.+..+|++...-+.+ - .... ...++++++.. ..+..++++.+.+|++|+++.+-..... ..++ -|.+..
T Consensus 92 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~~----~~l~~~~l~~~~ 167 (313)
T PRK12684 92 QGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADY----KELVSLPCYQWN 167 (313)
T ss_pred CCeEEEEechHHHHHHhHHHHHHHHHHCCCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCCC----CCceEEEeccce
Confidence 456788875443332 1 2211 11345555433 3467899999999999999986221111 1111 111112
Q ss_pred eEEEEEEEEeeeEeeecCCCCCccC---ccEEEecH-HH-HHHHHHHHhhcC--Ce-EEecCCHHHHHHHHHhcCCCCeE
Q 015945 182 LHIVGEVQLVVNHCLLGLPGVLKEE---LKRVFSHP-QA-LAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDTG 253 (398)
Q Consensus 182 l~I~~Ei~l~I~h~Ll~~~g~~l~~---I~~V~SHp-qa-l~QC~~fl~~~~--~~-~v~~~STA~Aa~~v~~~~~~~~A 253 (398)
+.+ +.+..|-+......++++ ..-|.-.. .. -.+...|+...+ .. ...++|......+|..+. + .
T Consensus 168 ~~~----v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~--G-v 240 (313)
T PRK12684 168 HCV----VVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGL--G-V 240 (313)
T ss_pred EEE----EeCCCCccccCCCcCHHHHhcCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhCC--c-e
Confidence 222 233344443322222222 22222111 11 233455665533 23 356677777777887642 3 5
Q ss_pred EEcCHHhHH
Q 015945 254 AVASAQAAE 262 (398)
Q Consensus 254 AI~s~~aA~ 262 (398)
|+.+..+++
T Consensus 241 ~~lp~~~~~ 249 (313)
T PRK12684 241 GIVADMAFD 249 (313)
T ss_pred EEeehhhcc
Confidence 666665543
No 221
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=38.21 E-value=39 Score=33.31 Aligned_cols=144 Identities=14% Similarity=0.029 Sum_probs=75.5
Q ss_pred CCceeEEEEEcCCCcHHHHHHHHhC----C-CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCe
Q 015945 108 DGTKVRVAYQGLPGAYSEAAARKAY----P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRL 182 (398)
Q Consensus 108 ~q~~~kVa~lGp~Gs~s~~AA~~~f----g-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l 182 (398)
.....+|+|....+-+--.-++.+| | ++++....+..++.+++.+|++|+|++..... ..-.....++
T Consensus 21 ~~~~v~~~y~~~~~~~~vA~~~g~f~~~~Gl~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~-------~~a~~~g~~~ 93 (320)
T PRK11480 21 QAVNVTVAYQTSAEPAKVAQADNTFAKESGATVDWRKFDSGASIVRALASGDVQIGNLGSSPL-------AVAASQQVPI 93 (320)
T ss_pred CCCeEEEEecCCCcHHHHHHHcCchHHHcCCeeEEEEeCCHHHHHHHHHCCCCCEECcCchHH-------HHHHHCCCCe
Confidence 4577899998533322211122234 3 57889999999999999999999997653211 0111122345
Q ss_pred EEEEEEEE-eeeEeeecCCCC-CccCc--cEEEecHHH--HHHHHHHHhhcC-----CeEEecCCHHHHHHHHHhcCCCC
Q 015945 183 HIVGEVQL-VVNHCLLGLPGV-LKEEL--KRVFSHPQA--LAQCEMTLSNLG-----IVRISADDTAGAAQMVASIGERD 251 (398)
Q Consensus 183 ~I~~Ei~l-~I~h~Ll~~~g~-~l~~I--~~V~SHpqa--l~QC~~fl~~~~-----~~~v~~~STA~Aa~~v~~~~~~~ 251 (398)
++++-... .....++++++. +++|. |+|...+-. ...-..||++.+ ++.+... .++++..+..+ .-+
T Consensus 94 ~~v~~~~~~~~~~~lv~~~~I~s~~DLkGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~-~~~~~~Al~~G-~VD 171 (320)
T PRK11480 94 EVFLLASKLGNSEALVVKKTISKPEDLIGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQ-PPAIIAAWQRG-DID 171 (320)
T ss_pred EEEEeeccCCcceEEEecCCCCChHHcCCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECC-cHHHHHHHHcC-CcC
Confidence 54432221 222456665543 33444 456543211 122356777643 3344433 44555555554 345
Q ss_pred eEEEcCHHh
Q 015945 252 TGAVASAQA 260 (398)
Q Consensus 252 ~AAI~s~~a 260 (398)
++++..+..
T Consensus 172 Aa~~~~p~~ 180 (320)
T PRK11480 172 GAYVWAPAV 180 (320)
T ss_pred EEEEcchHH
Confidence 555554443
No 222
>PRK08210 aspartate kinase I; Reviewed
Probab=38.10 E-value=4.6e+02 Score=26.86 Aligned_cols=96 Identities=14% Similarity=-0.007 Sum_probs=56.2
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecccccCCCCceEEEEEecCCC-------CCC---
Q 015945 228 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPI-------IAG--- 294 (398)
Q Consensus 228 ~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a---A~~ygL~il~~~I~D~~~N~TRF~vi~~~~~-------~~~--- 294 (398)
+++.+..-|..+|.++...+ +-+-.+.| |..+|.++.-.|..+... -|..- ...+. .+.
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 45566666777777766542 33444444 456789988888765322 34331 11110 000
Q ss_pred -CCCCceEEEEEE-eCCCcchHHHHHHHHHhCCceeeee
Q 015945 295 -TDRPYKTSIVFT-LEEGPGMLFKALAVFALRDINLTKI 331 (398)
Q Consensus 295 -~~~~~ktsi~f~-~~~~pGaL~~~L~~F~~~~INLt~I 331 (398)
....+-+.+.+. .++.||.+.++++.|+++|||+-.|
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 001223333332 3445999999999999999999988
No 223
>PRK09224 threonine dehydratase; Reviewed
Probab=37.59 E-value=81 Score=33.72 Aligned_cols=35 Identities=26% Similarity=0.392 Sum_probs=31.0
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeee
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 334 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESR 334 (398)
+..-+.|..|.+||+|.+.|+.+. -+-|+|.+|=|
T Consensus 422 ~e~~~~~~fPerpGal~~Fl~~l~-~~~~It~f~Yr 456 (504)
T PRK09224 422 DERLYRFEFPERPGALLKFLSTLG-THWNISLFHYR 456 (504)
T ss_pred ceEEEEEeCCCCCCHHHHHHHhcC-CCCeeEEEEEc
Confidence 455678999999999999999877 78999999998
No 224
>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=37.35 E-value=1.7e+02 Score=24.90 Aligned_cols=123 Identities=17% Similarity=0.121 Sum_probs=61.2
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc-
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 208 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~- 208 (398)
.|+++++.-. .+.++..+.+.+|++|+|++..+....+... ..|.+..+.++. +-.|-+.. +..+++++.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~---~~l~~~~~~lv~----~~~~p~~~-~~~~~~~L~~ 96 (198)
T cd08461 25 EAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLRS---RPLFEERYVCVT----RRGHPLLQ-GPLSLDQFCA 96 (198)
T ss_pred HCCCcEEEEeeCCcccHHHHHhcCCCcEEEecCccCCcccee---eeeecCcEEEEE----cCCChhhc-CCCCHHHHhh
Confidence 3566554332 3456788999999999999853322122111 112222332221 22222221 112222222
Q ss_pred --EEEecH-H-H-HHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHc
Q 015945 209 --RVFSHP-Q-A-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 264 (398)
Q Consensus 209 --~V~SHp-q-a-l~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~y 264 (398)
-|.-++ . . -.+..+|+.+.+. + ...++|...+..+++.+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~ 157 (198)
T cd08461 97 LDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAAT---DMVAFVPSRLVPNL 157 (198)
T ss_pred CCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcC---CeEEEchHHHHHhh
Confidence 232221 1 1 1234566666432 2 34566777777777764 46888888877654
No 225
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=37.32 E-value=1.5e+02 Score=23.78 Aligned_cols=76 Identities=17% Similarity=0.135 Sum_probs=39.8
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCc-HHHHHHHHH
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMAD-PRAQFALGH 378 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d-~~v~~al~~ 378 (398)
+..+.|.+.+..-.|.++|..--.+ -|.......|-+......+....+.|.|+-.|.... ..+.+|++.
T Consensus 8 ~~~~~~~~~~edhTl~n~L~~~l~~---------~pV~~a~Y~v~hp~~~~~~~~d~~~~~VeT~Gs~~P~~al~~Ai~~ 78 (86)
T cd00460 8 KNYVDFVLENEDHTLGNSLRRILLK---------SPVEFAAYYVEHPVKLQRTDEDKFILRIETVGSIPPEEALRRAVEI 78 (86)
T ss_pred CCEEEEEEeCCCchHHHHHHHHHhC---------CCceEEEEEeCCCccCCCCCCCeEEEEEEECCCCCHHHHHHHHHHH
Confidence 4567777776666677766654433 121111111111110111112457888888886533 356678888
Q ss_pred HHHhcC
Q 015945 379 LQEFAT 384 (398)
Q Consensus 379 L~~~~~ 384 (398)
|.+.+.
T Consensus 79 L~~~~~ 84 (86)
T cd00460 79 LRKKLE 84 (86)
T ss_pred HHHHHh
Confidence 877654
No 226
>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=37.00 E-value=2.5e+02 Score=23.52 Aligned_cols=32 Identities=19% Similarity=0.007 Sum_probs=23.3
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEee
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPI 162 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPI 162 (398)
.++++++.- ..+..++.+.+.+|++|+|++.-
T Consensus 25 ~~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~~ 57 (197)
T cd08438 25 RYPNIELELVEYGGKKVEQAVLNGELDVGITVL 57 (197)
T ss_pred HCcCeEEEEEEcCcHHHHHHHHcCCCCEEEEec
Confidence 355555432 34667889999999999999753
No 227
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=36.73 E-value=1.4e+02 Score=27.90 Aligned_cols=36 Identities=19% Similarity=0.262 Sum_probs=29.9
Q ss_pred eEEEEEEe--CCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 015945 300 KTSIVFTL--EEGPGMLFKALAVFALRDINLTKIESRPQR 337 (398)
Q Consensus 300 ktsi~f~~--~~~pGaL~~~L~~F~~~~INLt~IESRP~~ 337 (398)
++.+++++ +|+||-.+++-+.++++|.|+. +||-..
T Consensus 6 ~~~lviTviG~DrpGIVa~vs~~l~~~g~NI~--ds~~t~ 43 (190)
T PRK11589 6 QHYLVITALGADRPGIVNTITRHVSSCGCNIE--DSRLAM 43 (190)
T ss_pred ccEEEEEEEcCCCChHHHHHHHHHHHcCCCee--ehhhHh
Confidence 45667766 7999999999999999999987 667655
No 228
>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=36.66 E-value=72 Score=24.03 Aligned_cols=33 Identities=33% Similarity=0.407 Sum_probs=25.9
Q ss_pred eEEEEEE-eC-CCcchHHHHHHHHHhCCceeeeee
Q 015945 300 KTSIVFT-LE-EGPGMLFKALAVFALRDINLTKIE 332 (398)
Q Consensus 300 ktsi~f~-~~-~~pGaL~~~L~~F~~~~INLt~IE 332 (398)
+.++... +. +.||-+.++.+.+++.|||+..|-
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 3445555 44 489999999999999999999887
No 229
>PRK11260 cystine transporter subunit; Provisional
Probab=35.97 E-value=2.5e+02 Score=26.45 Aligned_cols=117 Identities=17% Similarity=0.095 Sum_probs=60.4
Q ss_pred CC-CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCC-----CCcc
Q 015945 132 YP-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG-----VLKE 205 (398)
Q Consensus 132 fg-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g-----~~l~ 205 (398)
.| .+++++. +|.++++++.+|++|+++-++.-+-+ -...++ ....+. .....++.+.+ .+++
T Consensus 78 lg~~~e~~~~-~~~~~~~~l~~G~~D~~~~~~~~~~~--r~~~~~--fs~p~~-------~~~~~~~~~~~~~~~~~~~~ 145 (266)
T PRK11260 78 LGVKASLKPT-KWDGMLASLDSKRIDVVINQVTISDE--RKKKYD--FSTPYT-------VSGIQALVKKGNEGTIKTAA 145 (266)
T ss_pred HCCeEEEEeC-CHHHHHHHHhcCCCCEEEeccccCHH--HHhccc--cCCcee-------ecceEEEEEcCCcCCCCCHH
Confidence 35 5677775 69999999999999998754321110 000110 001111 11122333221 1122
Q ss_pred Ccc--EEEecHHHHHHHHHHHhh--cCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHc
Q 015945 206 ELK--RVFSHPQALAQCEMTLSN--LGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIY 264 (398)
Q Consensus 206 ~I~--~V~SHpqal~QC~~fl~~--~~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~y 264 (398)
+++ +|-.-. .... ..|+.+ ++.+...+.+..++.+.+..+. -.++|+....+..+
T Consensus 146 dL~g~~Igv~~-G~~~-~~~l~~~~~~~~i~~~~~~~~~l~~L~~Gr--vD~~i~d~~~~~~~ 204 (266)
T PRK11260 146 DLKGKKVGVGL-GTNY-EQWLRQNVQGVDVRTYDDDPTKYQDLRVGR--IDAILVDRLAALDL 204 (266)
T ss_pred HcCCCEEEEec-CCcH-HHHHHHhCCCCceEecCCHHHHHHHHHcCC--CCEEEechHHHHHH
Confidence 221 222211 1111 346655 4667778889999988888753 34777776655443
No 230
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=35.71 E-value=5.2e+02 Score=29.62 Aligned_cols=127 Identities=11% Similarity=0.095 Sum_probs=75.7
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH---HcCCceeecccccCCCCceEEEEEecCCCCCC----CCCCce
Q 015945 228 GIVRISADDTAGAAQMVASIGERDTGAVASAQAAE---IYGLDILAEKIQDDDDNVTRFLILAREPIIAG----TDRPYK 300 (398)
Q Consensus 228 ~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~---~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~----~~~~~k 300 (398)
+++.+..-|..+|.+++..+ |.+-...|.+ .+|.++.-.|..+....-|..- ......+. ....+-
T Consensus 250 ~a~~i~~ls~~e~~el~~~g-----~~v~~~~a~~~a~~~~i~i~v~~~~~~~~~gT~I~--~~~~~~~~v~~It~~~~v 322 (861)
T PRK08961 250 DARLLTRLDYDEAQEIATTG-----AKVLHPRSIKPCRDAGIPMAILDTERPDLSGTSID--GDAEPVPGVKAISRKNGI 322 (861)
T ss_pred CceEecccCHHHHHHHHHCC-----CeEECHHHHHHHHHCCCCEEEEeCCCCCCCccEEe--CCCCCCCcceeEEEECCE
Confidence 45677777888888876642 5666666654 5899999888766544445442 11111110 011223
Q ss_pred EEEEEE---eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCC-CcHHHHHHH
Q 015945 301 TSIVFT---LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASM-ADPRAQFAL 376 (398)
Q Consensus 301 tsi~f~---~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~-~d~~v~~al 376 (398)
+-|.+. ..+.+|.+.++++.|+++|||+-.|.|-. ....|.++-.... .+..++.++
T Consensus 323 ~lItv~~~~~~~~~g~~a~if~~la~~~I~Vd~I~sse-------------------~sis~~i~~~~~~~~~~~~~~l~ 383 (861)
T PRK08961 323 VLVSMETIGMWQQVGFLADVFTLFKKHGLSVDLISSSE-------------------TNVTVSLDPSENLVNTDVLAALS 383 (861)
T ss_pred EEEEEecCCccccccHHHHHHHHHHHcCCeEEEEEcCC-------------------CEEEEEEccccccchHHHHHHHH
Confidence 333332 24679999999999999999999995321 2466777654321 123455555
Q ss_pred HHHH
Q 015945 377 GHLQ 380 (398)
Q Consensus 377 ~~L~ 380 (398)
++|+
T Consensus 384 ~~l~ 387 (861)
T PRK08961 384 ADLS 387 (861)
T ss_pred HHHh
Confidence 6664
No 231
>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=35.71 E-value=85 Score=25.09 Aligned_cols=38 Identities=24% Similarity=0.410 Sum_probs=29.7
Q ss_pred ccceEEEEEeecCCCcHHHHHHHHHHHHhcCc-----eEEEcc
Q 015945 354 YFDYLFYIDFEASMADPRAQFALGHLQEFATF-----LRVLGC 391 (398)
Q Consensus 354 ~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~~-----vkiLGs 391 (398)
.+.|+|-||+.|+..-..=+++|+.|+..... |+|-|+
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 36899999999987777778899999876543 677665
No 232
>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=35.23 E-value=1.9e+02 Score=21.91 Aligned_cols=27 Identities=22% Similarity=0.348 Sum_probs=23.6
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
+.+.+|.+.++++.|++++||+-.|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~~ 37 (80)
T cd04921 11 MVGVPGIAARIFSALARAGINVILISQ 37 (80)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEe
Confidence 456799999999999999999988854
No 233
>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=35.07 E-value=1e+02 Score=24.48 Aligned_cols=64 Identities=16% Similarity=0.055 Sum_probs=39.5
Q ss_pred CcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCC-CcHHHHHHHHHHHH
Q 015945 310 GPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASM-ADPRAQFALGHLQE 381 (398)
Q Consensus 310 ~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~-~d~~v~~al~~L~~ 381 (398)
.+|.++++=+.++.+|+|+..|...-... + ..+......|..-++++|.. +...++..|.++..
T Consensus 10 ~a~~ia~Vs~~lA~~~~NI~~I~~l~~~~-~-------~~~~~~~~~~~~e~~v~~~~~~~~~lr~~L~~la~ 74 (84)
T cd04871 10 TAEQLAAVTRVVADQGLNIDRIRRLSGRV-P-------LEEQDDSPKACVEFSVRGQPADLEALRAALLELAS 74 (84)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHhhccc-c-------ccccCCCCcEEEEEEEeCCCCCHHHHHHHHHHHhc
Confidence 68999999999999999999887641110 0 00101123466566666543 33466776776653
No 234
>COG3265 GntK Gluconate kinase [Carbohydrate transport and metabolism]
Probab=35.06 E-value=82 Score=28.68 Aligned_cols=78 Identities=15% Similarity=0.140 Sum_probs=50.1
Q ss_pred ccchhhcccCCCCCceeEEEEEcCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHcCC--ccEEEEeeccccccchHHh
Q 015945 96 PLSIMELSSSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWL--VDKAVLPIENSVGGSIHRN 173 (398)
Q Consensus 96 ~I~R~iis~s~~~q~~~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~--~d~gvVPIENS~~G~V~~t 173 (398)
+-||.+++...- ..++.|| .|+|.-...|..-....+.+.+=.+.-|++++.=. -|...|+|..+.+..|.+.
T Consensus 79 r~YRD~LR~~~~---~~~Fv~L--~g~~~~i~~Rm~~R~gHFM~~~ll~SQfa~LE~P~~de~vi~idi~~~~e~vv~~~ 153 (161)
T COG3265 79 RSYRDLLREANP---GLRFVYL--DGDFDLILERMKARKGHFMPASLLDSQFATLEEPGADEDVLTIDIDQPPEEVVAQA 153 (161)
T ss_pred HHHHHHHhccCC---CeEEEEe--cCCHHHHHHHHHhcccCCCCHHHHHHHHHHhcCCCCCCCEEEeeCCCCHHHHHHHH
Confidence 577888876643 2566665 78887766653222334444444556677776532 2677777778889888888
Q ss_pred HHhhh
Q 015945 174 YDLLL 178 (398)
Q Consensus 174 ld~L~ 178 (398)
+..+.
T Consensus 154 ~~~l~ 158 (161)
T COG3265 154 LAWLK 158 (161)
T ss_pred HHHHh
Confidence 87664
No 235
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=34.16 E-value=4.5e+02 Score=25.61 Aligned_cols=143 Identities=16% Similarity=0.149 Sum_probs=72.5
Q ss_pred ceeEEEEEcCCCcH--HHHH--HHHhCCCCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEE
Q 015945 110 TKVRVAYQGLPGAY--SEAA--ARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIV 185 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~--s~~A--A~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~ 185 (398)
+..+|++...-+.+ .... .+..++++.+.. .+..+.++.|.+|++|+|+.+-.....|.... .|.+..+.+
T Consensus 117 ~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~~-~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~---~l~~~~~~l- 191 (317)
T PRK11482 117 RTITIATTPSVGALVMPVIYQAIKTHYPQLLLRN-IPISDAENQLSQFQTDLIIDTHSCSNRTIQHH---VLFTDNVVL- 191 (317)
T ss_pred ceEEEEecHHHHHHHHHHHHHHHHHHCCCCEEEE-ecchhHHHHHHCCCcCEEEeccCCCCCceEEE---EEecCcEEE-
Confidence 45677765443332 1111 122455665432 24458899999999999998754333332221 122223322
Q ss_pred EEEEEeeeEeeecCCCCCccCccE----E-EecHHHHHHHHHHHhhc--CCe-EEecCCHHHHHHHHHhcCCCCeEEEcC
Q 015945 186 GEVQLVVNHCLLGLPGVLKEELKR----V-FSHPQALAQCEMTLSNL--GIV-RISADDTAGAAQMVASIGERDTGAVAS 257 (398)
Q Consensus 186 ~Ei~l~I~h~Ll~~~g~~l~~I~~----V-~SHpqal~QC~~fl~~~--~~~-~v~~~STA~Aa~~v~~~~~~~~AAI~s 257 (398)
..+-.|-|... ..+++++.. + ...+......++++... ... ...++|......+++.+ ...+|.+
T Consensus 192 ---v~~~~hpl~~~-~~~~~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~ilp 264 (317)
T PRK11482 192 ---VCRQGHPLLSL-EDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASS---DMLGIMP 264 (317)
T ss_pred ---EEeCCCCccCC-CCCHHHHhhCCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcC---CeeEEeH
Confidence 23445555432 334555542 2 22222212334555542 223 23556666667777754 4577888
Q ss_pred HHhHHHc
Q 015945 258 AQAAEIY 264 (398)
Q Consensus 258 ~~aA~~y 264 (398)
...+..+
T Consensus 265 ~~~~~~~ 271 (317)
T PRK11482 265 SRFYNLF 271 (317)
T ss_pred HHHHHHH
Confidence 8776543
No 236
>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=34.14 E-value=2.8e+02 Score=23.29 Aligned_cols=32 Identities=6% Similarity=-0.052 Sum_probs=22.4
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEee
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPI 162 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPI 162 (398)
.++++++.-. .+..++.+.+.+|++|+|+..-
T Consensus 25 ~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (196)
T cd08456 25 RHPDVTISIHTRDSPTVEQWLSAQQCDLGLVST 57 (196)
T ss_pred HCCCcEEEEEeCCHHHHHHHHHcCCccEEEEec
Confidence 3455544322 3556788999999999999753
No 237
>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=34.05 E-value=1.4e+02 Score=25.58 Aligned_cols=114 Identities=18% Similarity=0.134 Sum_probs=60.9
Q ss_pred CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCC---ccCcc--
Q 015945 134 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVL---KEELK-- 208 (398)
Q Consensus 134 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~---l~~I~-- 208 (398)
++++.+.. +.++.+++.+|++|+++.+...+.+. ...+. . ........+.++.+++.. +++++
T Consensus 39 ~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~~-----~~~~~-----~-~~~~~~~~~~~~~~~~~~~~~~~dl~g~ 106 (218)
T cd00134 39 KVKFVEVD-WDGLITALKSGKVDLIAAGMTITPER-----AKQVD-----F-SDPYYKSGQVILVKKGSPIKSVKDLKGK 106 (218)
T ss_pred eEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHHH-----Hhhcc-----C-cccceeccEEEEEECCCCCCChHHhCCC
Confidence 46677776 89999999999999998876211111 00000 0 001122234455544422 23322
Q ss_pred EEEecHHHHHHHHHHHhh-c-CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 209 RVFSHPQALAQCEMTLSN-L-GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 209 ~V~SHpqal~QC~~fl~~-~-~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
+|..-+ . .-...++.+ . ....+.+.|..++.+++..+. ..|++.....+..
T Consensus 107 ~i~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~--~d~~~~~~~~~~~ 159 (218)
T cd00134 107 KVAVQK-G-STAEKYLKKALPEAKVVSYDDNAEALAALENGR--ADAVIVDEIALAA 159 (218)
T ss_pred EEEEEc-C-chHHHHHHHhCCcccEEEeCCHHHHHHHHHcCC--ccEEEeccHHHHH
Confidence 222111 1 112344444 2 356778888899999998763 3466666555443
No 238
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=33.89 E-value=4.1e+02 Score=25.10 Aligned_cols=114 Identities=11% Similarity=0.009 Sum_probs=58.3
Q ss_pred hCCCCccc-cCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCccE
Q 015945 131 AYPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR 209 (398)
Q Consensus 131 ~fg~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~~ 209 (398)
.|+++++. ...+..++++.+.+|++|+|+..-.....+ +..+......+++++.++-.+..-..
T Consensus 114 ~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~---------------l~~~~l~~~~~~~v~~~~~~~~~~~~ 178 (275)
T PRK03601 114 NQEALQFEARIAQRQSLVKQLHERQLDLLITTEAPKMDE---------------FSSQLLGHFTLALYTSAPSKKKSELN 178 (275)
T ss_pred hCCCcEEEEEECChHHHHHHHHcCCCCEEEEcCCCccCC---------------ccEEEecceeEEEEecCchhhcccCC
Confidence 45566553 355667899999999999999753321111 11122222334444443321111111
Q ss_pred EE--ecHHHHHHHHHHHhhcCC-eEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 210 VF--SHPQALAQCEMTLSNLGI-VRISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 210 V~--SHpqal~QC~~fl~~~~~-~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
.+ ..+..+.+-..++...+. ....++|.....++|+.+ ...|+++...+.
T Consensus 179 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~~~p~~~~~ 231 (275)
T PRK03601 179 YIRLEWGADFQQHEAGLIGADEVPILTTSSAELARQLLATL---NGCAFLPVHWAK 231 (275)
T ss_pred eEEccCCccHhHHHHHhcccCCcceEEeCcHHHHHHHHHhC---CCEEEEcHHHHh
Confidence 11 122223222222222221 245677888888888865 347888887664
No 239
>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=33.63 E-value=3.8e+02 Score=25.43 Aligned_cols=110 Identities=10% Similarity=-0.004 Sum_probs=59.6
Q ss_pred ccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCC-----CccCc-----
Q 015945 138 VPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV-----LKEEL----- 207 (398)
Q Consensus 138 ~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~-----~l~~I----- 207 (398)
....+|.+++..+.+|++|+.+..+.-+-+. .+.+.-+.- +......++.+++. +++++
T Consensus 76 ~~~~~w~~~~~~l~~G~~Di~~~~~~~t~eR-----~~~~~fs~p------y~~~~~~~~~~~~~~~~i~~~~dl~~~~g 144 (275)
T TIGR02995 76 ASITEYGALIPGLQAGRFDAIAAGLFIKPER-----CKQVAFTQP------ILCDAEALLVKKGNPKGLKSYKDIAKNPD 144 (275)
T ss_pred eccCCHHHHHHHHHCCCcCEEeecccCCHHH-----Hhccccccc------eeecceeEEEECCCCCCCCCHHHhccCCC
Confidence 4567899999999999999866533211111 011100111 11122334444331 22333
Q ss_pred cEEEecHHHHHHHHHHHhhc---CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 208 KRVFSHPQALAQCEMTLSNL---GIVRISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 208 ~~V~SHpqal~QC~~fl~~~---~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
++|-....... .+||.+. ..+++.+.|..++.+++..+. -.++|+....+.
T Consensus 145 ~~Igv~~g~~~--~~~l~~~~~~~~~i~~~~~~~~~i~~L~~gr--vDa~i~d~~~~~ 198 (275)
T TIGR02995 145 AKIAAPGGGTE--EKLAREAGVKREQIIVVPDGQSGLKMVQDGR--ADAYSLTVLTIN 198 (275)
T ss_pred ceEEEeCCcHH--HHHHHHcCCChhhEEEeCCHHHHHHHHHcCC--CCEEecChHHHH
Confidence 24433332221 3466552 346778899999999999863 447787776544
No 240
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=33.52 E-value=4.2e+02 Score=25.72 Aligned_cols=144 Identities=13% Similarity=0.058 Sum_probs=68.4
Q ss_pred CceeEEEEEcCCCcH--HHHHH--HHhCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeE
Q 015945 109 GTKVRVAYQGLPGAY--SEAAA--RKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLH 183 (398)
Q Consensus 109 q~~~kVa~lGp~Gs~--s~~AA--~~~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~ 183 (398)
.+..+|++...-+.+ ..... ...++++.+.. ..+..++.+.+.+|++|+++.+-.......+. ...|.+..+.
T Consensus 92 ~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l~--~~~l~~~~~~ 169 (316)
T PRK12679 92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLV--AFPWFRWHHS 169 (316)
T ss_pred CceEEEEechHhhhcchHHHHHHHHHHCCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCCCCce--EEEccCCcEE
Confidence 356778875433321 22111 12356555432 34677899999999999999753211110010 0111222222
Q ss_pred EEEEEEEeeeEeeecCCCCCccCcc---EEEecHH--HHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEE
Q 015945 184 IVGEVQLVVNHCLLGLPGVLKEELK---RVFSHPQ--ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAV 255 (398)
Q Consensus 184 I~~Ei~l~I~h~Ll~~~g~~l~~I~---~V~SHpq--al~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI 255 (398)
++.+..|-|......+++++. -|.-++. .-.....|+...+. . ...++|+..+.++|..+ ...|+
T Consensus 170 ----~v~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g---~Gi~~ 242 (316)
T PRK12679 170 ----LLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALG---LGIGL 242 (316)
T ss_pred ----EEecCCCccccCCCCCHHHHhCCCeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcC---CcEEE
Confidence 233445554432222333332 2322221 12235566665433 2 34556677667777764 23566
Q ss_pred cCHHhH
Q 015945 256 ASAQAA 261 (398)
Q Consensus 256 ~s~~aA 261 (398)
.+..++
T Consensus 243 lp~~~~ 248 (316)
T PRK12679 243 VAEQSS 248 (316)
T ss_pred eccccc
Confidence 666543
No 241
>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=33.40 E-value=1.8e+02 Score=20.83 Aligned_cols=27 Identities=26% Similarity=0.347 Sum_probs=23.4
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 307 LEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 307 ~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
+++.||.+.++++.++..|||+-.|-.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 37 (66)
T cd04916 11 MKNTVGVSARATAALAKAGINIRMINQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 456899999999999999999988843
No 242
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=33.04 E-value=1.6e+02 Score=33.57 Aligned_cols=33 Identities=27% Similarity=0.306 Sum_probs=29.5
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeee
Q 015945 298 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTK 330 (398)
Q Consensus 298 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~ 330 (398)
+++|.|=+.-.|+||-|+.+.++|++.|+++..
T Consensus 789 ~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~ 821 (867)
T COG2844 789 NDKTVLEVRALDRPGLLAALAGVFADLGLSLHS 821 (867)
T ss_pred CCceEEEEEeCCcccHHHHHHHHHHhcccceee
Confidence 457888888899999999999999999999873
No 243
>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=32.87 E-value=1e+02 Score=26.67 Aligned_cols=32 Identities=13% Similarity=-0.067 Sum_probs=23.9
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEee
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPI 162 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPI 162 (398)
.++++++... .+..++.+.+.+|++|+|++.-
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (202)
T cd08468 25 LAPSVRLNLVHAEQKLPLDALLAGEIDFALGYS 57 (202)
T ss_pred hCCCCEEEEEECChHhHHHHHHCCCccEEEecc
Confidence 3566665433 4678999999999999999753
No 244
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=32.84 E-value=85 Score=29.14 Aligned_cols=49 Identities=27% Similarity=0.243 Sum_probs=37.2
Q ss_pred eeEEEEEcCCCcH--HHHHHHHhCCCCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 111 KVRVAYQGLPGAY--SEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 111 ~~kVa~lGp~Gs~--s~~AA~~~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
..+|+++ .||. .........+...+..+++..+++.++.+|++|..+..
T Consensus 146 gk~v~v~--~gt~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d 196 (275)
T COG0834 146 GKKVGVQ--LGTTDEAEEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSD 196 (275)
T ss_pred CCEEEEE--cCcchhHHHHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcc
Confidence 4678875 4555 44444434456889999999999999999999999875
No 245
>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=32.67 E-value=1.3e+02 Score=22.68 Aligned_cols=62 Identities=23% Similarity=0.267 Sum_probs=44.7
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcH-HHHHHHHHHHHh
Q 015945 304 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADP-RAQFALGHLQEF 382 (398)
Q Consensus 304 ~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~-~v~~al~~L~~~ 382 (398)
-|.+++..-++..+|.-.-..++.-..|...|.. ..|.|.|+-.|..+.. -+.+|++.|.+.
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 4556666678888998888889888888884432 4689999999986332 456777777654
No 246
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=31.70 E-value=3.4e+02 Score=28.60 Aligned_cols=49 Identities=12% Similarity=0.128 Sum_probs=34.2
Q ss_pred eeEEEEEcCCCcHHHHHHHH---hCCCCc--cccCCCHHHHHHHHHcCCccEEEEe
Q 015945 111 KVRVAYQGLPGAYSEAAARK---AYPKCE--TVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 111 ~~kVa~lGp~Gs~s~~AA~~---~fg~~~--~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
..+|++. .|+..+...+. .++... .....+.++++++|.+|++|+.++.
T Consensus 149 Gk~I~V~--~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d 202 (482)
T PRK10859 149 GGTLTVA--AGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIAD 202 (482)
T ss_pred CCeEEEE--CCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEEC
Confidence 4678875 56654443332 344433 4567899999999999999999884
No 247
>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=31.66 E-value=2.4e+02 Score=23.87 Aligned_cols=122 Identities=13% Similarity=0.001 Sum_probs=59.1
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc-
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 208 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~- 208 (398)
.++++++.-. .+..+..+.+.+|++|+|+..-.....+. ....|.+..+.++ .+-+|-+.. ...+++++.
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~~~~~-~~~~~~~l~~ 96 (200)
T cd08464 25 EAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWL---KREVLYTEGYACL----FDPQQLSLS-APLTLEDYVA 96 (200)
T ss_pred HCCCcEEEEecCCcccHHHHHhcCcccEEEecCCCCcccc---eeeeecccceEEE----EeCCCcccc-CCCCHHHHhc
Confidence 4566655333 34567789999999999997533211111 1111222233222 222232211 112233322
Q ss_pred --E-EEecHHH-HHHHHHHHhhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 209 --R-VFSHPQA-LAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 209 --~-V~SHpqa-l~QC~~fl~~~~~--~~-v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
. ++.+... ......|+.+.+. .. ..++|......+++.+ ...||.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 155 (200)
T cd08464 97 RPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGT---PLIATVPARLARA 155 (200)
T ss_pred CCcEEecCCCCCcchHHHHHHHcCCCcceEEEcCchhhHHHHHcCC---CceeecHHHHHHH
Confidence 1 2222111 1234566666443 22 3556666666666653 4589999888764
No 248
>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=30.89 E-value=3.3e+02 Score=23.00 Aligned_cols=121 Identities=16% Similarity=0.082 Sum_probs=58.5
Q ss_pred CCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCC-CCCccCcc-
Q 015945 132 YPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLP-GVLKEELK- 208 (398)
Q Consensus 132 fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~-g~~l~~I~- 208 (398)
++++++.. ..+..++.+.+.+|++|+|+..-.....+... ..|.+..+.++ .+-.|-+.... ..+++++.
T Consensus 27 ~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~pl~~~~~~~~~~dL~~ 99 (197)
T cd08425 27 YPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDA---QPLFDERLALV----VGATHPLAQRRTALTLDDLAA 99 (197)
T ss_pred CCCcEEEEEECcHHHHHHHHHcCCccEEEEecCCCCCCcEE---EEeccccEEEE----ecCCCchhHhcccCCHHHHhc
Confidence 45555433 24567899999999999999764322111111 11111122111 12222222211 12233322
Q ss_pred --EEE-ecH-HHHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 209 --RVF-SHP-QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 209 --~V~-SHp-qal~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
-|. ... .......+|+.+.+. + ...++|...+.++++.+ ...|+.+...++
T Consensus 100 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08425 100 EPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRG---RLATILPDAIAR 157 (197)
T ss_pred CCcEecCCCccHHHHHHHHHHHcCCCeeeEEeeCcHHHHHHHHhcC---CcEEeechhhhc
Confidence 222 111 122345667766443 2 23567777777777764 346777776543
No 249
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=30.54 E-value=4.4e+02 Score=24.38 Aligned_cols=118 Identities=14% Similarity=0.126 Sum_probs=67.0
Q ss_pred CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEE-----eeeEeeecCCCC---Ccc
Q 015945 134 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQL-----VVNHCLLGLPGV---LKE 205 (398)
Q Consensus 134 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l-----~I~h~Ll~~~g~---~l~ 205 (398)
.+++....++.+..+++.+|++|+++.+-. ....+-.+.++..++...- ...-.++++++. +++
T Consensus 30 ~v~~~~~~~~~~~~~~l~~g~~D~~~~~~~--------~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds~i~~l~ 101 (243)
T PF12974_consen 30 PVELVPADDYAEFIEALRSGEIDLAFMGPL--------PYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADSPITSLA 101 (243)
T ss_dssp EEEEE--SSHHHHHHHHHTTS-SEEE--HH--------HHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTSS--SHH
T ss_pred CEEEEEcCCHHHHHHHHHcCCccEEEECcH--------HHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCCCCCChh
Confidence 478899999999999999999999998621 1222223346666666655 333455565554 334
Q ss_pred Cc---cEEEecHHH---HHHHHHHH-hhcC------CeEEecCCHHHHHHHHHhcCCCCeEEEcCHHh
Q 015945 206 EL---KRVFSHPQA---LAQCEMTL-SNLG------IVRISADDTAGAAQMVASIGERDTGAVASAQA 260 (398)
Q Consensus 206 ~I---~~V~SHpqa---l~QC~~fl-~~~~------~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a 260 (398)
|+ +-.+..|.. .--.+.+| ++.+ ...+.+.|-..+++.+..+ .-+.|++.+...
T Consensus 102 dL~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G-~~Da~~~~~~~~ 168 (243)
T PF12974_consen 102 DLKGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNG-KADAAAIPSDAF 168 (243)
T ss_dssp HHGGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTT-SSSEEEEEHHHH
T ss_pred hcCCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcC-CccEEEEechhH
Confidence 44 234445543 34456677 5533 3456777777888888875 345555554433
No 250
>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=28.91 E-value=3.6e+02 Score=22.83 Aligned_cols=122 Identities=11% Similarity=-0.013 Sum_probs=59.2
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeecccc-ccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSV-GGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK 208 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~-~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~ 208 (398)
.++++++.. ..+..++.+.+.+|++|+|++.-.... .+.+ ....|.+..+.++ .+-+|-|......+++++.
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l--~~~~l~~~~~~~~----~~~~hpl~~~~~i~~~dL~ 98 (198)
T cd08437 25 TGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSAL--HSKIIKTQHFMII----VSKDHPLAKAKKVNFADLK 98 (198)
T ss_pred hCCceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCcccc--eEEEeecceEEEE----ecCCCcccccCcccHHHHc
Confidence 356655543 346788999999999999998532111 1000 0111122222221 2233333322223333332
Q ss_pred ---EEE-ecHH-HHHHHHHHHhhcC--Ce-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015945 209 ---RVF-SHPQ-ALAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDTGAVASAQAA 261 (398)
Q Consensus 209 ---~V~-SHpq-al~QC~~fl~~~~--~~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA 261 (398)
-|. .... --.+...|+.+.+ .+ ...++|...+.++++.+ ...|+.+...+
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 156 (198)
T cd08437 99 KENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVREN---VGIGFLTDIAV 156 (198)
T ss_pred CCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CcEEEEEhhhc
Confidence 232 1111 1234555665543 23 34566666677777764 34677776654
No 251
>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=28.87 E-value=2.5e+02 Score=25.99 Aligned_cols=108 Identities=19% Similarity=0.198 Sum_probs=60.8
Q ss_pred HHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeE---eeecCCCCCc---cC--ccEEEe-c
Q 015945 143 FEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNH---CLLGLPGVLK---EE--LKRVFS-H 213 (398)
Q Consensus 143 ~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h---~Ll~~~g~~l---~~--I~~V~S-H 213 (398)
..|+-..|++|.+|+|++= .|.+.+++..+..-..|...+ +++++++.+. ++ -++|.+ .
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 3478899999999999863 233344433332223344444 4445544322 22 145776 5
Q ss_pred HHHHHHHHHHHhhcC--CeEEecCCHHHHHHHHHhcCCCCeEEE----cCHHhHHHcCCceee
Q 015945 214 PQALAQCEMTLSNLG--IVRISADDTAGAAQMVASIGERDTGAV----ASAQAAEIYGLDILA 270 (398)
Q Consensus 214 pqal~QC~~fl~~~~--~~~v~~~STA~Aa~~v~~~~~~~~AAI----~s~~aA~~ygL~il~ 270 (398)
|. -.++|+.+.+ ++++..+.+-|+|-.+ + -+-|| .|-..-+.+||++++
T Consensus 117 p~---i~~~~f~~~Gi~v~ii~l~GsvE~aP~~---G--laD~IvDiv~TG~TL~~NgL~~ie 171 (182)
T TIGR00070 117 PN---LARRYFEKKGIDVEIIKLNGSVELAPLL---G--LADAIVDIVSTGTTLRENGLRIIE 171 (182)
T ss_pred HH---HHHHHHHHcCCeEEEEECcceeecccCC---C--ceeEEEEEeCCHHHHHHCCCEEee
Confidence 65 4567999865 4566665555543321 1 22244 255566789999995
No 252
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=28.78 E-value=80 Score=30.74 Aligned_cols=53 Identities=23% Similarity=0.219 Sum_probs=39.7
Q ss_pred ceeEEEEEc----CCCcHHHHHHHHhCC-----CCccccCCCHHHHHHHHHcCCccEEEEeec
Q 015945 110 TKVRVAYQG----LPGAYSEAAARKAYP-----KCETVPCDQFEAAFKAVELWLVDKAVLPIE 163 (398)
Q Consensus 110 ~~~kVa~lG----p~Gs~s~~AA~~~fg-----~~~~~~~~s~~~v~~aV~~g~~d~gvVPIE 163 (398)
...++++-- |.|.|+.++.. ..| ..++....+..+++..|+.|++|+|+|=..
T Consensus 134 ~~~~lai~~p~~~P~G~ya~~~l~-~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~s 195 (258)
T COG0725 134 PDVRLAIGDPKTVPAGKYAKEALE-LLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYVS 195 (258)
T ss_pred cCcEEEecCCCCCCchHHHHHHHH-HhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEEE
Confidence 345676653 67888887554 444 236778888899999999999999999754
No 253
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=28.72 E-value=3.3e+02 Score=25.48 Aligned_cols=40 Identities=10% Similarity=0.250 Sum_probs=28.5
Q ss_pred cHHHHHHHHhCC-CCccccCCCHHHHHHHHHcCCccEEEEeec
Q 015945 122 AYSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLPIE 163 (398)
Q Consensus 122 s~s~~AA~~~fg-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIE 163 (398)
.+-+.+++. .| ++++... +|..++.++++|++|+++-++.
T Consensus 54 di~~~ia~~-lg~~i~~~~~-pw~~~~~~l~~g~~D~~~~~~~ 94 (259)
T PRK15437 54 DLAKELCKR-INTQCTFVEN-PLDALIPSLKAKKIDAIMSSLS 94 (259)
T ss_pred HHHHHHHHH-cCCceEEEeC-CHHHHHHHHHCCCCCEEEecCC
Confidence 344455543 34 5677765 5999999999999998776654
No 254
>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=28.00 E-value=3.7e+02 Score=22.64 Aligned_cols=120 Identities=18% Similarity=0.160 Sum_probs=59.7
Q ss_pred CCCCcccc-CCCHHHHHHHHHcCCccEEEEeecccc--ccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc
Q 015945 132 YPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSV--GGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK 208 (398)
Q Consensus 132 fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~--~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~ 208 (398)
++++.+.. ..+..++.+.+.+|++|+|+....... .+... ..|.+..+.++. +-+|-+.. + .+++++.
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~---~~l~~~~~~~v~----~~~~~~~~-~-~~~~~l~ 96 (201)
T cd08418 26 FPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELIS---EPLFESDFVVVA----RKDHPLQG-A-RSLEELL 96 (201)
T ss_pred CCCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCCCCcceeE---EeecCCceEEEe----CCCCcccc-C-CCHHHHc
Confidence 45555433 245678999999999999997532211 11111 111222222221 11222211 1 1223322
Q ss_pred ---EEEec--HHHHHHHHHHHhhcC--Ce-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 209 ---RVFSH--PQALAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 209 ---~V~SH--pqal~QC~~fl~~~~--~~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
-|... ......+.+|+.+.+ .. ...++|...+.++|+.+ ...||.+...++.
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 156 (201)
T cd08418 97 DASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKA---DFLTILSRDMGRG 156 (201)
T ss_pred CCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhC---CEEEEeEHHHhhh
Confidence 23221 122334556666533 22 34567777777888865 4578888776653
No 255
>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=27.48 E-value=3.6e+02 Score=22.43 Aligned_cols=33 Identities=15% Similarity=0.047 Sum_probs=23.9
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeec
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIE 163 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIE 163 (398)
.++++.+.- ..+..++.+.+.+|++|+|+..-.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (194)
T cd08436 25 RHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLP 58 (194)
T ss_pred HCCCcEEEEecCCHHHHHHHHHcCCccEEEEecC
Confidence 456655433 235678899999999999998643
No 256
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=27.28 E-value=1.5e+02 Score=27.92 Aligned_cols=50 Identities=16% Similarity=0.188 Sum_probs=35.6
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhCC--CCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAYP--KCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~fg--~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
...+|++. .|+..+......+. +...+...+.++++++|.+|++|+.+..
T Consensus 132 ~g~~Igv~--~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 132 KGKHVGVL--QGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred CCCEEEEe--cCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeC
Confidence 34678884 67655443433332 3567778899999999999999998775
No 257
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=26.69 E-value=1.8e+02 Score=27.02 Aligned_cols=123 Identities=11% Similarity=-0.010 Sum_probs=62.1
Q ss_pred HHHHHHHHhCC-CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCC
Q 015945 123 YSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG 201 (398)
Q Consensus 123 ~s~~AA~~~fg-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g 201 (398)
+-+++++ ..| .+++.+. +|.++++++.+|++|+++..+.-+ ... ...++ + ...+ ......++.+++
T Consensus 53 l~~~ia~-~lg~~~~~~~~-~~~~~~~~l~~G~vDi~~~~~~~t-~~R-~~~~~-f-s~p~-------~~~~~~~~~~~~ 119 (247)
T PRK09495 53 LWAAIAK-ELKLDYTLKPM-DFSGIIPALQTKNVDLALAGITIT-DER-KKAID-F-SDGY-------YKSGLLVMVKAN 119 (247)
T ss_pred HHHHHHH-HhCCceEEEeC-CHHHHHHHHhCCCcCEEEecCccC-HHH-Hhhcc-c-cchh-------eecceEEEEECC
Confidence 4445454 345 4566655 699999999999999986544211 111 01110 0 0011 112223333222
Q ss_pred C----CccCcc--EEEecHHHHHHHHHHHhh--cCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 202 V----LKEELK--RVFSHPQALAQCEMTLSN--LGIVRISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 202 ~----~l~~I~--~V~SHpqal~QC~~fl~~--~~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
. ++++++ +|..-.. -.. ..|+.+ ++.+++...|..++.+++..+. -.|+|+....+.
T Consensus 120 ~~~~~~~~dL~g~~I~v~~g-~~~-~~~l~~~~~~~~i~~~~~~~~~~~~L~~gr--vDa~i~~~~~~~ 184 (247)
T PRK09495 120 NNDIKSVKDLDGKVVAVKSG-TGS-VDYAKANIKTKDLRQFPNIDNAYLELGTGR--ADAVLHDTPNIL 184 (247)
T ss_pred CCCCCChHHhCCCEEEEecC-chH-HHHHHhcCCCCceEEcCCHHHHHHHHHcCc--eeEEEeChHHHH
Confidence 1 233442 3433221 111 245655 3566777888888888887653 346666655443
No 258
>PRK09181 aspartate kinase; Validated
Probab=26.54 E-value=8e+02 Score=26.11 Aligned_cols=125 Identities=9% Similarity=0.008 Sum_probs=75.6
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecccccCCCCceEEEEEecCC-CCCC----CCCCc
Q 015945 228 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREP-IIAG----TDRPY 299 (398)
Q Consensus 228 ~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a---A~~ygL~il~~~I~D~~~N~TRF~vi~~~~-~~~~----~~~~~ 299 (398)
++..+..-|-.+|.++..-+ |-+-.+.+ |..+|.+|.-.|-.+...--|..- .... ..+. ....+
T Consensus 256 ~A~~i~~lsy~Ea~ELA~~G-----AkVLHp~ti~pa~~~~Ipi~V~nt~~p~~~GT~I~--~~~~~~~~~ik~It~~~~ 328 (475)
T PRK09181 256 KVVPIGRTNYDVADQLANLG-----MEAIHPKAAKGLRQAGIPLRIKNTFEPEHPGTLIT--KDYVSEQPRVEIIAGSDK 328 (475)
T ss_pred CCeEcCccCHHHHHHHHHcC-----chhcCHHHHHHHHHcCCeEEEecCCCCCCCCeEEe--cCcccccccceeEeccCC
Confidence 34566777888999987653 44444444 557899999988776443445442 1110 0010 01122
Q ss_pred eEEEEEE---eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHH
Q 015945 300 KTSIVFT---LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFAL 376 (398)
Q Consensus 300 ktsi~f~---~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al 376 (398)
-+.|-+. ..+.+|.+.++++.|+++|||+-.|-|- . -...|.|+-+ ...+.+++
T Consensus 329 ~~~i~i~~~~~~~~~g~~~~if~~l~~~~i~v~~i~ss---~----------------~sis~~v~~~----~~~~~~~~ 385 (475)
T PRK09181 329 VFALEVFDQDMVGEDGYDLEILEILTRHKVSYISKATN---A----------------NTITHYLWGS----LKTLKRVI 385 (475)
T ss_pred EEEEEEcCCCCCCcchHHHHHHHHHHHcCCeEEEEEec---C----------------cEEEEEEcCC----hHHHHHHH
Confidence 3333332 2357899999999999999999866332 1 2467777654 13566778
Q ss_pred HHHHHh
Q 015945 377 GHLQEF 382 (398)
Q Consensus 377 ~~L~~~ 382 (398)
++|++.
T Consensus 386 ~~L~~~ 391 (475)
T PRK09181 386 AELEKR 391 (475)
T ss_pred HHHHHh
Confidence 887753
No 259
>PLN02550 threonine dehydratase
Probab=26.43 E-value=2.5e+02 Score=30.95 Aligned_cols=70 Identities=17% Similarity=0.153 Sum_probs=46.9
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHH
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 379 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L 379 (398)
-.-+.|++|.+||+|.+.|+.|.. +-|+|.++=|-.... .. ..||-++-. +.....+++.|
T Consensus 510 E~l~~v~fPErpGAl~~Fl~~lg~-~~nITeF~YR~~~~~---------------~a-~vlvGi~v~--~~e~~~l~~~l 570 (591)
T PLN02550 510 ELLYRFVFPERPGALMKFLDAFSP-RWNISLFHYRGQGET---------------GA-NVLVGIQVP--PEEMQEFKSRA 570 (591)
T ss_pred eEEEEEEecCcCCHHHHHHHhhCC-CCceeeEEeecCCCC---------------Cc-cEEEEEeeC--HHHHHHHHHHH
Confidence 345778999999999999998873 368888888854432 11 345555532 35667777778
Q ss_pred HHhcCceEE
Q 015945 380 QEFATFLRV 388 (398)
Q Consensus 380 ~~~~~~vki 388 (398)
++..-.+..
T Consensus 571 ~~~gy~~~d 579 (591)
T PLN02550 571 NALGYEYQD 579 (591)
T ss_pred HHcCCCeEE
Confidence 766544443
No 260
>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=26.20 E-value=1.1e+02 Score=26.42 Aligned_cols=121 Identities=16% Similarity=0.066 Sum_probs=60.6
Q ss_pred hCCCCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc--
Q 015945 131 AYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK-- 208 (398)
Q Consensus 131 ~fg~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~-- 208 (398)
.|+++++.......++.+.+.+|++|+|+...+....+.. ...|.+..+.+ ..+-.|-+... ..+++++.
T Consensus 25 ~~P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~----v~~~~hpl~~~-~~~l~dl~~~ 96 (200)
T cd08460 25 EAPGVRLRFVPESDKDVDALREGRIDLEIGVLGPTGPEIR---VQTLFRDRFVG----VVRAGHPLARG-PITPERYAAA 96 (200)
T ss_pred HCCCCEEEEecCchhHHHHHHCCCccEEEecCCCCCcchh---eeeeeccceEE----EEeCCCCCCCC-CCCHHHHhcC
Confidence 3565554333222278899999999999984322111111 11112222222 22334444332 12333333
Q ss_pred -EEE-ecHH-HHHHHHHHHhhcCC---eEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 209 -RVF-SHPQ-ALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 209 -~V~-SHpq-al~QC~~fl~~~~~---~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
-|. +... .-.+..+|+.+.+. ....++|...+..+++.+ ...|+.+...++
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 153 (200)
T cd08460 97 PHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGS---DLIALVPERVTA 153 (200)
T ss_pred CCEEEecCCCCcchHHHHHHhcCCceeEEEEcCcHHHHHHHHhcC---CHHHHHHHHHHH
Confidence 222 2211 12346677766443 234677777788888764 346777776654
No 261
>PF08946 Osmo_CC: Osmosensory transporter coiled coil; InterPro: IPR015041 The osmosensory transporter coiled coil is a C-terminal domain found in various bacterial osmoprotective transporters, such as ProP, Proline/betaine transporter, Proline permease 2 and the citrate proton symporters. It adopts an antiparallel coiled-coil structure, and is essential for osmosensory and osmoprotectant transporter function []. ; PDB: 1R48_B.
Probab=25.89 E-value=32 Score=24.78 Aligned_cols=27 Identities=7% Similarity=-0.010 Sum_probs=22.7
Q ss_pred chhhhHHHhhhchhhHHHHHhhhhcccccccc
Q 015945 29 CGFGLDLRVLNKWECTCVGVLAQTHRAITPVE 60 (398)
Q Consensus 29 ~~lR~~Id~iD~~~~~i~~ll~~~~R~~~~~~ 60 (398)
+.+-.+|+.||.+ |-+|=.+ |-.|+.+
T Consensus 15 d~IEqkiedid~q---IaeLe~K--R~~Lv~q 41 (46)
T PF08946_consen 15 DNIEQKIEDIDEQ---IAELEAK--RQRLVDQ 41 (46)
T ss_dssp THHHHHHHHHHHH---HHHHHHH--HHHHHHH
T ss_pred HhHHHhHHHHHHH---HHHHHHH--HHHHHHh
Confidence 4567889999999 9999988 8887754
No 262
>PRK08055 chorismate mutase; Provisional
Probab=25.71 E-value=49 Score=30.72 Aligned_cols=26 Identities=19% Similarity=0.143 Sum_probs=22.8
Q ss_pred CcchhhhHHHhhhchhhHHHHHhhhhccccc
Q 015945 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAIT 57 (398)
Q Consensus 27 ~l~~lR~~Id~iD~~~~~i~~ll~~~~R~~~ 57 (398)
.|..+|-+||+++.+ |+.-|++ +...
T Consensus 116 dL~~vRp~l~~L~~~---il~~ia~--~l~~ 141 (181)
T PRK08055 116 DLSDVRQRIRQLDTQ---ILIQIAQ--RLKV 141 (181)
T ss_pred cHHHHHHHHHHHHHH---HHHHHHH--HHHh
Confidence 678999999999999 9999999 5543
No 263
>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=25.64 E-value=2.8e+02 Score=31.59 Aligned_cols=34 Identities=15% Similarity=0.309 Sum_probs=29.6
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeee
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIE 332 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IE 332 (398)
.-|-|.+..+|+||-|+++.++|+.+|+|+..=.
T Consensus 667 ~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~ 700 (850)
T TIGR01693 667 GGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQ 700 (850)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEE
Confidence 4577888889999999999999999999998443
No 264
>COG4472 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.58 E-value=73 Score=25.77 Aligned_cols=25 Identities=20% Similarity=0.274 Sum_probs=23.2
Q ss_pred cCCCCCCCCCCcchhhhHHHhhhch
Q 015945 17 FHKGLPDLVPNRCGFGLDLRVLNKW 41 (398)
Q Consensus 17 ~~~~~~~~~~~l~~lR~~Id~iD~~ 41 (398)
..+|.|+-.|+-++.|.+|+++|+.
T Consensus 46 llSGDPaYIpr~ndARn~IRk~eRD 70 (88)
T COG4472 46 LLSGDPAYIPRYNDARNQIRKLERD 70 (88)
T ss_pred hccCCccccCccccHHHHHHHHhHH
Confidence 4689999999999999999999998
No 265
>PLN02551 aspartokinase
Probab=25.28 E-value=4.5e+02 Score=28.36 Aligned_cols=99 Identities=14% Similarity=0.018 Sum_probs=62.4
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecccccCCCCceEEEEEecCCCC-CC---CCCCce
Q 015945 228 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPII-AG---TDRPYK 300 (398)
Q Consensus 228 ~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a---A~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~-~~---~~~~~k 300 (398)
++..+..-|-.+|.+++.-+ |-+-.+.+ |..++.+|.-+|--+...--|..-- ...... +- ....+-
T Consensus 293 ~A~~l~~lsy~Ea~elA~~G-----akVlhp~ai~pa~~~~Ipi~vknt~~p~~~GT~I~~-~~~~~~~~v~~It~~~~v 366 (521)
T PLN02551 293 NAVPVPYLTFDEAAELAYFG-----AQVLHPQSMRPAREGDIPVRVKNSYNPTAPGTLITK-TRDMSKAVLTSIVLKRNV 366 (521)
T ss_pred CceEecccCHHHHHHHHhCC-----CcccCHHHHHHHHHCCceEEEEecCCCCCCCcEEec-ccccCCCcccceecCCCe
Confidence 56778888999999987643 44444444 4578999999886654333454421 110000 00 112233
Q ss_pred EEEEEEe---CCCcchHHHHHHHHHhCCceeeeee
Q 015945 301 TSIVFTL---EEGPGMLFKALAVFALRDINLTKIE 332 (398)
Q Consensus 301 tsi~f~~---~~~pGaL~~~L~~F~~~~INLt~IE 332 (398)
+.|-+.- .+.+|.+.++++.|+++|||+-.|-
T Consensus 367 ~li~i~~~~m~~~~g~~arvf~~l~~~~I~Vd~Is 401 (521)
T PLN02551 367 TMLDIVSTRMLGQYGFLAKVFSTFEDLGISVDVVA 401 (521)
T ss_pred EEEEEecCCCCCcccHHHHHHHHHHHcCCcEEEEe
Confidence 3443422 3679999999999999999999994
No 266
>PRK05092 PII uridylyl-transferase; Provisional
Probab=25.26 E-value=3.3e+02 Score=31.50 Aligned_cols=34 Identities=15% Similarity=0.220 Sum_probs=29.7
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeee
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIE 332 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IE 332 (398)
+-|.|.+..+|+||-|.++.++|+.+|+|+..-.
T Consensus 731 ~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~ 764 (931)
T PRK05092 731 GVTEVTVLAADHPGLFSRIAGACAAAGANIVDAR 764 (931)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEE
Confidence 4678888889999999999999999999998544
No 267
>PF06153 DUF970: Protein of unknown function (DUF970); InterPro: IPR010375 This is a family of uncharacterised bacterial proteins.; PDB: 3M05_A.
Probab=24.76 E-value=2.2e+02 Score=24.35 Aligned_cols=53 Identities=15% Similarity=0.071 Sum_probs=36.3
Q ss_pred HHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHhcCce
Q 015945 316 KALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFL 386 (398)
Q Consensus 316 ~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~~~~v 386 (398)
++.+.|.++|+-.|+|-|.=- |+ +.++-.|.|-++ |++++++|+-+++.|..-
T Consensus 15 ~l~~~L~~~g~~~TkLsstGG-----------FL---r~GNtTlliGve----de~v~~vl~iIk~~c~~R 67 (109)
T PF06153_consen 15 DLSDALNENGFRVTKLSSTGG-----------FL---REGNTTLLIGVE----DEKVDEVLEIIKENCKKR 67 (109)
T ss_dssp HHHHHHHHTT--EEEEEEEET-----------TT---TEEEEEEEEEEE----GGGHHHHHHHHHHHH--E
T ss_pred HHHHHHHHCCceEEEEecccc-----------ee---ccCCEEEEEEec----HHHHHHHHHHHHHhhcCc
Confidence 445567999999999998732 22 235678888774 578999999999888753
No 268
>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=24.71 E-value=4.2e+02 Score=22.21 Aligned_cols=33 Identities=21% Similarity=0.179 Sum_probs=23.7
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeec
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIE 163 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIE 163 (398)
.++++++.. ..+..++.+.+.+|++|+|++...
T Consensus 26 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~ 59 (199)
T cd08451 26 AYPDVELTLEEANTAELLEALREGRLDAAFVRPP 59 (199)
T ss_pred HCCCcEEEEecCChHHHHHHHHCCCccEEEEecC
Confidence 456555433 335678899999999999998643
No 269
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=24.46 E-value=1.2e+02 Score=29.66 Aligned_cols=50 Identities=14% Similarity=0.131 Sum_probs=36.8
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhCC----CCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAYP----KCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~fg----~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
...+|+++ .|+..+...+.+.. +..++...+.++++++|.+|++|+.+..
T Consensus 152 ~Gk~V~v~--~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~d 205 (302)
T PRK10797 152 KGKAVVVT--SGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMD 205 (302)
T ss_pred CCCEEEEe--CCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEcc
Confidence 34678875 66655554544432 3578889999999999999999998754
No 270
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=24.14 E-value=4.3e+02 Score=24.29 Aligned_cols=63 Identities=19% Similarity=0.158 Sum_probs=43.1
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHH
Q 015945 300 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 379 (398)
Q Consensus 300 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L 379 (398)
-..+.-+..+.||-|..+++..++|||++--+-|+---.. .+-..+|=+++.... +++.+|
T Consensus 95 Viei~~~~~~~pgi~A~V~~~iak~gi~Irqi~~~dpe~~---------------~e~~l~IVte~~iP~----~li~el 155 (167)
T COG2150 95 VIEIYPEDARYPGILAGVASLIAKRGISIRQIISEDPELQ---------------EEPKLTIVTERPIPG----DLIDEL 155 (167)
T ss_pred EEEEEeccCCCccHHHHHHHHHHHcCceEEEEecCCcccC---------------CCceEEEEEeccCCH----HHHHHH
Confidence 3445555678999999999999999999999988843111 133556666776533 355555
Q ss_pred HH
Q 015945 380 QE 381 (398)
Q Consensus 380 ~~ 381 (398)
++
T Consensus 156 ~~ 157 (167)
T COG2150 156 KK 157 (167)
T ss_pred hc
Confidence 43
No 271
>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=24.03 E-value=4.6e+02 Score=22.44 Aligned_cols=122 Identities=16% Similarity=0.046 Sum_probs=58.9
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc-
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 208 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~- 208 (398)
.++++++.- ..+..++.+.+.+|++|+|+..-.-.....+. ...|.+.++.++ .+-+|-+......+++++.
T Consensus 25 ~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~~~v----~~~~hpl~~~~~i~~~~l~~ 98 (198)
T cd08443 25 RYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLI--TLPCYHWNRCVV----VKRDHPLADKQSISIEELAT 98 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccccccCCce--EeeeeeceEEEE----EcCCCccccCCCCCHHHHhc
Confidence 456655433 34667899999999999999752210111110 011112222221 2233444332222333332
Q ss_pred -EEEecHH--HH-HHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015945 209 -RVFSHPQ--AL-AQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAA 261 (398)
Q Consensus 209 -~V~SHpq--al-~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA 261 (398)
...+.+. .. .....|+.+.+. . ...+++.....++++.+ ...|+.+...+
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~~p~~~~ 155 (198)
T cd08443 99 YPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLG---LGVGVIASMAY 155 (198)
T ss_pred CCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CcEEEeecccc
Confidence 1222222 22 233455555443 2 34567777777788764 34666666544
No 272
>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=23.85 E-value=4.4e+02 Score=22.57 Aligned_cols=122 Identities=20% Similarity=0.164 Sum_probs=59.6
Q ss_pred hCCCCccccCC-CHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCcc-
Q 015945 131 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 208 (398)
Q Consensus 131 ~fg~~~~~~~~-s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I~- 208 (398)
.++++++.... +..++.+.+.+|++|+|+........+ +. ...+.+.++.+ ..+-.|-|... ..+++++.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~-~~--~~~l~~~~~~~----v~~~~h~l~~~-~~~~~dL~~ 96 (200)
T cd08467 25 RAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDG-LV--VRRLYDDGFAC----LVRHGHPALAQ-EWTLDDFAT 96 (200)
T ss_pred hCCCCEEEEecCCcccHHHHhhCCCcCEEEecCCCCCcc-ce--eEEeeeccEEE----EEcCCCccccC-CCCHHHHhC
Confidence 35666654333 455889999999999999753211111 11 01112222222 12333444322 12333322
Q ss_pred --EE-EecHHH-HHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 209 --RV-FSHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 209 --~V-~SHpqa-l~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
-| +.-... ......|+.+.+. . ...++|.....++|+.+ ...|+.+...+..
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08467 97 LRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAAT---DLIATVPRRVATQ 155 (200)
T ss_pred CCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcC---CeEEeeHHHHHHH
Confidence 22 111111 1233445555433 2 34567777777788764 3577888776654
No 273
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=23.80 E-value=2.4e+02 Score=29.55 Aligned_cols=70 Identities=21% Similarity=0.319 Sum_probs=52.2
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcHHHHHHHHHHHHh-
Q 015945 304 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF- 382 (398)
Q Consensus 304 ~f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~~v~~al~~L~~~- 382 (398)
-+...|+.|-.-++|..+..++|||..||--|.. ..|++|-. ++...++++..+|+..
T Consensus 4 eV~cedRlGltrelLdlLv~r~idl~~iEid~~~--------------------~IYln~p~-l~~~~fs~L~aei~~I~ 62 (511)
T COG3283 4 EVFCEDRLGLTRELLDLLVLRGIDLRGIEIDPIG--------------------RIYLNFPE-LEFESFSSLMAEIRRIP 62 (511)
T ss_pred EEEehhhhchHHHHHHHHHhcccCccceeecCCC--------------------eEEEeccc-cCHHHHHHHHHHHhcCC
Confidence 3456789999999999999999999999985532 56778743 5567778888888754
Q ss_pred -cCceEEEccccC
Q 015945 383 -ATFLRVLGCYPM 394 (398)
Q Consensus 383 -~~~vkiLGsYp~ 394 (398)
...|+..+--|.
T Consensus 63 GV~~vr~V~~mPs 75 (511)
T COG3283 63 GVTDVRTVPWMPS 75 (511)
T ss_pred CccceeeecCCcc
Confidence 445666665554
No 274
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=23.47 E-value=4.2e+02 Score=21.80 Aligned_cols=63 Identities=16% Similarity=0.098 Sum_probs=39.3
Q ss_pred eEEEEEcCCCcHHHHHHHHhCCCCccccCCC---HHHHHHHHHcCCccEEEEeeccccccchHHhHHhhh
Q 015945 112 VRVAYQGLPGAYSEAAARKAYPKCETVPCDQ---FEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL 178 (398)
Q Consensus 112 ~kVa~lGp~Gs~s~~AA~~~fg~~~~~~~~s---~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~ 178 (398)
+||++.|.+-|- .--+ .+|--....+.+ ..++++.+.. +-|||++-|.......+.+.++-+.
T Consensus 1 mkIaVIGD~dtv--~GFr-LaGi~~~~~~~~~ee~~~~l~~l~~-~~d~gII~Ite~~~~~i~e~i~~~~ 66 (100)
T PRK02228 1 MEIAVIGSPEFT--TGFR-LAGIRKVYEVPDDEKLDEAVEEVLE-DDDVGILVMHDDDLEKLPRRLRRTL 66 (100)
T ss_pred CEEEEEeCHHHH--HHHH-HcCCceEEeeCCHHHHHHHHHHHhh-CCCEEEEEEehhHhHhhHHHHHHHH
Confidence 589999874332 2112 345222333444 4555555533 4589999999998888888888644
No 275
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=23.32 E-value=2.5e+02 Score=32.14 Aligned_cols=32 Identities=9% Similarity=0.279 Sum_probs=28.7
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeee
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTK 330 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~ 330 (398)
+-|.|.+..+|+||-|+++-++|+.+|+|+..
T Consensus 676 ~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~ 707 (854)
T PRK01759 676 GGTEIFIYCQDQANLFLKVVSTIGAKKLSIHD 707 (854)
T ss_pred CeEEEEEEecCCccHHHHHHHHHHHCCCeEEE
Confidence 45778888899999999999999999999974
No 276
>PRK02047 hypothetical protein; Provisional
Probab=23.22 E-value=4.1e+02 Score=21.60 Aligned_cols=59 Identities=20% Similarity=0.311 Sum_probs=39.1
Q ss_pred CCCcchHHHHHHHHHhC--CceeeeeeeeeCCCCCCccccCCCCCCCcccce-EEEEEeecCCCcHHHHHHHHHHHHhc
Q 015945 308 EEGPGMLFKALAVFALR--DINLTKIESRPQRKRPLRVVDDSNKGSAKYFDY-LFYIDFEASMADPRAQFALGHLQEFA 383 (398)
Q Consensus 308 ~~~pGaL~~~L~~F~~~--~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y-~Ffvd~~g~~~d~~v~~al~~L~~~~ 383 (398)
++.++-...+.+++..+ ++....|.+|||+++ .| .+=|.+... +.+.+.++-++|.++-
T Consensus 24 ~~~~~~~~~v~~iv~~~~~~~~~~~i~~k~Ss~G----------------kY~Svtv~v~v~-s~eq~~~iY~~L~~~~ 85 (91)
T PRK02047 24 KAHPEFADTIFKVVSVHDPEFDLEKIEERPSSGG----------------NYTGLTITVRAT-SREQLDNIYRALTGHP 85 (91)
T ss_pred eCcHhHHHHHHHHHHHhCCCCccCceEEccCCCC----------------eEEEEEEEEEEC-CHHHHHHHHHHHhhCC
Confidence 45566666677777666 666788999999873 44 355555544 4467777777776543
No 277
>PRK06291 aspartate kinase; Provisional
Probab=23.05 E-value=8.9e+02 Score=25.44 Aligned_cols=98 Identities=12% Similarity=0.022 Sum_probs=60.4
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhH---HHcCCceeecccccCCCCceEEEEEecCC-CCCC----CCCCc
Q 015945 228 GIVRISADDTAGAAQMVASIGERDTGAVASAQAA---EIYGLDILAEKIQDDDDNVTRFLILAREP-IIAG----TDRPY 299 (398)
Q Consensus 228 ~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA---~~ygL~il~~~I~D~~~N~TRF~vi~~~~-~~~~----~~~~~ 299 (398)
+++.+..-|..+|.++..- + |-+-.+.|+ ..+|.++.-.|..+....-|..- .... ..+. ....+
T Consensus 248 ~a~~i~~l~~~ea~~l~~~----G-~~v~~~~a~~~~~~~~i~i~i~~~~~~~~~gt~i~--~~~~~~~~~V~~It~~~~ 320 (465)
T PRK06291 248 EARVIPKISYIEAMELSYF----G-AKVLHPRTIEPAMEKGIPVRVKNTFNPEFPGTLIT--SDSESSKRVVKAVTLIKN 320 (465)
T ss_pred CCeEccccCHHHHHHHHhC----C-CcccCHHHHHHHHHcCCcEEEecCCCCCCCceEEE--ecccccCcccceEEeeCC
Confidence 4666777777888777543 2 345555554 45899999988776555555542 2111 0000 01122
Q ss_pred eEEEEEE---eCCCcchHHHHHHHHHhCCceeeeee
Q 015945 300 KTSIVFT---LEEGPGMLFKALAVFALRDINLTKIE 332 (398)
Q Consensus 300 ktsi~f~---~~~~pGaL~~~L~~F~~~~INLt~IE 332 (398)
.+.+.+. ..+.||.+.++++.|+++|||+-.|-
T Consensus 321 valIsI~g~~m~~~~g~~arvf~~L~~~gI~V~mIs 356 (465)
T PRK06291 321 VALINISGAGMVGVPGTAARIFSALAEEGVNVIMIS 356 (465)
T ss_pred EEEEEEeCCCCCCCccHHHHHHHHHHHCCCcEEEEE
Confidence 2323232 23679999999999999999998884
No 278
>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=23.01 E-value=5e+02 Score=22.53 Aligned_cols=32 Identities=9% Similarity=-0.080 Sum_probs=23.0
Q ss_pred hCCCCccc-cCCCHHHHHHHHHcCCccEEEEee
Q 015945 131 AYPKCETV-PCDQFEAAFKAVELWLVDKAVLPI 162 (398)
Q Consensus 131 ~fg~~~~~-~~~s~~~v~~aV~~g~~d~gvVPI 162 (398)
.++++++. ...+..++.+.+.+|++|+|+...
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 25 EAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred HCCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 34555542 234667889999999999999854
No 279
>cd08429 PBP2_NhaR The C-terminal substrate binding domain of LysR-type transcriptional activator of the nhaA gene, encoding Na+/H+ antiporter, contains the type 2 periplasmic binding fold. NhaR is a positive regulator of the LysR family and is known to be an activator of the nhaA gene encoding a Na(+)/H(+) antiporter. In Escherichia coli, NhaA is the vital antiporter that protects against high sodium stress, and it is essential for growth in high sodium levels, while NhaB becomes essential only if NhaA is not available. The nhaA gene of nhaAR operon is induced by monovalent cations. The nhaR of the operon activates nhaAR, as well as the osmC transcription which is induced at elevated osmolarity. OsmC is transcribed from the two overlapping promoters (osmCp1 and osmP2) and that NhaR is shown to activate only the expression of osmCp1. NhaR also activates the transcription of the pgaABCD operon which is required for production of the biofilm adhesion, poly-beta-1,6-N-acetyl-d-glucosamine
Probab=22.56 E-value=5.2e+02 Score=22.56 Aligned_cols=122 Identities=11% Similarity=-0.034 Sum_probs=61.2
Q ss_pred hCCCCcc-ccCCCHHHHHHHHHcCCccEEEEeeccccccchHHh--HHhhhcCCeEEEEEEEEeeeEeeecCCCC---Cc
Q 015945 131 AYPKCET-VPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRN--YDLLLRHRLHIVGEVQLVVNHCLLGLPGV---LK 204 (398)
Q Consensus 131 ~fg~~~~-~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t--ld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~---~l 204 (398)
.++++++ +...+..++.+.|.+|++|+|+..-.. ...+... ..-|.+..+.++. +..|.. ..+.. ++
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~L~~~~~D~~i~~~~~--~~~~~~~~~~~~l~~~~~~~~~----~~~~~~-~~~~~~~~dL 97 (204)
T cd08429 25 LHEPIRLVCREGKLEQLLADLALHRLDMVLADRPM--PSSLDVKGYSHRLGECGVSFFA----APPLAK-RLEKPFPASL 97 (204)
T ss_pred hCCCcEEEEEeCCHHHHHHHHHcCCccEEEecCCC--ccccchheeeccccccceEEEe----cCCccc-ccccCCHhHh
Confidence 3565554 334578899999999999999965321 1111001 1122222332221 112211 11111 23
Q ss_pred cCccEEEecH-HH-HHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015945 205 EELKRVFSHP-QA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 262 (398)
Q Consensus 205 ~~I~~V~SHp-qa-l~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~ 262 (398)
.+..-|...+ .. ......|+.+.+. . ...++|.....++|+.+ ...++.++.++.
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~G---~Gv~~lp~~~~~ 157 (204)
T cd08429 98 DEAPLLLPGEDSALRRKLLQWFERQGLRPQIVGEFDDSALMKAFGQAG---AGIFAAPTVIAD 157 (204)
T ss_pred ccCCeeecCCCCcHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHcC---CCeEeccHHHHH
Confidence 3333343222 22 2345667766543 2 34566777777778765 346778887765
No 280
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=22.44 E-value=5.9e+02 Score=23.15 Aligned_cols=114 Identities=15% Similarity=0.145 Sum_probs=59.0
Q ss_pred CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCC----CccCc--
Q 015945 134 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV----LKEEL-- 207 (398)
Q Consensus 134 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~----~l~~I-- 207 (398)
.+++++ .+|.+++.++.+|++|+++.++..+.+-. ..+. ....+ ......++.+.+. .++++
T Consensus 64 ~~~~~~-~~~~~~~~~l~~G~~D~~~~~~~~~~~r~--~~~~--~s~p~-------~~~~~~~~~~~~~~~~~~~~dl~g 131 (250)
T TIGR01096 64 KCKFVE-QNFDGLIPSLKAKKVDAIMATMSITPKRQ--KQID--FSDPY-------YATGQGFVVKKGSDLAKTLEDLDG 131 (250)
T ss_pred eEEEEe-CCHHHHHHHHhCCCcCEEEecCccCHHHh--hccc--cccch-------hcCCeEEEEECCCCcCCChHHcCC
Confidence 467776 57999999999999999875443222110 0000 00000 0111222222221 12222
Q ss_pred cEEEecHHHHHHHHHHHhh--c-CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 208 KRVFSHPQALAQCEMTLSN--L-GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 208 ~~V~SHpqal~QC~~fl~~--~-~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
++|-. ....... .++.+ . +...+.+.|..++.+++..+. -.++|++...+..
T Consensus 132 ~~i~~-~~g~~~~-~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~--vD~~v~~~~~~~~ 186 (250)
T TIGR01096 132 KTVGV-QSGTTHE-QYLKDYFKPGVDIVEYDSYDNANMDLKAGR--IDAVFTDASVLAE 186 (250)
T ss_pred CEEEE-ecCchHH-HHHHHhccCCcEEEEcCCHHHHHHHHHcCC--CCEEEeCHHHHHH
Confidence 12322 1122222 34444 2 667788899999999988753 4477776665544
No 281
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=22.41 E-value=1.9e+02 Score=27.07 Aligned_cols=50 Identities=16% Similarity=0.174 Sum_probs=35.8
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhCC--CCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAYP--KCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~fg--~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
+..+|++. .|+..+.....++. +.+++...+.++++++|.+|++|+.+..
T Consensus 132 ~g~~Igv~--~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~ 183 (259)
T PRK15437 132 KGKRVGVL--QGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQD 183 (259)
T ss_pred CCCEEEEe--cCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEec
Confidence 45678885 56654443333332 3567888899999999999999998764
No 282
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=22.34 E-value=62 Score=25.52 Aligned_cols=77 Identities=17% Similarity=0.202 Sum_probs=49.5
Q ss_pred EEecHHHHHHHHHHHhhcCC-eEEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecccccCCCCceEEEEEec
Q 015945 210 VFSHPQALAQCEMTLSNLGI-VRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAR 288 (398)
Q Consensus 210 V~SHpqal~QC~~fl~~~~~-~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ygL~il~~~I~D~~~N~TRF~vi~~ 288 (398)
|-.||.-..-.+.+|...+. ....+.|..+|.+.+.... ++ .+|..-......|+.++. .|.... ..+++++++.
T Consensus 4 vd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~~-~d-~iiid~~~~~~~~~~~~~-~i~~~~-~~~~ii~~t~ 79 (112)
T PF00072_consen 4 VDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLKKHP-PD-LIIIDLELPDGDGLELLE-QIRQIN-PSIPIIVVTD 79 (112)
T ss_dssp EESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHST-ES-EEEEESSSSSSBHHHHHH-HHHHHT-TTSEEEEEES
T ss_pred EECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhcccC-ce-EEEEEeeecccccccccc-cccccc-ccccEEEecC
Confidence 44577777888889987787 6778888888888887653 44 333333222344544444 333333 7788888886
Q ss_pred CC
Q 015945 289 EP 290 (398)
Q Consensus 289 ~~ 290 (398)
..
T Consensus 80 ~~ 81 (112)
T PF00072_consen 80 ED 81 (112)
T ss_dssp ST
T ss_pred CC
Confidence 53
No 283
>PRK09269 chorismate mutase; Provisional
Probab=22.04 E-value=60 Score=30.43 Aligned_cols=24 Identities=21% Similarity=0.214 Sum_probs=21.9
Q ss_pred CCCcchhhhHHHhhhchhhHHHHHhhh
Q 015945 25 VPNRCGFGLDLRVLNKWECTCVGVLAQ 51 (398)
Q Consensus 25 ~~~l~~lR~~Id~iD~~~~~i~~ll~~ 51 (398)
.+.|.++|-+||+++.+ |+..|.+
T Consensus 122 ~~dL~~~Rp~l~~L~~~---il~~l~~ 145 (193)
T PRK09269 122 RPDLASIRPRLDRLQQE---LLDALAD 145 (193)
T ss_pred CCCHHHHHHHHHHHHHH---HHHHHHH
Confidence 35688999999999999 9999999
No 284
>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=21.96 E-value=1.9e+02 Score=26.30 Aligned_cols=22 Identities=9% Similarity=-0.079 Sum_probs=19.7
Q ss_pred CCCHHHHHHHHHcCCccEEEEe
Q 015945 140 CDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 140 ~~s~~~v~~aV~~g~~d~gvVP 161 (398)
..+..+++.+|.+|++|++++.
T Consensus 140 ~~~~~~~~~~l~~G~~Da~i~~ 161 (232)
T TIGR03871 140 ESPPGRMVEDLAAGEIDVAIVW 161 (232)
T ss_pred cCCHHHHHHHHHcCCcCEEEec
Confidence 3478999999999999999985
No 285
>PRK09466 metL bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional
Probab=21.83 E-value=1.2e+03 Score=26.60 Aligned_cols=99 Identities=8% Similarity=-0.066 Sum_probs=62.4
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecccccCCCCceEEEEEecCCCCC--C--CCCCce
Q 015945 228 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPIIA--G--TDRPYK 300 (398)
Q Consensus 228 ~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a---A~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~--~--~~~~~k 300 (398)
+++.+..-|-.+|.+++.-+ |-+-.+.+ |..+|.+|.-+|-.|...--|..- ....... . ....+-
T Consensus 245 ~A~~i~~isy~Ea~ela~~G-----akVlHp~ti~pa~~~~Ipi~V~ntf~p~~~GT~I~--~~~~~~~~v~~It~~~~v 317 (810)
T PRK09466 245 DACLLPLLRLDEASELARLA-----APVLHARTLQPVSGSDIDLQLRCSYQPEQGSTRIE--RVLASGTGARIVTSLDDV 317 (810)
T ss_pred CceEcccCCHHHHHHHHHcC-----ccccCHHHHHHHHHcCCeEEEecCCCCCCCceEEe--cCcccccceeeeeccCCE
Confidence 56777888999999987653 34444444 557899999998776554456542 1111000 0 111222
Q ss_pred EEEEEEeC---CCcchHHHHHHHHHhCCceeeeeee
Q 015945 301 TSIVFTLE---EGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 301 tsi~f~~~---~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
+.|-+... +.+|.+.++++.|+++|||+-.|.+
T Consensus 318 ~~i~i~~~~~~g~~g~~~~if~~l~~~~I~v~~i~~ 353 (810)
T PRK09466 318 CLIELQVPASHDFKLAQKELDQLLKRAQLRPLAVGV 353 (810)
T ss_pred EEEEEecCCcCCcchHHHHHHHHHHHCCCeEEEEEe
Confidence 33333222 4578899999999999999998843
No 286
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=21.64 E-value=4.1e+02 Score=21.04 Aligned_cols=66 Identities=12% Similarity=0.144 Sum_probs=41.1
Q ss_pred eEEEEEEeCCC----cchHHHHHHHHHhCCceeeeeeee-------eCCCCCCccccCCCCCCCcccceEEEEEeecCCC
Q 015945 300 KTSIVFTLEEG----PGMLFKALAVFALRDINLTKIESR-------PQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMA 368 (398)
Q Consensus 300 ktsi~f~~~~~----pGaL~~~L~~F~~~~INLt~IESR-------P~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~ 368 (398)
.+.+++...-. ...+.++-+.+.++|-.+.++++. |.++. ...|+|++.|+++.
T Consensus 4 E~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LaY~i~k~--------------~~G~Y~~~~f~~~~- 68 (92)
T PF01250_consen 4 ELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENWGKRRLAYPIKKQ--------------KEGHYFLFNFDASP- 68 (92)
T ss_dssp EEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEESSEETTE--------------CEEEEEEEEEEEST-
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEeecccccCCCCC--------------CEEEEEEEEEEeCH-
Confidence 34555554311 234566777889999999999985 44442 13578888998864
Q ss_pred cHHHHHHHHHHHH
Q 015945 369 DPRAQFALGHLQE 381 (398)
Q Consensus 369 d~~v~~al~~L~~ 381 (398)
..++++-+.|+.
T Consensus 69 -~~i~el~~~l~~ 80 (92)
T PF01250_consen 69 -SAIKELERKLRL 80 (92)
T ss_dssp -THHHHHHHHHHT
T ss_pred -HHHHHHHHHhcC
Confidence 455555555543
No 287
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=21.60 E-value=2.8e+02 Score=26.37 Aligned_cols=109 Identities=18% Similarity=0.154 Sum_probs=58.0
Q ss_pred HHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeE---eeecCCCCCc------cCccEEEec
Q 015945 143 FEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNH---CLLGLPGVLK------EELKRVFSH 213 (398)
Q Consensus 143 ~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h---~Ll~~~g~~l------~~I~~V~SH 213 (398)
..|+-..|+.|.+|+||+=-. .|.+.+-.+.--..|...+ +++++++... ..-++|.+.
T Consensus 54 ~~DIp~yV~~G~~DlGItG~D------------~l~E~~~~v~~l~dLgfG~crl~vAvp~~~~~~~~~~~~~~~rIATk 121 (215)
T PRK01686 54 ATDVPTYVEHGAADLGIVGKD------------VLLEHGKDLYEPLDLGIGKCRMSVAVPPGFDYAPAVKQGPRLRVATK 121 (215)
T ss_pred HHHHHHHHhCCCccEEEeeee------------EeeecCCCeEEEecCCccCEEEEEEEECcccccchhhccCCCEEEeC
Confidence 468899999999999997533 2222211111112233333 3444433221 122466666
Q ss_pred HHHHHHHHHHHhhcCC--eEEecCCHHHHHHHHHhcCCCCeEEEc----CHHhHHHcCCceee
Q 015945 214 PQALAQCEMTLSNLGI--VRISADDTAGAAQMVASIGERDTGAVA----SAQAAEIYGLDILA 270 (398)
Q Consensus 214 pqal~QC~~fl~~~~~--~~v~~~STA~Aa~~v~~~~~~~~AAI~----s~~aA~~ygL~il~ 270 (398)
.--+. ++|+++.++ +++..+..-|+|=.+ + -+-||+ +-..-+.+||++++
T Consensus 122 Yp~it--~~yf~~~gv~~~iv~l~GsvE~aP~~---G--lAD~IvDivsTG~TLr~NgL~~ie 177 (215)
T PRK01686 122 YPNIA--RRYFAEKGEQVEIIKLYGSVELAPLV---G--LADAIVDIVETGNTLRANGLVEVE 177 (215)
T ss_pred CHHHH--HHHHHHcCCeEEEEECcCceeecccc---C--CccEEEEeecChHHHHHCcCEEee
Confidence 55544 569988654 555555444443221 1 111332 55667889999997
No 288
>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=21.57 E-value=5.9e+02 Score=22.74 Aligned_cols=105 Identities=13% Similarity=-0.041 Sum_probs=66.0
Q ss_pred CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhh-hcCCeEEEEEEEEeeeEeeecCCCCCccCc-----
Q 015945 134 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLL-LRHRLHIVGEVQLVVNHCLLGLPGVLKEEL----- 207 (398)
Q Consensus 134 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L-~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I----- 207 (398)
++++....+..++++++.+|++|+++..... .+-.. ...++++++...-.-...++.+++..+.++
T Consensus 22 ~ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~--------~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DLkG 93 (216)
T PF09084_consen 22 DVEIVFFGGGGDVLEALASGKADIAVAGPDA--------VLFARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADLKG 93 (216)
T ss_dssp EEEEEEESSHHHHHHHHHTTSHSEEEEECHH--------HHHHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGGTT
T ss_pred EEEEEEecChhHHHHHHhcCCceEEeccchH--------HHHHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHhCC
Confidence 4788889999999999999999999876541 11111 234788888776555567777766433333
Q ss_pred cEEEecH--HHHHHHHHHHhhcC-----CeEEecCCHHHHHHHHHhc
Q 015945 208 KRVFSHP--QALAQCEMTLSNLG-----IVRISADDTAGAAQMVASI 247 (398)
Q Consensus 208 ~~V~SHp--qal~QC~~fl~~~~-----~~~v~~~STA~Aa~~v~~~ 247 (398)
|+|...+ .....-+.+|++.+ ++.+... ....+..+.++
T Consensus 94 K~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~-~~~~~~al~~g 139 (216)
T PF09084_consen 94 KKIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLG-PPELAQALLSG 139 (216)
T ss_dssp SEEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTT
T ss_pred CEEEEecCcchhHHHHHHHHHhccccccceeeeee-hhhhhhhhhcC
Confidence 3666655 33445566777643 3454443 45555555554
No 289
>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=21.23 E-value=5e+02 Score=21.80 Aligned_cols=123 Identities=12% Similarity=0.040 Sum_probs=59.6
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccc--cccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccC-
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENS--VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEE- 206 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS--~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~- 206 (398)
.++++++... .+..++.+.+.+|++|+|+...... ..+.... .|.+..+.+ ..+-.|-+......++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~l~~~---~l~~~~~~~----v~~~~hp~~~~~~~~~~~L 97 (199)
T cd08416 25 RRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDFEVV---PLFEDDIFL----AVPATSPLAASSEIDLRDL 97 (199)
T ss_pred hCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCCCCCeEEE---EeecceEEE----EECCCCcccccCccCHHHh
Confidence 3565554332 3556788999999999999864321 1111110 111112211 223334343222222222
Q ss_pred --ccEEE-ecHHH-HHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 207 --LKRVF-SHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 207 --I~~V~-SHpqa-l~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
..-|. +.... .....+++...+. . ...++|...+.++++.+ ...++++...++.
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 158 (199)
T cd08416 98 KDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGG---VGYALLPGRIADV 158 (199)
T ss_pred cCCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcC---CcEEEechhhhhh
Confidence 23332 22221 2234556655332 2 34566777777777764 3467777765543
No 290
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=21.12 E-value=7.4e+02 Score=23.73 Aligned_cols=53 Identities=19% Similarity=0.176 Sum_probs=32.4
Q ss_pred CceeEEEEEcCCCcH--HHHHH--HHhCCCCcccc-CCCHHHHHHHHHcCCccEEEEe
Q 015945 109 GTKVRVAYQGLPGAY--SEAAA--RKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 109 q~~~kVa~lGp~Gs~--s~~AA--~~~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVP 161 (398)
.+..+|++...-+.+ ..... +..++++++.- ..+..++.+.+.+|++|+|+.+
T Consensus 92 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~ 149 (309)
T PRK12682 92 SGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAT 149 (309)
T ss_pred CCeEEEeeCchHHHHHHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHcCCccEEEec
Confidence 356778765433321 11111 12345655543 3456889999999999999975
No 291
>PRK05473 hypothetical protein; Provisional
Probab=21.12 E-value=82 Score=25.77 Aligned_cols=25 Identities=20% Similarity=0.240 Sum_probs=23.7
Q ss_pred cCCCCCCCCCCcchhhhHHHhhhch
Q 015945 17 FHKGLPDLVPNRCGFGLDLRVLNKW 41 (398)
Q Consensus 17 ~~~~~~~~~~~l~~lR~~Id~iD~~ 41 (398)
.|+|.|.--++-...|..|.++++.
T Consensus 46 llSGDPaYItsh~nAR~lIrkiERD 70 (86)
T PRK05473 46 LLSGDPAYIPRHNDARNLIRKLERD 70 (86)
T ss_pred hccCCCCccCCcccHHHHHHHHhHH
Confidence 5899999999999999999999998
No 292
>PRK06635 aspartate kinase; Reviewed
Probab=21.04 E-value=2.9e+02 Score=28.25 Aligned_cols=28 Identities=25% Similarity=0.415 Sum_probs=24.9
Q ss_pred EeCCCcchHHHHHHHHHhCCceeeeeee
Q 015945 306 TLEEGPGMLFKALAVFALRDINLTKIES 333 (398)
Q Consensus 306 ~~~~~pGaL~~~L~~F~~~~INLt~IES 333 (398)
.+++.||.+.++++.|+++|||+..|.+
T Consensus 349 ~~~~~~g~~a~i~~~La~~~Ini~~i~s 376 (404)
T PRK06635 349 GMRSHPGVAAKMFEALAEEGINIQMIST 376 (404)
T ss_pred CCCCCchHHHHHHHHHHHCCCCEEEEEe
Confidence 3468899999999999999999999864
No 293
>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=20.98 E-value=5e+02 Score=21.69 Aligned_cols=33 Identities=18% Similarity=0.037 Sum_probs=23.7
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeec
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIE 163 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIE 163 (398)
.++++++.. ..+..+..+.+.+|++|+|++...
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (197)
T cd08449 25 QYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFA 58 (197)
T ss_pred HCCCeEEEEEECCHHHHHHHHhCCCccEEEeccc
Confidence 355655433 335788899999999999997543
No 294
>PRK07431 aspartate kinase; Provisional
Probab=20.93 E-value=3.1e+02 Score=29.77 Aligned_cols=128 Identities=13% Similarity=0.139 Sum_probs=69.2
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecccccCCCCceEEEEEecCCCC---------CCC
Q 015945 228 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPII---------AGT 295 (398)
Q Consensus 228 ~~~~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a---A~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~---------~~~ 295 (398)
+++.+..-+..+|.+++..+ +-+-...| +..+|.++.-.+--+. .--|.|. ...... ...
T Consensus 190 ~a~~i~~i~~~e~~el~~~G-----~~v~~~~a~~~~~~~~i~i~i~~~~~~-~~GT~i~--~~~~~~~~~~~~~~~~~i 261 (587)
T PRK07431 190 EAQLMDEISCDEMLELASLG-----ASVLHPRAVEIARNYGVPLVVRSSWSD-APGTLVT--SPPPRPRSLGGLELGKPV 261 (587)
T ss_pred CCeECCCcCHHHHHHHHhCC-----CceEhHHHHHHHHHcCCcEEEecCCCC-CCCeEEE--eCCcccccccchhccccc
Confidence 34556666677777765432 12333444 3457888887765532 2246553 211100 000
Q ss_pred C----CCceEEEE-EEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccceEEEEEeecCCCcH
Q 015945 296 D----RPYKTSIV-FTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADP 370 (398)
Q Consensus 296 ~----~~~ktsi~-f~~~~~pGaL~~~L~~F~~~~INLt~IESRP~~~~~~~~~~~~~~g~~~~~~y~Ffvd~~g~~~d~ 370 (398)
+ ..+..-+. ..+.+.+|.+.++++.|+++|||.-.|-.-++... ..++.|.|+-+- -.
T Consensus 262 ~gi~~~~~~a~itl~~~~~~~g~~a~if~~l~~~~I~v~~i~qs~~~~~--------------~~~isf~i~~~d---~~ 324 (587)
T PRK07431 262 DGVELDEDQAKVALLRVPDRPGIAAQLFEELAAQGVNVDLIIQSIHEGN--------------SNDIAFTVAENE---LK 324 (587)
T ss_pred ceEEEecCceEEEEecCCCcccHHHHHHHHHHHcCCcEEEEEeccCCCC--------------CccEEEEEeHHH---HH
Confidence 0 01111121 23467899999999999999999999965443221 136788885421 13
Q ss_pred HHHHHHHHHH
Q 015945 371 RAQFALGHLQ 380 (398)
Q Consensus 371 ~v~~al~~L~ 380 (398)
+..++|+++.
T Consensus 325 ~~~~~l~~l~ 334 (587)
T PRK07431 325 KAEAVAEAIA 334 (587)
T ss_pred HHHHHHHHHH
Confidence 3445555554
No 295
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=20.93 E-value=6.5e+02 Score=23.03 Aligned_cols=145 Identities=12% Similarity=0.042 Sum_probs=69.1
Q ss_pred CceeEEEEEcCCCc--HHHHHH--HHhCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeE
Q 015945 109 GTKVRVAYQGLPGA--YSEAAA--RKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLH 183 (398)
Q Consensus 109 q~~~kVa~lGp~Gs--~s~~AA--~~~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~ 183 (398)
.+..+|++...-+. +..... ...++++++.. ..+.++..+.+.+|++|+|++...+...+.+. ...|....+.
T Consensus 66 ~~~l~I~~~~~~~~~~~~~~l~~~~~~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~--~~~l~~~~~~ 143 (269)
T PRK11716 66 SGELSLFCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVA--FSPIDEIPLV 143 (269)
T ss_pred CceEEEEecchHHHHHHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcceE--EEEcccceEE
Confidence 35577776433322 122222 12355655533 35677899999999999999864332222111 1112222333
Q ss_pred EEEEEEEeeeEeeecCC----CCCccCccEEE-ecHHHHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEE
Q 015945 184 IVGEVQLVVNHCLLGLP----GVLKEELKRVF-SHPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAV 255 (398)
Q Consensus 184 I~~Ei~l~I~h~Ll~~~----g~~l~~I~~V~-SHpqal~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI 255 (398)
++ .+-+|.+.... -.++.+..-|. +.......-..|+...+. . ...++|.....+++..+ ...++
T Consensus 144 ~v----~~~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~ 216 (269)
T PRK11716 144 LI----APALPCPVRQQLSQEKPDWSRIPFILPEHGPARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALG---CGVGL 216 (269)
T ss_pred EE----EcCCcchhhhccccchhhHhhCCeeecCCCchHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcC---CCeEe
Confidence 22 23333222111 01222333332 111111223456655332 2 34566666666777764 34788
Q ss_pred cCHHhHH
Q 015945 256 ASAQAAE 262 (398)
Q Consensus 256 ~s~~aA~ 262 (398)
.+...++
T Consensus 217 ~p~~~~~ 223 (269)
T PRK11716 217 LPEVVLE 223 (269)
T ss_pred ccHHHhh
Confidence 8887665
No 296
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=20.85 E-value=6.1e+02 Score=24.34 Aligned_cols=87 Identities=14% Similarity=0.092 Sum_probs=54.8
Q ss_pred eEEEEE-cCCCcHHHHHHHHhC---C-CCccccCCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhh---cCCeE
Q 015945 112 VRVAYQ-GLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL---RHRLH 183 (398)
Q Consensus 112 ~kVa~l-Gp~Gs~s~~AA~~~f---g-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~---~~~l~ 183 (398)
.|||+. ||...+-+. +...+ | .++++.++++.+.=.+|.+|++|.-+.--. ..++... ..+|.
T Consensus 1 ikIG~~~~~~~~i~~~-v~~~~~~~Gi~vevv~f~D~~~~N~AL~~G~iDaN~fQh~--------~yl~~~n~~~~~~L~ 71 (237)
T PF03180_consen 1 IKIGVTPGPDAEILEA-VKEKLKKKGIDVEVVEFSDYVQPNEALADGEIDANFFQHI--------PYLEQFNKENGYNLV 71 (237)
T ss_dssp EEEEEETTCHHHHHHH-HHHHHHHTTEEEEEEEESSTTHHHHHHHTTSSSEEEEEEH--------HHHHHHHHHHT--EE
T ss_pred CEEEEeCCCHHHHHHH-HHHHHHhcCCeEEEEEecchhhcChHHHCCCcceeccCCH--------HHHHHHHHHCCCcEE
Confidence 378888 443444443 33333 3 478899999999999999999998876533 4444443 35688
Q ss_pred EEEEEEEeeeEeeecCCCCCccCcc
Q 015945 184 IVGEVQLVVNHCLLGLPGVLKEELK 208 (398)
Q Consensus 184 I~~Ei~l~I~h~Ll~~~g~~l~~I~ 208 (398)
.++.+++. ...|.+.+-.++++|.
T Consensus 72 ~v~~~~~~-p~glYS~k~~sl~~lp 95 (237)
T PF03180_consen 72 PVGPTYIE-PMGLYSKKYKSLDDLP 95 (237)
T ss_dssp EEEEEEE----EEEESSSSSGGGS-
T ss_pred EecceeEE-eEEEeecccCchhhcC
Confidence 78876665 3777776655555553
No 297
>PRK13584 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=20.83 E-value=2.3e+02 Score=26.89 Aligned_cols=110 Identities=14% Similarity=0.120 Sum_probs=61.2
Q ss_pred HHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeee---EeeecCCCCCccCccEEEecHHHHHH
Q 015945 143 FEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVN---HCLLGLPGVLKEELKRVFSHPQALAQ 219 (398)
Q Consensus 143 ~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~---h~Ll~~~g~~l~~I~~V~SHpqal~Q 219 (398)
..|+-..|+.|.+|+||+=-. .+.+++-.+..-..|... .+++++++. .+.++|.+..--+.
T Consensus 52 ~~DIp~yV~~G~aDlGI~G~D------------~l~E~~~~v~el~dLgfG~crl~vA~p~~~--~~~~rVATkyp~it- 116 (204)
T PRK13584 52 GSDVPIYVEQGMADIGIVGSD------------ILDERQYNVNNLLNMPFGACHFAVAAKPET--TNYRKIATSYVHTA- 116 (204)
T ss_pred HHHHHHHHhCCCccEEEeeee------------EeeccCCCeEEEecCCCCcEEEEEEEEcCC--CCceEEEeCcHHHH-
Confidence 457889999999999997533 222222122222233333 345555442 35578887766554
Q ss_pred HHHHHhhcCC--eEEecCCHHHHHHHHHhcCCCC-eEEE-cCHHhHHHcCCceeec
Q 015945 220 CEMTLSNLGI--VRISADDTAGAAQMVASIGERD-TGAV-ASAQAAEIYGLDILAE 271 (398)
Q Consensus 220 C~~fl~~~~~--~~v~~~STA~Aa~~v~~~~~~~-~AAI-~s~~aA~~ygL~il~~ 271 (398)
++|+.+.++ +++..+..-|.|=.+ +..+ .+=| .+-..-+.+||.+++.
T Consensus 117 -~~yf~~~Gi~~~ii~l~GsvElaP~~---GlAD~IvDiv~TG~TLr~NgL~~~e~ 168 (204)
T PRK13584 117 -ETYFKSKGIDVELIKLNGSVELACVV---DMVDGIVDIVQTGTTLKANGLVEKQH 168 (204)
T ss_pred -HHHHHHcCCeEEEEECCCceeecccc---CCccEEEEEECccHHHHHCCCEEEEE
Confidence 679988654 555554443433221 1111 1122 3556678899998853
No 298
>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=20.41 E-value=5.3e+02 Score=21.77 Aligned_cols=120 Identities=13% Similarity=0.012 Sum_probs=58.5
Q ss_pred hCCCCccccC-CCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCCCccCc--
Q 015945 131 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 207 (398)
Q Consensus 131 ~fg~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~~l~~I-- 207 (398)
.++++++... .+..++.+.+.+|++|+|++..+....+... ..+.+..+.+ ..+-.|.+...+..+++++
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08457 25 LRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFL---IETRSLPAVV----AVPMGHPLAQLDVVSPQDLAG 97 (196)
T ss_pred HCCCeEEEEEecCcHHHHHHHHcCCccEEEeccCCCCCCcEE---EEeccCCeEE----EeeCCCccccCCccCHHHhCC
Confidence 4565554332 2346888999999999999864432222111 1112222222 2233444433322233333
Q ss_pred -cEEE-ecHH-HHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHh
Q 015945 208 -KRVF-SHPQ-ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQA 260 (398)
Q Consensus 208 -~~V~-SHpq-al~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~a 260 (398)
.-|. ++.. ......+|+.+.+. . ...++|...+.++++.+ ...++.+...
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~ 153 (196)
T cd08457 98 ERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREG---LGIAIIDPAT 153 (196)
T ss_pred CceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcC---CeEEEEChHH
Confidence 3333 2222 22445666665432 2 34566666666777664 3456665543
No 299
>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=20.40 E-value=5.1e+02 Score=21.55 Aligned_cols=115 Identities=15% Similarity=-0.026 Sum_probs=60.4
Q ss_pred hCCCCcccc-CCCHHHHHHHHHcCCccEEEEeeccccccchHHhHHhhhcCCeEEEEEEEEeeeEeeecCCCC-------
Q 015945 131 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV------- 202 (398)
Q Consensus 131 ~fg~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~tld~L~~~~l~I~~Ei~l~I~h~Ll~~~g~------- 202 (398)
.|+++++.- ..+..++.+.+.+|++|+|+..-.....+ +..+.......++++.++-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~---------------~~~~~l~~~~~~~v~~~~~~~~~~~~ 89 (193)
T cd08442 25 RYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPR---------------LEQEPVFQEELVLVSPKGHPPVSRAE 89 (193)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEEeCCCCCCC---------------cEEEEeecCcEEEEecCCCcccccHH
Confidence 356655433 34567889999999999999753221111 1112222222333333221
Q ss_pred CccCccEEEec-H-HHHHHHHHHHhhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015945 203 LKEELKRVFSH-P-QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 263 (398)
Q Consensus 203 ~l~~I~~V~SH-p-qal~QC~~fl~~~~~--~-~v~~~STA~Aa~~v~~~~~~~~AAI~s~~aA~~ 263 (398)
++.+..-|.-. . ....+...|+.+.+. . ...++|...+.+++.++ ...|+.+...++.
T Consensus 90 ~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 152 (193)
T cd08442 90 DLAGSTLLAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAG---MGIALLPRSVLDS 152 (193)
T ss_pred HhCCCceEEecCCCcHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHhC---CcEEEcCHHHHhh
Confidence 12222333211 1 122446677766432 2 34567777777777764 3478888877653
No 300
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=20.33 E-value=2.2e+02 Score=26.74 Aligned_cols=50 Identities=20% Similarity=0.171 Sum_probs=34.9
Q ss_pred ceeEEEEEcCCCcHHHHHHHHhC---C-----CCccccCCCHHHHHHHHHcCCccEEEEe
Q 015945 110 TKVRVAYQGLPGAYSEAAARKAY---P-----KCETVPCDQFEAAFKAVELWLVDKAVLP 161 (398)
Q Consensus 110 ~~~kVa~lGp~Gs~s~~AA~~~f---g-----~~~~~~~~s~~~v~~aV~~g~~d~gvVP 161 (398)
+..+|++ .+.|+-.+.+.+.++ | +++++..+. .++..++.+|++|.++++
T Consensus 120 kGk~i~~-~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~iDa~~~~ 177 (252)
T PF13379_consen 120 KGKKIAV-PFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGEIDAAVLW 177 (252)
T ss_dssp STEEEEE-SSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-SEEEEE
T ss_pred CCcEEEE-cCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCCcCEEEec
Confidence 5567775 456777776665444 2 367777777 999999999999999986
No 301
>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]
Probab=20.25 E-value=4.2e+02 Score=26.38 Aligned_cols=36 Identities=11% Similarity=0.160 Sum_probs=31.4
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeee
Q 015945 299 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 334 (398)
Q Consensus 299 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IESR 334 (398)
+...+.++.++.+|-.+.+-+.+..+|.|+++-...
T Consensus 6 ~~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf 41 (287)
T COG0788 6 DTFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQF 41 (287)
T ss_pred cceEEEEecCCCCCcHHHHHHHHHHcCCceeecccc
Confidence 356788899999999999999999999999977666
Done!