Query 015464
Match_columns 406
No_of_seqs 308 out of 1289
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 06:33:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/015464.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/015464hhsearch_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 1.8E-93 3.8E-98 725.1 31.6 357 25-404 4-379 (386)
2 PLN02317 arogenate dehydratase 100.0 6.2E-88 1.3E-92 676.9 34.9 320 78-405 61-380 (382)
3 COG0077 PheA Prephenate dehydr 100.0 8.3E-87 1.8E-91 643.0 31.7 271 119-404 2-276 (279)
4 PRK11899 prephenate dehydratas 100.0 5.7E-85 1.2E-89 636.5 33.6 274 118-405 3-277 (279)
5 PRK11898 prephenate dehydratas 100.0 6.4E-78 1.4E-82 589.5 33.5 270 120-404 2-279 (283)
6 KOG2797 Prephenate dehydratase 100.0 5.3E-78 1.1E-82 575.9 22.9 291 110-405 81-373 (377)
7 PF00800 PDT: Prephenate dehyd 100.0 4.9E-52 1.1E-56 382.3 17.3 177 122-298 1-181 (181)
8 PRK06034 hypothetical protein; 100.0 4.7E-29 1E-33 241.6 6.5 160 18-197 1-171 (279)
9 cd04904 ACT_AAAH ACT domain of 99.9 2E-21 4.4E-26 153.8 9.5 73 309-397 1-73 (74)
10 cd04931 ACT_PAH ACT domain of 99.8 3E-20 6.4E-25 152.7 10.2 71 304-389 10-80 (90)
11 cd04930 ACT_TH ACT domain of t 99.8 5.2E-20 1.1E-24 157.8 9.4 76 306-397 39-114 (115)
12 cd04929 ACT_TPH ACT domain of 99.8 5.6E-20 1.2E-24 145.8 8.2 71 309-395 1-71 (74)
13 cd04905 ACT_CM-PDT C-terminal 99.8 2.1E-19 4.5E-24 143.8 11.3 80 308-401 1-80 (80)
14 cd04880 ACT_AAAH-PDT-like ACT 99.8 7.5E-19 1.6E-23 138.7 10.0 75 310-398 1-75 (75)
15 TIGR01268 Phe4hydrox_tetr phen 99.7 4.9E-17 1.1E-21 166.2 10.4 80 306-400 14-94 (436)
16 TIGR01270 Trp_5_monoox tryptop 99.6 7.7E-15 1.7E-19 150.7 10.0 77 304-396 27-104 (464)
17 PRK11199 tyrA bifunctional cho 99.3 5.9E-13 1.3E-17 135.8 2.9 134 27-172 4-152 (374)
18 TIGR01801 CM_A chorismate muta 99.2 1.1E-12 2.4E-17 110.2 -0.5 73 26-107 4-84 (102)
19 TIGR01807 CM_P2 chorismate mut 99.2 1.8E-12 3.9E-17 103.2 0.4 66 28-102 1-76 (76)
20 TIGR01799 CM_T chorismate muta 99.2 2.7E-12 5.9E-17 103.9 -1.0 71 28-107 1-80 (83)
21 TIGR01797 CM_P_1 chorismate mu 99.2 3.2E-12 7E-17 103.5 -1.0 70 28-106 1-79 (83)
22 PRK07248 hypothetical protein; 99.1 4.7E-12 1E-16 103.4 -0.5 71 27-106 2-80 (87)
23 TIGR01803 CM-like chorismate m 99.1 4.1E-12 8.8E-17 102.7 -0.9 69 28-105 1-78 (82)
24 TIGR01805 CM_mono_grmpos monof 99.1 1.5E-11 3.2E-16 99.1 -0.6 69 28-105 1-77 (81)
25 COG1605 PheA Chorismate mutase 99.0 2.3E-11 5E-16 102.1 -1.0 75 26-109 8-92 (101)
26 PRK07075 isochorismate-pyruvat 99.0 2.9E-11 6.2E-16 101.5 -0.4 75 26-109 8-90 (101)
27 PRK06285 chorismate mutase; Pr 99.0 2.3E-11 5E-16 101.2 -1.3 73 25-106 6-87 (96)
28 TIGR01795 CM_mono_cladeE monof 99.0 3.2E-11 7E-16 99.9 -1.2 74 25-106 2-83 (94)
29 PRK09239 chorismate mutase; Pr 99.0 2.2E-11 4.8E-16 102.7 -2.2 79 20-107 4-91 (104)
30 TIGR01791 CM_archaeal chorisma 99.0 4.3E-11 9.3E-16 96.8 -1.0 69 28-105 1-78 (83)
31 PRK12595 bifunctional 3-deoxy- 98.9 2.9E-10 6.2E-15 115.5 -0.7 71 27-106 5-83 (360)
32 PRK06443 chorismate mutase; Va 98.8 2.4E-09 5.2E-14 97.2 3.2 82 27-131 6-95 (177)
33 PF01817 CM_2: Chorismate muta 98.8 3.3E-10 7.2E-15 90.9 -2.9 66 32-106 1-75 (81)
34 TIGR01808 CM_M_hiGC-arch monof 98.7 1.8E-09 3.8E-14 85.7 0.1 63 27-104 1-71 (74)
35 PRK08818 prephenate dehydrogen 98.7 2.6E-08 5.6E-13 101.6 8.1 65 307-387 294-359 (370)
36 PRK07857 hypothetical protein; 98.7 5.9E-09 1.3E-13 87.8 1.7 58 18-81 20-85 (106)
37 TIGR01269 Tyr_3_monoox tyrosin 98.6 1.1E-07 2.3E-12 97.5 9.0 73 307-392 36-109 (457)
38 smart00830 CM_2 Chorismate mut 98.5 1.5E-08 3.2E-13 80.6 -1.2 65 32-105 1-74 (79)
39 KOG3820 Aromatic amino acid hy 98.4 7.7E-07 1.7E-11 89.5 8.6 76 306-397 34-109 (461)
40 cd04886 ACT_ThrD-II-like C-ter 98.0 4.9E-05 1.1E-09 57.7 9.3 68 312-392 2-69 (73)
41 PF01842 ACT: ACT domain; Int 98.0 3.3E-05 7.1E-10 58.1 8.0 38 309-346 1-38 (66)
42 TIGR01806 CM_mono2 chorismate 97.5 1.2E-05 2.6E-10 69.1 -1.8 56 45-106 9-73 (114)
43 cd04882 ACT_Bt0572_2 C-termina 97.3 0.0016 3.5E-08 48.7 8.0 59 311-390 2-60 (65)
44 cd04884 ACT_CBS C-terminal ACT 97.2 0.0028 6E-08 49.2 8.6 65 311-390 2-66 (72)
45 PRK06737 acetolactate synthase 97.2 0.0038 8.3E-08 49.9 9.5 69 309-394 3-71 (76)
46 cd04878 ACT_AHAS N-terminal AC 97.1 0.0058 1.3E-07 45.9 9.7 67 310-393 2-68 (72)
47 cd04874 ACT_Af1403 N-terminal 97.1 0.0055 1.2E-07 46.2 9.1 64 310-392 2-65 (72)
48 cd04883 ACT_AcuB C-terminal AC 97.1 0.0049 1.1E-07 47.3 8.7 64 309-391 2-65 (72)
49 PF13710 ACT_5: ACT domain; PD 96.9 0.0062 1.4E-07 46.7 8.0 61 317-394 1-61 (63)
50 PRK09269 chorismate mutase; Pr 96.9 0.00015 3.2E-09 67.9 -1.5 56 45-106 37-101 (193)
51 cd02116 ACT ACT domains are co 96.8 0.0072 1.6E-07 41.7 7.4 58 312-387 2-59 (60)
52 cd04888 ACT_PheB-BS C-terminal 96.7 0.015 3.3E-07 44.9 9.3 73 310-398 2-76 (76)
53 PRK08055 chorismate mutase; Pr 96.7 0.00026 5.5E-09 65.6 -1.2 55 45-105 30-93 (181)
54 PF13291 ACT_4: ACT domain; PD 96.7 0.016 3.5E-07 45.7 9.1 70 306-391 4-73 (80)
55 cd04902 ACT_3PGDH-xct C-termin 96.6 0.014 3.1E-07 44.5 7.8 35 311-345 2-36 (73)
56 cd04908 ACT_Bt0572_1 N-termina 96.5 0.02 4.4E-07 43.6 8.4 35 310-344 3-37 (66)
57 TIGR00119 acolac_sm acetolacta 96.5 0.026 5.6E-07 51.2 10.1 70 310-396 3-72 (157)
58 cd04909 ACT_PDH-BS C-terminal 96.5 0.0092 2E-07 45.6 6.2 36 310-345 3-38 (69)
59 cd04903 ACT_LSD C-terminal ACT 96.5 0.018 3.9E-07 43.1 7.8 62 311-391 2-63 (71)
60 PRK11895 ilvH acetolactate syn 96.4 0.029 6.3E-07 51.1 10.3 71 309-396 3-73 (161)
61 PRK11152 ilvM acetolactate syn 96.4 0.034 7.4E-07 44.4 9.3 66 308-391 3-68 (76)
62 CHL00100 ilvH acetohydroxyacid 96.3 0.02 4.3E-07 52.8 8.4 71 309-396 3-73 (174)
63 cd04879 ACT_3PGDH-like ACT_3PG 96.3 0.026 5.7E-07 42.0 7.7 62 311-391 2-63 (71)
64 cd04887 ACT_MalLac-Enz ACT_Mal 96.1 0.034 7.3E-07 42.9 7.7 63 311-390 2-64 (74)
65 PRK04435 hypothetical protein; 96.1 0.06 1.3E-06 48.2 10.4 78 306-399 67-146 (147)
66 cd04885 ACT_ThrD-I Tandem C-te 96.1 0.019 4.1E-07 44.2 6.2 61 312-390 2-62 (68)
67 PRK08178 acetolactate synthase 96.0 0.077 1.7E-06 44.3 9.6 71 308-396 8-78 (96)
68 PRK13562 acetolactate synthase 96.0 0.07 1.5E-06 43.4 9.1 70 309-395 3-73 (84)
69 cd04896 ACT_ACR-like_3 ACT dom 95.9 0.051 1.1E-06 43.3 7.8 63 311-388 3-69 (75)
70 cd04881 ACT_HSDH-Hom ACT_HSDH_ 95.7 0.076 1.6E-06 40.5 8.0 64 311-390 3-66 (79)
71 cd04901 ACT_3PGDH C-terminal A 95.6 0.031 6.8E-07 42.3 5.5 60 311-391 2-61 (69)
72 cd04872 ACT_1ZPV ACT domain pr 95.3 0.089 1.9E-06 42.4 7.7 66 309-389 2-68 (88)
73 cd04906 ACT_ThrD-I_1 First of 95.3 0.13 2.7E-06 41.5 8.5 68 311-396 4-71 (85)
74 PRK00194 hypothetical protein; 95.2 0.11 2.3E-06 42.0 7.8 36 308-343 3-38 (90)
75 cd04926 ACT_ACR_4 C-terminal 95.2 0.13 2.7E-06 40.1 7.9 36 309-344 2-37 (72)
76 cd04873 ACT_UUR-ACR-like ACT d 95.1 0.2 4.3E-06 37.6 8.6 36 310-345 2-37 (70)
77 PRK08198 threonine dehydratase 95.1 0.15 3.2E-06 52.7 10.4 76 307-396 326-402 (404)
78 PRK08577 hypothetical protein; 95.1 0.29 6.3E-06 42.9 10.6 69 308-391 56-124 (136)
79 COG4492 PheB ACT domain-contai 94.9 0.13 2.9E-06 45.2 7.9 77 306-399 70-149 (150)
80 cd04870 ACT_PSP_1 CT domains f 94.9 0.22 4.7E-06 39.0 8.6 61 313-388 4-64 (75)
81 cd04876 ACT_RelA-SpoT ACT dom 94.9 0.31 6.7E-06 35.1 9.0 63 312-391 2-64 (71)
82 cd04877 ACT_TyrR N-terminal AC 94.8 0.2 4.3E-06 39.0 7.9 59 311-390 3-61 (74)
83 cd04875 ACT_F4HF-DF N-terminal 94.7 0.12 2.5E-06 40.3 6.5 33 311-343 2-34 (74)
84 PF13740 ACT_6: ACT domain; PD 94.7 0.18 3.8E-06 39.7 7.5 59 313-387 7-65 (76)
85 cd04899 ACT_ACR-UUR-like_2 C-t 94.7 0.29 6.2E-06 37.1 8.5 36 310-345 2-37 (70)
86 cd04889 ACT_PDH-BS-like C-term 94.6 0.11 2.3E-06 38.0 5.8 34 312-345 2-35 (56)
87 TIGR01127 ilvA_1Cterm threonin 94.4 0.22 4.8E-06 50.9 9.6 72 308-393 305-377 (380)
88 COG2061 ACT-domain-containing 94.2 0.35 7.5E-06 43.6 8.9 74 308-397 5-79 (170)
89 cd04895 ACT_ACR_1 ACT domain-c 94.0 0.39 8.4E-06 38.0 8.0 29 309-337 2-30 (72)
90 PRK06382 threonine dehydratase 93.8 0.34 7.5E-06 50.2 9.6 36 307-342 329-364 (406)
91 PRK08526 threonine dehydratase 93.7 1.4 3.1E-05 45.8 13.9 209 161-393 167-398 (403)
92 cd04869 ACT_GcvR_2 ACT domains 93.4 0.62 1.3E-05 36.4 8.3 35 311-345 2-36 (81)
93 PRK08639 threonine dehydratase 92.7 1.6 3.5E-05 45.5 12.5 74 307-397 335-409 (420)
94 PRK07334 threonine dehydratase 91.8 0.98 2.1E-05 46.8 9.7 76 306-395 324-400 (403)
95 TIGR01124 ilvA_2Cterm threonin 91.1 4 8.6E-05 43.7 13.5 205 162-397 166-395 (499)
96 cd04893 ACT_GcvR_1 ACT domains 91.1 1.9 4.2E-05 33.9 8.5 64 311-390 4-67 (77)
97 cd04900 ACT_UUR-like_1 ACT dom 90.9 1.6 3.5E-05 33.7 7.9 32 309-340 2-33 (73)
98 COG1707 ACT domain-containing 90.8 0.72 1.6E-05 42.3 6.5 61 311-389 5-65 (218)
99 cd04935 ACT_AKiii-DAPDC_1 ACT 89.9 2.1 4.6E-05 33.7 7.8 62 316-397 12-74 (75)
100 PRK11589 gcvR glycine cleavage 89.3 1.8 4E-05 40.4 8.1 36 310-345 97-132 (190)
101 cd04897 ACT_ACR_3 ACT domain-c 89.1 3.1 6.7E-05 33.1 8.1 29 309-337 2-30 (75)
102 COG2716 GcvR Glycine cleavage 89.1 1.9 4E-05 39.7 7.7 74 313-399 97-171 (176)
103 COG0440 IlvH Acetolactate synt 88.9 2.2 4.8E-05 38.9 8.0 73 308-397 4-76 (163)
104 TIGR02079 THD1 threonine dehyd 88.8 3.2 6.9E-05 43.2 10.4 73 307-395 324-396 (409)
105 COG4747 ACT domain-containing 86.9 4.5 9.7E-05 35.2 8.2 38 310-347 71-108 (142)
106 cd04932 ACT_AKiii-LysC-EC_1 AC 86.8 4.3 9.3E-05 32.0 7.7 58 315-391 11-69 (75)
107 PLN02550 threonine dehydratase 86.6 8.1 0.00018 42.3 12.1 208 162-397 258-487 (591)
108 COG3830 ACT domain-containing 86.3 1.9 4.1E-05 35.6 5.4 69 313-396 8-78 (90)
109 cd04927 ACT_ACR-like_2 Second 86.0 7 0.00015 30.7 8.6 27 312-338 4-30 (76)
110 cd04912 ACT_AKiii-LysC-EC-like 85.0 6.9 0.00015 30.4 8.1 56 315-389 11-67 (75)
111 PRK09224 threonine dehydratase 84.3 6.9 0.00015 41.9 10.2 72 307-396 327-398 (504)
112 cd04934 ACT_AK-Hom3_1 CT domai 84.1 4.3 9.4E-05 31.8 6.5 55 317-391 13-67 (73)
113 cd04907 ACT_ThrD-I_2 Second of 83.8 11 0.00024 30.2 8.8 63 310-391 3-65 (81)
114 PRK06349 homoserine dehydrogen 83.7 4.3 9.2E-05 42.5 8.2 64 310-390 350-413 (426)
115 PRK13011 formyltetrahydrofolat 83.6 7.5 0.00016 38.6 9.5 67 308-389 7-75 (286)
116 PRK12483 threonine dehydratase 82.9 7.9 0.00017 41.7 10.0 73 306-397 343-416 (521)
117 cd08417 PBP2_Nitroaromatics_li 82.9 30 0.00065 29.8 13.1 122 139-271 25-155 (200)
118 cd04891 ACT_AK-LysC-DapG-like_ 81.0 7.4 0.00016 27.6 6.4 30 314-343 7-36 (61)
119 PF12974 Phosphonate-bd: ABC t 79.8 2.8 6E-05 39.6 4.7 84 118-210 104-202 (243)
120 cd04925 ACT_ACR_2 ACT domain-c 79.8 16 0.00035 28.3 8.3 32 311-342 3-34 (74)
121 PRK06545 prephenate dehydrogen 79.4 6.8 0.00015 39.9 7.7 40 308-347 290-329 (359)
122 PRK13010 purU formyltetrahydro 78.4 11 0.00024 37.5 8.6 66 310-390 11-80 (289)
123 TIGR00691 spoT_relA (p)ppGpp s 76.3 18 0.0004 40.2 10.5 69 306-391 608-676 (683)
124 cd08411 PBP2_OxyR The C-termin 76.2 50 0.0011 28.4 13.0 123 139-271 26-157 (200)
125 COG0317 SpoT Guanosine polypho 75.9 18 0.00039 40.4 10.0 70 306-392 625-694 (701)
126 PRK11092 bifunctional (p)ppGpp 75.7 14 0.0003 41.4 9.3 69 306-391 624-692 (702)
127 TIGR01693 UTase_glnD [Protein- 75.4 16 0.00035 41.7 9.9 51 306-371 777-827 (850)
128 PRK11151 DNA-binding transcrip 75.3 63 0.0014 31.2 13.0 123 138-270 115-246 (305)
129 PRK11790 D-3-phosphoglycerate 74.1 8.6 0.00019 40.1 6.8 63 308-392 338-401 (409)
130 cd04913 ACT_AKii-LysC-BS-like_ 72.9 17 0.00036 27.0 6.6 27 314-340 8-34 (75)
131 PF12727 PBP_like: PBP superfa 72.7 39 0.00084 31.4 10.2 133 144-281 14-168 (193)
132 TIGR01728 SsuA_fam ABC transpo 72.5 59 0.0013 30.6 11.8 139 121-269 2-159 (288)
133 TIGR00363 lipoprotein, YaeC fa 72.2 91 0.002 30.4 13.1 147 118-276 18-200 (258)
134 PRK05007 PII uridylyl-transfer 71.9 9.6 0.00021 43.7 7.1 36 306-341 806-843 (884)
135 PF00497 SBP_bac_3: Bacterial 71.0 13 0.00028 33.3 6.5 50 119-170 110-160 (225)
136 PRK05092 PII uridylyl-transfer 70.6 20 0.00044 41.3 9.4 36 307-342 842-877 (931)
137 PRK10872 relA (p)ppGpp synthet 70.0 31 0.00068 38.8 10.3 68 307-390 665-732 (743)
138 cd08445 PBP2_BenM_CatM_CatR Th 69.4 76 0.0016 27.6 12.8 121 139-269 26-158 (203)
139 PF00585 Thr_dehydrat_C: C-ter 69.2 14 0.0003 30.2 5.7 67 307-391 9-75 (91)
140 COG4747 ACT domain-containing 68.9 5.9 0.00013 34.5 3.5 29 311-339 6-34 (142)
141 cd04890 ACT_AK-like_1 ACT doma 68.7 18 0.0004 26.5 5.8 51 316-387 11-61 (62)
142 KOG2663 Acetolactate synthase, 68.4 16 0.00035 35.8 6.6 74 306-398 75-150 (309)
143 PRK09508 leuO leucine transcri 67.6 30 0.00066 33.8 8.8 122 139-271 137-266 (314)
144 PRK15007 putative ABC transpor 67.3 17 0.00036 33.8 6.6 50 118-169 125-174 (243)
145 cd08452 PBP2_AlsR The C-termin 67.1 84 0.0018 27.2 14.0 122 139-270 25-157 (197)
146 TIGR00719 sda_beta L-serine de 66.7 24 0.00053 33.2 7.6 55 308-378 148-203 (208)
147 cd04933 ACT_AK1-AT_1 ACT domai 65.3 25 0.00055 28.0 6.3 57 316-391 12-72 (78)
148 PRK13581 D-3-phosphoglycerate 62.8 18 0.00039 39.0 6.6 105 265-389 387-514 (526)
149 TIGR00655 PurU formyltetrahydr 62.6 48 0.001 32.8 9.1 65 311-390 3-71 (280)
150 PRK06027 purU formyltetrahydro 62.1 50 0.0011 32.8 9.1 34 310-343 8-41 (286)
151 cd04928 ACT_TyrKc Uncharacteri 61.8 55 0.0012 25.5 7.4 35 311-345 4-38 (68)
152 TIGR01096 3A0103s03R lysine-ar 61.2 25 0.00055 32.6 6.6 49 119-169 131-180 (250)
153 cd08435 PBP2_GbpR The C-termin 60.9 1E+02 0.0023 26.2 12.6 122 139-270 25-158 (201)
154 PRK01759 glnD PII uridylyl-tra 60.6 29 0.00062 39.8 8.0 32 306-337 781-812 (854)
155 PRK11242 DNA-binding transcrip 60.4 1.4E+02 0.0031 28.3 11.9 121 140-270 117-247 (296)
156 cd00134 PBPb Bacterial peripla 59.6 30 0.00064 30.0 6.4 50 119-170 105-154 (218)
157 cd08453 PBP2_IlvR The C-termin 59.1 1.2E+02 0.0025 26.1 13.2 123 139-270 25-160 (200)
158 PF13379 NMT1_2: NMT1-like fam 58.5 64 0.0014 30.5 9.0 144 118-267 6-180 (252)
159 PRK09959 hybrid sensory histid 58.2 16 0.00035 42.7 5.6 49 119-169 164-212 (1197)
160 cd08440 PBP2_LTTR_like_4 TThe 58.2 1.1E+02 0.0024 25.7 12.9 122 139-270 25-155 (197)
161 PRK11260 cystine transporter s 58.1 27 0.00059 33.2 6.4 49 119-169 149-197 (266)
162 cd08486 PBP2_CbnR The C-termin 57.9 1.3E+02 0.0028 26.2 12.3 121 139-269 26-157 (198)
163 PRK10859 membrane-bound lytic 57.4 44 0.00095 35.4 8.3 113 142-270 81-207 (482)
164 smart00062 PBPb Bacterial peri 56.7 1.2E+02 0.0027 25.9 10.0 112 142-269 40-158 (219)
165 PRK09495 glnH glutamine ABC tr 55.9 30 0.00065 32.4 6.2 49 119-169 131-179 (247)
166 PRK03381 PII uridylyl-transfer 55.5 47 0.001 37.6 8.6 37 308-344 707-743 (774)
167 PRK11063 metQ DL-methionine tr 54.7 2.2E+02 0.0047 27.9 13.5 107 119-234 32-151 (271)
168 PRK09959 hybrid sensory histid 54.6 19 0.00042 42.1 5.5 50 119-170 407-456 (1197)
169 smart00079 PBPe Eukaryotic hom 54.6 28 0.0006 29.2 5.2 47 120-169 14-71 (134)
170 cd08446 PBP2_Chlorocatechol Th 54.3 1.4E+02 0.003 25.5 13.7 122 139-270 26-158 (198)
171 PF00497 SBP_bac_3: Bacterial 53.5 68 0.0015 28.5 7.9 125 131-272 28-166 (225)
172 cd04923 ACT_AK-LysC-DapG-like_ 53.4 65 0.0014 23.0 6.4 27 315-341 10-36 (63)
173 cd08462 PBP2_NodD The C-termin 53.2 1.5E+02 0.0033 25.6 10.4 121 139-271 25-155 (200)
174 PRK09034 aspartate kinase; Rev 53.1 2.7E+02 0.0059 29.4 13.3 128 235-389 233-372 (454)
175 PRK10341 DNA-binding transcrip 52.8 2.3E+02 0.0049 27.5 12.2 120 139-270 122-252 (312)
176 cd08450 PBP2_HcaR The C-termin 51.9 1.5E+02 0.0032 25.2 11.9 32 139-170 25-57 (196)
177 PRK04374 PII uridylyl-transfer 51.8 76 0.0016 36.5 9.5 37 306-342 794-832 (869)
178 cd08412 PBP2_PAO1_like The C-t 51.5 1.5E+02 0.0033 25.1 13.4 122 139-270 25-154 (198)
179 smart00062 PBPb Bacterial peri 51.4 44 0.00096 28.8 6.2 51 119-171 106-156 (219)
180 cd04936 ACT_AKii-LysC-BS-like_ 51.3 73 0.0016 22.7 6.4 27 315-341 10-36 (63)
181 cd04911 ACT_AKiii-YclM-BS_1 AC 51.2 68 0.0015 25.6 6.5 57 316-392 12-68 (76)
182 PRK10820 DNA-binding transcrip 51.2 40 0.00087 36.2 6.9 59 311-390 3-61 (520)
183 PF13840 ACT_7: ACT domain ; P 50.6 95 0.0021 23.4 7.1 33 308-340 8-42 (65)
184 cd04868 ACT_AK-like ACT domain 49.8 40 0.00086 23.3 4.6 27 317-343 12-38 (60)
185 TIGR01327 PGDH D-3-phosphoglyc 49.7 31 0.00068 37.1 5.8 104 266-389 387-513 (525)
186 PRK12683 transcriptional regul 48.6 2.7E+02 0.0058 27.1 12.8 121 139-269 118-248 (309)
187 cd08421 PBP2_LTTR_like_1 The C 48.4 1.7E+02 0.0037 24.8 12.8 122 139-270 25-155 (198)
188 PF03466 LysR_substrate: LysR 47.7 1.8E+02 0.004 25.0 13.0 123 139-271 31-162 (209)
189 cd08466 PBP2_LeuO The C-termin 47.0 1.8E+02 0.004 24.8 10.5 123 139-272 25-156 (200)
190 PF12916 DUF3834: Protein of u 46.7 27 0.00059 32.9 4.1 71 118-193 67-142 (201)
191 cd08461 PBP2_DntR_like_3 The C 46.3 1.6E+02 0.0034 25.2 8.8 123 139-272 25-157 (198)
192 cd04924 ACT_AK-Arch_2 ACT doma 46.3 1E+02 0.0022 22.2 6.6 27 315-341 11-37 (66)
193 PRK11482 putative DNA-binding 45.3 3.1E+02 0.0067 26.9 13.1 122 139-272 142-271 (317)
194 PRK11589 gcvR glycine cleavage 45.1 92 0.002 29.1 7.4 36 308-345 6-43 (190)
195 PRK00275 glnD PII uridylyl-tra 45.0 93 0.002 35.9 8.9 36 307-342 813-850 (895)
196 PRK03059 PII uridylyl-transfer 44.9 1E+02 0.0022 35.4 9.2 36 307-342 785-822 (856)
197 cd08459 PBP2_DntR_NahR_LinR_li 44.8 2E+02 0.0043 24.6 10.3 122 139-271 25-155 (201)
198 KOG3217 Protein tyrosine phosp 44.8 20 0.00043 32.4 2.7 63 323-403 58-124 (159)
199 cd04914 ACT_AKi-DapG-BS_1 ACT 44.6 33 0.00071 26.1 3.7 28 315-343 9-36 (67)
200 cd08413 PBP2_CysB_like The C-t 44.4 2.1E+02 0.0045 24.7 12.5 122 139-270 25-156 (198)
201 cd04892 ACT_AK-like_2 ACT doma 43.6 1.1E+02 0.0024 21.4 6.5 27 315-341 10-36 (65)
202 cd04922 ACT_AKi-HSDH-ThrA_2 AC 43.1 66 0.0014 23.4 5.1 27 315-341 11-37 (66)
203 TIGR01729 taurine_ABC_bnd taur 42.8 3.1E+02 0.0068 26.4 11.2 116 142-266 28-156 (300)
204 TIGR02424 TF_pcaQ pca operon t 42.7 3.1E+02 0.0067 26.2 12.5 122 139-270 118-251 (300)
205 TIGR00656 asp_kin_monofn aspar 42.6 3.6E+02 0.0077 27.6 12.1 97 236-341 189-296 (401)
206 PRK12684 transcriptional regul 42.3 3.3E+02 0.0072 26.5 12.4 142 118-270 93-249 (313)
207 PRK11917 bifunctional adhesin/ 41.4 1.1E+02 0.0025 29.1 7.8 49 118-168 147-199 (259)
208 PRK09906 DNA-binding transcrip 41.0 3.2E+02 0.007 25.9 13.7 122 139-270 115-247 (296)
209 PF11966 SSURE: Fibronectin-bi 41.0 61 0.0013 25.9 4.6 38 362-399 18-60 (81)
210 TIGR03427 ABC_peri_uca ABC tra 40.8 3.9E+02 0.0085 26.9 12.6 131 142-280 36-179 (328)
211 cd04918 ACT_AK1-AT_2 ACT domai 40.7 1.5E+02 0.0033 22.0 7.5 36 308-343 3-38 (65)
212 cd04919 ACT_AK-Hom3_2 ACT doma 40.6 79 0.0017 23.1 5.2 26 316-341 12-37 (66)
213 PRK11480 tauA taurine transpor 40.5 35 0.00077 33.7 4.2 141 118-267 23-179 (320)
214 cd08437 PBP2_MleR The substrat 40.4 2.3E+02 0.005 24.1 12.3 122 139-269 25-156 (198)
215 cd08456 PBP2_LysR The C-termin 40.4 2.3E+02 0.0049 24.0 10.6 122 139-270 25-155 (196)
216 TIGR01096 3A0103s03R lysine-ar 40.1 2.8E+02 0.0061 25.5 10.1 115 142-272 64-187 (250)
217 PRK08210 aspartate kinase I; R 39.7 4.4E+02 0.0095 27.1 13.1 96 236-339 193-303 (403)
218 COG0834 HisJ ABC-type amino ac 39.6 66 0.0014 30.0 5.7 50 119-170 146-197 (275)
219 cd08426 PBP2_LTTR_like_5 The C 39.6 2.4E+02 0.0051 24.0 13.2 122 139-270 25-155 (199)
220 TIGR02995 ectoine_ehuB ectoine 39.5 66 0.0014 30.8 5.8 49 119-169 144-193 (275)
221 PF03401 TctC: Tripartite tric 39.4 47 0.001 32.4 4.8 133 118-255 105-261 (274)
222 cd08427 PBP2_LTTR_like_2 The C 39.2 2.4E+02 0.0051 23.8 13.2 121 139-270 25-153 (195)
223 PRK11553 alkanesulfonate trans 39.1 1.7E+02 0.0037 28.5 8.8 50 118-168 27-83 (314)
224 cd08468 PBP2_Pa0477 The C-term 38.9 2.6E+02 0.0055 24.2 9.8 123 139-272 25-158 (202)
225 PRK12679 cbl transcriptional r 38.8 3.8E+02 0.0082 26.1 11.2 122 139-269 118-248 (316)
226 cd04871 ACT_PSP_2 ACT domains 38.5 85 0.0018 25.1 5.4 64 318-389 10-74 (84)
227 cd04937 ACT_AKi-DapG-BS_2 ACT 38.4 1.3E+02 0.0029 22.2 6.2 27 315-341 11-37 (64)
228 TIGR01098 3A0109s03R phosphate 38.2 60 0.0013 30.3 5.2 89 118-209 140-238 (254)
229 cd00134 PBPb Bacterial peripla 38.1 1.7E+02 0.0037 25.1 7.9 114 142-271 39-159 (218)
230 TIGR00070 hisG ATP phosphoribo 38.1 1.1E+02 0.0024 28.5 6.7 107 152-278 50-171 (182)
231 PRK08961 bifunctional aspartat 38.0 6.3E+02 0.014 29.1 14.1 129 235-389 249-388 (861)
232 PF07485 DUF1529: Domain of Un 37.0 2.2E+02 0.0048 24.8 8.0 51 319-385 67-117 (123)
233 PRK13584 hisG ATP phosphoribos 35.7 1.2E+02 0.0027 28.7 6.7 110 151-279 52-168 (204)
234 PRK12680 transcriptional regul 35.7 4.4E+02 0.0096 26.0 13.0 144 118-270 93-250 (327)
235 COG2844 GlnD UTP:GlnB (protein 34.8 1.7E+02 0.0036 33.6 8.4 32 306-337 789-820 (867)
236 PRK12727 flagellar biosynthesi 34.5 72 0.0016 34.8 5.5 115 20-152 254-392 (559)
237 PF09084 NMT1: NMT1/THI5 like; 34.4 3.5E+02 0.0075 24.4 14.7 106 142-255 22-139 (216)
238 PRK15437 histidine ABC transpo 34.3 3E+02 0.0065 25.8 9.4 43 128-171 52-94 (259)
239 PRK09224 threonine dehydratase 34.2 1E+02 0.0022 33.1 6.6 35 307-342 422-456 (504)
240 TIGR03339 phn_lysR aminoethylp 34.2 3.9E+02 0.0084 24.9 13.8 119 139-267 109-236 (279)
241 PF01193 RNA_pol_L: RNA polyme 33.9 1.2E+02 0.0026 22.9 5.3 62 312-390 2-64 (66)
242 COG2107 Predicted periplasmic 33.9 74 0.0016 31.4 5.0 53 118-172 94-146 (272)
243 cd08416 PBP2_MdcR The C-termin 33.3 3E+02 0.0065 23.3 12.8 123 139-271 25-158 (199)
244 cd08465 PBP2_ToxR The C-termin 33.0 3.2E+02 0.007 23.6 10.2 33 139-171 25-58 (200)
245 cd04921 ACT_AKi-HSDH-ThrA-like 32.3 2.2E+02 0.0048 21.5 6.8 27 315-341 11-37 (80)
246 cd08460 PBP2_DntR_like_1 The C 31.8 89 0.0019 27.0 5.0 121 139-270 25-153 (200)
247 PRK06526 transposase; Provisio 31.5 91 0.002 30.3 5.3 115 69-196 50-168 (254)
248 cd08449 PBP2_XapR The C-termin 31.3 3.2E+02 0.0069 23.0 12.9 33 139-171 25-58 (197)
249 cd08443 PBP2_CysB The C-termin 30.8 3.5E+02 0.0076 23.3 12.8 122 139-269 25-155 (198)
250 PRK15010 ABC transporter lysin 30.7 4.6E+02 0.0099 24.6 11.5 113 142-270 66-188 (260)
251 PRK12682 transcriptional regul 30.5 5E+02 0.011 25.0 13.3 121 139-270 118-249 (309)
252 cd08420 PBP2_CysL_like C-termi 30.4 3.3E+02 0.0071 22.8 12.3 122 139-270 25-158 (201)
253 cd08438 PBP2_CidR The C-termin 30.2 3.3E+02 0.0072 22.8 13.1 32 139-170 25-57 (197)
254 cd08425 PBP2_CynR The C-termin 30.1 3.4E+02 0.0074 23.0 10.1 122 139-270 26-157 (197)
255 PRK06635 aspartate kinase; Rev 30.0 1.8E+02 0.0038 29.9 7.4 29 315-343 270-298 (404)
256 cd08418 PBP2_TdcA The C-termin 29.9 3.4E+02 0.0074 22.9 11.4 121 139-271 25-156 (201)
257 PRK05007 PII uridylyl-transfer 29.7 2.3E+02 0.0049 32.8 8.8 34 307-340 700-733 (884)
258 cd08451 PBP2_BudR The C-termin 29.3 3.5E+02 0.0076 22.8 13.9 122 139-270 26-159 (199)
259 COG2150 Predicted regulator of 29.3 2.4E+02 0.0053 25.9 7.1 62 309-389 96-157 (167)
260 TIGR02995 ectoine_ehuB ectoine 28.7 4.8E+02 0.01 24.8 9.9 112 145-271 75-199 (275)
261 COG0725 ModA ABC-type molybdat 28.4 92 0.002 30.4 4.7 52 119-171 135-195 (258)
262 COG3283 TyrR Transcriptional r 28.3 1.9E+02 0.004 30.4 6.9 71 312-403 4-76 (511)
263 cd08444 PBP2_Cbl The C-termina 28.3 3.8E+02 0.0083 23.0 13.7 122 139-270 25-156 (198)
264 PRK15010 ABC transporter lysin 28.2 1.8E+02 0.0039 27.4 6.7 50 118-169 132-183 (260)
265 PRK11139 DNA-binding transcrip 28.1 4.3E+02 0.0092 25.2 9.4 118 140-271 120-246 (297)
266 TIGR01693 UTase_glnD [Protein- 27.8 2.4E+02 0.0053 32.2 8.7 33 307-339 667-699 (850)
267 PRK10797 glutamate and asparta 27.5 1.2E+02 0.0025 30.0 5.4 49 119-169 153-205 (302)
268 PF12974 Phosphonate-bd: ABC t 26.7 5.1E+02 0.011 24.0 9.5 116 142-267 30-167 (243)
269 PRK15437 histidine ABC transpo 26.6 1.9E+02 0.0041 27.3 6.5 50 118-169 132-183 (259)
270 PRK10859 membrane-bound lytic 26.4 3E+02 0.0065 29.1 8.5 49 119-169 149-202 (482)
271 cd08436 PBP2_LTTR_like_3 The C 26.1 3.9E+02 0.0084 22.3 12.9 33 139-171 25-58 (194)
272 cd00460 RNAP_RPB11_RPB3 RPB11 26.0 3E+02 0.0064 22.1 6.6 76 308-392 8-84 (86)
273 PRK08055 chorismate mutase; Pr 25.7 49 0.0011 30.8 2.2 28 25-57 114-141 (181)
274 cd04916 ACT_AKiii-YclM-BS_2 AC 25.5 84 0.0018 22.8 3.1 27 315-341 11-37 (66)
275 cd08469 PBP2_PnbR The C-termin 25.5 4.6E+02 0.0099 22.9 9.3 32 139-170 25-57 (221)
276 PRK05092 PII uridylyl-transfer 25.3 3.5E+02 0.0075 31.4 9.4 34 307-340 731-764 (931)
277 PRK01759 glnD PII uridylyl-tra 25.2 2.4E+02 0.0051 32.5 7.9 36 307-342 676-713 (854)
278 cd08467 PBP2_SyrM The C-termin 25.0 4.4E+02 0.0096 22.6 9.7 122 139-271 25-155 (200)
279 cd08464 PBP2_DntR_like_2 The C 24.7 4.3E+02 0.0093 22.3 9.2 122 139-271 25-155 (200)
280 PRK01686 hisG ATP phosphoribos 24.5 2.3E+02 0.0051 27.0 6.6 112 151-279 54-178 (215)
281 cd08457 PBP2_OccR The C-termin 24.3 4.4E+02 0.0096 22.3 13.2 120 139-268 25-153 (196)
282 PRK09181 aspartate kinase; Val 23.7 9.1E+02 0.02 25.8 13.1 125 236-390 256-391 (475)
283 PRK03601 transcriptional regul 23.2 6.5E+02 0.014 23.8 14.2 114 139-270 114-231 (275)
284 cd08442 PBP2_YofA_SoxR_like Th 23.0 4.5E+02 0.0098 22.0 12.8 122 139-271 25-152 (193)
285 COG3181 Uncharacterized protei 22.7 85 0.0019 31.8 3.4 91 127-217 157-264 (319)
286 PF00072 Response_reg: Respons 22.3 56 0.0012 25.9 1.7 77 218-298 4-81 (112)
287 PRK11716 DNA-binding transcrip 22.1 6.2E+02 0.013 23.2 13.2 123 139-270 92-223 (269)
288 COG0788 PurU Formyltetrahydrof 21.9 5.2E+02 0.011 25.8 8.4 36 307-342 6-41 (287)
289 PRK09466 metL bifunctional asp 21.5 1.2E+03 0.027 26.7 12.7 100 235-341 244-353 (810)
290 cd08485 PBP2_ClcR The C-termin 21.3 5.3E+02 0.011 22.1 13.4 122 139-270 26-158 (198)
291 TIGR03871 ABC_peri_MoxJ_2 quin 21.2 2.2E+02 0.0047 26.0 5.7 49 119-169 104-161 (232)
292 cd08441 PBP2_MetR The C-termin 21.2 5.1E+02 0.011 21.9 11.9 123 139-271 25-156 (198)
293 PF01250 Ribosomal_S6: Ribosom 21.1 4.3E+02 0.0093 21.0 8.1 65 308-388 4-79 (92)
294 CHL00180 rbcR LysR transcripti 20.6 7.6E+02 0.016 23.7 14.9 142 118-269 95-255 (305)
295 PLN02551 aspartokinase 20.6 1.1E+03 0.024 25.5 13.5 100 235-340 292-401 (521)
296 PRK15421 DNA-binding transcrip 20.1 8.1E+02 0.018 23.9 12.6 121 139-269 114-242 (317)
297 cd08433 PBP2_Nac The C-teminal 20.1 5.3E+02 0.012 21.7 13.2 122 139-270 25-155 (198)
No 1
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=100.00 E-value=1.8e-93 Score=725.05 Aligned_cols=357 Identities=30% Similarity=0.471 Sum_probs=323.7
Q ss_pred CCCchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhc-cCCCCccccccccc
Q 015464 25 VPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDS-QSSGFHKDLNLLPT 95 (406)
Q Consensus 25 ~~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~-~~~~l~~d~i~l~~ 95 (406)
..+|+++|.+||+||.+ |++||+| |++++.+|| | | |+|+|| +++++|+... ..++++++.++
T Consensus 4 ~~~L~~lR~~ID~ID~~---ii~Ll~~--R~~~~~~I~~~K~~~~~pi~dp~RE-~~vl~~~~~~a~~~~l~~~~i~--- 74 (386)
T PRK10622 4 ENPLLALREKISALDEK---LLALLAE--RRELAVEVAKAKLLSHRPVRDIDRE-RDLLERLITLGKAHHLDAHYIT--- 74 (386)
T ss_pred hhHHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCcChHHH-HHHHHHHHHhcccCCCCHHHHH---
Confidence 45799999999999999 9999999 999999999 4 6 999999 7777777664 45899999999
Q ss_pred hhcccccccccccccCC---C--CCCCCccEEEEEcCCCcHHHHHHHHHCCC----CceeccCCHHHHHHHHHcCCccEE
Q 015464 96 LVYGQIAEPLSIMELSS---S--PDDGTKVRVAYQGLPGAYSEAAARKAYPK----CETVPCDQFEAAFKAVELWLVDKA 166 (406)
Q Consensus 96 ~I~ReImr~~~~~eis~---~--~~~~~~~~Va~lGp~Gs~s~~AA~~~f~~----~~~~~~~s~~~v~~aV~~g~~d~g 166 (406)
.||+.||..|...|... . .......+||||||+|||||+||+++|+. ...++|.||++||++|++|++|+|
T Consensus 75 ~if~~ii~~S~~~Q~~~~~~~~~~~~~~~~~va~lGp~GtfSh~Aa~~~~~~~~~~~~~~~~~s~~~v~~av~~g~~d~g 154 (386)
T PRK10622 75 RLFQLIIEDSVLTQQALLQQHLNKTNPHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYA 154 (386)
T ss_pred HHHHHHHHHHHHHhhhhhhccccccccccceEEEECCCCcHHHHHHHHhhccccccccccCCCCHHHHHHHHHCCCCCEE
Confidence 99999998876544311 0 11124578999999999999999988863 223489999999999999999999
Q ss_pred EEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCccEEEechHHHHHHHHHHhh-cCCeEEeccCH
Q 015464 167 VLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSN-LGIVRISADDT 245 (406)
Q Consensus 167 vVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~~VySHpqal~QC~~~L~~-~~~~~i~~~sT 245 (406)
|||||||++|+|.+|||+|.+++++|+||+.+||+|||++.+|.++++|++||||||||+||++||++ |+++.++++||
T Consensus 155 VvPiENS~~G~V~~t~DlL~~~~l~I~~E~~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~p~~~~~~~~sT 234 (386)
T PRK10622 155 VLPIENTSSGAINDVYDLLQHTSLSIVGEMTLPIDHCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRYPHWKIEYTEST 234 (386)
T ss_pred EEEEecCCceehHHHHHHHhcCCCEEEEEEEEEEEEEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHCCCceEEEcCCh
Confidence 99999999999999999999999999999999999999999999999999999999999999999998 58999999999
Q ss_pred HHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecCccCCCCCeeEEEEEecCCCCCCCCCCceEEEEEEeCCCcchHHHH
Q 015464 246 AGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLFKA 325 (406)
Q Consensus 246 A~Aa~~v~~~~~~~~AAIas~~aA~~ygL~il~~~I~d~~~N~TRF~vi~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~ 325 (406)
|+||+.|++.++++.|||||+.||++|||+||+++|||.++|+|||+||++++..+....++||||+|+++|+||+|+++
T Consensus 235 a~Aa~~v~~~~~~~~AAI~s~~aa~~ygL~vl~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~~ 314 (386)
T PRK10622 235 AAAMEKVAQANSPHVAALGSEAGGALYGLQVLERNLANQQQNITRFIVLARKAINVSDQVPAKTTLLMATGQQAGALVEA 314 (386)
T ss_pred HHHHHHHHhcCCCCEEEECCHHHHHHcCCcChhhcCcCCccccceEEEEecCCCCCCCCCCCcEEEEEEcCCCCcHHHHH
Confidence 99999999887778999999999999999999999999999999999999987433333457999999999999999999
Q ss_pred HHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcCCceEEEccccCCC
Q 015464 326 LAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDT 404 (406)
Q Consensus 326 L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~~~vrvLGsYp~~~ 404 (406)
|++|+.+|||||||||||+++++ |+|.||||++|+..++.++++|++|++.|.++|+|||||...
T Consensus 315 L~~Fa~~giNLtkIeSRP~~~~~--------------~~Y~Ffid~eg~~~d~~~~~aL~~l~~~~~~~kvLGsYp~~~ 379 (386)
T PRK10622 315 LLVLRNHNLIMTKLESRPIHGNP--------------WEEMFYLDVQANLRSAEMQKALKELGEITRSLKVLGCYPSEN 379 (386)
T ss_pred HHHHHHcCCCeeEEEeeecCCCC--------------ceEEEEEEEeCCCCCHHHHHHHHHHHHhcCcEEEeeeecCCc
Confidence 99999999999999999999876 999999999999999999999999999999999999999764
No 2
>PLN02317 arogenate dehydratase
Probab=100.00 E-value=6.2e-88 Score=676.92 Aligned_cols=320 Identities=81% Similarity=1.238 Sum_probs=293.9
Q ss_pred hhhccCCCCccccccccchhcccccccccccccCCCCCCCCccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHH
Q 015464 78 SQDSQSSGFHKDLNLLPTLVYGQIAEPLSIMELSSSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKA 157 (406)
Q Consensus 78 l~~~~~~~l~~d~i~l~~~I~ReImr~~~~~eis~~~~~~~~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~a 157 (406)
....+...+.+|...|| |++..++++.........+|+||||+|||||+||+++|++.++++|++|++||++
T Consensus 61 ~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~rVaylGp~GtfSe~AA~~~f~~~e~vp~~sf~~vf~A 132 (382)
T PLN02317 61 VVATQSVSFHRDLSGLP--------RPLSITDLSPSPMHGSKLRVAYQGVPGAYSEAAARKAYPNCEAVPCEQFEAAFQA 132 (382)
T ss_pred ccccccccccccccccc--------ccccHhhhcccccCCCCcEEEEECCCcCHHHHHHHHhhCcCceeecCCHHHHHHH
Confidence 33344455555554433 6666555654444445789999999999999999999998899999999999999
Q ss_pred HHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCccEEEechHHHHHHHHHHhhcCC
Q 015464 158 VELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLGI 237 (406)
Q Consensus 158 V~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~~VySHpqal~QC~~~L~~~~~ 237 (406)
|++|++|+||||||||++|+|.+|||+|.+++++|+||+.+||+|||++++|.++++|++||||||||+||++||+++++
T Consensus 133 Ve~g~ad~gVvPIENS~~GsV~~t~DlL~~~~l~IvgEv~l~I~h~Ll~~~g~~l~~Ik~VySHPQALaQC~~~L~~~~~ 212 (382)
T PLN02317 133 VELWLADRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEELKRVISHPQALAQCENTLTKLGV 212 (382)
T ss_pred HHCCCCCEEEEEEeccCccchHHHHHHHhcCCCEEEEEEEEEeeeEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHcCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecCccCCCCCeeEEEEEecCCCCCCCCCCceEEEEEEeCC
Q 015464 238 VRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEE 317 (406)
Q Consensus 238 ~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ygL~il~~~I~d~~~N~TRF~vi~~~~~~~~~~~~~ktsi~f~~~~ 317 (406)
+++++.|||+||++|++.+.++.|||||+.||++|||+||+++|||+++|+|||+||+|++..+..++.+||||+|++++
T Consensus 213 ~~~~~~sTA~AA~~Va~~~~~~~AAIaS~~aA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KTSivfsl~~ 292 (382)
T PLN02317 213 VREAVDDTAGAAKMVAANGLRDTAAIASARAAELYGLDILAEGIQDDSDNVTRFLMLAREPIIPRTDRPFKTSIVFSLEE 292 (382)
T ss_pred eEEEcCCHHHHHHHHHhcCCCCceeecCHHHHHHcCCcchhhhhcCCCCCeeeEEEEecCCcCCCCCCCccEEEEEEcCC
Confidence 99999999999999998777789999999999999999999999999999999999999876554556779999999999
Q ss_pred CcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcCCceEEE
Q 015464 318 GPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVL 397 (406)
Q Consensus 318 ~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~~~vrvL 397 (406)
+||+|+++|++|+.+|||||||||||++++|++++||+|.|.++.|+|.|||||||++.|++++++|++|++++.++|+|
T Consensus 293 ~pG~L~k~L~~Fa~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~eY~FyVD~eg~~~d~~~~~aL~~L~~~~~~lrvL 372 (382)
T PLN02317 293 GPGVLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNSGTAKYFDYLFYVDFEASMADPRAQNALAHLQEFATFLRVL 372 (382)
T ss_pred CCchHHHHHHHHHHCCCCEEEEEeeecCCCCccccccccccccccccEEEEEEEEcCcCCHHHHHHHHHHHHhcCeEEEE
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCCC
Q 015464 398 GCYPMDTT 405 (406)
Q Consensus 398 GsYp~~~~ 405 (406)
||||++.+
T Consensus 373 GsYp~~~~ 380 (382)
T PLN02317 373 GSYPMDMT 380 (382)
T ss_pred eeeecCCC
Confidence 99998765
No 3
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=8.3e-87 Score=643.01 Aligned_cols=271 Identities=48% Similarity=0.747 Sum_probs=257.8
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCCC-CceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEE
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYPK-CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQ 197 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~~-~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~ 197 (406)
.++|+||||+|||||+||+++|++ .+..+|.||++||++|++|++||||||||||++|+|++|+|+|...+++|+||+.
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 478999999999999999999997 7999999999999999999999999999999999999999999999999999999
Q ss_pred EeeeeEeecCCCCCccCccEEEechHHHHHHHHHHhhc--CCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCc
Q 015464 198 LVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLD 275 (406)
Q Consensus 198 l~I~h~L~~~~g~~l~~I~~VySHpqal~QC~~~L~~~--~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ygL~ 275 (406)
+||+|||+++.+.++++|++|||||||++||++||+++ ++++++++|||+||+++++.++...|||||+.||++|||+
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 7999999999999999999888899999999999999999
Q ss_pred eeecCccCCCCCeeEEEEEecC-CCCCCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccC
Q 015464 276 ILAEKIQDDDDNVTRFLILARE-PIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDD 354 (406)
Q Consensus 276 il~~~I~d~~~N~TRF~vi~~~-~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~ 354 (406)
||++||||.++|+|||+||+|. +.. ..++..||||+|+++|+||+|+++|++|+.||||||||||||+++.+
T Consensus 162 il~~~I~D~~~N~TRF~vl~r~~~~~-~~~~~~kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~~~------ 234 (279)
T COG0077 162 ILAENIEDEPNNRTRFLVLSRRKPPS-VSDGPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTGL------ 234 (279)
T ss_pred hHhhcccCCCCCeEEEEEEeccCCCC-cCCCCceEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCCCC------
Confidence 9999999999999999999985 321 11245799999999999999999999999999999999999999876
Q ss_pred CCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcCCceEEEccccCCC
Q 015464 355 SNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDT 404 (406)
Q Consensus 355 ~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~~~vrvLGsYp~~~ 404 (406)
|+|+||||++||.+++.+++||++|++.+.++|+|||||...
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 999999999999999999999999999999999999999865
No 4
>PRK11899 prephenate dehydratase; Provisional
Probab=100.00 E-value=5.7e-85 Score=636.48 Aligned_cols=274 Identities=45% Similarity=0.663 Sum_probs=259.9
Q ss_pred CccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEE
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQ 197 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~ 197 (406)
.+++||||||+|||||+||+++|++.++++|.||++||++|++|++|+||||||||++|+|.+|+|+|.+++++|+||+.
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 45789999999999999999999988999999999999999999999999999999999999999999999999999999
Q ss_pred EeeeeEeecCCCCCccCccEEEechHHHHHHHHHHhhcCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCcee
Q 015464 198 LVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDIL 277 (406)
Q Consensus 198 l~I~h~L~~~~g~~l~~I~~VySHpqal~QC~~~L~~~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ygL~il 277 (406)
+||+|||++.+|.++++|++||||||||+||++||++++++.+++.|||+||++|++.++++.|||||+.||++|||+||
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 99999999999999999999999999999999999998999999999999999999877788999999999999999999
Q ss_pred ecCccCCCCCeeEEEEEecCCCC-CCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCC
Q 015464 278 AEKIQDDDDNVTRFLILAREPII-AGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSN 356 (406)
Q Consensus 278 ~~~I~d~~~N~TRF~vi~~~~~~-~~~~~~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~ 356 (406)
+++|||.++|+|||+||+|++.. +...+.+||||+|+++|+||+|+++|++|+.+|||||||||||+++++
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 99999999999999999998642 222345699999999999999999999999999999999999999876
Q ss_pred CCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcCCceEEEccccCCCC
Q 015464 357 KGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDTT 405 (406)
Q Consensus 357 ~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~~~vrvLGsYp~~~~ 405 (406)
|+|.||||++|+.+|++++++|++|++.+.++|+|||||....
T Consensus 235 ------~~Y~F~id~eg~~~d~~v~~aL~~l~~~~~~~kvLGsYp~~~~ 277 (279)
T PRK11899 235 ------TATQFYADIEGHPEDRNVALALEELRFFSEEVRILGVYPAHPF 277 (279)
T ss_pred ------ceEEEEEEEECCCCCHHHHHHHHHHHHhcCcEEEeeeecCccc
Confidence 9999999999999999999999999999999999999998654
No 5
>PRK11898 prephenate dehydratase; Provisional
Probab=100.00 E-value=6.4e-78 Score=589.48 Aligned_cols=270 Identities=44% Similarity=0.618 Sum_probs=252.8
Q ss_pred cEEEEEcCCCcHHHHHHHHHCCC---CceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccC-CeEEEEE
Q 015464 120 VRVAYQGLPGAYSEAAARKAYPK---CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRH-RLHIVGE 195 (406)
Q Consensus 120 ~~Va~lGp~Gs~s~~AA~~~f~~---~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~-~l~I~gE 195 (406)
++||||||+|||||+||+++|+. .++++|+||++||++|++|++||||||||||++|+|.+|||+|.++ +++|+||
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 7899999999999999999999999999999999999999999775 8999999
Q ss_pred EEEeeeeEeecCCCCCccCccEEEechHHHHHHHHHHhh--cCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcC
Q 015464 196 VQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSN--LGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYG 273 (406)
Q Consensus 196 ~~l~I~h~L~~~~g~~l~~I~~VySHpqal~QC~~~L~~--~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~yg 273 (406)
+.+||+|||+++++.. ++|++||||||||+||++||++ ++++.+.++|||+||+++++++..+.|||+|+.||++||
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 9999999999999999999998 489999999999999999987767789999999999999
Q ss_pred CceeecCccCCCCCeeEEEEEecCCC-CCCCCCCceEEEEEEeCCC-cchHHHHHHHHHhCCceeeeeEeeeCCCCCCcc
Q 015464 274 LDILAEKIQDDDDNVTRFLILAREPI-IAGTDRPYKTSIVFTLEEG-PGMLFKALAVFALRDINLTKIESRPQRKRPLRV 351 (406)
Q Consensus 274 L~il~~~I~d~~~N~TRF~vi~~~~~-~~~~~~~~ktsi~f~~~~~-pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~ 351 (406)
|+||++||||.++|+|||+||+|++. .+...+.+||||+|+++++ ||+|+++|++|+.+|||||||||||+++++
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 99999999999999999999999864 2233457799999999875 999999999999999999999999999875
Q ss_pred ccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcCCceEEEccccCCC
Q 015464 352 VDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDT 404 (406)
Q Consensus 352 ~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~~~vrvLGsYp~~~ 404 (406)
|+|.|||||+|+.++++++++|++|++.+.++|+|||||...
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=5.3e-78 Score=575.89 Aligned_cols=291 Identities=71% Similarity=1.120 Sum_probs=278.4
Q ss_pred cCCCCCCCCccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCC
Q 015464 110 LSSSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHR 189 (406)
Q Consensus 110 is~~~~~~~~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~ 189 (406)
++.+.......+|+|||++|+|||.||.+.|++++.++|+.|+.+|++|+.+.+|++|||||||+.|+|.++||||.+++
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 44444444667899999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eEEEEEEEEeeeeEeecCCCCCccCccEEEechHHHHHHHHHHhh--cCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHH
Q 015464 190 LHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSN--LGIVRISADDTAGAAQMVASIGERDTGAVASAQ 267 (406)
Q Consensus 190 l~I~gE~~l~I~h~L~~~~g~~l~~I~~VySHpqal~QC~~~L~~--~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~ 267 (406)
++|+||+.+||+|||++.+|+..+++++|.||||||+||+.||++ +++.++.++|||+||+.++.++..+++||+|+.
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 458999999999999999999888999999999
Q ss_pred hHHHcCCceeecCccCCCCCeeEEEEEecCCCCCCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCC
Q 015464 268 AAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347 (406)
Q Consensus 268 aA~~ygL~il~~~I~d~~~N~TRF~vi~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~ 347 (406)
||++|||.||++||||+.+|+|||+++.|++.+|..++..||||+|...++||.|+++|++|+.|+||||+|||||.+..
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 99999999999999999999999999999999999899999999999999999999999999999999999999999999
Q ss_pred CCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcCCceEEEccccCCCC
Q 015464 348 PLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFLRVLGCYPMDTT 405 (406)
Q Consensus 348 p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~~~vrvLGsYp~~~~ 405 (406)
|+||+|| .++|+|.||||+|..+.+++.++++.+++++++++|+|||||++.+
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 3779999999999999999999999999999999999999999864
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=4.9e-52 Score=382.27 Aligned_cols=177 Identities=48% Similarity=0.768 Sum_probs=164.2
Q ss_pred EEEEcCCCcHHHHHHHHHC--CCCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEe
Q 015464 122 VAYQGLPGAYSEAAARKAY--PKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLV 199 (406)
Q Consensus 122 Va~lGp~Gs~s~~AA~~~f--~~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~ 199 (406)
|+||||+|||||+||++|| ++.++++++||++||++|.++++|+||||||||++|.|.+|+|+|.+.+++|+||+.+|
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 47899999999999999999999999999999999999999999999999999999999
Q ss_pred eeeEeecCCCCCccCccEEEechHHHHHHHHHHhhc--CCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCcee
Q 015464 200 VNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDIL 277 (406)
Q Consensus 200 I~h~L~~~~g~~l~~I~~VySHpqal~QC~~~L~~~--~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ygL~il 277 (406)
|+|||+++++.++++|++|||||||++||++||+++ +++++.+.||++||+.|+..+.++.|||+|+.||++|||+||
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 999999999988999999999999999999999984 899999999999999988877789999999999999999999
Q ss_pred ecCccCCCCCeeEEEEEecCC
Q 015464 278 AEKIQDDDDNVTRFLILAREP 298 (406)
Q Consensus 278 ~~~I~d~~~N~TRF~vi~~~~ 298 (406)
+++|||.++|+|||+||+|++
T Consensus 161 ~~~I~d~~~N~TRF~vi~~~~ 181 (181)
T PF00800_consen 161 ARNIQDNPNNYTRFLVIGKEP 181 (181)
T ss_dssp ECS-SSSTT-EEEEEEEECCT
T ss_pred hhcCCCCCCCeEeEEEEecCC
Confidence 999999999999999999874
No 8
>PRK06034 hypothetical protein; Provisional
Probab=99.95 E-value=4.7e-29 Score=241.60 Aligned_cols=160 Identities=13% Similarity=0.076 Sum_probs=139.7
Q ss_pred cCCCCCCCCCchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C------C-CCCchhhHHHHHhhhhccCCCCcc
Q 015464 18 HKGLPDLVPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R------P-YTPDVQSSEANERSQDSQSSGFHK 88 (406)
Q Consensus 18 ~~~~~~~~~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K------~-~~P~RE~a~i~~rl~~~~~~~l~~ 88 (406)
|+..|+-..+|++||.+||+||++ |++||+| |++++.+++ | | |+|+|| +++++|+.+.+.+++++
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 566777789999999999999999 9999999 999999999 4 5 999999 88999999999999999
Q ss_pred ccccccchhcccccccccccccCCCCCCCCccEE-EEEcCCCcHHHHHHHHHCC-CCceeccCCHHHHHHHHHcCCccEE
Q 015464 89 DLNLLPTLVYGQIAEPLSIMELSSSPDDGTKVRV-AYQGLPGAYSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKA 166 (406)
Q Consensus 89 d~i~l~~~I~ReImr~~~~~eis~~~~~~~~~~V-a~lGp~Gs~s~~AA~~~f~-~~~~~~~~s~~~v~~aV~~g~~d~g 166 (406)
+.++ .|||+|| +.|+..|.+.+| +|+||+|+|+|+||++||| ..+.++|.||++||++|++|++|||
T Consensus 75 ~~ie---~Ifr~Ii--------s~Sr~lQ~~~~V~a~lG~~gs~s~~AA~~~FG~s~~~~~~~s~~dVf~AV~~g~adyG 143 (279)
T PRK06034 75 DTVE---SIWRVII--------ATFTYVQAPFSVHADGSGGEAAMRDSARFHFGFTVPYVPHFSAQAVVEAVARSKGDLG 143 (279)
T ss_pred HHHH---HHHHHHH--------HHHHHhcCCceEEEEeCCccHHHHHHHHHHhccccCCccCCCHHHHHHHHHcCCCCEE
Confidence 9999 9999995 444556667889 9999999999999999999 5788999999999999999999999
Q ss_pred EEeeecccccccccccchhccCCeEEEEEEE
Q 015464 167 VLPIENSVGGSIHRNYDLLLRHRLHIVGEVQ 197 (406)
Q Consensus 167 vVPIENS~~G~V~~t~DlL~~~~l~I~gE~~ 197 (406)
||||+++ .+.+|..+.. ....+|++...
T Consensus 144 VVPI~~~-~~~WW~~L~~--~~~~~iiarlP 171 (279)
T PRK06034 144 LVSLTSS-DTPWWGRLEA--EGAPKIIARLP 171 (279)
T ss_pred EEECCCC-CCcHHHHhcc--CCCCeEEEeCC
Confidence 9999544 5788866543 45577775543
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=2e-21 Score=153.81 Aligned_cols=73 Identities=34% Similarity=0.559 Sum_probs=68.7
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHH
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 388 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~ 388 (406)
|||+|+++|+||+|+++|+.|+.+|||||||||||+++++ |+|.|||||+| .++.+++++++|+
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 6899999999999999999999999999999999999875 99999999999 5678999999999
Q ss_pred HcCCceEEE
Q 015464 389 EFATFLRVL 397 (406)
Q Consensus 389 ~~~~~vrvL 397 (406)
+.+..+|++
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=99.83 E-value=3e-20 Score=152.69 Aligned_cols=71 Identities=35% Similarity=0.585 Sum_probs=66.0
Q ss_pred CCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHH
Q 015464 304 DRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFA 383 (406)
Q Consensus 304 ~~~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~a 383 (406)
+..+||||+|+++|+||+|+++|++|+.+||||+||||||++..+ |+|.|||||+|+ .+++++++
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 345689999999999999999999999999999999999998865 999999999998 68999999
Q ss_pred HHHHHH
Q 015464 384 LGHLQE 389 (406)
Q Consensus 384 l~~L~~ 389 (406)
|++|++
T Consensus 75 l~~L~~ 80 (90)
T cd04931 75 IKSLRN 80 (90)
T ss_pred HHHHHH
Confidence 999986
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=5.2e-20 Score=157.83 Aligned_cols=76 Identities=28% Similarity=0.400 Sum_probs=70.1
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
++||||+|+++|+||+|+++|++|+.+|||||||||||++..+ |+|.|||||+|+.+ .++++|+
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 4589999999999999999999999999999999999998865 99999999999863 6999999
Q ss_pred HHHHcCCceEEE
Q 015464 386 HLQEFATFLRVL 397 (406)
Q Consensus 386 ~L~~~~~~vrvL 397 (406)
+|+..+.++|+-
T Consensus 103 ~L~~~~~~~kv~ 114 (115)
T cd04930 103 SLRQVAEDVRLT 114 (115)
T ss_pred HHHHhcCeeEec
Confidence 999999998863
No 12
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.81 E-value=5.6e-20 Score=145.78 Aligned_cols=71 Identities=30% Similarity=0.440 Sum_probs=65.1
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHH
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 388 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~ 388 (406)
||++|+++|+||+|+++|++|+.+||||+||||||++..+ |+|.|||||+|+. .+++.++++|+
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 5899999999999999999999999999999999999865 9999999999986 48999999999
Q ss_pred HcCCceE
Q 015464 389 EFATFLR 395 (406)
Q Consensus 389 ~~~~~vr 395 (406)
+.+...+
T Consensus 65 ~~~~~~~ 71 (74)
T cd04929 65 REVASVN 71 (74)
T ss_pred Hhccccc
Confidence 8877543
No 13
>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=2.1e-19 Score=143.81 Aligned_cols=80 Identities=54% Similarity=0.928 Sum_probs=75.4
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 387 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L 387 (406)
|+|++|.++|+||+|.++|+.|+++||||++|+|||.+... |+|.||||++++.++++++++++.|
T Consensus 1 ~~sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~--------------~~~~f~vd~~~~~~~~~~~~~l~~l 66 (80)
T cd04905 1 KTSIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGL--------------WEYVFFIDFEGHIEDPNVAEALEEL 66 (80)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCC--------------ceEEEEEEEECCCCCHHHHHHHHHH
Confidence 58999999999999999999999999999999999997643 8999999999987789999999999
Q ss_pred HHcCCceEEEcccc
Q 015464 388 QEFATFLRVLGCYP 401 (406)
Q Consensus 388 ~~~~~~vrvLGsYp 401 (406)
+..+.++|+|||||
T Consensus 67 ~~~~~~~~~lG~y~ 80 (80)
T cd04905 67 KRLTEFVKVLGSYP 80 (80)
T ss_pred HHhCCeEEEeeeeC
Confidence 99999999999997
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=7.5e-19 Score=138.70 Aligned_cols=75 Identities=52% Similarity=0.826 Sum_probs=71.2
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
|++|+++|+||+|+++|++|+.+|+||++|||||.++.+ |+|.||||++|+..+.++++++++|++
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 588999999999999999999999999999999998764 999999999998778999999999999
Q ss_pred cCCceEEEc
Q 015464 390 FATFLRVLG 398 (406)
Q Consensus 390 ~~~~vrvLG 398 (406)
.+.++|+||
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=99.70 E-value=4.9e-17 Score=166.25 Aligned_cols=80 Identities=35% Similarity=0.614 Sum_probs=74.8
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
.+||||+|+++|+||+|+++|++|+.+|||||||||||++..+ |+|.|||||+|+. +++++++|+
T Consensus 14 ~~KTSLiFsL~d~pGaL~~vL~vFa~~gINLthIESRPsk~~~--------------~eY~FFVD~eg~~-~~~v~~aL~ 78 (436)
T TIGR01268 14 IAKTSLIFSLKEEAGALAETLKLFQAHDVNLTHIESRPSKTHP--------------GEYEFFVEFDEAS-DRKLEGVIE 78 (436)
T ss_pred CCeEEEEEEcCCCCcHHHHHHHHHHHCCCCeeEEecccCCCCC--------------ccEEEEEEEecCc-cHHHHHHHH
Confidence 3489999999999999999999999999999999999999865 9999999999986 589999999
Q ss_pred HHHHcC-CceEEEccc
Q 015464 386 HLQEFA-TFLRVLGCY 400 (406)
Q Consensus 386 ~L~~~~-~~vrvLGsY 400 (406)
+|++.+ ..+++||+-
T Consensus 79 ~Lk~~~~~~vkiLGs~ 94 (436)
T TIGR01268 79 HLRQKAEVTVNILSRD 94 (436)
T ss_pred HHHHhccceEEEeCCC
Confidence 999999 899999984
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=99.57 E-value=7.7e-15 Score=150.70 Aligned_cols=77 Identities=29% Similarity=0.292 Sum_probs=70.0
Q ss_pred CCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccce-EEEEEEEecCCCcHHHHH
Q 015464 304 DRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFD-YLFYIDFEASMADPRAQF 382 (406)
Q Consensus 304 ~~~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~-Y~Ffid~e~~~~~~~~~~ 382 (406)
.+..||||+|+++|+||+|+++|++|+.+||||+||||||++..+ |+ |.|||||+|+. .++++
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 356799999999999999999999999999999999999998764 89 99999999975 68999
Q ss_pred HHHHHHHcCCceEE
Q 015464 383 ALGHLQEFATFLRV 396 (406)
Q Consensus 383 al~~L~~~~~~vrv 396 (406)
+|++|++.+..+.+
T Consensus 91 aL~~Lk~~~~~~~~ 104 (464)
T TIGR01270 91 AMDLLKSGLDVHEV 104 (464)
T ss_pred HHHHHHHhccccee
Confidence 99999998887555
No 17
>PRK11199 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
Probab=99.32 E-value=5.9e-13 Score=135.75 Aligned_cols=134 Identities=13% Similarity=0.124 Sum_probs=99.5
Q ss_pred CchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchh
Q 015464 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLV 97 (406)
Q Consensus 27 ~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I 97 (406)
+|+++|.+||+||++ |++||++ |++++.+|| | | |+|+|| +.+++++.. ....+++++.++ .|
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 667766655 445899999999 99
Q ss_pred ccccccccccccc---CCCCCCCCccEEEEEcCCCcHHHHHHHHHCC---CCceeccCCHHHHHHHHHcCCccEEEEeee
Q 015464 98 YGQIAEPLSIMEL---SSSPDDGTKVRVAYQGLPGAYSEAAARKAYP---KCETVPCDQFEAAFKAVELWLVDKAVLPIE 171 (406)
Q Consensus 98 ~ReImr~~~~~ei---s~~~~~~~~~~Va~lGp~Gs~s~~AA~~~f~---~~~~~~~~s~~~v~~aV~~g~~d~gvVPIE 171 (406)
||.||..+...|. +....+ ...+|+++|+-|.++.-.|+.+.. .+.....+++.+.-+++.+ +|+.++.+.
T Consensus 75 ~~~i~~~s~~~q~~~~~~~~~~-~~~~I~IiGG~GlmG~slA~~l~~~G~~V~~~d~~~~~~~~~~~~~--aDlVilavP 151 (374)
T PRK11199 75 LRRVMRESYSSENDKGFKTLNP-DLRPVVIVGGKGQLGRLFAKMLTLSGYQVRILEQDDWDRAEDILAD--AGMVIVSVP 151 (374)
T ss_pred HHHHHHHHHHHhHHhcccccCc-ccceEEEEcCCChhhHHHHHHHHHCCCeEEEeCCCcchhHHHHHhc--CCEEEEeCc
Confidence 9999988775554 222332 457899999889998877764432 2344444444444455554 455555554
Q ss_pred c
Q 015464 172 N 172 (406)
Q Consensus 172 N 172 (406)
.
T Consensus 152 ~ 152 (374)
T PRK11199 152 I 152 (374)
T ss_pred H
Confidence 3
No 18
>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=99.23 E-value=1.1e-12 Score=110.22 Aligned_cols=73 Identities=10% Similarity=0.120 Sum_probs=67.0
Q ss_pred CCchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccccchh
Q 015464 26 PNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPTLV 97 (406)
Q Consensus 26 ~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~~~~~l~~d~i~l~~~I 97 (406)
.+|++||.+||+||.+ |++||++ |+.++.+|| | | |+|+|| .++++++.+...|++|++.++ .|
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 889999999888999999999 99
Q ss_pred cccccccccc
Q 015464 98 YGQIAEPLSI 107 (406)
Q Consensus 98 ~ReImr~~~~ 107 (406)
|+.||..|..
T Consensus 75 f~~I~~~Sr~ 84 (102)
T TIGR01801 75 FKEIFKASLA 84 (102)
T ss_pred HHHHHHHHHH
Confidence 9999876643
No 19
>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=99.22 E-value=1.8e-12 Score=103.22 Aligned_cols=66 Identities=12% Similarity=0.237 Sum_probs=61.2
Q ss_pred chhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-------C-CCCchhhHHHHHhhhhccCCCCccccccccchh
Q 015464 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-------P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPTLV 97 (406)
Q Consensus 28 l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-------~-~~P~RE~a~i~~rl~~~~~~~l~~d~i~l~~~I 97 (406)
|.+||.+||+||.+ |++||++ |+.++.++| | | |+|+|| ..+++++.....++++++.++ .|
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 888899999888999999999 99
Q ss_pred ccccc
Q 015464 98 YGQIA 102 (406)
Q Consensus 98 ~ReIm 102 (406)
|+.||
T Consensus 72 f~~I~ 76 (76)
T TIGR01807 72 FREIM 76 (76)
T ss_pred HHHHC
Confidence 99985
No 20
>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=99.17 E-value=2.7e-12 Score=103.91 Aligned_cols=71 Identities=14% Similarity=0.180 Sum_probs=62.4
Q ss_pred chhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchhc
Q 015464 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLVY 98 (406)
Q Consensus 28 l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I~ 98 (406)
|+++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| +.+++++.. +..++++++.++ .||
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 777777666 445899999999 999
Q ss_pred ccccccccc
Q 015464 99 GQIAEPLSI 107 (406)
Q Consensus 99 ReImr~~~~ 107 (406)
+.||..|..
T Consensus 72 ~~i~~~s~~ 80 (83)
T TIGR01799 72 RRFMRESYA 80 (83)
T ss_pred HHHHHHHHH
Confidence 999877753
No 21
>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=99.16 E-value=3.2e-12 Score=103.54 Aligned_cols=70 Identities=11% Similarity=0.090 Sum_probs=62.3
Q ss_pred chhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhcc-CCCCccccccccchhc
Q 015464 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQ-SSGFHKDLNLLPTLVY 98 (406)
Q Consensus 28 l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~~-~~~l~~d~i~l~~~I~ 98 (406)
|.++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| ..+++++.... .++|+++.++ .||
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 77888887755 4999999999 999
Q ss_pred cccccccc
Q 015464 99 GQIAEPLS 106 (406)
Q Consensus 99 ReImr~~~ 106 (406)
+.||..|.
T Consensus 72 ~~ii~~S~ 79 (83)
T TIGR01797 72 QLIIEDSV 79 (83)
T ss_pred HHHHHHHH
Confidence 99976653
No 22
>PRK07248 hypothetical protein; Provisional
Probab=99.15 E-value=4.7e-12 Score=103.36 Aligned_cols=71 Identities=7% Similarity=0.068 Sum_probs=63.9
Q ss_pred CchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccccchhc
Q 015464 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPTLVY 98 (406)
Q Consensus 27 ~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~~~~~l~~d~i~l~~~I~ 98 (406)
+|+++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| ..++.++.....++++++.++ .||
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 689999999999999 9999999 999999999 4 6 999999 888899888777888888888 999
Q ss_pred cccccccc
Q 015464 99 GQIAEPLS 106 (406)
Q Consensus 99 ReImr~~~ 106 (406)
|.||..|.
T Consensus 73 ~~I~~~S~ 80 (87)
T PRK07248 73 KDIMKRSR 80 (87)
T ss_pred HHHHHHHH
Confidence 99986664
No 23
>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=99.15 E-value=4.1e-12 Score=102.69 Aligned_cols=69 Identities=10% Similarity=0.081 Sum_probs=61.5
Q ss_pred chhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchhc
Q 015464 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLVY 98 (406)
Q Consensus 28 l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I~ 98 (406)
|+++|.+||+||.+ |++||++ |+.++.++| | | |+|+|| +.+++++.. +..++++++.++ .||
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 777777766 445999999999 999
Q ss_pred ccccccc
Q 015464 99 GQIAEPL 105 (406)
Q Consensus 99 ReImr~~ 105 (406)
+.||..|
T Consensus 72 ~~ii~~s 78 (82)
T TIGR01803 72 AQIIHWY 78 (82)
T ss_pred HHHHHHH
Confidence 9997665
No 24
>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=99.07 E-value=1.5e-11 Score=99.14 Aligned_cols=69 Identities=9% Similarity=0.052 Sum_probs=61.7
Q ss_pred chhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccccchhcc
Q 015464 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPTLVYG 99 (406)
Q Consensus 28 l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~~~~~l~~d~i~l~~~I~R 99 (406)
|.++|.+||+||.+ |++||++ |++++.+|| | | |+|+|| ..++.++.....+.++++.++ .||+
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 888889888777777888888 9999
Q ss_pred cccccc
Q 015464 100 QIAEPL 105 (406)
Q Consensus 100 eImr~~ 105 (406)
.||..|
T Consensus 72 ~I~~~S 77 (81)
T TIGR01805 72 NIMDIS 77 (81)
T ss_pred HHHHHH
Confidence 997554
No 25
>COG1605 PheA Chorismate mutase [Amino acid transport and metabolism]
Probab=99.04 E-value=2.3e-11 Score=102.13 Aligned_cols=75 Identities=17% Similarity=0.321 Sum_probs=67.3
Q ss_pred CCchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C------C-CCCchhhHHHHHhhh-hccCCCCccccccccc
Q 015464 26 PNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R------P-YTPDVQSSEANERSQ-DSQSSGFHKDLNLLPT 95 (406)
Q Consensus 26 ~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K------~-~~P~RE~a~i~~rl~-~~~~~~l~~d~i~l~~ 95 (406)
..|..+|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| +.+++|+. .+..+++++++++
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 3789999999999999 9999999 999999999 3 6 999999 77788877 6999999999999
Q ss_pred hhcccccccccccc
Q 015464 96 LVYGQIAEPLSIME 109 (406)
Q Consensus 96 ~I~ReImr~~~~~e 109 (406)
.+|++||+.+...+
T Consensus 79 ~~f~~i~~~~~~~q 92 (101)
T COG1605 79 RLFREIMEASKAVQ 92 (101)
T ss_pred HHHHHHHHHHHHHH
Confidence 99999998875443
No 26
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=99.04 E-value=2.9e-11 Score=101.55 Aligned_cols=75 Identities=9% Similarity=0.115 Sum_probs=64.3
Q ss_pred CCchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchh
Q 015464 26 PNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLV 97 (406)
Q Consensus 26 ~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I 97 (406)
.+|+++|.+||+||.+ |++||++ |+.++.++| | | |+|+|| ..++.++.. +..++++++.++ .|
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 3689999999999999 9999999 999999999 5 6 999999 667776655 555999999999 99
Q ss_pred cccccccccccc
Q 015464 98 YGQIAEPLSIME 109 (406)
Q Consensus 98 ~ReImr~~~~~e 109 (406)
|+.||..+-..|
T Consensus 79 f~~Ii~~~i~~q 90 (101)
T PRK07075 79 FAQLIHWYIAQQ 90 (101)
T ss_pred HHHHHHHHHHHH
Confidence 999987664433
No 27
>PRK06285 chorismate mutase; Provisional
Probab=99.03 E-value=2.3e-11 Score=101.19 Aligned_cols=73 Identities=11% Similarity=0.232 Sum_probs=63.7
Q ss_pred CCCchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccc
Q 015464 25 VPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPT 95 (406)
Q Consensus 25 ~~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~ 95 (406)
..+|.+||.+||+||.+ |++||++ |+.++.+|| | | |+|+|| ..++.++.. +..++++++.++
T Consensus 6 ~~~L~elR~~ID~ID~~---iv~Ll~~--R~~l~~~I~~~K~~~~~~v~dp~RE-~~vl~~~~~~a~~~~l~~~~i~--- 76 (96)
T PRK06285 6 EKRLNEIRKRIDEIDEQ---IIDLIAE--RTSLAKEIAELKKSLGMPIFDPERE-DYIHEKIRKLCEEHNIDENIGL--- 76 (96)
T ss_pred HHHHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHcCCCCCChHHH-HHHHHHHHHHhhhCCCCHHHHH---
Confidence 35799999999999999 9999999 999999999 4 6 999999 667777666 556999999999
Q ss_pred hhccccccccc
Q 015464 96 LVYGQIAEPLS 106 (406)
Q Consensus 96 ~I~ReImr~~~ 106 (406)
.||+.||..|-
T Consensus 77 ~if~~Ii~~s~ 87 (96)
T PRK06285 77 KIMKILMEHSK 87 (96)
T ss_pred HHHHHHHHHHH
Confidence 99999976653
No 28
>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=99.01 E-value=3.2e-11 Score=99.95 Aligned_cols=74 Identities=9% Similarity=0.106 Sum_probs=64.1
Q ss_pred CCCchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccccch
Q 015464 25 VPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPTL 96 (406)
Q Consensus 25 ~~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~~~~~l~~d~i~l~~~ 96 (406)
+..|.++|.+||+||.+ |++||++ |+.++.++| | | |+|+||.+.+.+....+...+|+++.++ .
T Consensus 2 ~~~L~~lR~~ID~ID~q---Lv~LL~~--R~~~~~~ia~~K~~~~~~v~dp~Re~~vl~~~~~~a~~~gl~p~~~e---~ 73 (94)
T TIGR01795 2 VAELKALRQSIDNIDAA---VIHMLAE--RFKCTSQVGVLKANAGLAPADPAREDYQIARLRRLAIDAGLDPEFAE---K 73 (94)
T ss_pred chhHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHHHCCCCHHHHH---H
Confidence 45899999999999999 9999999 999999999 5 6 9999995544444555899999999999 9
Q ss_pred hccccccccc
Q 015464 97 VYGQIAEPLS 106 (406)
Q Consensus 97 I~ReImr~~~ 106 (406)
||+.|++++-
T Consensus 74 i~~~i~~esi 83 (94)
T TIGR01795 74 FLNFIVTEVI 83 (94)
T ss_pred HHHHHHHHHH
Confidence 9999987764
No 29
>PRK09239 chorismate mutase; Provisional
Probab=99.01 E-value=2.2e-11 Score=102.73 Aligned_cols=79 Identities=11% Similarity=0.119 Sum_probs=68.6
Q ss_pred CCCCCCCCchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCcccc
Q 015464 20 GLPDLVPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDL 90 (406)
Q Consensus 20 ~~~~~~~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~ 90 (406)
..|.+..+|++||.+||+||.+ |++||++ |+.++.++| | | |+|+|| ..++.++.. +...+|++++
T Consensus 4 ~~~~~~~~L~~lR~~ID~ID~e---Iv~LLa~--R~~l~~~Ia~~K~~~~~~i~dp~RE-~~vl~~~~~~a~~~gl~p~~ 77 (104)
T PRK09239 4 EQARAPAELAALRQSIDNIDAA---LIHMLAE--RFKCTQAVGVLKAEHGLPPADPARE-AYQIERLRQLAKDANLDPDF 77 (104)
T ss_pred ccHHHHHHHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHHCCCCCCCHHHH-HHHHHHHHHHHHHCCCCHHH
Confidence 3566777899999999999999 9999999 999999999 4 6 999999 666666655 7778999999
Q ss_pred ccccchhcccccccccc
Q 015464 91 NLLPTLVYGQIAEPLSI 107 (406)
Q Consensus 91 i~l~~~I~ReImr~~~~ 107 (406)
++ .||+-|++++-.
T Consensus 78 ~~---~i~~~ii~esir 91 (104)
T PRK09239 78 AE---KFLNFIIKEVIR 91 (104)
T ss_pred HH---HHHHHHHHHHHH
Confidence 99 999999877743
No 30
>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=98.99 E-value=4.3e-11 Score=96.77 Aligned_cols=69 Identities=9% Similarity=0.109 Sum_probs=59.8
Q ss_pred chhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchhc
Q 015464 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLVY 98 (406)
Q Consensus 28 l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I~ 98 (406)
|.++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| ..+..++.+ ....+++++.++ .||
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 777777765 444789999999 999
Q ss_pred ccccccc
Q 015464 99 GQIAEPL 105 (406)
Q Consensus 99 ReImr~~ 105 (406)
+.||..|
T Consensus 72 ~~i~~~s 78 (83)
T TIGR01791 72 EILMSLS 78 (83)
T ss_pred HHHHHHH
Confidence 9997554
No 31
>PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed
Probab=98.87 E-value=2.9e-10 Score=115.47 Aligned_cols=71 Identities=13% Similarity=0.134 Sum_probs=66.2
Q ss_pred CchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccccchhc
Q 015464 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPTLVY 98 (406)
Q Consensus 27 ~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~~~~~l~~d~i~l~~~I~ 98 (406)
+|++||.+||+||.+ |++||+| |++++.+|| | | |+|+|| .++++++.+.+.++++++.++ .||
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 589999999999999 9999999 999999999 4 6 999999 889999999888999999999 999
Q ss_pred cccccccc
Q 015464 99 GQIAEPLS 106 (406)
Q Consensus 99 ReImr~~~ 106 (406)
|+||+.|.
T Consensus 76 ~~I~~~Sr 83 (360)
T PRK12595 76 KEIFKASL 83 (360)
T ss_pred HHHHHHHH
Confidence 99997654
No 32
>PRK06443 chorismate mutase; Validated
Probab=98.81 E-value=2.4e-09 Score=97.20 Aligned_cols=82 Identities=5% Similarity=0.009 Sum_probs=62.0
Q ss_pred CchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccccchhc
Q 015464 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPTLVY 98 (406)
Q Consensus 27 ~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~~~~~l~~d~i~l~~~I~ 98 (406)
+|++||.+||+||.+ |++||+| |++++.++| | | |+|+|| .++++++.+.+. ||
T Consensus 6 dLeeLR~eID~ID~e---IL~LL~k--Rm~la~eIg~~K~~~g~pI~Dp~RE-~eVLerl~~~n~-------------If 66 (177)
T PRK06443 6 DMEDLRSEILENTMD---IIELIEK--RRELARMIGIIKMRNGLSIRDSERE-NYVKNNLKSDNP-------------LL 66 (177)
T ss_pred cHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHhcCCCCCCChHHH-HHHHHHHHHhCH-------------HH
Confidence 589999999999999 9999999 999999999 4 6 999999 889999876552 88
Q ss_pred ccccccccccccCCCCCCCCccEEEEEcCCCcH
Q 015464 99 GQIAEPLSIMELSSSPDDGTKVRVAYQGLPGAY 131 (406)
Q Consensus 99 ReImr~~~~~eis~~~~~~~~~~Va~lGp~Gs~ 131 (406)
++||..+...+ .++.....|...|-.|++
T Consensus 67 ~eIms~Sr~~Q----~~~~~~~~i~~sg~y~~~ 95 (177)
T PRK06443 67 NMIFEATIHYQ----KNISLNINIEVSGDYDSL 95 (177)
T ss_pred HHHHHHHHHHH----hcccccceeeeecchHHH
Confidence 99875553322 122223356665544544
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=98.78 E-value=3.3e-10 Score=90.88 Aligned_cols=66 Identities=20% Similarity=0.337 Sum_probs=58.3
Q ss_pred hhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchhccccc
Q 015464 32 GLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLVYGQIA 102 (406)
Q Consensus 32 R~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I~ReIm 102 (406)
|.+||+||.+ |++||++ |+.++.++| | | |+|+|| ..++.++.+ +..++++++.++ .||+.||
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 8999999999 9999999 999999999 4 6 999999 777777777 445999999999 9999998
Q ss_pred cccc
Q 015464 103 EPLS 106 (406)
Q Consensus 103 r~~~ 106 (406)
..|.
T Consensus 72 ~~s~ 75 (81)
T PF01817_consen 72 EESR 75 (81)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6653
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=98.74 E-value=1.8e-09 Score=85.73 Aligned_cols=63 Identities=10% Similarity=-0.024 Sum_probs=51.1
Q ss_pred CchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhccCCCCccccccccchhc
Q 015464 27 NRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDSQSSGFHKDLNLLPTLVY 98 (406)
Q Consensus 27 ~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~~~~~l~~d~i~l~~~I~ 98 (406)
+|+.+|.+||+||.+ |++||++ |+.++.++| | | |+|+|| .++++++.+.. +. +|.+|
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--PE-------GKDLA 65 (74)
T ss_pred CHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHHhCCCCCCChHHH-HHHHHHHHHhC--CC-------CHHHH
Confidence 478899999999999 9999999 999999999 4 6 999999 88888885433 21 23666
Q ss_pred cccccc
Q 015464 99 GQIAEP 104 (406)
Q Consensus 99 ReImr~ 104 (406)
+.|++.
T Consensus 66 e~i~~~ 71 (74)
T TIGR01808 66 IKLLRV 71 (74)
T ss_pred HHHHHh
Confidence 666543
No 35
>PRK08818 prephenate dehydrogenase; Provisional
Probab=98.73 E-value=2.6e-08 Score=101.62 Aligned_cols=65 Identities=26% Similarity=0.335 Sum_probs=53.4
Q ss_pred ceEEEEEEeC-CCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 307 YKTSIVFTLE-EGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 307 ~ktsi~f~~~-~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
.-++|+|+++ |+||+|+++|++|+.+|||||+||| .+.++ |+|.|||||++..+-..+..+-.
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 55554 99999999998654444444444
Q ss_pred HH
Q 015464 386 HL 387 (406)
Q Consensus 386 ~L 387 (406)
++
T Consensus 358 ~~ 359 (370)
T PRK08818 358 EI 359 (370)
T ss_pred hh
Confidence 44
No 36
>PRK07857 hypothetical protein; Provisional
Probab=98.69 E-value=5.9e-09 Score=87.84 Aligned_cols=58 Identities=10% Similarity=0.040 Sum_probs=51.4
Q ss_pred cCCCCCCCCCchhhhhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhhc
Q 015464 18 HKGLPDLVPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQDS 81 (406)
Q Consensus 18 ~~~~~~~~~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~~ 81 (406)
.++-|.--.+|.++|.+||+||.+ |++||++ |+.++.+|| | | |+|+|| .++++|+.+.
T Consensus 20 ~~~~p~~~~~L~~lR~eID~ID~e---Il~LL~e--R~~la~eIg~~K~~~g~pI~dp~RE-~eVl~rl~~~ 85 (106)
T PRK07857 20 GTDDPLSDAEIDELREEIDRLDAE---ILALVKR--RTEVSQAIGKARMASGGTRLVHSRE-MKVIERYREE 85 (106)
T ss_pred CCCCCcchhhHHHHHHHHHHHHHH---HHHHHHH--HHHHHHHHHHHHhccCCCccChHHH-HHHHHHHHHH
Confidence 355677778999999999999999 9999999 999999999 4 6 999999 8888888653
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=98.62 E-value=1.1e-07 Score=97.55 Aligned_cols=73 Identities=21% Similarity=0.269 Sum_probs=60.2
Q ss_pred ceEEEEEEeCCC-cchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 307 YKTSIVFTLEEG-PGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 307 ~ktsi~f~~~~~-pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
..++++|+++++ +|+|.++|.+|..++|||++|||||++... .| ..+|.|||||+++ ..++..++.
T Consensus 36 ~~~~~~~~~~~~~~g~L~~~l~~f~~~~inl~hiEsr~~~~~~--------~~---~~~~~~~v~~~~~--~~~~~~~~~ 102 (457)
T TIGR01269 36 AMQNNQFYIRTKEISSLHRILKYIETFKLNLVHFETRPTRTLS--------NA---DVDYSCLITLEAN--EINMSLLIE 102 (457)
T ss_pred cceeEEEEeccCcchhHHHHHHHHHHcCCcEEEeecCCccccC--------CC---CCceEEEEEEecc--HhhHHHHHH
Confidence 357788888754 999999999999999999999999987542 11 2479999999976 477999999
Q ss_pred HHHHcCC
Q 015464 386 HLQEFAT 392 (406)
Q Consensus 386 ~L~~~~~ 392 (406)
.|++.+.
T Consensus 103 ~l~~~~~ 109 (457)
T TIGR01269 103 SLRGNSF 109 (457)
T ss_pred HHHhhhc
Confidence 9998765
No 38
>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=98.49 E-value=1.5e-08 Score=80.64 Aligned_cols=65 Identities=23% Similarity=0.429 Sum_probs=56.0
Q ss_pred hhHHhhhcccchHHHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchhccccc
Q 015464 32 GLDLRVLNKWECTCVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLVYGQIA 102 (406)
Q Consensus 32 R~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I~ReIm 102 (406)
|.+||.||.+ |++||++ |+.++.++| | | |+|+|| ..++.++.. +...+++++.++ .||+.||
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 7899999999 9999999 999999999 4 6 999999 666666555 667788999999 9999997
Q ss_pred ccc
Q 015464 103 EPL 105 (406)
Q Consensus 103 r~~ 105 (406)
..+
T Consensus 72 ~~s 74 (79)
T smart00830 72 EAS 74 (79)
T ss_pred HHH
Confidence 655
No 39
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=98.42 E-value=7.7e-07 Score=89.55 Aligned_cols=76 Identities=28% Similarity=0.410 Sum_probs=64.6
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
...++++|++++++|+|.++|++|..+++|+.||||||++... .+|.|||+++... .++.++++
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 4478999999999999999999999999999999999997642 4699999999864 48888999
Q ss_pred HHHHcCCceEEE
Q 015464 386 HLQEFATFLRVL 397 (406)
Q Consensus 386 ~L~~~~~~vrvL 397 (406)
.|+..+..+...
T Consensus 98 ~lrq~~~~~~~~ 109 (461)
T KOG3820|consen 98 LLRQNHVALSYF 109 (461)
T ss_pred HHHHhcccceec
Confidence 999887544433
No 40
>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=98.02 E-value=4.9e-05 Score=57.66 Aligned_cols=68 Identities=21% Similarity=0.194 Sum_probs=54.1
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcC
Q 015464 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFA 391 (406)
Q Consensus 312 ~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~ 391 (406)
.+.++|+||.|.++++.|+..|+|++.|.+++....- ..+.+.+++.++.. +...++.+++.|+..+
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 01567888888874 4577888999998765
Q ss_pred C
Q 015464 392 T 392 (406)
Q Consensus 392 ~ 392 (406)
-
T Consensus 69 ~ 69 (73)
T cd04886 69 Y 69 (73)
T ss_pred C
Confidence 3
No 41
>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=3.3e-05 Score=58.08 Aligned_cols=38 Identities=18% Similarity=0.377 Sum_probs=34.9
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCC
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~ 346 (406)
+.|.+.++|+||.|.++++.|+++|||+..+.+++.+.
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 42
>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=97.50 E-value=1.2e-05 Score=69.11 Aligned_cols=56 Identities=13% Similarity=0.128 Sum_probs=48.1
Q ss_pred HHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchhccccccccc
Q 015464 45 CVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLVYGQIAEPLS 106 (406)
Q Consensus 45 l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I~ReImr~~~ 106 (406)
|++||++ |+.++.+|| | | |+|+|| ..+++++.. +..++|+++.++ .||+.||..+.
T Consensus 9 Lv~Ll~e--R~~la~eVa~~K~~~~~pI~Dp~RE-~~Vl~~~~~~a~~~gL~~~~i~---~if~~Ii~~Sk 73 (114)
T TIGR01806 9 LVDAANE--RLQLADDVAGYKARNNLPIEDSPRE-EQVLDSLRAQAQSAGLDPDYVT---RFFQAQINANK 73 (114)
T ss_pred HHHHHHH--HHHHHHHHHHHHHHCCCCCCChHHH-HHHHHHHHHHhHcCCCCHHHHH---HHHHHHHHHHH
Confidence 9999999 999999999 4 6 999999 777777766 445999999999 99999986543
No 43
>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=97.29 E-value=0.0016 Score=48.70 Aligned_cols=59 Identities=22% Similarity=0.265 Sum_probs=43.4
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
+.+.++|+||.|.++++.|+.+|+|+..+...+.... ....+++.++. ...+++.|++.
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 4568899999999999999999999999987665321 23456666654 34566666654
No 44
>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=97.20 E-value=0.0028 Score=49.16 Aligned_cols=65 Identities=14% Similarity=0.125 Sum_probs=44.3
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
+.+.++|+||+|.++++.++.+|+|+..+...+..... +....+|.+++.. ...++.+++.|++.
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 45688999999999999999999999999766653221 1223444444422 22366777777654
No 45
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=97.19 E-value=0.0038 Score=49.86 Aligned_cols=69 Identities=12% Similarity=0.248 Sum_probs=53.2
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHH
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 388 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~ 388 (406)
-+|.+-+.|+||.|.++++.|+.||.|+..|..-|+... .-+.+-|-+.| ++..+..+.++|+
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 356677789999999999999999999999998887642 34566666665 4577888888888
Q ss_pred HcCCce
Q 015464 389 EFATFL 394 (406)
Q Consensus 389 ~~~~~v 394 (406)
+.-.=+
T Consensus 66 KLidV~ 71 (76)
T PRK06737 66 KLINVL 71 (76)
T ss_pred CCcCEE
Confidence 765433
No 46
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=97.13 E-value=0.0058 Score=45.91 Aligned_cols=67 Identities=18% Similarity=0.236 Sum_probs=50.8
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
+|.+...|+||.|.++++.|+.+|+|+.++.+.+.+.. ....+++.++. .. ..+..++++|++
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 46778899999999999999999999999998764221 12345555554 34 788999999987
Q ss_pred cCCc
Q 015464 390 FATF 393 (406)
Q Consensus 390 ~~~~ 393 (406)
...-
T Consensus 65 ~~~v 68 (72)
T cd04878 65 LVDV 68 (72)
T ss_pred CccE
Confidence 6543
No 47
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.07 E-value=0.0055 Score=46.23 Aligned_cols=64 Identities=19% Similarity=0.238 Sum_probs=48.0
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
+|.+..+|+||.|.++++.|+.+++|+.++...+... +.+.+++++++. ..+..+++.|++
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 4667889999999999999999999999998765432 245567888764 345567777775
Q ss_pred cCC
Q 015464 390 FAT 392 (406)
Q Consensus 390 ~~~ 392 (406)
...
T Consensus 63 ~~~ 65 (72)
T cd04874 63 LPI 65 (72)
T ss_pred CCC
Confidence 443
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=97.05 E-value=0.0049 Score=47.26 Aligned_cols=64 Identities=16% Similarity=0.280 Sum_probs=45.3
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHH
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 388 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~ 388 (406)
+.+.+.++|+||.|.++++.|+.+|+|+.++...+.... ....++|.+++. +.. .+++.|+
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 357788999999999999999999999999976654321 234556666653 222 5566666
Q ss_pred HcC
Q 015464 389 EFA 391 (406)
Q Consensus 389 ~~~ 391 (406)
+..
T Consensus 63 ~~G 65 (72)
T cd04883 63 RAG 65 (72)
T ss_pred HCC
Confidence 543
No 49
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=96.91 E-value=0.0062 Score=46.68 Aligned_cols=61 Identities=18% Similarity=0.263 Sum_probs=47.4
Q ss_pred CCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcCCce
Q 015464 317 EGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFATFL 394 (406)
Q Consensus 317 ~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~~~v 394 (406)
|+||+|.+++++|..||+|+..|..-|+... .-+.+-+.++|. +..+..+..+|++...-+
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 467888888874 357778888888765533
No 50
>PRK09269 chorismate mutase; Provisional
Probab=96.88 E-value=0.00015 Score=67.87 Aligned_cols=56 Identities=16% Similarity=0.165 Sum_probs=48.2
Q ss_pred HHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchhccccccccc
Q 015464 45 CVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLVYGQIAEPLS 106 (406)
Q Consensus 45 l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I~ReImr~~~ 106 (406)
|++||+| |+.++.+|+ | | |+|+|| +.+++++.. +..++|+++.++ .||+.||..+.
T Consensus 37 Lv~Li~e--Rl~la~~VA~~K~~~~~pI~Dp~RE-~~VL~~v~~~A~~~gLdp~~v~---~iF~~~I~aSk 101 (193)
T PRK09269 37 LVDLAAQ--RLALADPVALSKWDSGKPIEDPPRE-AQVLANVEAQAPAHGVDPDYVR---RFFRDQIEANK 101 (193)
T ss_pred HHHHHHH--HHHHHHHHHHHHHhCCCCCCChHHH-HHHHHHHHHHhhcCCCCHHHHH---HHHHHHHHHHH
Confidence 9999999 999999999 5 6 999999 777777766 445999999999 99999985543
No 51
>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=96.84 E-value=0.0072 Score=41.70 Aligned_cols=58 Identities=28% Similarity=0.316 Sum_probs=43.7
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHH
Q 015464 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 387 (406)
Q Consensus 312 ~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L 387 (406)
.+..+++||.|.++++.|+.+|+|+.++.+++... + +...|++.++... ....++++|
T Consensus 2 ~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~-~--------------~~~~~~~~~~~~~---~~~~~~~~l 59 (60)
T cd02116 2 TVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGD-G--------------GEADIFIVVDGDG---DLEKLLEAL 59 (60)
T ss_pred EEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcCC-C--------------CeEEEEEEEechH---HHHHHHHHh
Confidence 46678899999999999999999999999887643 1 4567777776532 455555544
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=96.74 E-value=0.015 Score=44.90 Aligned_cols=73 Identities=23% Similarity=0.250 Sum_probs=49.7
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
+|.+..+|+||.|.++++.++..|+|+..+.+..... +.+...|-++. +..+..+..+++.|++
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 5777889999999999999999999999998742211 11344444444 3333367777887775
Q ss_pred c--CCceEEEc
Q 015464 390 F--ATFLRVLG 398 (406)
Q Consensus 390 ~--~~~vrvLG 398 (406)
. ...++++|
T Consensus 66 i~~V~~v~~~~ 76 (76)
T cd04888 66 IDGVEKVELVG 76 (76)
T ss_pred CCCeEEEEEeC
Confidence 4 33455555
No 53
>PRK08055 chorismate mutase; Provisional
Probab=96.72 E-value=0.00026 Score=65.57 Aligned_cols=55 Identities=7% Similarity=0.060 Sum_probs=47.0
Q ss_pred HHHHhhhhcccccccccC--C-----C-CCCchhhHHHHHhhhh-ccCCCCccccccccchhcccccccc
Q 015464 45 CVGVLAQTHRAITPVEDD--R-----P-YTPDVQSSEANERSQD-SQSSGFHKDLNLLPTLVYGQIAEPL 105 (406)
Q Consensus 45 l~~Ll~~~~R~~~~~~v~--K-----~-~~P~RE~a~i~~rl~~-~~~~~l~~d~i~l~~~I~ReImr~~ 105 (406)
|++|+++ |+.++.+|+ | | |+|+|| +.+++++.. +...|++++.++ .+|+.+|..+
T Consensus 30 Lv~Li~e--Rl~la~~VA~~K~~~~~PI~Dp~RE-~~VL~~v~~~A~~~GLdp~~i~---~~F~~~I~as 93 (181)
T PRK08055 30 LATLINE--RLSYMKDVAGYKAEHHLPIEDLTQE-QKVLAEAEEEAASNGLDPESIK---PFIVAQMDAA 93 (181)
T ss_pred HHHHHHH--HHHHHHHHHHHHHhCCCCCCChHHH-HHHHHHHHHHhhhCCCCHHHHH---HHHHHHHHHH
Confidence 9999999 999999999 4 7 999999 777777666 545679999999 9999998553
No 54
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=96.68 E-value=0.016 Score=45.72 Aligned_cols=70 Identities=14% Similarity=0.263 Sum_probs=52.2
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
.+.+.|.+...|+||.|.++.++++..|+|+..+.....+.. ..+.+.++++-. +-..+..+++
T Consensus 4 ~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~---------------~~~~~~l~v~V~-d~~~L~~ii~ 67 (80)
T PF13291_consen 4 SFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDD---------------GTARITLTVEVK-DLEHLNQIIR 67 (80)
T ss_dssp -EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ET---------------TEEEEEEEEEES-SHHHHHHHHH
T ss_pred EEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccC---------------CEEEEEEEEEEC-CHHHHHHHHH
Confidence 567889999999999999999999999999999999997521 245566666553 4478888899
Q ss_pred HHHHcC
Q 015464 386 HLQEFA 391 (406)
Q Consensus 386 ~L~~~~ 391 (406)
.|++.-
T Consensus 68 ~L~~i~ 73 (80)
T PF13291_consen 68 KLRQIP 73 (80)
T ss_dssp HHCTST
T ss_pred HHHCCC
Confidence 887643
No 55
>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=96.55 E-value=0.014 Score=44.54 Aligned_cols=35 Identities=17% Similarity=0.312 Sum_probs=30.9
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCC
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~ 345 (406)
+++..+|+||.|.++++.|+++|+|+..+.+.+..
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~ 36 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDE 36 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccC
Confidence 46688999999999999999999999999877653
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=96.51 E-value=0.02 Score=43.57 Aligned_cols=35 Identities=20% Similarity=0.313 Sum_probs=31.2
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeC
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~ 344 (406)
-|.+.++|+||.|.++++.|+++|+|+..+..-+.
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 35668899999999999999999999999987664
No 57
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=96.48 E-value=0.026 Score=51.24 Aligned_cols=70 Identities=17% Similarity=0.254 Sum_probs=54.0
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
.|.+.++|+||.|.++.+.|+.+|+|+..+-.-|.... ..+.+.+-+++ ++..+..+.++|.+
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 46677899999999999999999999999988887421 34566666666 46778888888887
Q ss_pred cCCceEE
Q 015464 390 FATFLRV 396 (406)
Q Consensus 390 ~~~~vrv 396 (406)
.-.=+++
T Consensus 66 li~V~~V 72 (157)
T TIGR00119 66 LVDVIKV 72 (157)
T ss_pred CccEEEE
Confidence 6553333
No 58
>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=96.47 E-value=0.0092 Score=45.56 Aligned_cols=36 Identities=17% Similarity=0.346 Sum_probs=31.7
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCC
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~ 345 (406)
.+.+.++|+||.|.++++.|+.+|+|+..+...+.+
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~ 38 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIR 38 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEee
Confidence 466788999999999999999999999999877654
No 59
>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=0.018 Score=43.13 Aligned_cols=62 Identities=16% Similarity=0.306 Sum_probs=44.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
|.+..+|+||.|.++++.|+.+|+|+..+...+.... ......++++.. .+.+++++|++.
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 122334666553 344677777754
Q ss_pred C
Q 015464 391 A 391 (406)
Q Consensus 391 ~ 391 (406)
-
T Consensus 63 ~ 63 (71)
T cd04903 63 P 63 (71)
T ss_pred C
Confidence 3
No 60
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=96.45 E-value=0.029 Score=51.09 Aligned_cols=71 Identities=17% Similarity=0.250 Sum_probs=54.6
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHH
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 388 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~ 388 (406)
-.|.+.++|+||.|.++.+.|+.||+|+..+-.-|.... ..+.+.+-+++ ++..+..+.++|.
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 356677899999999999999999999999988887421 34556666666 4577888888888
Q ss_pred HcCCceEE
Q 015464 389 EFATFLRV 396 (406)
Q Consensus 389 ~~~~~vrv 396 (406)
+.-.=+++
T Consensus 66 KLidV~~V 73 (161)
T PRK11895 66 KLIDVLKV 73 (161)
T ss_pred ccccEEEE
Confidence 76554443
No 61
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=96.40 E-value=0.034 Score=44.40 Aligned_cols=66 Identities=9% Similarity=0.167 Sum_probs=48.0
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 387 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L 387 (406)
|-+|.+.+.|+||+|.++++.|+.||.|+..|-.-|+... .-...-+-++ ++..+..+.++|
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 3457777889999999999999999999999999987532 1122222332 456777778888
Q ss_pred HHcC
Q 015464 388 QEFA 391 (406)
Q Consensus 388 ~~~~ 391 (406)
.+.-
T Consensus 65 ~KL~ 68 (76)
T PRK11152 65 NKLV 68 (76)
T ss_pred hcCc
Confidence 7653
No 62
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=96.30 E-value=0.02 Score=52.84 Aligned_cols=71 Identities=15% Similarity=0.237 Sum_probs=53.3
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHH
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 388 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~ 388 (406)
-.|.+...|+||.|.++.+.|+.||+|+..+.+.|.... +...+-+.+.++. ..+..+.++|+
T Consensus 3 ~~isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~---------------~~sr~TIvv~~~~--~~ieqL~kQL~ 65 (174)
T CHL00100 3 HTLSVLVEDESGVLTRIAGLFARRGFNIESLAVGPAEQK---------------GISRITMVVPGDD--RTIEQLTKQLY 65 (174)
T ss_pred EEEEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCC---------------CccEEEEEEECCH--HHHHHHHHHHH
Confidence 356667789999999999999999999999999886642 2346677777642 33667777777
Q ss_pred HcCCceEE
Q 015464 389 EFATFLRV 396 (406)
Q Consensus 389 ~~~~~vrv 396 (406)
+.+.-+++
T Consensus 66 KLidVl~V 73 (174)
T CHL00100 66 KLVNILKV 73 (174)
T ss_pred HHhHhhEE
Confidence 77665544
No 63
>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=96.25 E-value=0.026 Score=42.01 Aligned_cols=62 Identities=15% Similarity=0.247 Sum_probs=44.4
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
+.+..+|+||.|.++++.|+.+|+|+.++.+.+.... ..+...++++.. ...+++++|++.
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 133445566432 244666777654
Q ss_pred C
Q 015464 391 A 391 (406)
Q Consensus 391 ~ 391 (406)
-
T Consensus 63 ~ 63 (71)
T cd04879 63 P 63 (71)
T ss_pred C
Confidence 3
No 64
>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=96.11 E-value=0.034 Score=42.86 Aligned_cols=63 Identities=16% Similarity=0.223 Sum_probs=45.6
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
|.+...|+||.|.++.+.++..|+|+..++++..... .....|-+++. +...++.++..|+..
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 12333434443 336677778877653
No 65
>PRK04435 hypothetical protein; Provisional
Probab=96.10 E-value=0.06 Score=48.18 Aligned_cols=78 Identities=19% Similarity=0.185 Sum_probs=56.3
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
..+++|.+.+.|+||.|.++++.++..|+|+..|...-.... .....|=||.. ..+..+.++++
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 GKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQG--------------RANVTISIDTS--SMEGDIDELLE 130 (147)
T ss_pred CcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCC--------------EEEEEEEEEeC--ChHHHHHHHHH
Confidence 347889999999999999999999999999999986421111 13455555653 23347888888
Q ss_pred HHHHc--CCceEEEcc
Q 015464 386 HLQEF--ATFLRVLGC 399 (406)
Q Consensus 386 ~L~~~--~~~vrvLGs 399 (406)
.|+.. ...++++|.
T Consensus 131 ~L~~i~gV~~V~i~~~ 146 (147)
T PRK04435 131 KLRNLDGVEKVELIGM 146 (147)
T ss_pred HHHcCCCcEEEEEEec
Confidence 88754 446777774
No 66
>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=96.09 E-value=0.019 Score=44.19 Aligned_cols=61 Identities=23% Similarity=0.190 Sum_probs=43.5
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 312 ~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
.+.++++||+|.++++.++. |.|++.+.=|-.... .....+=+++.+ ...++++++.|++.
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~~--------------~~~v~v~ie~~~---~~~~~~i~~~L~~~ 62 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGGD--------------EARVLVGIQVPD---REDLAELKERLEAL 62 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCCC--------------ceEEEEEEEeCC---HHHHHHHHHHHHHc
Confidence 46789999999999999999 999999977654311 134444445443 25677777777764
No 67
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=95.97 E-value=0.077 Score=44.27 Aligned_cols=71 Identities=18% Similarity=0.337 Sum_probs=52.9
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 387 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L 387 (406)
+-.|.+-+.|+||.|.++-+.|+.||.|+..|-.-|+... .-..+.|-+. ++..+..++++|
T Consensus 8 ~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~~---------------~iSRmtivv~---~~~~i~Qi~kQL 69 (96)
T PRK08178 8 NVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQDG---------------DKSRIWLLVN---DDQRLEQMISQI 69 (96)
T ss_pred CEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCCC---------------CceEEEEEEc---CchHHHHHHHHH
Confidence 4556667789999999999999999999999988887642 1234555444 246888889998
Q ss_pred HHcCCceEE
Q 015464 388 QEFATFLRV 396 (406)
Q Consensus 388 ~~~~~~vrv 396 (406)
++.-.=+++
T Consensus 70 ~KLidVikV 78 (96)
T PRK08178 70 EKLEDVLKV 78 (96)
T ss_pred hCCcCEEEE
Confidence 877554443
No 68
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=95.97 E-value=0.07 Score=43.42 Aligned_cols=70 Identities=10% Similarity=0.117 Sum_probs=50.9
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEe-cCCCcHHHHHHHHHH
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFE-ASMADPRAQFALGHL 387 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e-~~~~~~~~~~al~~L 387 (406)
-.|.+-+.|+||.|.++-+.|+.||+|+..|---|+... .=..+=|-++ | ++..+..+.++|
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 346666789999999999999999999999998887642 1123334443 4 456778888888
Q ss_pred HHcCCceE
Q 015464 388 QEFATFLR 395 (406)
Q Consensus 388 ~~~~~~vr 395 (406)
++.-.=++
T Consensus 66 ~KlidVik 73 (84)
T PRK13562 66 KQQINVLT 73 (84)
T ss_pred hCCccEEE
Confidence 87655443
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=95.86 E-value=0.051 Score=43.32 Aligned_cols=63 Identities=17% Similarity=0.280 Sum_probs=42.9
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceee--eeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCC-CcHH-HHHHHHH
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLT--KIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASM-ADPR-AQFALGH 386 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLt--kIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~-~~~~-~~~al~~ 386 (406)
|-+...|+||-|+++.++|+..|+++. ||.|--...+ -.=.||||.+|.. .++. .+.+-+.
T Consensus 3 lev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Ger---------------v~D~Fyv~~~g~kl~d~~~~~~L~~~ 67 (75)
T cd04896 3 LQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYR---------------EVDLFIVQSDGKKIMDPKKQAALCAR 67 (75)
T ss_pred EEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCE---------------EEEEEEEeCCCCccCCHHHHHHHHHH
Confidence 456778999999999999999999987 6664332221 2348999987754 4443 3333334
Q ss_pred HH
Q 015464 387 LQ 388 (406)
Q Consensus 387 L~ 388 (406)
|.
T Consensus 68 L~ 69 (75)
T cd04896 68 LR 69 (75)
T ss_pred HH
Confidence 44
No 70
>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=95.67 E-value=0.076 Score=40.45 Aligned_cols=64 Identities=14% Similarity=0.248 Sum_probs=46.0
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
|.+...|+||.|.++++.|+.+|+|+.++.+.+..... .....|-++. .+...++++++.|++.
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~-------------~~~~~i~~~~---~~~~~l~~~i~~L~~~ 66 (79)
T cd04881 3 LRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGGE-------------TAPVVIVTHE---TSEAALNAALAEIEAL 66 (79)
T ss_pred EEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCC-------------ceeEEEEEcc---CCHHHHHHHHHHHHcC
Confidence 45677899999999999999999999999887643210 1233333332 3567888899988854
No 71
>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=95.59 E-value=0.031 Score=42.27 Aligned_cols=60 Identities=18% Similarity=0.217 Sum_probs=43.4
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
+++...|+||.|.++++.|+.+|+|+..+.+++.. + .-...++++.. ..++++++|++.
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~-~----------------~a~~~~~~~~~----~l~~li~~l~~~ 60 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRG-E----------------IGYVVIDIDSE----VSEELLEALRAI 60 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCC-C----------------EEEEEEEcCCC----CCHHHHHHHHcC
Confidence 56677899999999999999999999998776532 1 22334466654 445677777754
Q ss_pred C
Q 015464 391 A 391 (406)
Q Consensus 391 ~ 391 (406)
-
T Consensus 61 ~ 61 (69)
T cd04901 61 P 61 (69)
T ss_pred C
Confidence 3
No 72
>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=95.35 E-value=0.089 Score=42.44 Aligned_cols=66 Identities=17% Similarity=0.238 Sum_probs=46.1
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEec-CCCcHHHHHHHHHH
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEA-SMADPRAQFALGHL 387 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~-~~~~~~~~~al~~L 387 (406)
-.+.+.-+|+||-+.++.+.|+.+|+|+..+++.-..+ .+...+-+++.+ ..+-..+.+.+..|
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 45677889999999999999999999999998775221 133445555554 23345666666666
Q ss_pred HH
Q 015464 388 QE 389 (406)
Q Consensus 388 ~~ 389 (406)
.+
T Consensus 67 ~~ 68 (88)
T cd04872 67 GK 68 (88)
T ss_pred HH
Confidence 53
No 73
>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=95.33 E-value=0.13 Score=41.52 Aligned_cols=68 Identities=16% Similarity=0.151 Sum_probs=43.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
+.+.++|+||+|.++|+.++.. |++.+.=+-.... .....+-+++.++ ...++.+++.|++.
T Consensus 4 l~v~ipD~PG~L~~ll~~l~~a--nI~~~~y~~~~~~--------------~~~v~i~ie~~~~--~~~~~~i~~~L~~~ 65 (85)
T cd04906 4 LAVTIPERPGSFKKFCELIGPR--NITEFNYRYADEK--------------DAHIFVGVSVANG--AEELAELLEDLKSA 65 (85)
T ss_pred EEEecCCCCcHHHHHHHHhCCC--ceeEEEEEccCCC--------------eeEEEEEEEeCCc--HHHHHHHHHHHHHC
Confidence 6678899999999999999944 5554443332211 1344555666541 25566777777776
Q ss_pred CCceEE
Q 015464 391 ATFLRV 396 (406)
Q Consensus 391 ~~~vrv 396 (406)
.-.+..
T Consensus 66 G~~~~~ 71 (85)
T cd04906 66 GYEVVD 71 (85)
T ss_pred CCCeEE
Confidence 555544
No 74
>PRK00194 hypothetical protein; Validated
Probab=95.24 E-value=0.11 Score=42.02 Aligned_cols=36 Identities=19% Similarity=0.230 Sum_probs=31.6
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeee
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP 343 (406)
+-.+.+.-+|+||.+.++.+.|+.+|+|+..+++.-
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~ 38 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTI 38 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHh
Confidence 445677778999999999999999999999998774
No 75
>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=95.20 E-value=0.13 Score=40.13 Aligned_cols=36 Identities=22% Similarity=0.328 Sum_probs=31.4
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeC
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~ 344 (406)
|-|.+..+|+||.|+++.++|+.+|+|+......+.
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 76
>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=95.13 E-value=0.2 Score=37.62 Aligned_cols=36 Identities=17% Similarity=0.214 Sum_probs=31.9
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCC
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~ 345 (406)
-|.+..+|+||.|.++.+.|+.+|+|+..+......
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~ 37 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTG 37 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecC
Confidence 356788999999999999999999999999887754
No 77
>PRK08198 threonine dehydratase; Provisional
Probab=95.11 E-value=0.15 Score=52.73 Aligned_cols=76 Identities=16% Similarity=0.168 Sum_probs=55.9
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeee-CCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP-QRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP-~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
....+.+.++|+||.|.++|+.++..|.|+..|.-.. ..+.| .+...+.|.+|.. +...++++++
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 3568889999999999999999999999999997654 33222 1345666676663 3346778899
Q ss_pred HHHHcCCceEE
Q 015464 386 HLQEFATFLRV 396 (406)
Q Consensus 386 ~L~~~~~~vrv 396 (406)
.|++..-.+++
T Consensus 392 ~L~~~G~~v~~ 402 (404)
T PRK08198 392 ALRDAGYEVKV 402 (404)
T ss_pred HHHHCCCeEEE
Confidence 99877655554
No 78
>PRK08577 hypothetical protein; Provisional
Probab=95.05 E-value=0.29 Score=42.93 Aligned_cols=69 Identities=17% Similarity=0.295 Sum_probs=49.0
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 387 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L 387 (406)
...|.+...|+||.|.++++.|+.+|+|+..+.++...... .+.-.|-+|+... +..+.+++++|
T Consensus 56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~-------------~~~i~l~vev~~~--~~~l~~l~~~L 120 (136)
T PRK08577 56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGE-------------LAECVIIVDLSKS--DIDLEELEEEL 120 (136)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCC-------------EEEEEEEEEeCCc--hhhHHHHHHHH
Confidence 56778888999999999999999999999999988765321 1122333455432 24577788888
Q ss_pred HHcC
Q 015464 388 QEFA 391 (406)
Q Consensus 388 ~~~~ 391 (406)
++..
T Consensus 121 ~~l~ 124 (136)
T PRK08577 121 KKLE 124 (136)
T ss_pred HcCC
Confidence 7643
No 79
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=94.94 E-value=0.13 Score=45.20 Aligned_cols=77 Identities=21% Similarity=0.321 Sum_probs=60.4
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeee-EeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKI-ESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFAL 384 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkI-ESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al 384 (406)
....++.+.+.|+.|.|.++|.+.++.++|..-| ++-|..++ .+-..-+|..+ .+..+.+++
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 4477899999999999999999999999999888 45676654 24566667763 457888899
Q ss_pred HHHHH--cCCceEEEcc
Q 015464 385 GHLQE--FATFLRVLGC 399 (406)
Q Consensus 385 ~~L~~--~~~~vrvLGs 399 (406)
++|+. ....|+++|+
T Consensus 133 ~kl~k~e~V~kVeivgs 149 (150)
T COG4492 133 EKLRKVEGVEKVEIVGS 149 (150)
T ss_pred HHHhcccceeEEEEeec
Confidence 98874 4556888886
No 80
>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=94.94 E-value=0.22 Score=38.96 Aligned_cols=61 Identities=11% Similarity=0.072 Sum_probs=43.8
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHH
Q 015464 313 FTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 388 (406)
Q Consensus 313 f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~ 388 (406)
+.=+|+||-+.++-+.|+.+|+|+..++++=..+ .+...|.+++....+-..+++.|+.+.
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 4447999999999999999999999998665432 245556666643333456677776665
No 81
>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=94.94 E-value=0.31 Score=35.06 Aligned_cols=63 Identities=16% Similarity=0.189 Sum_probs=44.6
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcC
Q 015464 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFA 391 (406)
Q Consensus 312 ~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~ 391 (406)
.+..+++||.+.++++.|+.+++|+.+++...... ....+.+.++.. ....+..+++.|+..-
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 112234444432 3456777888877543
No 82
>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=94.75 E-value=0.2 Score=39.02 Aligned_cols=59 Identities=20% Similarity=0.356 Sum_probs=46.8
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
|.+...|++|.|.+++++++..|+|+..+++++. + + .+++++.. +-..+..+++.|+..
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 5567789999999999999999999999999763 1 2 66677754 446778888888754
No 83
>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=94.75 E-value=0.12 Score=40.26 Aligned_cols=33 Identities=12% Similarity=0.225 Sum_probs=29.6
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeee
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP 343 (406)
|.+.-+|+||-+.++.+.|+.+|+|+..+++.-
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 446668999999999999999999999998884
No 84
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=94.71 E-value=0.18 Score=39.73 Aligned_cols=59 Identities=17% Similarity=0.225 Sum_probs=37.0
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHH
Q 015464 313 FTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 387 (406)
Q Consensus 313 f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L 387 (406)
+.=+|+||-++.+.+.++.+|.|+..++-.-..+ .+...+-|++... .-.+++++|.++
T Consensus 7 v~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~---------------~f~~~~~v~~~~~-~~~~l~~~L~~l 65 (76)
T PF13740_consen 7 VVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGG---------------RFTLIMLVSIPED-SLERLESALEEL 65 (76)
T ss_dssp EEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETT---------------EEEEEEEEEESHH-HHHHHHHHHHHH
T ss_pred EEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcC---------------eEEEEEEEEeCcc-cHHHHHHHHHHH
Confidence 3347999999999999999999998777766543 1344444455422 224556666665
No 85
>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=94.67 E-value=0.29 Score=37.07 Aligned_cols=36 Identities=19% Similarity=0.253 Sum_probs=31.9
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCC
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~ 345 (406)
-|.+..+|+||.|.++.+.|+.+|+|+.++...+..
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 86
>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=94.62 E-value=0.11 Score=38.00 Aligned_cols=34 Identities=26% Similarity=0.362 Sum_probs=30.5
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCC
Q 015464 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (406)
Q Consensus 312 ~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~ 345 (406)
.+.++|+||.|.++++.|..+|+|+..+...+..
T Consensus 2 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~ 35 (56)
T cd04889 2 SVFVENKPGRLAEVTEILAEAGINIKAISIAETR 35 (56)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEcc
Confidence 4577899999999999999999999999887765
No 87
>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=94.43 E-value=0.22 Score=50.91 Aligned_cols=72 Identities=22% Similarity=0.244 Sum_probs=49.4
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEee-eCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR-PQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 386 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESR-P~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~ 386 (406)
...|.+.++|+||.|.++++.++..|.|++.|.-+ ..+..+ .......|.+|.. +....+.+++.
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 222222 0233444555543 23556678888
Q ss_pred HHHcCCc
Q 015464 387 LQEFATF 393 (406)
Q Consensus 387 L~~~~~~ 393 (406)
|++..-.
T Consensus 371 L~~~G~~ 377 (380)
T TIGR01127 371 LRDMGYN 377 (380)
T ss_pred HHHcCCc
Confidence 8765433
No 88
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=94.20 E-value=0.35 Score=43.59 Aligned_cols=74 Identities=22% Similarity=0.338 Sum_probs=52.7
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeee-eEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTK-IESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 386 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtk-IESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~ 386 (406)
+.++.+.++|+||.|.++|+.++..|.|+.. |.||--+..| .--.-|-|++. .++..++.++.
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 5678889999999999999999999999875 5788765433 22333444553 24667778888
Q ss_pred HHHcCCceEEE
Q 015464 387 LQEFATFLRVL 397 (406)
Q Consensus 387 L~~~~~~vrvL 397 (406)
+++....++-.
T Consensus 69 ~e~~Gi~I~~~ 79 (170)
T COG2061 69 LEEEGIIIIRF 79 (170)
T ss_pred HHhCCcEEEEe
Confidence 86666555444
No 89
>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=93.99 E-value=0.39 Score=37.95 Aligned_cols=29 Identities=28% Similarity=0.436 Sum_probs=25.7
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceee
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLT 337 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLt 337 (406)
|-|-+..+|+||-|+++.++|+..|+++.
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~ 30 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCIT 30 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEE
Confidence 44557778999999999999999999987
No 90
>PRK06382 threonine dehydratase; Provisional
Probab=93.81 E-value=0.34 Score=50.19 Aligned_cols=36 Identities=19% Similarity=0.255 Sum_probs=33.0
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEee
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESR 342 (406)
.++.|.+.++|+||.|.++++.|+..|+|+++|+-.
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 377888899999999999999999999999999873
No 91
>PRK08526 threonine dehydratase; Provisional
Probab=93.70 E-value=1.4 Score=45.76 Aligned_cols=209 Identities=18% Similarity=0.151 Sum_probs=110.8
Q ss_pred CCccEEEEeeecccccccccccchhc--cCCeEEEEEEEEeee---eEeecCCCCCccCccEE----Ee---chHHHHHH
Q 015464 161 WLVDKAVLPIENSVGGSIHRNYDLLL--RHRLHIVGEVQLVVN---HCLLGLPGVLKEELKRV----FS---HPQALAQC 228 (406)
Q Consensus 161 g~~d~gvVPIENS~~G~V~~t~DlL~--~~~l~I~gE~~l~I~---h~L~~~~g~~l~~I~~V----yS---Hpqal~QC 228 (406)
+..|+.|+|+- ..|.+.-....|. ..+.+|+|--.-.-. ..+-..+......+.++ .. -|..+..|
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 4555555555553 346777664432111 01111000111222221 11 16677777
Q ss_pred HHHHhhcCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecCccCCCCCeeEEEEEecCCCCCC------
Q 015464 229 EMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAG------ 302 (406)
Q Consensus 229 ~~~L~~~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ygL~il~~~I~d~~~N~TRF~vi~~~~~~~~------ 302 (406)
+++++. +..++-.....|.+.+.+.. + -.+.+..|+-+-+|.--...+ ..+.+=-++++-....+.
T Consensus 245 ~~~vd~--~v~V~d~ei~~A~~~l~~~~--g-i~ve~aga~~lAall~~~~~~---~~~~~Vv~ilsGGnid~~~~~~i~ 316 (403)
T PRK08526 245 LECVDD--FVQVDDEEIANAILFLLEKQ--K-IVVEGAGAASVAALLHQKIDL---KKGKKIGVVLSGGNIDVQMLNIII 316 (403)
T ss_pred HHhCCE--EEEECHHHHHHHHHHHHHhc--C-cEeeHHHHHHHHHHHhCcccc---ccCCeEEEEECCCCCCHHHHHHHH
Confidence 766642 22333444556666666542 2 223444555555543111111 122232333332221110
Q ss_pred ----CCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEe-eeCCCCCCccccCCCCCCCccceEEEEEEEecCCCc
Q 015464 303 ----TDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIES-RPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMAD 377 (406)
Q Consensus 303 ----~~~~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIES-RP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~ 377 (406)
.....+..+.+.++++||+|.++++.++..+.|++.|+= |.....+ .++-...|.+|.. +.
T Consensus 317 ~~~l~~~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~~~~~-------------~~~~~~~~~~e~~-~~ 382 (403)
T PRK08526 317 EKGLIKSYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFSTKLD-------------YGDAMISITLETK-GK 382 (403)
T ss_pred HHHHHhcCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEeccCCCC-------------CccEEEEEEEEeC-CH
Confidence 012346778899999999999999999999999999976 5444322 1234555666654 34
Q ss_pred HHHHHHHHHHHHcCCc
Q 015464 378 PRAQFALGHLQEFATF 393 (406)
Q Consensus 378 ~~~~~al~~L~~~~~~ 393 (406)
..++++++.|++..-.
T Consensus 383 ~~~~~~~~~l~~~g~~ 398 (403)
T PRK08526 383 EHQEEIRKILTEKGFN 398 (403)
T ss_pred HHHHHHHHHHHHCCCC
Confidence 6777888888765433
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=93.39 E-value=0.62 Score=36.40 Aligned_cols=35 Identities=17% Similarity=0.397 Sum_probs=30.2
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCC
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~ 345 (406)
+.+..+|+||-+.++-+.|+.+|+|+..+++.-..
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~ 36 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYS 36 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence 45667899999999999999999999999886543
No 93
>PRK08639 threonine dehydratase; Validated
Probab=92.68 E-value=1.6 Score=45.50 Aligned_cols=74 Identities=16% Similarity=0.218 Sum_probs=49.6
Q ss_pred ceEEEEEEeCCCcchHHHHHH-HHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 307 YKTSIVFTLEEGPGMLFKALA-VFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~-~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
.+..+.|.++++||+|.++|+ ++.... |++.|+-|.....+ .+ ...|.+|.. +...++++++
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 13 344555543 2346677777
Q ss_pred HHHHcCCceEEE
Q 015464 386 HLQEFATFLRVL 397 (406)
Q Consensus 386 ~L~~~~~~vrvL 397 (406)
.|++..-.++.+
T Consensus 398 ~L~~~Gy~~~~~ 409 (420)
T PRK08639 398 RMEAFGPSYIDI 409 (420)
T ss_pred HHHHCCCceEEC
Confidence 887765444443
No 94
>PRK07334 threonine dehydratase; Provisional
Probab=91.83 E-value=0.98 Score=46.76 Aligned_cols=76 Identities=14% Similarity=0.168 Sum_probs=55.1
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeC-CCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ-RKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFAL 384 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~-~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al 384 (406)
.+.+.|.+...|+||.|.++++.++..++|+.++.++.. +..+ . ..+...|-|++. +...+.+++
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 456899999999999999999999999999999998864 1111 0 113334444443 446888999
Q ss_pred HHHHHcCCceE
Q 015464 385 GHLQEFATFLR 395 (406)
Q Consensus 385 ~~L~~~~~~vr 395 (406)
..|++..-.+.
T Consensus 390 ~~Lr~~g~~~~ 400 (403)
T PRK07334 390 AALRAAGFEAR 400 (403)
T ss_pred HHHHHcCCeeE
Confidence 99987655444
No 95
>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=91.09 E-value=4 Score=43.71 Aligned_cols=205 Identities=19% Similarity=0.239 Sum_probs=107.3
Q ss_pred CccEEEEeeecccccccccccchhc--cCCeEEEEEEEEeeeeEeec--CCC--CCccC---------ccEEEechHHHH
Q 015464 162 LVDKAVLPIENSVGGSIHRNYDLLL--RHRLHIVGEVQLVVNHCLLG--LPG--VLKEE---------LKRVFSHPQALA 226 (406)
Q Consensus 162 ~~d~gvVPIENS~~G~V~~t~DlL~--~~~l~I~gE~~l~I~h~L~~--~~g--~~l~~---------I~~VySHpqal~ 226 (406)
..|+.++|+- ..|.+.-..-.|. ..+.+|+|--...-. ++.. ..| ..+.. ++.+ =+..+.
T Consensus 166 ~~D~vvvpvG--gGGliaGia~~lk~~~p~~kVIgVep~~~~-~~~~s~~~g~~~~~~~~~t~adgiav~~~--g~~~~~ 240 (499)
T TIGR01124 166 PLDAVFVPVG--GGGLAAGVAALIKQLMPEIKVIGVEPTDSD-CMKQALDAGEPVDLDQVGLFADGVAVKRV--GDETFR 240 (499)
T ss_pred CCCEEEEccC--ccHHHHHHHHHHHHhCCCCEEEEEEECCCh-HHHHHHhcCCceeCCCCCCccCcccCCCc--cHHHHH
Confidence 5899999975 4555555544443 235677665442211 1100 001 01111 1122 245666
Q ss_pred HHHHHHhhcCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecCccCCCCCeeEEEEEecCCCCCC----
Q 015464 227 QCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAG---- 302 (406)
Q Consensus 227 QC~~~L~~~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ygL~il~~~I~d~~~N~TRF~vi~~~~~~~~---- 302 (406)
-|+++++. +-.+.......|.+.+.+.. -.-+.+..|+.+.+|.-+.+... . .+.|=-+|++-......
T Consensus 241 ~~~~~vd~--vv~V~d~ei~~ai~~l~~~~---gii~EpagA~~lAal~~~~~~~~-~-~~~~vv~i~sG~n~~~~~l~~ 313 (499)
T TIGR01124 241 LCQQYLDD--IVTVDTDEVCAAIKDLFEDT---RAVAEPAGALALAGLKKYVALHG-I-RGQTLVAILSGANMNFHRLRY 313 (499)
T ss_pred HHHHhCCE--EEEECHHHHHHHHHHHHHhc---CcEEechHHHHHHHHHHhhhhcC-C-CCCeEEEEECCCCCCHHHHHH
Confidence 66666532 22233334556666676642 12334445556666554433211 1 12232223332211100
Q ss_pred ------CCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCC
Q 015464 303 ------TDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMA 376 (406)
Q Consensus 303 ------~~~~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~ 376 (406)
-.......+.+++|++||+|.+.++.+.. -|+|.++=|-.... .=..||.++.. +
T Consensus 314 ~~~r~~~~~~re~~l~V~iPerPGal~~f~~~i~~--~nItef~yr~~~~~----------------~a~v~vgie~~-~ 374 (499)
T TIGR01124 314 VSERCELGEQREALLAVTIPEQPGSFLKFCELLGN--RNITEFNYRYADRK----------------DAHIFVGVQLS-N 374 (499)
T ss_pred HHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhh--cceEEEEEEecCCC----------------eEEEEEEEEeC-C
Confidence 11234678889999999999999999997 48898888863321 22345566654 3
Q ss_pred cHHHHHHHHHHHHcCCceEEE
Q 015464 377 DPRAQFALGHLQEFATFLRVL 397 (406)
Q Consensus 377 ~~~~~~al~~L~~~~~~vrvL 397 (406)
...++.+++.|++..-.+..+
T Consensus 375 ~~~~~~l~~~L~~~Gy~~~dl 395 (499)
T TIGR01124 375 PQERQEILARLNDGGYSVVDL 395 (499)
T ss_pred HHHHHHHHHHHHHcCCCeEEC
Confidence 467788888887765444443
No 96
>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=91.08 E-value=1.9 Score=33.89 Aligned_cols=64 Identities=16% Similarity=0.052 Sum_probs=42.7
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
|.+.-+|+||-.+++-+.++++|.|+..+...-..+ .|-+..-++++. .....+++.++.+.+.
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 456678999999999999999999999776665221 133333445442 2335666667766533
No 97
>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=90.95 E-value=1.6 Score=33.73 Aligned_cols=32 Identities=13% Similarity=0.305 Sum_probs=27.4
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeE
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIE 340 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIE 340 (406)
+.|.+..+|+||-|+++-++|+.+|+|+..-.
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 34667778999999999999999999999543
No 98
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=90.84 E-value=0.72 Score=42.28 Aligned_cols=61 Identities=20% Similarity=0.252 Sum_probs=46.6
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
|.+...|+||.|.++-.+.+.+|.|+|..+..-.+... .-..|.++||-. ....++++|+.
T Consensus 5 lsi~~enk~GvL~~ltgiiae~ggNIt~~q~~~~~~g~---------------~~~iYmEiEgi~---d~e~l~~~lks 65 (218)
T COG1707 5 LSIIAENKPGVLRDLTGIIAEEGGNITYAQQFLEKDGE---------------KALIYMEIEGID---DFEKLLERLKS 65 (218)
T ss_pred eEEEeecCccHHHHHHHHHHhcCCceEeeehhhhccCc---------------eEEEEEEeeCCC---CHHHHHHHhhc
Confidence 44556799999999999999999999999887665421 347788999853 34566777764
No 99
>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=89.90 E-value=2.1 Score=33.71 Aligned_cols=62 Identities=11% Similarity=0.227 Sum_probs=45.8
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecC-CCcHHHHHHHHHHHHcCCce
Q 015464 316 EEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEAS-MADPRAQFALGHLQEFATFL 394 (406)
Q Consensus 316 ~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~-~~~~~~~~al~~L~~~~~~v 394 (406)
++.||.+.++++.|+++|||+-.|-+ +. .++.|-|+-... ..+..++.++++|++.+ .+
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 257777765432 23348889999998854 35
Q ss_pred EEE
Q 015464 395 RVL 397 (406)
Q Consensus 395 rvL 397 (406)
.++
T Consensus 72 ~~~ 74 (75)
T cd04935 72 KII 74 (75)
T ss_pred EEe
Confidence 543
No 100
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=89.28 E-value=1.8 Score=40.43 Aligned_cols=36 Identities=19% Similarity=0.377 Sum_probs=30.2
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCC
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~ 345 (406)
.+.+.-.|+||-++++-+.|+.+|||+..+.|+=..
T Consensus 97 ~v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~ 132 (190)
T PRK11589 97 WVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQP 132 (190)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCChhheEEeeec
Confidence 344455799999999999999999999999998543
No 101
>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=89.07 E-value=3.1 Score=33.13 Aligned_cols=29 Identities=14% Similarity=0.298 Sum_probs=25.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceee
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLT 337 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLt 337 (406)
|-|-+..+|+||-|+++...|.+.|+++.
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~ 30 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVF 30 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEE
Confidence 34557789999999999999999999987
No 102
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=89.05 E-value=1.9 Score=39.73 Aligned_cols=74 Identities=22% Similarity=0.277 Sum_probs=51.6
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCc-HHHHHHHHHHHHcC
Q 015464 313 FTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMAD-PRAQFALGHLQEFA 391 (406)
Q Consensus 313 f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~-~~~~~al~~L~~~~ 391 (406)
+...|+||-+.++-+.|..+||||..++||-... | | ...-.|.+++-.+..- -.+..+.++++.+|
T Consensus 97 v~a~DrpgIv~~~T~lf~~~~inie~L~~~~~~a-~---------~---s~~~lfha~it~~lPa~~~i~~l~~~f~al~ 163 (176)
T COG2716 97 VDANDRPGIVEEFTALFDGHGINIENLVSRTYPA-P---------G---SSAPLFHAQITARLPANLSISALRDAFEALC 163 (176)
T ss_pred EEecCCccHHHHHHHHHHhcCCchhhceeeeeec-C---------C---CCccceehhhhccCCCcCcHHHHHHHHHHHH
Confidence 4447999999999999999999999999985432 1 1 1345899998554321 24445555666677
Q ss_pred CceEEEcc
Q 015464 392 TFLRVLGC 399 (406)
Q Consensus 392 ~~vrvLGs 399 (406)
..+.+=|+
T Consensus 164 ~~L~v~~~ 171 (176)
T COG2716 164 DELNVDGS 171 (176)
T ss_pred Hhhcceee
Confidence 76666554
No 103
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=88.88 E-value=2.2 Score=38.94 Aligned_cols=73 Identities=18% Similarity=0.307 Sum_probs=52.4
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 387 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L 387 (406)
+-.+.+-+.|+||.|.++.+.|+.+|.|+-.|---|+-... .-.--+-..| ++..+..+.++|
T Consensus 4 ~rilsvlv~ne~GvLsRv~glfsrRG~NIeSltv~~tE~~~---------------~SRiTivv~g--~~~~~EQi~kQL 66 (163)
T COG0440 4 RRILSLLVENEPGVLSRVTGLFSRRGYNIESLTVGPTETPG---------------LSRITIVVSG--DEQVLEQIIKQL 66 (163)
T ss_pred eEEEEEEEECCCCeeehhhHHHHhcCcccceEEEEecCCCC---------------ceEEEEEEcC--CcchHHHHHHHH
Confidence 34456667899999999999999999999999888875431 1122333344 456777888888
Q ss_pred HHcCCceEEE
Q 015464 388 QEFATFLRVL 397 (406)
Q Consensus 388 ~~~~~~vrvL 397 (406)
.+.-.-+|++
T Consensus 67 ~kLidV~kV~ 76 (163)
T COG0440 67 NKLIDVLKVL 76 (163)
T ss_pred HhhccceeEE
Confidence 8776666665
No 104
>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=88.82 E-value=3.2 Score=43.17 Aligned_cols=73 Identities=15% Similarity=0.103 Sum_probs=47.9
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHH
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 386 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~ 386 (406)
.+..+.|.++++||+|.++|+.....+-|+++++-|..... ..-...|.+|.. +...++++++.
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 36788899999999999999944445559998888762211 122344555543 23566777777
Q ss_pred HHHcCCceE
Q 015464 387 LQEFATFLR 395 (406)
Q Consensus 387 L~~~~~~vr 395 (406)
|++..-.++
T Consensus 388 L~~~Gy~~~ 396 (409)
T TIGR02079 388 MAAADIHYE 396 (409)
T ss_pred HHHCCCCeE
Confidence 777644443
No 105
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=86.91 E-value=4.5 Score=35.21 Aligned_cols=38 Identities=29% Similarity=0.339 Sum_probs=32.8
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCC
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~ 347 (406)
-+.+..+|+||+|.+++.+|..++||+--|.-.-.+++
T Consensus 71 VlaVEmeD~PG~l~~I~~vl~d~diNldYiYAFv~ek~ 108 (142)
T COG4747 71 VLAVEMEDVPGGLSRIAEVLGDADINLDYIYAFVTEKQ 108 (142)
T ss_pred EEEEEecCCCCcHHHHHHHHhhcCcCceeeeeeeecCc
Confidence 35678899999999999999999999998887776653
No 106
>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=86.81 E-value=4.3 Score=31.96 Aligned_cols=58 Identities=19% Similarity=0.299 Sum_probs=42.0
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHH-HHHHHHHHcC
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQ-FALGHLQEFA 391 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~-~al~~L~~~~ 391 (406)
.++.||.+.++++.|+.+|||+-.|-+ +. .++.|=|+-.-...+..++ .++++|++.+
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 2577777753322234565 6788888744
No 107
>PLN02550 threonine dehydratase
Probab=86.61 E-value=8.1 Score=42.30 Aligned_cols=208 Identities=14% Similarity=0.129 Sum_probs=108.5
Q ss_pred CccEEEEeeecccccccccccchhc--cCCeEEEEEEEEeee---eEeecCCCCCccCccE----EE---echHHHHHHH
Q 015464 162 LVDKAVLPIENSVGGSIHRNYDLLL--RHRLHIVGEVQLVVN---HCLLGLPGVLKEELKR----VF---SHPQALAQCE 229 (406)
Q Consensus 162 ~~d~gvVPIENS~~G~V~~t~DlL~--~~~l~I~gE~~l~I~---h~L~~~~g~~l~~I~~----Vy---SHpqal~QC~ 229 (406)
..|+.+||+- ..|.+.-..-.+. ..+++|+|--.-.-. ..+-..+.+.++.+.+ +. .-++.+.-|+
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 4899999985 3555555544443 356777765542211 0111110011111111 11 1145666666
Q ss_pred HHHhhcCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecCccCCCCCeeEEEEEecCCCCCC-------
Q 015464 230 MTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAG------- 302 (406)
Q Consensus 230 ~~L~~~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ygL~il~~~I~d~~~N~TRF~vi~~~~~~~~------- 302 (406)
+++.. +-.|......+|.+.+.+.. + ..+-+..|+.+.+|.-..+... .+ +.+=-+|++-......
T Consensus 336 ~~vD~--vV~Vsd~eI~~Ai~~l~e~~--g-ivvEpAGA~alAall~~~~~~~-~~-g~~Vv~vlsGgNid~~~l~~v~~ 408 (591)
T PLN02550 336 ELVDG--VVLVSRDAICASIKDMFEEK--R-SILEPAGALALAGAEAYCKYYG-LK-DENVVAITSGANMNFDRLRIVTE 408 (591)
T ss_pred hhCCE--EEEECHHHHHHHHHHHHHHC--C-CEEeHHHHHHHHHHHHHHHhcC-CC-CCeEEEEecCCCCCHHHHHHHHH
Confidence 65432 23334444667777777642 1 2233344555555543332111 11 2222223322211100
Q ss_pred ---CCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHH
Q 015464 303 ---TDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPR 379 (406)
Q Consensus 303 ---~~~~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~ 379 (406)
.....+..+.+.++++||+|.++++.+... |++.|+=|-... .+-..+|.+|.. ....
T Consensus 409 ~~~~~~~r~~~~~v~ipd~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v~v~ie~~-~~~~ 469 (591)
T PLN02550 409 LADVGRQQEAVLATFMPEEPGSFKRFCELVGPM--NITEFKYRYSSE----------------KEALVLYSVGVH-TEQE 469 (591)
T ss_pred HHHhccCCEEEEEEEcCCCCCHHHHHHHHhhhh--cceEEEEEecCC----------------CceEEEEEEEeC-CHHH
Confidence 112235678889999999999999999986 999998776321 223455666654 4467
Q ss_pred HHHHHHHHHHcCCceEEE
Q 015464 380 AQFALGHLQEFATFLRVL 397 (406)
Q Consensus 380 ~~~al~~L~~~~~~vrvL 397 (406)
++.+++.|++..-.++.|
T Consensus 470 ~~~i~~~l~~~g~~~~~l 487 (591)
T PLN02550 470 LQALKKRMESAQLRTVNL 487 (591)
T ss_pred HHHHHHHHHHCCCCeEeC
Confidence 888888888765444433
No 108
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=86.30 E-value=1.9 Score=35.58 Aligned_cols=69 Identities=13% Similarity=0.188 Sum_probs=47.5
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecC-CCcHHHHH-HHHHHHHc
Q 015464 313 FTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEAS-MADPRAQF-ALGHLQEF 390 (406)
Q Consensus 313 f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~-~~~~~~~~-al~~L~~~ 390 (406)
+.=+|+||--+.+-++++.+|+|+..|+---..+ .+...+++|+.-. .+-..+++ +-++.++.
T Consensus 8 V~GkDr~GIva~is~vLAe~~vNIldisQtvm~~---------------~ftm~~lV~~~~~~~d~~~lr~~l~~~~~~l 72 (90)
T COG3830 8 VIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDG---------------FFTMIMLVDISKEVVDFAALRDELAAEGKKL 72 (90)
T ss_pred EEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhh---------------hceeeeEEcCChHhccHHHHHHHHHHHHHhc
Confidence 3337999999999999999999999987655543 4778899999532 22234444 33345555
Q ss_pred CCceEE
Q 015464 391 ATFLRV 396 (406)
Q Consensus 391 ~~~vrv 396 (406)
...+++
T Consensus 73 gv~V~v 78 (90)
T COG3830 73 GVDVRV 78 (90)
T ss_pred CcEEEE
Confidence 555553
No 109
>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=86.04 E-value=7 Score=30.69 Aligned_cols=27 Identities=11% Similarity=0.250 Sum_probs=23.9
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeee
Q 015464 312 VFTLEEGPGMLFKALAVFALRDINLTK 338 (406)
Q Consensus 312 ~f~~~~~pGaL~~~L~~Fa~~~INLtk 338 (406)
-+..+|+||-|+++.++|+.+|+|+..
T Consensus 4 ei~~~Dr~gLfa~i~~~l~~~~l~I~~ 30 (76)
T cd04927 4 KLFCSDRKGLLHDVTEVLYELELTIER 30 (76)
T ss_pred EEEECCCCCHHHHHHHHHHHCCCeEEE
Confidence 345679999999999999999999984
No 110
>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=85.01 E-value=6.9 Score=30.41 Aligned_cols=56 Identities=14% Similarity=0.230 Sum_probs=42.8
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCC-cHHHHHHHHHHHH
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMA-DPRAQFALGHLQE 389 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~-~~~~~~al~~L~~ 389 (406)
+.+.||.+.++++.|+.+|||+-.+-+.+ -...|.|+-+.... +..++.++++|++
T Consensus 11 l~~~~g~~~~if~~L~~~~I~v~~i~~s~-------------------~~is~~v~~~~~~~~~~~~~~~~~~l~~ 67 (75)
T cd04912 11 MLGAHGFLAKVFEIFAKHGLSVDLISTSE-------------------VSVSLTLDPTKNLSDQLLLDALVKDLSQ 67 (75)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEcCC-------------------cEEEEEEEchhhccchHHHHHHHHHHHh
Confidence 45679999999999999999998886421 26788887654322 3578888888887
No 111
>PRK09224 threonine dehydratase; Reviewed
Probab=84.30 E-value=6.9 Score=41.92 Aligned_cols=72 Identities=14% Similarity=0.214 Sum_probs=49.6
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHH
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 386 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~ 386 (406)
....+.+++|++||+|.+.++.+. +-|+|.++=|-.... .=..+|.++....+..++.+++.
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 467888999999999999999999 689999987774321 22345555544222346777788
Q ss_pred HHHcCCceEE
Q 015464 387 LQEFATFLRV 396 (406)
Q Consensus 387 L~~~~~~vrv 396 (406)
|++..-.++.
T Consensus 389 L~~~gy~~~~ 398 (504)
T PRK09224 389 LRAHGYPVVD 398 (504)
T ss_pred HHHcCCCeEE
Confidence 8765444433
No 112
>cd04934 ACT_AK-Hom3_1 CT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydro
Probab=84.11 E-value=4.3 Score=31.82 Aligned_cols=55 Identities=16% Similarity=0.268 Sum_probs=43.0
Q ss_pred CCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcC
Q 015464 317 EGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFA 391 (406)
Q Consensus 317 ~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~ 391 (406)
..||.+.++++.|+++|||+-.|-+ .. .++.|-++-.. ..++.++.++++|++.+
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 36788887642 33358889999998843
No 113
>cd04907 ACT_ThrD-I_2 Second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes the second of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=83.85 E-value=11 Score=30.21 Aligned_cols=63 Identities=22% Similarity=0.248 Sum_probs=44.0
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
-+.|+.|++||+|.+.|+.+. -+-|+|.++=|-.... .+ .-||-++-. ++.+..+++.|++
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 467889999999999999993 3889999998875432 12 244444432 2366777777776
Q ss_pred cC
Q 015464 390 FA 391 (406)
Q Consensus 390 ~~ 391 (406)
..
T Consensus 64 ~g 65 (81)
T cd04907 64 LG 65 (81)
T ss_pred cC
Confidence 43
No 114
>PRK06349 homoserine dehydrogenase; Provisional
Probab=83.72 E-value=4.3 Score=42.49 Aligned_cols=64 Identities=17% Similarity=0.258 Sum_probs=46.1
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
-|.+.+.|+||.|.++-+.|+.++||+..+...+.... ..+..+.++. ..+..+++++++|++
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 45566689999999999999999999999887764321 1233333332 245789999998875
Q ss_pred c
Q 015464 390 F 390 (406)
Q Consensus 390 ~ 390 (406)
.
T Consensus 413 l 413 (426)
T PRK06349 413 L 413 (426)
T ss_pred C
Confidence 4
No 115
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=83.63 E-value=7.5 Score=38.61 Aligned_cols=67 Identities=9% Similarity=0.212 Sum_probs=46.5
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEe--cCCCcHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFE--ASMADPRAQFALG 385 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e--~~~~~~~~~~al~ 385 (406)
+..|.+.-+|+||-..++-+.|+.+|+|+..+.+.-.... ..|...++++ ...+...++++|+
T Consensus 7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~---------------~~F~m~~~~~~p~~~~~~~L~~~L~ 71 (286)
T PRK13011 7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLS---------------GRFFMRVEFHSEEGLDEDALRAGFA 71 (286)
T ss_pred eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCC---------------CeEEEEEEEecCCCCCHHHHHHHHH
Confidence 3445566689999999999999999999999999833222 2333344553 2333567777777
Q ss_pred HHHH
Q 015464 386 HLQE 389 (406)
Q Consensus 386 ~L~~ 389 (406)
.+.+
T Consensus 72 ~l~~ 75 (286)
T PRK13011 72 PIAA 75 (286)
T ss_pred HHHH
Confidence 7754
No 116
>PRK12483 threonine dehydratase; Reviewed
Probab=82.92 E-value=7.9 Score=41.72 Aligned_cols=73 Identities=16% Similarity=0.160 Sum_probs=51.1
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHH-HHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRA-QFAL 384 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~-~~al 384 (406)
..+..+.++++++||+|.++++.+... |++.++=+-... .+=..+|.+|.... ... +.++
T Consensus 343 ~r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v~v~ie~~~~-~~~~~~i~ 403 (521)
T PRK12483 343 QREAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYRYADA----------------REAHLFVGVQTHPR-HDPRAQLL 403 (521)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEEecCC----------------CeeEEEEEEEeCCh-hhhHHHHH
Confidence 347788899999999999999999987 999998875221 12345566665422 344 7788
Q ss_pred HHHHHcCCceEEE
Q 015464 385 GHLQEFATFLRVL 397 (406)
Q Consensus 385 ~~L~~~~~~vrvL 397 (406)
+.|++..-.++.+
T Consensus 404 ~~l~~~g~~~~dl 416 (521)
T PRK12483 404 ASLRAQGFPVLDL 416 (521)
T ss_pred HHHHHCCCCeEEC
Confidence 8887765555544
No 117
>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=82.88 E-value=30 Score=29.79 Aligned_cols=122 Identities=20% Similarity=0.119 Sum_probs=66.4
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCccE
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR 217 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~~ 217 (406)
.++++++.. ..+..++.+.+.+|++|+|++.-.+...+.. ...|.+.++.++. +-.|-+.. +..+++++..
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v~----~~~~~~~~-~~~~~~~L~~ 96 (200)
T cd08417 25 EAPGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLR---SQPLFEDRFVCVA----RKDHPLAG-GPLTLEDYLA 96 (200)
T ss_pred hCCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccCCCccc---hhhhhcCceEEEe----cCCCcccc-cccCHHHHhC
Confidence 346655433 3466789999999999999986543322211 1223344444432 33344433 2233444432
Q ss_pred ----EEechHH-HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 218 ----VFSHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 218 ----VySHpqa-l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
++.+... ......|+...+. + ...++|...+.+++..+ ...|+.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08417 97 APHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGT---DLIATVPRRLAEA 155 (200)
T ss_pred CCeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcC---CeeeeccHHHHHh
Confidence 2333222 2345566666443 2 34566677777777764 3577888776654
No 118
>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=81.00 E-value=7.4 Score=27.60 Aligned_cols=30 Identities=23% Similarity=0.327 Sum_probs=25.8
Q ss_pred EeCCCcchHHHHHHHHHhCCceeeeeEeee
Q 015464 314 TLEEGPGMLFKALAVFALRDINLTKIESRP 343 (406)
Q Consensus 314 ~~~~~pGaL~~~L~~Fa~~~INLtkIESRP 343 (406)
..++.||.+.++++.|+.+|||+..|..-+
T Consensus 7 ~~~~~~~~~~~i~~~L~~~~i~i~~i~~~~ 36 (61)
T cd04891 7 GVPDKPGVAAKIFSALAEAGINVDMIVQSV 36 (61)
T ss_pred cCCCCCcHHHHHHHHHHHcCCcEEEEEEcC
Confidence 357889999999999999999998886544
No 119
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=79.85 E-value=2.8 Score=39.61 Aligned_cols=84 Identities=18% Similarity=0.176 Sum_probs=56.2
Q ss_pred CccEEEEEcCCCcHHHHHHHHHC-C----C----CceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhc--
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAY-P----K----CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL-- 186 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f-~----~----~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~-- 186 (406)
...+|++-.+..+.+..+.+.++ . + ...+...+.++++.+|.+|++|.|+++- .+++.+.
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 35688887665444566666555 2 1 2455778999999999999999999873 3444333
Q ss_pred ----cCCeEEEEEEEEeeeeEeecCCCC
Q 015464 187 ----RHRLHIVGEVQLVVNHCLLGLPGV 210 (406)
Q Consensus 187 ----~~~l~I~gE~~l~I~h~L~~~~g~ 210 (406)
..+++|.++...-..+.+++.++.
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 347999999887777788877663
No 120
>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=79.81 E-value=16 Score=28.34 Aligned_cols=32 Identities=28% Similarity=0.361 Sum_probs=26.6
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEee
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESR 342 (406)
|-+..+|+||-|+++-++|+.+|+|+..-...
T Consensus 3 ~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~ 34 (74)
T cd04925 3 IELTGTDRPGLLSEVFAVLADLHCNVVEARAW 34 (74)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCCcEEEEEEE
Confidence 44556799999999999999999999854444
No 121
>PRK06545 prephenate dehydrogenase; Validated
Probab=79.45 E-value=6.8 Score=39.88 Aligned_cols=40 Identities=13% Similarity=0.304 Sum_probs=35.5
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCC
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~ 347 (406)
-..+.+.++|+||.|.+++..++..|||+..|+-.-++..
T Consensus 290 ~~~~~v~v~d~pg~~~~~~~~~~~~~i~i~~~~i~~~~~~ 329 (359)
T PRK06545 290 FYDLYVDVPDEPGVIARVTAILGEEGISIENLRILEARED 329 (359)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHcCCCeecceeeeccCC
Confidence 4668889999999999999999999999999988777654
No 122
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=78.39 E-value=11 Score=37.51 Aligned_cols=66 Identities=9% Similarity=0.172 Sum_probs=46.9
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEec----CCCcHHHHHHHH
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEA----SMADPRAQFALG 385 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~----~~~~~~~~~al~ 385 (406)
-|.+.-+|+||-.+++=+.++++|+|+..+... .... ...|+..++++. ..+...++.+++
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 345566899999999999999999999999886 2111 146666666662 233467777777
Q ss_pred HHHHc
Q 015464 386 HLQEF 390 (406)
Q Consensus 386 ~L~~~ 390 (406)
++.+.
T Consensus 76 ~l~~~ 80 (289)
T PRK13010 76 PVAEK 80 (289)
T ss_pred HHHHH
Confidence 76543
No 123
>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=76.33 E-value=18 Score=40.24 Aligned_cols=69 Identities=13% Similarity=0.132 Sum_probs=50.5
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
.+.+.|.+...|++|.|.++.+.++..++|+..+.++-... ..+.+-++++-. +-..+..++.
T Consensus 608 ~f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~----------------~~~~~~~~ieV~-~~~~L~~ii~ 670 (683)
T TIGR00691 608 RFIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGK----------------REAILNITVEIK-NYKHLLKIML 670 (683)
T ss_pred eeEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCC----------------CEEEEEEEEEEC-CHHHHHHHHH
Confidence 35667888889999999999999999999999999864321 123333444432 3467888888
Q ss_pred HHHHcC
Q 015464 386 HLQEFA 391 (406)
Q Consensus 386 ~L~~~~ 391 (406)
.|+..-
T Consensus 671 ~L~~i~ 676 (683)
T TIGR00691 671 KIKTKN 676 (683)
T ss_pred HHhCCC
Confidence 887653
No 124
>cd08411 PBP2_OxyR The C-terminal substrate-binding domain of the LysR-type transcriptional regulator OxyR, a member of the type 2 periplasmic binding fold protein superfamily. OxyR senses hydrogen peroxide and is activated through the formation of an intramolecular disulfide bond. The OxyR activation induces the transcription of genes necessary for the bacterial defense against oxidative stress. The OxyR of LysR-type transcriptional regulator family is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repre
Probab=76.16 E-value=50 Score=28.42 Aligned_cols=123 Identities=20% Similarity=0.117 Sum_probs=63.2
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc--
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I-- 215 (406)
.|+++++.-. .+..++.+.+.+|++|+|+..-.....+. ....|.+..+.++. +-+|-+......+++++
T Consensus 26 ~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~pl~~~~~~~~~~l~~ 98 (200)
T cd08411 26 AYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGL---EEEPLFDEPFLLAV----PKDHPLAKRKSVTPEDLAG 98 (200)
T ss_pred HCCCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCCCCCc---eEEEeeccceEEEe----cCCCCccccCccCHHHHcC
Confidence 4566665443 46788999999999999997543221111 11122233333221 22232322222222222
Q ss_pred -cEEE-ech-HHHHHHHHHHhhcCC---eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 216 -KRVF-SHP-QALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 216 -~~Vy-SHp-qal~QC~~~L~~~~~---~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
.-|. +.. ....+...|+.+.+. ..+.++|...+.+++..+ ...|+.+...++.
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 245677778888888775 3578888887764
No 125
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=75.87 E-value=18 Score=40.37 Aligned_cols=70 Identities=17% Similarity=0.226 Sum_probs=54.0
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
.+.+.|.+...|++|.|.+++++++..++|+.++.++...++ .+.+.++++-+ +-..+..++.
T Consensus 625 ~f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~~----------------~~~~~~~i~v~-n~~~L~~i~~ 687 (701)
T COG0317 625 VYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQ----------------FATMQFTIEVK-NLNHLGRVLA 687 (701)
T ss_pred ceEEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCCc----------------eEEEEEEEEEC-cHHHHHHHHH
Confidence 467788888899999999999999999999999999987332 34555566554 3367778888
Q ss_pred HHHHcCC
Q 015464 386 HLQEFAT 392 (406)
Q Consensus 386 ~L~~~~~ 392 (406)
.|+....
T Consensus 688 ~l~~~~~ 694 (701)
T COG0317 688 RLKQLPD 694 (701)
T ss_pred HHhcCCC
Confidence 8876543
No 126
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=75.71 E-value=14 Score=41.36 Aligned_cols=69 Identities=13% Similarity=0.192 Sum_probs=50.0
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
.+.+.|.+...|++|.|.++...++..++|+..+.++..+.. .+...++++-. +-..+..++.
T Consensus 624 ~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~----------------~~~~~~~ieV~-~~~~L~~i~~ 686 (702)
T PRK11092 624 EFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGR----------------VYSAFIRLTAR-DRVHLANIMR 686 (702)
T ss_pred eeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCC----------------EEEEEEEEEEC-CHHHHHHHHH
Confidence 346677888899999999999999999999999998754321 22333344432 2367888888
Q ss_pred HHHHcC
Q 015464 386 HLQEFA 391 (406)
Q Consensus 386 ~L~~~~ 391 (406)
.|+..-
T Consensus 687 ~Lr~i~ 692 (702)
T PRK11092 687 KIRVMP 692 (702)
T ss_pred HHhCCC
Confidence 887543
No 127
>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=75.37 E-value=16 Score=41.65 Aligned_cols=51 Identities=12% Similarity=0.180 Sum_probs=41.5
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEE
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDF 371 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~ 371 (406)
.+.|.|-+...|+||-|+++.++|+.+|||+......-...+ ..-.|||..
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 457888899999999999999999999999997666654432 355899965
No 128
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=75.32 E-value=63 Score=31.23 Aligned_cols=123 Identities=16% Similarity=0.121 Sum_probs=67.4
Q ss_pred HHCCCCceeccC-CHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc
Q 015464 138 KAYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK 216 (406)
Q Consensus 138 ~~f~~~~~~~~~-s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~ 216 (406)
+.++++++.... +.+++++.+.+|++|+|+++......+-.. ..|.+.++.++ .+-+|-+...+..+++++.
T Consensus 115 ~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~~----~~~~hpl~~~~~i~~~~L~ 187 (305)
T PRK11151 115 QTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIE---VPLFDEPMLLA----VYEDHPWANRDRVPMSDLA 187 (305)
T ss_pred HHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCeEE---EEeccCcEEEE----ecCCCCcccCCccCHHHhc
Confidence 346777765444 578999999999999999876544333222 22233343333 2334444332223333332
Q ss_pred --EEEechHH---HHHHHHHHhhcCC---eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 217 --RVFSHPQA---LAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 217 --~VySHpqa---l~QC~~~L~~~~~---~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
..++++.. ..+...|+...+. ..+.++|...++++++.+ ...+|.+...+.
T Consensus 188 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~ilp~~~~~ 246 (305)
T PRK11151 188 GEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAG---SGITLLPALAVP 246 (305)
T ss_pred CCCeEeecCCccHHHHHHHHHHHCCCCCCceEEeccHHHHHHHHHcC---CCEEEeeHHhhh
Confidence 12222221 1344455544322 245678888888888764 357888887664
No 129
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=74.05 E-value=8.6 Score=40.06 Aligned_cols=63 Identities=24% Similarity=0.311 Sum_probs=45.0
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceE-EEEEEEecCCCcHHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDY-LFYIDFEASMADPRAQFALGH 386 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y-~Ffid~e~~~~~~~~~~al~~ 386 (406)
.-.|++...|+||.+.+++++++++|||+..+..+... +| +.-||+++... + +++++
T Consensus 338 ~~rlii~h~d~pG~ia~it~~l~~~~iNI~~m~~~~~~------------------~~A~~iie~D~~~~-~---~~~~~ 395 (409)
T PRK11790 338 GHRLLHIHENRPGVLAAINQIFAEQGINIAAQYLQTDG------------------EIGYVVIDVDADYA-E---EALDA 395 (409)
T ss_pred CceEEEEeCCCCCHHHHHHHHHHhcCCCHHHheeccCC------------------CEEEEEEEeCCCCc-H---HHHHH
Confidence 45677788999999999999999999999877764322 23 33449988653 2 45666
Q ss_pred HHHcCC
Q 015464 387 LQEFAT 392 (406)
Q Consensus 387 L~~~~~ 392 (406)
|++.-.
T Consensus 396 i~~i~~ 401 (409)
T PRK11790 396 LKAIPG 401 (409)
T ss_pred HHcCCC
Confidence 665443
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=72.92 E-value=17 Score=26.96 Aligned_cols=27 Identities=26% Similarity=0.404 Sum_probs=23.8
Q ss_pred EeCCCcchHHHHHHHHHhCCceeeeeE
Q 015464 314 TLEEGPGMLFKALAVFALRDINLTKIE 340 (406)
Q Consensus 314 ~~~~~pGaL~~~L~~Fa~~~INLtkIE 340 (406)
.+++.||.+.++++.++..|||+.-+-
T Consensus 8 ~~~~~~g~~~~i~~~L~~~~I~i~~i~ 34 (75)
T cd04913 8 GVPDKPGVAAKIFGALAEANINVDMIV 34 (75)
T ss_pred CCCCCCcHHHHHHHHHHHcCCeEEEEE
Confidence 357889999999999999999998664
No 131
>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=72.68 E-value=39 Score=31.38 Aligned_cols=133 Identities=22% Similarity=0.168 Sum_probs=74.0
Q ss_pred ceeccCCHHHHHHHHHcCCccEEEEeeeccccccc--ccccchhccCCeEEEEEEEEeeeeEeecCCC-----CCccCc-
Q 015464 144 ETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSI--HRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG-----VLKEEL- 215 (406)
Q Consensus 144 ~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V--~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g-----~~l~~I- 215 (406)
...+..|. +.+.++.+|.+|++.+=+.....|.. ...-++|...++.++.-. .=...|+.++| ..++|+
T Consensus 14 ~~~~~gS~-~gl~~L~~g~~~iAg~h~~~~~~~~~n~~~~~~~l~g~~~v~v~~~--~r~~Gl~v~~~np~~i~~~~dL~ 90 (193)
T PF12727_consen 14 AVQYTGSR-AGLSALARGEADIAGIHLPDPESGEYNIPFVRRLLPGIEVVLVRLA--RREQGLIVRPGNPKGITSLEDLA 90 (193)
T ss_pred EEEecCCH-HHHHHHHCCCceEEEecCCCCcccccchHHHHHhcCCCcEEEEeee--EEeeeEEEeCCCCccCCCHHHhc
Confidence 34444443 66788889999999886654433331 112223333344443222 22346666666 234444
Q ss_pred --cEEEechHHHHHHHHHHhh----cCC-----e--EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH-cCCceeecCc
Q 015464 216 --KRVFSHPQALAQCEMTLSN----LGI-----V--RISADDTAGAAQMVASIGERDTGAVASAQAAEI-YGLDILAEKI 281 (406)
Q Consensus 216 --~~VySHpqal~QC~~~L~~----~~~-----~--~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~-ygL~il~~~I 281 (406)
...+--.|.=+=.+.+|+. .++ . -..+.|..+.|..|+.+ ...++++.+.+|+. |||.++.=.-
T Consensus 91 ~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G--~AD~G~g~~~~A~~~~gL~Fvpl~~ 168 (193)
T PF12727_consen 91 DPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASG--KADAGIGIRAAAEEFYGLDFVPLAE 168 (193)
T ss_pred cCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcC--CCCEEeehHHHHHhhcCCCcEEccc
Confidence 2223333333335555554 222 1 12456667778888875 35789999999975 7999876433
No 132
>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=72.48 E-value=59 Score=30.56 Aligned_cols=139 Identities=17% Similarity=0.061 Sum_probs=71.2
Q ss_pred EEEEEcCCCcHHHHHH--HHHCC------CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEE
Q 015464 121 RVAYQGLPGAYSEAAA--RKAYP------KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHI 192 (406)
Q Consensus 121 ~Va~lGp~Gs~s~~AA--~~~f~------~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I 192 (406)
+|+|+.. +......| +.+|. ++++....+..++++++.+|++|+|++..... +.. .-...++.+
T Consensus 2 ~vg~~~~-~~~~~~~a~~~g~f~~~g~~l~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~----~~~---~~~g~~~~~ 73 (288)
T TIGR01728 2 RIGYQKN-GHSALALAKEKGLLEKELGKTKVEWVEFPAGPPALEALGAGSLDFGYIGPGPA----LFA---YAAGADIKA 73 (288)
T ss_pred eEEecCC-CchHHHHHHHhCHHHHhhCCceEEEEecCCCcHHHHHHhcCCccccccCCcHH----HHH---HhcCCCEEE
Confidence 6788764 43222222 33442 35677888888999999999999997643311 110 001125555
Q ss_pred EEEEEEeeeeEeecCCCC---CccCc--cEEEechH--HHHHHHHHHhhcCCe---E-EeccCHHHHHHHHHhcCCCCeE
Q 015464 193 VGEVQLVVNHCLLGLPGV---LKEEL--KRVFSHPQ--ALAQCEMTLSNLGIV---R-ISADDTAGAAQMVASIGERDTG 261 (406)
Q Consensus 193 ~gE~~l~I~h~L~~~~g~---~l~~I--~~VySHpq--al~QC~~~L~~~~~~---~-i~~~sTA~Aa~~v~~~~~~~~A 261 (406)
++-..-.-..+++++++. +++|+ ++|...+- .......+|.+.|+. + +...+.+.+.+.+..+. -.|
T Consensus 74 i~~~~~~~~~~~v~~~~~~i~s~~dL~Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~--vda 151 (288)
T TIGR01728 74 VGLVSDNKATAIVVIKGSPIRTVADLKGKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQ--VDA 151 (288)
T ss_pred EEEecCCCceEEEECCCCCCCCHHHcCCCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCC--CCE
Confidence 554332123555555432 23333 24553221 123344566654432 1 22345667777777653 235
Q ss_pred EEcCHHhH
Q 015464 262 AVASAQAA 269 (406)
Q Consensus 262 AIas~~aA 269 (406)
++.++..+
T Consensus 152 ~~~~~p~~ 159 (288)
T TIGR01728 152 WAIWEPWG 159 (288)
T ss_pred EEeccchH
Confidence 55554433
No 133
>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=72.16 E-value=91 Score=30.41 Aligned_cols=147 Identities=18% Similarity=0.127 Sum_probs=79.8
Q ss_pred CccEEEEE-cCCCcHHHHHHHHHCC----CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchh-cc--CC
Q 015464 118 TKVRVAYQ-GLPGAYSEAAARKAYP----KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLL-LR--HR 189 (406)
Q Consensus 118 ~~~~Va~l-Gp~Gs~s~~AA~~~f~----~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL-~~--~~ 189 (406)
...+|+++ |+....-+.+...+|. +++++.++++.+..+|+.+|++|.+..= ... .+... .. .+
T Consensus 18 ~~l~vG~~~~~~~~~~~~~~~~~~~~~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~q-------~~~-~l~~~~~~~g~~ 89 (258)
T TIGR00363 18 LHIKVGVISGAEQQVAEVAAKVAKEKYGLDVELVEFNDYALPNEAVSKGDLDANAFQ-------HKP-YLDQDAKAKGYK 89 (258)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCEEEEEEeCCcHHHHHHHHcCCCCeEecC-------CHH-HHHHHHHhCCCc
Confidence 35889998 4444444555665553 5789999999999999999999986431 111 11111 12 34
Q ss_pred eEEEEEEEEeeeeEeecCCCCCccCcc---EEEec--hHHHHHHHHHHhhcC-----------------------CeEEe
Q 015464 190 LHIVGEVQLVVNHCLLGLPGVLKEELK---RVFSH--PQALAQCEMTLSNLG-----------------------IVRIS 241 (406)
Q Consensus 190 l~I~gE~~l~I~h~L~~~~g~~l~~I~---~VySH--pqal~QC~~~L~~~~-----------------------~~~i~ 241 (406)
+.++|...+- ...+.+.+-.++++++ +|.-. |.-.++.-..|.+.| ++++.
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 1233444334566764 55433 333333334555522 34444
Q ss_pred ccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCce
Q 015464 242 ADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDI 276 (406)
Q Consensus 242 ~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ygL~i 276 (406)
... +..++.+.++ . -.||+....-+...||..
T Consensus 169 l~~-~~~~~al~~g-~-vDaa~v~~~~~~~agl~~ 200 (258)
T TIGR00363 169 LET-SQLPRALDDP-K-VDLAVINTTYAGQVGLNP 200 (258)
T ss_pred cCH-HHHHHHhhcc-c-ccEEEEChHHHHHcCCCc
Confidence 443 3344444332 1 246666666677777763
No 134
>PRK05007 PII uridylyl-transferase; Provisional
Probab=71.89 E-value=9.6 Score=43.71 Aligned_cols=36 Identities=22% Similarity=0.365 Sum_probs=30.9
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeEe
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLT--KIES 341 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLt--kIES 341 (406)
.+.|.|-+...|+||-|+++.++|...|||+. ||-+
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 45677888899999999999999999999987 5544
No 135
>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=71.02 E-value=13 Score=33.25 Aligned_cols=50 Identities=20% Similarity=0.232 Sum_probs=38.7
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCC-CCceeccCCHHHHHHHHHcCCccEEEEee
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLPI 170 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~-~~~~~~~~s~~~v~~aV~~g~~d~gvVPI 170 (406)
..+|++. .|++........+. ..+++.+.|.++++++|.+|++|+.+++-
T Consensus 110 ~~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~~ 160 (225)
T PF00497_consen 110 GKRIGVV--RGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVDE 160 (225)
T ss_dssp TSEEEEE--TTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEEH
T ss_pred Ccccccc--cchhHHHHhhhhccchhhhcccccHHHHHHHHhcCCeeeeeccc
Confidence 3578886 55555544444565 77888999999999999999999998863
No 136
>PRK05092 PII uridylyl-transferase; Provisional
Probab=70.59 E-value=20 Score=41.28 Aligned_cols=36 Identities=17% Similarity=0.250 Sum_probs=31.2
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEee
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESR 342 (406)
+.|.|.+..+|+||-|+++.++|+..|||+..-...
T Consensus 842 ~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~ 877 (931)
T PRK05092 842 RFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIA 877 (931)
T ss_pred CeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEE
Confidence 357778888999999999999999999999965555
No 137
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=69.97 E-value=31 Score=38.85 Aligned_cols=68 Identities=19% Similarity=0.253 Sum_probs=49.2
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHH
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 386 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~ 386 (406)
+.+.|.+...|++|.|.++.++++..++|+..+.++..++.. ...-.|-|++. +-..+..++..
T Consensus 665 ~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~~-------------~~~~~~~ieV~---~~~~L~~l~~~ 728 (743)
T PRK10872 665 YSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQQ-------------LATIDMTIEIY---NLQVLGRVLGK 728 (743)
T ss_pred eEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCC-------------EEEEEEEEEEC---CHHHHHHHHHH
Confidence 456777888999999999999999999999999987644210 12234444543 23677888888
Q ss_pred HHHc
Q 015464 387 LQEF 390 (406)
Q Consensus 387 L~~~ 390 (406)
|+..
T Consensus 729 L~~i 732 (743)
T PRK10872 729 LNQV 732 (743)
T ss_pred HhcC
Confidence 8754
No 138
>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=69.40 E-value=76 Score=27.55 Aligned_cols=121 Identities=14% Similarity=0.045 Sum_probs=61.1
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCC-CCCccCc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLP-GVLKEEL- 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~-g~~l~~I- 215 (406)
.++++++... .+..++.+.+.+|++|+|+........|.... .|.+..+.++ .+-+|-|.... ..+++++
T Consensus 26 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~l~~~~~~~v----~~~~hpl~~~~~~i~~~dL~ 98 (203)
T cd08445 26 AAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRRI---VLREEPLVVA----LPAGHPLAQEKAPLTLAQLA 98 (203)
T ss_pred HCCCeEEEEEeCChHHHHHHHHcCCCcEEEecCCCCCCCceeE---EEEeccEEEE----eeCCCCCccCCCCcCHHHhc
Confidence 3566655433 35789999999999999996432111221111 1122233222 23334443332 2333333
Q ss_pred --cEEEechH---H-HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015464 216 --KRVFSHPQ---A-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAA 269 (406)
Q Consensus 216 --~~VySHpq---a-l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA 269 (406)
.-|.-... . ..+..+|+.+.+. . ...++|...+.++++.+ ...++.+...+
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 158 (203)
T cd08445 99 DEPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAG---EGVTLVPASVQ 158 (203)
T ss_pred CCCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcC---CCeEEehHHhh
Confidence 23331111 1 2344556665432 2 34567777777888765 34677776644
No 139
>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=69.17 E-value=14 Score=30.23 Aligned_cols=67 Identities=16% Similarity=0.221 Sum_probs=42.6
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHH
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH 386 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~ 386 (406)
.+..+.|+.|++||+|.+.|+.+..++ |+|.++=|-..... . .-+|-++-. +....+.+++.
T Consensus 9 ~E~~~~v~~PE~pGal~~F~~~l~~~~-nITeF~YR~~~~~~--------------a--~vlvgi~v~-~~~~~~~l~~~ 70 (91)
T PF00585_consen 9 REALFAVEFPERPGALKRFLDALGPRN-NITEFHYRYSGDDF--------------A--RVLVGIEVP-DAEDLEELIER 70 (91)
T ss_dssp -EEEEEEE--BSTTHCHHHHHCCSSSE--EEEEEEE-TTTSC--------------S--EEEEEEE-S-STHHHHHHHHH
T ss_pred CEEEEEEECCCCccHHHHHHHHhCCCc-eEEEEEEcCCCCCe--------------e--eEEEEEEeC-CHHHHHHHHHH
Confidence 466788999999999999999887655 59999888765421 2 334444433 23457778887
Q ss_pred HHHcC
Q 015464 387 LQEFA 391 (406)
Q Consensus 387 L~~~~ 391 (406)
|++..
T Consensus 71 L~~~g 75 (91)
T PF00585_consen 71 LKALG 75 (91)
T ss_dssp HTSSS
T ss_pred HHHcC
Confidence 87653
No 140
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=68.95 E-value=5.9 Score=34.48 Aligned_cols=29 Identities=28% Similarity=0.332 Sum_probs=24.5
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeee
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKI 339 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkI 339 (406)
|.+-+.|+||-|.++++.++.+|||+.-+
T Consensus 6 ISvFlENk~GRL~~~~~~L~eagINiRA~ 34 (142)
T COG4747 6 ISVFLENKPGRLASVANKLKEAGINIRAF 34 (142)
T ss_pred EEEEecCCcchHHHHHHHHHHcCCceEEE
Confidence 44446899999999999999999998643
No 141
>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=68.71 E-value=18 Score=26.47 Aligned_cols=51 Identities=18% Similarity=0.234 Sum_probs=37.2
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHH
Q 015464 316 EEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHL 387 (406)
Q Consensus 316 ~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L 387 (406)
.+.+|...++++.|+++|||.-.|.+ +. .+..|+++-.-. +..++.++++|
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 46799999999999999999999954 11 368888876321 24555665554
No 142
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=68.36 E-value=16 Score=35.83 Aligned_cols=74 Identities=19% Similarity=0.247 Sum_probs=53.6
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEE--EEEEecCCCcHHHHHH
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLF--YIDFEASMADPRAQFA 383 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~F--fid~e~~~~~~~~~~a 383 (406)
..+-.|-.-+.|+||.|.++=++|+.||.|+-.+----...+ -.| -|=+.| .|.-++.+
T Consensus 75 ~krHvinclVqnEpGvlsRisGvlAaRGfNIdSLvVc~tevk-----------------~LsrmTIVl~G--td~VveQa 135 (309)
T KOG2663|consen 75 VKRHVINCLVQNEPGVLSRISGVLAARGFNIDSLVVCLTEVK-----------------ALSRMTIVLQG--TDGVVEQA 135 (309)
T ss_pred ccceeEEEEecCCchHHHHHHHHHHhccCCchheeeechhhh-----------------hhhhceEEEec--cHHHHHHH
Confidence 345566666789999999999999999999765544333322 133 455556 46889999
Q ss_pred HHHHHHcCCceEEEc
Q 015464 384 LGHLQEFATFLRVLG 398 (406)
Q Consensus 384 l~~L~~~~~~vrvLG 398 (406)
.++|++...-+++|.
T Consensus 136 ~rQiedlVnV~aVlD 150 (309)
T KOG2663|consen 136 RRQIEDLVNVYAVLD 150 (309)
T ss_pred HHHHHHhhhhheeee
Confidence 999998877777664
No 143
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=67.61 E-value=30 Score=33.78 Aligned_cols=122 Identities=14% Similarity=0.010 Sum_probs=67.6
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCccE
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR 217 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~~ 217 (406)
.++++.+... .+..++++.+.+|++|+|+++-+....+... ..|.+.++.++ .+.+|-+. ....+++++..
T Consensus 137 ~~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~l~~---~~l~~~~~~lv----~~~~hpl~-~~~~~~~~L~~ 208 (314)
T PRK09508 137 IAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFTS---VPLFKDELVLV----ASKNHPRI-KGPITEEQLYN 208 (314)
T ss_pred hCCCcEEEEEeCcchhHHHHHhcCCccEEEecCCCCccccce---eeeecCceEEE----EcCCCCcc-CCCCCHHHHhh
Confidence 4566665433 3567889999999999999975432222111 12233333332 23444443 22234444431
Q ss_pred ----EEechHHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 218 ----VFSHPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 218 ----VySHpqal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
+++++....+...|+.+.+. . ...++|.....+.|+.+ ...++.+...++.
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 266 (314)
T PRK09508 209 EQHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQT---HLVAIAPRWLAEE 266 (314)
T ss_pred CCCEEecCCCCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhC---ChHHHHHHHHHHH
Confidence 23333333444667766443 2 34677777777888764 3467788877764
No 144
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=67.26 E-value=17 Score=33.80 Aligned_cols=50 Identities=20% Similarity=0.199 Sum_probs=38.9
Q ss_pred CccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
...+|++. .|+.........++....+..++..+++.+|.+|++|+.+++
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 34578886 565555545556777888889999999999999999999875
No 145
>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=67.07 E-value=84 Score=27.18 Aligned_cols=122 Identities=10% Similarity=-0.021 Sum_probs=61.1
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc--
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I-- 215 (406)
.|+++++.- ..+..++.+.+.+|++|+|++.-.....|... ..|.+..+.+ ..+-.|-+......+++++
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~l----v~~~~hpl~~~~~~~~~~L~~ 97 (197)
T cd08452 25 KFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHI---ETVQSSPCVL----ALPKQHPLASKEEITIEDLRD 97 (197)
T ss_pred HCCCcEEEEEecChHHHHHHHHCCCccEEEeeCCCCCCCeeE---EEeeeccEEE----EEeCCCccccCCCCCHHHhcC
Confidence 467666543 34677899999999999999853221111111 1122222222 2233454433222223332
Q ss_pred -cEEEechH----HHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 -KRVFSHPQ----ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 -~~VySHpq----al~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
.-|...+. ...+..+|+.+.+. . ...++|...+.+.++.+ ...|+.+...+.
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 246777776543
No 146
>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=66.73 E-value=24 Score=33.20 Aligned_cols=55 Identities=16% Similarity=0.253 Sum_probs=42.5
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeE-eeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIE-SRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADP 378 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIE-SRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~ 378 (406)
-..+++.-.|+||.+.++-+.+.+++||+.... +|-.++ .+=.-.+.++....++
T Consensus 148 g~~L~~~~~D~PG~Ig~vg~~Lg~~~iNIa~m~v~r~~~g----------------~~Ai~vl~vD~~v~~~ 203 (208)
T TIGR00719 148 HPAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIG----------------NIALLTIEIDKNIDDH 203 (208)
T ss_pred ccEEEEEeCCCCChHHHHHHHHHhCCccEEEEEEEecCCC----------------CEEEEEEEeCCCCCHH
Confidence 356788889999999999999999999998764 443332 3557788998876554
No 147
>cd04933 ACT_AK1-AT_1 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the first of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine. This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. Like the Escherichia coli AKIII (LysC), Arabidopsis AK1 binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. A loop in common is involved in the binding of both Lys and S-adenosylmethionine providing an explanation for the synergistic inhibition by these effectors. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=65.29 E-value=25 Score=27.97 Aligned_cols=57 Identities=14% Similarity=0.180 Sum_probs=39.8
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCC----CcHHHHHHHHHHHHcC
Q 015464 316 EEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASM----ADPRAQFALGHLQEFA 391 (406)
Q Consensus 316 ~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~----~~~~~~~al~~L~~~~ 391 (406)
++.||.+.++++.|+++|||.-.|-+ .. .++.|-|+-..-. -+..++.+..+|++.+
T Consensus 12 ~~~~g~~a~IF~~La~~~InVDmI~q---s~----------------~sISftV~~sd~~~~~~~~~~l~~~~~~~~~~~ 72 (78)
T cd04933 12 LGQYGFLAKVFSIFETLGISVDVVAT---SE----------------VSISLTLDPSKLWSRELIQQELDHVVEELEKDA 72 (78)
T ss_pred CCccCHHHHHHHHHHHcCCcEEEEEe---cC----------------CEEEEEEEhhhhhhhhhHHHHHHHHHHHHHHcC
Confidence 57799999999999999999999965 11 2577877653210 0125556666676654
No 148
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=62.78 E-value=18 Score=38.95 Aligned_cols=105 Identities=14% Similarity=0.238 Sum_probs=66.7
Q ss_pred CHHhHHHcCCceeecCc--cCCCCCeeEEEEEecCCCC-------CC-------------CCCCceEEEEEEeCCCcchH
Q 015464 265 SAQAAEIYGLDILAEKI--QDDDDNVTRFLILAREPII-------AG-------------TDRPYKTSIVFTLEEGPGML 322 (406)
Q Consensus 265 s~~aA~~ygL~il~~~I--~d~~~N~TRF~vi~~~~~~-------~~-------------~~~~~ktsi~f~~~~~pGaL 322 (406)
+..-|+-.|+++-.... .+.-.|.-++.+-+..... -+ .-.++-..+++...|+||.+
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 33558888888654332 3334677677665443110 00 00123456777788999999
Q ss_pred HHHHHHHHhCCceeeeeE-eeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 323 FKALAVFALRDINLTKIE-SRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 323 ~~~L~~Fa~~~INLtkIE-SRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
.++.+.|+.++||+.... +|-.++ .+....++++....+ +++++|++
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 467888899887653 34555554
No 149
>TIGR00655 PurU formyltetrahydrofolate deformylase. This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.
Probab=62.59 E-value=48 Score=32.84 Aligned_cols=65 Identities=11% Similarity=0.224 Sum_probs=44.0
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecC---CCcHHHHHHHHH-
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEAS---MADPRAQFALGH- 386 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~---~~~~~~~~al~~- 386 (406)
|.+.-+|+||-.+++=+.++++|+|++.+...=.... ..|.-.++++.. .+...+++++++
T Consensus 3 itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~---------------~~F~mr~~v~~~~~~~~~~~l~~~l~~~ 67 (280)
T TIGR00655 3 LLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPET---------------GRFFMRVEFQLEGFRLEESSLLAAFKSA 67 (280)
T ss_pred EEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCC---------------CeEEEEEEEEeCCCCCCHHHHHHHHHHH
Confidence 4566799999999999999999999999877643221 122223344432 234677777777
Q ss_pred HHHc
Q 015464 387 LQEF 390 (406)
Q Consensus 387 L~~~ 390 (406)
+.+.
T Consensus 68 ~~~~ 71 (280)
T TIGR00655 68 LAEK 71 (280)
T ss_pred HHHH
Confidence 5543
No 150
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=62.11 E-value=50 Score=32.77 Aligned_cols=34 Identities=9% Similarity=0.159 Sum_probs=28.8
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeEeee
Q 015464 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (406)
Q Consensus 310 si~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP 343 (406)
.|.+.-+|+||-..++-+.|+.+|+|+..+.+.=
T Consensus 8 vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~ 41 (286)
T PRK06027 8 VLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFV 41 (286)
T ss_pred EEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEE
Confidence 3444558999999999999999999999888765
No 151
>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=61.83 E-value=55 Score=25.49 Aligned_cols=35 Identities=14% Similarity=0.268 Sum_probs=28.5
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCC
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~ 345 (406)
|++..+|+||-+.++-++|+.+|+|+..=....++
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 56667899999999999999999999965444443
No 152
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=61.22 E-value=25 Score=32.61 Aligned_cols=49 Identities=16% Similarity=0.193 Sum_probs=38.6
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCC-CCceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~-~~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
..+|++. .|+........++. +.++..+.+.++++++|.+|++|+.++.
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 4578775 56655555555676 6788889999999999999999999884
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=60.92 E-value=1e+02 Score=26.16 Aligned_cols=122 Identities=15% Similarity=0.108 Sum_probs=61.4
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecc--cccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENS--VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS--~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I 215 (406)
.|+++++... .+..++.+.+.+|++|+|++..... ..|... ..|.+..+.++ .+-+|-+...+..+++++
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 4566655433 4678899999999999999754322 122111 12223333332 233344433322333333
Q ss_pred c---EEEe-chH-HHHHHHHHHhhcCC---e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 K---RVFS-HPQ-ALAQCEMTLSNLGI---V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 ~---~VyS-Hpq-al~QC~~~L~~~~~---~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
. -|.. ... -.....+|+...+. . ...+++...+.+++..+ ...|+.+...++
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 24556666666777764 357888887775
No 154
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=60.60 E-value=29 Score=39.78 Aligned_cols=32 Identities=22% Similarity=0.294 Sum_probs=29.0
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLT 337 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLt 337 (406)
.+.|.|=+..+|+||-|+++-++|...||++.
T Consensus 781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~ 812 (854)
T PRK01759 781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLL 812 (854)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEE
Confidence 45687888899999999999999999999987
No 155
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=60.37 E-value=1.4e+02 Score=28.32 Aligned_cols=121 Identities=15% Similarity=0.049 Sum_probs=61.5
Q ss_pred CCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCC-CCccC---
Q 015464 140 YPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG-VLKEE--- 214 (406)
Q Consensus 140 f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g-~~l~~--- 214 (406)
|++..+.. ..+..++.+.+.+|++|+|+++-+....+... ..|.+.++.++ .+-+|-|...+. .++++
T Consensus 117 ~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~~----~~~~~pl~~~~~~i~~~~L~~ 189 (296)
T PRK11242 117 YPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA---QPLFTETLALV----VGRHHPLAARRKALTLDELAD 189 (296)
T ss_pred CCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCCCCcceeE---EEeeeccEEEE----EcCCCcccccCCCcCHHHHhC
Confidence 56665544 34668899999999999999865433333222 12222333322 222233322211 22222
Q ss_pred ccEEEechHHH--HHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 215 LKRVFSHPQAL--AQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 215 I~~VySHpqal--~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
-.-|.-.+... ..-..|+.+.+. + .+.++|-..+.+++..+ ...++.++..+.
T Consensus 190 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 247 (296)
T PRK11242 190 EPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG---RLATLLPAAIAR 247 (296)
T ss_pred CCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhC---CeEEEeehhhcc
Confidence 22343333322 223455655443 2 34566666777777765 246677776554
No 156
>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=59.56 E-value=30 Score=30.04 Aligned_cols=50 Identities=28% Similarity=0.312 Sum_probs=37.7
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEee
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPI 170 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPI 170 (406)
..+|++. .|+..+......++...+..+.+.++++++|.+|++|.+++.-
T Consensus 105 g~~i~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 154 (218)
T cd00134 105 GKKVAVQ--KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDE 154 (218)
T ss_pred CCEEEEE--cCchHHHHHHHhCCcccEEEeCCHHHHHHHHHcCCccEEEecc
Confidence 4578776 4544444555566666788999999999999999999888753
No 157
>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=59.10 E-value=1.2e+02 Score=26.12 Aligned_cols=123 Identities=14% Similarity=0.033 Sum_probs=62.4
Q ss_pred HCCCCceeccC-CHHHHHHHHHcCCccEEEEeeeccccccccccc--chhccCCeEEEEEEEEeeeeEeecCCCCCccCc
Q 015464 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNY--DLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (406)
Q Consensus 139 ~f~~~~~~~~~-s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~--DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I 215 (406)
.|+++++.... +..+..+.+.+|++|+|+..-.... .....+ ..|.+.++.+ ..+-.|-+...+..+++++
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 35666654433 5678899999999999997532110 001111 1223333333 2333444433322333333
Q ss_pred ---cEEE-echH---HHHHHHHHHhhcCC--eE-EeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 ---KRVF-SHPQ---ALAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 ---~~Vy-SHpq---al~QC~~~L~~~~~--~~-i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
.-|. +... ....+..|+.+.+. +. ..++|...+.++++.+ ...++.+...++
T Consensus 99 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08453 99 AAEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAG---MGVALVPASLRN 160 (200)
T ss_pred ccCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcC---CcEEEeEhHHhh
Confidence 3333 2211 23456777777543 22 3556666666667664 346777776543
No 158
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=58.55 E-value=64 Score=30.50 Aligned_cols=144 Identities=12% Similarity=0.048 Sum_probs=76.2
Q ss_pred CccEEEEEcCCCcHHHHHHH--HHC---C-CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeE
Q 015464 118 TKVRVAYQGLPGAYSEAAAR--KAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLH 191 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~--~~f---~-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~ 191 (406)
...+|+|+...+.+....+. .+| | ++++....+..++.+++.+|++|++.+ ......+.-... .-...++.
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 45789997544433333332 234 2 578899999999999999999999999 443322211100 00011333
Q ss_pred EEEEEEEeeeeEeecCC------C-CCccCc---------cEEEe-chH--HHHHHHHHHhhcC------CeEEeccCHH
Q 015464 192 IVGEVQLVVNHCLLGLP------G-VLKEEL---------KRVFS-HPQ--ALAQCEMTLSNLG------IVRISADDTA 246 (406)
Q Consensus 192 I~gE~~l~I~h~L~~~~------g-~~l~~I---------~~VyS-Hpq--al~QC~~~L~~~~------~~~i~~~sTA 246 (406)
+.+-...-- .+++.+. + .+++|+ ++|.. ++- .....+.+|++.+ ++++.+.. .
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 333222111 2444442 2 234555 46665 553 3345678888732 35556655 7
Q ss_pred HHHHHHHhcCCCCeEEEcCHH
Q 015464 247 GAAQMVASIGERDTGAVASAQ 267 (406)
Q Consensus 247 ~Aa~~v~~~~~~~~AAIas~~ 267 (406)
++.+.+..++ -+.+++..+.
T Consensus 161 ~~~~al~~g~-iDa~~~~eP~ 180 (252)
T PF13379_consen 161 EMVAALRAGE-IDAAVLWEPF 180 (252)
T ss_dssp HHHHHHHTTS--SEEEEETTH
T ss_pred HHHHHHhCCC-cCEEEecCCH
Confidence 7777777653 4444444444
No 159
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=58.22 E-value=16 Score=42.73 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=41.2
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
..+|++. .|+..+...+.+|++.+++.++|..+++++|.+|++|..+..
T Consensus 164 ~~~i~~~--~g~~~~~~~~~~~p~~~i~~~~s~~~al~av~~G~~Da~i~~ 212 (1197)
T PRK09959 164 PVNIARV--ANYPPDEVIHQSFPKATIISFTNLYQALASVSAGQNDYFIGS 212 (1197)
T ss_pred CeEEEEe--CCCCCHHHHHHhCCCCEEEeCCCHHHHHHHHHcCCCCEEEcc
Confidence 4567775 466667777888999999999999999999999999988775
No 160
>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=58.21 E-value=1.1e+02 Score=25.68 Aligned_cols=122 Identities=21% Similarity=0.083 Sum_probs=60.1
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.++++++.-. .+..+..+.+.+|++|+|+..-+....|... ..|.+.++.++ .+-+|-+...+..+++++.
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 3566654433 3567899999999999999854321111111 11122222222 2223333222222233332
Q ss_pred --EE-EechHH-HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 217 --RV-FSHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 217 --~V-ySHpqa-l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
-| +++... .....+|+.+.+. + ...++|...+.+++..+ ...|+.+...+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (197)
T cd08440 98 YPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAG---LGVAVLPALALP 155 (197)
T ss_pred CCEEecCCCccHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEcchhHHH
Confidence 22 222221 1233445555332 2 34567777777777764 357777776654
No 161
>PRK11260 cystine transporter subunit; Provisional
Probab=58.14 E-value=27 Score=33.20 Aligned_cols=49 Identities=12% Similarity=0.139 Sum_probs=38.7
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
..+|++. .|+......+..++..++..+++..+++++|.+|++|+.+.+
T Consensus 149 g~~Igv~--~G~~~~~~l~~~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d 197 (266)
T PRK11260 149 GKKVGVG--LGTNYEQWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVD 197 (266)
T ss_pred CCEEEEe--cCCcHHHHHHHhCCCCceEecCCHHHHHHHHHcCCCCEEEec
Confidence 3467763 666555555667777788899999999999999999999884
No 162
>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=57.89 E-value=1.3e+02 Score=26.22 Aligned_cols=121 Identities=8% Similarity=-0.030 Sum_probs=62.7
Q ss_pred HCCCCcee-ccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc--
Q 015464 139 AYPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (406)
Q Consensus 139 ~f~~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I-- 215 (406)
.++++++. ...+..++.+.+.+|++|+|++.-.....|.. ...|.+.++.+ .++-+|-+......+++++
T Consensus 26 ~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~~~~~~---~~~l~~~~~~l----v~~~~h~l~~~~~i~~~dL~~ 98 (198)
T cd08486 26 STPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIE---IVNIAQEDLYL----AVHRSQSGKFGKTCKLADLRA 98 (198)
T ss_pred hCCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCCCCceE---EEEEeeccEEE----EecCCCccccCCcccHHHHcC
Confidence 45766543 33567899999999999999974321111111 11122223222 2344454433333344444
Q ss_pred -cEEEech----HHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015464 216 -KRVFSHP----QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAA 269 (406)
Q Consensus 216 -~~VySHp----qal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA 269 (406)
.-|.-.+ ....+..+++.+.+. + ...+++......+++.+ ...+|.+..++
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~ 157 (198)
T cd08486 99 VELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG---AASSIVPASVA 157 (198)
T ss_pred CCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---ceEEEcchhhc
Confidence 3332222 234566677766442 3 33566666666666653 45677776543
No 163
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=57.44 E-value=44 Score=35.38 Aligned_cols=113 Identities=16% Similarity=0.047 Sum_probs=59.1
Q ss_pred CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCC----CccCcc-
Q 015464 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV----LKEELK- 216 (406)
Q Consensus 142 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~----~l~~I~- 216 (406)
.++++...+|++++.++.+|++|+++..+.-+.+-. ..+.-+ .-++.+...|+.+++. ++++++
T Consensus 81 ~~e~v~~~~~~~ll~aL~~G~iDi~~~~lt~T~eR~-----~~~~FS------~Py~~~~~~lv~r~~~~~i~~l~dL~G 149 (482)
T PRK10859 81 KLEIKVRDNISQLFDALDKGKADLAAAGLTYTPERL-----KQFRFG------PPYYSVSQQLVYRKGQPRPRSLGDLKG 149 (482)
T ss_pred cEEEEecCCHHHHHHHHhCCCCCEEeccCcCChhhh-----ccCccc------CCceeeeEEEEEeCCCCCCCCHHHhCC
Confidence 567777889999999999999998754443221110 000001 1112233444444432 223332
Q ss_pred -EEEe-----chHHHHHHHHHHhh-cCCe--EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 217 -RVFS-----HPQALAQCEMTLSN-LGIV--RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 217 -~VyS-----Hpqal~QC~~~L~~-~~~~--~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
+|.. +.+.+. ++... +++. .+...|+.++.+.|..+. -.++|+....+.
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 3443 344578889999998763 346777665544
No 164
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=56.74 E-value=1.2e+02 Score=25.86 Aligned_cols=112 Identities=20% Similarity=0.109 Sum_probs=61.0
Q ss_pred CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCC---CccCc--c
Q 015464 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV---LKEEL--K 216 (406)
Q Consensus 142 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~---~l~~I--~ 216 (406)
.+++.+. ++.++.+++.+|++|+++.....+.+..- .+. ...........++.+++. +++++ +
T Consensus 40 ~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~~~-----~~~------~~~~~~~~~~~~~~~~~~~~~~~~dL~g~ 107 (219)
T smart00062 40 KVEFVEV-SFDNLLTALKSGKIDVVAAGMTITPERAK-----QVD------FSDPYYKSGQVILVRKDSPIKSLEDLKGK 107 (219)
T ss_pred eEEEEec-cHHHHHHHHHCCcccEEeccccCCHHHHh-----hee------eccceeeceeEEEEecCCCCCChHHhCCC
Confidence 4677777 89999999999999999876432211100 000 011111222455555442 22333 2
Q ss_pred EEEechHHHHHHHHHHhh--cCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015464 217 RVFSHPQALAQCEMTLSN--LGIVRISADDTAGAAQMVASIGERDTGAVASAQAA 269 (406)
Q Consensus 217 ~VySHpqal~QC~~~L~~--~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA 269 (406)
+|..-+ . .-...++.. ++...+.+.+..++.+++..+. -.|++.....+
T Consensus 108 ~i~~~~-g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~--~d~~~~~~~~~ 158 (219)
T smart00062 108 KVAVVA-G-TTGEELLKKLYPEAKIVSYDSQAEALAALKAGR--ADAAVADAPAL 158 (219)
T ss_pred EEEEec-C-ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCc--ccEEEeccHHH
Confidence 333322 1 123345544 3567778888888888887653 34566555543
No 165
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=55.92 E-value=30 Score=32.41 Aligned_cols=49 Identities=14% Similarity=0.054 Sum_probs=37.5
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
..+|++. .|+......+..++..++..+++.++++++|.+|++|+.+.-
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 455555555556666778889999999999999999988764
No 166
>PRK03381 PII uridylyl-transferase; Provisional
Probab=55.54 E-value=47 Score=37.60 Aligned_cols=37 Identities=11% Similarity=0.183 Sum_probs=30.9
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeC
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~ 344 (406)
-|-|.+..+|+||-|+++-++|+.+|+|+..-...-.
T Consensus 707 ~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~ 743 (774)
T PRK03381 707 ATVLEVRAADRPGLLARLARALERAGVDVRWARVATL 743 (774)
T ss_pred eEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeec
Confidence 4667778899999999999999999999996554443
No 167
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=54.73 E-value=2.2e+02 Score=27.90 Aligned_cols=107 Identities=17% Similarity=0.149 Sum_probs=59.9
Q ss_pred ccEEEEE-cCCCcHHHHHHHHHC---C-CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhc--cCCeE
Q 015464 119 KVRVAYQ-GLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL--RHRLH 191 (406)
Q Consensus 119 ~~~Va~l-Gp~Gs~s~~AA~~~f---~-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~--~~~l~ 191 (406)
..+|++. ++.....+.+...++ | +++++..+++.+..+++.+|++|.... ..+..... .+. ..++.
T Consensus 32 ~I~IG~~~~~~~~~~~~~~~~l~~~~G~~Vel~~f~~~~~~~~ALa~GdID~~~~-----qh~~~l~~--~~~~~g~~l~ 104 (271)
T PRK11063 32 HIKVGVIVGAEQQVAEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAF-----QHKPYLDQ--QIKDRGYKLV 104 (271)
T ss_pred cEEEEeCCCChHHHHHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHcCCcceecc-----cCHHHHHH--HHHHcCCcEE
Confidence 4789987 444434444433333 4 688999999999999999999998751 11111111 111 23566
Q ss_pred EEEEEEE-eeeeEeecCCCCCccCcc---EEEec--hHHHHHHHHHHhh
Q 015464 192 IVGEVQL-VVNHCLLGLPGVLKEELK---RVFSH--PQALAQCEMTLSN 234 (406)
Q Consensus 192 I~gE~~l-~I~h~L~~~~g~~l~~I~---~VySH--pqal~QC~~~L~~ 234 (406)
++|-..+ |+ .+....=.+++|++ +|... |.-.+.+-.+|.+
T Consensus 105 ~~~~~~vvp~--~~ys~~i~si~DL~~Gk~IAip~d~~n~~r~L~lL~~ 151 (271)
T PRK11063 105 AVGNTFVYPI--AGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQK 151 (271)
T ss_pred EEeEEEEEEe--eccccCCCCHHHhcCCCEEEecCCCccHHHHHHHHHH
Confidence 6665433 33 22222222455653 66544 5555555556665
No 168
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=54.60 E-value=19 Score=42.10 Aligned_cols=50 Identities=24% Similarity=0.216 Sum_probs=41.3
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEee
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPI 170 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPI 170 (406)
..+||+. .|+..+...++.+++.+++.++|..+++++|.+|++|.++.+.
T Consensus 407 g~~vav~--~g~~~~~~~~~~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~~ 456 (1197)
T PRK09959 407 GMKVAIP--YYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDALVATQ 456 (1197)
T ss_pred CCEEEEe--CCcchHHHHHHHCCCcEEEEcCCHHHHHHHHHcCCCCEEehhh
Confidence 4678885 5666666666788889999999999999999999999988653
No 169
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=54.57 E-value=28 Score=29.22 Aligned_cols=47 Identities=9% Similarity=0.055 Sum_probs=36.7
Q ss_pred cEEEEEcCCCcHHHHHHHHHCCC-----------CceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 120 VRVAYQGLPGAYSEAAARKAYPK-----------CETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 120 ~~Va~lGp~Gs~s~~AA~~~f~~-----------~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
.+|+++ .||..+..++.+.+. .++..+++..+++.+|.+|+ |..+..
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 578886 788888888765543 25678899999999999999 966665
No 170
>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=54.29 E-value=1.4e+02 Score=25.51 Aligned_cols=122 Identities=12% Similarity=0.044 Sum_probs=60.7
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCcc---C
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKE---E 214 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~---~ 214 (406)
.++++++.-. .+..+..+.+.+|++|+|+.+-.....+... ..|.+..+.+ ..+-+|-+...+..+++ +
T Consensus 26 ~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----v~~~~~pl~~~~~~~~~~l~~ 98 (198)
T cd08446 26 ARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAV---ENVAQERLYL----AVPKSHPLAARPAVSLADLRN 98 (198)
T ss_pred HCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecCCCCCCcee---EEeeeccEEE----EEeCCCCcccCCccCHHHHcC
Confidence 4566654433 4677889999999999999754322111111 1112223322 22333433322212222 2
Q ss_pred ccEEE-ech---HHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 215 LKRVF-SHP---QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 215 I~~Vy-SHp---qal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
..-|. ... ....+...|+.+.+. . ...++|...+.++++.+ ...++.+...+.
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 34567777777777764 347777776554
No 171
>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=53.45 E-value=68 Score=28.48 Aligned_cols=125 Identities=17% Similarity=0.099 Sum_probs=70.9
Q ss_pred HHHHHHHHHCC-CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCC
Q 015464 131 YSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG 209 (406)
Q Consensus 131 ~s~~AA~~~f~-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g 209 (406)
+-.+++++. + +.++++. +|.+++..+.+|++|+++-++..+.+- ...+.... -.......++.+++
T Consensus 28 l~~~i~~~~-g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~r----------~~~~~~s~-p~~~~~~~~~~~~~ 94 (225)
T PF00497_consen 28 LLRAIAKRL-GIKIEFVPM-PWSRLLEMLENGKADIIIGGLSITPER----------AKKFDFSD-PYYSSPYVLVVRKG 94 (225)
T ss_dssp HHHHHHHHH-TCEEEEEEE-EGGGHHHHHHTTSSSEEESSEB-BHHH----------HTTEEEES-ESEEEEEEEEEETT
T ss_pred HHHHHHhhc-ccccceeec-ccccccccccccccccccccccccccc----------cccccccc-cccchhheeeeccc
Confidence 334444433 4 5678888 999999999999999987555432221 01111111 12233455555543
Q ss_pred C-----C---ccCc--cEEEechHHHHHHHHHHhh--c-CCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHc
Q 015464 210 V-----L---KEEL--KRVFSHPQALAQCEMTLSN--L-GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (406)
Q Consensus 210 ~-----~---l~~I--~~VySHpqal~QC~~~L~~--~-~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~y 272 (406)
. . ++++ ++|..-.-.. -.++|.+ + +++.+.+.|..++.+++..+ .-.|+|+....+..+
T Consensus 95 ~~~~~~~~~~~~dl~~~~i~~~~g~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~i~~~~~~~~~ 166 (225)
T PF00497_consen 95 DAPPIKTIKSLDDLKGKRIGVVRGSS--YADYLKQQYPSNINIVEVDSPEEALEALLSG--RIDAFIVDESTAEYL 166 (225)
T ss_dssp STCSTSSHSSGGGGTTSEEEEETTSH--HHHHHHHHTHHTSEEEEESSHHHHHHHHHTT--SSSEEEEEHHHHHHH
T ss_pred cccccccccchhhhcCcccccccchh--HHHHhhhhccchhhhcccccHHHHHHHHhcC--Ceeeeeccchhhhhh
Confidence 1 1 2244 2343333221 1223333 2 67888899999999998876 345888877766543
No 172
>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=53.43 E-value=65 Score=22.97 Aligned_cols=27 Identities=26% Similarity=0.426 Sum_probs=23.8
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
+.+.||.+.++++.++.++||+-.|-+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04923 10 MRSHPGVAAKMFKALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEc
Confidence 456799999999999999999998864
No 173
>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=53.17 E-value=1.5e+02 Score=25.61 Aligned_cols=121 Identities=15% Similarity=0.116 Sum_probs=59.1
Q ss_pred HCCCCceeccC-CHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~~-s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.++++++.... +. +..+.+.+|++|+|+++-+....+... .-|.+..+.++ .+-+|-+.. ...+++++.
T Consensus 25 ~~P~i~l~i~~~~~-~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~hpl~~-~~~~~~~l~~ 95 (200)
T cd08462 25 EAPGVRFELLPPDD-QPHELLERGEVDLLIAPERFMSDGHPS---EPLFEEEFVCV----VWADNPLVG-GELTAEQYFS 95 (200)
T ss_pred HCCCCEEEEecCCh-hHHHHHhcCCeeEEEecCCCCCCCcee---eeeeccceEEE----EcCCCCccC-CCCCHHHHhh
Confidence 45666544332 44 999999999999999864322222111 11122222221 233444432 223344443
Q ss_pred --EEE-echHHH-HHHHH-HHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 217 --RVF-SHPQAL-AQCEM-TLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 217 --~Vy-SHpqal-~QC~~-~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
-|. +..... ....+ ++.+.+. . .+.++|.....++|+.+ ...||.+...++.
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 34566666777777764 3578888877654
No 174
>PRK09034 aspartate kinase; Reviewed
Probab=53.11 E-value=2.7e+02 Score=29.36 Aligned_cols=128 Identities=15% Similarity=0.085 Sum_probs=75.1
Q ss_pred cCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecCccCCCCCeeEEEEEecCCCCC-C-----CCC
Q 015464 235 LGIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPIIA-G-----TDR 305 (406)
Q Consensus 235 ~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~a---A~~ygL~il~~~I~d~~~N~TRF~vi~~~~~~~-~-----~~~ 305 (406)
++++.+..-|-.+|.++...+ |-+-.+.| |..++++|.-.|..+....-|..- ....... . ...
T Consensus 233 ~~A~~l~~lsy~Ea~ela~~G-----akvlhp~ai~~a~~~~Ipi~v~~~~~p~~~GT~I~--~~~~~~~~~~Vk~It~~ 305 (454)
T PRK09034 233 KNPKSIKEITYREMRELSYAG-----FSVFHDEALIPAYRGGIPINIKNTNNPEDPGTLIV--PDRDNKNKNPITGIAGD 305 (454)
T ss_pred CCCeECCccCHHHHHHHHhCC-----cccCCHHHHHHHHHcCCCEEEEcCCCCCCCccEEE--eccccCccccceEEEec
Confidence 356677788888988886542 33444444 345899999998876544445442 2211100 0 001
Q ss_pred CceEEEEEE---eCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHH
Q 015464 306 PYKTSIVFT---LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQF 382 (406)
Q Consensus 306 ~~ktsi~f~---~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~ 382 (406)
.+-+.|.+. ....||.+.++++.|+++|||.-.| |+. . .+..|+|+=+ ..+......
T Consensus 306 ~~i~~Itv~~~~~~~~~g~~a~if~~la~~~I~Vd~i---~ss-~---------------~sis~~v~~~-~~~~a~~~~ 365 (454)
T PRK09034 306 KGFTSIYISKYLMNREVGFGRKVLQILEDHGISYEHM---PSG-I---------------DDLSIIIRER-QLTPKKEDE 365 (454)
T ss_pred CCEEEEEEccCCCCCCccHHHHHHHHHHHcCCeEEEE---cCC-C---------------cEEEEEEeHH-HhhHHHHHH
Confidence 222333332 2457899999999999999999988 221 1 3678888742 221112255
Q ss_pred HHHHHHH
Q 015464 383 ALGHLQE 389 (406)
Q Consensus 383 al~~L~~ 389 (406)
++++|+.
T Consensus 366 l~~el~~ 372 (454)
T PRK09034 366 ILAEIKQ 372 (454)
T ss_pred HHHHHHH
Confidence 6666653
No 175
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=52.84 E-value=2.3e+02 Score=27.54 Aligned_cols=120 Identities=18% Similarity=0.183 Sum_probs=59.3
Q ss_pred HCCCCcee-ccCCHHHHHHHHHcCCccEEEEeeeccc--ccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc
Q 015464 139 AYPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENSV--GGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (406)
Q Consensus 139 ~f~~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIENS~--~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I 215 (406)
.++++++. ...+..++++.|.+|++|+|+++..+.. .+.. ...|.+..+.++. +-+|-+.. ..+++++
T Consensus 122 ~~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~---~~~l~~~~~~lv~----~~~~pl~~--~i~~~dL 192 (312)
T PRK10341 122 VFPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLH---VEPLFESEFVLVA----SKSRTCTG--TTTLESL 192 (312)
T ss_pred hCCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCcccccCCee---EEEEecccEEEEE----cCCCchhc--cCCHHHH
Confidence 35666653 3345689999999999999998754321 1111 1112222332221 11222211 1122222
Q ss_pred c---EEEech--HHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 K---RVFSHP--QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 ~---~VySHp--qal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
. -|.--+ ....+..+|+.+.+. . .+.++|.....+.+..+ ...++.+...++
T Consensus 193 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 252 (312)
T PRK10341 193 KNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA---DFLTVIPCDMTS 252 (312)
T ss_pred hCCCeEccCCCCcHHHHHHHHHHHcCcCCCceEEecCHHHHHHHHHhC---CcEEEeeHHhcC
Confidence 2 222111 122344456655432 2 35677777777777764 346777776554
No 176
>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=51.91 E-value=1.5e+02 Score=25.18 Aligned_cols=32 Identities=13% Similarity=-0.043 Sum_probs=24.0
Q ss_pred HCCCCceeccC-CHHHHHHHHHcCCccEEEEee
Q 015464 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPI 170 (406)
Q Consensus 139 ~f~~~~~~~~~-s~~~v~~aV~~g~~d~gvVPI 170 (406)
.++++++.-.. +..++++.+.+|++|+|++.-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08450 25 EHPDLDVELSSLFSPQLAEALMRGKLDVAFMRP 57 (196)
T ss_pred hCCCcEEEEEecChHHHHHHHhcCCccEEEEeC
Confidence 45666654433 567889999999999999754
No 177
>PRK04374 PII uridylyl-transferase; Provisional
Probab=51.77 E-value=76 Score=36.51 Aligned_cols=37 Identities=19% Similarity=0.389 Sum_probs=30.9
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeEee
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLT--KIESR 342 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLt--kIESR 342 (406)
.+.|.|-+...|+||-|+++-++|+..|+|+. ||.+.
T Consensus 794 ~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~ 832 (869)
T PRK04374 794 GRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATF 832 (869)
T ss_pred CCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEec
Confidence 34677778889999999999999999999998 45444
No 178
>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=51.46 E-value=1.5e+02 Score=25.12 Aligned_cols=122 Identities=15% Similarity=0.041 Sum_probs=61.2
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCcc---C
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKE---E 214 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~---~ 214 (406)
.++++++.- ..+..++.+.+.+|++|+|++.-.....|... ..|.+..+.+ ..+-+|-|...+..+++ +
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 456655433 34678899999999999999854322222111 1112222221 12334444332222233 2
Q ss_pred ccEEE-echHHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 215 LKRVF-SHPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 215 I~~Vy-SHpqal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
..-|. .......+-.+|+.+.+. . ...++|...+.+++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (198)
T cd08412 98 EPLILLDLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANG---LGYSLLNDRPYR 154 (198)
T ss_pred CcEEecCchhHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CCEEEeeccccc
Confidence 23333 222222333455555443 2 33567777777777764 347777776655
No 179
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=51.38 E-value=44 Score=28.76 Aligned_cols=51 Identities=27% Similarity=0.312 Sum_probs=37.0
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEeee
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIE 171 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPIE 171 (406)
..+|++.. |+........++....+....+..+++.+|.+|++|+++++-.
T Consensus 106 g~~i~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~ 156 (219)
T smart00062 106 GKKVAVVA--GTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADAP 156 (219)
T ss_pred CCEEEEec--CccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEeccH
Confidence 35787753 4433433343455677888999999999999999999988644
No 180
>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=51.29 E-value=73 Score=22.67 Aligned_cols=27 Identities=26% Similarity=0.431 Sum_probs=23.8
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
+.+.||.+.++++.++.+|||+-.|-+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04936 10 MRSHPGVAAKMFEALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 456799999999999999999988864
No 181
>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=51.24 E-value=68 Score=25.60 Aligned_cols=57 Identities=19% Similarity=0.203 Sum_probs=40.4
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHcCC
Q 015464 316 EEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEFAT 392 (406)
Q Consensus 316 ~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~~ 392 (406)
....|-+.++|++|+.+||+.-++ |+.- -+....|+=.. ..++..+.++++|++.+.
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 6542 23444554322 333488899999988654
No 182
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=51.23 E-value=40 Score=36.18 Aligned_cols=59 Identities=20% Similarity=0.345 Sum_probs=44.3
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc
Q 015464 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF 390 (406)
Q Consensus 311 i~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~ 390 (406)
+-+...|+.|--.++|..|..++|||..||=-|.. ..|++|. +.+....+.++.+++..
T Consensus 3 l~~~~~dr~g~~~~~l~~~~~~~~~~~~~e~~~~~--------------------~~~~~~~-~~~~~~~~~~~~~~~~~ 61 (520)
T PRK10820 3 LEVFCEDRLGLTRELLDLLVLRSIDLRGIEIDPIG--------------------RIYLNFA-ELEFESFSSLMAEIRRI 61 (520)
T ss_pred EEEEeeccccHHHHHHHHHHhcCCCccEEEEcCCC--------------------eEEEeCC-CcChhhHHHHHHHHhcC
Confidence 34566799999999999999999999999975531 3677776 34445566777777543
No 183
>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=50.62 E-value=95 Score=23.42 Aligned_cols=33 Identities=33% Similarity=0.407 Sum_probs=25.7
Q ss_pred eEEEEEE-eC-CCcchHHHHHHHHHhCCceeeeeE
Q 015464 308 KTSIVFT-LE-EGPGMLFKALAVFALRDINLTKIE 340 (406)
Q Consensus 308 ktsi~f~-~~-~~pGaL~~~L~~Fa~~~INLtkIE 340 (406)
+.++.-. +. +.||.+.++.+.+++.|||+.-|-
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 3445544 44 489999999999999999998887
No 184
>cd04868 ACT_AK-like ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes each of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). Typically, AK consists of two ACT domains in a tandem repeat, but the second ACT domain is inserted within the first, resulting in, what is normally the terminal beta strand of ACT2, formed from a region N-terminal of ACT1. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Aspartokinase is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. One mechanism for the regulation of this pathway is by the production of several isoenzymes of aspartokinase with different repressors and allosteric inhibitors. Pairs of ACT domains are proposed to specifically bind am
Probab=49.81 E-value=40 Score=23.27 Aligned_cols=27 Identities=26% Similarity=0.359 Sum_probs=23.6
Q ss_pred CCcchHHHHHHHHHhCCceeeeeEeee
Q 015464 317 EGPGMLFKALAVFALRDINLTKIESRP 343 (406)
Q Consensus 317 ~~pGaL~~~L~~Fa~~~INLtkIESRP 343 (406)
+.+|.+.++++.+++++||+..+..-.
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~~~~ 38 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMISQSE 38 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEEcCC
Confidence 578999999999999999999886544
No 185
>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=49.71 E-value=31 Score=37.09 Aligned_cols=104 Identities=16% Similarity=0.294 Sum_probs=65.1
Q ss_pred HHhHHHcCCceeecCccC--CCCCeeEEEEEecCCCC-------CCC-------C------CCceEEEEEEeCCCcchHH
Q 015464 266 AQAAEIYGLDILAEKIQD--DDDNVTRFLILAREPII-------AGT-------D------RPYKTSIVFTLEEGPGMLF 323 (406)
Q Consensus 266 ~~aA~~ygL~il~~~I~d--~~~N~TRF~vi~~~~~~-------~~~-------~------~~~ktsi~f~~~~~pGaL~ 323 (406)
...|+..|++|....... .-.|.-++-+-+..... -+. + .+.-..+++...|+||.+.
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 356888999986654432 23466566554332110 000 0 1123456777789999999
Q ss_pred HHHHHHHhCCceeeeeE-eeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHH
Q 015464 324 KALAVFALRDINLTKIE-SRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQE 389 (406)
Q Consensus 324 ~~L~~Fa~~~INLtkIE-SRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~ 389 (406)
++.+.+..++||+.... +|-.++ .+....++++....+ +++++|++
T Consensus 467 ~v~~~L~~~~iNIa~m~~~R~~~g----------------~~al~~i~~D~~v~~----~~l~~i~~ 513 (525)
T TIGR01327 467 KVGTLLGTAGINIASMQLGRKEKG----------------GEALMLLSLDQPVPD----EVLEEIKA 513 (525)
T ss_pred HHHhHHhhcCCChHHcEeecCCCC----------------CeEEEEEEcCCCCCH----HHHHHHhc
Confidence 99999999999998764 554332 467888899887653 34555543
No 186
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=48.59 E-value=2.7e+02 Score=27.13 Aligned_cols=121 Identities=12% Similarity=-0.007 Sum_probs=61.3
Q ss_pred HCCCCcee-ccCCHHHHHHHHHcCCccEEEEeeecc-cccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc-
Q 015464 139 AYPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENS-VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL- 215 (406)
Q Consensus 139 ~f~~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIENS-~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I- 215 (406)
.++++.+. ...+..++.+.|.+|++|+|+.+-... ..+. ...-|.+.++. +..+.+|-|...+..+++++
T Consensus 118 ~~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~l---~~~~l~~~~~~----~v~~~~hpl~~~~~~~~~~L~ 190 (309)
T PRK12683 118 VFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDL---VSFPYYSWHHV----VVVPKGHPLTGRENLTLEAIA 190 (309)
T ss_pred HCCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCCc---eEEEcccCeEE----EEecCCCCcccCCccCHHHHh
Confidence 35666543 335788999999999999999753211 1121 11112222332 23455555543333333333
Q ss_pred --cEEEech--HHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015464 216 --KRVFSHP--QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAA 269 (406)
Q Consensus 216 --~~VySHp--qal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA 269 (406)
.-|.-.+ .--.+...|+.+.+. . ...++|.......|..+. + .++.+...+
T Consensus 191 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~--G-i~~lp~~~~ 248 (309)
T PRK12683 191 EYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELGM--G-VGIVAAMAY 248 (309)
T ss_pred cCCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhCC--C-eEEeehhhc
Confidence 3332211 123456667776543 3 234556655566666542 3 455555443
No 187
>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=48.37 E-value=1.7e+02 Score=24.85 Aligned_cols=122 Identities=18% Similarity=0.062 Sum_probs=61.0
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.++++++.-. .+..++.+.+.+|++|+|++.-.-...+.. ...|.+.++.++ .+-.|-+...+..+++++.
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 4566655433 456789999999999999986432111111 112223333332 2223333322222333332
Q ss_pred --EEEech-H-HHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 217 --RVFSHP-Q-ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 217 --~VySHp-q-al~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
-|.-.+ . ...++..++...+. . ...++|...+..++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08421 98 HDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAG---LGIGIVPESAAR 155 (198)
T ss_pred CceEeecCCcchHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CCeEEccchhhh
Confidence 222111 1 11234445444333 2 34567777777777764 347777777665
No 188
>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=47.74 E-value=1.8e+02 Score=25.00 Aligned_cols=123 Identities=18% Similarity=0.078 Sum_probs=67.7
Q ss_pred HCCCCce-eccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc--
Q 015464 139 AYPKCET-VPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (406)
Q Consensus 139 ~f~~~~~-~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I-- 215 (406)
.++++++ +...+..++.+.+.+|++|+|+........|..... |.+..+. +..+-+|-|......+++++
T Consensus 31 ~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~---l~~~~~~----~~~~~~~pl~~~~~i~~~dL~~ 103 (209)
T PF03466_consen 31 RHPNIRIEIREGDSDELIEALRSGELDLAITFGPPPPPGLESEP---LGEEPLV----LVVSPDHPLAQKKPITLEDLAD 103 (209)
T ss_dssp HSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSSSSTTEEEEE---EEEEEEE----EEEETTSGGGTTSSSSGGGGTT
T ss_pred HCCCcEEEEEeccchhhhHHHhcccccEEEEEeecccccccccc---ccceeee----eeeeccccccccccchhhhhhh
Confidence 4566654 344566899999999999999998765222221111 1111111 11222333333323334444
Q ss_pred -cEEEec--hHHHHHHHHHHhhcCCe---EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 216 -KRVFSH--PQALAQCEMTLSNLGIV---RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 216 -~~VySH--pqal~QC~~~L~~~~~~---~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
.-|.-. ..-..+..+++.+.+.. ...++|...+..++..+ ...++.+...+..
T Consensus 104 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 162 (209)
T PF03466_consen 104 YPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASG---DGIAILPDSLAQD 162 (209)
T ss_dssp SEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTT---SEBEEEEHHHHHH
T ss_pred ccccccccccccccccccccccccccccccccccchhhhccccccc---cceeecCcccccc
Confidence 333322 12345666666665442 34677888888888764 4678888887753
No 189
>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=46.98 E-value=1.8e+02 Score=24.78 Aligned_cols=123 Identities=16% Similarity=0.066 Sum_probs=62.5
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.++++++... .+..++.+.+.+|++|+|++--.....+.. ...|.+.++.++. +-.|-+.. ...+++++.
T Consensus 25 ~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~lv~----~~~~~~~~-~~~~~~~L~~ 96 (200)
T cd08466 25 LAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFK---SELLFEDELVCVA----RKDHPRIQ-GSLSLEQYLA 96 (200)
T ss_pred HCCCCEEEEecCchHhHHHHHHcCCccEEEecccCCCCCce---eeeecccceEEEE----eCCCCCCC-CCcCHHHHhh
Confidence 3566665433 467789999999999999974222111111 1122333433332 23343332 123344442
Q ss_pred --EEEechHH-HHHHHHHHhhcCC---e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHc
Q 015464 217 --RVFSHPQA-LAQCEMTLSNLGI---V-RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (406)
Q Consensus 217 --~VySHpqa-l~QC~~~L~~~~~---~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~y 272 (406)
-+.-.++. ..+-..|+.+.+. . ...++|.....++++.+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~~ 156 (200)
T cd08466 97 EKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQT---DLIAIAPRWLADQY 156 (200)
T ss_pred CCcEEecCCCCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCC---CeehhhHHHHHHHh
Confidence 22222221 1233455554332 2 34566666666777654 35778888777643
No 190
>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=46.75 E-value=27 Score=32.90 Aligned_cols=71 Identities=28% Similarity=0.223 Sum_probs=41.7
Q ss_pred CccEEEEEcCCCcHHHHHHHHHC---C-CCceeccCCHHHHHHHHHcCCccEEEEeeeccccccccccc-chhccCCeEE
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNY-DLLLRHRLHI 192 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f---~-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~-DlL~~~~l~I 192 (406)
+..+|+++= +|+-.+.-+|.+. + .++++..++|.++++++++|++|-+||+.+-+. ..++ |+|.+.++++
T Consensus 67 ~~~rI~vwR-kGsaADvl~Ral~d~~~~~~EvVytdD~~~i~~Ml~~g~vdsAVv~~~~~~----G~~fEdl~~~~g~~~ 141 (201)
T PF12916_consen 67 GKPRIAVWR-KGSAADVLTRALLDLKGIKAEVVYTDDMSEIVKMLNEGEVDSAVVGSEFSK----GETFEDLLGSLGLYA 141 (201)
T ss_dssp TSSEEEESS-TTSHHHHHHHHHHHHH--T-EEEE---HHHHHHHHHTT-E--EEEETTT-------EEHHHHHHHTT---
T ss_pred CCceEEEEe-cccHHHHHHHHHHhhccccceeEEecCHHHHHHHHhcCceeeeeecchhcc----chhHHHHHhhcCCCC
Confidence 445888885 7877665555433 3 689999999999999999999999999944322 3344 4666777776
Q ss_pred E
Q 015464 193 V 193 (406)
Q Consensus 193 ~ 193 (406)
=
T Consensus 142 P 142 (201)
T PF12916_consen 142 P 142 (201)
T ss_dssp -
T ss_pred C
Confidence 3
No 191
>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=46.30 E-value=1.6e+02 Score=25.18 Aligned_cols=123 Identities=17% Similarity=0.124 Sum_probs=62.7
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.|+++++.-. .+.++..+.+.+|++|+|++..+....+... ..|.+.++.++. +-.|-+.. +..+++++.
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 4566665443 3456788999999999999854322222111 122233333322 22232222 222233332
Q ss_pred --EEEechHH---HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHc
Q 015464 217 --RVFSHPQA---LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (406)
Q Consensus 217 --~VySHpqa---l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~y 272 (406)
-|.-++.. -.+-.+|+.+.+. + ...++|...+...+..+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~ 157 (198)
T cd08461 97 LDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAAT---DMVAFVPSRLVPNL 157 (198)
T ss_pred CCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcC---CeEEEchHHHHHhh
Confidence 23222111 1234566665443 2 34566777777777764 46888888877654
No 192
>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=46.29 E-value=1e+02 Score=22.20 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=23.5
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
+++.+|.+.++++.++++|||+--|-.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~q 37 (66)
T cd04924 11 MRGTPGVAGRVFGALGKAGINVIMISQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 356799999999999999999987754
No 193
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=45.27 E-value=3.1e+02 Score=26.89 Aligned_cols=122 Identities=17% Similarity=0.167 Sum_probs=65.8
Q ss_pred HCCCCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCccE-
Q 015464 139 AYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR- 217 (406)
Q Consensus 139 ~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~~- 217 (406)
.++++.+.. .+..+.++.|.+|++|+|+.+-.....|... ..|.+..+.++ .+-+|-|... ..+++++..
T Consensus 142 ~~P~i~i~~-~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~lv----~~~~hpl~~~-~~~~~dL~~~ 212 (317)
T PRK11482 142 HYPQLLLRN-IPISDAENQLSQFQTDLIIDTHSCSNRTIQH---HVLFTDNVVLV----CRQGHPLLSL-EDDEETLDNA 212 (317)
T ss_pred HCCCCEEEE-ecchhHHHHHHCCCcCEEEeccCCCCCceEE---EEEecCcEEEE----EeCCCCccCC-CCCHHHHhhC
Confidence 456666543 2446889999999999999875533333222 12233334332 4555655432 345565542
Q ss_pred ----EEechHHHHHHHHHHhhc--CCe-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHc
Q 015464 218 ----VFSHPQALAQCEMTLSNL--GIV-RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (406)
Q Consensus 218 ----VySHpqal~QC~~~L~~~--~~~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~y 272 (406)
|...+......++++... ... ...++|.......++.+ ...+|.+...+..+
T Consensus 213 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~ilp~~~~~~~ 271 (317)
T PRK11482 213 EHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASS---DMLGIMPSRFYNLF 271 (317)
T ss_pred CCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcC---CeeEEeHHHHHHHH
Confidence 222222212234455441 223 33556666666777754 45778888776543
No 194
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=45.13 E-value=92 Score=29.08 Aligned_cols=36 Identities=19% Similarity=0.262 Sum_probs=29.8
Q ss_pred eEEEEEEe--CCCcchHHHHHHHHHhCCceeeeeEeeeCC
Q 015464 308 KTSIVFTL--EEGPGMLFKALAVFALRDINLTKIESRPQR 345 (406)
Q Consensus 308 ktsi~f~~--~~~pGaL~~~L~~Fa~~~INLtkIESRP~~ 345 (406)
++.+++++ +|+||-..++-+.++++|.|+. +||-..
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 45666666 7999999999999999999987 667654
No 195
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=44.98 E-value=93 Score=35.90 Aligned_cols=36 Identities=25% Similarity=0.329 Sum_probs=30.6
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeEee
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLT--KIESR 342 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLt--kIESR 342 (406)
+-|-|.+...|+||-|+++-++|+..|+|+. +|.+.
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 4567777889999999999999999999997 55554
No 196
>PRK03059 PII uridylyl-transferase; Provisional
Probab=44.94 E-value=1e+02 Score=35.35 Aligned_cols=36 Identities=19% Similarity=0.359 Sum_probs=30.6
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeEee
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLT--KIESR 342 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLt--kIESR 342 (406)
+.|-|.+..+|+||-|+++-++|+..|+|+. ||-+.
T Consensus 785 ~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~ 822 (856)
T PRK03059 785 QYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTL 822 (856)
T ss_pred CEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeec
Confidence 4677778889999999999999999999998 45544
No 197
>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=44.83 E-value=2e+02 Score=24.62 Aligned_cols=122 Identities=18% Similarity=0.148 Sum_probs=61.4
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.|+++++.-. .+..++.+.+.+|++|+|+.+......+.. ...|.+..+.+ ..+-+|-+...+ .+++++.
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 4566655433 345688899999999999986432111111 11122223322 233344333221 3333332
Q ss_pred --EEEechH--HHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 217 --RVFSHPQ--ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 217 --~VySHpq--al~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
-|...+. ...+..+|+.+.+. . .+.++|.....++++.+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (201)
T cd08459 97 ARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQT---DLVATVPERLARL 155 (201)
T ss_pred CCcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcC---CEEEecHHHHHHH
Confidence 2332221 12345566666443 3 23455555555666654 4588888877764
No 198
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=44.76 E-value=20 Score=32.37 Aligned_cols=63 Identities=17% Similarity=0.285 Sum_probs=40.9
Q ss_pred HHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHH--HHH--cCCceEEEc
Q 015464 323 FKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGH--LQE--FATFLRVLG 398 (406)
Q Consensus 323 ~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~--L~~--~~~~vrvLG 398 (406)
.+.+++.+.|||-++|. +|+++... |.++ |.--.|++.++.+++.. .+. .-..|..||
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 68899999999997765 67776532 2222 33334677888877663 221 223489999
Q ss_pred cccCC
Q 015464 399 CYPMD 403 (406)
Q Consensus 399 sYp~~ 403 (406)
+|-..
T Consensus 120 sy~~~ 124 (159)
T KOG3217|consen 120 SYDKN 124 (159)
T ss_pred ccCCC
Confidence 99643
No 199
>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=44.59 E-value=33 Score=26.11 Aligned_cols=28 Identities=11% Similarity=0.143 Sum_probs=24.2
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEeee
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIESRP 343 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIESRP 343 (406)
.++.||.+.++++.++.+|||+-.| ++-
T Consensus 9 ~~~~~~~~a~if~~La~~~InvDmI-~~~ 36 (67)
T cd04914 9 KDNENDLQQRVFKALANAGISVDLI-NVS 36 (67)
T ss_pred CCCCccHHHHHHHHHHHcCCcEEEE-Eec
Confidence 3467999999999999999999999 443
No 200
>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=44.45 E-value=2.1e+02 Score=24.71 Aligned_cols=122 Identities=14% Similarity=0.023 Sum_probs=61.2
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecc-cccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENS-VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL- 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS-~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I- 215 (406)
.|+++++... .+..++.+.+.+|++|+|+.+-... ..+... ..|.+.++.+ ..+.+|-|......+++++
T Consensus 25 ~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~---~~l~~~~~~~----v~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08413 25 RYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLVT---LPCYRWNHCV----IVPPGHPLADLGPLTLEDLA 97 (198)
T ss_pred hCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCcEE---EEeeeeeEEE----EecCCCcccccCCCCHHHHh
Confidence 4566654433 3567899999999999999853211 111111 1112222222 2334454443323333333
Q ss_pred --cEEEec-hH-HHHHHHHHHhhcCC---eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 --KRVFSH-PQ-ALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 --~~VySH-pq-al~QC~~~L~~~~~---~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
.-|.-. .. -..+.+.|+++.+. ....++|......+++.+. ..|+.+...+.
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~---Gi~~lp~~~~~ 156 (198)
T cd08413 98 QYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGL---GVGIIAEMAYD 156 (198)
T ss_pred cCCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhCC---CEEEccccccC
Confidence 223211 11 22345566665443 2345677777777877652 36677665443
No 201
>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=43.63 E-value=1.1e+02 Score=21.38 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=23.2
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
..+.+|.+.++++.|++++|++-.+..
T Consensus 10 ~~~~~~~~~~i~~~l~~~~i~v~~i~~ 36 (65)
T cd04892 10 MRGTPGVAARIFSALAEAGINIIMISQ 36 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 346789999999999999999987754
No 202
>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=43.11 E-value=66 Score=23.36 Aligned_cols=27 Identities=19% Similarity=0.389 Sum_probs=23.7
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
+.+.||.+.++++.+++.|||+-.|-.
T Consensus 11 ~~~~~~~~~~i~~~l~~~~I~v~~i~~ 37 (66)
T cd04922 11 MAGTPGVAATFFSALAKANVNIRAIAQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 457799999999999999999988853
No 203
>TIGR01729 taurine_ABC_bnd taurine ABC transporter, periplasmic binding protein. This model identifies a cluster of ABC transporter periplasmic substrate binding proteins, apparently specific for taurine. Transport systems for taurine (NH2-CH2-CH2-SO3H), sulfonates, and sulfate esters import sulfur when sulfate levels are low. The most closely related proteins outside this family are putative aliphatic sulfonate binding proteins (TIGR01728).
Probab=42.77 E-value=3.1e+02 Score=26.42 Aligned_cols=116 Identities=11% Similarity=-0.054 Sum_probs=60.4
Q ss_pred CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEE-EeeeeEeecCCCC---CccCc--
Q 015464 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQ-LVVNHCLLGLPGV---LKEEL-- 215 (406)
Q Consensus 142 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~-l~I~h~L~~~~g~---~l~~I-- 215 (406)
++++....+..+.++++..|++|++++..... +. . .-...++.++.-.. ..-.+.|+++++. +++|+
T Consensus 28 ~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~~~----~~-a--~~~g~~~~~v~~~~~~~~~~~lv~~~~s~I~s~~DLkG 100 (300)
T TIGR01729 28 TIDWRKFDSGADISTALASGNVPIGVIGSSPL----AA-A--ASRGVPIELFWILDNIGKSEALVAREGSGIEKPEDLKG 100 (300)
T ss_pred eeEEEecCcHHHHHHHHHcCCCCEeccCCCHH----HH-H--HHCCCCeEEEEEeccCCccceEEecCCCCCCChhHcCC
Confidence 67889999999999999999999997532211 00 0 00112344432211 1112567777653 23344
Q ss_pred cEEEechHH--HHHHHHHHhhcCC-----eEEeccCHHHHHHHHHhcCCCCeEEEcCH
Q 015464 216 KRVFSHPQA--LAQCEMTLSNLGI-----VRISADDTAGAAQMVASIGERDTGAVASA 266 (406)
Q Consensus 216 ~~VySHpqa--l~QC~~~L~~~~~-----~~i~~~sTA~Aa~~v~~~~~~~~AAIas~ 266 (406)
|+|..++-. ...-..||++.+. +.+.. +.++++..+..+ .-+.+++...
T Consensus 101 K~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~G-~vDa~~~~~p 156 (300)
T TIGR01729 101 KNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQRG-DIDAAYVWPP 156 (300)
T ss_pred CEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHcC-CcCEEEEecH
Confidence 356554321 1223457766443 34444 345556666554 3344444443
No 204
>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=42.66 E-value=3.1e+02 Score=26.16 Aligned_cols=122 Identities=17% Similarity=0.138 Sum_probs=62.0
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeeccc--ccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSV--GGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~--~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I 215 (406)
.|+++.+... .+..++.+.+.+|++|+|++...+.. .+... .-|.+..+.++ .+-.|-|...+..+++++
T Consensus 118 ~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~---~~l~~~~~~~~----~~~~hpl~~~~~i~~~dL 190 (300)
T TIGR02424 118 RAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGLSF---EHLYNEPVVFV----VRAGHPLLAAPSLPVASL 190 (300)
T ss_pred hCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCcccccceee---eeecCCceEEE----EcCCCccccCCCCCHHHH
Confidence 4566655433 36678899999999999997543321 11111 11223333222 222344433322233333
Q ss_pred c--EEEechHH---HHHHHHHHhhcCC----eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 K--RVFSHPQA---LAQCEMTLSNLGI----VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 ~--~VySHpqa---l~QC~~~L~~~~~----~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
. ..+..+.. ......|+.+.+. ....++|......++..+ ...++.+...++
T Consensus 191 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 251 (300)
T TIGR02424 191 ADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQES---DAIWIISRGVVA 251 (300)
T ss_pred hCCCEEecCCCCchHHHHHHHHHHCCCCCCCceEEeccHHHHHHHHHhC---CceEeCcHHHHh
Confidence 2 12222221 1334556665332 235677777777777764 346677777664
No 205
>TIGR00656 asp_kin_monofn aspartate kinase, monofunctional class. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. The protein slr0657 from Synechocystis PCC6803 is extended by a duplication of the C-terminal region corresponding to the beta chain. Incorporation of a second copy of the C-terminal domain may be quite common in this subgroup of aspartokinases.
Probab=42.57 E-value=3.6e+02 Score=27.63 Aligned_cols=97 Identities=19% Similarity=0.121 Sum_probs=60.0
Q ss_pred CCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecCccCCCCCeeEEEEEecCCC-CCCC----CCCc
Q 015464 236 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPI-IAGT----DRPY 307 (406)
Q Consensus 236 ~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~a---A~~ygL~il~~~I~d~~~N~TRF~vi~~~~~-~~~~----~~~~ 307 (406)
+++.+..-|..+|.++...+ |-+-...| |..++.+|.-.|..+.. --|.. ..... .+.- ...+
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 56677777888888887642 33444444 44589999888765433 22333 22211 1100 0122
Q ss_pred eEEEEEE---eCCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 308 KTSIVFT---LEEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 308 ktsi~f~---~~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
.+-+.+. +.+.||.+.++++.|++++||+-.|..
T Consensus 260 va~vsv~g~~~~~~~g~~~~if~~L~~~~I~i~~i~~ 296 (401)
T TIGR00656 260 VTRVTVHGLGMLGKRGFLARIFGALAERNINVDLISQ 296 (401)
T ss_pred EEEEEEecCCCCCCccHHHHHHHHHHHcCCcEEEEEc
Confidence 3333333 567899999999999999999988754
No 206
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=42.34 E-value=3.3e+02 Score=26.46 Aligned_cols=142 Identities=14% Similarity=0.016 Sum_probs=67.9
Q ss_pred CccEEEEEcCCCcH-H-HHHH--HHHCCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccc--hhccCCe
Q 015464 118 TKVRVAYQGLPGAY-S-EAAA--RKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRL 190 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~-s-~~AA--~~~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~D--lL~~~~l 190 (406)
+..+|++...-+.+ - .... ...++++.+.. ..+..++++.+.+|++|+++.+-.... ...++ -|.+..+
T Consensus 93 g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~----~~~l~~~~l~~~~~ 168 (313)
T PRK12684 93 GNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIAD----YKELVSLPCYQWNH 168 (313)
T ss_pred CeEEEEechHHHHHHhHHHHHHHHHHCCCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCC----CCCceEEEeccceE
Confidence 45677764433322 1 1111 12346665543 346789999999999999997622111 11111 1112222
Q ss_pred EEEEEEEEeeeeEeecCCCCCccCc---cEEEech-H-HHHHHHHHHhhcC--Ce-EEeccCHHHHHHHHHhcCCCCeEE
Q 015464 191 HIVGEVQLVVNHCLLGLPGVLKEEL---KRVFSHP-Q-ALAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDTGA 262 (406)
Q Consensus 191 ~I~gE~~l~I~h~L~~~~g~~l~~I---~~VySHp-q-al~QC~~~L~~~~--~~-~i~~~sTA~Aa~~v~~~~~~~~AA 262 (406)
.+ ..+..|-+......+++++ .-|.-.. . --.+...|+...+ .. ...++|......+|..+. + .+
T Consensus 169 ~~----v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~--G-v~ 241 (313)
T PRK12684 169 CV----VVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELGL--G-VG 241 (313)
T ss_pred EE----EeCCCCccccCCCcCHHHHhcCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhCC--c-eE
Confidence 22 2344444433222222222 2222111 1 1233455665533 23 356677777777777642 3 56
Q ss_pred EcCHHhHH
Q 015464 263 VASAQAAE 270 (406)
Q Consensus 263 Ias~~aA~ 270 (406)
+.+..+++
T Consensus 242 ~lp~~~~~ 249 (313)
T PRK12684 242 IVADMAFD 249 (313)
T ss_pred Eeehhhcc
Confidence 65655543
No 207
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=41.44 E-value=1.1e+02 Score=29.09 Aligned_cols=49 Identities=12% Similarity=0.064 Sum_probs=32.6
Q ss_pred CccEEEEEcCCCcHHHHHHHHHC----CCCceeccCCHHHHHHHHHcCCccEEEE
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAY----PKCETVPCDQFEAAFKAVELWLVDKAVL 168 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f----~~~~~~~~~s~~~v~~aV~~g~~d~gvV 168 (406)
...+|+++ .|+..+.....+. ....+...++..+++++|..|++|..+.
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 34678885 4443332222221 2356778899999999999999998765
No 208
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=41.00 E-value=3.2e+02 Score=25.95 Aligned_cols=122 Identities=11% Similarity=-0.012 Sum_probs=63.0
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCcc---C
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKE---E 214 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~---~ 214 (406)
.++++.+... .+.+++++.+.+|++|+|++.-+....+. ....|.+.++.++ .+-.|-|......+++ +
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 4677665443 35678999999999999998654211111 1122333344333 2333434322222223 3
Q ss_pred ccEEEech---HH-HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 215 LKRVFSHP---QA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 215 I~~VySHp---qa-l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
..-|.--+ .. ..+...|+...++ . ...++|...+...|+.+ ...++.+...++
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 34566777777777764 235666665543
No 209
>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=41.00 E-value=61 Score=25.94 Aligned_cols=38 Identities=24% Similarity=0.410 Sum_probs=30.5
Q ss_pred cceEEEEEEEecCCCcHHHHHHHHHHHHcCCc-----eEEEcc
Q 015464 362 YFDYLFYIDFEASMADPRAQFALGHLQEFATF-----LRVLGC 399 (406)
Q Consensus 362 ~~~Y~Ffid~e~~~~~~~~~~al~~L~~~~~~-----vrvLGs 399 (406)
.+.|+|-||+.|+..-..=|++|+.|+..... |+|-|.
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 36899999999987777888999999876543 777765
No 210
>TIGR03427 ABC_peri_uca ABC transporter periplasmic binding protein, urea carboxylase region. Members of this family are ABC transporter periplasmic binding proteins associated with the urea carboxylase/allophanate hydrolase pathway, an alternative to urease for urea degradation. The protein is restricted to bacteria with the pathway, with its gene close to the urea carboxylase and allophanate hydrolase genes. The substrate for this transporter therefore is likely to be urea or a compound from which urea is easily derived.
Probab=40.81 E-value=3.9e+02 Score=26.87 Aligned_cols=131 Identities=11% Similarity=0.039 Sum_probs=67.6
Q ss_pred CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEE-EeeeeEeecCCCCCccCc--cEE
Q 015464 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQ-LVVNHCLLGLPGVLKEEL--KRV 218 (406)
Q Consensus 142 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~-l~I~h~L~~~~g~~l~~I--~~V 218 (406)
++++...++..++++++..|.+|+|.+--...+..... ...++.|+.-.. -.-...+++++..+++|. |+|
T Consensus 36 ~Ve~~~f~~~~~~l~Al~aG~iD~~~~g~~~~~~~~~a------~g~~~~iv~v~~~~~g~~~ivv~~i~svaDLKGKkI 109 (328)
T TIGR03427 36 TIEVVQINDYVESINQYTAGKFDGCTMTNMDALTIPAA------GGVDTTALIVGDFSNGNDGIVLKGGKSLADLKGQKV 109 (328)
T ss_pred eEEEEECCChHHHHHHHHcCCCCEEeecCHHHHHHHHh------CCCCeEEEEEEccCCCceEEEECCCCCHHHcCCCEE
Confidence 57889999999999999999999986521110000000 112233322111 111134555544456666 477
Q ss_pred EechHHHHH--HHHHHhhcC-----CeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH---HcCCceeecC
Q 015464 219 FSHPQALAQ--CEMTLSNLG-----IVRISADDTAGAAQMVASIGERDTGAVASAQAAE---IYGLDILAEK 280 (406)
Q Consensus 219 ySHpqal~Q--C~~~L~~~~-----~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~---~ygL~il~~~ 280 (406)
..++-...+ ....|++.| ++.+.... +.+...+..+ .-+.+++-....+. ..|.++|...
T Consensus 110 av~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~~-~d~~aAl~~G-~VDAa~~~eP~~s~~~~~~g~~~l~~~ 179 (328)
T TIGR03427 110 NLVELSVSHYLLARALESVGLSEKDVKVVNTSD-ADIVAAFITK-DVTAVVTWNPQLSEIKAQPGANEVFDS 179 (328)
T ss_pred eccCCChHHHHHHHHHHHcCCCHHHeEEEeCCh-HHHHHHHhcC-CCcEEEEcCchHHHHHhCCCcEEeccc
Confidence 665543332 334455533 45566544 4555554443 34555554444332 2466666543
No 211
>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=40.69 E-value=1.5e+02 Score=22.03 Aligned_cols=36 Identities=17% Similarity=0.239 Sum_probs=28.1
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeee
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP 343 (406)
+.|++=.+...+|.+.++++.|++.|||+..|-.=+
T Consensus 3 ~VsvVG~~~~~~~~~~~i~~aL~~~~I~v~~i~~g~ 38 (65)
T cd04918 3 IISLIGNVQRSSLILERAFHVLYTKGVNVQMISQGA 38 (65)
T ss_pred EEEEECCCCCCccHHHHHHHHHHHCCCCEEEEEecC
Confidence 456665555679999999999999999997775333
No 212
>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=40.55 E-value=79 Score=23.10 Aligned_cols=26 Identities=19% Similarity=0.226 Sum_probs=23.0
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 316 EEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 316 ~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
.+.||.+.++++.+++.|||+--|-.
T Consensus 12 ~~~~~~~~~if~~L~~~~I~v~~i~q 37 (66)
T cd04919 12 KNMIGIAGRMFTTLADHRINIEMISQ 37 (66)
T ss_pred CCCcCHHHHHHHHHHHCCCCEEEEEe
Confidence 46799999999999999999988854
No 213
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=40.52 E-value=35 Score=33.74 Aligned_cols=141 Identities=15% Similarity=0.025 Sum_probs=72.6
Q ss_pred CccEEEEEcCCCcHHHHHHHHHC----C-CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEE
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAY----P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHI 192 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f----~-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I 192 (406)
...+|+|+...+.+--.-++.+| | ++++....+..++.+++.+|++|+|.+.....+.. .....++.+
T Consensus 23 ~~v~~~y~~~~~~~~vA~~~g~f~~~~Gl~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~~~a-------~~~g~~~~~ 95 (320)
T PRK11480 23 VNVTVAYQTSAEPAKVAQADNTFAKESGATVDWRKFDSGASIVRALASGDVQIGNLGSSPLAVA-------ASQQVPIEV 95 (320)
T ss_pred CeEEEEecCCCcHHHHHHHcCchHHHcCCeeEEEEeCCHHHHHHHHHCCCCCEECcCchHHHHH-------HHCCCCeEE
Confidence 56899998543323221123234 3 57899999999999999999999997654311100 001223444
Q ss_pred EEEEEE-eeeeEeecCCCC-CccCc--cEEEechHH--HHHHHHHHhhcCC-----eEEeccCHHHHHHHHHhcCCCCeE
Q 015464 193 VGEVQL-VVNHCLLGLPGV-LKEEL--KRVFSHPQA--LAQCEMTLSNLGI-----VRISADDTAGAAQMVASIGERDTG 261 (406)
Q Consensus 193 ~gE~~l-~I~h~L~~~~g~-~l~~I--~~VySHpqa--l~QC~~~L~~~~~-----~~i~~~sTA~Aa~~v~~~~~~~~A 261 (406)
++-... .....++++++. +++|+ |+|...+-. ...-..+|++.|. +.+... .+.++..+..+ .-+.+
T Consensus 96 v~~~~~~~~~~~lv~~~~I~s~~DLkGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~-~~~~~~Al~~G-~VDAa 173 (320)
T PRK11480 96 FLLASKLGNSEALVVKKTISKPEDLIGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQ-PPAIIAAWQRG-DIDGA 173 (320)
T ss_pred EEeeccCCcceEEEecCCCCChHHcCCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECC-cHHHHHHHHcC-CcCEE
Confidence 332211 122355555543 33444 456643211 1223567776443 333433 34555555554 34444
Q ss_pred EEcCHH
Q 015464 262 AVASAQ 267 (406)
Q Consensus 262 AIas~~ 267 (406)
++....
T Consensus 174 ~~~~p~ 179 (320)
T PRK11480 174 YVWAPA 179 (320)
T ss_pred EEcchH
Confidence 444443
No 214
>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=40.43 E-value=2.3e+02 Score=24.12 Aligned_cols=122 Identities=11% Similarity=0.004 Sum_probs=60.6
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeeccc-ccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSV-GGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~-~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~ 216 (406)
.++++++.-. .+..++.+.+.+|++|+|++.-.... .+.+ ....|.+..+.++ .+-+|-|......+++++.
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 4566665443 46788999999999999998532110 1111 1112223333332 2333434332223333332
Q ss_pred ---EEE-echH-HHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015464 217 ---RVF-SHPQ-ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAA 269 (406)
Q Consensus 217 ---~Vy-SHpq-al~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA 269 (406)
-|. .... --.+...++.+.+. + ...++|...+.++++++ ...++.+...+
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 156 (198)
T cd08437 99 KENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVREN---VGIGFLTDIAV 156 (198)
T ss_pred CCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CcEEEEEhhhc
Confidence 222 1111 12345556655432 3 34566666666777764 24677776654
No 215
>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=40.36 E-value=2.3e+02 Score=24.00 Aligned_cols=122 Identities=13% Similarity=0.036 Sum_probs=58.4
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc--
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I-- 215 (406)
.++++++.-. .+..++.+.+.+|++|+|+..-.....+... ..|.+..+.+ ..+-.|-+...+...++++
T Consensus 25 ~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08456 25 RHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIER---ERLLRIDGVC----VLPPGHRLAVKKVLTPSDLEG 97 (196)
T ss_pred HCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCeeE---EEeeccCeEE----EecCCCchhccCccCHHHcCC
Confidence 4566554333 3556788999999999999753322111111 1112222222 1222333332222223333
Q ss_pred -cEEE-echHHH-HHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 -KRVF-SHPQAL-AQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 -~~Vy-SHpqal-~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
.-|. .+.... .....|+.+.+. . ...++|...+.+++.++ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (196)
T cd08456 98 EPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAG---VGVSVVNPLTAL 155 (196)
T ss_pred CcEEEecCCcchHHHHHHHHHHCCCCcceEEEEccHHHHHHHHHcC---CeEEEeChhhhc
Confidence 2332 222222 234555655432 2 34566666677777764 346666666544
No 216
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=40.13 E-value=2.8e+02 Score=25.48 Aligned_cols=115 Identities=15% Similarity=0.126 Sum_probs=60.2
Q ss_pred CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCC----CccCc--
Q 015464 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV----LKEEL-- 215 (406)
Q Consensus 142 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~----~l~~I-- 215 (406)
.+++++ .+|.+++.++.+|++|+++.++..+.+-. ..+. ....+. .....++.+.+. .++++
T Consensus 64 ~~~~~~-~~~~~~~~~l~~G~~D~~~~~~~~~~~r~--~~~~--~s~p~~-------~~~~~~~~~~~~~~~~~~~dl~g 131 (250)
T TIGR01096 64 KCKFVE-QNFDGLIPSLKAKKVDAIMATMSITPKRQ--KQID--FSDPYY-------ATGQGFVVKKGSDLAKTLEDLDG 131 (250)
T ss_pred eEEEEe-CCHHHHHHHHhCCCcCEEEecCccCHHHh--hccc--cccchh-------cCCeEEEEECCCCcCCChHHcCC
Confidence 567777 57999999999999999875443222110 0010 000110 111222222221 12222
Q ss_pred cEEEechHHHHHHHHHHhh--c-CCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHc
Q 015464 216 KRVFSHPQALAQCEMTLSN--L-GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (406)
Q Consensus 216 ~~VySHpqal~QC~~~L~~--~-~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~y 272 (406)
++|-. ....... .++.+ . +...+.+.|..++.+++..+. -.++|++...+..+
T Consensus 132 ~~i~~-~~g~~~~-~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~--vD~~v~~~~~~~~~ 187 (250)
T TIGR01096 132 KTVGV-QSGTTHE-QYLKDYFKPGVDIVEYDSYDNANMDLKAGR--IDAVFTDASVLAEG 187 (250)
T ss_pred CEEEE-ecCchHH-HHHHHhccCCcEEEEcCCHHHHHHHHHcCC--CCEEEeCHHHHHHH
Confidence 12222 1222222 34443 2 667788899999999988753 45777776665543
No 217
>PRK08210 aspartate kinase I; Reviewed
Probab=39.75 E-value=4.4e+02 Score=27.09 Aligned_cols=96 Identities=14% Similarity=-0.007 Sum_probs=55.6
Q ss_pred CCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecCccCCCCCeeEEEEEecCCC-------CCC---
Q 015464 236 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPI-------IAG--- 302 (406)
Q Consensus 236 ~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~a---A~~ygL~il~~~I~d~~~N~TRF~vi~~~~~-------~~~--- 302 (406)
+++.+..-|..+|.++...+ +-+-...| |..+|.+|.-.+..+... -|..- ...+. .+.
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 45666666777777766542 23444444 345788888887765322 34331 11110 000
Q ss_pred -CCCCceEEEEEE-eCCCcchHHHHHHHHHhCCceeeee
Q 015464 303 -TDRPYKTSIVFT-LEEGPGMLFKALAVFALRDINLTKI 339 (406)
Q Consensus 303 -~~~~~ktsi~f~-~~~~pGaL~~~L~~Fa~~~INLtkI 339 (406)
....+-+-|.+. .+..||.+.++++.|+++|||+-.|
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 001223333333 3445999999999999999999988
No 218
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=39.60 E-value=66 Score=30.02 Aligned_cols=50 Identities=26% Similarity=0.226 Sum_probs=37.9
Q ss_pred ccEEEEEcCCCcH--HHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEee
Q 015464 119 KVRVAYQGLPGAY--SEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPI 170 (406)
Q Consensus 119 ~~~Va~lGp~Gs~--s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPI 170 (406)
..+|+++ .|+. .........+...+..+++..+++.++.+|++|..+..-
T Consensus 146 gk~v~v~--~gt~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d~ 197 (275)
T COG0834 146 GKKVGVQ--LGTTDEAEEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSDS 197 (275)
T ss_pred CCEEEEE--cCcchhHHHHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcch
Confidence 3677776 5555 444444344578899999999999999999999998753
No 219
>cd08426 PBP2_LTTR_like_5 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=39.59 E-value=2.4e+02 Score=23.96 Aligned_cols=122 Identities=15% Similarity=0.063 Sum_probs=61.3
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc--
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I-- 215 (406)
.++++++... .+..+..+.+.+|++|+|+..-+....+.. ...|.+.++.++ .+-+|-+...+..+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~hpl~~~~~~~~~~l~~ 97 (199)
T cd08426 25 RYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIR---VHSRQPAPIGAV----VPPGHPLARQPSVTLAQLAG 97 (199)
T ss_pred hCCCeEEEEEeCCcHHHHHHHHCCCccEEEecCCCCCCCeE---EEeeccCcEEEE----ecCCCCcccCCccCHHHHhC
Confidence 3565554333 356788999999999999975332222211 112222233222 233333332222223332
Q ss_pred -cEEEechH--HHHHHHHHHhhcCC---eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 -KRVFSHPQ--ALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 -~~VySHpq--al~QC~~~L~~~~~---~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
.-|.-.+. .......|+.+.+. ....++|...+.+++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (199)
T cd08426 98 YPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAG---GGISLLTELAVR 155 (199)
T ss_pred CCeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcC---CCEEEEchHhhh
Confidence 23322211 12334556655332 234577777777888765 346777776554
No 220
>TIGR02995 ectoine_ehuB ectoine/hydroxyectoine ABC transporter solute-binding protein. Members of this family are the extracellular solute-binding proteins of ABC transporters that closely resemble amino acid transporters. The member from Sinorhizobium meliloti is involved in ectoine uptake, both for osmoprotection and for catabolism. All other members of the seed alignment are found associated with ectoine catabolic genes.
Probab=39.52 E-value=66 Score=30.82 Aligned_cols=49 Identities=20% Similarity=0.181 Sum_probs=36.4
Q ss_pred ccEEEEEcCCCcHHHHHHHHH-CCCCceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 119 KVRVAYQGLPGAYSEAAARKA-YPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~-f~~~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
..+|+++ .|+....+.+.. +...+++.++|.++++++|.+|++|+.+..
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 3578875 566555555432 344567888999999999999999988875
No 221
>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=39.36 E-value=47 Score=32.41 Aligned_cols=133 Identities=18% Similarity=0.133 Sum_probs=71.6
Q ss_pred CccEEEEEcCCCcHHHHHHHHHC---C-CCceeccCCHHHHHHHHHcCCccEEEEeeecc----cccccccc-------c
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENS----VGGSIHRN-------Y 182 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f---~-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS----~~G~V~~t-------~ 182 (406)
+..+++..| .|+.+|.++..++ | +.+.+++++-.++..++..|++|+++....+. -.|.+... +
T Consensus 105 ~~~~~g~~g-~g~~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~~~~~~~~~~G~~k~Lav~~~~r~ 183 (274)
T PF03401_consen 105 GKLTFGSSG-PGSSDHLAAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSPGEALPYVEAGDLKPLAVFSDERS 183 (274)
T ss_dssp CC-EEEESS-TTSHHHHHHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHTTSEEEEEECSSS-B
T ss_pred CCeEEEecC-CCchHHHHHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecHHHHHHHHhCCCceEEEEecCccc
Confidence 345666655 4788887765443 3 56889999999999999999999998765422 23443311 1
Q ss_pred chhc------cCCeEEEEEEEEeeeeEeecCCCCCccCccEEEechHH---HHHHHHHHhhcCCeEEeccCHHHHHHHHH
Q 015464 183 DLLL------RHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQA---LAQCEMTLSNLGIVRISADDTAGAAQMVA 253 (406)
Q Consensus 183 DlL~------~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~~VySHpqa---l~QC~~~L~~~~~~~i~~~sTA~Aa~~v~ 253 (406)
+.|. +.++ .++.+...+.+++++|++.+-+.++..--+. ....++|+++.+.... ..+..+..+.+.
T Consensus 184 ~~~pdvPT~~E~G~---~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~~g~~~~-~~~~~~~~~~l~ 259 (274)
T PF03401_consen 184 PALPDVPTFKEQGY---PDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEKMGLEPV-YMDGEEFDAFLA 259 (274)
T ss_dssp TTCTTS-BTTTTT----TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHHHTEEEE-CESHHHHHHHHH
T ss_pred cccCCCCCHHHhCc---cceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHHCCCcCC-CCCHHHHHHHHH
Confidence 1111 1111 0223455678888888753333322211111 1233445555555443 566667777766
Q ss_pred hc
Q 015464 254 SI 255 (406)
Q Consensus 254 ~~ 255 (406)
++
T Consensus 260 ~~ 261 (274)
T PF03401_consen 260 EE 261 (274)
T ss_dssp HH
T ss_pred HH
Confidence 54
No 222
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=39.16 E-value=2.4e+02 Score=23.81 Aligned_cols=121 Identities=16% Similarity=0.033 Sum_probs=58.5
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecc--cccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENS--VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS--~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I 215 (406)
.++++++... .+.+++.+.+.+|++|+|+..-... ..+.. ...|.+..+.++.- -+|-+.... ..+.+-
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~---~~~l~~~~~~~v~~----~~~p~~~~~-~~l~~~ 96 (195)
T cd08427 25 RHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLPKDLV---WTPLVREPLVLIAP----AELAGDDPR-ELLATQ 96 (195)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCCCEEEEcCCCCccccCce---EEEcccCcEEEEEC----CCCCcchHH-HHhcCC
Confidence 4566665433 3568899999999999999853221 11111 12222333322211 112111100 012222
Q ss_pred cEEE-echHHH-HHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 KRVF-SHPQAL-AQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 ~~Vy-SHpqal-~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
.-|. .+.... .+...|+.+.+. . ...++|...+.++++.+ ...|+.+...++
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 153 (195)
T cd08427 97 PFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQG---LGVAIVPDIAVP 153 (195)
T ss_pred CeEEecCCchHHHHHHHHHHHcCCCCCeEEEeccHHHHHHHHHhC---CcEEEccHHHHh
Confidence 2222 121111 334566665433 2 34566666677777764 357788877665
No 223
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=39.09 E-value=1.7e+02 Score=28.48 Aligned_cols=50 Identities=18% Similarity=0.156 Sum_probs=32.0
Q ss_pred CccEEEEEcCCCcHHHHHH-----HHHCCC--CceeccCCHHHHHHHHHcCCccEEEE
Q 015464 118 TKVRVAYQGLPGAYSEAAA-----RKAYPK--CETVPCDQFEAAFKAVELWLVDKAVL 168 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA-----~~~f~~--~~~~~~~s~~~v~~aV~~g~~d~gvV 168 (406)
...+|++...... ...+. ++.+++ +++....+..++.+++.+|++|+|+.
T Consensus 27 ~~lrIg~~~~~~~-~~l~~~~~~~~~~~p~v~ie~~~~~~~~~~~~aL~~G~iDia~~ 83 (314)
T PRK11553 27 EALRIGYQKGSIG-LVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGST 83 (314)
T ss_pred CeEEEEeCCCchH-HHHHHhhCHHHHhCCCCeeEEEECCCcHHHHHHHHcCCCCEEcc
Confidence 5678888643221 12221 112333 45667767789999999999999985
No 224
>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=38.89 E-value=2.6e+02 Score=24.15 Aligned_cols=123 Identities=14% Similarity=0.055 Sum_probs=60.7
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecc--cccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENS--VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS--~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I 215 (406)
.++++++... .+..++.+.+.+|++|+|++.-... ....+. ...|.+..+.++ .+-+|-+.. ..+++++
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~--~~~l~~~~~~~~----~~~~hpl~~--~~~~~~L 96 (202)
T cd08468 25 LAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIE--ERDWWEDTYVVI----ASRDHPRLS--RLTLDAF 96 (202)
T ss_pred hCCCCEEEEEECChHhHHHHHHCCCccEEEecccccccCCCCEE--EEEEecCcEEEE----EeCCCCCcC--CCCHHHH
Confidence 4566665444 4578999999999999999853321 011110 011122222221 122232221 1233332
Q ss_pred c---EEEec--hHHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHc
Q 015464 216 K---RVFSH--PQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (406)
Q Consensus 216 ~---~VySH--pqal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~y 272 (406)
. -|... ...-.+..+++.+.+. + .+.++|......+++.+ +..++.+..+++.+
T Consensus 97 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~---~~~~~~p~~~~~~~ 158 (202)
T cd08468 97 LAERHLVVTPWNEDRGVVDQVLEKQGLEREIALQLPNVLNAPFIVASS---DLLMTLPRQAARAL 158 (202)
T ss_pred hhCCCeEEecCCCCCchHHHHHHHcCCCceEEEEcChhHhHHHHHhcC---CeeeecHHHHHHHh
Confidence 1 12111 1112345556655443 2 34666766666666543 45778888877653
No 225
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=38.83 E-value=3.8e+02 Score=26.10 Aligned_cols=122 Identities=11% Similarity=0.023 Sum_probs=60.2
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.++++.+.- ..+..++.+.+.+|++|+++.+-.......+ ....|.+..+. +.++.+|-|......+++++.
T Consensus 118 ~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l--~~~~l~~~~~~----~v~~~~hpl~~~~~i~~~~L~~ 191 (316)
T PRK12679 118 LFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQL--VAFPWFRWHHS----LLVPHDHPLTQITPLTLESIAK 191 (316)
T ss_pred HCCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCCCCc--eEEEccCCcEE----EEecCCCccccCCCCCHHHHhC
Confidence 356655433 3467789999999999999975321111011 01112222222 234555555433223333332
Q ss_pred --EEEechH--HHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015464 217 --RVFSHPQ--ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAA 269 (406)
Q Consensus 217 --~VySHpq--al~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA 269 (406)
-|.-++. .-.....|+...+. . ...++|+..+..+|..+ ...|+.+..++
T Consensus 192 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g---~Gi~~lp~~~~ 248 (316)
T PRK12679 192 WPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALG---LGIGLVAEQSS 248 (316)
T ss_pred CCeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcC---CcEEEeccccc
Confidence 2322221 22235556665443 2 34556666666677664 23566666543
No 226
>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=38.48 E-value=85 Score=25.06 Aligned_cols=64 Identities=17% Similarity=0.090 Sum_probs=39.3
Q ss_pred CcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCC-CcHHHHHHHHHHHH
Q 015464 318 GPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASM-ADPRAQFALGHLQE 389 (406)
Q Consensus 318 ~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~-~~~~~~~al~~L~~ 389 (406)
.+|.++++=+.++.+|+|+..|...-.. .++ .+......|..-+++++.. +...++.+|.++.+
T Consensus 10 ~a~~ia~Vs~~lA~~~~NI~~I~~l~~~-~~~-------~~~~~~~~~~~e~~v~~~~~~~~~lr~~L~~la~ 74 (84)
T cd04871 10 TAEQLAAVTRVVADQGLNIDRIRRLSGR-VPL-------EEQDDSPKACVEFSVRGQPADLEALRAALLELAS 74 (84)
T ss_pred CHHHHHHHHHHHHHcCCCHHHHHHhhcc-ccc-------cccCCCCcEEEEEEEeCCCCCHHHHHHHHHHHhc
Confidence 7899999999999999999988763111 000 0000123455555665543 33567777776653
No 227
>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=38.39 E-value=1.3e+02 Score=22.17 Aligned_cols=27 Identities=15% Similarity=0.365 Sum_probs=23.0
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
+.+.||.+.++++.+++.|||+..+-+
T Consensus 11 ~~~~~gi~~~if~aL~~~~I~v~~~~~ 37 (64)
T cd04937 11 IRGVPGVMAKIVGALSKEGIEILQTAD 37 (64)
T ss_pred ccCCcCHHHHHHHHHHHCCCCEEEEEc
Confidence 357899999999999999999975553
No 228
>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=38.24 E-value=60 Score=30.29 Aligned_cols=89 Identities=16% Similarity=0.051 Sum_probs=49.0
Q ss_pred CccEEEEEcCCCcHHHHH----HHHHCC------CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhcc
Q 015464 118 TKVRVAYQGLPGAYSEAA----ARKAYP------KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLR 187 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~A----A~~~f~------~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~ 187 (406)
...+|++.++.++..+.. ..+..+ ...+....++.+++++|.+|++|.++.+-. ...+...+..+ ..
T Consensus 140 ~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~~Da~~~~~~-~~~~~~~~~~~--~~ 216 (254)
T TIGR01098 140 KGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGKVDAATNNSS-AIGRLKKRGPS--DM 216 (254)
T ss_pred cCCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCCCCeEEecHH-HHHHHHHhCcc--ch
Confidence 346899887654332222 222333 145667778999999999999999998743 22221211111 01
Q ss_pred CCeEEEEEEEEeeeeEeecCCC
Q 015464 188 HRLHIVGEVQLVVNHCLLGLPG 209 (406)
Q Consensus 188 ~~l~I~gE~~l~I~h~L~~~~g 209 (406)
.++.+.++......+.++.+++
T Consensus 217 ~~~~~~~~~~~~~~~~~~~~~~ 238 (254)
T TIGR01098 217 KKVRVIWKSPLIPNDPIAVRKD 238 (254)
T ss_pred hheEEEEecCCCCCCCEEEECC
Confidence 2466776543333344444444
No 229
>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=38.09 E-value=1.7e+02 Score=25.07 Aligned_cols=114 Identities=18% Similarity=0.180 Sum_probs=61.5
Q ss_pred CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCC---ccCcc--
Q 015464 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVL---KEELK-- 216 (406)
Q Consensus 142 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~---l~~I~-- 216 (406)
++++.+.. +.++.+++.+|++|+++.+...+.+.. ..+. . ..........++.+++.. +++++
T Consensus 39 ~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~~~--~~~~--------~-~~~~~~~~~~~~~~~~~~~~~~~dl~g~ 106 (218)
T cd00134 39 KVKFVEVD-WDGLITALKSGKVDLIAAGMTITPERA--KQVD--------F-SDPYYKSGQVILVKKGSPIKSVKDLKGK 106 (218)
T ss_pred eEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHHHH--hhcc--------C-cccceeccEEEEEECCCCCCChHHhCCC
Confidence 56777777 899999999999999988762221110 0000 0 001112233445544432 23332
Q ss_pred EEEechHHHHHHHHHHhh-c-CCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 217 RVFSHPQALAQCEMTLSN-L-GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 217 ~VySHpqal~QC~~~L~~-~-~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
+|..- .. .-...++.+ . ....+.+.+...+++++..+. ..|++.....+..
T Consensus 107 ~i~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~--~d~~~~~~~~~~~ 159 (218)
T cd00134 107 KVAVQ-KG-STAEKYLKKALPEAKVVSYDDNAEALAALENGR--ADAVIVDEIALAA 159 (218)
T ss_pred EEEEE-cC-chHHHHHHHhCCcccEEEeCCHHHHHHHHHcCC--ccEEEeccHHHHH
Confidence 22221 11 112234444 2 356778888889999988763 4566766655544
No 230
>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=38.09 E-value=1.1e+02 Score=28.49 Aligned_cols=107 Identities=20% Similarity=0.186 Sum_probs=58.9
Q ss_pred HHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeee---eEeecCCCCCc---cC--ccEEEe-ch
Q 015464 152 EAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVN---HCLLGLPGVLK---EE--LKRVFS-HP 222 (406)
Q Consensus 152 ~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~---h~L~~~~g~~l---~~--I~~VyS-Hp 222 (406)
.|+-..|++|.+|+|++= .|.|.+++..+..-..|... .++++.++.+. ++ -++|.+ .|
T Consensus 50 ~Dip~yV~~G~aDlGI~G------------~D~l~E~~~~v~~~~dL~fg~crl~vA~p~~~~~~~~~~l~~~rIATkyp 117 (182)
T TIGR00070 50 QDIPTYVEHGAADLGITG------------YDVLLESGADVYELLDLGFGKCRLVLAVPQESDISSVEDLKGKRIATKYP 117 (182)
T ss_pred chhHHHHhCCCccEEEec------------chhhhhCCCCEEEEeecCcCceEEEEEEECCCCCCChHHhCCCEEEECCH
Confidence 478899999999999863 23333333222222223333 34445544322 22 135766 66
Q ss_pred HHHHHHHHHHhhcCC--eEEeccCHHHHHHHHHhcCCCCeEEE----cCHHhHHHcCCceee
Q 015464 223 QALAQCEMTLSNLGI--VRISADDTAGAAQMVASIGERDTGAV----ASAQAAEIYGLDILA 278 (406)
Q Consensus 223 qal~QC~~~L~~~~~--~~i~~~sTA~Aa~~v~~~~~~~~AAI----as~~aA~~ygL~il~ 278 (406)
. -.++|+++.++ +++..+..-++|-. - .-+-|| .+-..-+.+||++++
T Consensus 118 ~---i~~~~f~~~Gi~v~ii~l~GsvE~aP~---~--GlaD~IvDiv~TG~TL~~NgL~~ie 171 (182)
T TIGR00070 118 N---LARRYFEKKGIDVEIIKLNGSVELAPL---L--GLADAIVDIVSTGTTLRENGLRIIE 171 (182)
T ss_pred H---HHHHHHHHcCCeEEEEECcceeecccC---C--CceeEEEEEeCCHHHHHHCCCEEee
Confidence 5 45679998765 45555544444322 1 122244 255667789999995
No 231
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=38.05 E-value=6.3e+02 Score=29.06 Aligned_cols=129 Identities=11% Similarity=0.092 Sum_probs=76.8
Q ss_pred cCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH---HcCCceeecCccCCCCCeeEEEEEecCCCCCC----CCCCc
Q 015464 235 LGIVRISADDTAGAAQMVASIGERDTGAVASAQAAE---IYGLDILAEKIQDDDDNVTRFLILAREPIIAG----TDRPY 307 (406)
Q Consensus 235 ~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~---~ygL~il~~~I~d~~~N~TRF~vi~~~~~~~~----~~~~~ 307 (406)
++++.+..-|..+|.+++..+ |.+-...|++ .+|.+|.-.+..+....-|..- ......+. ....+
T Consensus 249 ~~a~~i~~ls~~e~~el~~~g-----~~v~~~~a~~~a~~~~i~i~v~~~~~~~~~gT~I~--~~~~~~~~v~~It~~~~ 321 (861)
T PRK08961 249 PDARLLTRLDYDEAQEIATTG-----AKVLHPRSIKPCRDAGIPMAILDTERPDLSGTSID--GDAEPVPGVKAISRKNG 321 (861)
T ss_pred CCceEecccCHHHHHHHHHCC-----CeEECHHHHHHHHHCCCCEEEEeCCCCCCCccEEe--CCCCCCCcceeEEEECC
Confidence 355677777888888776542 5666666654 5899998888765443444432 11111111 01122
Q ss_pred eEEEEEE---eCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCC-CcHHHHHH
Q 015464 308 KTSIVFT---LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASM-ADPRAQFA 383 (406)
Q Consensus 308 ktsi~f~---~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~-~~~~~~~a 383 (406)
-+-|.+. ..+.+|.+.++++.|+++|||+-.|.|-. ....|.++-.... .+..++.+
T Consensus 322 v~lItv~~~~~~~~~g~~a~if~~la~~~I~Vd~I~sse-------------------~sis~~i~~~~~~~~~~~~~~l 382 (861)
T PRK08961 322 IVLVSMETIGMWQQVGFLADVFTLFKKHGLSVDLISSSE-------------------TNVTVSLDPSENLVNTDVLAAL 382 (861)
T ss_pred EEEEEEecCCccccccHHHHHHHHHHHcCCeEEEEEcCC-------------------CEEEEEEccccccchHHHHHHH
Confidence 3333332 23679999999999999999999994321 3567777654321 12345555
Q ss_pred HHHHHH
Q 015464 384 LGHLQE 389 (406)
Q Consensus 384 l~~L~~ 389 (406)
+++|+.
T Consensus 383 ~~~l~~ 388 (861)
T PRK08961 383 SADLSQ 388 (861)
T ss_pred HHHHhh
Confidence 666653
No 232
>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=37.05 E-value=2.2e+02 Score=24.78 Aligned_cols=51 Identities=12% Similarity=0.158 Sum_probs=39.3
Q ss_pred cchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHH
Q 015464 319 PGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALG 385 (406)
Q Consensus 319 pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~ 385 (406)
+..+-.+++.+..+||.+|-|..--...+| -.||+-++++-+-..+...+.
T Consensus 67 ~~EV~pvi~aL~~~GI~vtAlHNH~l~e~P----------------rl~ymH~~~~gdp~~lA~~vr 117 (123)
T PF07485_consen 67 EDEVNPVISALRKNGIEVTALHNHWLFEQP----------------RLFYMHIWGVGDPAKLARKVR 117 (123)
T ss_pred HHHHHHHHHHHHHCCceEEEEecccccCCC----------------CEEEEEEEecCCHHHHHHHHH
Confidence 345777888899999999999999988877 389999999754444444433
No 233
>PRK13584 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=35.68 E-value=1.2e+02 Score=28.73 Aligned_cols=110 Identities=14% Similarity=0.120 Sum_probs=60.7
Q ss_pred HHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeee---eEeecCCCCCccCccEEEechHHHHH
Q 015464 151 FEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVN---HCLLGLPGVLKEELKRVFSHPQALAQ 227 (406)
Q Consensus 151 ~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~---h~L~~~~g~~l~~I~~VySHpqal~Q 227 (406)
..|+-..|+.|.+|+||+=-. .|.+.+-.+..-..|... .++++.|+. .+.++|.+..--+.
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 357889999999999998533 333222122222233333 345555442 35578887766554
Q ss_pred HHHHHhhcCC--eEEeccCHHHHHHHHHhcCCCC-eEEE-cCHHhHHHcCCceeec
Q 015464 228 CEMTLSNLGI--VRISADDTAGAAQMVASIGERD-TGAV-ASAQAAEIYGLDILAE 279 (406)
Q Consensus 228 C~~~L~~~~~--~~i~~~sTA~Aa~~v~~~~~~~-~AAI-as~~aA~~ygL~il~~ 279 (406)
++|+++.|+ +.+..+..-+.|=.+ +..+ .+=| .+-..-+.+||.++++
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 679988765 444444333332221 1111 1122 3566778999998854
No 234
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=35.67 E-value=4.4e+02 Score=25.96 Aligned_cols=144 Identities=14% Similarity=0.059 Sum_probs=74.2
Q ss_pred CccEEEEEcCCCcHH--HHH--HHHHCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEE
Q 015464 118 TKVRVAYQGLPGAYS--EAA--ARKAYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHI 192 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s--~~A--A~~~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I 192 (406)
+..+|++...-+.+- ... -.+.++++.+... .+.+++.+.+.+|++|+|+++-.....+... ...|.+..+.+
T Consensus 93 g~lrIg~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~~l 170 (327)
T PRK12680 93 GQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGI--AVPLYRWRRLV 170 (327)
T ss_pred eEEEEEecchhHHHhhHHHHHHHHHHCCCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCCcce--EEEeeccceEE
Confidence 456777765444321 111 1224566665443 3568999999999999999864321111111 11122333332
Q ss_pred EEEEEEeeeeEeecC-CCCCccCc---cEEEech-HHH-HHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEE
Q 015464 193 VGEVQLVVNHCLLGL-PGVLKEEL---KRVFSHP-QAL-AQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAV 263 (406)
Q Consensus 193 ~gE~~l~I~h~L~~~-~g~~l~~I---~~VySHp-qal-~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAI 263 (406)
.++..|-|... ....++++ .-|..-+ ... ....+|+...+. . ...++|.....++|..+ ...|+
T Consensus 171 ----~~~~~hpl~~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G---~Gia~ 243 (327)
T PRK12680 171 ----VVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAG---LGVGL 243 (327)
T ss_pred ----EEeCCChhhccCCCCCHHHHhcCCEEEecCCCchHHHHHHHHHHCCCCCcEEEEECCHHHHHHHHHcC---CCEEE
Confidence 34556666532 22333333 3332222 122 445667766443 2 34666777777777764 23566
Q ss_pred cCHHhHH
Q 015464 264 ASAQAAE 270 (406)
Q Consensus 264 as~~aA~ 270 (406)
.+..++.
T Consensus 244 lp~~~~~ 250 (327)
T PRK12680 244 LAEMAVN 250 (327)
T ss_pred eechhcc
Confidence 6666554
No 235
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=34.85 E-value=1.7e+02 Score=33.56 Aligned_cols=32 Identities=28% Similarity=0.314 Sum_probs=29.1
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee
Q 015464 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLT 337 (406)
Q Consensus 306 ~~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLt 337 (406)
+++|.|-+.-.|+||-|+.+.++|+..++++.
T Consensus 789 ~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~ 820 (867)
T COG2844 789 NDKTVLEVRALDRPGLLAALAGVFADLGLSLH 820 (867)
T ss_pred CCceEEEEEeCCcccHHHHHHHHHHhccccee
Confidence 45788888889999999999999999999987
No 236
>PRK12727 flagellar biosynthesis regulator FlhF; Provisional
Probab=34.50 E-value=72 Score=34.78 Aligned_cols=115 Identities=19% Similarity=0.120 Sum_probs=57.5
Q ss_pred CCCCCCCCchhhhhHHhhhcccchHHHHHhhhhcccccccccCCC-CCCchhhHHHHHhhhhccCCCCccccccccchhc
Q 015464 20 GLPDLVPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDDRP-YTPDVQSSEANERSQDSQSSGFHKDLNLLPTLVY 98 (406)
Q Consensus 20 ~~~~~~~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~~~~v~K~-~~P~RE~a~i~~rl~~~~~~~l~~d~i~l~~~I~ 98 (406)
+.|.....|.++|.|| .. |.+||.+ ++..... +.. -.|-|. .++++|. ..++.++++. .++
T Consensus 254 ~~~~~~~~l~~m~~El----~~---lR~lle~--q~~~l~~-~~~~~~P~~~--~l~~~L~---~~Gvs~~la~---~L~ 315 (559)
T PRK12727 254 PAPQNDEELKQLRGEL----AL---MRQMIER--EMNRLTD-ERLRGSPVRA--QALELMD---DYGFDAGLTR---DVA 315 (559)
T ss_pred CCCCCHHHHHHHHHHH----HH---HHHHHHH--HHHhhhh-hhhccChHHH--HHHHHHH---HCCCCHHHHH---HHH
Confidence 4556667788899999 44 6666766 4433221 211 344443 3345553 4556666655 555
Q ss_pred cccccccccc--------------ccCCCCCCCCccEEEEEcCCCc-----HHHHHHHHH--C-C-CCceeccCCHH
Q 015464 99 GQIAEPLSIM--------------ELSSSPDDGTKVRVAYQGLPGA-----YSEAAARKA--Y-P-KCETVPCDQFE 152 (406)
Q Consensus 99 ReImr~~~~~--------------eis~~~~~~~~~~Va~lGp~Gs-----~s~~AA~~~--f-~-~~~~~~~~s~~ 152 (406)
.++....... .+..+........|++.||.|+ ...+|++.. . + .+-++..+++.
T Consensus 316 ~~l~~~~~~~~~~~~l~~~L~~~l~v~~~~~l~~G~vIaLVGPtGvGKTTtaakLAa~la~~~~gkkVaLIdtDtyR 392 (559)
T PRK12727 316 MQIPADTELHRGRGLMLGLLSKRLPVAPVDPLERGGVIALVGPTGAGKTTTIAKLAQRFAAQHAPRDVALVTTDTQR 392 (559)
T ss_pred HhhhcccchhhHHHHHHHHHHHhcCcCccccccCCCEEEEECCCCCCHHHHHHHHHHHHHHhcCCCceEEEeccccc
Confidence 5543211000 0111112224567899999885 223443311 1 2 35566666654
No 237
>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=34.44 E-value=3.5e+02 Score=24.36 Aligned_cols=106 Identities=14% Similarity=0.026 Sum_probs=66.6
Q ss_pred CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCcc---Cc--c
Q 015464 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKE---EL--K 216 (406)
Q Consensus 142 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~---~I--~ 216 (406)
+++++...+..++++++.+|++|+++......+ ...-...++.+++...-.-...|+++++..+. |+ |
T Consensus 22 ~ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~-------~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DLkGK 94 (216)
T PF09084_consen 22 DVEIVFFGGGGDVLEALASGKADIAVAGPDAVL-------FARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADLKGK 94 (216)
T ss_dssp EEEEEEESSHHHHHHHHHTTSHSEEEEECHHHH-------HHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGGTTS
T ss_pred EEEEEEecChhHHHHHHhcCCceEEeccchHHH-------HHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHhCCC
Confidence 578899999999999999999999987654222 11112346888887765555778877664333 33 3
Q ss_pred EEEech--HHHHHHHHHHhhcC-----CeEEeccCHHHHHHHHHhc
Q 015464 217 RVFSHP--QALAQCEMTLSNLG-----IVRISADDTAGAAQMVASI 255 (406)
Q Consensus 217 ~VySHp--qal~QC~~~L~~~~-----~~~i~~~sTA~Aa~~v~~~ 255 (406)
+|...+ .....-+.+|++.+ ++.+... ....+..+.++
T Consensus 95 ~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~-~~~~~~al~~g 139 (216)
T PF09084_consen 95 KIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLG-PPELAQALLSG 139 (216)
T ss_dssp EEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTT
T ss_pred EEEEecCcchhHHHHHHHHHhccccccceeeeee-hhhhhhhhhcC
Confidence 666666 34445567777644 3444443 45555555554
No 238
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=34.28 E-value=3e+02 Score=25.83 Aligned_cols=43 Identities=9% Similarity=0.189 Sum_probs=29.7
Q ss_pred CCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEeee
Q 015464 128 PGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIE 171 (406)
Q Consensus 128 ~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPIE 171 (406)
.-.+-+++++..--++++++. +|..+++++++|++|+++-++.
T Consensus 52 ~vdi~~~ia~~lg~~i~~~~~-pw~~~~~~l~~g~~D~~~~~~~ 94 (259)
T PRK15437 52 DIDLAKELCKRINTQCTFVEN-PLDALIPSLKAKKIDAIMSSLS 94 (259)
T ss_pred eHHHHHHHHHHcCCceEEEeC-CHHHHHHHHHCCCCCEEEecCC
Confidence 333444555533226777775 5999999999999998776664
No 239
>PRK09224 threonine dehydratase; Reviewed
Probab=34.20 E-value=1e+02 Score=33.10 Aligned_cols=35 Identities=26% Similarity=0.392 Sum_probs=30.8
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEee
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESR 342 (406)
+..-+.|..|++||+|.+.|+.+. -+-|+|.+|=|
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 455678899999999999999887 78999999998
No 240
>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=34.18 E-value=3.9e+02 Score=24.87 Aligned_cols=119 Identities=21% Similarity=0.135 Sum_probs=61.8
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc--
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I-- 215 (406)
.++++++.- ..+..+.++.+.+|++|+|++.-..+..+.. ...|.+..+.++ .+-+|-|...+..+++++
T Consensus 109 ~~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~lv----~s~~~pl~~~~~i~~~~L~~ 181 (279)
T TIGR03339 109 RYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLD---RVVLGNDPLVAV----VHRQHPLAERESVTLEELAG 181 (279)
T ss_pred HCCCcEEEEEECCHHHHHHHHHcCCCcEEEEecccCCCceE---EEEcCCceEEEE----ECCCCccccCCCcCHHHHhC
Confidence 356665543 3577899999999999999985433322211 111222233222 122333332222333333
Q ss_pred -cEEEech--HHHHHHHHHHhhcCC---eEEeccCHHHHHHHHHhcCCCCeEEEcCHH
Q 015464 216 -KRVFSHP--QALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQ 267 (406)
Q Consensus 216 -~~VySHp--qal~QC~~~L~~~~~---~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~ 267 (406)
.-|...+ ........|+.+.+. ....++|...+.+++..+ ...++.+..
T Consensus 182 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~ 236 (279)
T TIGR03339 182 QPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAG---LGVSVVSAA 236 (279)
T ss_pred CCeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcC---CCEEEcchh
Confidence 3333222 123456677766432 234577777777777764 235666654
No 241
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=33.92 E-value=1.2e+02 Score=22.88 Aligned_cols=62 Identities=23% Similarity=0.267 Sum_probs=45.2
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCc-HHHHHHHHHHHHc
Q 015464 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMAD-PRAQFALGHLQEF 390 (406)
Q Consensus 312 ~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~-~~~~~al~~L~~~ 390 (406)
-|.+.+..-++..+|.-.-..++.-..|...|.. ..|.|.|+-.|+.+- .-+.+|++.|.+.
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 4566666778899999998899888888884422 468999999988532 3556777777654
No 242
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=33.86 E-value=74 Score=31.41 Aligned_cols=53 Identities=36% Similarity=0.293 Sum_probs=38.2
Q ss_pred CccEEEEEcCCCcHHHHHHHHHCCCCceeccCCHHHHHHHHHcCCccEEEEeeec
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIEN 172 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPIEN 172 (406)
...+||+-|+-- -+++..|.+++..++++. -|+++..||.+|++|.|++--|.
T Consensus 94 ~~~rvavpG~~T-TA~lL~rl~~p~~~~V~m-~fdeI~~Avl~G~VDaGvlIHE~ 146 (272)
T COG2107 94 KGKRVAVPGEMT-TAALLFRLAYPKAEIVYM-PFDEIIPAVLEGKVDAGVLIHEE 146 (272)
T ss_pred ccceEecCCccc-HHHHHHHHhCCCceEEEe-eHHHHHHHHHcCCCccceEEeeh
Confidence 456787755433 235556666677666554 58999999999999999997764
No 243
>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=33.29 E-value=3e+02 Score=23.30 Aligned_cols=123 Identities=12% Similarity=0.037 Sum_probs=61.1
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecc--cccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccC-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENS--VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEE- 214 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS--~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~- 214 (406)
.++++++.-. .+..+..+.+.+|++|+|+...... ..+... ..|.+.++.+ ..+-.|-+......++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~l~~---~~l~~~~~~~----v~~~~hp~~~~~~~~~~~L 97 (199)
T cd08416 25 RRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDFEV---VPLFEDDIFL----AVPATSPLAASSEIDLRDL 97 (199)
T ss_pred hCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCCCCCeEE---EEeecceEEE----EECCCCcccccCccCHHHh
Confidence 4566654433 3556788999999999999864321 111111 1112222222 223344443322222333
Q ss_pred --ccEEE-echHH-HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 215 --LKRVF-SHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 215 --I~~Vy-SHpqa-l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
..-|. +.... .....+++...+. . ...++|...+.+++..+ ...++++...++.
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 2234556655432 2 34566777777777764 3467777765543
No 244
>cd08465 PBP2_ToxR The C-terminal substrate binding domain of LysR-type transcriptional regulator ToxR regulates the expression of the toxoflavin biosynthesis genes; contains the type 2 periplasmic bindinig fold. In soil bacterium Burkholderia glumae, ToxR regulates the toxABCDE and toxFGHI operons in the presence of toxoflavin as a coinducer. Additionally, the expression of both operons requires a transcriptional activator, ToxJ, whose expression is regulated by the TofI or TofR quorum-sensing system. The biosynthesis of toxoflavin is suggested to be synthesized in a pathway common to the synthesis of riboflavin. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After
Probab=33.05 E-value=3.2e+02 Score=23.58 Aligned_cols=33 Identities=18% Similarity=0.032 Sum_probs=24.9
Q ss_pred HCCCCcee-ccCCHHHHHHHHHcCCccEEEEeee
Q 015464 139 AYPKCETV-PCDQFEAAFKAVELWLVDKAVLPIE 171 (406)
Q Consensus 139 ~f~~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIE 171 (406)
.++++++. ...+..++.+.+.+|++|+|+...+
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~ 58 (200)
T cd08465 25 EAPGIDLAVSQASREAMLAQVADGEIDLALGVFP 58 (200)
T ss_pred HCCCcEEEEecCChHhHHHHHHCCCccEEEeccc
Confidence 35666653 3357889999999999999997543
No 245
>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=32.35 E-value=2.2e+02 Score=21.53 Aligned_cols=27 Identities=22% Similarity=0.348 Sum_probs=23.6
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
+.+.+|.+.++++.|++++||+-.|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~~ 37 (80)
T cd04921 11 MVGVPGIAARIFSALARAGINVILISQ 37 (80)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEe
Confidence 456799999999999999999988854
No 246
>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=31.80 E-value=89 Score=27.01 Aligned_cols=121 Identities=16% Similarity=0.066 Sum_probs=61.6
Q ss_pred HCCCCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc--
Q 015464 139 AYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK-- 216 (406)
Q Consensus 139 ~f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~-- 216 (406)
.|+++++.......+..+.+.+|++|+|++.......+.. ...|.+..+.+ ..+-+|-|... ..+++++.
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 4566655444322278899999999999984322111111 11122223322 22344544332 12334333
Q ss_pred -EEE-echH-HHHHHHHHHhhcCC---eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 217 -RVF-SHPQ-ALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 217 -~Vy-SHpq-al~QC~~~L~~~~~---~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
-|. +... .-.+..+|+.+.+. ....++|...+..+++.+ ...|+.+...++
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 153 (200)
T cd08460 97 PHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGS---DLIALVPERVTA 153 (200)
T ss_pred CCEEEecCCCCcchHHHHHHhcCCceeEEEEcCcHHHHHHHHhcC---CHHHHHHHHHHH
Confidence 222 2111 12346677766443 234577777777887764 346777776654
No 247
>PRK06526 transposase; Provisional
Probab=31.49 E-value=91 Score=30.26 Aligned_cols=115 Identities=19% Similarity=0.122 Sum_probs=54.5
Q ss_pred hhhHHHHHhhhhccCCCCccccccccchhcccccccccccccCCCCCCCCccEEEEEcCCCcH-HHHHHH---HHCCCCc
Q 015464 69 VQSSEANERSQDSQSSGFHKDLNLLPTLVYGQIAEPLSIMELSSSPDDGTKVRVAYQGLPGAY-SEAAAR---KAYPKCE 144 (406)
Q Consensus 69 RE~a~i~~rl~~~~~~~l~~d~i~l~~~I~ReImr~~~~~eis~~~~~~~~~~Va~lGp~Gs~-s~~AA~---~~f~~~~ 144 (406)
|+...+.+|+..+.+.. +..+..+...-.+.+.+. ...+..++........|.+.||.|+- ||+|.- .......
T Consensus 50 R~~~~~~~~lk~a~~p~-~~~le~fd~~~~~~~~~~-~~~~l~~~~fi~~~~nlll~Gp~GtGKThLa~al~~~a~~~g~ 127 (254)
T PRK06526 50 RESHGGEGRIRAARFPA-RKSLEEFDFDHQRSLKRD-TIAHLGTLDFVTGKENVVFLGPPGTGKTHLAIGLGIRACQAGH 127 (254)
T ss_pred HHHHHHHHHHHhCCCCC-CCChhhccCccCCCcchH-HHHHHhcCchhhcCceEEEEeCCCCchHHHHHHHHHHHHHCCC
Confidence 55455555555444332 234444332323333222 11223344333345678999999984 565531 1111112
Q ss_pred eeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEE
Q 015464 145 TVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEV 196 (406)
Q Consensus 145 ~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~ 196 (406)
-+.+.+..+.++.+.... ..|.....+.-+.+.++-|+.|+
T Consensus 128 ~v~f~t~~~l~~~l~~~~-----------~~~~~~~~l~~l~~~dlLIIDD~ 168 (254)
T PRK06526 128 RVLFATAAQWVARLAAAH-----------HAGRLQAELVKLGRYPLLIVDEV 168 (254)
T ss_pred chhhhhHHHHHHHHHHHH-----------hcCcHHHHHHHhccCCEEEEccc
Confidence 234456666666665331 23444444444455566666555
No 248
>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=31.27 E-value=3.2e+02 Score=23.00 Aligned_cols=33 Identities=18% Similarity=0.054 Sum_probs=24.1
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeee
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIE 171 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIE 171 (406)
.++++++... .+..+..+.+.+|++|+|++...
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (197)
T cd08449 25 QYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFA 58 (197)
T ss_pred HCCCeEEEEEECCHHHHHHHHhCCCccEEEeccc
Confidence 3566654433 35788899999999999997543
No 249
>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=30.84 E-value=3.5e+02 Score=23.31 Aligned_cols=122 Identities=16% Similarity=0.049 Sum_probs=60.4
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.++++++.-. .+..++.+.+.+|++|+|+..-.-.....+. ...|.+.++.++ .+-+|.+......+++++.
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 4676665433 4677899999999999999752210111111 111222233222 2334444332223333332
Q ss_pred -EEEechH--HH-HHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015464 217 -RVFSHPQ--AL-AQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAA 269 (406)
Q Consensus 217 -~VySHpq--al-~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA 269 (406)
...+++. .. .....|+.+.+. . ...+++.....++++.+ ...|+.+...+
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~~p~~~~ 155 (198)
T cd08443 99 YPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLG---LGVGVIASMAY 155 (198)
T ss_pred CCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CcEEEeecccc
Confidence 2223332 22 233445555443 2 34567777777777764 23566666544
No 250
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=30.75 E-value=4.6e+02 Score=24.61 Aligned_cols=113 Identities=15% Similarity=0.154 Sum_probs=59.9
Q ss_pred CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCC----CccCcc-
Q 015464 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV----LKEELK- 216 (406)
Q Consensus 142 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~----~l~~I~- 216 (406)
.+++++ .+|.++++++..|++|+++-++.-+.+-. ..+...+-+ +.....++++++. +++++.
T Consensus 66 ~~~~~~-~~~~~~~~~l~~g~~Di~~~~~~~t~eR~----------~~~~fs~p~-~~~~~~~~~~~~~~~~~~~~dl~g 133 (260)
T PRK15010 66 KCTWVA-SDFDALIPSLKAKKIDAIISSLSITDKRQ----------QEIAFSDKL-YAADSRLIAAKGSPIQPTLDSLKG 133 (260)
T ss_pred ceEEEe-CCHHHHHHHHHCCCCCEEEecCcCCHHHH----------hhcccccce-EeccEEEEEECCCCCCCChhHcCC
Confidence 566666 47999999999999998775443221111 001111111 1223444444432 122332
Q ss_pred -EEEechHHHHHHHHHHh----hcCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 217 -RVFSHPQALAQCEMTLS----NLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 217 -~VySHpqal~QC~~~L~----~~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
+|--..-... ..|+. ..++..+.+.+..++.+++..+. -.|.|++...+.
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 3333222111 12333 23567777888888888888753 457777766553
No 251
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=30.47 E-value=5e+02 Score=25.00 Aligned_cols=121 Identities=12% Similarity=0.011 Sum_probs=58.9
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccc--hhccCCeEEEEEEEEeeeeEeecCCCCCccCc
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~D--lL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I 215 (406)
.++++++.- ..+..++.+.+.+|++|+|+.+-.... ...++ .|.+..+ -+.++..|-|......+++++
T Consensus 118 ~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~----~~~l~~~~l~~~~~----~~~~~~~~pl~~~~~~~~~~L 189 (309)
T PRK12682 118 RYPKVNLSLHQGSPDEIARMVISGEADIGIATESLAD----DPDLATLPCYDWQH----AVIVPPDHPLAQEERITLEDL 189 (309)
T ss_pred hCCCeEEEEecCCHHHHHHHHHcCCccEEEecCcccC----CCcceEEEeeeeeE----EEEecCCCccccCCCcCHHHH
Confidence 356666543 345688999999999999997532110 11111 0111111 122333343332212223333
Q ss_pred ---cEEE-echHH-HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 ---KRVF-SHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 ---~~Vy-SHpqa-l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
.-|. +.... ..+-..|+...+. + ...++|.....++|..+. ..++.+...++
T Consensus 190 ~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~---Gi~~lp~~~~~ 249 (309)
T PRK12682 190 AEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGL---GVGIVAEMAYR 249 (309)
T ss_pred hcCCceeeCCCccHHHHHHHHHHHcCCCCcEEEEeCCHHHHHHHHHhCC---ceEEehhhhhh
Confidence 2222 11111 1233445555443 2 346778888888888752 35666665543
No 252
>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=30.44 E-value=3.3e+02 Score=22.83 Aligned_cols=122 Identities=18% Similarity=0.142 Sum_probs=61.5
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccC---
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEE--- 214 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~--- 214 (406)
.++++++.. ..+..++.+.+.+|++|+|++.......+... ..|.+..+.++ .+-+|-+......++++
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 356655432 34567889999999999999864432222111 11223333332 22233333222222333
Q ss_pred ccEEEechH--HHHHHHHHHhhcC-----C-eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 215 LKRVFSHPQ--ALAQCEMTLSNLG-----I-VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 215 I~~VySHpq--al~QC~~~L~~~~-----~-~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
..-|...+. -..+..+|+...+ . ....+++...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08420 98 EPWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAG---LGISILSRLAVR 158 (201)
T ss_pred CCEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcC---CCEEEeeHHHHH
Confidence 333332221 1234555665321 2 234567777777777764 357788777654
No 253
>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=30.18 E-value=3.3e+02 Score=22.84 Aligned_cols=32 Identities=19% Similarity=0.007 Sum_probs=23.6
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEee
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPI 170 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPI 170 (406)
.++++++.- ..+..++.+.+.+|++|+|++.-
T Consensus 25 ~~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~~ 57 (197)
T cd08438 25 RYPNIELELVEYGGKKVEQAVLNGELDVGITVL 57 (197)
T ss_pred HCcCeEEEEEEcCcHHHHHHHHcCCCCEEEEec
Confidence 356665433 34667889999999999999753
No 254
>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=30.11 E-value=3.4e+02 Score=22.96 Aligned_cols=122 Identities=16% Similarity=0.074 Sum_probs=60.3
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCC-CCCccCcc
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLP-GVLKEELK 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~-g~~l~~I~ 216 (406)
.++++.+.-. .+..++.+.+.+|++|+++..-.....+... ..|.+..+.++ .+-.|-+.... ..+++++.
T Consensus 26 ~~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~pl~~~~~~~~~~dL~ 98 (197)
T cd08425 26 RYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDA---QPLFDERLALV----VGATHPLAQRRTALTLDDLA 98 (197)
T ss_pred HCCCcEEEEEECcHHHHHHHHHcCCccEEEEecCCCCCCcEE---EEeccccEEEE----ecCCCchhHhcccCCHHHHh
Confidence 3566654433 4567899999999999999764322221111 11222222222 22233332221 12333332
Q ss_pred ---EEE-ec-hHHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 217 ---RVF-SH-PQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 217 ---~Vy-SH-pqal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
-|. .. ........+|+.+.+. + ...++|...+.++++.+ ...|+.+...++
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08425 99 AEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRG---RLATILPDAIAR 157 (197)
T ss_pred cCCcEecCCCccHHHHHHHHHHHcCCCeeeEEeeCcHHHHHHHHhcC---CcEEeechhhhc
Confidence 222 11 1122345666666443 2 23567777777777764 346777766543
No 255
>PRK06635 aspartate kinase; Reviewed
Probab=29.99 E-value=1.8e+02 Score=29.93 Aligned_cols=29 Identities=21% Similarity=0.364 Sum_probs=25.5
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEeee
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIESRP 343 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIESRP 343 (406)
..++||.|.++++.|+++|||+-.|.+-.
T Consensus 270 ~~~~~g~l~~i~~~L~~~~I~i~~is~s~ 298 (404)
T PRK06635 270 VPDKPGIAAQIFGALAEANINVDMIVQNV 298 (404)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEecC
Confidence 56889999999999999999999885543
No 256
>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=29.92 E-value=3.4e+02 Score=22.91 Aligned_cols=121 Identities=17% Similarity=0.160 Sum_probs=61.6
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeeccc--ccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSV--GGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~--~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I 215 (406)
.++++.+... .+..+..+.+.+|++|+|+....... .+.. ...|.+.++.++. +-+|-+.. + .+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~---~~~l~~~~~~~v~----~~~~~~~~-~-~~~~~l 95 (201)
T cd08418 25 QFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELI---SEPLFESDFVVVA----RKDHPLQG-A-RSLEEL 95 (201)
T ss_pred HCCCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCCCCccee---EEeecCCceEEEe----CCCCcccc-C-CCHHHH
Confidence 3566654333 45678999999999999998532211 1111 1112233333322 12222211 1 123333
Q ss_pred c---EEEec--hHHHHHHHHHHhhcC--Ce-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 216 K---RVFSH--PQALAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 216 ~---~VySH--pqal~QC~~~L~~~~--~~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
. -|... ......+.+++...+ .. ...++|...+..+|+.+ ...||.+...++.
T Consensus 96 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 156 (201)
T cd08418 96 LDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKA---DFLTILSRDMGRG 156 (201)
T ss_pred cCCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhC---CEEEEeEHHHhhh
Confidence 2 23221 122344556666533 22 34567777777888765 3578888776654
No 257
>PRK05007 PII uridylyl-transferase; Provisional
Probab=29.71 E-value=2.3e+02 Score=32.76 Aligned_cols=34 Identities=15% Similarity=0.160 Sum_probs=29.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeE
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIE 340 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIE 340 (406)
+-|.|.+..+|+||-|+++.++|+.+|+|+..-.
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 3577778889999999999999999999998443
No 258
>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=29.31 E-value=3.5e+02 Score=22.81 Aligned_cols=122 Identities=19% Similarity=0.170 Sum_probs=59.0
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecc-cccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENS-VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL- 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS-~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I- 215 (406)
.++++.+... .+..++.+.+.+|++|+|+++.... ..+... ..|.+..+.++ .+.+|-+......+++++
T Consensus 26 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~~l~~~~~~~~~dL~ 98 (199)
T cd08451 26 AYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVL---ELLLEEPMLVA----LPAGHPLARERSIPLAALA 98 (199)
T ss_pred HCCCcEEEEecCChHHHHHHHHCCCccEEEEecCCCCCCceeE---EEeecccEEEE----ecCCCCCcccCccCHHHhc
Confidence 4566654333 3567889999999999999864322 111111 11222233332 233444443222233333
Q ss_pred --cEEE-echH---HHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 --KRVF-SHPQ---ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 --~~Vy-SHpq---al~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
.-|. +... ...+-..|+.+.+. . ...++|...+.+.+..+ ...++.+...++
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 159 (199)
T cd08451 99 DEPFILFPRPVGPGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAG---LGVSIVPASMRQ 159 (199)
T ss_pred CCCEEEecCCcChhHHHHHHHHHHHcCCceeeEEehhhHHHHHHHHHcC---CCEEEechHHHh
Confidence 2232 1111 11233344544343 2 23455666666666654 346777776665
No 259
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=29.29 E-value=2.4e+02 Score=25.90 Aligned_cols=62 Identities=19% Similarity=0.164 Sum_probs=42.9
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHH
Q 015464 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQ 388 (406)
Q Consensus 309 tsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~ 388 (406)
..+.-+..+.||-|..+++..++|||++--+-|+----. .+=..+|=+++... .+++.+|+
T Consensus 96 iei~~~~~~~pgi~A~V~~~iak~gi~Irqi~~~dpe~~---------------~e~~l~IVte~~iP----~~li~el~ 156 (167)
T COG2150 96 IEIYPEDARYPGILAGVASLIAKRGISIRQIISEDPELQ---------------EEPKLTIVTERPIP----GDLIDELK 156 (167)
T ss_pred EEEEeccCCCccHHHHHHHHHHHcCceEEEEecCCcccC---------------CCceEEEEEeccCC----HHHHHHHh
Confidence 345555668999999999999999999999988843111 12355666676543 35666665
Q ss_pred H
Q 015464 389 E 389 (406)
Q Consensus 389 ~ 389 (406)
+
T Consensus 157 ~ 157 (167)
T COG2150 157 K 157 (167)
T ss_pred c
Confidence 4
No 260
>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=28.74 E-value=4.8e+02 Score=24.76 Aligned_cols=112 Identities=10% Similarity=-0.012 Sum_probs=60.6
Q ss_pred eeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCC-----CccCc----
Q 015464 145 TVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV-----LKEEL---- 215 (406)
Q Consensus 145 ~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~-----~l~~I---- 215 (406)
.....+|.+++..+.+|++|+.+..+.-+-+.. +.+.-+.- ++.....++.+++. +++++
T Consensus 75 ~~~~~~w~~~~~~l~~G~~Di~~~~~~~t~eR~-----~~~~fs~p------y~~~~~~~~~~~~~~~~i~~~~dl~~~~ 143 (275)
T TIGR02995 75 NASITEYGALIPGLQAGRFDAIAAGLFIKPERC-----KQVAFTQP------ILCDAEALLVKKGNPKGLKSYKDIAKNP 143 (275)
T ss_pred eeccCCHHHHHHHHHCCCcCEEeecccCCHHHH-----hccccccc------eeecceeEEEECCCCCCCCCHHHhccCC
Confidence 356678999999999999998665432111111 00000010 11112334444332 22333
Q ss_pred -cEEEechHHHHHHHHHHhhc---CCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 216 -KRVFSHPQALAQCEMTLSNL---GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 216 -~~VySHpqal~QC~~~L~~~---~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
++|-....... .+||++. ..+++.+.|..++.+.+..+. -.++|+....+..
T Consensus 144 g~~Igv~~g~~~--~~~l~~~~~~~~~i~~~~~~~~~i~~L~~gr--vDa~i~d~~~~~~ 199 (275)
T TIGR02995 144 DAKIAAPGGGTE--EKLAREAGVKREQIIVVPDGQSGLKMVQDGR--ADAYSLTVLTIND 199 (275)
T ss_pred CceEEEeCCcHH--HHHHHHcCCChhhEEEeCCHHHHHHHHHcCC--CCEEecChHHHHH
Confidence 24433332221 3466552 346778889999999999863 4578887765543
No 261
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=28.38 E-value=92 Score=30.43 Aligned_cols=52 Identities=23% Similarity=0.201 Sum_probs=39.4
Q ss_pred ccEEEEE----cCCCcHHHHHHHHHCC-----CCceeccCCHHHHHHHHHcCCccEEEEeee
Q 015464 119 KVRVAYQ----GLPGAYSEAAARKAYP-----KCETVPCDQFEAAFKAVELWLVDKAVLPIE 171 (406)
Q Consensus 119 ~~~Va~l----Gp~Gs~s~~AA~~~f~-----~~~~~~~~s~~~v~~aV~~g~~d~gvVPIE 171 (406)
..++++- .|.|.|+.++-. ..| ..+++...+..+++..|+.|++|+|+|=..
T Consensus 135 ~~~lai~~p~~~P~G~ya~~~l~-~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~s 195 (258)
T COG0725 135 DVRLAIGDPKTVPAGKYAKEALE-LLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYVS 195 (258)
T ss_pred CcEEEecCCCCCCchHHHHHHHH-HhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEEE
Confidence 4566665 367888887654 333 236788889999999999999999999654
No 262
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=28.30 E-value=1.9e+02 Score=30.40 Aligned_cols=71 Identities=21% Similarity=0.327 Sum_probs=52.9
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHHHHHHHc-
Q 015464 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFALGHLQEF- 390 (406)
Q Consensus 312 ~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al~~L~~~- 390 (406)
-+...|+-|-.-++|..+..++|||..||--|.. ..|++|.. ++-..++.++.+|+..
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 3456789999999999999999999999986643 45677743 4556778888888754
Q ss_pred -CCceEEEccccCC
Q 015464 391 -ATFLRVLGCYPMD 403 (406)
Q Consensus 391 -~~~vrvLGsYp~~ 403 (406)
...||..+--|..
T Consensus 63 GV~~vr~V~~mPse 76 (511)
T COG3283 63 GVTDVRTVPWMPSE 76 (511)
T ss_pred CccceeeecCCcch
Confidence 4457777666654
No 263
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=28.28 E-value=3.8e+02 Score=22.97 Aligned_cols=122 Identities=14% Similarity=0.024 Sum_probs=62.2
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEeeec-ccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCcc---
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIEN-SVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKE--- 213 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIEN-S~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~--- 213 (406)
.|+++.+.- ..+..++.+.+.+|++|+|+..-.. ...+.. ...|.+..+. +..+.+|-+...+..+++
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~~l~~~~~~----~~~~~~hpl~~~~~~~~~~l~ 97 (198)
T cd08444 25 QFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPELV---SFPYYDWHHH----IIVPVGHPLESITPLTIETIA 97 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEeccccCCCcCcE---Eeecccccee----EEecCCCccccCCCcCHHHHh
Confidence 467665433 3466788999999999999974210 011111 1111122221 233444554432222333
Q ss_pred CccEEEechH-H-HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 214 ELKRVFSHPQ-A-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 214 ~I~~VySHpq-a-l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
+..-|.-++. . -.++..|+.+.+. + ...++|...+.+++..+ ...++.+...+.
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08444 98 KWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLG---MGIGIVAEMAFE 156 (198)
T ss_pred CCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcC---CcEEeccHHHHh
Confidence 3334433332 2 2345667766443 2 34567777777777764 346777766554
No 264
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=28.18 E-value=1.8e+02 Score=27.44 Aligned_cols=50 Identities=16% Similarity=0.188 Sum_probs=35.9
Q ss_pred CccEEEEEcCCCcHHHHHHHHHCC--CCceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAYP--KCETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f~--~~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
...+|++. .|+..+......+. +..++...+.++.+++|..|++|+.+..
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 34578875 66654444433332 3567788999999999999999998765
No 265
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=28.09 E-value=4.3e+02 Score=25.23 Aligned_cols=118 Identities=15% Similarity=-0.037 Sum_probs=57.1
Q ss_pred CCCCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc---c
Q 015464 140 YPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL---K 216 (406)
Q Consensus 140 f~~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I---~ 216 (406)
++++.+.-..+ +..+.+.+|++|+|++..+....|.... .|.+..+.++ .+-.|.+......+++++ .
T Consensus 120 ~p~i~i~l~~~--~~~~~l~~g~~Dl~i~~~~~~~~~l~~~---~l~~~~~~~~----~~~~~~~~~~~~i~~~dL~~~p 190 (297)
T PRK11139 120 HPDIDVRLKAV--DRLEDFLRDDVDVAIRYGRGNWPGLRVE---KLLDEYLLPV----CSPALLNGGKPLKTPEDLARHT 190 (297)
T ss_pred CCCceEEEEeC--CChhhhccCCCCEEEEeCCCCCCCceEE---EeccceeEEE----eCHHHhcccCCCCCHHHhhcCc
Confidence 45544333222 2346778899999998765433332221 1222233322 233343332222333333 2
Q ss_pred EEEechHHHHHHHHHHhhcCC-----e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 217 RVFSHPQALAQCEMTLSNLGI-----V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 217 ~VySHpqal~QC~~~L~~~~~-----~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
-|...+ ......|+...+. . .+.+++...+...|..+ ...|+.+...++.
T Consensus 191 ~i~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 246 (297)
T PRK11139 191 LLHDDS--REDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG---QGVALGNRVLAQP 246 (297)
T ss_pred eEeecC--cccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhC---CCeEecchhhhHH
Confidence 333222 2345567765322 2 23456666666666653 3467777766654
No 266
>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=27.76 E-value=2.4e+02 Score=32.21 Aligned_cols=33 Identities=15% Similarity=0.301 Sum_probs=28.9
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeee
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKI 339 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkI 339 (406)
.-|-|.+..+|+||-|+++.++|+.+|+|+..=
T Consensus 667 ~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A 699 (850)
T TIGR01693 667 GGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDA 699 (850)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEE
Confidence 457788888999999999999999999999843
No 267
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=27.46 E-value=1.2e+02 Score=29.95 Aligned_cols=49 Identities=14% Similarity=0.133 Sum_probs=36.6
Q ss_pred ccEEEEEcCCCcHHHHHHHHHCC----CCceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 119 KVRVAYQGLPGAYSEAAARKAYP----KCETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~f~----~~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
..+|+++ .|+.++...+.+.. +..++.+.+.++++++|.+|++|+.+..
T Consensus 153 Gk~V~v~--~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~d 205 (302)
T PRK10797 153 GKAVVVT--SGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMD 205 (302)
T ss_pred CCEEEEe--CCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEcc
Confidence 4578775 66655555554432 3678899999999999999999998754
No 268
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=26.73 E-value=5.1e+02 Score=24.05 Aligned_cols=116 Identities=15% Similarity=0.153 Sum_probs=65.8
Q ss_pred CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhc-cCCeEEEEEEEE-----eeeeEeecCCCC---Cc
Q 015464 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL-RHRLHIVGEVQL-----VVNHCLLGLPGV---LK 212 (406)
Q Consensus 142 ~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~-~~~l~I~gE~~l-----~I~h~L~~~~g~---~l 212 (406)
.+++....++.+..+++.+|++|+++.+-. .+-.+. +.++..++...- ...-.++++++. ++
T Consensus 30 ~v~~~~~~~~~~~~~~l~~g~~D~~~~~~~---------~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds~i~~l 100 (243)
T PF12974_consen 30 PVELVPADDYAEFIEALRSGEIDLAFMGPL---------PYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADSPITSL 100 (243)
T ss_dssp EEEEE--SSHHHHHHHHHTTS-SEEE--HH---------HHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTSS--SH
T ss_pred CEEEEEcCCHHHHHHHHHcCCccEEEECcH---------HHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCCCCCCh
Confidence 478899999999999999999999988621 222222 346666665554 333345566554 34
Q ss_pred cCc---cEEEechHH---HHHHHHHH-hhcC------CeEEeccCHHHHHHHHHhcCCCCeEEEcCHH
Q 015464 213 EEL---KRVFSHPQA---LAQCEMTL-SNLG------IVRISADDTAGAAQMVASIGERDTGAVASAQ 267 (406)
Q Consensus 213 ~~I---~~VySHpqa---l~QC~~~L-~~~~------~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~ 267 (406)
+|+ +-.+..|.. .--.+.+| ++.| ...+.+.+-..++..|..+ .-+.|++.+..
T Consensus 101 ~dL~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G-~~Da~~~~~~~ 167 (243)
T PF12974_consen 101 ADLKGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNG-KADAAAIPSDA 167 (243)
T ss_dssp HHHGGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTT-SSSEEEEEHHH
T ss_pred hhcCCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcC-CccEEEEechh
Confidence 444 344555553 34456677 5543 3456777778888888875 34555554433
No 269
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=26.65 E-value=1.9e+02 Score=27.27 Aligned_cols=50 Identities=16% Similarity=0.174 Sum_probs=35.8
Q ss_pred CccEEEEEcCCCcHHHHHHHHHCC--CCceeccCCHHHHHHHHHcCCccEEEEe
Q 015464 118 TKVRVAYQGLPGAYSEAAARKAYP--KCETVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 118 ~~~~Va~lGp~Gs~s~~AA~~~f~--~~~~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
...+|++. .|+..+.....++. +.+++...+.++++++|..|++|+.+..
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 44578886 56654443333332 4667889999999999999999998764
No 270
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=26.39 E-value=3e+02 Score=29.12 Aligned_cols=49 Identities=12% Similarity=0.128 Sum_probs=34.2
Q ss_pred ccEEEEEcCCCcHHHHHHHH---HCCCCc--eeccCCHHHHHHHHHcCCccEEEEe
Q 015464 119 KVRVAYQGLPGAYSEAAARK---AYPKCE--TVPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~---~f~~~~--~~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
..+|++. .|+..+..... .++... ...+.+.++++++|.+|++|+.++.
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 3578875 56554443322 345443 4567899999999999999999884
No 271
>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=26.12 E-value=3.9e+02 Score=22.32 Aligned_cols=33 Identities=15% Similarity=0.049 Sum_probs=24.3
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeee
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIE 171 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIE 171 (406)
.|+++.+.-. .+..++.+.+.+|++|+|+..-.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (194)
T cd08436 25 RHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLP 58 (194)
T ss_pred HCCCcEEEEecCCHHHHHHHHHcCCccEEEEecC
Confidence 4566654433 35678899999999999998644
No 272
>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=25.99 E-value=3e+02 Score=22.05 Aligned_cols=76 Identities=17% Similarity=0.135 Sum_probs=39.1
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCc-HHHHHHHHH
Q 015464 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMAD-PRAQFALGH 386 (406)
Q Consensus 308 ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~-~~~~~al~~ 386 (406)
+..+.|.+.+..-.|..+|..-..+ -|...-.-+|.+..-........+.|.|+-.|+..- ..+..|++.
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 4567777776666677777655444 121110001111000000112357888888886432 466778888
Q ss_pred HHHcCC
Q 015464 387 LQEFAT 392 (406)
Q Consensus 387 L~~~~~ 392 (406)
|.+.+.
T Consensus 79 L~~~~~ 84 (86)
T cd00460 79 LRKKLE 84 (86)
T ss_pred HHHHHh
Confidence 877654
No 273
>PRK08055 chorismate mutase; Provisional
Probab=25.65 E-value=49 Score=30.79 Aligned_cols=28 Identities=18% Similarity=0.109 Sum_probs=23.8
Q ss_pred CCCchhhhhHHhhhcccchHHHHHhhhhccccc
Q 015464 25 VPNRCGFGLDLRVLNKWECTCVGVLAQTHRAIT 57 (406)
Q Consensus 25 ~~~l~~lR~~ID~iD~~~~~l~~Ll~~~~R~~~ 57 (406)
+++|+.+|-+||+++.+ |+..|++ ++..
T Consensus 114 ~~dL~~vRp~l~~L~~~---il~~ia~--~l~~ 141 (181)
T PRK08055 114 PQDLSDVRQRIRQLDTQ---ILIQIAQ--RLKV 141 (181)
T ss_pred CCcHHHHHHHHHHHHHH---HHHHHHH--HHHh
Confidence 34688999999999999 9999999 5544
No 274
>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=25.54 E-value=84 Score=22.76 Aligned_cols=27 Identities=26% Similarity=0.347 Sum_probs=23.4
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeEe
Q 015464 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 315 ~~~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
+.+.||.+.++++.++..|||+-.|-.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 37 (66)
T cd04916 11 MKNTVGVSARATAALAKAGINIRMINQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 456799999999999999999988843
No 275
>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=25.47 E-value=4.6e+02 Score=22.90 Aligned_cols=32 Identities=9% Similarity=-0.080 Sum_probs=23.3
Q ss_pred HCCCCcee-ccCCHHHHHHHHHcCCccEEEEee
Q 015464 139 AYPKCETV-PCDQFEAAFKAVELWLVDKAVLPI 170 (406)
Q Consensus 139 ~f~~~~~~-~~~s~~~v~~aV~~g~~d~gvVPI 170 (406)
.++++++. ...+..++.+.+.+|++|+|+...
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 25 EAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred HCCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 35665543 234667889999999999999854
No 276
>PRK05092 PII uridylyl-transferase; Provisional
Probab=25.29 E-value=3.5e+02 Score=31.41 Aligned_cols=34 Identities=15% Similarity=0.220 Sum_probs=29.5
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeE
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIE 340 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIE 340 (406)
+-|.|.+..+|+||-|.++.++|+.+|+|+..-.
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 4577888889999999999999999999998544
No 277
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=25.21 E-value=2.4e+02 Score=32.48 Aligned_cols=36 Identities=11% Similarity=0.281 Sum_probs=30.3
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeEee
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLT--KIESR 342 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLt--kIESR 342 (406)
+-|.|.+..+|+||-|+++-++|+.+|+|+. +|.+.
T Consensus 676 ~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~ 713 (854)
T PRK01759 676 GGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITS 713 (854)
T ss_pred CeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEc
Confidence 3577888889999999999999999999997 45443
No 278
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=24.97 E-value=4.4e+02 Score=22.60 Aligned_cols=122 Identities=20% Similarity=0.156 Sum_probs=60.8
Q ss_pred HCCCCceeccC-CHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~~-s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.++++++.... +..++.+.+.+|++|+|+.....-. +.+. ...|.+.++.++ .+-+|-|... ..+++++.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~-~~~~--~~~l~~~~~~~v----~~~~h~l~~~-~~~~~dL~~ 96 (200)
T cd08467 25 RAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPP-DGLV--VRRLYDDGFACL----VRHGHPALAQ-EWTLDDFAT 96 (200)
T ss_pred hCCCCEEEEecCCcccHHHHhhCCCcCEEEecCCCCC-ccce--eEEeeeccEEEE----EcCCCccccC-CCCHHHHhC
Confidence 46777655443 4558899999999999997532111 1111 111223333322 2334444322 23333322
Q ss_pred --EE-EechHH-HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 217 --RV-FSHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 217 --~V-ySHpqa-l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
-| +.-... ......|+.+.+. . ...++|.....++|+.+ ...|+.+...+..
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08467 97 LRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAAT---DLIATVPRRVATQ 155 (200)
T ss_pred CCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcC---CeEEeeHHHHHHH
Confidence 12 111111 1233445555443 2 34567777777777764 3477777776654
No 279
>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=24.71 E-value=4.3e+02 Score=22.32 Aligned_cols=122 Identities=13% Similarity=0.001 Sum_probs=59.9
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.++++++.-. .+..+..+.+.+|++|+|+..-.....+. ....|.+..+.++ .+-+|-+.. ...+++++.
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 4566665433 34567789999999999997533211111 1112223333222 222332211 112333322
Q ss_pred --E-EEechHH-HHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 217 --R-VFSHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 217 --~-VySHpqa-l~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
. ++.+... ......|+.+.+. . ...++|......++..+ ...||.+...++.
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 1234566665443 2 23556666565666553 3588999888764
No 280
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=24.47 E-value=2.3e+02 Score=27.00 Aligned_cols=112 Identities=19% Similarity=0.148 Sum_probs=57.6
Q ss_pred HHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeee---eEeecCCCCCc------cCccEEEec
Q 015464 151 FEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVN---HCLLGLPGVLK------EELKRVFSH 221 (406)
Q Consensus 151 ~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~---h~L~~~~g~~l------~~I~~VySH 221 (406)
..|+-.-|+.|.+|+||+=-. .|.+.+-.+.--..|... .++++.++... ..-++|.+-
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 458889999999999998533 222222111111122222 33444433221 122466665
Q ss_pred hHHHHHHHHHHhhcCC--eEEeccCHHHHHHHHHhcCCCC-eEEE-cCHHhHHHcCCceeec
Q 015464 222 PQALAQCEMTLSNLGI--VRISADDTAGAAQMVASIGERD-TGAV-ASAQAAEIYGLDILAE 279 (406)
Q Consensus 222 pqal~QC~~~L~~~~~--~~i~~~sTA~Aa~~v~~~~~~~-~AAI-as~~aA~~ygL~il~~ 279 (406)
.--+. ++|+++.++ +++..+..-++|=.+ +..+ .+=| .+-..-+.+||++++.
T Consensus 122 Yp~it--~~yf~~~gv~~~iv~l~GsvE~aP~~---GlAD~IvDivsTG~TLr~NgL~~ie~ 178 (215)
T PRK01686 122 YPNIA--RRYFAEKGEQVEIIKLYGSVELAPLV---GLADAIVDIVETGNTLRANGLVEVEE 178 (215)
T ss_pred CHHHH--HHHHHHcCCeEEEEECcCceeecccc---CCccEEEEeecChHHHHHCcCEEeeE
Confidence 55444 569988765 444444433333211 1111 1112 3566678899999963
No 281
>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=24.32 E-value=4.4e+02 Score=22.34 Aligned_cols=120 Identities=13% Similarity=0.024 Sum_probs=59.9
Q ss_pred HCCCCceeccC-CHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc--
Q 015464 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (406)
Q Consensus 139 ~f~~~~~~~~~-s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I-- 215 (406)
.++++++.... +..++.+.+.+|++|+|++..+....+... ..|.+..+.++ .+-.|.+...+..+++++
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~~----~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08457 25 LRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFL---IETRSLPAVVA----VPMGHPLAQLDVVSPQDLAG 97 (196)
T ss_pred HCCCeEEEEEecCcHHHHHHHHcCCccEEEeccCCCCCCcEE---EEeccCCeEEE----eeCCCccccCCccCHHHhCC
Confidence 45666554333 346888999999999999865432222111 11222233222 233444443333333333
Q ss_pred -cEEE-echH-HHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHh
Q 015464 216 -KRVF-SHPQ-ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQA 268 (406)
Q Consensus 216 -~~Vy-SHpq-al~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~a 268 (406)
.-|. ++.. ......+|+.+.+. . ...++|...+.+.++.+ ...++.+...
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 34566666666677664 2355665443
No 282
>PRK09181 aspartate kinase; Validated
Probab=23.72 E-value=9.1e+02 Score=25.77 Aligned_cols=125 Identities=9% Similarity=-0.002 Sum_probs=75.0
Q ss_pred CCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecCccCCCCCeeEEEEEecCC-CCC---C-CCCCc
Q 015464 236 GIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREP-IIA---G-TDRPY 307 (406)
Q Consensus 236 ~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~a---A~~ygL~il~~~I~d~~~N~TRF~vi~~~~-~~~---~-~~~~~ 307 (406)
.+..+..-|-.+|.++..-+ |-+-.+.+ |..+|.+|.-.|-.+...-=|..- .... ..+ . ....+
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 34567778888888886643 44444444 456899998888765333344432 1110 001 0 01122
Q ss_pred eEEEEEE---eCCCcchHHHHHHHHHhCCceeeeeEeeeCCCCCCccccCCCCCCCccceEEEEEEEecCCCcHHHHHHH
Q 015464 308 KTSIVFT---LEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMADPRAQFAL 384 (406)
Q Consensus 308 ktsi~f~---~~~~pGaL~~~L~~Fa~~~INLtkIESRP~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~~~~~~~al 384 (406)
-+.|-+. ..+.+|.+.++++.|+++|||+-.|-|- . -+..|.|+-+ ...++.++
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 2257899999999999999999866332 1 2577888664 13567778
Q ss_pred HHHHHc
Q 015464 385 GHLQEF 390 (406)
Q Consensus 385 ~~L~~~ 390 (406)
++|++.
T Consensus 386 ~~L~~~ 391 (475)
T PRK09181 386 AELEKR 391 (475)
T ss_pred HHHHHh
Confidence 887753
No 283
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=23.16 E-value=6.5e+02 Score=23.83 Aligned_cols=114 Identities=11% Similarity=0.012 Sum_probs=57.3
Q ss_pred HCCCCcee-ccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCccE
Q 015464 139 AYPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR 217 (406)
Q Consensus 139 ~f~~~~~~-~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~~ 217 (406)
.|+++++. -.....++++.+.+|++|+|+..-.....+ +..+......+++++.++-.+..-..
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 45666653 355667899999999999999754321111 11111112223344433321111111
Q ss_pred E--EechHHHHHHHHHHhhcCC-eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 218 V--FSHPQALAQCEMTLSNLGI-VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 218 V--ySHpqal~QC~~~L~~~~~-~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
. +.++..+.+-..++...+. ....++|.....++|+.+ ...|+++...++
T Consensus 179 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~~~p~~~~~ 231 (275)
T PRK03601 179 YIRLEWGADFQQHEAGLIGADEVPILTTSSAELARQLLATL---NGCAFLPVHWAK 231 (275)
T ss_pred eEEccCCccHhHHHHHhcccCCcceEEeCcHHHHHHHHHhC---CCEEEEcHHHHh
Confidence 1 1122223222222222122 245677777888888864 347888877664
No 284
>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=23.02 E-value=4.5e+02 Score=21.96 Aligned_cols=122 Identities=14% Similarity=-0.018 Sum_probs=60.8
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCccE
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR 217 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~~ 217 (406)
.|+++++.-. .+..++.+.+.+|++|+|++.-.....+... ..|.+.++.++. +-+|-+... -.++.+..-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v~----~~~~~~~~~-~~~l~~~~~ 96 (193)
T cd08442 25 RYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQ---EPVFQEELVLVS----PKGHPPVSR-AEDLAGSTL 96 (193)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEEeCCCCCCCcEE---EEeecCcEEEEe----cCCCccccc-HHHhCCCce
Confidence 4676654433 4567889999999999999753321111111 111222222221 122222110 011223333
Q ss_pred EEec-h-HHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 218 VFSH-P-QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 218 VySH-p-qal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
|.-. . ....+...|+.+.+. . ...++|...+..++.++ ...++.+...++.
T Consensus 97 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 152 (193)
T cd08442 97 LAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAG---MGIALLPRSVLDS 152 (193)
T ss_pred EEecCCCcHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHhC---CcEEEcCHHHHhh
Confidence 3211 1 122446677766432 2 34567777777777764 3477888877653
No 285
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.68 E-value=85 Score=31.83 Aligned_cols=91 Identities=18% Similarity=0.095 Sum_probs=57.6
Q ss_pred CCCcHHHHHHHHHC---C-CCceeccCCHHHHHHHHHcCCccEEEEeeecccccccccccchhc---cCCeEE------E
Q 015464 127 LPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL---RHRLHI------V 193 (406)
Q Consensus 127 p~Gs~s~~AA~~~f---~-~~~~~~~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~---~~~l~I------~ 193 (406)
+.|+..|+++..++ | +...+|++.-.++..++..|.+|.++-=+.++....=.-++.+|. +..+.. +
T Consensus 157 g~Gs~dhl~~~~~~k~~Gi~~~~Vpy~g~gea~taLlgg~v~a~~~~~se~~~~vksG~lr~Lav~s~eRl~~~pdvPT~ 236 (319)
T COG3181 157 GLGSADHLAGALFAKAAGIKITYVPYKGGGEALTALLGGHVDAGSTNLSELLSQVKSGTLRLLAVFSEERLPGLPDVPTL 236 (319)
T ss_pred CCCcHHHHHHHHHHHHhCCceeEEeecCccHHHHHHhcCceeeeecChhhhhhhhccCceEEEEeechhhcCCCCCCCCh
Confidence 35778888765443 2 567899999999999999999999887664443333333444442 111111 1
Q ss_pred E----EEEEeeeeEeecCCCCCccCccE
Q 015464 194 G----EVQLVVNHCLLGLPGVLKEELKR 217 (406)
Q Consensus 194 g----E~~l~I~h~L~~~~g~~l~~I~~ 217 (406)
. .+.+++.+.+.+.+|++-+.|.+
T Consensus 237 ~E~G~~~~~~~wrgvfap~g~~~e~~~~ 264 (319)
T COG3181 237 KEQGYDVVMSIWRGVFAPAGTPDEIIAK 264 (319)
T ss_pred HhcCCceeeeeeeEEEeCCCCCHHHHHH
Confidence 1 12267778888888876555544
No 286
>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=22.29 E-value=56 Score=25.90 Aligned_cols=77 Identities=17% Similarity=0.203 Sum_probs=48.8
Q ss_pred EEechHHHHHHHHHHhhcCC-eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHHcCCceeecCccCCCCCeeEEEEEec
Q 015464 218 VFSHPQALAQCEMTLSNLGI-VRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAR 296 (406)
Q Consensus 218 VySHpqal~QC~~~L~~~~~-~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ygL~il~~~I~d~~~N~TRF~vi~~ 296 (406)
|-.||.-..-.+.+|+..+. ....+.|..+|.+.+.... ++ .+|..-......|+.++.. |.... ..+++++++.
T Consensus 4 vd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~~-~d-~iiid~~~~~~~~~~~~~~-i~~~~-~~~~ii~~t~ 79 (112)
T PF00072_consen 4 VDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLKKHP-PD-LIIIDLELPDGDGLELLEQ-IRQIN-PSIPIIVVTD 79 (112)
T ss_dssp EESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHST-ES-EEEEESSSSSSBHHHHHHH-HHHHT-TTSEEEEEES
T ss_pred EECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhcccC-ce-EEEEEeeeccccccccccc-ccccc-ccccEEEecC
Confidence 44677778888889988788 6778888888888887653 44 3343332223444444333 32222 6788888886
Q ss_pred CC
Q 015464 297 EP 298 (406)
Q Consensus 297 ~~ 298 (406)
..
T Consensus 80 ~~ 81 (112)
T PF00072_consen 80 ED 81 (112)
T ss_dssp ST
T ss_pred CC
Confidence 54
No 287
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=22.06 E-value=6.2e+02 Score=23.24 Aligned_cols=123 Identities=13% Similarity=0.056 Sum_probs=61.2
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCC----CCCcc
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLP----GVLKE 213 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~----g~~l~ 213 (406)
.++++++... .+.++..+.+.+|++|+|++...+...+.+. ...|...++.++ .+-+|.+.... -.++.
T Consensus 92 ~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~--~~~l~~~~~~~v----~~~~~~~~~~~~~~~~~~l~ 165 (269)
T PRK11716 92 EHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVA--FSPIDEIPLVLI----APALPCPVRQQLSQEKPDWS 165 (269)
T ss_pred HCCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcceE--EEEcccceEEEE----EcCCcchhhhccccchhhHh
Confidence 3566665443 4677899999999999999864432222111 122233333333 23333322211 11233
Q ss_pred CccEEE-echHHHHHHHHHHhhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 214 ELKRVF-SHPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 214 ~I~~Vy-SHpqal~QC~~~L~~~~~--~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
+..-|. +.......-..|+...+. . ...++|......++..+ ...++.+...++
T Consensus 166 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 223 (269)
T PRK11716 166 RIPFILPEHGPARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALG---CGVGLLPEVVLE 223 (269)
T ss_pred hCCeeecCCCchHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcC---CCeEeccHHHhh
Confidence 333332 111111223456655332 2 34566666666677664 347888887765
No 288
>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]
Probab=21.89 E-value=5.2e+02 Score=25.81 Aligned_cols=36 Identities=11% Similarity=0.160 Sum_probs=31.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeEee
Q 015464 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (406)
Q Consensus 307 ~ktsi~f~~~~~pGaL~~~L~~Fa~~~INLtkIESR 342 (406)
+...+.++.++.||-.+++-+....+|.|+.+-...
T Consensus 6 ~~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf 41 (287)
T COG0788 6 DTFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQF 41 (287)
T ss_pred cceEEEEecCCCCCcHHHHHHHHHHcCCceeecccc
Confidence 346678899999999999999999999999976655
No 289
>PRK09466 metL bifunctional aspartate kinase II/homoserine dehydrogenase II; Provisional
Probab=21.55 E-value=1.2e+03 Score=26.65 Aligned_cols=100 Identities=8% Similarity=-0.083 Sum_probs=62.4
Q ss_pred cCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecCccCCCCCeeEEEEEecCCCCC---C-CCCCc
Q 015464 235 LGIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILAREPIIA---G-TDRPY 307 (406)
Q Consensus 235 ~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~a---A~~ygL~il~~~I~d~~~N~TRF~vi~~~~~~~---~-~~~~~ 307 (406)
++++.+..-|-.+|.++..-+ |-+-.+.+ |..+|.+|.-.|-.|...--|+.. ...+... . ....+
T Consensus 244 ~~A~~i~~isy~Ea~ela~~G-----akVlHp~ti~pa~~~~Ipi~V~ntf~p~~~GT~I~--~~~~~~~~v~~It~~~~ 316 (810)
T PRK09466 244 KDACLLPLLRLDEASELARLA-----APVLHARTLQPVSGSDIDLQLRCSYQPEQGSTRIE--RVLASGTGARIVTSLDD 316 (810)
T ss_pred CCceEcccCCHHHHHHHHHcC-----ccccCHHHHHHHHHcCCeEEEecCCCCCCCceEEe--cCcccccceeeeeccCC
Confidence 356778888999999987653 34444444 456899999988775444355542 1111100 0 11122
Q ss_pred eEEEEEEeC---CCcchHHHHHHHHHhCCceeeeeEe
Q 015464 308 KTSIVFTLE---EGPGMLFKALAVFALRDINLTKIES 341 (406)
Q Consensus 308 ktsi~f~~~---~~pGaL~~~L~~Fa~~~INLtkIES 341 (406)
-+.|-+... ..||.+.++++.|+++|||+-.|-+
T Consensus 317 v~~i~i~~~~~~g~~g~~~~if~~l~~~~I~v~~i~~ 353 (810)
T PRK09466 317 VCLIELQVPASHDFKLAQKELDQLLKRAQLRPLAVGV 353 (810)
T ss_pred EEEEEEecCCcCCcchHHHHHHHHHHHCCCeEEEEEe
Confidence 333333222 4588899999999999999998843
No 290
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=21.26 E-value=5.3e+02 Score=22.12 Aligned_cols=122 Identities=11% Similarity=-0.018 Sum_probs=60.2
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCc--
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I-- 215 (406)
.++++++... .+.++.++.+.+|++|+|+++-.....|.... .|.+.++.++ .+-.|.+......+++++
T Consensus 26 ~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~l~~~---~l~~~~~~~~----~~~~~~~~~~~~v~~~~L~~ 98 (198)
T cd08485 26 VAPSATVSLTQMSKNRQIEALDAGTIDIGFGRFYPYQEGVVVR---NVTNERLFLG----AQKSRARSFGEQVHCSALRN 98 (198)
T ss_pred hCCCcEEEEEECCHHHHHHHHHcCCccEEEecCCCCCCCeEEE---EeeccceEEE----eCCCCccccCCCcCHHHHhc
Confidence 4566665443 35678999999999999998532222222221 1122233322 223333322222333333
Q ss_pred -cEEE-echH--H-HHHHHHHHhhcC--Ce-EEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 216 -KRVF-SHPQ--A-LAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 216 -~~Vy-SHpq--a-l~QC~~~L~~~~--~~-~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
.-|. .++. . -.+-.+|+.+.+ .+ ...++|.....++|+.+ ...||.+...++
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (198)
T cd08485 99 EPLILFPREGRPSFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAG---VGVTIVPETVAM 158 (198)
T ss_pred CCeEecCCCCCccHHHHHHHHHHHcCCCcceEEEcCcHHHHHHHHHcC---CceEECcchhhc
Confidence 2332 2211 1 223334555433 22 34566777777777764 346777776554
No 291
>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=21.19 E-value=2.2e+02 Score=26.01 Aligned_cols=49 Identities=12% Similarity=0.049 Sum_probs=31.4
Q ss_pred ccEEEEEcCCCcHHHHHHHHH-C-CCCc-e------eccCCHHHHHHHHHcCCccEEEEe
Q 015464 119 KVRVAYQGLPGAYSEAAARKA-Y-PKCE-T------VPCDQFEAAFKAVELWLVDKAVLP 169 (406)
Q Consensus 119 ~~~Va~lGp~Gs~s~~AA~~~-f-~~~~-~------~~~~s~~~v~~aV~~g~~d~gvVP 169 (406)
..+|++. .|+..+.+.... + .... . ....+..+++.+|.+|++|.+++.
T Consensus 104 g~~V~v~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~ 161 (232)
T TIGR03871 104 KLRIGVF--AGTPPAHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVW 161 (232)
T ss_pred CCeEEEE--cCChHHHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEec
Confidence 3578775 466655544322 2 1211 1 123478999999999999999985
No 292
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=21.15 E-value=5.1e+02 Score=21.91 Aligned_cols=123 Identities=20% Similarity=0.142 Sum_probs=61.5
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.|+++.+.-. .+..+..+.+.+|++|+|+..-.....+.. ...|.+..+.++ .+.+|-+......+++++.
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08441 25 RWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIA---YEPLFDYEVVLV----VAPDHPLAAKEFITPEDLAD 97 (198)
T ss_pred hCCCeEEEEEeCCchhHHHHHHcCCceEEEecCCcCCCCcE---EEEccCCcEEEE----EcCCCChHHcccCCHHHhcC
Confidence 4566655443 355788999999999999974221111111 112223333322 2333434322222333332
Q ss_pred -EEEech--HH-HHHHHHHHhhcCC---eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHHH
Q 015464 217 -RVFSHP--QA-LAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (406)
Q Consensus 217 -~VySHp--qa-l~QC~~~L~~~~~---~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~~ 271 (406)
....++ .. ......|+.+.+. ....++|...+.++++.+ ...++.+...++.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 156 (198)
T cd08441 98 ETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASG---RGVAALPNWAVRE 156 (198)
T ss_pred CceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhC---CcEEEeeHHHHHH
Confidence 122222 11 2334556655432 234677777777777765 3466777765543
No 293
>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=21.08 E-value=4.3e+02 Score=21.01 Aligned_cols=65 Identities=12% Similarity=0.168 Sum_probs=40.9
Q ss_pred eEEEEEEeCCC----cchHHHHHHHHHhCCceeeeeEee-------eCCCCCCccccCCCCCCCccceEEEEEEEecCCC
Q 015464 308 KTSIVFTLEEG----PGMLFKALAVFALRDINLTKIESR-------PQRKRPLRVVDDSNKGSAKYFDYLFYIDFEASMA 376 (406)
Q Consensus 308 ktsi~f~~~~~----pGaL~~~L~~Fa~~~INLtkIESR-------P~~~~p~~~~~~~~~g~~~~~~Y~Ffid~e~~~~ 376 (406)
.+.+++...-. ...+.++-+.+..+|-.+.++++. |+++.. -.|+|++.|+++.
T Consensus 4 E~~~il~~~~~~~~~~~~~~~~~~~i~~~gg~v~~~~~~G~r~LaY~i~k~~--------------~G~Y~~~~f~~~~- 68 (92)
T PF01250_consen 4 ELMFILRPDLSEEEIKKLIERVKKIIEKNGGVVRSVENWGKRRLAYPIKKQK--------------EGHYFLFNFDASP- 68 (92)
T ss_dssp EEEEEE-TTSCHHHHHHHHHHHHHHHHHTTEEEEEEEEEEEEEESSEETTEC--------------EEEEEEEEEEEST-
T ss_pred eEEEEECCCCCHHHHHHHHHHHHHHHHHCCCEEEEEEEEeecccccCCCCCC--------------EEEEEEEEEEeCH-
Confidence 35556654322 235567777889999999999985 554431 4577888998874
Q ss_pred cHHHHHHHHHHH
Q 015464 377 DPRAQFALGHLQ 388 (406)
Q Consensus 377 ~~~~~~al~~L~ 388 (406)
..++.+-..|+
T Consensus 69 -~~i~el~~~l~ 79 (92)
T PF01250_consen 69 -SAIKELERKLR 79 (92)
T ss_dssp -THHHHHHHHHH
T ss_pred -HHHHHHHHHhc
Confidence 34555444554
No 294
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=20.58 E-value=7.6e+02 Score=23.66 Aligned_cols=142 Identities=15% Similarity=0.133 Sum_probs=69.5
Q ss_pred CccEEEEEcCCCc-HHHHH-H--HHHCCCCceec-cCCHHHHHHHHHcCCccEEEEeee--ccc-ccccccccchhccCC
Q 015464 118 TKVRVAYQGLPGA-YSEAA-A--RKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIE--NSV-GGSIHRNYDLLLRHR 189 (406)
Q Consensus 118 ~~~~Va~lGp~Gs-~s~~A-A--~~~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIE--NS~-~G~V~~t~DlL~~~~ 189 (406)
+..+|++..+-+. +.... + .+.++++.+.- ..+..++.+.+.+|++|+|+.+-. +.. .+.. ...|.+..
T Consensus 95 g~l~ig~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~---~~~l~~~~ 171 (305)
T CHL00180 95 GTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKILE---ITPYVEDE 171 (305)
T ss_pred ceEEEEEcCcchHhHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEEcCccCccccccee---EEEeccCc
Confidence 5677877765543 22222 1 22456665543 336788999999999999998421 110 1111 11122223
Q ss_pred eEEEEEEEEeeeeEeecCCCCCccCc---cEEEech-HHH-HHHHHHHhhcCC------eEEeccCHHHHHHHHHhcCCC
Q 015464 190 LHIVGEVQLVVNHCLLGLPGVLKEEL---KRVFSHP-QAL-AQCEMTLSNLGI------VRISADDTAGAAQMVASIGER 258 (406)
Q Consensus 190 l~I~gE~~l~I~h~L~~~~g~~l~~I---~~VySHp-qal-~QC~~~L~~~~~------~~i~~~sTA~Aa~~v~~~~~~ 258 (406)
+.++ .+-+|-|......+++++ .-|.... ..+ .+-.+|+...+. ..+.++|...+...++++
T Consensus 172 ~~~v----~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--- 244 (305)
T CHL00180 172 LALI----IPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAVQSG--- 244 (305)
T ss_pred EEEE----ECCCCccccCCccCHHHHccCCceEecCCCcHHHHHHHHHHHcCCCcccceEEEEeCCHHHHHHHHHcC---
Confidence 3332 233444443333333333 3333222 222 223445554332 235677777777788764
Q ss_pred CeEEEcCHHhH
Q 015464 259 DTGAVASAQAA 269 (406)
Q Consensus 259 ~~AAIas~~aA 269 (406)
...++.+...+
T Consensus 245 ~g~~~lp~~~~ 255 (305)
T CHL00180 245 LGAAFVSVSAI 255 (305)
T ss_pred CcEEEeEhHHH
Confidence 23555554443
No 295
>PLN02551 aspartokinase
Probab=20.57 E-value=1.1e+03 Score=25.52 Aligned_cols=100 Identities=14% Similarity=0.053 Sum_probs=62.3
Q ss_pred cCCeEEeccCHHHHHHHHHhcCCCCeEEEcCHHh---HHHcCCceeecCccCCCCCeeEEEEEecC-CC--CCC-CCCCc
Q 015464 235 LGIVRISADDTAGAAQMVASIGERDTGAVASAQA---AEIYGLDILAEKIQDDDDNVTRFLILARE-PI--IAG-TDRPY 307 (406)
Q Consensus 235 ~~~~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~a---A~~ygL~il~~~I~d~~~N~TRF~vi~~~-~~--~~~-~~~~~ 307 (406)
+++..+..-|-.+|.++..-+ |-|-.+.| |..++.+|.-+|--+...--|..-- ... +. ... ....+
T Consensus 292 ~~A~~l~~lsy~Ea~elA~~G-----akVlhp~ai~pa~~~~Ipi~vknt~~p~~~GT~I~~-~~~~~~~~v~~It~~~~ 365 (521)
T PLN02551 292 PNAVPVPYLTFDEAAELAYFG-----AQVLHPQSMRPAREGDIPVRVKNSYNPTAPGTLITK-TRDMSKAVLTSIVLKRN 365 (521)
T ss_pred CCceEecccCHHHHHHHHhCC-----CcccCHHHHHHHHHCCceEEEEecCCCCCCCcEEec-ccccCCCcccceecCCC
Confidence 356778888999999987643 44444444 4568999998886553323344311 110 00 000 11223
Q ss_pred eEEEEEEe---CCCcchHHHHHHHHHhCCceeeeeE
Q 015464 308 KTSIVFTL---EEGPGMLFKALAVFALRDINLTKIE 340 (406)
Q Consensus 308 ktsi~f~~---~~~pGaL~~~L~~Fa~~~INLtkIE 340 (406)
-+.|-+.- .+.||.+.++++.|+++|||.-.|-
T Consensus 366 v~li~i~~~~m~~~~g~~arvf~~l~~~~I~Vd~Is 401 (521)
T PLN02551 366 VTMLDIVSTRMLGQYGFLAKVFSTFEDLGISVDVVA 401 (521)
T ss_pred eEEEEEecCCCCCcccHHHHHHHHHHHcCCcEEEEe
Confidence 34444432 2579999999999999999999993
No 296
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=20.15 E-value=8.1e+02 Score=23.85 Aligned_cols=121 Identities=20% Similarity=0.128 Sum_probs=59.7
Q ss_pred HCCCCceec-cCCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccCcc-
Q 015464 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (406)
Q Consensus 139 ~f~~~~~~~-~~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~I~- 216 (406)
.++++.+.. ..+-.++.+.+.+|++|+|+++-.....+.. +..|.+..+.++ ++..|-+......+++++.
T Consensus 114 ~~P~i~l~~~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~lv----~~~~hpl~~~~~i~~~~L~~ 186 (317)
T PRK15421 114 NWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLH---YSPMFDYEVRLV----LAPDHPLAAKTRITPEDLAS 186 (317)
T ss_pred HCCCceEEEEeCccHHHHHHHHCCCcCEEEecCcccCCCce---EEEeccceEEEE----EcCCCCccccCcCCHHHhCC
Confidence 356665433 3346688999999999999986321111111 111222233322 3344444333233334432
Q ss_pred -EEEech---HHHHHHHHHHhhcCC--eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhH
Q 015464 217 -RVFSHP---QALAQCEMTLSNLGI--VRISADDTAGAAQMVASIGERDTGAVASAQAA 269 (406)
Q Consensus 217 -~VySHp---qal~QC~~~L~~~~~--~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA 269 (406)
..+..+ ........|+...+. ..+.++|.....+.|..+ ...+|.+...+
T Consensus 187 ~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~i~p~~~~ 242 (317)
T PRK15421 187 ETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAAR---MGIAALPHWVV 242 (317)
T ss_pred CcEEecCCchhhHHHHHHHHHHhCCCCceeecCCHHHHHHHHHhC---CcEEEecchhc
Confidence 122221 223344555555443 334566777666777764 23566666544
No 297
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=20.14 E-value=5.3e+02 Score=21.72 Aligned_cols=122 Identities=19% Similarity=0.089 Sum_probs=60.6
Q ss_pred HCCCCceecc-CCHHHHHHHHHcCCccEEEEeeecccccccccccchhccCCeEEEEEEEEeeeeEeecCCCCCccC---
Q 015464 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEE--- 214 (406)
Q Consensus 139 ~f~~~~~~~~-~s~~~v~~aV~~g~~d~gvVPIENS~~G~V~~t~DlL~~~~l~I~gE~~l~I~h~L~~~~g~~l~~--- 214 (406)
.++++++... .+..++.+.+.+|++|+|+..-.....+.. ...|.+..+.++ .+-+|-+...+..++++
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~~~~~~~~~~~~~l~~ 97 (198)
T cd08433 25 RYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLS---TEPLLEEDLFLV----GPADAPLPRGAPVPLAELAR 97 (198)
T ss_pred HCCCcEEEEEecCcHHHHHHHhCCCCcEEEEeCCCCCCCee---EEEeccccEEEE----ecCCCccccCCCCCHHHhCC
Confidence 4566655433 355788999999999999975332221111 111222222222 23333333222222222
Q ss_pred ccEEE-echHH-HHHHHHHHhhcCC---eEEeccCHHHHHHHHHhcCCCCeEEEcCHHhHH
Q 015464 215 LKRVF-SHPQA-LAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (406)
Q Consensus 215 I~~Vy-SHpqa-l~QC~~~L~~~~~---~~i~~~sTA~Aa~~v~~~~~~~~AAIas~~aA~ 270 (406)
..-|. .+... ...+.+|+...+. ....++|...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08433 98 LPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAG---LGYTILPASAVA 155 (198)
T ss_pred CceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcC---CcEEEcchhhhh
Confidence 22222 22222 2345566665443 234577777777777764 346677766543
Done!