Query 016702
Match_columns 384
No_of_seqs 299 out of 1298
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 09:13:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016702.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016702hhsearch_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 5.2E-94 1.1E-98 723.8 32.1 332 37-382 16-379 (386)
2 COG0077 PheA Prephenate dehydr 100.0 1.2E-91 2.5E-96 673.0 31.4 271 97-382 2-276 (279)
3 PRK11899 prephenate dehydratas 100.0 1.4E-89 3.1E-94 664.4 33.0 274 95-382 2-276 (279)
4 PLN02317 arogenate dehydratase 100.0 1.5E-89 3.3E-94 684.5 33.4 306 78-383 75-380 (382)
5 PRK11898 prephenate dehydratas 100.0 2.8E-82 6E-87 615.8 32.8 271 97-382 1-279 (283)
6 KOG2797 Prephenate dehydratase 100.0 8.7E-76 1.9E-80 558.6 23.1 299 80-383 73-373 (377)
7 PF00800 PDT: Prephenate dehyd 100.0 7.2E-56 1.6E-60 404.8 15.7 177 100-276 1-181 (181)
8 PRK06034 hypothetical protein; 99.9 2.1E-25 4.6E-30 215.0 8.8 135 37-174 20-170 (279)
9 cd04904 ACT_AAAH ACT domain of 99.9 1.1E-21 2.3E-26 154.5 9.4 73 287-375 1-73 (74)
10 cd04931 ACT_PAH ACT domain of 99.8 1.3E-20 2.7E-25 154.1 10.1 70 284-368 12-81 (90)
11 cd04930 ACT_TH ACT domain of t 99.8 2.2E-20 4.7E-25 159.3 9.0 76 284-375 39-114 (115)
12 cd04905 ACT_CM-PDT C-terminal 99.8 8E-20 1.7E-24 145.3 11.2 80 286-379 1-80 (80)
13 cd04929 ACT_TPH ACT domain of 99.8 3.1E-20 6.8E-25 146.5 8.1 71 287-373 1-71 (74)
14 cd04880 ACT_AAAH-PDT-like ACT 99.8 3.7E-19 7.9E-24 139.5 9.9 75 288-376 1-75 (75)
15 TIGR01268 Phe4hydrox_tetr phen 99.7 3.4E-17 7.4E-22 166.4 10.4 79 285-378 15-94 (436)
16 TIGR01270 Trp_5_monoox tryptop 99.6 5.3E-15 1.1E-19 151.1 9.9 76 283-374 28-104 (464)
17 PRK08818 prephenate dehydrogen 98.7 2.1E-08 4.6E-13 101.5 8.0 65 285-365 294-359 (370)
18 TIGR01269 Tyr_3_monoox tyrosin 98.6 1.1E-07 2.3E-12 97.1 8.7 73 286-371 37-110 (457)
19 TIGR01807 CM_P2 chorismate mut 98.6 3.2E-08 6.9E-13 78.4 2.4 51 37-87 10-67 (76)
20 TIGR01801 CM_A chorismate muta 98.5 4.5E-08 9.8E-13 82.0 2.0 51 37-87 15-70 (102)
21 TIGR01805 CM_mono_grmpos monof 98.5 4.5E-08 9.7E-13 78.4 0.9 51 37-87 10-65 (81)
22 TIGR01797 CM_P_1 chorismate mu 98.4 5.1E-08 1.1E-12 78.5 0.5 51 37-87 10-66 (83)
23 PRK07248 hypothetical protein; 98.4 1E-07 2.2E-12 77.3 2.0 51 37-87 12-67 (87)
24 KOG3820 Aromatic amino acid hy 98.3 1.6E-06 3.6E-11 86.9 8.4 73 285-373 35-107 (461)
25 TIGR01803 CM-like chorismate m 98.3 3.5E-07 7.5E-12 73.5 1.7 51 37-87 10-66 (82)
26 TIGR01799 CM_T chorismate muta 98.2 5.5E-07 1.2E-11 72.5 1.7 51 37-87 10-66 (83)
27 PRK07857 hypothetical protein; 98.2 7.5E-07 1.6E-11 74.9 2.4 42 37-78 39-85 (106)
28 TIGR01808 CM_M_hiGC-arch monof 98.2 8.3E-07 1.8E-11 70.1 2.2 44 37-80 11-59 (74)
29 cd04886 ACT_ThrD-II-like C-ter 98.2 1.8E-05 4E-10 59.5 9.1 69 290-371 2-70 (73)
30 PRK06285 chorismate mutase; Pr 98.1 9.3E-07 2E-11 73.1 1.6 51 37-87 18-74 (96)
31 PRK07075 isochorismate-pyruvat 98.1 1.5E-06 3.2E-11 72.7 2.7 51 37-87 19-74 (101)
32 PRK11199 tyrA bifunctional cho 98.1 3E-06 6.5E-11 86.0 4.5 81 37-117 14-118 (374)
33 PF01842 ACT: ACT domain; Int 98.1 2.3E-05 5E-10 58.5 8.0 38 287-324 1-38 (66)
34 TIGR01791 CM_archaeal chorisma 98.1 1.5E-06 3.2E-11 69.8 1.4 50 37-86 10-65 (83)
35 PF01817 CM_2: Chorismate muta 98.0 6.7E-07 1.5E-11 71.2 -0.7 51 37-87 6-62 (81)
36 COG1605 PheA Chorismate mutase 98.0 3E-06 6.4E-11 70.8 2.7 51 37-87 19-76 (101)
37 PRK06443 chorismate mutase; Va 98.0 2.3E-06 5.1E-11 77.6 2.2 71 37-113 16-96 (177)
38 PRK12595 bifunctional 3-deoxy- 98.0 2.4E-06 5.3E-11 86.4 2.2 51 37-87 15-70 (360)
39 TIGR01795 CM_mono_cladeE monof 97.8 5.9E-06 1.3E-10 68.2 1.2 44 37-80 14-62 (94)
40 PRK09239 chorismate mutase; Pr 97.8 7E-06 1.5E-10 69.0 1.6 50 37-86 21-76 (104)
41 smart00830 CM_2 Chorismate mut 97.8 1.8E-05 3.9E-10 62.4 3.1 47 37-83 6-57 (79)
42 TIGR01806 CM_mono2 chorismate 97.6 4.5E-05 9.8E-10 65.1 3.0 48 40-87 7-60 (114)
43 cd04882 ACT_Bt0572_2 C-termina 97.4 0.001 2.2E-08 49.5 7.9 60 289-369 2-61 (65)
44 cd04884 ACT_CBS C-terminal ACT 97.4 0.0012 2.6E-08 50.9 8.5 65 289-368 2-66 (72)
45 cd04878 ACT_AHAS N-terminal AC 97.3 0.0036 7.7E-08 46.7 9.6 68 288-372 2-69 (72)
46 cd04874 ACT_Af1403 N-terminal 97.3 0.0027 5.9E-08 47.5 9.0 64 288-370 2-65 (72)
47 cd04883 ACT_AcuB C-terminal AC 97.2 0.0031 6.7E-08 48.0 9.2 65 287-370 2-66 (72)
48 PRK06737 acetolactate synthase 97.1 0.0045 9.7E-08 49.3 9.3 71 287-374 3-73 (76)
49 PRK09269 chorismate mutase; Pr 97.1 0.00039 8.4E-09 64.7 3.4 49 39-87 34-88 (193)
50 PRK08055 chorismate mutase; Pr 97.1 0.00042 9.1E-09 63.8 3.2 47 40-87 28-81 (181)
51 cd02116 ACT ACT domains are co 96.9 0.0053 1.2E-07 42.0 7.4 58 290-365 2-59 (60)
52 PF13710 ACT_5: ACT domain; PD 96.9 0.0067 1.4E-07 46.3 7.9 62 295-373 1-62 (63)
53 cd04888 ACT_PheB-BS C-terminal 96.8 0.013 2.8E-07 45.0 9.1 73 288-376 2-76 (76)
54 cd04908 ACT_Bt0572_1 N-termina 96.7 0.014 3E-07 44.3 8.3 35 288-322 3-37 (66)
55 cd04903 ACT_LSD C-terminal ACT 96.7 0.01 2.2E-07 44.1 7.6 63 289-370 2-64 (71)
56 PRK11152 ilvM acetolactate syn 96.6 0.022 4.7E-07 45.3 9.2 67 286-370 3-69 (76)
57 PRK11895 ilvH acetolactate syn 96.6 0.02 4.2E-07 51.9 10.1 71 287-374 3-73 (161)
58 TIGR00119 acolac_sm acetolacta 96.6 0.019 4.1E-07 51.8 10.0 70 288-374 3-72 (157)
59 cd04909 ACT_PDH-BS C-terminal 96.6 0.016 3.4E-07 44.0 8.1 36 288-323 3-38 (69)
60 PF13291 ACT_4: ACT domain; PD 96.6 0.023 5.1E-07 44.5 9.3 71 284-370 4-74 (80)
61 cd04902 ACT_3PGDH-xct C-termin 96.6 0.0092 2E-07 45.3 6.8 61 289-368 2-62 (73)
62 cd04879 ACT_3PGDH-like ACT_3PG 96.5 0.016 3.4E-07 42.9 7.5 63 289-370 2-64 (71)
63 cd04885 ACT_ThrD-I Tandem C-te 96.4 0.01 2.2E-07 45.4 6.0 62 290-369 2-63 (68)
64 cd04887 ACT_MalLac-Enz ACT_Mal 96.3 0.021 4.5E-07 43.7 7.6 63 289-368 2-64 (74)
65 CHL00100 ilvH acetohydroxyacid 96.3 0.018 3.9E-07 52.8 8.4 72 286-374 2-73 (174)
66 cd04896 ACT_ACR-like_3 ACT dom 96.3 0.02 4.4E-07 45.4 7.3 64 288-366 2-69 (75)
67 PRK13562 acetolactate synthase 96.1 0.047 1E-06 44.3 8.8 72 287-374 3-74 (84)
68 cd04881 ACT_HSDH-Hom ACT_HSDH_ 96.0 0.043 9.3E-07 41.5 7.9 64 289-368 3-66 (79)
69 PRK08178 acetolactate synthase 95.9 0.086 1.9E-06 43.8 9.7 71 286-374 8-78 (96)
70 PRK04435 hypothetical protein; 95.9 0.075 1.6E-06 47.3 9.9 77 285-377 68-146 (147)
71 cd04901 ACT_3PGDH C-terminal A 95.9 0.019 4.2E-07 43.1 5.3 61 289-370 2-62 (69)
72 cd04906 ACT_ThrD-I_1 First of 95.8 0.068 1.5E-06 42.8 8.3 69 289-375 4-72 (85)
73 PRK08198 threonine dehydratase 95.7 0.077 1.7E-06 54.3 10.7 77 285-375 326-403 (404)
74 cd04926 ACT_ACR_4 C-terminal 95.7 0.062 1.3E-06 41.6 7.7 36 287-322 2-37 (72)
75 cd04873 ACT_UUR-ACR-like ACT d 95.4 0.14 3E-06 38.2 8.5 36 288-323 2-37 (70)
76 cd04899 ACT_ACR-UUR-like_2 C-t 95.3 0.15 3.2E-06 38.4 8.3 38 287-324 1-38 (70)
77 cd04876 ACT_RelA-SpoT ACT dom 95.3 0.18 3.9E-06 36.0 8.5 64 290-370 2-65 (71)
78 cd04895 ACT_ACR_1 ACT domain-c 95.2 0.081 1.8E-06 41.6 6.8 29 287-315 2-30 (72)
79 cd04872 ACT_1ZPV ACT domain pr 95.2 0.1 2.2E-06 41.8 7.6 67 287-368 2-69 (88)
80 PF13740 ACT_6: ACT domain; PD 95.2 0.11 2.4E-06 40.6 7.5 35 289-323 3-39 (76)
81 PRK00194 hypothetical protein; 95.1 0.11 2.4E-06 41.6 7.7 36 286-321 3-38 (90)
82 cd04870 ACT_PSP_1 CT domains f 95.1 0.17 3.8E-06 39.2 8.5 62 291-367 4-65 (75)
83 PRK08577 hypothetical protein; 95.1 0.51 1.1E-05 41.1 12.1 70 286-370 56-125 (136)
84 cd04875 ACT_F4HF-DF N-terminal 95.0 0.096 2.1E-06 40.4 6.7 33 289-321 2-34 (74)
85 cd04877 ACT_TyrR N-terminal AC 95.0 0.21 4.6E-06 38.6 8.6 61 288-369 2-62 (74)
86 TIGR01127 ilvA_1Cterm threonin 94.9 0.14 3.1E-06 51.9 9.3 73 286-372 305-378 (380)
87 PRK06382 threonine dehydratase 94.8 0.15 3.2E-06 52.5 9.4 74 285-372 329-403 (406)
88 cd04889 ACT_PDH-BS-like C-term 94.8 0.089 1.9E-06 38.2 5.7 34 290-323 2-35 (56)
89 COG2061 ACT-domain-containing 94.5 0.26 5.7E-06 44.2 8.8 74 286-375 5-79 (170)
90 PRK08526 threonine dehydratase 94.2 0.86 1.9E-05 47.0 13.2 217 131-373 161-400 (403)
91 COG4492 PheB ACT domain-contai 93.7 0.34 7.4E-06 42.5 7.7 77 284-377 70-149 (150)
92 PRK08639 threonine dehydratase 93.7 0.77 1.7E-05 47.5 11.8 74 285-375 335-409 (420)
93 cd04869 ACT_GcvR_2 ACT domains 93.5 0.56 1.2E-05 36.4 8.3 34 289-322 2-35 (81)
94 PRK07334 threonine dehydratase 93.5 0.49 1.1E-05 48.6 10.0 76 285-374 325-401 (403)
95 cd04900 ACT_UUR-like_1 ACT dom 92.4 1.2 2.5E-05 34.4 8.4 32 287-318 2-33 (73)
96 cd04897 ACT_ACR_3 ACT domain-c 92.3 0.64 1.4E-05 36.9 6.9 29 287-315 2-30 (75)
97 COG4747 ACT domain-containing 92.0 0.94 2E-05 39.2 8.0 38 287-324 70-107 (142)
98 cd04893 ACT_GcvR_1 ACT domains 91.2 1.9 4.1E-05 33.7 8.5 64 289-368 4-67 (77)
99 TIGR01124 ilvA_2Cterm threonin 91.1 3.2 6.9E-05 44.1 12.7 72 285-375 324-395 (499)
100 TIGR02079 THD1 threonine dehyd 90.9 1.3 2.9E-05 45.6 9.4 74 285-374 324-397 (409)
101 PRK11589 gcvR glycine cleavage 90.8 1.3 2.8E-05 41.2 8.3 35 289-323 98-132 (190)
102 COG2716 GcvR Glycine cleavage 90.2 1.4 2.9E-05 40.4 7.7 74 291-377 97-171 (176)
103 cd04927 ACT_ACR-like_2 Second 89.7 2.9 6.3E-05 32.7 8.4 27 290-316 4-30 (76)
104 cd04935 ACT_AKiii-DAPDC_1 ACT 89.1 2.8 6.1E-05 32.8 7.9 63 293-375 11-74 (75)
105 COG0440 IlvH Acetolactate synt 88.9 2.1 4.6E-05 38.9 7.9 74 286-376 4-77 (163)
106 cd04912 ACT_AKiii-LysC-EC-like 88.6 3.3 7.1E-05 32.1 8.0 56 293-367 11-67 (75)
107 cd04932 ACT_AKiii-LysC-EC_1 AC 88.4 3.5 7.6E-05 32.3 8.0 62 293-374 11-73 (75)
108 COG1707 ACT domain-containing 88.1 1.8 3.9E-05 39.6 6.9 61 289-367 5-65 (218)
109 cd04907 ACT_ThrD-I_2 Second of 88.0 4.2 9.2E-05 32.4 8.4 65 288-371 3-67 (81)
110 PRK13011 formyltetrahydrofolat 87.6 3.6 7.7E-05 40.6 9.3 67 286-367 7-75 (286)
111 COG3830 ACT domain-containing 87.5 1.5 3.3E-05 36.0 5.5 66 294-374 11-78 (90)
112 cd08445 PBP2_BenM_CatM_CatR Th 86.2 21 0.00047 30.8 13.1 141 97-247 2-158 (203)
113 PRK09224 threonine dehydratase 86.1 4.7 0.0001 42.8 9.9 73 285-375 327-399 (504)
114 cd08417 PBP2_Nitroaromatics_li 86.1 20 0.00044 30.5 13.4 121 118-249 26-155 (200)
115 PRK12483 threonine dehydratase 86.0 4.6 9.9E-05 43.2 9.7 72 285-375 344-416 (521)
116 cd04934 ACT_AK-Hom3_1 CT domai 85.8 6.4 0.00014 30.7 8.1 55 295-369 13-67 (73)
117 PLN02550 threonine dehydratase 84.5 5.3 0.00012 43.4 9.4 71 286-375 417-487 (591)
118 cd04925 ACT_ACR_2 ACT domain-c 83.8 9.2 0.0002 29.5 8.2 32 289-320 3-34 (74)
119 PRK11151 DNA-binding transcrip 83.6 23 0.0005 34.0 12.8 144 95-248 90-246 (305)
120 cd08411 PBP2_OxyR The C-termin 83.6 27 0.00059 29.8 12.5 123 117-249 26-157 (200)
121 PRK06349 homoserine dehydrogen 83.4 4.3 9.4E-05 42.1 8.0 64 288-368 350-413 (426)
122 cd04891 ACT_AK-LysC-DapG-like_ 83.0 5.3 0.00012 28.1 6.2 31 291-321 6-36 (61)
123 PF12974 Phosphonate-bd: ABC t 82.7 1.1 2.3E-05 42.1 3.0 83 96-187 104-201 (243)
124 PRK11790 D-3-phosphoglycerate 82.4 3.1 6.8E-05 43.0 6.5 63 286-370 338-401 (409)
125 TIGR01728 SsuA_fam ABC transpo 80.8 8.2 0.00018 36.2 8.3 138 98-245 1-157 (288)
126 PRK06545 prephenate dehydrogen 80.5 6.1 0.00013 39.9 7.7 40 286-325 290-329 (359)
127 PRK13010 purU formyltetrahydro 80.0 9.4 0.0002 37.8 8.6 66 288-368 11-80 (289)
128 cd08452 PBP2_AlsR The C-termin 79.7 39 0.00085 29.1 13.1 123 116-248 24-157 (197)
129 TIGR00363 lipoprotein, YaeC fa 79.1 42 0.00091 32.5 12.7 110 96-213 18-139 (258)
130 PRK05007 PII uridylyl-transfer 78.7 4.4 9.6E-05 46.1 6.6 56 284-356 806-864 (884)
131 PRK15007 putative ABC transpor 78.6 4.7 0.0001 37.2 5.8 49 97-147 126-174 (243)
132 TIGR01693 UTase_glnD [Protein- 78.5 8.3 0.00018 43.6 8.7 54 284-352 777-831 (850)
133 KOG2663 Acetolactate synthase, 78.0 6.5 0.00014 38.3 6.5 73 285-376 76-150 (309)
134 PF00585 Thr_dehydrat_C: C-ter 77.9 6.5 0.00014 32.0 5.7 68 285-370 9-76 (91)
135 cd04913 ACT_AKii-LysC-BS-like_ 77.2 15 0.00033 27.0 7.3 28 291-318 7-34 (75)
136 cd08435 PBP2_GbpR The C-termin 76.2 47 0.001 28.1 12.2 122 117-248 25-158 (201)
137 PRK06027 purU formyltetrahydro 75.8 15 0.00032 36.3 8.6 64 288-368 8-76 (286)
138 PRK11092 bifunctional (p)ppGpp 75.7 13 0.00028 41.3 9.0 69 285-370 625-693 (702)
139 PF00497 SBP_bac_3: Bacterial 75.4 5.6 0.00012 35.3 5.1 48 98-147 111-159 (225)
140 TIGR01096 3A0103s03R lysine-ar 74.5 7.1 0.00015 36.1 5.8 49 97-147 131-180 (250)
141 cd00134 PBPb Bacterial peripla 74.0 8.5 0.00018 33.2 5.9 50 97-148 105-154 (218)
142 PRK10872 relA (p)ppGpp synthet 73.7 17 0.00037 40.6 9.3 69 285-369 665-733 (743)
143 PRK05092 PII uridylyl-transfer 73.4 16 0.00034 41.9 9.2 53 285-352 842-895 (931)
144 TIGR00719 sda_beta L-serine de 72.6 15 0.00032 34.5 7.4 58 286-359 148-206 (208)
145 TIGR00691 spoT_relA (p)ppGpp s 72.6 18 0.00039 40.1 9.1 69 285-370 609-677 (683)
146 COG0317 SpoT Guanosine polypho 72.3 23 0.0005 39.3 9.7 69 285-370 626-694 (701)
147 PRK09508 leuO leucine transcri 72.2 16 0.00035 35.4 7.9 122 117-249 137-266 (314)
148 PRK09959 hybrid sensory histid 71.6 5.1 0.00011 46.4 4.9 51 96-148 406-456 (1197)
149 PRK11260 cystine transporter s 70.8 9.1 0.0002 36.2 5.7 48 98-147 150-197 (266)
150 cd08450 PBP2_HcaR The C-termin 70.3 66 0.0014 27.2 11.6 122 117-248 25-156 (196)
151 TIGR00655 PurU formyltetrahydr 70.0 25 0.00054 34.6 8.6 65 289-368 3-71 (280)
152 PF13379 NMT1_2: NMT1-like fam 69.5 23 0.00051 33.2 8.2 145 95-245 5-180 (252)
153 PRK01759 glnD PII uridylyl-tra 69.5 9.3 0.0002 43.3 6.2 32 284-315 781-812 (854)
154 cd04890 ACT_AK-like_1 ACT doma 69.0 18 0.00039 26.4 5.8 51 294-365 11-61 (62)
155 TIGR03339 phn_lysR aminoethylp 68.8 1E+02 0.0022 28.7 12.6 139 95-245 86-236 (279)
156 PRK13581 D-3-phosphoglycerate 68.7 12 0.00025 40.0 6.5 106 242-367 386-514 (526)
157 PRK09959 hybrid sensory histid 68.2 7.4 0.00016 45.0 5.3 49 97-147 164-212 (1197)
158 cd08412 PBP2_PAO1_like The C-t 67.9 74 0.0016 26.8 12.6 122 117-248 25-154 (198)
159 PRK11242 DNA-binding transcrip 67.7 91 0.002 29.5 11.9 121 118-248 117-247 (296)
160 smart00062 PBPb Bacterial peri 67.5 13 0.00028 31.8 5.6 51 97-149 106-156 (219)
161 PRK09495 glnH glutamine ABC tr 66.8 12 0.00025 35.0 5.4 49 97-147 131-179 (247)
162 cd08486 PBP2_CbnR The C-termin 66.7 85 0.0018 27.1 13.2 140 97-246 2-156 (198)
163 cd08446 PBP2_Chlorocatechol Th 66.7 80 0.0017 26.8 12.7 122 117-248 26-158 (198)
164 cd08420 PBP2_CysL_like C-termi 66.5 57 0.0012 27.4 9.4 122 117-248 25-158 (201)
165 smart00079 PBPe Eukaryotic hom 66.3 16 0.00034 30.5 5.6 47 98-147 14-71 (134)
166 PF12727 PBP_like: PBP superfa 64.9 41 0.00089 31.0 8.6 130 122-256 14-165 (193)
167 PRK09906 DNA-binding transcrip 64.7 1.3E+02 0.0028 28.5 12.8 141 96-247 90-246 (296)
168 cd08459 PBP2_DntR_NahR_LinR_li 64.4 89 0.0019 26.6 10.3 122 117-249 25-155 (201)
169 smart00062 PBPb Bacterial peri 64.3 88 0.0019 26.5 10.2 110 121-246 41-157 (219)
170 cd08462 PBP2_NodD The C-termin 64.1 70 0.0015 27.5 9.6 121 117-249 25-155 (200)
171 cd08453 PBP2_IlvR The C-termin 63.4 94 0.002 26.5 13.6 121 118-248 26-160 (200)
172 cd04928 ACT_TyrKc Uncharacteri 62.9 70 0.0015 24.8 8.5 36 289-324 4-39 (68)
173 COG4747 ACT domain-containing 62.8 11 0.00024 32.8 3.9 28 290-317 7-34 (142)
174 cd04933 ACT_AK1-AT_1 ACT domai 62.6 30 0.00065 27.4 6.2 58 293-369 11-72 (78)
175 PRK11063 metQ DL-methionine tr 61.8 63 0.0014 31.4 9.7 110 96-214 31-153 (271)
176 PRK11589 gcvR glycine cleavage 61.6 35 0.00076 31.7 7.5 37 286-324 6-44 (190)
177 cd08413 PBP2_CysB_like The C-t 61.5 1.1E+02 0.0023 26.4 11.3 121 117-247 25-155 (198)
178 cd08451 PBP2_BudR The C-termin 61.4 99 0.0022 26.1 13.4 123 116-248 25-159 (199)
179 PRK12683 transcriptional regul 61.2 1.6E+02 0.0035 28.4 12.9 142 95-246 92-247 (309)
180 PF03401 TctC: Tripartite tric 60.8 13 0.00029 36.0 4.7 135 94-233 103-261 (274)
181 cd08440 PBP2_LTTR_like_4 TThe 60.6 99 0.0021 25.8 12.8 122 117-248 25-155 (197)
182 PRK11482 putative DNA-binding 59.8 1.6E+02 0.0036 28.6 12.3 142 96-249 117-270 (317)
183 cd08466 PBP2_LeuO The C-termin 58.8 1.1E+02 0.0024 25.9 10.5 122 117-249 25-155 (200)
184 TIGR01327 PGDH D-3-phosphoglyc 58.6 18 0.00039 38.6 5.6 105 243-367 386-513 (525)
185 cd08461 PBP2_DntR_like_3 The C 58.3 84 0.0018 26.6 9.0 123 117-250 25-157 (198)
186 TIGR02424 TF_pcaQ pca operon t 57.9 1.7E+02 0.0037 27.7 12.2 145 94-248 91-251 (300)
187 PRK03381 PII uridylyl-transfer 57.6 37 0.00081 38.1 8.1 53 286-353 707-760 (774)
188 PF03466 LysR_substrate: LysR 57.6 1.2E+02 0.0026 25.9 13.5 122 117-248 31-161 (209)
189 cd08421 PBP2_LTTR_like_1 The C 57.3 1.2E+02 0.0026 25.6 11.9 122 117-248 25-155 (198)
190 PRK12679 cbl transcriptional r 57.2 1.5E+02 0.0033 28.6 11.6 143 95-246 92-247 (316)
191 PRK11716 DNA-binding transcrip 57.1 97 0.0021 28.5 9.8 145 95-248 66-223 (269)
192 cd08485 PBP2_ClcR The C-termin 56.2 1.3E+02 0.0028 25.8 11.7 142 97-248 2-158 (198)
193 PRK04374 PII uridylyl-transfer 56.1 53 0.0011 37.5 9.0 52 285-353 795-849 (869)
194 cd08437 PBP2_MleR The substrat 55.3 1.3E+02 0.0028 25.5 12.3 121 117-247 25-156 (198)
195 cd08468 PBP2_Pa0477 The C-term 54.9 53 0.0012 28.3 7.2 121 117-249 25-157 (202)
196 PRK12684 transcriptional regul 54.8 1.8E+02 0.004 28.0 11.7 144 94-248 91-249 (313)
197 PRK11553 alkanesulfonate trans 54.8 58 0.0013 31.5 8.2 53 93-146 24-83 (314)
198 cd04923 ACT_AK-LysC-DapG-like_ 54.6 59 0.0013 23.0 6.3 27 293-319 10-36 (63)
199 cd08426 PBP2_LTTR_like_5 The C 54.4 1.3E+02 0.0029 25.3 13.2 122 117-248 25-155 (199)
200 PRK10341 DNA-binding transcrip 54.1 1.7E+02 0.0036 28.2 11.2 119 118-248 123-252 (312)
201 TIGR02995 ectoine_ehuB ectoine 53.9 23 0.00049 33.8 5.0 49 97-147 144-193 (275)
202 TIGR01098 3A0109s03R phosphate 53.6 24 0.00051 32.8 5.0 88 97-187 141-238 (254)
203 PRK11917 bifunctional adhesin/ 53.5 39 0.00085 32.1 6.6 48 97-146 148-199 (259)
204 KOG3217 Protein tyrosine phosp 52.6 13 0.00029 33.3 2.8 63 301-381 58-124 (159)
205 COG2107 Predicted periplasmic 52.5 24 0.00053 34.5 4.9 52 96-149 94-145 (272)
206 cd04871 ACT_PSP_2 ACT domains 52.5 39 0.00085 26.9 5.4 66 294-367 7-74 (84)
207 PRK10820 DNA-binding transcrip 52.4 35 0.00075 36.4 6.6 59 289-368 3-61 (520)
208 cd04936 ACT_AKii-LysC-BS-like_ 50.9 73 0.0016 22.5 6.3 27 293-319 10-36 (63)
209 PRK12680 transcriptional regul 50.8 2.5E+02 0.0055 27.5 12.8 146 94-248 91-250 (327)
210 PRK09986 DNA-binding transcrip 50.4 2.2E+02 0.0048 26.7 12.6 144 95-248 96-255 (294)
211 PRK00275 glnD PII uridylyl-tra 49.5 65 0.0014 36.9 8.5 36 285-320 813-850 (895)
212 PRK03059 PII uridylyl-transfer 48.9 76 0.0016 36.2 8.8 36 285-320 785-822 (856)
213 cd08444 PBP2_Cbl The C-termina 48.6 1.7E+02 0.0038 25.0 12.8 122 117-248 25-156 (198)
214 PRK10859 membrane-bound lytic 48.5 83 0.0018 33.0 8.6 48 98-147 150-202 (482)
215 cd08425 PBP2_CynR The C-termin 48.0 1.7E+02 0.0037 24.7 10.7 120 118-247 27-156 (197)
216 cd04868 ACT_AK-like ACT domain 47.7 41 0.0009 23.0 4.4 27 295-321 12-38 (60)
217 cd08443 PBP2_CysB The C-termin 47.5 1.8E+02 0.0039 24.9 12.8 123 116-247 24-155 (198)
218 PRK09034 aspartate kinase; Rev 47.1 3.6E+02 0.0078 28.2 13.3 127 214-367 234-372 (454)
219 cd04924 ACT_AK-Arch_2 ACT doma 46.9 93 0.002 22.3 6.4 27 293-319 11-37 (66)
220 PRK09224 threonine dehydratase 46.6 47 0.001 35.4 6.4 35 285-320 422-456 (504)
221 PF00497 SBP_bac_3: Bacterial 46.4 69 0.0015 28.1 6.7 122 111-249 30-165 (225)
222 cd08460 PBP2_DntR_like_1 The C 46.0 51 0.0011 28.3 5.6 121 117-248 25-153 (200)
223 cd08457 PBP2_OccR The C-termin 45.9 1.9E+02 0.004 24.5 12.6 120 117-246 25-153 (196)
224 cd04892 ACT_AK-like_2 ACT doma 45.7 1E+02 0.0022 21.5 6.4 27 293-319 10-36 (65)
225 TIGR03871 ABC_peri_MoxJ_2 quin 45.7 44 0.00095 30.4 5.4 49 97-147 104-161 (232)
226 COG0725 ModA ABC-type molybdat 45.1 31 0.00066 33.5 4.4 52 97-149 135-195 (258)
227 cd08438 PBP2_CidR The C-termin 44.7 1.9E+02 0.004 24.2 13.4 32 117-148 25-57 (197)
228 TIGR00656 asp_kin_monofn aspar 44.6 2.9E+02 0.0064 28.0 11.7 97 214-319 189-296 (401)
229 PF09084 NMT1: NMT1/THI5 like; 44.1 2.4E+02 0.0051 25.3 14.3 105 121-233 23-139 (216)
230 PF07485 DUF1529: Domain of Un 44.1 81 0.0018 27.3 6.4 51 297-363 67-117 (123)
231 PRK10859 membrane-bound lytic 42.4 90 0.002 32.8 7.7 28 120-147 81-108 (482)
232 cd04914 ACT_AKi-DapG-BS_1 ACT 42.2 38 0.00083 25.6 3.7 28 293-321 9-36 (67)
233 COG2844 GlnD UTP:GlnB (protein 41.6 85 0.0018 35.6 7.5 32 284-315 789-820 (867)
234 cd04911 ACT_AKiii-YclM-BS_1 AC 41.6 1.2E+02 0.0025 24.2 6.4 57 294-370 12-68 (76)
235 PRK11139 DNA-binding transcrip 40.4 2.4E+02 0.0051 26.8 9.8 105 133-249 133-246 (297)
236 cd08414 PBP2_LTTR_aromatics_li 40.3 2.2E+02 0.0047 23.8 11.7 32 118-149 26-58 (197)
237 TIGR03427 ABC_peri_uca ABC tra 40.2 3.8E+02 0.0082 26.8 11.5 130 120-257 36-178 (328)
238 cd04922 ACT_AKi-HSDH-ThrA_2 AC 40.1 69 0.0015 23.1 4.8 27 293-319 11-37 (66)
239 CHL00180 rbcR LysR transcripti 40.1 3.4E+02 0.0074 25.9 14.8 142 94-245 93-253 (305)
240 cd04937 ACT_AKi-DapG-BS_2 ACT 40.0 1.2E+02 0.0026 22.3 6.1 33 287-319 4-37 (64)
241 KOG0850 Transcription factor D 39.6 40 0.00087 32.5 4.1 67 19-85 111-190 (245)
242 PRK15421 DNA-binding transcrip 38.9 3.7E+02 0.0081 26.1 11.6 143 95-247 88-242 (317)
243 PRK15010 ABC transporter lysin 38.8 72 0.0016 29.9 5.8 49 97-147 133-183 (260)
244 cd08464 PBP2_DntR_like_2 The C 38.7 2.4E+02 0.0052 23.7 8.8 122 117-249 25-155 (200)
245 TIGR00070 hisG ATP phosphoribo 38.0 1E+02 0.0022 28.6 6.4 108 129-256 49-171 (182)
246 cd08441 PBP2_MetR The C-termin 37.7 2.5E+02 0.0054 23.7 12.3 141 98-248 2-155 (198)
247 cd04919 ACT_AK-Hom3_2 ACT doma 37.5 85 0.0018 22.8 4.9 26 294-319 12-37 (66)
248 cd08436 PBP2_LTTR_like_3 The C 37.5 2.4E+02 0.0052 23.4 12.6 122 116-247 24-155 (194)
249 TIGR01729 taurine_ABC_bnd taur 37.5 3.6E+02 0.0079 25.7 10.6 137 99-245 2-157 (300)
250 cd08416 PBP2_MdcR The C-termin 37.0 2.5E+02 0.0055 23.5 13.0 122 117-248 25-157 (199)
251 COG0834 HisJ ABC-type amino ac 36.2 46 0.001 30.8 4.0 48 98-147 147-196 (275)
252 PRK11062 nhaR transcriptional 35.6 4E+02 0.0086 25.4 10.9 145 95-250 92-249 (296)
253 PF01193 RNA_pol_L: RNA polyme 35.4 1.5E+02 0.0032 22.3 6.0 63 290-369 2-65 (66)
254 cd08447 PBP2_LTTR_aromatics_li 35.2 2.7E+02 0.0059 23.3 11.4 121 118-248 26-157 (198)
255 PF13840 ACT_7: ACT domain ; P 34.0 85 0.0018 23.6 4.4 33 286-318 8-42 (65)
256 PRK11480 tauA taurine transpor 34.0 51 0.0011 32.4 4.1 143 93-245 20-179 (320)
257 cd04918 ACT_AK1-AT_2 ACT domai 32.5 2.1E+02 0.0045 21.2 7.3 34 286-319 3-36 (65)
258 PF11966 SSURE: Fibronectin-bi 32.1 1E+02 0.0022 24.6 4.6 38 340-377 18-60 (81)
259 PRK05007 PII uridylyl-transfer 32.1 1.8E+02 0.004 33.2 8.6 32 286-317 701-732 (884)
260 cd08433 PBP2_Nac The C-teminal 32.0 3.1E+02 0.0067 23.0 12.9 122 117-248 25-155 (198)
261 PRK15437 histidine ABC transpo 31.0 1.1E+02 0.0024 28.6 5.7 49 97-147 133-183 (259)
262 cd08465 PBP2_ToxR The C-termin 30.8 3.4E+02 0.0074 23.2 8.7 118 118-245 26-152 (200)
263 PF12916 DUF3834: Protein of u 30.3 79 0.0017 29.8 4.3 73 95-172 66-143 (201)
264 TIGR01693 UTase_glnD [Protein- 30.2 2E+02 0.0043 32.7 8.4 32 286-317 668-699 (850)
265 PRK02047 hypothetical protein; 29.8 3.1E+02 0.0066 22.3 7.6 60 294-370 24-86 (91)
266 PRK10216 DNA-binding transcrip 29.6 2.7E+02 0.0057 26.9 8.3 146 97-248 98-262 (319)
267 cd08418 PBP2_TdcA The C-termin 29.6 3.4E+02 0.0073 22.7 10.6 121 117-249 25-156 (201)
268 PRK10797 glutamate and asparta 29.4 89 0.0019 30.5 4.9 48 98-147 154-205 (302)
269 TIGR01096 3A0103s03R lysine-ar 28.8 4.2E+02 0.009 24.1 9.1 114 120-249 64-186 (250)
270 cd08483 PBP2_HvrB The C-termin 28.7 1.1E+02 0.0024 25.7 4.8 116 118-248 26-149 (190)
271 PRK10837 putative DNA-binding 28.3 5E+02 0.011 24.2 12.8 55 94-148 87-146 (290)
272 PRK08210 aspartate kinase I; R 28.2 2.2E+02 0.0048 29.1 7.7 95 215-317 194-303 (403)
273 TIGR00149 TIGR00149_YbjQ secon 28.0 38 0.00081 29.7 1.8 18 333-353 104-121 (132)
274 cd00134 PBPb Bacterial peripla 27.7 3.7E+02 0.0081 22.7 8.8 114 120-249 39-159 (218)
275 PRK01759 glnD PII uridylyl-tra 27.1 2E+02 0.0044 32.8 7.8 31 286-316 677-707 (854)
276 PRK05092 PII uridylyl-transfer 27.1 2.9E+02 0.0063 31.8 9.1 34 285-318 731-764 (931)
277 cd08427 PBP2_LTTR_like_2 The C 27.1 3.7E+02 0.008 22.3 12.0 121 117-248 25-153 (195)
278 PRK08961 bifunctional aspartat 27.0 7.8E+02 0.017 28.1 12.4 128 214-367 250-388 (861)
279 PRK04998 hypothetical protein; 27.0 3.3E+02 0.0072 21.8 7.2 60 294-370 23-83 (88)
280 cd08423 PBP2_LTTR_like_6 The C 26.9 3.7E+02 0.0081 22.4 11.5 121 118-248 26-160 (200)
281 PRK15437 histidine ABC transpo 26.4 4.4E+02 0.0096 24.5 9.0 28 120-148 66-93 (259)
282 PRK06635 aspartate kinase; Rev 26.2 2.2E+02 0.0048 29.0 7.3 29 293-321 270-298 (404)
283 cd08419 PBP2_CbbR_RubisCO_like 26.1 3.8E+02 0.0083 22.2 14.0 122 117-248 24-154 (197)
284 TIGR02122 TRAP_TAXI TRAP trans 25.5 1.1E+02 0.0024 29.3 4.7 50 97-147 141-197 (320)
285 cd08458 PBP2_NocR The C-termin 25.5 4.1E+02 0.009 22.4 14.3 121 117-247 25-154 (196)
286 TIGR03427 ABC_peri_uca ABC tra 25.1 82 0.0018 31.6 3.8 48 97-147 106-160 (328)
287 cd08448 PBP2_LTTR_aromatics_li 25.1 4E+02 0.0087 22.1 14.3 122 117-248 25-157 (197)
288 COG0788 PurU Formyltetrahydrof 24.7 4.3E+02 0.0093 26.2 8.4 35 286-320 7-41 (287)
289 TIGR00787 dctP tripartite ATP- 24.6 3.4E+02 0.0075 25.6 7.9 151 102-258 3-196 (257)
290 cd08469 PBP2_PnbR The C-termin 24.6 4.6E+02 0.01 22.7 9.5 32 117-148 25-57 (221)
291 PRK01686 hisG ATP phosphoribos 24.3 2.2E+02 0.0047 27.1 6.3 138 97-257 3-178 (215)
292 PRK00341 hypothetical protein; 24.2 3.9E+02 0.0085 21.7 7.1 60 294-370 25-86 (91)
293 cd08467 PBP2_SyrM The C-termin 24.2 4.5E+02 0.0097 22.4 9.8 122 117-249 25-155 (200)
294 PRK11074 putative DNA-binding 24.2 3.8E+02 0.0083 25.5 8.3 147 94-249 90-247 (300)
295 PRK09084 aspartate kinase III; 24.0 8.4E+02 0.018 25.5 11.7 100 214-319 234-342 (448)
296 KOG4028 Uncharacterized conser 23.8 59 0.0013 28.8 2.2 34 98-131 108-142 (175)
297 PF06153 DUF970: Protein of un 23.4 2.3E+02 0.0049 24.2 5.6 53 301-371 14-66 (109)
298 cd08442 PBP2_YofA_SoxR_like Th 23.4 4.3E+02 0.0093 21.9 12.2 121 117-248 25-151 (193)
299 cd08449 PBP2_XapR The C-termin 23.2 4.4E+02 0.0095 21.9 11.9 33 117-149 25-58 (197)
300 PLN02550 threonine dehydratase 22.9 3.3E+02 0.0071 29.9 8.1 67 288-373 512-578 (591)
301 cd04916 ACT_AKiii-YclM-BS_2 AC 22.6 1E+02 0.0022 22.1 3.1 26 293-318 11-36 (66)
302 PF03180 Lipoprotein_9: NLPA l 22.6 3E+02 0.0064 26.4 6.9 84 98-194 1-95 (237)
303 PF09084 NMT1: NMT1/THI5 like; 22.6 2.5E+02 0.0054 25.1 6.2 51 97-150 93-150 (216)
304 cd04921 ACT_AKi-HSDH-ThrA-like 22.5 3.4E+02 0.0073 20.3 7.6 27 293-319 11-37 (80)
305 PF13379 NMT1_2: NMT1-like fam 22.4 1.9E+02 0.0041 27.0 5.6 50 96-147 120-177 (252)
306 COG2150 Predicted regulator of 22.0 1.3E+02 0.0028 27.5 4.0 35 287-321 96-130 (167)
307 COG3978 Acetolactate synthase 21.8 4.3E+02 0.0093 21.5 6.5 50 290-352 7-56 (86)
308 COG3482 Uncharacterized conser 21.7 1.3E+02 0.0027 29.0 4.1 45 99-146 3-47 (237)
309 TIGR02122 TRAP_TAXI TRAP trans 21.7 2E+02 0.0042 27.6 5.6 55 94-148 28-90 (320)
310 PF01894 UPF0047: Uncharacteri 21.6 44 0.00094 28.7 0.9 17 333-352 92-108 (118)
311 COG3181 Uncharacterized protei 21.4 97 0.0021 31.3 3.5 97 99-195 150-264 (319)
312 cd00460 RNAP_RPB11_RPB3 RPB11 21.4 4E+02 0.0087 21.1 6.5 74 286-370 8-84 (86)
313 COG3283 TyrR Transcriptional r 21.3 2.8E+02 0.006 29.0 6.7 71 290-381 4-76 (511)
314 PRK15385 magnesium transport p 20.9 6.3E+02 0.014 24.2 8.7 66 288-368 144-212 (225)
315 TIGR01098 3A0109s03R phosphate 20.9 2.4E+02 0.0052 25.9 5.9 55 95-149 31-94 (254)
316 PHA03169 hypothetical protein; 20.2 4E+02 0.0087 27.6 7.4 66 283-361 320-385 (413)
No 1
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=100.00 E-value=5.2e-94 Score=723.80 Aligned_cols=332 Identities=31% Similarity=0.439 Sum_probs=304.8
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCccc-------ee-eccCCCCc-----
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD-------FT-VTPNDGTK----- 97 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~-------i~-~s~~~~~~----- 97 (384)
-+|.+|++||+||++++.+||++|++.| + + ||+++|+++...+. ++++.+. || .|+..|..
T Consensus 16 ~ID~~ii~Ll~~R~~~~~~I~~~K~~~~~pi~dp~RE~~vl~~~~~~a~~~~l~~~~i~~if~~ii~~S~~~Q~~~~~~~ 95 (386)
T PRK10622 16 ALDEKLLALLAERRELAVEVAKAKLLSHRPVRDIDRERDLLERLITLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQH 95 (386)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHhhhhhhcc
Confidence 8999999999999999999999999988 3 4 99999999998886 7787753 34 34444433
Q ss_pred --------eEEEEECCCCcHHHHHHHHHCCC----CcccCCCCHHHHHHHHHhCCCCeEEEeeecccccccccccccccc
Q 016702 98 --------VRISFKGLPGSFSEDAALKAYPK----CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLR 165 (384)
Q Consensus 98 --------~~Va~LGP~GTfS~~AA~~~f~~----~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~ 165 (384)
++||||||+|||||+||+++|+. ...+||+||++||++|++|++||||||||||++|+|.+|||+|.+
T Consensus 96 ~~~~~~~~~~va~lGp~GtfSh~Aa~~~~~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~DlL~~ 175 (386)
T PRK10622 96 LNKTNPHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVLPIENTSSGAINDVYDLLQH 175 (386)
T ss_pred ccccccccceEEEECCCCcHHHHHHHHhhccccccccccCCCCHHHHHHHHHCCCCCEEEEEEecCCceehHHHHHHHhc
Confidence 78999999999999999999863 234589999999999999999999999999999999999999999
Q ss_pred CCeEEEEEEEEeeeeeeecCCCCCcCCccEEEecHHHHHHHHHHHHhc-CCeEEecCCHHHHHHHHHhcCCCCeEEEcCH
Q 016702 166 HRLHIVGEVQLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL-GVARENVDDTASAAQYVASNGLRDAGAVASA 244 (384)
Q Consensus 166 ~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~VySHpqAl~QC~~fL~~~-~~~~i~~~STA~AA~~v~~~~~~~~AAIas~ 244 (384)
++++|+||+.+||+|||++.++.++++|++||||||||+||++||+++ +++.++++|||+||+++++.++++.|||||+
T Consensus 176 ~~l~I~~E~~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~ 255 (386)
T PRK10622 176 TSLSIVGEMTLPIDHCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRYPHWKIEYTESTAAAMEKVAQANSPHVAALGSE 255 (386)
T ss_pred CCCEEEEEEEEEEEEEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHCCCceEEEcCChHHHHHHHHhcCCCCEEEECCH
Confidence 999999999999999999999999999999999999999999999997 7899999999999999998777789999999
Q ss_pred HHHHHcCCceeeccccCCCCCeeEEEEEeeCCCCCCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 016702 245 RAAEIYGLNILADRIQDEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (384)
Q Consensus 245 ~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~ 324 (384)
.||++|||+||+++|||.++|+|||+||++++..++....+||||+|+++|+||+|+++|++|+.+|||||||||||.++
T Consensus 256 ~aa~~ygL~vl~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~~L~~Fa~~giNLtkIeSRP~~~ 335 (386)
T PRK10622 256 AGGALYGLQVLERNLANQQQNITRFIVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTKLESRPIHG 335 (386)
T ss_pred HHHHHcCCcChhhcCcCCccccceEEEEecCCCCCCCCCCCcEEEEEEcCCCCcHHHHHHHHHHHcCCCeeEEEeeecCC
Confidence 99999999999999999999999999999987433333346999999999999999999999999999999999999998
Q ss_pred CCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCC
Q 016702 325 RPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDA 382 (384)
Q Consensus 325 ~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~~vkvLGsYp~~~ 382 (384)
.+ |+|+||||++||.+|+.++++|++|++.+.++|+|||||...
T Consensus 336 ~~--------------~~Y~Ffid~eg~~~d~~~~~aL~~l~~~~~~~kvLGsYp~~~ 379 (386)
T PRK10622 336 NP--------------WEEMFYLDVQANLRSAEMQKALKELGEITRSLKVLGCYPSEN 379 (386)
T ss_pred CC--------------ceEEEEEEEeCCCCCHHHHHHHHHHHHhcCcEEEeeeecCCc
Confidence 75 999999999999999999999999999999999999999763
No 2
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=1.2e-91 Score=673.04 Aligned_cols=271 Identities=47% Similarity=0.714 Sum_probs=258.0
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCC-CcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEE
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPK-CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQ 175 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~-~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~ 175 (384)
+++|+||||+|||||+||+++|++ .+..||+||+|||++|++|++||||||||||++|+|++|+|+|..++|+|+||+.
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 689999999999999999999998 7999999999999999999999999999999999999999999999999999999
Q ss_pred EeeeeeeecCCCCCcCCccEEEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHHcCCc
Q 016702 176 LAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLN 253 (384)
Q Consensus 176 l~I~h~Ll~~~g~~l~~I~~VySHpqAl~QC~~fL~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ygL~ 253 (384)
+||+|||+++.+.++++|++|||||||++||++||+++ +++.++++|||+||+++++.++...|||||+.||++|||+
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 99999999998889999999999999999999999998 6999999999999999999877899999999999999999
Q ss_pred eeeccccCCCCCeeEEEEEeeC-CCCCCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccC
Q 016702 254 ILADRIQDEPDNITRFLVLARD-PIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDD 332 (384)
Q Consensus 254 il~~~I~D~~~N~TRF~vi~~~-~~~~~~~~~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~ 332 (384)
+|++||||.++|+|||+||+|. +..... ...||||+|+++|+||+|+++|++|+.||||||||||||+++.+
T Consensus 162 il~~~I~D~~~N~TRF~vl~r~~~~~~~~-~~~kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~~~------ 234 (279)
T COG0077 162 ILAENIEDEPNNRTRFLVLSRRKPPSVSD-GPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTGL------ 234 (279)
T ss_pred hHhhcccCCCCCeEEEEEEeccCCCCcCC-CCceEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCCCC------
Confidence 9999999999999999999985 322222 34699999999999999999999999999999999999999875
Q ss_pred CCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCC
Q 016702 333 SNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDA 382 (384)
Q Consensus 333 ~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~~vkvLGsYp~~~ 382 (384)
|+|+||||++||.+|+.+++||++|+..+.++|+|||||...
T Consensus 235 --------~~Y~F~iD~eg~~~~~~v~~AL~el~~~t~~~kilGsYp~~~ 276 (279)
T COG0077 235 --------GEYLFFIDIEGHIDDPLVKEALEELKEITEFVKILGSYPSAR 276 (279)
T ss_pred --------eeEEEEEEEecCcCcHhHHHHHHHHHhheeEEEEEeeccccc
Confidence 999999999999999999999999999999999999999864
No 3
>PRK11899 prephenate dehydratase; Provisional
Probab=100.00 E-value=1.4e-89 Score=664.42 Aligned_cols=274 Identities=41% Similarity=0.577 Sum_probs=259.8
Q ss_pred CCceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEE
Q 016702 95 GTKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEV 174 (384)
Q Consensus 95 ~~~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi 174 (384)
.+++|||||||+|||||+||+++|++.+++||.||++||++|++|++||||||||||++|+|.+|+|+|.+++++|+||+
T Consensus 2 ~~~~kvaylGp~GsfS~~Aa~~~~~~~~~v~~~s~~~vf~av~~g~~d~gVvPiENS~~G~V~~~~Dll~~~~l~Iv~E~ 81 (279)
T PRK11899 2 SKTNRIAFQGEPGANSHLACRDAFPDMEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVADIHHLLPESGLHIVGEY 81 (279)
T ss_pred CCCCEEEEECCCCCHHHHHHHHhcCcCceeecCCHHHHHHHHHCCCCCEEEEEeeccCCccHHHHHHHHhcCCCEEEEEE
Confidence 46789999999999999999999998889999999999999999999999999999999999999999999999999999
Q ss_pred EEeeeeeeecCCCCCcCCccEEEecHHHHHHHHHHHHhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHHcCCce
Q 016702 175 QLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNI 254 (384)
Q Consensus 175 ~l~I~h~Ll~~~g~~l~~I~~VySHpqAl~QC~~fL~~~~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ygL~i 254 (384)
.+||+|||++.++.++++|++||||||||+||++||++++++.+++.|||+||+++++.++++.|||||+.||++|||+|
T Consensus 82 ~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAIas~~aa~~YgL~i 161 (279)
T PRK11899 82 FLPIRHQLMALPGATLEEIKTVHSHPHALGQCRKIIRALGLKPVVAADTAGAARLVAERGDPSMAALASRLAAELYGLDI 161 (279)
T ss_pred EEEeeEEEecCCCCCHHHCeEEEEeHHHHHHHHHHHHHcCCeEEEcCChHHHHHHHHhcCCCCeeEeCCHHHHHHcCCcc
Confidence 99999999999998999999999999999999999999999999999999999999987777899999999999999999
Q ss_pred eeccccCCCCCeeEEEEEeeCCCC-CCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCC
Q 016702 255 LADRIQDEPDNITRFLVLARDPII-PRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (384)
Q Consensus 255 l~~~I~D~~~N~TRF~vi~~~~~~-~~~~~~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~ 333 (384)
|+++|||.++|+|||+||++++.. +...+.+||||+|+++|+||+|+++|++|+.+|||||||||||.++++
T Consensus 162 l~~~IqD~~~N~TRF~vi~~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~------- 234 (279)
T PRK11899 162 LAENIEDADHNTTRFVVLSREADWAARGDGPIVTTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSF------- 234 (279)
T ss_pred hhhcccCCcccceeEEEEecCCCCCCCCCCCceEEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCC-------
Confidence 999999999999999999998642 222334699999999999999999999999999999999999999875
Q ss_pred CCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCC
Q 016702 334 NNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDA 382 (384)
Q Consensus 334 ~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~~vkvLGsYp~~~ 382 (384)
|+|+||||++||.+|++++++|++|++.+.++|+|||||...
T Consensus 235 -------~~Y~F~id~eg~~~d~~v~~aL~~l~~~~~~~kvLGsYp~~~ 276 (279)
T PRK11899 235 -------TATQFYADIEGHPEDRNVALALEELRFFSEEVRILGVYPAHP 276 (279)
T ss_pred -------ceEEEEEEEECCCCCHHHHHHHHHHHHhcCcEEEeeeecCcc
Confidence 999999999999999999999999999999999999999754
No 4
>PLN02317 arogenate dehydratase
Probab=100.00 E-value=1.5e-89 Score=684.50 Aligned_cols=306 Identities=75% Similarity=1.223 Sum_probs=287.1
Q ss_pred hCCCCCCccceeeccCCCCceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEeeecccccccc
Q 016702 78 SLPKPLTVADFTVTPNDGTKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIH 157 (384)
Q Consensus 78 ~n~GPL~~e~i~~s~~~~~~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~ 157 (384)
..+.||....++.+..-..+++||||||+|||||+||+++|++.+++||+||++||++|++|++||||||||||++|+|.
T Consensus 75 ~~~~~~~~~~~~~~~~~~~~~rVaylGp~GtfSe~AA~~~f~~~e~vp~~sf~~vf~AVe~g~ad~gVvPIENS~~GsV~ 154 (382)
T PLN02317 75 GLPRPLSITDLSPSPMHGSKLRVAYQGVPGAYSEAAARKAYPNCEAVPCEQFEAAFQAVELWLADRAVLPIENSLGGSIH 154 (382)
T ss_pred cccccccHhhhcccccCCCCcEEEEECCCcCHHHHHHHHhhCcCceeecCCHHHHHHHHHCCCCCEEEEEEeccCccchH
Confidence 45667766556644555667899999999999999999999988999999999999999999999999999999999999
Q ss_pred ccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCccEEEecHHHHHHHHHHHHhcCCeEEecCCHHHHHHHHHhcCCCC
Q 016702 158 RNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLRD 237 (384)
Q Consensus 158 ~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~VySHpqAl~QC~~fL~~~~~~~i~~~STA~AA~~v~~~~~~~ 237 (384)
+|||+|.+++++|+||+.+||+|||++++|.++++|++||||||||+||++||++++++++++.|||+||++|++.+.++
T Consensus 155 ~t~DlL~~~~l~IvgEv~l~I~h~Ll~~~g~~l~~Ik~VySHPQALaQC~~~L~~~~~~~~~~~sTA~AA~~Va~~~~~~ 234 (382)
T PLN02317 155 RNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEELKRVISHPQALAQCENTLTKLGVVREAVDDTAGAAKMVAANGLRD 234 (382)
T ss_pred HHHHHHhcCCCEEEEEEEEEeeeEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHcCCeEEEcCCHHHHHHHHHhcCCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999877778
Q ss_pred eEEEcCHHHHHHcCCceeeccccCCCCCeeEEEEEeeCCCCCCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeee
Q 016702 238 AGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKI 317 (384)
Q Consensus 238 ~AAIas~~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkI 317 (384)
.|||||+.||++|||+||+++|||.++|+|||+||++++..|.....+||||+|+++|+||+|+++|++|+.+|||||||
T Consensus 235 ~AAIaS~~aA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KTSivfsl~~~pG~L~k~L~~Fa~~~INLtkI 314 (382)
T PLN02317 235 TAAIASARAAELYGLDILAEGIQDDSDNVTRFLMLAREPIIPRTDRPFKTSIVFSLEEGPGVLFKALAVFALRDINLTKI 314 (382)
T ss_pred ceeecCHHHHHHcCCcchhhhhcCCCCCeeeEEEEecCCcCCCCCCCccEEEEEEcCCCCchHHHHHHHHHHCCCCEEEE
Confidence 99999999999999999999999999999999999998765544445699999999999999999999999999999999
Q ss_pred eeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCCC
Q 016702 318 ESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDAT 383 (384)
Q Consensus 318 ESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~~vkvLGsYp~~~~ 383 (384)
||||.++.++++.|+...|..+.|+|.|||||+|+..|++++++|++|++.+.++|+|||||...+
T Consensus 315 ESRP~~~~~~~~~~~~~~~~~~~~eY~FyVD~eg~~~d~~~~~aL~~L~~~~~~lrvLGsYp~~~~ 380 (382)
T PLN02317 315 ESRPQRKRPLRVVDDSNSGTAKYFDYLFYVDFEASMADPRAQNALAHLQEFATFLRVLGSYPMDMT 380 (382)
T ss_pred EeeecCCCCccccccccccccccccEEEEEEEEcCcCCHHHHHHHHHHHHhcCeEEEEeeeecCCC
Confidence 999999999999999999999999999999999999999999999999999999999999998765
No 5
>PRK11898 prephenate dehydratase; Provisional
Probab=100.00 E-value=2.8e-82 Score=615.85 Aligned_cols=271 Identities=44% Similarity=0.610 Sum_probs=252.8
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCC---CcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccC-CeEEEE
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPK---CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRH-RLHIVG 172 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~---~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~-~l~I~g 172 (384)
+++||||||+|||||+||.++|+. .++++|+||++||++|++|++||||||||||++|+|.+|||+|.++ +++|+|
T Consensus 1 ~~~va~lGp~Gs~s~~Aa~~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~v~~~~d~L~~~~~~~iv~ 80 (283)
T PRK11898 1 MMKIAYLGPEGTFTEAAALKFFPADGEAELVPYDSIPDVLDAVEAGEVDYAVVPIENSIEGSVNPTLDYLAHGSPLQIVA 80 (283)
T ss_pred CcEEEEECCCCCHHHHHHHHhhccccccceEecCCHHHHHHHHHcCCCCEEEEEecccCceecHHHHHHhccCCCcEEEE
Confidence 468999999999999999999975 6899999999999999999999999999999999999999999775 899999
Q ss_pred EEEEeeeeeeecCCCCCcCCccEEEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHHc
Q 016702 173 EVQLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIY 250 (384)
Q Consensus 173 Ei~l~I~h~Ll~~~g~~l~~I~~VySHpqAl~QC~~fL~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~y 250 (384)
|+.+||+|||+++++.. ++|++||||||||+||++||+++ +++.+++.|||+||+++++++..+.|||||+.||++|
T Consensus 81 E~~l~I~~~L~~~~~~~-~~i~~V~SHpqal~QC~~~l~~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y 159 (283)
T PRK11898 81 EIVLPIAQHLLVHPGHA-AKIRTVYSHPQALAQCRKWLAEHLPGAELEPANSTAAAAQYVAEHPDEPIAAIASELAAELY 159 (283)
T ss_pred EEEeeeeEEEeCCCCCh-hcCeEEEEeHHHHHHHHHHHHhcCCCCEEEEcCchHHHHHHHhcCCCCCeEEECCHHHHHHc
Confidence 99999999999998765 99999999999999999999997 7899999999999999998766678999999999999
Q ss_pred CCceeeccccCCCCCeeEEEEEeeCCC-CCCCCCCceEEEEEEeCC-CcchHHHHHHHHHhCCceeeeeeeeeCCCCCCc
Q 016702 251 GLNILADRIQDEPDNITRFLVLARDPI-IPRTDKLFKTSIVFTLDE-GPGVLFKALAVFALREINLTKIESRPQRKRPLR 328 (384)
Q Consensus 251 gL~il~~~I~D~~~N~TRF~vi~~~~~-~~~~~~~~Ktsl~f~~~~-~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~ 328 (384)
||+||++||||.++|+|||+||++++. .+...+.+||||+|++++ +||+|+++|++|+.+|||||||||||+++.+
T Consensus 160 gL~il~~~I~d~~~N~TRF~vi~~~~~~~~~~~~~~ktslif~l~~~~pGsL~~~L~~F~~~~INLt~IeSRP~~~~~-- 237 (283)
T PRK11898 160 GLEILAEDIQDYPNNRTRFWLLGRKKPPPPLRTGGDKTSLVLTLPNNLPGALYKALSEFAWRGINLTRIESRPTKTGL-- 237 (283)
T ss_pred CCcEehhcCCCCCccceEEEEEEcCcccCCCCCCCCeEEEEEEeCCCCccHHHHHHHHHHHCCCCeeeEecccCCCCC--
Confidence 999999999999999999999999864 222234569999999987 5999999999999999999999999999875
Q ss_pred cccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCC
Q 016702 329 VVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDA 382 (384)
Q Consensus 329 ~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~~vkvLGsYp~~~ 382 (384)
|+|.|||||+||.+|++++++|++|++.+.++|+|||||...
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=8.7e-76 Score=558.62 Aligned_cols=299 Identities=66% Similarity=1.115 Sum_probs=281.9
Q ss_pred CCCCCccceeeccCCCCceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEeeecccccccccc
Q 016702 80 PKPLTVADFTVTPNDGTKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRN 159 (384)
Q Consensus 80 ~GPL~~e~i~~s~~~~~~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~t 159 (384)
+.|+....+..+..-....+|+||||+|+|||.||.+.|++.+-+||..|+.+|++|+...+||+|+|||||+.|+|...
T Consensus 73 ~~pl~~~~l~psp~~~s~lRva~qg~pgaysesaa~ka~pn~~avpc~~f~~afqave~w~vD~AVLPiENS~gGsIhrn 152 (377)
T KOG2797|consen 73 PQPLTSTDLSPSPMHGSTLRVAYQGVPGAYSESAALKAYPNCEAVPCDQFEAAFQAVELWIVDYAVLPIENSTGGSIHRN 152 (377)
T ss_pred CCcchhhhcccCCCCCceEEEEeecCCchhhhhhhhhhcCCcccccHhHHHHHHHHHHHhhccceeeeeeccCCceeeec
Confidence 44555444555666677899999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccccCCeEEEEEEEEeeeeeeecCCCCCcCCccEEEecHHHHHHHHHHHHhcC--CeEEecCCHHHHHHHHHhcCCCC
Q 016702 160 YDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQLG--VARENVDDTASAAQYVASNGLRD 237 (384)
Q Consensus 160 lDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~VySHpqAl~QC~~fL~~~~--~~~i~~~STA~AA~~v~~~~~~~ 237 (384)
||||.++.+.|+||+.+||+|||++.+|...+++++|.||||||+||..||.+.+ +.++.++|||+||+.++.+...+
T Consensus 153 YDLLlrh~lhiVgEv~vPvhHCLi~~~gv~~e~~~~VlSHPQal~Qce~~L~~l~~~~~r~a~~dTa~Aa~~~s~~~~~d 232 (377)
T KOG2797|consen 153 YDLLLRHRLHIVGEVQVPVHHCLIALPGVRKEEVVRVLSHPQALGQCECSLTKLGPNAAREAVSDTAGAAEQISASNTAD 232 (377)
T ss_pred hHHHhhcchheeeEEecceeeeEecCCCCChhheeeeecCcHHHHHHHHHHHhcccceeeeeccchHHHHHHHHhccccc
Confidence 9999999999999999999999999999999999999999999999999999974 88999999999999999988889
Q ss_pred eEEEcCHHHHHHcCCceeeccccCCCCCeeEEEEEeeCCCCCCCCCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeee
Q 016702 238 AGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKI 317 (384)
Q Consensus 238 ~AAIas~~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkI 317 (384)
++||+|+.||++|||.||+++|||+.+|.|||++|.|++.+|..+...||||+|...+.||.|+++|++|+-|+||||+|
T Consensus 233 ~~AIASe~aA~ly~l~Il~~~IqDd~~NvTRFLmLar~p~ip~t~rl~ktsivf~~~~gp~vLfkvl~vfa~r~inltkI 312 (377)
T KOG2797|consen 233 TAAIASERAAELYGLNILEKNIQDDLGNVTRFLMLAREPIIPDTDRLFKTSIVFFREKGPGVLFKVLSVFAFRSINLTKI 312 (377)
T ss_pred HHHHHHHHHHHHhcchhhhhhcccccCCeeEEEEEeccCCCCCCCccceeeEEEEeecCCchHHHHHHHHHhhhceeeee
Confidence 99999999999999999999999999999999999999999987778999999999999999999999999999999999
Q ss_pred eeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhcCceEEEccccCCCC
Q 016702 318 ESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDAT 383 (384)
Q Consensus 318 ESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~~vkvLGsYp~~~~ 383 (384)
||||.+..|+|+.|+ .+.|+|.||||+|..+.+++.++++.++++.+.++++|||||.+.+
T Consensus 313 esRP~h~~p~r~v~~-----~k~f~ylFyidfeasmae~~aq~al~~~~e~~sflrvlGsyp~d~t 373 (377)
T KOG2797|consen 313 ESRPFHNRPLRVVDD-----SKNFEYLFYIDFEASMAEPRAQNALGEVQEFTSFLRVLGSYPMDMT 373 (377)
T ss_pred ecccccCCCcccccc-----cccccEEEEEEEEeccCcHHHHHHHHHHHHHHHHHHHhcCCccccc
Confidence 999999999888776 4569999999999999999999999999999999999999998764
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=7.2e-56 Score=404.77 Aligned_cols=177 Identities=47% Similarity=0.723 Sum_probs=164.0
Q ss_pred EEEECCCCcHHHHHHHHHC--CCCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEe
Q 016702 100 ISFKGLPGSFSEDAALKAY--PKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLA 177 (384)
Q Consensus 100 Va~LGP~GTfS~~AA~~~f--~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~ 177 (384)
||||||+|||||+||+++| ++.++++|+||++||++|++|++||||||||||++|.|.+|+|+|.+++++|+||+.+|
T Consensus 1 Ia~LGP~GT~S~~Aa~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~~vvPiENs~~G~V~~t~d~L~~~~l~i~~e~~l~ 80 (181)
T PF00800_consen 1 IAYLGPEGTFSHEAAQQYFGGPDAEIVPCDSFEEVFDAVEEGEADYGVVPIENSLEGSVSETLDLLIDSDLYIVGEIVLP 80 (181)
T ss_dssp EEEESSTTSHHHHHHCCCCTTTCSEEEEESSHHHHHHHHHCTSSSEEEEEEECTTTCECHHHHHHHHTSSCEEEEEEEEE
T ss_pred CEEeCCCCCHHHHHHHHHHHhhccceEecCCHHHHHHHHHcCCCceEEEeEeeecCCEeHHHHHHHhcCCceEEEEEEec
Confidence 7999999999999999999 46899999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeecCCCCCcCCccEEEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHHcCCcee
Q 016702 178 ANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNIL 255 (384)
Q Consensus 178 I~h~Ll~~~g~~l~~I~~VySHpqAl~QC~~fL~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ygL~il 255 (384)
|+|||+++++.++++|++|||||||++||++||+++ +++.+++.||++||++++..+.+..|||+|+.||++|||++|
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 999999999988999999999999999999999997 799999999999999987777788999999999999999999
Q ss_pred eccccCCCCCeeEEEEEeeCC
Q 016702 256 ADRIQDEPDNITRFLVLARDP 276 (384)
Q Consensus 256 ~~~I~D~~~N~TRF~vi~~~~ 276 (384)
+++|||.++|+|||+||++++
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 999999999999999999864
No 8
>PRK06034 hypothetical protein; Provisional
Probab=99.92 E-value=2.1e-25 Score=214.99 Aligned_cols=135 Identities=8% Similarity=-0.042 Sum_probs=115.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCC-C--C--C-chhHHHHHhhhhCCCCCCccc-------ee-eccCCCCceEE-E
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSS-N--V--N-DVPGKLCKDLISLPKPLTVAD-------FT-VTPNDGTKVRI-S 101 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~-~--~--~-RE~~il~~~~~~n~GPL~~e~-------i~-~s~~~~~~~~V-a 101 (384)
-+|.||++||+||++++.+||++|++. + + + ||+++|+++...|+|+|+.+. || .|+.+|++.+| +
T Consensus 20 ~ID~eLl~LL~eR~~lv~~Va~~K~~~~~~pv~dP~RE~evl~rl~~~~~g~L~~~~ie~Ifr~Iis~Sr~lQ~~~~V~a 99 (279)
T PRK06034 20 AIDEELHQLLMERGDIIDRLIAVKRTQEVGSAFRPGREADMMRRLVSRHRGILPLDTVESIWRVIIATFTYVQAPFSVHA 99 (279)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccCCCCccChHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCceEEE
Confidence 789999999999999999999999986 3 3 4 999999999999999999874 56 46789999999 9
Q ss_pred EECCCCcHHHHHHHHHCCC-CcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEE
Q 016702 102 FKGLPGSFSEDAALKAYPK-CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEV 174 (384)
Q Consensus 102 ~LGP~GTfS~~AA~~~f~~-~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi 174 (384)
||||+|||||+||++|||. .++++|.||++||++|++|++|||||||+++ .+..+..|.. ....+|++-.
T Consensus 100 ~lG~~gs~s~~AA~~~FG~s~~~~~~~s~~dVf~AV~~g~adyGVVPI~~~-~~~WW~~L~~--~~~~~iiarl 170 (279)
T PRK06034 100 DGSGGEAAMRDSARFHFGFTVPYVPHFSAQAVVEAVARSKGDLGLVSLTSS-DTPWWGRLEA--EGAPKIIARL 170 (279)
T ss_pred EeCCccHHHHHHHHHHhccccCCccCCCHHHHHHHHHcCCCCEEEEECCCC-CCcHHHHhcc--CCCCeEEEeC
Confidence 9999999999999999995 6889999999999999999999999999544 4555543332 4457776543
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=99.86 E-value=1.1e-21 Score=154.51 Aligned_cols=73 Identities=34% Similarity=0.571 Sum_probs=68.7
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHH
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 366 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~ 366 (384)
|||+|+++|+||+|+++|+.|+.+|||||||||||.++.+ |+|.|||||+| +++.+++++++|+
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 HhcCceEEE
Q 016702 367 EFATFLRVL 375 (384)
Q Consensus 367 ~~~~~vkvL 375 (384)
+.+..+|++
T Consensus 65 ~~~~~~~~~ 73 (74)
T cd04904 65 RVVADVNIL 73 (74)
T ss_pred HhcCeEEEc
Confidence 999999885
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=99.84 E-value=1.3e-20 Score=154.11 Aligned_cols=70 Identities=34% Similarity=0.537 Sum_probs=65.5
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHH
Q 016702 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 363 (384)
Q Consensus 284 ~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~ 363 (384)
.+||||+|+++|+||+|+++|++|+.+||||+||||||++..+ |+|.|||||+|+ .+++++++|+
T Consensus 12 ~~ktslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~--------------~~Y~FfVDieg~-~~~~~~~~l~ 76 (90)
T cd04931 12 NGVISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNK--------------DEYEFFINLDKK-SAPALDPIIK 76 (90)
T ss_pred CCcEEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCC--------------ceEEEEEEEEcC-CCHHHHHHHH
Confidence 4689999999999999999999999999999999999998864 999999999999 7899999999
Q ss_pred HHHHh
Q 016702 364 HLQEF 368 (384)
Q Consensus 364 ~L~~~ 368 (384)
+|++.
T Consensus 77 ~L~~~ 81 (90)
T cd04931 77 SLRND 81 (90)
T ss_pred HHHHH
Confidence 99863
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=99.82 E-value=2.2e-20 Score=159.27 Aligned_cols=76 Identities=28% Similarity=0.370 Sum_probs=70.0
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHH
Q 016702 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 363 (384)
Q Consensus 284 ~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~ 363 (384)
.+||||+|+++|+||+|+++|++|+.+|||||||||||++..+ |+|.|||||+|+.+ .++++|+
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 3589999999999999999999999999999999999998864 99999999999864 5999999
Q ss_pred HHHHhcCceEEE
Q 016702 364 HLQEFATFLRVL 375 (384)
Q Consensus 364 ~L~~~~~~vkvL 375 (384)
+|+..+..+++-
T Consensus 103 ~L~~~~~~~kv~ 114 (115)
T cd04930 103 SLRQVAEDVRLT 114 (115)
T ss_pred HHHHhcCeeEec
Confidence 999999988863
No 12
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=99.82 E-value=8e-20 Score=145.26 Aligned_cols=80 Identities=54% Similarity=0.946 Sum_probs=75.7
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 365 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L 365 (384)
|+|++|.++|+||+|.++|+.|+++||||++|+|||.+... |+|.||||++|+.++++++++++.|
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 HHhcCceEEEcccc
Q 016702 366 QEFATFLRVLGCYP 379 (384)
Q Consensus 366 ~~~~~~vkvLGsYp 379 (384)
+..+.++|+||+||
T Consensus 67 ~~~~~~~~~lG~y~ 80 (80)
T cd04905 67 KRLTEFVKVLGSYP 80 (80)
T ss_pred HHhCCeEEEeeeeC
Confidence 99999999999997
No 13
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.82 E-value=3.1e-20 Score=146.51 Aligned_cols=71 Identities=30% Similarity=0.456 Sum_probs=65.2
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHH
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 366 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~ 366 (384)
||++|+++|+||+|+++|++|+.+||||+||||||++..+ |+|.|||||+||. .++++++++|+
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 6899999999999999999999999999999999998864 9999999999987 38999999999
Q ss_pred HhcCceE
Q 016702 367 EFATFLR 373 (384)
Q Consensus 367 ~~~~~vk 373 (384)
+.+...+
T Consensus 65 ~~~~~~~ 71 (74)
T cd04929 65 REVASVN 71 (74)
T ss_pred Hhccccc
Confidence 9877644
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=99.79 E-value=3.7e-19 Score=139.53 Aligned_cols=75 Identities=52% Similarity=0.844 Sum_probs=71.3
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
|++|+++|+||+|.++|+.|+.+|+||++|||||.++.+ |+|.||||++|+.++.++++++++|++
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 588999999999999999999999999999999998864 999999999998888999999999999
Q ss_pred hcCceEEEc
Q 016702 368 FATFLRVLG 376 (384)
Q Consensus 368 ~~~~vkvLG 376 (384)
.+.++|+||
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=3.4e-17 Score=166.44 Aligned_cols=79 Identities=34% Similarity=0.648 Sum_probs=74.5
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
+||||+|+++|+||+|+++|++|+.+|||||||||||++..+ |+|.|||||+|+. +++++++|++
T Consensus 15 ~KTSLiFsL~d~pGaL~~vL~vFa~~gINLthIESRPsk~~~--------------~eY~FFVD~eg~~-~~~v~~aL~~ 79 (436)
T TIGR01268 15 AKTSLIFSLKEEAGALAETLKLFQAHDVNLTHIESRPSKTHP--------------GEYEFFVEFDEAS-DRKLEGVIEH 79 (436)
T ss_pred CeEEEEEEcCCCCcHHHHHHHHHHHCCCCeeEEecccCCCCC--------------ccEEEEEEEecCc-cHHHHHHHHH
Confidence 489999999999999999999999999999999999998865 9999999999987 5899999999
Q ss_pred HHHhc-CceEEEccc
Q 016702 365 LQEFA-TFLRVLGCY 378 (384)
Q Consensus 365 L~~~~-~~vkvLGsY 378 (384)
|++.+ ..+++||+-
T Consensus 80 Lk~~~~~~vkiLGs~ 94 (436)
T TIGR01268 80 LRQKAEVTVNILSRD 94 (436)
T ss_pred HHHhccceEEEeCCC
Confidence 99999 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=99.58 E-value=5.3e-15 Score=151.07 Aligned_cols=76 Identities=29% Similarity=0.318 Sum_probs=69.5
Q ss_pred CCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCccccc-EEEEEEeecCCCcHHHHHH
Q 016702 283 KLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFD-YLFYIDFEASMADPRAQNA 361 (384)
Q Consensus 283 ~~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~-Y~FfID~eg~~~d~~v~~a 361 (384)
+..||||+|+++|+||+|+++|++|+.+|||||||||||++..+ |+ |.|||||+|+. ++++++
T Consensus 28 ~~~ktSLIFsL~d~pGaL~~vL~vFa~~gINLThIESRPsk~~~--------------~e~Y~FfVD~Eg~~--~~l~~a 91 (464)
T TIGR01270 28 GVQRLSIIFSLSNVVGDLSKAIAIFQDRHINILHLESRDSKDGT--------------SKTMDVLVDVELFH--YGLQEA 91 (464)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHCCCCEEEEECCcCCCCC--------------CccEEEEEEEEcCH--HHHHHH
Confidence 35699999999999999999999999999999999999998764 99 99999999976 689999
Q ss_pred HHHHHHhcCceEE
Q 016702 362 LGHLQEFATFLRV 374 (384)
Q Consensus 362 l~~L~~~~~~vkv 374 (384)
|++|++.+..+.+
T Consensus 92 L~~Lk~~~~~~~~ 104 (464)
T TIGR01270 92 MDLLKSGLDVHEV 104 (464)
T ss_pred HHHHHHhccccee
Confidence 9999998887555
No 17
>PRK08818 prephenate dehydrogenase; Provisional
Probab=98.74 E-value=2.1e-08 Score=101.51 Aligned_cols=65 Identities=26% Similarity=0.343 Sum_probs=53.7
Q ss_pred ceEEEEEEeC-CCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHH
Q 016702 285 FKTSIVFTLD-EGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 363 (384)
Q Consensus 285 ~Ktsl~f~~~-~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~ 363 (384)
.-++|+|.++ |+||+|+++|++|+.+|||||+||| .+.++ |+|.|||||++..+-..+..+-.
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 3689999997 9999999999999999999999999 55543 99999999999654455555555
Q ss_pred HH
Q 016702 364 HL 365 (384)
Q Consensus 364 ~L 365 (384)
++
T Consensus 358 ~~ 359 (370)
T PRK08818 358 EI 359 (370)
T ss_pred hh
Confidence 44
No 18
>TIGR01269 Tyr_3_monoox tyrosine 3-monooxygenase, tetrameric. This model describes tyrosine 3-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tryptophan 5-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=98.62 E-value=1.1e-07 Score=97.14 Aligned_cols=73 Identities=22% Similarity=0.255 Sum_probs=60.3
Q ss_pred eEEEEEEeCCC-cchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 286 KTSIVFTLDEG-PGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 286 Ktsl~f~~~~~-pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
.++++|+++++ +|+|.++|++|+.++|||++|||||++... .+ ..+|.|||||+++. .++.++++.
T Consensus 37 ~~~~~~~~~~~~~g~L~~~l~~f~~~~inl~hiEsr~~~~~~--------~~---~~~~~~~v~~~~~~--~~~~~~~~~ 103 (457)
T TIGR01269 37 MQNNQFYIRTKEISSLHRILKYIETFKLNLVHFETRPTRTLS--------NA---DVDYSCLITLEANE--INMSLLIES 103 (457)
T ss_pred ceeEEEEeccCcchhHHHHHHHHHHcCCcEEEeecCCccccC--------CC---CCceEEEEEEeccH--hhHHHHHHH
Confidence 57888888754 999999999999999999999999987542 01 24699999999864 779999999
Q ss_pred HHHhcCc
Q 016702 365 LQEFATF 371 (384)
Q Consensus 365 L~~~~~~ 371 (384)
|++.+..
T Consensus 104 l~~~~~~ 110 (457)
T TIGR01269 104 LRGNSFI 110 (457)
T ss_pred HHhhhcc
Confidence 9987653
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=98.56 E-value=3.2e-08 Score=78.36 Aligned_cols=51 Identities=10% Similarity=-0.055 Sum_probs=46.5
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCC--CC--C--C-chhHHHHHhhhhCCCCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKS--SN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~--~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (384)
.+|.||++||++|+.++.+||++|+. .| + + ||+++|.++...++||++.+.
T Consensus 10 ~iD~~iv~Ll~~R~~~~~~i~~~K~~~~~~~~i~d~~Re~~vl~~~~~~~~~~l~~~~ 67 (76)
T TIGR01807 10 AIDDRILDLLSERATYAQAVGELKGSGASGASFYRPEREAQVIRRLQNLNKGPLDQEA 67 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcCChHHHHHHHHHHHHhccCCCCHHH
Confidence 79999999999999999999999998 66 3 5 999999999999999998754
No 20
>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=98.50 E-value=4.5e-08 Score=81.95 Aligned_cols=51 Identities=12% Similarity=-0.024 Sum_probs=47.5
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCCCCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (384)
-+|.+|++||++|++++.+||++|++.| + + ||+++|+++...++||++.+.
T Consensus 15 ~ID~eIl~LL~eR~~~~~~Ig~~K~~~~~~i~dp~RE~~vl~~~~~~~~g~l~~~~ 70 (102)
T TIGR01801 15 QLNRQILALISRRGEVVAQIGHAKSAQGPNHYDPAREEQMLNELIKINPGPFPTAT 70 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCChHHHHHHHHHHHHhcCCCCCHHH
Confidence 7999999999999999999999999888 3 4 999999999999999999874
No 21
>TIGR01805 CM_mono_grmpos monofunctional chorismate mutase, gram positive-type, clade 2. This model represents a clade of chorismate mutase proteins/domains from gram positive species. The sequence from Enterococcus is fused to the C-terminus of an aparrent acetyltransferase, and the seuence from Clostridium acetobutylicum (but not perfringens) is fused to the N-terminus of shikimate-5-dehydrogenase, another enzyme of the chorismate pathway. All the other members of this clade are mono-functional. Members of this clade from Streptococcus and Lactococcus have been found which represent the sole chorismate mutase domain in their respective genomes which also exhibit evidence of the enzymes of both the upstream and downstream branches of the chorismate pathways.
Probab=98.46 E-value=4.5e-08 Score=78.43 Aligned_cols=51 Identities=6% Similarity=-0.104 Sum_probs=46.5
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCCCCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (384)
-+|.||++||++|++++.+||++|.+.| + + ||++++.++...+++|++.+.
T Consensus 10 ~iD~~i~~Ll~~R~~~~~~i~~~K~~~~~~i~d~~RE~~vl~~~~~~~~~~~~~~~ 65 (81)
T TIGR01805 10 EIDDKLVVLFEERMEVVKEIAAYKKKNGIPIFDSKREQEIIDKCTKNVENKEYRET 65 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcccCCCHHH
Confidence 7899999999999999999999999988 3 5 999999999999999887653
No 22
>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=98.43 E-value=5.1e-08 Score=78.54 Aligned_cols=51 Identities=10% Similarity=-0.124 Sum_probs=46.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (384)
-+|.||++||++|+.++.+||++|.+.| + | ||+++|.++...+. ++|+.+.
T Consensus 10 ~ID~~lv~Ll~~R~~~~~~i~~~K~~~~~~v~dp~RE~~vl~~~~~~~~~~~l~~~~ 66 (83)
T TIGR01797 10 AIDEKLLKLLAERRELAFEVGKSKLLSHRPVRDIERERDLLQRLITLGKAYHLDAHY 66 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhhhCCCCHHH
Confidence 7899999999999999999999999888 3 5 99999999999886 8898764
No 23
>PRK07248 hypothetical protein; Provisional
Probab=98.41 E-value=1e-07 Score=77.33 Aligned_cols=51 Identities=10% Similarity=-0.095 Sum_probs=46.8
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCCCCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (384)
-+|.+|++||++|+.++.+||++|.+.| + + ||++++.++...+++|+.++.
T Consensus 12 ~iD~~i~~Ll~~R~~l~~~I~~~K~~~~~~v~d~~RE~~vl~~~~~~~~~~~~~~~ 67 (87)
T PRK07248 12 QIDDQLVALLEKRMALVEQVVAYKKATGKPVLDTKREQVILDKVSSLVENKAYQET 67 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcccCCCHHH
Confidence 7899999999999999999999999988 3 4 999999999999999987654
No 24
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=98.32 E-value=1.6e-06 Score=86.87 Aligned_cols=73 Identities=29% Similarity=0.445 Sum_probs=63.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
..++++|++++++|+|.++|+.|..+++|+.||||||++... .+|.|||+++... .++.++++.
T Consensus 35 ~~~~~if~~r~~~~~l~~~Lk~f~~~~vnl~HiEsR~s~~~~--------------~~~evlv~~~~~~--~~l~~~i~~ 98 (461)
T KOG3820|consen 35 ARISLIFSLRNKVGALARALKAFEEFHVNLLHIESRPSERRS--------------SGYEVLVELDATR--GQLIQAIEL 98 (461)
T ss_pred ceEEEEEEecccchHHHHHHHHhhhcCceEEEeecccccccC--------------CCceEEEeeccch--hhHHHHHHH
Confidence 368899999999999999999999999999999999997653 4699999999865 478889999
Q ss_pred HHHhcCceE
Q 016702 365 LQEFATFLR 373 (384)
Q Consensus 365 L~~~~~~vk 373 (384)
|+..+..+.
T Consensus 99 lrq~~~~~~ 107 (461)
T KOG3820|consen 99 LRQNHVALS 107 (461)
T ss_pred HHHhcccce
Confidence 988865433
No 25
>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=98.26 E-value=3.5e-07 Score=73.50 Aligned_cols=51 Identities=10% Similarity=-0.082 Sum_probs=45.3
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (384)
.+|.||++||++|+.++.+||++|+..+ + + ||++++.++...+. ++++++.
T Consensus 10 ~ID~~lv~Ll~~R~~~~~~ia~~K~~~~~~v~d~~Re~~vl~~~~~~a~~~gl~~~~ 66 (82)
T TIGR01803 10 RIDLALVQALGRRMDYVKRASEFKRSHEAAIPAPERVAAVLPNAARWAEENGLDPPF 66 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHHcCCCHHH
Confidence 7899999999999999999999999877 3 4 99999999988775 7788753
No 26
>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=98.20 E-value=5.5e-07 Score=72.49 Aligned_cols=51 Identities=6% Similarity=-0.083 Sum_probs=44.7
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (384)
-+|.+|++||++|+.++.+||++|.+.| + + ||++++.++...+. ++++++.
T Consensus 10 ~ID~~il~Ll~~R~~~~~~ia~~K~~~~~~v~d~~RE~~vl~~~~~~a~~~gl~~~~ 66 (83)
T TIGR01799 10 GVDQELLHLLAKRLELVAQVGKVKHAAGLPIYAPEREAAMLAARREEAEKAGIAPDL 66 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhhcCCCCHHH
Confidence 7899999999999999999999999988 3 4 99999999888665 6677653
No 27
>PRK07857 hypothetical protein; Provisional
Probab=98.20 E-value=7.5e-07 Score=74.91 Aligned_cols=42 Identities=7% Similarity=-0.158 Sum_probs=38.7
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhh
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLIS 78 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~ 78 (384)
-+|.||++||++|+.++.+||++|++.| + + ||+++|+++.+.
T Consensus 39 ~ID~eIl~LL~eR~~la~eIg~~K~~~g~pI~dp~RE~eVl~rl~~~ 85 (106)
T PRK07857 39 RLDAEILALVKRRTEVSQAIGKARMASGGTRLVHSREMKVIERYREE 85 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCCccChHHHHHHHHHHHHH
Confidence 6899999999999999999999999988 3 4 999999999874
No 28
>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=98.18 E-value=8.3e-07 Score=70.13 Aligned_cols=44 Identities=9% Similarity=-0.145 Sum_probs=40.2
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP 80 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~ 80 (384)
.+|.||++||++|+.++.+||++|+..| + + ||++++.++...++
T Consensus 11 ~ID~~ii~LL~~R~~~~~~i~~~K~~~~~~i~d~~RE~~vl~~~~~~~~ 59 (74)
T TIGR01808 11 RLDAEILALVKRRAEISQAIGKARMASGGTRLVHSREMKVIERYSELGP 59 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhCC
Confidence 7899999999999999999999999988 3 4 99999999988663
No 29
>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=98.15 E-value=1.8e-05 Score=59.55 Aligned_cols=69 Identities=20% Similarity=0.180 Sum_probs=54.8
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhc
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFA 369 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~ 369 (384)
.+.++|+||.|.++++.|+..|+|++.|.++|..... . .+.+.+++.++.. +...++.+++.|++.+
T Consensus 2 ~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~---------~---~~~~~~~i~v~~~-~~~~l~~l~~~l~~~g 68 (73)
T cd04886 2 RVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTL---------P---LGEVEVELTLETR-GAEHIEEIIAALREAG 68 (73)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCC---------C---CceEEEEEEEEeC-CHHHHHHHHHHHHHcC
Confidence 4678999999999999999999999999999864310 0 1567888888874 4577889999998876
Q ss_pred Cc
Q 016702 370 TF 371 (384)
Q Consensus 370 ~~ 371 (384)
..
T Consensus 69 ~~ 70 (73)
T cd04886 69 YD 70 (73)
T ss_pred CE
Confidence 43
No 30
>PRK06285 chorismate mutase; Provisional
Probab=98.13 E-value=9.3e-07 Score=73.15 Aligned_cols=51 Identities=8% Similarity=-0.167 Sum_probs=45.5
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (384)
.+|.+|++||++|+.++.+||++|+..| + | ||++++.++...+. ++++++.
T Consensus 18 ~ID~~iv~Ll~~R~~l~~~I~~~K~~~~~~v~dp~RE~~vl~~~~~~a~~~~l~~~~ 74 (96)
T PRK06285 18 EIDEQIIDLIAERTSLAKEIAELKKSLGMPIFDPEREDYIHEKIRKLCEEHNIDENI 74 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhhhCCCCHHH
Confidence 7999999999999999999999999988 3 5 99999999988774 8887653
No 31
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=98.12 E-value=1.5e-06 Score=72.73 Aligned_cols=51 Identities=10% Similarity=-0.087 Sum_probs=44.8
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC-C--C-chhHHHHHhhhhCC-CCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN-V--N-DVPGKLCKDLISLP-KPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~-~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (384)
.+|.+|++||++|+.++.+||++|+... + + ||+++|.++...+. ++++.+.
T Consensus 19 ~ID~~iv~LL~eR~~~~~~ia~~K~~~~~i~d~~Re~~vl~~~~~~a~~~gl~~~~ 74 (101)
T PRK07075 19 RLDRDIIAALGRRMQYVKAASRFKPSEASIPAPERVAAMLPERRRWAEQAGLDADF 74 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCcCCCCCChHHHHHHHHHHHHHhhcCCCCHHH
Confidence 7999999999999999999999999755 4 4 99999999988776 8888753
No 32
>PRK11199 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
Probab=98.08 E-value=3e-06 Score=86.04 Aligned_cols=81 Identities=7% Similarity=-0.081 Sum_probs=62.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCccc-------ee-eccCC--------
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD-------FT-VTPND-------- 94 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~-------i~-~s~~~-------- 94 (384)
.+|.||++||++|++++.+||++|++.+ + + ||++++.++...+. ++++++. || .|+..
T Consensus 14 ~iD~~iv~Ll~~R~~~~~~ia~~K~~~~~~v~d~~Re~~vl~~~~~~~~~~~l~~~~~~~i~~~i~~~s~~~q~~~~~~~ 93 (374)
T PRK11199 14 EVDKQLLELLAKRLELVAQVGEVKSRHGLPIYVPEREAAMLASRRAEAEALGVPPDLIEDVLRRVMRESYSSENDKGFKT 93 (374)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHhHHhcccc
Confidence 8999999999999999999999999988 3 4 99999999888765 6676653 44 23321
Q ss_pred --CCceEEEEECCCCcHHHHHHHHH
Q 016702 95 --GTKVRISFKGLPGSFSEDAALKA 117 (384)
Q Consensus 95 --~~~~~Va~LGP~GTfS~~AA~~~ 117 (384)
+..++|++.|-.|....--|+.+
T Consensus 94 ~~~~~~~I~IiGG~GlmG~slA~~l 118 (374)
T PRK11199 94 LNPDLRPVVIVGGKGQLGRLFAKML 118 (374)
T ss_pred cCcccceEEEEcCCChhhHHHHHHH
Confidence 23478999985577766555544
No 33
>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=98.06 E-value=2.3e-05 Score=58.46 Aligned_cols=38 Identities=18% Similarity=0.372 Sum_probs=34.9
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~ 324 (384)
+.+.+..+|+||.|.++++.|+++|||+..+.+++.+.
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 45778889999999999999999999999999999865
No 34
>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=98.06 E-value=1.5e-06 Score=69.84 Aligned_cols=50 Identities=6% Similarity=-0.072 Sum_probs=42.6
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCcc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVA 86 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e 86 (384)
.+|.||++||++|+.++.+||++|++.| + | ||++++.++..... ..++++
T Consensus 10 ~iD~~i~~Ll~~R~~l~~~i~~~K~~~g~~i~d~~RE~~v~~~~~~~~~~~~l~~~ 65 (83)
T TIGR01791 10 EIDKSILDLIEKRIKIARKIGEIKHNNGLPITDEEREERVIERLRNTARNLGLDVL 65 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHhcCCCHH
Confidence 7999999999999999999999999988 3 4 99999999875443 346654
No 35
>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=98.05 E-value=6.7e-07 Score=71.20 Aligned_cols=51 Identities=8% Similarity=-0.147 Sum_probs=45.8
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (384)
.+|.+|++||.+|+.++.+||++|.+.| + + ||++++.++..... ++++++.
T Consensus 6 ~iD~~i~~Ll~~R~~l~~~i~~~K~~~~~~i~d~~RE~~v~~~~~~~~~~~~l~~~~ 62 (81)
T PF01817_consen 6 EIDREIVDLLAERMDLVRKIAEYKKENGLPIFDPDREEEVLERLRELAEEGGLDPEF 62 (81)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSTHHHHHHHHHHHHHHHHHTTSEHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHHHHhHhCCCCHHH
Confidence 6899999999999999999999999998 3 4 99999999988777 8888653
No 36
>COG1605 PheA Chorismate mutase [Amino acid transport and metabolism]
Probab=98.03 E-value=3e-06 Score=70.80 Aligned_cols=51 Identities=8% Similarity=-0.100 Sum_probs=45.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC-C----C-chhHHHHHhh-hhCCCCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN-V----N-DVPGKLCKDL-ISLPKPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~-~----~-RE~~il~~~~-~~n~GPL~~e~ 87 (384)
-+|.+|++||++|+.++++||++|.++| . + ||++||+++. ..+.++++++.
T Consensus 19 ~iD~~ll~Ll~eR~~l~~~Va~~K~~~g~~pi~d~~RE~~vl~~~~~~~~~~~l~~~~ 76 (101)
T COG1605 19 EIDRELLDLLAERLELAKEVGEAKAASGKLPIYDPEREEQVLERLRAEAEKGGLDPEL 76 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCHHH
Confidence 3899999999999999999999999887 2 4 9999999998 57888888764
No 37
>PRK06443 chorismate mutase; Validated
Probab=98.02 E-value=2.3e-06 Score=77.59 Aligned_cols=71 Identities=8% Similarity=-0.132 Sum_probs=53.5
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCCCCCCccceee-ccCCC----CceEEEEECCC
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVADFTV-TPNDG----TKVRISFKGLP 106 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~i~~-s~~~~----~~~~Va~LGP~ 106 (384)
-+|.||++||++|++++.+||++|++.| + | ||+++++++.+.|+ +-. .||+ |+..| .+..|-..|
T Consensus 16 ~ID~eIL~LL~kRm~la~eIg~~K~~~g~pI~Dp~RE~eVLerl~~~n~--If~-eIms~Sr~~Q~~~~~~~~i~~sg-- 90 (177)
T PRK06443 16 ENTMDIIELIEKRRELARMIGIIKMRNGLSIRDSERENYVKNNLKSDNP--LLN-MIFEATIHYQKNISLNINIEVSG-- 90 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhCH--HHH-HHHHHHHHHHhcccccceeeeec--
Confidence 7899999999999999999999999988 3 4 99999999999885 332 3553 55443 344555554
Q ss_pred CcHHHHH
Q 016702 107 GSFSEDA 113 (384)
Q Consensus 107 GTfS~~A 113 (384)
.|-..|
T Consensus 91 -~y~~~~ 96 (177)
T PRK06443 91 -DYDSLI 96 (177)
T ss_pred -chHHHH
Confidence 455544
No 38
>PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed
Probab=98.01 E-value=2.4e-06 Score=86.37 Aligned_cols=51 Identities=6% Similarity=-0.185 Sum_probs=47.5
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCCCCCCccc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (384)
-+|+||++||+||++++.+||++|++.| + + ||+++|+++...+.|||+.+.
T Consensus 15 ~ID~eIl~LL~~R~~~~~~I~~~K~~~g~pi~dp~RE~~vl~~~~~~~~g~l~~~~ 70 (360)
T PRK12595 15 EINLQLLELLSKRGELVQEIGEEKTKQGTKRYDPVREREMLDMIAENNEGPFEDST 70 (360)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhccCCCCHHH
Confidence 7999999999999999999999999988 3 4 999999999999999999863
No 39
>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=97.83 E-value=5.9e-06 Score=68.23 Aligned_cols=44 Identities=0% Similarity=-0.191 Sum_probs=39.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP 80 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~ 80 (384)
.+|.||++||++|+.++.+||++|...| + | ||++++.++...+.
T Consensus 14 ~ID~qLv~LL~~R~~~~~~ia~~K~~~~~~v~dp~Re~~vl~~~~~~a~ 62 (94)
T TIGR01795 14 NIDAAVIHMLAERFKCTSQVGVLKANAGLAPADPAREDYQIARLRRLAI 62 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHH
Confidence 7999999999999999999999999988 3 4 99999999876443
No 40
>PRK09239 chorismate mutase; Provisional
Probab=97.83 E-value=7e-06 Score=69.04 Aligned_cols=50 Identities=2% Similarity=-0.182 Sum_probs=43.0
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCcc
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVA 86 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e 86 (384)
.+|.+|++||++|+.++.+||++|+..| + | ||++++.++...+. ..|+++
T Consensus 21 ~ID~eIv~LLa~R~~l~~~Ia~~K~~~~~~i~dp~RE~~vl~~~~~~a~~~gl~p~ 76 (104)
T PRK09239 21 NIDAALIHMLAERFKCTQAVGVLKAEHGLPPADPAREAYQIERLRQLAKDANLDPD 76 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCHH
Confidence 7999999999999999999999999888 3 5 99999999877665 445543
No 41
>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=97.78 E-value=1.8e-05 Score=62.40 Aligned_cols=47 Identities=6% Similarity=-0.055 Sum_probs=41.7
Q ss_pred cchhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCCCCC
Q 016702 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPL 83 (384)
Q Consensus 37 ~~~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~GPL 83 (384)
.+|.+|++||.+|+.++.+||++|...| + + ||++++.++........
T Consensus 6 ~iD~~ii~Ll~~R~~l~~~i~~~K~~~~~~i~d~~Re~~vl~~~~~~a~~~~ 57 (79)
T smart00830 6 AIDDQILALLAERAALAREVARLKAKNGLPIYDPEREAEVLERLRALAEGPG 57 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCChHHHHHHHHHHHHHcccCC
Confidence 6899999999999999999999999877 3 4 99999999988776543
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=97.59 E-value=4.5e-05 Score=65.14 Aligned_cols=48 Identities=10% Similarity=0.005 Sum_probs=42.0
Q ss_pred hhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 016702 40 GGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (384)
Q Consensus 40 ~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (384)
.+|++||++|+.++.+||++|...| + + ||++++.++...+. ++|+.+.
T Consensus 7 ~eLv~Ll~eR~~la~eVa~~K~~~~~pI~Dp~RE~~Vl~~~~~~a~~~gL~~~~ 60 (114)
T TIGR01806 7 GQLVDAANERLQLADDVAGYKARNNLPIEDSPREEQVLDSLRAQAQSAGLDPDY 60 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCChHHHHHHHHHHHHHhHcCCCCHHH
Confidence 5899999999999999999999888 4 4 99999999988776 7777653
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=97.39 E-value=0.001 Score=49.45 Aligned_cols=60 Identities=22% Similarity=0.282 Sum_probs=43.6
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
+.+.++|+||.|.++++.|+++|+|+..+...|.... ....+++.+++ .+.+++.|++.
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~---------------~~~~v~~~ve~------~~~~~~~L~~~ 60 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKG---------------GKALLIFRTED------IEKAIEVLQER 60 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCC---------------CeEEEEEEeCC------HHHHHHHHHHC
Confidence 4568899999999999999999999999987665421 23455666654 34566666654
Q ss_pred c
Q 016702 369 A 369 (384)
Q Consensus 369 ~ 369 (384)
.
T Consensus 61 G 61 (65)
T cd04882 61 G 61 (65)
T ss_pred C
Confidence 3
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=97.39 E-value=0.0012 Score=50.89 Aligned_cols=65 Identities=12% Similarity=0.140 Sum_probs=45.0
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
+.+.++|+||+|.++++.++++|+|+..+...+..... +....+|.+++...+ .++.+++.|++.
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~--------------~~~~~~v~v~~e~~~-~~~~i~~~L~~~ 66 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPD--------------GMRRVFIRVTPMDRS-KENELIEELKAK 66 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCC--------------CccEEEEEEEEecch-HHHHHHHHHhCc
Confidence 55688999999999999999999999999766543221 223345555542222 366777777655
No 45
>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=97.26 E-value=0.0036 Score=46.71 Aligned_cols=68 Identities=19% Similarity=0.268 Sum_probs=51.5
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
+|.+..+|+||.|.++++.|+.+++|+..+...+.+.. ....+++.++. .+ +.+.+++++|++
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 46778899999999999999999999999998765321 12345555554 34 789999999987
Q ss_pred hcCce
Q 016702 368 FATFL 372 (384)
Q Consensus 368 ~~~~v 372 (384)
...-.
T Consensus 65 ~~~v~ 69 (72)
T cd04878 65 LVDVL 69 (72)
T ss_pred CccEE
Confidence 76543
No 46
>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=97.25 E-value=0.0027 Score=47.53 Aligned_cols=64 Identities=19% Similarity=0.263 Sum_probs=48.3
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
.|.+..+|+||.|.++++.|+++++|+.++...+... ..+.+++++++. ..+..+++.|++
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 4667789999999999999999999999998766432 235567888875 245567777776
Q ss_pred hcC
Q 016702 368 FAT 370 (384)
Q Consensus 368 ~~~ 370 (384)
...
T Consensus 63 ~~~ 65 (72)
T cd04874 63 LPI 65 (72)
T ss_pred CCC
Confidence 543
No 47
>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=97.23 E-value=0.0031 Score=48.05 Aligned_cols=65 Identities=17% Similarity=0.340 Sum_probs=45.9
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHH
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 366 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~ 366 (384)
+.+.+.++|+||.|.++++.|+++|+|+.++..-+.... ....++|.+++. ++ ..+++.|+
T Consensus 2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~---------------~~~~v~i~v~~~--~~--~~~~~~L~ 62 (72)
T cd04883 2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEE---------------DNKILVFRVQTM--NP--RPIIEDLR 62 (72)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCC---------------CeEEEEEEEecC--CH--HHHHHHHH
Confidence 457788999999999999999999999999976554331 234456666652 22 15666666
Q ss_pred HhcC
Q 016702 367 EFAT 370 (384)
Q Consensus 367 ~~~~ 370 (384)
+..-
T Consensus 63 ~~G~ 66 (72)
T cd04883 63 RAGY 66 (72)
T ss_pred HCCC
Confidence 6543
No 48
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=97.13 E-value=0.0045 Score=49.26 Aligned_cols=71 Identities=14% Similarity=0.244 Sum_probs=54.3
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHH
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 366 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~ 366 (384)
-+|.+-+.|+||.|.+++..|+.||.|+..|..-|+... .-+.+-|-+.| +|..+.++.++|.
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 456777789999999999999999999999998887542 22455555555 4577888888888
Q ss_pred HhcCceEE
Q 016702 367 EFATFLRV 374 (384)
Q Consensus 367 ~~~~~vkv 374 (384)
+.-.=+++
T Consensus 66 KLidV~~V 73 (76)
T PRK06737 66 KLINVLQV 73 (76)
T ss_pred CCcCEEEE
Confidence 77654443
No 49
>PRK09269 chorismate mutase; Provisional
Probab=97.10 E-value=0.00039 Score=64.67 Aligned_cols=49 Identities=8% Similarity=-0.031 Sum_probs=42.6
Q ss_pred hhhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 016702 39 RGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (384)
Q Consensus 39 ~~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (384)
=.+|++||+||+.++.+|+.+|...| | + ||+++|.++...+. ++++.+.
T Consensus 34 l~~Lv~Li~eRl~la~~VA~~K~~~~~pI~Dp~RE~~VL~~v~~~A~~~gLdp~~ 88 (193)
T PRK09269 34 LTPLVDLAAQRLALADPVALSKWDSGKPIEDPPREAQVLANVEAQAPAHGVDPDY 88 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHhhcCCCCHHH
Confidence 36899999999999999999999988 4 4 99999999988776 7777653
No 50
>PRK08055 chorismate mutase; Provisional
Probab=97.06 E-value=0.00042 Score=63.82 Aligned_cols=47 Identities=11% Similarity=0.057 Sum_probs=40.9
Q ss_pred hhHHHHHHHHHHHHHHhhhccCCCC--C--C-chhHHHHHhhhhCC--CCCCccc
Q 016702 40 GGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP--KPLTVAD 87 (384)
Q Consensus 40 ~~il~LLn~Ra~~a~eig~~K~~~~--~--~-RE~~il~~~~~~n~--GPL~~e~ 87 (384)
.+|++||+||+.++.+|+++|...| + + ||+++|.++...+. | ++.+.
T Consensus 28 ~~Lv~Li~eRl~la~~VA~~K~~~~~PI~Dp~RE~~VL~~v~~~A~~~G-Ldp~~ 81 (181)
T PRK08055 28 GALATLINERLSYMKDVAGYKAEHHLPIEDLTQEQKVLAEAEEEAASNG-LDPES 81 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHhhhCC-CCHHH
Confidence 4799999999999999999999988 4 4 99999999988776 4 76653
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=96.94 E-value=0.0053 Score=41.97 Aligned_cols=58 Identities=28% Similarity=0.328 Sum_probs=43.5
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHH
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 365 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L 365 (384)
.+..+++||.+.++++.|+.+++++.++.+++... . +...|++.++... .++.++++|
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 4566777776532 455555554
No 52
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=96.88 E-value=0.0067 Score=46.29 Aligned_cols=62 Identities=19% Similarity=0.296 Sum_probs=48.2
Q ss_pred CCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhcCceE
Q 016702 295 EGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLR 373 (384)
Q Consensus 295 ~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~~vk 373 (384)
|+||.|.+++..|..+|+|+..|..-|+... .-+.+.|.++|. +..+..+.+.|.+...-++
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~---------------~~~riti~v~~~--~~~i~~l~~Ql~KlidV~~ 62 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDP---------------GISRITIVVSGD--DREIEQLVKQLEKLIDVVK 62 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-SST---------------TEEEEEEEEES---CCHHHHHHHHHHCSTTEEE
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecCCC---------------CEEEEEEEEeeC--chhHHHHHHHHhccCCeEe
Confidence 6899999999999999999999999995442 357788888874 4678888888888765443
No 53
>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=96.79 E-value=0.013 Score=45.02 Aligned_cols=73 Identities=23% Similarity=0.278 Sum_probs=50.7
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
+|.+..+|+||.|.++++.+++.|+|+..+.+...... .+...|-|+. +..+..+..+++.|++
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~--------------~~~i~~~v~v--~~~~~~l~~l~~~L~~ 65 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHG--------------RANVTISIDT--STMNGDIDELLEELRE 65 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCC--------------eEEEEEEEEc--CchHHHHHHHHHHHhc
Confidence 57788899999999999999999999999987432111 1344555555 3233367788888875
Q ss_pred hc--CceEEEc
Q 016702 368 FA--TFLRVLG 376 (384)
Q Consensus 368 ~~--~~vkvLG 376 (384)
.- ..|+++|
T Consensus 66 i~~V~~v~~~~ 76 (76)
T cd04888 66 IDGVEKVELVG 76 (76)
T ss_pred CCCeEEEEEeC
Confidence 43 3466655
No 54
>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=96.67 E-value=0.014 Score=44.26 Aligned_cols=35 Identities=17% Similarity=0.293 Sum_probs=31.1
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 322 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~ 322 (384)
-|.+.++|+||.|.++++.|+++|+|+..+..-|.
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 35678899999999999999999999999987664
No 55
>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=96.67 E-value=0.01 Score=44.12 Aligned_cols=63 Identities=17% Similarity=0.355 Sum_probs=44.9
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
|.+..+|+||.|.++++.|+++|+|+..+...+..... .....|+++.. .+.+++++|++.
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~---------------~~~i~i~v~~~----~~~~~i~~l~~~ 62 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGD---------------QALMVIEVDQP----IDEEVIEEIKKI 62 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCC---------------eEEEEEEeCCC----CCHHHHHHHHcC
Confidence 56778899999999999999999999999887642211 12334666553 344677777764
Q ss_pred cC
Q 016702 369 AT 370 (384)
Q Consensus 369 ~~ 370 (384)
-.
T Consensus 63 ~~ 64 (71)
T cd04903 63 PN 64 (71)
T ss_pred CC
Confidence 43
No 56
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=96.60 E-value=0.022 Score=45.35 Aligned_cols=67 Identities=10% Similarity=0.162 Sum_probs=49.9
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 365 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L 365 (384)
|-+|.+.+.|+||.|.+++..|+.||.|+..|.--|+.... .+.-.+-+ + ++..+..+.++|
T Consensus 3 ~~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~~-------------~sriti~v--~---~~~~i~ql~kQL 64 (76)
T PRK11152 3 QHQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDAQ-------------NINIELTV--A---SERPIDLLSSQL 64 (76)
T ss_pred eEEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCCC-------------EEEEEEEE--C---CCchHHHHHHHH
Confidence 45677778999999999999999999999999998875421 12222332 2 466778888888
Q ss_pred HHhcC
Q 016702 366 QEFAT 370 (384)
Q Consensus 366 ~~~~~ 370 (384)
.+.-.
T Consensus 65 ~KL~d 69 (76)
T PRK11152 65 NKLVD 69 (76)
T ss_pred hcCcC
Confidence 87654
No 57
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=96.59 E-value=0.02 Score=51.93 Aligned_cols=71 Identities=17% Similarity=0.265 Sum_probs=54.9
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHH
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 366 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~ 366 (384)
-.|.+.++|+||.|.++.+.|++||+|+..+-.-|.... ..+.+.|-++| ++..+.++.++|.
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 457777899999999999999999999999988887432 23455666666 5678889999998
Q ss_pred HhcCceEE
Q 016702 367 EFATFLRV 374 (384)
Q Consensus 367 ~~~~~vkv 374 (384)
+.-.=+++
T Consensus 66 KLidV~~V 73 (161)
T PRK11895 66 KLIDVLKV 73 (161)
T ss_pred ccccEEEE
Confidence 87654444
No 58
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=96.59 E-value=0.019 Score=51.79 Aligned_cols=70 Identities=17% Similarity=0.269 Sum_probs=54.3
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
.|.+.+.|+||.|.++.+.|+++|+|+..+-.-|.... ..+.+.|-+++ ++..+.++.++|.+
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 56677899999999999999999999999988887432 23456666666 56788888888887
Q ss_pred hcCceEE
Q 016702 368 FATFLRV 374 (384)
Q Consensus 368 ~~~~vkv 374 (384)
.-.=+++
T Consensus 66 li~V~~V 72 (157)
T TIGR00119 66 LVDVIKV 72 (157)
T ss_pred CccEEEE
Confidence 7654444
No 59
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.57 E-value=0.016 Score=43.96 Aligned_cols=36 Identities=19% Similarity=0.352 Sum_probs=31.5
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~ 323 (384)
.+.+.++|+||.|.++++.|+.+|+|+..+...+.+
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~ 38 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIR 38 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEee
Confidence 466788999999999999999999999999876653
No 60
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=96.57 E-value=0.023 Score=44.47 Aligned_cols=71 Identities=14% Similarity=0.253 Sum_probs=52.0
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHH
Q 016702 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 363 (384)
Q Consensus 284 ~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~ 363 (384)
.+.+.|.+...|+||.|.++++.++..|+|+..+..++.+.. ..+.+.++++-. +-..+..+++
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 457889999999999999999999999999999999997521 234555555543 4478889999
Q ss_pred HHHHhcC
Q 016702 364 HLQEFAT 370 (384)
Q Consensus 364 ~L~~~~~ 370 (384)
.|++.-.
T Consensus 68 ~L~~i~~ 74 (80)
T PF13291_consen 68 KLRQIPG 74 (80)
T ss_dssp HHCTSTT
T ss_pred HHHCCCC
Confidence 9886543
No 61
>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=96.57 E-value=0.0092 Score=45.29 Aligned_cols=61 Identities=16% Similarity=0.278 Sum_probs=43.5
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
+++..+|+||.|.++++.|+++|+|+..+.+.+.... ......+++++.. .+ .++++|++.
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~---------------~~~~~~i~v~~~~-~~---~~~~~l~~~ 62 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPG---------------GEALMVLSVDEPV-PD---EVLEELRAL 62 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCC---------------CEEEEEEEeCCCC-CH---HHHHHHHcC
Confidence 4667899999999999999999999999987665322 2345666887733 33 444555443
No 62
>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=96.49 E-value=0.016 Score=42.94 Aligned_cols=63 Identities=16% Similarity=0.264 Sum_probs=45.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
+.+..+|+||.|.++++.|+++|+|+.++.+.+.... ..+...++++.. ...+++++|++.
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 5677899999999999999999999999999875321 123445566432 244667777665
Q ss_pred cC
Q 016702 369 AT 370 (384)
Q Consensus 369 ~~ 370 (384)
-.
T Consensus 63 ~~ 64 (71)
T cd04879 63 PG 64 (71)
T ss_pred CC
Confidence 43
No 63
>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=96.38 E-value=0.01 Score=45.41 Aligned_cols=62 Identities=23% Similarity=0.220 Sum_probs=44.4
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhc
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFA 369 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~ 369 (384)
.+.+|++||+|.++++.++. +.|++.+.=|-.... .....+=|++.+ ...++++++.|++..
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~~--------------~~~v~v~ie~~~---~~~~~~i~~~L~~~G 63 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGGD--------------EARVLVGIQVPD---REDLAELKERLEALG 63 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCCC--------------ceEEEEEEEeCC---HHHHHHHHHHHHHcC
Confidence 57889999999999999999 999999976654311 134444455543 256677777777654
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=96.34 E-value=0.021 Score=43.72 Aligned_cols=63 Identities=14% Similarity=0.217 Sum_probs=46.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
|.+..+|+||.|.++.+.++..|+|+..++++..+.. .....|-|++. +.+.++.+++.|+..
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 6678899999999999999999999999999864321 12334444443 236677788887754
No 65
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=96.34 E-value=0.018 Score=52.79 Aligned_cols=72 Identities=18% Similarity=0.316 Sum_probs=54.1
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 365 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L 365 (384)
|-.|.+...|+||.|.++.+.|+.||+|+..+.+.|..... ...+-|.+.+. +..+.++.++|
T Consensus 2 ~~~isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~~---------------~sr~TIvv~~~--~~~ieqL~kQL 64 (174)
T CHL00100 2 KHTLSVLVEDESGVLTRIAGLFARRGFNIESLAVGPAEQKG---------------ISRITMVVPGD--DRTIEQLTKQL 64 (174)
T ss_pred eEEEEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCCC---------------ccEEEEEEECC--HHHHHHHHHHH
Confidence 34566777899999999999999999999999998865431 23566667663 23377777788
Q ss_pred HHhcCceEE
Q 016702 366 QEFATFLRV 374 (384)
Q Consensus 366 ~~~~~~vkv 374 (384)
.+.+.-+++
T Consensus 65 ~KLidVl~V 73 (174)
T CHL00100 65 YKLVNILKV 73 (174)
T ss_pred HHHhHhhEE
Confidence 877765554
No 66
>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=96.29 E-value=0.02 Score=45.40 Aligned_cols=64 Identities=17% Similarity=0.238 Sum_probs=43.5
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceee--eeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCC-CcHHHH-HHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLT--KIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASM-ADPRAQ-NALG 363 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLt--kIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~-~d~~v~-~al~ 363 (384)
-|-+..+|+||-|+++.+.|++.|+++. ||.|--... .-.=.||||.+|.. .|+.-+ .+-+
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Ge---------------rv~D~Fyv~~~g~kl~d~~~~~~L~~ 66 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGY---------------REVDLFIVQSDGKKIMDPKKQAALCA 66 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccC---------------EEEEEEEEeCCCCccCCHHHHHHHHH
Confidence 3556779999999999999999999987 565332211 13458999988854 554433 3333
Q ss_pred HHH
Q 016702 364 HLQ 366 (384)
Q Consensus 364 ~L~ 366 (384)
.|.
T Consensus 67 ~L~ 69 (75)
T cd04896 67 RLR 69 (75)
T ss_pred HHH
Confidence 443
No 67
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=96.14 E-value=0.047 Score=44.27 Aligned_cols=72 Identities=11% Similarity=0.161 Sum_probs=52.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHH
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 366 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~ 366 (384)
-.|.+-+.|+||.|.++-..|++||+|+..|.--|+.... ...+.+-++. | ++..+.++.++|+
T Consensus 3 ~~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~~-------------iSRmtivv~~-~--d~~~ieqI~kQL~ 66 (84)
T PRK13562 3 RILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQPG-------------ISNMEIQVDI-Q--DDTSLHILIKKLK 66 (84)
T ss_pred EEEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCCCC-------------ceEEEEEEeC-C--CHHHHHHHHHHHh
Confidence 4566667899999999999999999999999988876432 1233333332 3 4567788889998
Q ss_pred HhcCceEE
Q 016702 367 EFATFLRV 374 (384)
Q Consensus 367 ~~~~~vkv 374 (384)
+.-.=+++
T Consensus 67 KlidVikV 74 (84)
T PRK13562 67 QQINVLTV 74 (84)
T ss_pred CCccEEEE
Confidence 87654444
No 68
>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=96.02 E-value=0.043 Score=41.50 Aligned_cols=64 Identities=16% Similarity=0.259 Sum_probs=46.4
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
|.+...|+||.|.++++.|+.+|+|+.++.+++..... .....|-++. .+...++++++.|++.
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 45677899999999999999999999999887653211 1223333332 3467888899998864
No 69
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=95.95 E-value=0.086 Score=43.79 Aligned_cols=71 Identities=20% Similarity=0.376 Sum_probs=53.8
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 365 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L 365 (384)
+-.|.+-+.|+||.|.++-..|+.||.|+..|-.-|+.... -..+.|-+. +|..+.++.++|
T Consensus 8 ~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~~~---------------iSRmtivv~---~~~~i~Qi~kQL 69 (96)
T PRK08178 8 NVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQDGD---------------KSRIWLLVN---DDQRLEQMISQI 69 (96)
T ss_pred CEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCCCC---------------ceEEEEEEc---CchHHHHHHHHH
Confidence 45677778899999999999999999999999888875431 123444443 357889999999
Q ss_pred HHhcCceEE
Q 016702 366 QEFATFLRV 374 (384)
Q Consensus 366 ~~~~~~vkv 374 (384)
++.-.=+++
T Consensus 70 ~KLidVikV 78 (96)
T PRK08178 70 EKLEDVLKV 78 (96)
T ss_pred hCCcCEEEE
Confidence 887665544
No 70
>PRK04435 hypothetical protein; Provisional
Probab=95.88 E-value=0.075 Score=47.28 Aligned_cols=77 Identities=18% Similarity=0.216 Sum_probs=56.5
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
.+++|.+.++|+||.|.++++.++..|+|+..|........ .....|=||... .+..+.++++.
T Consensus 68 r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g--------------~a~vs~tVevs~--~~~~L~~Li~~ 131 (147)
T PRK04435 68 KIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQG--------------RANVTISIDTSS--MEGDIDELLEK 131 (147)
T ss_pred cEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCC--------------EEEEEEEEEeCC--hHHHHHHHHHH
Confidence 47889999999999999999999999999999986422111 134566666632 23478888888
Q ss_pred HHHh--cCceEEEcc
Q 016702 365 LQEF--ATFLRVLGC 377 (384)
Q Consensus 365 L~~~--~~~vkvLGs 377 (384)
|+.. ...|+++|.
T Consensus 132 L~~i~gV~~V~i~~~ 146 (147)
T PRK04435 132 LRNLDGVEKVELIGM 146 (147)
T ss_pred HHcCCCcEEEEEEec
Confidence 8854 346777774
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=95.87 E-value=0.019 Score=43.14 Aligned_cols=61 Identities=20% Similarity=0.237 Sum_probs=44.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
+++...|+||.|.++++.|+++|+|+..+.+++..+ .-...++++.. ..++++++|++.
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~-----------------~a~~~~~~~~~----~l~~li~~l~~~ 60 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGE-----------------IGYVVIDIDSE----VSEELLEALRAI 60 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCC-----------------EEEEEEEcCCC----CCHHHHHHHHcC
Confidence 566778999999999999999999999987765431 12334466654 345677777765
Q ss_pred cC
Q 016702 369 AT 370 (384)
Q Consensus 369 ~~ 370 (384)
-.
T Consensus 61 ~~ 62 (69)
T cd04901 61 PG 62 (69)
T ss_pred CC
Confidence 43
No 72
>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=95.76 E-value=0.068 Score=42.80 Aligned_cols=69 Identities=16% Similarity=0.175 Sum_probs=44.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
+.+.+||+||+|.++|+.++..||+ .+.=+-.... .....+-|++.+. ...++++++.|++.
T Consensus 4 l~v~ipD~PG~L~~ll~~l~~anI~--~~~y~~~~~~--------------~~~v~i~ie~~~~--~~~~~~i~~~L~~~ 65 (85)
T cd04906 4 LAVTIPERPGSFKKFCELIGPRNIT--EFNYRYADEK--------------DAHIFVGVSVANG--AEELAELLEDLKSA 65 (85)
T ss_pred EEEecCCCCcHHHHHHHHhCCCcee--EEEEEccCCC--------------eeEEEEEEEeCCc--HHHHHHHHHHHHHC
Confidence 6678899999999999999955554 4433322111 1345555676541 25567777888776
Q ss_pred cCceEEE
Q 016702 369 ATFLRVL 375 (384)
Q Consensus 369 ~~~vkvL 375 (384)
.-.+.++
T Consensus 66 G~~~~~~ 72 (85)
T cd04906 66 GYEVVDL 72 (85)
T ss_pred CCCeEEC
Confidence 6655554
No 73
>PRK08198 threonine dehydratase; Provisional
Probab=95.74 E-value=0.077 Score=54.31 Aligned_cols=77 Identities=16% Similarity=0.182 Sum_probs=56.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeee-CCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP-QRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 363 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP-~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~ 363 (384)
...+|.+.++|+||.|.++|+.++..|.|+..|.-.+ ..+.+ .....+.|.+|.. +...++++++
T Consensus 326 r~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~~~~~~~-------------~~~~~v~v~ie~~-~~~~~~~l~~ 391 (404)
T PRK08198 326 RYLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDRFSPDLR-------------LGEVEVELTLETR-GPEHIEEILD 391 (404)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEEccCCCC-------------CceEEEEEEEEeC-CHHHHHHHHH
Confidence 3568889999999999999999999999999987654 33322 1234555666653 2346778899
Q ss_pred HHHHhcCceEEE
Q 016702 364 HLQEFATFLRVL 375 (384)
Q Consensus 364 ~L~~~~~~vkvL 375 (384)
.|++..-.++++
T Consensus 392 ~L~~~G~~v~~~ 403 (404)
T PRK08198 392 ALRDAGYEVKVV 403 (404)
T ss_pred HHHHCCCeEEEc
Confidence 998877666543
No 74
>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=95.73 E-value=0.062 Score=41.63 Aligned_cols=36 Identities=19% Similarity=0.302 Sum_probs=31.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 322 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~ 322 (384)
|-+.+..+|+||.|+++.+.|+.+|+|+......+.
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 457788899999999999999999999998776654
No 75
>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=95.41 E-value=0.14 Score=38.17 Aligned_cols=36 Identities=17% Similarity=0.194 Sum_probs=31.9
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~ 323 (384)
-+.+..+|+||.|.++.+.|+.+|+|+..+...+..
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~ 37 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTG 37 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecC
Confidence 366788999999999999999999999999887754
No 76
>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=95.29 E-value=0.15 Score=38.40 Aligned_cols=38 Identities=21% Similarity=0.245 Sum_probs=32.9
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~ 324 (384)
|-+.+..+|+||.|.++.+.|+.+++|+.++...+..+
T Consensus 1 ~~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~ 38 (70)
T cd04899 1 TVLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGE 38 (70)
T ss_pred CEEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCC
Confidence 34667789999999999999999999999999887643
No 77
>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=95.28 E-value=0.18 Score=36.01 Aligned_cols=64 Identities=16% Similarity=0.213 Sum_probs=44.7
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhc
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFA 369 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~ 369 (384)
.+..+|+||.+.++++.|+++++|+..++..+.... ...+.+.++.. +...+..+++.|+..-
T Consensus 2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~----------------~~~~~~~~~~~-~~~~~~~~~~~l~~~~ 64 (71)
T cd04876 2 RVEAIDRPGLLADITTVIAEEKINILSVNTRTDDDG----------------LATIRLTLEVR-DLEHLARIMRKLRQIP 64 (71)
T ss_pred EEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCCC----------------EEEEEEEEEEC-CHHHHHHHHHHHhCCC
Confidence 456789999999999999999999999988764311 12233444332 3456777888877654
Q ss_pred C
Q 016702 370 T 370 (384)
Q Consensus 370 ~ 370 (384)
.
T Consensus 65 ~ 65 (71)
T cd04876 65 G 65 (71)
T ss_pred C
Confidence 3
No 78
>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=95.24 E-value=0.081 Score=41.62 Aligned_cols=29 Identities=24% Similarity=0.416 Sum_probs=26.1
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceee
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLT 315 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLt 315 (384)
|-|-+..+|+||-|+++.++|++.|+++.
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~ 30 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCIT 30 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEE
Confidence 45667789999999999999999999998
No 79
>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=95.19 E-value=0.1 Score=41.77 Aligned_cols=67 Identities=16% Similarity=0.232 Sum_probs=46.0
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeec-CCCcHHHHHHHHHH
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEA-SMADPRAQNALGHL 365 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg-~~~d~~v~~al~~L 365 (384)
-.+.+.-+|+||-+.++.+.|+.+|+|+..++..-..+ .+...+-+++.+ ..+-..+++.|+.|
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 45667779999999999999999999999998764211 133444555543 22335666666666
Q ss_pred HHh
Q 016702 366 QEF 368 (384)
Q Consensus 366 ~~~ 368 (384)
.+.
T Consensus 67 ~~~ 69 (88)
T cd04872 67 GKE 69 (88)
T ss_pred HHH
Confidence 543
No 80
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=95.17 E-value=0.11 Score=40.63 Aligned_cols=35 Identities=20% Similarity=0.313 Sum_probs=25.7
Q ss_pred EEEEe--CCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 016702 289 IVFTL--DEGPGVLFKALAVFALREINLTKIESRPQR 323 (384)
Q Consensus 289 l~f~~--~~~pGaL~~~L~~F~~~~INLtkIESRP~~ 323 (384)
+++++ +|+||-++.+.+.++++|.|+..++-.-..
T Consensus 3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~ 39 (76)
T PF13740_consen 3 LVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLG 39 (76)
T ss_dssp EEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEET
T ss_pred EEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEc
Confidence 44444 899999999999999999999877666543
No 81
>PRK00194 hypothetical protein; Validated
Probab=95.15 E-value=0.11 Score=41.57 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=31.4
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeee
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP 321 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP 321 (384)
+-.+.+.-+|+||.+.++.+.|+.+|+|+..+++.-
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~ 38 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTI 38 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHh
Confidence 445667779999999999999999999999998774
No 82
>cd04870 ACT_PSP_1 CT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_1 CD includes the first of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.14 E-value=0.17 Score=39.24 Aligned_cols=62 Identities=11% Similarity=0.083 Sum_probs=44.1
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 291 FTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 291 f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
+.=+|+||-++++-+.|+.+|+|+..++++-..+ .+...|.+++....+-..+++.|+.+.+
T Consensus 4 v~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~---------------~f~~~~~v~~p~~~~~~~l~~~l~~l~~ 65 (75)
T cd04870 4 VTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHG---------------RLSLGILVQIPDSADSEALLKDLLFKAH 65 (75)
T ss_pred EEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcC---------------eeEEEEEEEcCCCCCHHHHHHHHHHHHH
Confidence 4448999999999999999999999998765432 2445566665433234667777776653
No 83
>PRK08577 hypothetical protein; Provisional
Probab=95.06 E-value=0.51 Score=41.10 Aligned_cols=70 Identities=17% Similarity=0.313 Sum_probs=50.1
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 365 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L 365 (384)
...|.+...|+||.|.++++.|+.+++|+..+.++...... .+.-.|-+|+... +..+.+++++|
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 56778888999999999999999999999999988764321 1122334555432 24577888888
Q ss_pred HHhcC
Q 016702 366 QEFAT 370 (384)
Q Consensus 366 ~~~~~ 370 (384)
++.-.
T Consensus 121 ~~l~~ 125 (136)
T PRK08577 121 KKLEE 125 (136)
T ss_pred HcCCC
Confidence 76543
No 84
>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=95.01 E-value=0.096 Score=40.44 Aligned_cols=33 Identities=12% Similarity=0.220 Sum_probs=29.5
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeee
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRP 321 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP 321 (384)
|.+.-+|+||-+.++.+.|+.+|+|+..+++.-
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 345668999999999999999999999998884
No 85
>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=94.98 E-value=0.21 Score=38.60 Aligned_cols=61 Identities=18% Similarity=0.348 Sum_probs=48.1
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
.|.+...|++|.|.++++.++..|+|+..+++++. + + .+++++.. +-..+..+++.|++
T Consensus 2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~------------------~-i~l~i~v~-~~~~L~~li~~L~~ 60 (74)
T cd04877 2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-G------------------R-IYLNFPTI-EFEKLQTLMPEIRR 60 (74)
T ss_pred EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-C------------------e-EEEEeEec-CHHHHHHHHHHHhC
Confidence 35667789999999999999999999999999764 2 3 66777653 44677888888876
Q ss_pred hc
Q 016702 368 FA 369 (384)
Q Consensus 368 ~~ 369 (384)
.-
T Consensus 61 i~ 62 (74)
T cd04877 61 ID 62 (74)
T ss_pred CC
Confidence 53
No 86
>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=94.86 E-value=0.14 Score=51.88 Aligned_cols=73 Identities=21% Similarity=0.319 Sum_probs=49.4
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeee-eCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESR-PQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESR-P~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
+..|.+.++|+||.|.++++.+++.+.|++.|.-+ ..+..+ .+ .+...+-||..+ ....+++++.
T Consensus 305 ~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~r~~~~~~--------~~---~~~v~v~vet~~---~~~~~~i~~~ 370 (380)
T TIGR01127 305 KVRIETVLPDRPGALYHLLESIAEARANIVKIDHDRLSKEIP--------PG---FAMVEITLETRG---KEHLDEILKI 370 (380)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeccccCCC--------Cc---eEEEEEEEEeCC---HHHHHHHHHH
Confidence 44788899999999999999999999999999654 323222 01 133444444432 3456678888
Q ss_pred HHHhcCce
Q 016702 365 LQEFATFL 372 (384)
Q Consensus 365 L~~~~~~v 372 (384)
|++..-.+
T Consensus 371 L~~~G~~v 378 (380)
T TIGR01127 371 LRDMGYNF 378 (380)
T ss_pred HHHcCCcc
Confidence 87765444
No 87
>PRK06382 threonine dehydratase; Provisional
Probab=94.81 E-value=0.15 Score=52.47 Aligned_cols=74 Identities=18% Similarity=0.295 Sum_probs=49.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeee-eeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIES-RPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 363 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIES-RP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~ 363 (384)
.++.|.+.++|+||+|.++++.|..+|+|+++|+- |...... .+ .....|-||..+. ...+++++
T Consensus 329 ~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~~~~~~~~~--------~~---~~~v~i~vet~~~---~~~~~v~~ 394 (406)
T PRK06382 329 QLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEVDNLRKETP--------PG---FQSVTFTVNVRGQ---DHLDRILN 394 (406)
T ss_pred CEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEEeeccccCC--------CC---cEEEEEEEEeCCH---HHHHHHHH
Confidence 47788899999999999999999999999999987 3221111 01 1334455555421 23346777
Q ss_pred HHHHhcCce
Q 016702 364 HLQEFATFL 372 (384)
Q Consensus 364 ~L~~~~~~v 372 (384)
.|++..-.+
T Consensus 395 ~L~~~Gy~~ 403 (406)
T PRK06382 395 ALREMGYKF 403 (406)
T ss_pred HHHHCCCCe
Confidence 777665443
No 88
>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=94.80 E-value=0.089 Score=38.21 Aligned_cols=34 Identities=24% Similarity=0.342 Sum_probs=30.4
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~ 323 (384)
.+.++|+||.|.++++.|.++|+|+..+...+..
T Consensus 2 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~ 35 (56)
T cd04889 2 SVFVENKPGRLAEVTEILAEAGINIKAISIAETR 35 (56)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEcc
Confidence 4577899999999999999999999999877765
No 89
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=94.51 E-value=0.26 Score=44.23 Aligned_cols=74 Identities=22% Similarity=0.342 Sum_probs=52.7
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeee-eeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTK-IESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtk-IESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
+.++.+.++|+||-|.++|++++..|.|+.. |.||-.+..| .----|-|++.. .+..++.++.
T Consensus 5 ritldIEL~D~PGQLl~vLqPls~~g~NiItIiH~r~kk~g~---------------r~pV~i~~~~d~-~~~~~~i~~~ 68 (170)
T COG2061 5 RITLDIELKDKPGQLLKVLQPLSKTGANIITIIHSRDKKYGP---------------RVPVQIVFEGDR-EDKDAKIIRL 68 (170)
T ss_pred EEEEEEEecCCCcchhhhhcchhhcCccEEEEEeecCcccCC---------------ceeEEEEEEecc-cHHHHHHHHH
Confidence 5688899999999999999999999999875 5788655432 122334444432 3567778888
Q ss_pred HHHhcCceEEE
Q 016702 365 LQEFATFLRVL 375 (384)
Q Consensus 365 L~~~~~~vkvL 375 (384)
+++....++-.
T Consensus 69 ~e~~Gi~I~~~ 79 (170)
T COG2061 69 LEEEGIIIIRF 79 (170)
T ss_pred HHhCCcEEEEe
Confidence 87766655544
No 90
>PRK08526 threonine dehydratase; Provisional
Probab=94.15 E-value=0.86 Score=47.02 Aligned_cols=217 Identities=18% Similarity=0.166 Sum_probs=110.2
Q ss_pred HHHHHHHhCCCCeEEEeeeccccccccccccccc--cCCeEEEEEEEEeee---eeeecCCCCCcCCccEEE----e---
Q 016702 131 DTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL--RHRLHIVGEVQLAAN---FCLLALPGIKADQLKRVL----S--- 198 (384)
Q Consensus 131 ~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~--~~~l~I~gEi~l~I~---h~Ll~~~g~~l~~I~~Vy----S--- 198 (384)
|+++.+ +..|+-|+|+- ..|.+.-+...|. ..+.+|+|--.-.-. ..+-..+......+.++. .
T Consensus 161 EI~eq~--~~~D~vvvpvG--gGGl~aGia~~~k~~~p~~kvigVep~~~~~~~~s~~~g~~~~~~~~~tiadgiav~~~ 236 (403)
T PRK08526 161 EMLDEI--SDLDMVVVPVG--GGGLISGIASAAKQINPNIKIIGVGAKGAPAMYESFHAKKIINSKSVRTIADGIAVRDA 236 (403)
T ss_pred HHHHhc--CCCCEEEEecC--hHHHHHHHHHHHHHhCCCCEEEEEEECCCChHHHHHHcCCcccCCCCCceeccccCCCC
Confidence 444444 35899999984 4555555555443 345777664432111 011111101112222221 1
Q ss_pred cHHHHHHHHHHHHhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHHcCCceeeccccCCCCCeeEEEEEeeCCCC
Q 016702 199 HPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDPII 278 (384)
Q Consensus 199 HpqAl~QC~~fL~~~~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~ 278 (384)
-|..+..|++++++ +..++-....+|.+.+++.. +. .+.+..|+-+-+|.--...+ ..+.+=-+|++--...
T Consensus 237 ~~~~~~~~~~~vd~--~v~V~d~ei~~A~~~l~~~~--gi-~ve~aga~~lAall~~~~~~---~~~~~Vv~ilsGGnid 308 (403)
T PRK08526 237 SPINLAIILECVDD--FVQVDDEEIANAILFLLEKQ--KI-VVEGAGAASVAALLHQKIDL---KKGKKIGVVLSGGNID 308 (403)
T ss_pred CHHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhc--Cc-EeeHHHHHHHHHHHhCcccc---ccCCeEEEEECCCCCC
Confidence 16666666665542 22233334555666666542 22 22333344444442111111 1122222233221111
Q ss_pred CC--------C--CCCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeee-eeCCCCCCccccCCCCCCcccccEEEEE
Q 016702 279 PR--------T--DKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIES-RPQRKRPLRVVDDSNNGTAKYFDYLFYI 347 (384)
Q Consensus 279 ~~--------~--~~~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIES-RP~~~~~~~~~~~~~~~~~~~~~Y~FfI 347 (384)
+. + ...-+..+.+.++|+||+|.++++.+...+.|++.|+= |.....+ ..+-...|
T Consensus 309 ~~~~~~i~~~~l~~~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~~~~~-------------~~~~~~~~ 375 (403)
T PRK08526 309 VQMLNIIIEKGLIKSYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFSTKLD-------------YGDAMISI 375 (403)
T ss_pred HHHHHHHHHHHHHhcCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEeccCCCC-------------CccEEEEE
Confidence 00 0 12236788899999999999999999999999999976 6544322 12234455
Q ss_pred EeecCCCcHHHHHHHHHHHHhcCceE
Q 016702 348 DFEASMADPRAQNALGHLQEFATFLR 373 (384)
Q Consensus 348 D~eg~~~d~~v~~al~~L~~~~~~vk 373 (384)
.+|.. +.+.++++++.|++..-.++
T Consensus 376 ~~e~~-~~~~~~~~~~~l~~~g~~~~ 400 (403)
T PRK08526 376 TLETK-GKEHQEEIRKILTEKGFNFY 400 (403)
T ss_pred EEEeC-CHHHHHHHHHHHHHCCCCeE
Confidence 55543 34677888888877654443
No 91
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=93.67 E-value=0.34 Score=42.53 Aligned_cols=77 Identities=21% Similarity=0.320 Sum_probs=60.1
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHH
Q 016702 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIE-SRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNAL 362 (384)
Q Consensus 284 ~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIE-SRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al 362 (384)
..+.+|.+.+.|+.|.|.++|...++.++|+..|. +-|..+. -+-..-||..+ .+..+.+++
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 34779999999999999999999999999998885 5676553 24556667764 457788999
Q ss_pred HHHHH--hcCceEEEcc
Q 016702 363 GHLQE--FATFLRVLGC 377 (384)
Q Consensus 363 ~~L~~--~~~~vkvLGs 377 (384)
++|++ ....|.++|+
T Consensus 133 ~kl~k~e~V~kVeivgs 149 (150)
T COG4492 133 EKLRKVEGVEKVEIVGS 149 (150)
T ss_pred HHHhcccceeEEEEeec
Confidence 99885 3556888875
No 92
>PRK08639 threonine dehydratase; Validated
Probab=93.65 E-value=0.77 Score=47.50 Aligned_cols=74 Identities=15% Similarity=0.246 Sum_probs=50.2
Q ss_pred ceEEEEEEeCCCcchHHHHHH-HHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALA-VFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 363 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~-~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~ 363 (384)
.+..+.|.+||+||+|.++|+ +++... |++.|+-|.....+ .. ...|.+|.. +.+.++++++
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 234444443 2356777888
Q ss_pred HHHHhcCceEEE
Q 016702 364 HLQEFATFLRVL 375 (384)
Q Consensus 364 ~L~~~~~~vkvL 375 (384)
.|++..-.++.+
T Consensus 398 ~L~~~Gy~~~~~ 409 (420)
T PRK08639 398 RMEAFGPSYIDI 409 (420)
T ss_pred HHHHCCCceEEC
Confidence 888776655544
No 93
>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=93.53 E-value=0.56 Score=36.37 Aligned_cols=34 Identities=18% Similarity=0.417 Sum_probs=29.6
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 322 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~ 322 (384)
+.+..+|+||-+.++-+.|+.+|+|+..+++...
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~ 35 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETY 35 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeee
Confidence 4466789999999999999999999999988554
No 94
>PRK07334 threonine dehydratase; Provisional
Probab=93.51 E-value=0.49 Score=48.62 Aligned_cols=76 Identities=13% Similarity=0.172 Sum_probs=56.1
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeC-CCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ-RKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 363 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~-~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~ 363 (384)
..+.|.+...|+||.|.++++.+++.++|+..+.++.. +..+. + .+...|-|++. +.+.+.++++
T Consensus 325 y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~--------~---~~~i~l~i~V~---d~~~L~~vi~ 390 (403)
T PRK07334 325 RLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPA--------K---GAELELVIETR---DAAHLQEVIA 390 (403)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCC--------C---eEEEEEEEEeC---CHHHHHHHHH
Confidence 46899999999999999999999999999999998854 11110 1 13344445552 3478889999
Q ss_pred HHHHhcCceEE
Q 016702 364 HLQEFATFLRV 374 (384)
Q Consensus 364 ~L~~~~~~vkv 374 (384)
.|++....+.+
T Consensus 391 ~Lr~~g~~~~~ 401 (403)
T PRK07334 391 ALRAAGFEARL 401 (403)
T ss_pred HHHHcCCeeEe
Confidence 99987655544
No 95
>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=92.41 E-value=1.2 Score=34.37 Aligned_cols=32 Identities=13% Similarity=0.283 Sum_probs=27.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeee
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIE 318 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIE 318 (384)
+-+.+..+|+||-|+++-.+|+.+|+|+..-.
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 34667788999999999999999999999543
No 96
>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=92.31 E-value=0.64 Score=36.88 Aligned_cols=29 Identities=10% Similarity=0.256 Sum_probs=25.7
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceee
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLT 315 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLt 315 (384)
|-|-+..+|+||-|+++...|.+.|+++.
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~ 30 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVF 30 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEE
Confidence 44557789999999999999999999987
No 97
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=92.04 E-value=0.94 Score=39.18 Aligned_cols=38 Identities=24% Similarity=0.302 Sum_probs=32.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~ 324 (384)
.-+.+..+|+||.|.+++.+|.+++||+--|.---.++
T Consensus 70 dVlaVEmeD~PG~l~~I~~vl~d~diNldYiYAFv~ek 107 (142)
T COG4747 70 DVLAVEMEDVPGGLSRIAEVLGDADINLDYIYAFVTEK 107 (142)
T ss_pred eEEEEEecCCCCcHHHHHHHHhhcCcCceeeeeeeecC
Confidence 34567889999999999999999999999887776654
No 98
>cd04893 ACT_GcvR_1 ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. This CD includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein, and other related domains. The glycine cleavage enzyme system in Escherichia coli provides one-carbon units for cellular methylation reactions. This enzyme system, encoded by the gcvTHP operon and lpd gene, catalyzes the cleavage of glycine into CO2 + NH3 and transfers a one-carbon unit to tetrahydrofolate, producing 5,10-methylenetetrahydrofolate. The gcvTHP operon is activated by the GcvA protein in response to glycine and repressed by a GcvA/GcvR interaction in the absence of glycine. It has been proposed that the co-activator glycine acts through a mechanism of de-repression by binding to GcvR and preventing GcvR from interacting with GcvA to block GcvA's activator function. Evidence also suggests that GcvR int
Probab=91.18 E-value=1.9 Score=33.69 Aligned_cols=64 Identities=16% Similarity=0.062 Sum_probs=42.5
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
|.+.-||+||-.+++-+.++++|.|+..+...-..+ .+-+..-++++. .+-+.+++.++.+.+.
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 445569999999999999999999999776654211 133333445442 2235677777776643
No 99
>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=91.10 E-value=3.2 Score=44.11 Aligned_cols=72 Identities=19% Similarity=0.266 Sum_probs=51.6
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
....+.+++|++||+|.++++.+.. -|+|.++=|-.... +=..||-++-. +...++++++.
T Consensus 324 re~~l~V~iPerPGal~~f~~~i~~--~nItef~yr~~~~~----------------~a~v~vgie~~-~~~~~~~l~~~ 384 (499)
T TIGR01124 324 REALLAVTIPEQPGSFLKFCELLGN--RNITEFNYRYADRK----------------DAHIFVGVQLS-NPQERQEILAR 384 (499)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhhh--cceEEEEEEecCCC----------------eEEEEEEEEeC-CHHHHHHHHHH
Confidence 4678889999999999999999997 48888888753221 11244555543 34677888888
Q ss_pred HHHhcCceEEE
Q 016702 365 LQEFATFLRVL 375 (384)
Q Consensus 365 L~~~~~~vkvL 375 (384)
|++..-.+..+
T Consensus 385 L~~~Gy~~~dl 395 (499)
T TIGR01124 385 LNDGGYSVVDL 395 (499)
T ss_pred HHHcCCCeEEC
Confidence 88776655554
No 100
>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=90.88 E-value=1.3 Score=45.63 Aligned_cols=74 Identities=15% Similarity=0.137 Sum_probs=48.5
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
-+..+.|.+|++||+|.++|+.....+-|+++++-|..... + ..+..+=||+.+ ...++++++.
T Consensus 324 r~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~y~~~~~~----------~---~~~v~v~iE~~~---~~h~~~i~~~ 387 (409)
T TIGR02079 324 LKHYFIVRFPQRPGALREFLNDVLGPNDDITRFEYTKKSNR----------E---TGPALIGIELND---KEDFAGLLER 387 (409)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeecCCC----------C---eEEEEEEEEeCC---HHHHHHHHHH
Confidence 36788899999999999999944445559998887752211 1 133343344433 3566777778
Q ss_pred HHHhcCceEE
Q 016702 365 LQEFATFLRV 374 (384)
Q Consensus 365 L~~~~~~vkv 374 (384)
|++..-.+++
T Consensus 388 L~~~Gy~~~~ 397 (409)
T TIGR02079 388 MAAADIHYED 397 (409)
T ss_pred HHHCCCCeEE
Confidence 8776655544
No 101
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=90.76 E-value=1.3 Score=41.17 Aligned_cols=35 Identities=20% Similarity=0.407 Sum_probs=29.9
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~ 323 (384)
+.+.-+|+||-++++-+.|+.+|||+..+.++-.+
T Consensus 98 v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~ 132 (190)
T PRK11589 98 VQVEVADSPHLIERFTALFDSHHMNIAELVSRTQP 132 (190)
T ss_pred EEEEECCCCCHHHHHHHHHHHcCCChhheEEeeec
Confidence 44445899999999999999999999999998543
No 102
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=90.23 E-value=1.4 Score=40.44 Aligned_cols=74 Identities=20% Similarity=0.253 Sum_probs=51.7
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCc-HHHHHHHHHHHHhc
Q 016702 291 FTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMAD-PRAQNALGHLQEFA 369 (384)
Q Consensus 291 f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d-~~v~~al~~L~~~~ 369 (384)
+...||||-+.++-+.|..|||||-.++||-.+-. + ...-.|++++.-+..- -++..+.++++..|
T Consensus 97 v~a~DrpgIv~~~T~lf~~~~inie~L~~~~~~a~----------~---s~~~lfha~it~~lPa~~~i~~l~~~f~al~ 163 (176)
T COG2716 97 VDANDRPGIVEEFTALFDGHGINIENLVSRTYPAP----------G---SSAPLFHAQITARLPANLSISALRDAFEALC 163 (176)
T ss_pred EEecCCccHHHHHHHHHHhcCCchhhceeeeeecC----------C---CCccceehhhhccCCCcCcHHHHHHHHHHHH
Confidence 44579999999999999999999999999743321 1 1346899998766422 34445555666677
Q ss_pred CceEEEcc
Q 016702 370 TFLRVLGC 377 (384)
Q Consensus 370 ~~vkvLGs 377 (384)
..+.+=|+
T Consensus 164 ~~L~v~~~ 171 (176)
T COG2716 164 DELNVDGS 171 (176)
T ss_pred Hhhcceee
Confidence 66665443
No 103
>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=89.74 E-value=2.9 Score=32.71 Aligned_cols=27 Identities=15% Similarity=0.252 Sum_probs=24.1
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeee
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTK 316 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtk 316 (384)
-+..+|+||-|+++.+.|+.+|+|+..
T Consensus 4 ei~~~Dr~gLfa~i~~~l~~~~l~I~~ 30 (76)
T cd04927 4 KLFCSDRKGLLHDVTEVLYELELTIER 30 (76)
T ss_pred EEEECCCCCHHHHHHHHHHHCCCeEEE
Confidence 355689999999999999999999984
No 104
>cd04935 ACT_AKiii-DAPDC_1 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. This CD includes the first of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=89.12 E-value=2.8 Score=32.79 Aligned_cols=63 Identities=11% Similarity=0.231 Sum_probs=46.6
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecC-CCcHHHHHHHHHHHHhcCc
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEAS-MADPRAQNALGHLQEFATF 371 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~-~~d~~v~~al~~L~~~~~~ 371 (384)
.++.||.+.++++.|+++|||+-.|-+ +. ..+.|-|+-... ..+..+++++++|++.+ .
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~vDmI~~-s~------------------~~isftv~~~~~~~~~~~~~~l~~el~~~~-~ 70 (75)
T cd04935 11 MWQQVGFLADVFAPFKKHGVSVDLVST-SE------------------TNVTVSLDPDPNGLDPDVLDALLDDLNQIC-R 70 (75)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe-CC------------------CEEEEEEeCcccccchHHHHHHHHHHHhce-E
Confidence 357899999999999999999999965 11 247788775432 23348889999999854 3
Q ss_pred eEEE
Q 016702 372 LRVL 375 (384)
Q Consensus 372 vkvL 375 (384)
|.++
T Consensus 71 v~~~ 74 (75)
T cd04935 71 VKII 74 (75)
T ss_pred EEEe
Confidence 5543
No 105
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=88.88 E-value=2.1 Score=38.87 Aligned_cols=74 Identities=18% Similarity=0.318 Sum_probs=53.9
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 365 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L 365 (384)
+-.+.+.+.|+||.|.++...|+.+|.|+-.|--=|+-... .=.--|-..| ++..++++.+.|
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 44566667899999999999999999999999888875532 1122233334 557788888888
Q ss_pred HHhcCceEEEc
Q 016702 366 QEFATFLRVLG 376 (384)
Q Consensus 366 ~~~~~~vkvLG 376 (384)
.+.-.-+|++-
T Consensus 67 ~kLidV~kV~d 77 (163)
T COG0440 67 NKLIDVLKVLD 77 (163)
T ss_pred HhhccceeEEE
Confidence 88777666653
No 106
>cd04912 ACT_AKiii-LysC-EC-like_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC) and plants, (Zea mays Ask1, Ask2, and Arabidopsis thaliana AK1). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Like the A. thaliana AK1 (AK1-AT), the E. coli AKIII (LysC) has two bound feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. The lysine-sensitive plant isoenzyme is synergistically inhibited by S-adenosylmethionine. A homolog of this group appears to be the Saccharomyces cerevisiae AK (Hom3) which clusters with this group as well. Members of this CD
Probab=88.61 E-value=3.3 Score=32.07 Aligned_cols=56 Identities=14% Similarity=0.221 Sum_probs=43.6
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCC-cHHHHHHHHHHHH
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMA-DPRAQNALGHLQE 367 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~-d~~v~~al~~L~~ 367 (384)
+.+.||.+.++++.|+++|||+-.+-+.+ -...|.|+-+.... +..++.++++|++
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 46789999999999999999998886422 24788888754322 3588889999988
No 107
>cd04932 ACT_AKiii-LysC-EC_1 ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in bacteria (Escherichia coli (EC) LysC). Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The E. coli AKIII (LysC) binds two feedback allosteric inhibitor lysine molecules at the dimer interface located between the ACT1 domain of two subunits. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=88.38 E-value=3.5 Score=32.30 Aligned_cols=62 Identities=19% Similarity=0.288 Sum_probs=44.1
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHH-HHHHHHHHhcCc
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQ-NALGHLQEFATF 371 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~-~al~~L~~~~~~ 371 (384)
.++.||.+.++++.|+++|||+-.|-+ +. -++.|=|+-.-...|..++ +++++|++.+ .
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~VDmI~~-s~------------------~~iSftv~~~d~~~~~~~~~~l~~~l~~~~-~ 70 (75)
T cd04932 11 MLHAQGFLAKVFGILAKHNISVDLITT-SE------------------ISVALTLDNTGSTSDQLLTQALLKELSQIC-D 70 (75)
T ss_pred CCCCcCHHHHHHHHHHHcCCcEEEEee-cC------------------CEEEEEEeccccchhHHHHHHHHHHHHhcc-E
Confidence 467899999999999999999999965 11 2477777753222234565 7888888844 3
Q ss_pred eEE
Q 016702 372 LRV 374 (384)
Q Consensus 372 vkv 374 (384)
|++
T Consensus 71 v~~ 73 (75)
T cd04932 71 VKV 73 (75)
T ss_pred EEe
Confidence 443
No 108
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=88.05 E-value=1.8 Score=39.62 Aligned_cols=61 Identities=21% Similarity=0.284 Sum_probs=46.2
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
|.+...|+||.|.++-.+++.+|.|+|.....-.+.. ..-..|.++||-. | .+.++++|+.
T Consensus 5 lsi~~enk~GvL~~ltgiiae~ggNIt~~q~~~~~~g---------------~~~~iYmEiEgi~-d--~e~l~~~lks 65 (218)
T COG1707 5 LSIIAENKPGVLRDLTGIIAEEGGNITYAQQFLEKDG---------------EKALIYMEIEGID-D--FEKLLERLKS 65 (218)
T ss_pred eEEEeecCccHHHHHHHHHHhcCCceEeeehhhhccC---------------ceEEEEEEeeCCC-C--HHHHHHHhhc
Confidence 4455679999999999999999999999987766542 1346788999964 3 3456677664
No 109
>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=88.02 E-value=4.2 Score=32.43 Aligned_cols=65 Identities=20% Similarity=0.189 Sum_probs=44.5
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
.+.|++|.+||+|.+.|+.+.. +-|+|.++=|-..... +. -||=++-. ++.+.++++.|++
T Consensus 3 ~~~v~iPErpGal~~Fl~~l~p-~~~ITeF~YR~~~~~~--------------a~--vlvGi~~~--~~~~~~l~~~l~~ 63 (81)
T cd04907 3 LFRFEFPERPGALKKFLNELLP-KWNITLFHYRNQGSDY--------------GR--VLVGIQVP--DADLDELKERLDA 63 (81)
T ss_pred EEEEEcCCCCCHHHHHHHHhCC-CCeEeEEEEecCCCCc--------------ee--EEEEEEeC--hHHHHHHHHHHHH
Confidence 4678899999999999999943 7899999988754321 22 33444322 2367777778877
Q ss_pred hcCc
Q 016702 368 FATF 371 (384)
Q Consensus 368 ~~~~ 371 (384)
..-.
T Consensus 64 ~g~~ 67 (81)
T cd04907 64 LGYP 67 (81)
T ss_pred cCCC
Confidence 5443
No 110
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=87.59 E-value=3.6 Score=40.63 Aligned_cols=67 Identities=9% Similarity=0.220 Sum_probs=46.2
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEee--cCCCcHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFE--ASMADPRAQNALG 363 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~e--g~~~d~~v~~al~ 363 (384)
+..+.+.-+|+||-..++-+.|+.+|+|+..+.+.-.... ..|...++++ ...+-..++++|+
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 3345556689999999999999999999999999733332 1233333443 3333567787787
Q ss_pred HHHH
Q 016702 364 HLQE 367 (384)
Q Consensus 364 ~L~~ 367 (384)
.+.+
T Consensus 72 ~l~~ 75 (286)
T PRK13011 72 PIAA 75 (286)
T ss_pred HHHH
Confidence 7754
No 111
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=87.46 E-value=1.5 Score=35.98 Aligned_cols=66 Identities=15% Similarity=0.298 Sum_probs=46.9
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCc-HHHHH-HHHHHHHhcCc
Q 016702 294 DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMAD-PRAQN-ALGHLQEFATF 371 (384)
Q Consensus 294 ~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d-~~v~~-al~~L~~~~~~ 371 (384)
+|+||-...+-.+|+++|+|+..|+---.++ .+...+++|+.-..-| ..+++ +-++.++....
T Consensus 11 kDr~GIva~is~vLAe~~vNIldisQtvm~~---------------~ftm~~lV~~~~~~~d~~~lr~~l~~~~~~lgv~ 75 (90)
T COG3830 11 KDRVGIVAAVSRVLAEHGVNILDISQTVMDG---------------FFTMIMLVDISKEVVDFAALRDELAAEGKKLGVD 75 (90)
T ss_pred CCCCchhHHHHHHHHHcCCcEEEHHHHHHhh---------------hceeeeEEcCChHhccHHHHHHHHHHHHHhcCcE
Confidence 7999999999999999999999997655443 3678899999633222 44444 33345566666
Q ss_pred eEE
Q 016702 372 LRV 374 (384)
Q Consensus 372 vkv 374 (384)
|++
T Consensus 76 V~v 78 (90)
T COG3830 76 VRV 78 (90)
T ss_pred EEE
Confidence 654
No 112
>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=86.15 E-value=21 Score=30.82 Aligned_cols=141 Identities=15% Similarity=0.060 Sum_probs=69.8
Q ss_pred ceEEEEECCCCcH-HHHHH---HHHCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEE
Q 016702 97 KVRISFKGLPGSF-SEDAA---LKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIV 171 (384)
Q Consensus 97 ~~~Va~LGP~GTf-S~~AA---~~~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~ 171 (384)
..+||+..+-+.+ --.+. .+.+++.++... .+.+++.+.+.+|++|+|+........+... ..|.+.++.++
T Consensus 2 ~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v 78 (203)
T cd08445 2 TFSIGFVPSTLYGLLPELIRRFRQAAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRR---IVLREEPLVVA 78 (203)
T ss_pred eEEEEEehHHHHhHHHHHHHHHHHHCCCeEEEEEeCChHHHHHHHHcCCCcEEEecCCCCCCCcee---EEEEeccEEEE
Confidence 3566666544332 11121 223566554433 3578999999999999999743211122211 11222233322
Q ss_pred EEEEEeeeeeeecCC-CCCcCCc---cEEEecHH---H-HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEE
Q 016702 172 GEVQLAANFCLLALP-GIKADQL---KRVLSHPQ---A-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGA 240 (384)
Q Consensus 172 gEi~l~I~h~Ll~~~-g~~l~~I---~~VySHpq---A-l~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AA 240 (384)
.+-+|-|.... ..+++++ .-|.-... . ..+..+|+.+.+. . ...++|...+.++++.+ ...+
T Consensus 79 ----~~~~hpl~~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~ 151 (203)
T cd08445 79 ----LPAGHPLAQEKAPLTLAQLADEPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAG---EGVT 151 (203)
T ss_pred ----eeCCCCCccCCCCcCHHHhcCCCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcC---CCeE
Confidence 23445454332 2333333 33331111 1 2345567766543 2 34466777777777764 3567
Q ss_pred EcCHHHH
Q 016702 241 VASARAA 247 (384)
Q Consensus 241 Ias~~aA 247 (384)
+.+...+
T Consensus 152 ~~p~~~~ 158 (203)
T cd08445 152 LVPASVQ 158 (203)
T ss_pred EehHHhh
Confidence 7776544
No 113
>PRK09224 threonine dehydratase; Reviewed
Probab=86.14 E-value=4.7 Score=42.84 Aligned_cols=73 Identities=15% Similarity=0.241 Sum_probs=49.8
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
....+.+++|++||+|.++++.+. +-|+|.++=|-.... +=..+|-++....+..++++++.
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 367888999999999999999998 688888887764321 11244555543222236777888
Q ss_pred HHHhcCceEEE
Q 016702 365 LQEFATFLRVL 375 (384)
Q Consensus 365 L~~~~~~vkvL 375 (384)
|++..-.++.+
T Consensus 389 L~~~gy~~~~l 399 (504)
T PRK09224 389 LRAHGYPVVDL 399 (504)
T ss_pred HHHcCCCeEEC
Confidence 87765555444
No 114
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=86.14 E-value=20 Score=30.55 Aligned_cols=121 Identities=21% Similarity=0.120 Sum_probs=66.4
Q ss_pred CCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCccE-
Q 016702 118 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR- 195 (384)
Q Consensus 118 f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~- 195 (384)
+++.++.. ..+-.++.+.+.+|++|+|+++-.+...+.. ...|.+.++.++ .+-.|-+.. +..+++++..
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~~~~~-~~~~~~~L~~~ 97 (200)
T cd08417 26 APGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLR---SQPLFEDRFVCV----ARKDHPLAG-GPLTLEDYLAA 97 (200)
T ss_pred CCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccCCCccc---hhhhhcCceEEE----ecCCCcccc-cccCHHHHhCC
Confidence 45544432 3466789999999999999987544322222 123334455443 233454433 2233444432
Q ss_pred --E-EecHHH-HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 196 --V-LSHPQA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 196 --V-ySHpqA-l~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
| +.+... ......|+.+++.. ...++|...+.+++..+ ...|+.+...++.
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08417 98 PHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGT---DLIATVPRRLAEA 155 (200)
T ss_pred CeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcC---CeeeeccHHHHHh
Confidence 2 333222 24456777766542 34456666666777664 4577777766653
No 115
>PRK12483 threonine dehydratase; Reviewed
Probab=86.04 E-value=4.6 Score=43.24 Aligned_cols=72 Identities=17% Similarity=0.174 Sum_probs=51.0
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHH-HHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRA-QNALG 363 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v-~~al~ 363 (384)
.+..+.+.+|++||+|.++++.+..+ |++.++=|-... .+=..+|.+|..- .+.. +++++
T Consensus 344 r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v~v~ie~~~-~~~~~~~i~~ 404 (521)
T PRK12483 344 REAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYRYADA----------------REAHLFVGVQTHP-RHDPRAQLLA 404 (521)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEEecCC----------------CeeEEEEEEEeCC-hhhhHHHHHH
Confidence 47788999999999999999999988 999988774221 1223555565432 2344 78888
Q ss_pred HHHHhcCceEEE
Q 016702 364 HLQEFATFLRVL 375 (384)
Q Consensus 364 ~L~~~~~~vkvL 375 (384)
.|++..-.++.+
T Consensus 405 ~l~~~g~~~~dl 416 (521)
T PRK12483 405 SLRAQGFPVLDL 416 (521)
T ss_pred HHHHCCCCeEEC
Confidence 888776656554
No 116
>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=85.81 E-value=6.4 Score=30.68 Aligned_cols=55 Identities=16% Similarity=0.272 Sum_probs=43.4
Q ss_pred CCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhc
Q 016702 295 EGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFA 369 (384)
Q Consensus 295 ~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~ 369 (384)
..||.+.++++.|+++|||+-.|-+-. .++.|-++-. +..++.+++++++|++.+
T Consensus 13 ~~~g~~~~If~~la~~~I~vd~I~~s~-------------------~~isftv~~~-~~~~~~l~~l~~el~~~~ 67 (73)
T cd04934 13 LSHGFLARIFAILDKYRLSVDLISTSE-------------------VHVSMALHME-NAEDTNLDAAVKDLQKLG 67 (73)
T ss_pred cccCHHHHHHHHHHHcCCcEEEEEeCC-------------------CEEEEEEehh-hcChHHHHHHHHHHHHhe
Confidence 469999999999999999999996611 3588888764 333458999999999843
No 117
>PLN02550 threonine dehydratase
Probab=84.49 E-value=5.3 Score=43.40 Aligned_cols=71 Identities=13% Similarity=0.116 Sum_probs=52.1
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 365 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L 365 (384)
+..+.+.++++||+|.++++.+... |++.|+=|-... .+=..+|.+|.. +...++++++.|
T Consensus 417 ~~~~~v~ipd~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v~v~ie~~-~~~~~~~i~~~l 477 (591)
T PLN02550 417 EAVLATFMPEEPGSFKRFCELVGPM--NITEFKYRYSSE----------------KEALVLYSVGVH-TEQELQALKKRM 477 (591)
T ss_pred EEEEEEEcCCCCCHHHHHHHHhhhh--cceEEEEEecCC----------------CceEEEEEEEeC-CHHHHHHHHHHH
Confidence 5678889999999999999999986 999998776221 123455566554 456788889999
Q ss_pred HHhcCceEEE
Q 016702 366 QEFATFLRVL 375 (384)
Q Consensus 366 ~~~~~~vkvL 375 (384)
++..-.++.|
T Consensus 478 ~~~g~~~~~l 487 (591)
T PLN02550 478 ESAQLRTVNL 487 (591)
T ss_pred HHCCCCeEeC
Confidence 8876555444
No 118
>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=83.84 E-value=9.2 Score=29.55 Aligned_cols=32 Identities=28% Similarity=0.351 Sum_probs=26.7
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeee
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESR 320 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESR 320 (384)
|-+..+|+||-|+++-..|+.+|+|+..-...
T Consensus 3 ~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~ 34 (74)
T cd04925 3 IELTGTDRPGLLSEVFAVLADLHCNVVEARAW 34 (74)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCCcEEEEEEE
Confidence 44566899999999999999999999854443
No 119
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=83.62 E-value=23 Score=34.00 Aligned_cols=144 Identities=13% Similarity=0.094 Sum_probs=78.3
Q ss_pred CCceEEEEECCCCc--HHHH--HHHHHCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeE
Q 016702 95 GTKVRISFKGLPGS--FSED--AALKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (384)
Q Consensus 95 ~~~~~Va~LGP~GT--fS~~--AA~~~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~ 169 (384)
.+..+|+....-+. +.+. ...+.++++++... .+.+++++++.+|++|+||++......+... ..|.+.++.
T Consensus 90 ~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~ 166 (305)
T PRK11151 90 SGPLHIGLIPTVGPYLLPHIIPMLHQTFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIE---VPLFDEPML 166 (305)
T ss_pred CceEEEEecchhHHHHHHHHHHHHHHHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCeEE---EEeccCcEE
Confidence 45677777544332 1111 22344676665443 3689999999999999999976554444222 233344444
Q ss_pred EEEEEEEeeeeeeecCCCCCcCCc---cEEEecH-HH-HHHHHHHHHhcCC---eEEecCCHHHHHHHHHhcCCCCeEEE
Q 016702 170 IVGEVQLAANFCLLALPGIKADQL---KRVLSHP-QA-LASSDIVLTQLGV---ARENVDDTASAAQYVASNGLRDAGAV 241 (384)
Q Consensus 170 I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp-qA-l~QC~~fL~~~~~---~~i~~~STA~AA~~v~~~~~~~~AAI 241 (384)
++ .+-+|-+...+..+++++ .-|...+ .. ..+...|+..++. ....++|...+.++++.+ ...+|
T Consensus 167 ~~----~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~i 239 (305)
T PRK11151 167 LA----VYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAG---SGITL 239 (305)
T ss_pred EE----ecCCCCcccCCccCHHHhcCCCeEeecCCccHHHHHHHHHHHCCCCCCceEEeccHHHHHHHHHcC---CCEEE
Confidence 43 233454443332333333 2232211 11 2345556655432 235677777777887764 46777
Q ss_pred cCHHHHH
Q 016702 242 ASARAAE 248 (384)
Q Consensus 242 as~~aA~ 248 (384)
.+...+.
T Consensus 240 lp~~~~~ 246 (305)
T PRK11151 240 LPALAVP 246 (305)
T ss_pred eeHHhhh
Confidence 7777664
No 120
>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=83.58 E-value=27 Score=29.83 Aligned_cols=123 Identities=15% Similarity=0.115 Sum_probs=64.4
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc--
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (384)
.|++.++.-. .+..++.+.+.+|++|+|+..-.....+. ....|.+.++.++. +-.|-+......+++++
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 3566554333 46789999999999999997543222211 11223333333322 22333322222222222
Q ss_pred -cEEE-ecH-HHHHHHHHHHHhcCC---eEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 194 -KRVL-SHP-QALASSDIVLTQLGV---ARENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 194 -~~Vy-SHp-qAl~QC~~fL~~~~~---~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
.-|. +.. ....+..+|+.+++. ....++|...+.+++..+ ...|+.+...++.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 157 (200)
T cd08411 99 ERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAG---LGITLLPELAVPS 157 (200)
T ss_pred CceEecCCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CCEEEeCHHHhcc
Confidence 2232 111 123344556665543 245667777777777774 4678888777663
No 121
>PRK06349 homoserine dehydrogenase; Provisional
Probab=83.41 E-value=4.3 Score=42.11 Aligned_cols=64 Identities=19% Similarity=0.272 Sum_probs=46.5
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
-|.+.+.|+||.|.++-+.|.+++||+..+...+.... ..+..+.++- ..+..+++++++|++
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 45556689999999999999999999999887764321 1234444432 335788999998886
Q ss_pred h
Q 016702 368 F 368 (384)
Q Consensus 368 ~ 368 (384)
.
T Consensus 413 l 413 (426)
T PRK06349 413 L 413 (426)
T ss_pred C
Confidence 4
No 122
>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=83.05 E-value=5.3 Score=28.14 Aligned_cols=31 Identities=26% Similarity=0.289 Sum_probs=26.3
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeeeeee
Q 016702 291 FTLDEGPGVLFKALAVFALREINLTKIESRP 321 (384)
Q Consensus 291 f~~~~~pGaL~~~L~~F~~~~INLtkIESRP 321 (384)
+..++.||.+.++++.|+++|||+..|..-+
T Consensus 6 ~~~~~~~~~~~~i~~~L~~~~i~i~~i~~~~ 36 (61)
T cd04891 6 KGVPDKPGVAAKIFSALAEAGINVDMIVQSV 36 (61)
T ss_pred ecCCCCCcHHHHHHHHHHHcCCcEEEEEEcC
Confidence 3457889999999999999999998876544
No 123
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=82.71 E-value=1.1 Score=42.06 Aligned_cols=83 Identities=17% Similarity=0.161 Sum_probs=56.8
Q ss_pred CceEEEEECCCCcHHHHHHHHHC-CC--------CcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccc--
Q 016702 96 TKVRISFKGLPGSFSEDAALKAY-PK--------CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL-- 164 (384)
Q Consensus 96 ~~~~Va~LGP~GTfS~~AA~~~f-~~--------~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~-- 164 (384)
+..+|++-.|..+..+.+....+ .. ...++..+.++++.+|.+|++|.|+++- .+++.+.
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 45799998776555577766655 22 1345678999999999999999999873 3444443
Q ss_pred ----cCCeEEEEEEEEeeeeeeecCCC
Q 016702 165 ----RHRLHIVGEVQLAANFCLLALPG 187 (384)
Q Consensus 165 ----~~~l~I~gEi~l~I~h~Ll~~~g 187 (384)
..+++|.++...-..+.+++.++
T Consensus 175 ~~~~~~~~rvl~~s~~~p~~~~~~~~~ 201 (243)
T PF12974_consen 175 GPDIPSQLRVLWTSPPYPNWPLVASPD 201 (243)
T ss_dssp -HHHHTTEEEEEEEEEEE--EEEEETT
T ss_pred cCcccccEEEEEEeCCCCCcEEEEeCC
Confidence 24799999987766777888765
No 124
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=82.44 E-value=3.1 Score=43.00 Aligned_cols=63 Identities=24% Similarity=0.336 Sum_probs=45.6
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccE-EEEEEeecCCCcHHHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDY-LFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y-~FfID~eg~~~d~~v~~al~~ 364 (384)
.-.|++.-.|+||.+.+++++++++|||+-.+..+... +| +..||+++... + +++++
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 56677788999999999999999999999877664322 23 33449988653 3 45666
Q ss_pred HHHhcC
Q 016702 365 LQEFAT 370 (384)
Q Consensus 365 L~~~~~ 370 (384)
|++.-.
T Consensus 396 i~~i~~ 401 (409)
T PRK11790 396 LKAIPG 401 (409)
T ss_pred HHcCCC
Confidence 665444
No 125
>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=80.77 E-value=8.2 Score=36.16 Aligned_cols=138 Identities=15% Similarity=0.029 Sum_probs=72.0
Q ss_pred eEEEEECCCCcHH-HHHH-HHHCC------CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeE
Q 016702 98 VRISFKGLPGSFS-EDAA-LKAYP------KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (384)
Q Consensus 98 ~~Va~LGP~GTfS-~~AA-~~~f~------~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~ 169 (384)
++|+|+.. +... ..|. +.+|. ++++++..+..++++++.+|++|+|++.....+ .. .-...++.
T Consensus 1 l~vg~~~~-~~~~~~~a~~~g~f~~~g~~l~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~----~~---~~~g~~~~ 72 (288)
T TIGR01728 1 VRIGYQKN-GHSALALAKEKGLLEKELGKTKVEWVEFPAGPPALEALGAGSLDFGYIGPGPAL----FA---YAAGADIK 72 (288)
T ss_pred CeEEecCC-CchHHHHHHHhCHHHHhhCCceEEEEecCCCcHHHHHHhcCCccccccCCcHHH----HH---HhcCCCEE
Confidence 47899865 3322 2332 23442 356778888889999999999999987543111 10 00112555
Q ss_pred EEEEEEEeeeeeeecCCCC---CcCCcc--EEEecHH--HHHHHHHHHHhcCCe---E-EecCCHHHHHHHHHhcCCCCe
Q 016702 170 IVGEVQLAANFCLLALPGI---KADQLK--RVLSHPQ--ALASSDIVLTQLGVA---R-ENVDDTASAAQYVASNGLRDA 238 (384)
Q Consensus 170 I~gEi~l~I~h~Ll~~~g~---~l~~I~--~VySHpq--Al~QC~~fL~~~~~~---~-i~~~STA~AA~~v~~~~~~~~ 238 (384)
+++-..-.-..+++++++. +++|++ +|...+- .-..-..+|.++|+. . ....+.+++.+.+..+. -.
T Consensus 73 ~i~~~~~~~~~~~v~~~~~~i~s~~dL~Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~--vd 150 (288)
T TIGR01728 73 AVGLVSDNKATAIVVIKGSPIRTVADLKGKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQ--VD 150 (288)
T ss_pred EEEEecCCCceEEEECCCCCCCCHHHcCCCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCC--CC
Confidence 5554332123455554432 233432 4543221 123445577766542 1 22245667777776652 34
Q ss_pred EEEcCHH
Q 016702 239 GAVASAR 245 (384)
Q Consensus 239 AAIas~~ 245 (384)
|++..+.
T Consensus 151 a~~~~~p 157 (288)
T TIGR01728 151 AWAIWEP 157 (288)
T ss_pred EEEeccc
Confidence 5555443
No 126
>PRK06545 prephenate dehydrogenase; Validated
Probab=80.53 E-value=6.1 Score=39.90 Aligned_cols=40 Identities=15% Similarity=0.310 Sum_probs=35.3
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCC
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR 325 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~ 325 (384)
-..+.+.++|+||.|.+++..+...|||+..|+-..++..
T Consensus 290 ~~~~~v~v~d~pg~~~~~~~~~~~~~i~i~~~~i~~~~~~ 329 (359)
T PRK06545 290 FYDLYVDVPDEPGVIARVTAILGEEGISIENLRILEARED 329 (359)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHcCCCeecceeeeccCC
Confidence 4568889999999999999999999999999988776654
No 127
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=80.02 E-value=9.4 Score=37.75 Aligned_cols=66 Identities=9% Similarity=0.186 Sum_probs=47.0
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeec----CCCcHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEA----SMADPRAQNALG 363 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg----~~~d~~v~~al~ 363 (384)
-|.+.-+|+||-.+++=+.++++|+|+..+... .... ...|+..++++. ..+...++++|+
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 345555999999999999999999999999886 2111 135766666662 233467888887
Q ss_pred HHHHh
Q 016702 364 HLQEF 368 (384)
Q Consensus 364 ~L~~~ 368 (384)
++.+.
T Consensus 76 ~l~~~ 80 (289)
T PRK13010 76 PVAEK 80 (289)
T ss_pred HHHHH
Confidence 77543
No 128
>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=79.67 E-value=39 Score=29.06 Aligned_cols=123 Identities=10% Similarity=0.013 Sum_probs=61.9
Q ss_pred HHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcC---
Q 016702 116 KAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD--- 191 (384)
Q Consensus 116 ~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~--- 191 (384)
+.|++.++.- ..+..++.+.+.+|++|+|++.-.....|.. ...|.+.++.+ ..+-.|-+......+++
T Consensus 24 ~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~l----v~~~~hpl~~~~~~~~~~L~ 96 (197)
T cd08452 24 KKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALH---IETVQSSPCVL----ALPKQHPLASKEEITIEDLR 96 (197)
T ss_pred HHCCCcEEEEEecChHHHHHHHHCCCccEEEeeCCCCCCCee---EEEeeeccEEE----EEeCCCccccCCCCCHHHhc
Confidence 3466655432 2467889999999999999985322111211 11222223322 23445555432222232
Q ss_pred CccEEEecHH----HHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 192 QLKRVLSHPQ----ALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 192 ~I~~VySHpq----Al~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
+..-|...+. ...+-.+|+.+.+. . ...++|...+.++++.+ ...|+.+...+.
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 157 (197)
T cd08452 97 DEPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAG---IGVTFVPSSAKK 157 (197)
T ss_pred CCCEEeccCCcchhHHHHHHHHHHHcCCCccceeecccHHHHHHHHHcC---CCEEEchHHHhh
Confidence 3333332111 22344456666543 2 23466666666777664 346666765543
No 129
>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=79.08 E-value=42 Score=32.52 Aligned_cols=110 Identities=16% Similarity=0.109 Sum_probs=62.1
Q ss_pred CceEEEEE-CCCCcHHHHHHHHHCC----CCcccCCCCHHHHHHHHHhCCCCeEEEeeecccccccccccccccc--CCe
Q 016702 96 TKVRISFK-GLPGSFSEDAALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLR--HRL 168 (384)
Q Consensus 96 ~~~~Va~L-GP~GTfS~~AA~~~f~----~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~--~~l 168 (384)
+++|||++ ||....-+.|...+|. +++++.+++..+..+|+.+|++|.+..=.. ......... .++
T Consensus 18 ~~l~vG~~~~~~~~~~~~~~~~~~~~~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~q~~-------~~l~~~~~~~g~~l 90 (258)
T TIGR00363 18 LHIKVGVISGAEQQVAEVAAKVAKEKYGLDVELVEFNDYALPNEAVSKGDLDANAFQHK-------PYLDQDAKAKGYKL 90 (258)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCEEEEEEeCCcHHHHHHHHcCCCCeEecCCH-------HHHHHHHHhCCCcE
Confidence 46999998 5554444555555553 368889999999999999999998763111 111111112 355
Q ss_pred EEEEEEEEeeeeeeecCCCCCcCCcc---EEEec--HHHHHHHHHHHHhc
Q 016702 169 HIVGEVQLAANFCLLALPGIKADQLK---RVLSH--PQALASSDIVLTQL 213 (384)
Q Consensus 169 ~I~gEi~l~I~h~Ll~~~g~~l~~I~---~VySH--pqAl~QC~~fL~~~ 213 (384)
.++|-..+ ....+.+.+-.+++|++ +|.-. |.-.++.-..|.+.
T Consensus 91 v~v~~~~~-~p~~~ys~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~~a 139 (258)
T TIGR00363 91 VAVGNTFV-YPLAGYSKKIKNVNELQDGAKVAVPNDPTNLGRALLLLQKQ 139 (258)
T ss_pred EEEeeeEE-ecccccCcCCCCHHHcCCCCEEEEeCCcchHHHHHHHHHHc
Confidence 56653322 11234444444667774 55332 33334444466663
No 130
>PRK05007 PII uridylyl-transferase; Provisional
Probab=78.66 E-value=4.4 Score=46.05 Aligned_cols=56 Identities=18% Similarity=0.236 Sum_probs=41.5
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeeeeeCCCCCCccccCCCCCCcccccEEEEE-EeecCCCcH
Q 016702 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLT--KIESRPQRKRPLRVVDDSNNGTAKYFDYLFYI-DFEASMADP 356 (384)
Q Consensus 284 ~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLt--kIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfI-D~eg~~~d~ 356 (384)
.+.|.|-+..+|+||-|+++.++|.+.||++. ||.+.= . .-.=.||| |-+|..-++
T Consensus 806 ~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~g--e---------------ra~DvFyV~~~~g~~l~~ 864 (884)
T PRK05007 806 DRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIG--E---------------RVEDLFILATADRRALNE 864 (884)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccC--c---------------eEEEEEEEEcCCCCcCCH
Confidence 35788889999999999999999999999997 454421 1 12458999 666664343
No 131
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=78.64 E-value=4.7 Score=37.20 Aligned_cols=49 Identities=14% Similarity=0.219 Sum_probs=40.1
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..+||+. .|++......+.++..+.+++++.++.+.+|.+|++|+.+.+
T Consensus 126 g~~Igv~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~grvDa~i~~ 174 (243)
T PRK15007 126 GKKVGVQ--NGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGD 174 (243)
T ss_pred CCeEEEe--cCcHHHHHHHHhCCCCeEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 4588884 677766666666777888889999999999999999999875
No 132
>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=78.47 E-value=8.3 Score=43.56 Aligned_cols=54 Identities=11% Similarity=0.102 Sum_probs=42.6
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEe-ecC
Q 016702 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDF-EAS 352 (384)
Q Consensus 284 ~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~-eg~ 352 (384)
.+.|.+-+..+|+||-|+++.+.|+.+|||+......-.... -.-.|||.. .|.
T Consensus 777 ~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~---------------~~d~F~v~~~~g~ 831 (850)
T TIGR01693 777 RKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEK---------------AEDVFYVTDLFGL 831 (850)
T ss_pred CCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCcc---------------ceeEEEEECCCCC
Confidence 347888899999999999999999999999997766654332 356899965 344
No 133
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=77.97 E-value=6.5 Score=38.31 Aligned_cols=73 Identities=21% Similarity=0.269 Sum_probs=54.5
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEE--EEEeecCCCcHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLF--YIDFEASMADPRAQNAL 362 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~F--fID~eg~~~d~~v~~al 362 (384)
.|-.|-+-+.|+||.|.++-.+|+.||.|+-.+----...+ -.| =|=+.| .|.-++++.
T Consensus 76 krHvinclVqnEpGvlsRisGvlAaRGfNIdSLvVc~tevk-----------------~LsrmTIVl~G--td~VveQa~ 136 (309)
T KOG2663|consen 76 KRHVINCLVQNEPGVLSRISGVLAARGFNIDSLVVCLTEVK-----------------ALSRMTIVLQG--TDGVVEQAR 136 (309)
T ss_pred cceeEEEEecCCchHHHHHHHHHHhccCCchheeeechhhh-----------------hhhhceEEEec--cHHHHHHHH
Confidence 35666667789999999999999999999876554443332 234 455666 578999999
Q ss_pred HHHHHhcCceEEEc
Q 016702 363 GHLQEFATFLRVLG 376 (384)
Q Consensus 363 ~~L~~~~~~vkvLG 376 (384)
++|++...-+++|.
T Consensus 137 rQiedlVnV~aVlD 150 (309)
T KOG2663|consen 137 RQIEDLVNVYAVLD 150 (309)
T ss_pred HHHHHhhhhheeee
Confidence 99998877666663
No 134
>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=77.90 E-value=6.5 Score=32.01 Aligned_cols=68 Identities=16% Similarity=0.222 Sum_probs=43.2
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
.+..+.|++|.+||+|.+.|+.+..++ |+|.++=|-..... . .-+|=++-. +.+..+.+++.
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 467888999999999999999987665 58988888765421 1 233444432 23457788888
Q ss_pred HHHhcC
Q 016702 365 LQEFAT 370 (384)
Q Consensus 365 L~~~~~ 370 (384)
|++..-
T Consensus 71 L~~~gy 76 (91)
T PF00585_consen 71 LKALGY 76 (91)
T ss_dssp HTSSS-
T ss_pred HHHcCC
Confidence 876643
No 135
>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=77.22 E-value=15 Score=26.98 Aligned_cols=28 Identities=29% Similarity=0.355 Sum_probs=24.3
Q ss_pred EEeCCCcchHHHHHHHHHhCCceeeeee
Q 016702 291 FTLDEGPGVLFKALAVFALREINLTKIE 318 (384)
Q Consensus 291 f~~~~~pGaL~~~L~~F~~~~INLtkIE 318 (384)
+.+++.||.+.++++.+++.|||+.-+-
T Consensus 7 ~~~~~~~g~~~~i~~~L~~~~I~i~~i~ 34 (75)
T cd04913 7 RGVPDKPGVAAKIFGALAEANINVDMIV 34 (75)
T ss_pred CCCCCCCcHHHHHHHHHHHcCCeEEEEE
Confidence 3457899999999999999999998664
No 136
>cd08435 PBP2_GbpR The C-terminal substrate binding domain of galactose-binding protein regulator contains the type 2 periplasmic binding fold. Galactose-binding protein regulator (GbpR), a member of the LysR family of bacterial transcriptional regulators, regulates the expression of chromosomal virulence gene chvE. The chvE gene is involved in the uptake of specific sugars, in chemotaxis to these sugars, and in the VirA-VirG two-component signal transduction system. In the presence of an inducing sugar such as L-arabinose, D-fucose, or D-galactose, GbpR activates chvE expression, while in the absence of an inducing sugar, GbpR represses expression. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a ma
Probab=76.19 E-value=47 Score=28.10 Aligned_cols=122 Identities=14% Similarity=0.095 Sum_probs=61.9
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeecc--ccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS--~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (384)
.|++.++.. ..+..++.+.+.+|++|+|++..... ..|.. ...|.+.++.++ .+-+|-+...+..+++|+
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~~l~~~~~~~~~dL 97 (201)
T cd08435 25 RHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLA---SEELADEPLVVV----ARPGHPLARRARLTLADL 97 (201)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCCCCcE---EEEcccCcEEEE----EeCCCcCcccCCcCHHHH
Confidence 456654433 34678999999999999999853221 12211 122233344332 333444443322333333
Q ss_pred c---EEEec-HH-HHHHHHHHHHhcCCe----EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 194 K---RVLSH-PQ-ALASSDIVLTQLGVA----RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 194 ~---~VySH-pq-Al~QC~~fL~~~~~~----~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
. -|..- .. -.....+|+.+.+.. ...+++...+.+++..+ ...|+.+...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08435 98 ADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARS---DMLAVLPRSVAE 158 (201)
T ss_pred hcCCEEecCCCCcHHHHHHHHHHHcCCCCCCceEEEccHHHHHHHHhcC---CeEEEeEHHHhh
Confidence 2 22211 11 112345556555432 23455666666666664 456777777665
No 137
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=75.80 E-value=15 Score=36.26 Aligned_cols=64 Identities=11% Similarity=0.131 Sum_probs=43.2
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCC-----CcHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASM-----ADPRAQNAL 362 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~-----~d~~v~~al 362 (384)
.+.+.-+|+||-..++-+.|+.+|+|+..+.+.-... +. .|++-++.+. +-..++++|
T Consensus 8 vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~----------------~g-~F~m~i~v~~~~~~~~~~~L~~~L 70 (286)
T PRK06027 8 VLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPE----------------TG-RFFMRVEFEGDGLIFNLETLRADF 70 (286)
T ss_pred EEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCC----------------CC-eEEEEEEEEeCCCCCCHHHHHHHH
Confidence 3444458999999999999999999999888764221 12 2555443333 225677777
Q ss_pred HHHHHh
Q 016702 363 GHLQEF 368 (384)
Q Consensus 363 ~~L~~~ 368 (384)
+.|.+.
T Consensus 71 ~~l~~~ 76 (286)
T PRK06027 71 AALAEE 76 (286)
T ss_pred HHHHHH
Confidence 777653
No 138
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=75.67 E-value=13 Score=41.27 Aligned_cols=69 Identities=12% Similarity=0.190 Sum_probs=49.4
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
..+.|.+...|++|.|.++...++..++|+..+.++..+.. .+.-.|-|++. +-..+..++..
T Consensus 625 ~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~--------------~~~~~~~ieV~---~~~~L~~i~~~ 687 (702)
T PRK11092 625 FIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGR--------------VYSAFIRLTAR---DRVHLANIMRK 687 (702)
T ss_pred eEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCC--------------EEEEEEEEEEC---CHHHHHHHHHH
Confidence 45667788899999999999999999999999998754321 12223334442 23678888888
Q ss_pred HHHhcC
Q 016702 365 LQEFAT 370 (384)
Q Consensus 365 L~~~~~ 370 (384)
|+..-.
T Consensus 688 Lr~i~~ 693 (702)
T PRK11092 688 IRVMPD 693 (702)
T ss_pred HhCCCC
Confidence 886543
No 139
>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=75.36 E-value=5.6 Score=35.32 Aligned_cols=48 Identities=25% Similarity=0.262 Sum_probs=38.8
Q ss_pred eEEEEECCCCcHHHHHHHHHCC-CCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 98 VRISFKGLPGSFSEDAALKAYP-KCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 98 ~~Va~LGP~GTfS~~AA~~~f~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
.+|++. .|++......+.+. ..+++.+.+.++++++|.+|++|+.+++
T Consensus 111 ~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~ 159 (225)
T PF00497_consen 111 KRIGVV--RGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVD 159 (225)
T ss_dssp SEEEEE--TTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEE
T ss_pred cccccc--cchhHHHHhhhhccchhhhcccccHHHHHHHHhcCCeeeeecc
Confidence 578874 56666655555565 6788899999999999999999999986
No 140
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=74.53 E-value=7.1 Score=36.05 Aligned_cols=49 Identities=10% Similarity=0.127 Sum_probs=40.3
Q ss_pred ceEEEEECCCCcHHHHHHHHHCC-CCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALKAYP-KCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..+|++ ..|+..+......++ +.+++.+.+.++++++|.+|++|+.|+.
T Consensus 131 g~~i~~--~~g~~~~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~ 180 (250)
T TIGR01096 131 GKTVGV--QSGTTHEQYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTD 180 (250)
T ss_pred CCEEEE--ecCchHHHHHHHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 457887 467777776666777 6778889999999999999999999984
No 141
>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=73.97 E-value=8.5 Score=33.21 Aligned_cols=50 Identities=24% Similarity=0.314 Sum_probs=39.3
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEee
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPI 148 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPi 148 (384)
..+|++. .|+..+....+.++.....++.+.++++++|.+|++|+++++-
T Consensus 105 g~~i~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 154 (218)
T cd00134 105 GKKVAVQ--KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDE 154 (218)
T ss_pred CCEEEEE--cCchHHHHHHHhCCcccEEEeCCHHHHHHHHHcCCccEEEecc
Confidence 3578877 5655566666666666788999999999999999999988763
No 142
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=73.66 E-value=17 Score=40.60 Aligned_cols=69 Identities=17% Similarity=0.259 Sum_probs=49.5
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
..+.|.+...|++|.|.++.+.++..++|+..+.++..+... ...-.|-|++. +-..+..++..
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 345677788999999999999999999999999987654211 12233444553 23677888888
Q ss_pred HHHhc
Q 016702 365 LQEFA 369 (384)
Q Consensus 365 L~~~~ 369 (384)
|+..-
T Consensus 729 L~~i~ 733 (743)
T PRK10872 729 LNQVP 733 (743)
T ss_pred HhcCC
Confidence 87653
No 143
>PRK05092 PII uridylyl-transferase; Provisional
Probab=73.41 E-value=16 Score=41.89 Aligned_cols=53 Identities=17% Similarity=0.204 Sum_probs=40.5
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEE-EeecC
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYI-DFEAS 352 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfI-D~eg~ 352 (384)
..|.|.+..+|+||-|+++.+.|+.+|||+..-...-... ...-.||| |-+|.
T Consensus 842 ~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~---------------~~~D~F~v~d~~g~ 895 (931)
T PRK05092 842 RFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGE---------------RAVDVFYVTDLFGL 895 (931)
T ss_pred CeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCC---------------EEEEEEEEeCCCCC
Confidence 3577888889999999999999999999999665543222 13468999 55555
No 144
>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=72.63 E-value=15 Score=34.48 Aligned_cols=58 Identities=17% Similarity=0.245 Sum_probs=44.6
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIE-SRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQ 359 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIE-SRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~ 359 (384)
-..|++.-.|+||.+.++-+.|.+++||+.... +|-.++ .+=+-.|.++....++.++
T Consensus 148 g~~L~~~~~D~PG~Ig~vg~~Lg~~~iNIa~m~v~r~~~g----------------~~Ai~vl~vD~~v~~~vl~ 206 (208)
T TIGR00719 148 HPAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIG----------------NIALLTIEIDKNIDDHIKD 206 (208)
T ss_pred ccEEEEEeCCCCChHHHHHHHHHhCCccEEEEEEEecCCC----------------CEEEEEEEeCCCCCHHHHh
Confidence 356788889999999999999999999998774 343332 3467888999887665443
No 145
>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Probab=72.55 E-value=18 Score=40.07 Aligned_cols=69 Identities=14% Similarity=0.152 Sum_probs=49.3
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
..+.|.+...|++|.|.++.+.++..++|+..+.++-... ..+.+.++++- .+-..+..++..
T Consensus 609 f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~----------------~~~~~~~~ieV-~~~~~L~~ii~~ 671 (683)
T TIGR00691 609 FIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGK----------------REAILNITVEI-KNYKHLLKIMLK 671 (683)
T ss_pred eEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCC----------------CEEEEEEEEEE-CCHHHHHHHHHH
Confidence 4567788889999999999999999999999999864321 11233333332 233678888888
Q ss_pred HHHhcC
Q 016702 365 LQEFAT 370 (384)
Q Consensus 365 L~~~~~ 370 (384)
|+..-.
T Consensus 672 L~~i~~ 677 (683)
T TIGR00691 672 IKTKND 677 (683)
T ss_pred HhCCCC
Confidence 876543
No 146
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=72.30 E-value=23 Score=39.28 Aligned_cols=69 Identities=16% Similarity=0.239 Sum_probs=52.4
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 364 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~ 364 (384)
..+.|.+...|++|.|.++++.++..++|+.++.++...+. .+.+.++++-+ +-..+..++..
T Consensus 626 f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~~----------------~~~~~~~i~v~-n~~~L~~i~~~ 688 (701)
T COG0317 626 YPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQ----------------FATMQFTIEVK-NLNHLGRVLAR 688 (701)
T ss_pred eEEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCCc----------------eEEEEEEEEEC-cHHHHHHHHHH
Confidence 45677788889999999999999999999999999987332 24555555543 23667788888
Q ss_pred HHHhcC
Q 016702 365 LQEFAT 370 (384)
Q Consensus 365 L~~~~~ 370 (384)
|+....
T Consensus 689 l~~~~~ 694 (701)
T COG0317 689 LKQLPD 694 (701)
T ss_pred HhcCCC
Confidence 876654
No 147
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=72.15 E-value=16 Score=35.39 Aligned_cols=122 Identities=16% Similarity=0.021 Sum_probs=67.9
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCccE
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR 195 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~ 195 (384)
.+++.++... .+-.++++.+.+|++|+|+++-+-...+... ..|.+.++.++ .+-.|-+. ....+++++..
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 3566554432 3568899999999999999975422222111 12233344332 34455553 22234444431
Q ss_pred ----EEecHHHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 196 ----VLSHPQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 196 ----VySHpqAl~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
+++++....+...|+.+.+.. ...++|......+++.+ ...++.+...++.
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 266 (314)
T PRK09508 209 EQHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQT---HLVAIAPRWLAEE 266 (314)
T ss_pred CCCEEecCCCCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhC---ChHHHHHHHHHHH
Confidence 233333334456777766532 34567777777777764 3567778777654
No 148
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=71.64 E-value=5.1 Score=46.36 Aligned_cols=51 Identities=16% Similarity=0.111 Sum_probs=44.1
Q ss_pred CceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEee
Q 016702 96 TKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPI 148 (384)
Q Consensus 96 ~~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPi 148 (384)
...+||+ +.|++.+....+.+++.+++.+++.++++.+|.+|++|+.|.+.
T Consensus 406 ~g~~vav--~~g~~~~~~~~~~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~~ 456 (1197)
T PRK09959 406 KGMKVAI--PYYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDALVATQ 456 (1197)
T ss_pred cCCEEEE--eCCcchHHHHHHHCCCcEEEEcCCHHHHHHHHHcCCCCEEehhh
Confidence 3568888 57888888878889989999999999999999999999998753
No 149
>PRK11260 cystine transporter subunit; Provisional
Probab=70.77 E-value=9.1 Score=36.21 Aligned_cols=48 Identities=8% Similarity=0.070 Sum_probs=39.7
Q ss_pred eEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 98 VRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 98 ~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
.+|+. ..|+..+....+.++..++..+++..+.++++.+|++|+.+.+
T Consensus 150 ~~Igv--~~G~~~~~~l~~~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d 197 (266)
T PRK11260 150 KKVGV--GLGTNYEQWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVD 197 (266)
T ss_pred CEEEE--ecCCcHHHHHHHhCCCCceEecCCHHHHHHHHHcCCCCEEEec
Confidence 47776 6777766666667777788889999999999999999999885
No 150
>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=70.28 E-value=66 Score=27.19 Aligned_cols=122 Identities=21% Similarity=0.121 Sum_probs=58.8
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCcc-
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (384)
.+++.++.-. .+..++++.+.+|++|+|++.-.....+.. ...|.+..+.+ ..+-.|-|...+..+++|+.
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~pl~~~~~~~~~dl~~ 97 (196)
T cd08450 25 EHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGID---YQLLLKEPLIV----VLPADHRLAGREKIPPQDLAG 97 (196)
T ss_pred hCCCcEEEEEecChHHHHHHHhcCCccEEEEeCCCCCCCcE---EEEEEccceEE----EecCCCCcccCceECHHHhCC
Confidence 3566554433 356789999999999999976432111111 11122222222 22333444332212233332
Q ss_pred --EEE-ecHH--HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 195 --RVL-SHPQ--ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 195 --~Vy-SHpq--Al~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
-|. ++.. ...+...|+.+.+.. ...++|...+..+++.+ ...|+.+...+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 156 (196)
T cd08450 98 ENFISPAPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVAST---LGCALLPLYANN 156 (196)
T ss_pred CCeEeecCCCchHHHHHHHHHHHCCCCcEeeeeechHHHHHHHHhcC---CcEEEeehhhhh
Confidence 222 2221 123356677766543 23455666666666654 345566655443
No 151
>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=69.95 E-value=25 Score=34.63 Aligned_cols=65 Identities=11% Similarity=0.224 Sum_probs=44.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecC---CCcHHHHHHHHH-
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEAS---MADPRAQNALGH- 364 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~---~~d~~v~~al~~- 364 (384)
|.+.-+|+||-.+++-+.++++|+|++.+...-.... ..|.-.++++.. .+.+.+++++++
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 4556699999999999999999999998877643221 122223344432 334677887777
Q ss_pred HHHh
Q 016702 365 LQEF 368 (384)
Q Consensus 365 L~~~ 368 (384)
+.+.
T Consensus 68 ~~~~ 71 (280)
T TIGR00655 68 LAEK 71 (280)
T ss_pred HHHH
Confidence 6543
No 152
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=69.50 E-value=23 Score=33.25 Aligned_cols=145 Identities=15% Similarity=0.074 Sum_probs=77.9
Q ss_pred CCceEEEEECCCCcHHHHHHHH--HCC----CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCe
Q 016702 95 GTKVRISFKGLPGSFSEDAALK--AYP----KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRL 168 (384)
Q Consensus 95 ~~~~~Va~LGP~GTfS~~AA~~--~f~----~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l 168 (384)
..+++|||+...+.+.-..|.+ +|. +++++.+.+-.++.+++.+|++|++.+ ...+..+.-.-. .-...++
T Consensus 5 ~~~l~ig~~~~~~~~p~~~a~~~g~f~~~G~~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~--~~~~~~~ 81 (252)
T PF13379_consen 5 PTTLRIGYLPGPDYAPLYVAQEKGLFEKEGLDVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGA--GGPDVDI 81 (252)
T ss_dssp ESEEEEEETSSGGGHHHHHHHHTTHHHHTTSCEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTT--TT----E
T ss_pred CcEEEEEeecchHHHHHHHHHHcChHHHcCCEEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCC--CCcccce
Confidence 3568999985444444333432 342 367889999999999999999999999 443332221111 0001233
Q ss_pred EEEEEEEEeeeeeeecCC------C-CCcCCc---------cEEEe-cHHH--HHHHHHHHHhcC------CeEEecCCH
Q 016702 169 HIVGEVQLAANFCLLALP------G-IKADQL---------KRVLS-HPQA--LASSDIVLTQLG------VARENVDDT 223 (384)
Q Consensus 169 ~I~gEi~l~I~h~Ll~~~------g-~~l~~I---------~~VyS-HpqA--l~QC~~fL~~~~------~~~i~~~ST 223 (384)
.+.+-...- ...++.+. + .+++|+ ++|.. ++-. .-..+.+|++.+ ++.+.+..
T Consensus 82 ~~~~~~~~~-g~~lvv~~~~~~~~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~- 159 (252)
T PF13379_consen 82 VVLAGLSQN-GNALVVRNDLKDASDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP- 159 (252)
T ss_dssp EEEEECSBS-SEEEEECGGGTTCSTTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-
T ss_pred EEeeccCCC-ceEEEEcCccccCCCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-
Confidence 333322211 12344442 2 244555 46665 5533 345678998863 34555555
Q ss_pred HHHHHHHHhcCCCCeEEEcCHH
Q 016702 224 ASAAQYVASNGLRDAGAVASAR 245 (384)
Q Consensus 224 A~AA~~v~~~~~~~~AAIas~~ 245 (384)
.++...++.+ .-+.+++.-+.
T Consensus 160 ~~~~~al~~g-~iDa~~~~eP~ 180 (252)
T PF13379_consen 160 PEMVAALRAG-EIDAAVLWEPF 180 (252)
T ss_dssp HHHHHHHHTT-S-SEEEEETTH
T ss_pred HHHHHHHhCC-CcCEEEecCCH
Confidence 7777777765 23445544444
No 153
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=69.47 E-value=9.3 Score=43.31 Aligned_cols=32 Identities=22% Similarity=0.231 Sum_probs=29.2
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee
Q 016702 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLT 315 (384)
Q Consensus 284 ~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLt 315 (384)
.+.|.|=+..+|+||-|+++.++|.+.||++.
T Consensus 781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~ 812 (854)
T PRK01759 781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLL 812 (854)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEE
Confidence 34788888999999999999999999999987
No 154
>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=68.98 E-value=18 Score=26.36 Aligned_cols=51 Identities=18% Similarity=0.250 Sum_probs=37.5
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHH
Q 016702 294 DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 365 (384)
Q Consensus 294 ~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L 365 (384)
.+.||...++++.|++++||+-.|.+ +. -...|+|+-.-. +..+++++++|
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 358888877322 34666666655
No 155
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=68.78 E-value=1e+02 Score=28.69 Aligned_cols=139 Identities=16% Similarity=0.148 Sum_probs=72.2
Q ss_pred CCceEEEEECCCCcHHHHHHH---HHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEE
Q 016702 95 GTKVRISFKGLPGSFSEDAAL---KAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHI 170 (384)
Q Consensus 95 ~~~~~Va~LGP~GTfS~~AA~---~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I 170 (384)
.+..+|++.++ .+--.+.. +.+++.++.- ..+..++++.+.+|++|+|++.......+.. ...|...++.+
T Consensus 86 ~~~l~ig~~~~--~~~~~~l~~~~~~~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~l 160 (279)
T TIGR03339 86 EGSLRIAATAP--YYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLD---RVVLGNDPLVA 160 (279)
T ss_pred ceEEEEeCchH--HHHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEecccCCCceE---EEEcCCceEEE
Confidence 45678887643 12222211 2356655433 3578899999999999999985443322211 12222333333
Q ss_pred EEEEEEeeeeeeecCCCCCcCC---ccEEEecH--HHHHHHHHHHHhcCC---eEEecCCHHHHHHHHHhcCCCCeEEEc
Q 016702 171 VGEVQLAANFCLLALPGIKADQ---LKRVLSHP--QALASSDIVLTQLGV---ARENVDDTASAAQYVASNGLRDAGAVA 242 (384)
Q Consensus 171 ~gEi~l~I~h~Ll~~~g~~l~~---I~~VySHp--qAl~QC~~fL~~~~~---~~i~~~STA~AA~~v~~~~~~~~AAIa 242 (384)
+ .+-+|-|...+..++++ ..-|...+ ........|+.+.+. ....++|...+.+++..+ ...++.
T Consensus 161 v----~s~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~l 233 (279)
T TIGR03339 161 V----VHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAG---LGVSVV 233 (279)
T ss_pred E----ECCCCccccCCCcCHHHHhCCCeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcC---CCEEEc
Confidence 2 22234343332233333 33343222 223567778877653 234567777777777764 345666
Q ss_pred CHH
Q 016702 243 SAR 245 (384)
Q Consensus 243 s~~ 245 (384)
+..
T Consensus 234 p~~ 236 (279)
T TIGR03339 234 SAA 236 (279)
T ss_pred chh
Confidence 654
No 156
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=68.65 E-value=12 Score=40.05 Aligned_cols=106 Identities=15% Similarity=0.201 Sum_probs=67.7
Q ss_pred cCHHHHHHcCCceeeccc--cCCCCCeeEEEEEeeCCCC-------CCC-------------CCCceEEEEEEeCCCcch
Q 016702 242 ASARAAEIYGLNILADRI--QDEPDNITRFLVLARDPII-------PRT-------------DKLFKTSIVFTLDEGPGV 299 (384)
Q Consensus 242 as~~aA~~ygL~il~~~I--~D~~~N~TRF~vi~~~~~~-------~~~-------------~~~~Ktsl~f~~~~~pGa 299 (384)
-+..-|+-.|+++-.... .+...|+-++.+-+..... -.+ -..+..++++...|+||.
T Consensus 386 nA~~iA~e~GI~~~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~ggg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~ 465 (526)
T PRK13581 386 NAPLLAKERGIEVEESKSEESPDYSNLITVTVTTDDGERSVAGTVFGDGEPRIVEIDGYRVDAKPEGHMLIIRNRDRPGV 465 (526)
T ss_pred CHHHHHHHcCCEEEEEEecCCCCCCCEEEEEEEeCCeEEEEEEEEecCCceEEEEECCEEEEeeCCceEEEEEeCCcCCh
Confidence 344668888888754332 3334676677664433110 000 012345677777999999
Q ss_pred HHHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 300 LFKALAVFALREINLTKIE-SRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 300 L~~~L~~F~~~~INLtkIE-SRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
+.++.+.|.+++||+.... +|-.++ .+.+..|+++....+ +++++|++
T Consensus 466 I~~v~~~L~~~~iNIa~m~~~r~~~g----------------~~al~~i~~D~~v~~----~~l~~i~~ 514 (526)
T PRK13581 466 IGKVGTLLGEAGINIAGMQLGRREAG----------------GEALMVLSVDDPVPE----EVLEELRA 514 (526)
T ss_pred hHHHHHHHhhcCCCchhcEeccCCCC----------------CeEEEEEECCCCCCH----HHHHHHhc
Confidence 9999999999999998775 453222 457888999887754 35555554
No 157
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=68.17 E-value=7.4 Score=45.04 Aligned_cols=49 Identities=12% Similarity=0.181 Sum_probs=42.9
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..+|+. +.|++.+..++++|++.+++.++|..+++++|.+|++|+.|..
T Consensus 164 ~~~i~~--~~g~~~~~~~~~~~p~~~i~~~~s~~~al~av~~G~~Da~i~~ 212 (1197)
T PRK09959 164 PVNIAR--VANYPPDEVIHQSFPKATIISFTNLYQALASVSAGQNDYFIGS 212 (1197)
T ss_pred CeEEEE--eCCCCCHHHHHHhCCCCEEEeCCCHHHHHHHHHcCCCCEEEcc
Confidence 456776 5588888888889999999999999999999999999998875
No 158
>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=67.85 E-value=74 Score=26.84 Aligned_cols=122 Identities=15% Similarity=0.056 Sum_probs=61.8
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCc---CC
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---DQ 192 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l---~~ 192 (384)
.+++.++.. ..+..++++.+.+|++|+|++.-.....|... ..|.+..+.+ ..+-.|-|...+..++ .+
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 456654432 34678899999999999999854322222111 1222222221 2233454443222222 33
Q ss_pred ccEEE-ecHHHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 193 LKRVL-SHPQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 193 I~~Vy-SHpqAl~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
..-|. .......+-.+|+.+.+.. ...++|...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (198)
T cd08412 98 EPLILLDLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANG---LGYSLLNDRPYR 154 (198)
T ss_pred CcEEecCchhHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CCEEEeeccccc
Confidence 33333 2222223344566665532 23456677777777664 356777766554
No 159
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=67.68 E-value=91 Score=29.45 Aligned_cols=121 Identities=16% Similarity=0.065 Sum_probs=62.6
Q ss_pred CCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCC-CCcC---C
Q 016702 118 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPG-IKAD---Q 192 (384)
Q Consensus 118 f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g-~~l~---~ 192 (384)
|++..+... .+..++.+.+.+|++|+|+++......+... ..|.+.++.++ .+-.|-|...+. .+++ +
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 455555443 4568899999999999999875544333222 22223333332 233333432221 2222 2
Q ss_pred ccEEEecHHHH--HHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 193 LKRVLSHPQAL--ASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 193 I~~VySHpqAl--~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
-.-|.-.+... ..-..|+.+.+.. ...++|-..+.+++..+ ...++.++..+.
T Consensus 190 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 247 (296)
T PRK11242 190 EPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG---RLATLLPAAIAR 247 (296)
T ss_pred CCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhC---CeEEEeehhhcc
Confidence 23343333322 2334566665533 24456666666777764 346677766554
No 160
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=67.46 E-value=13 Score=31.84 Aligned_cols=51 Identities=24% Similarity=0.319 Sum_probs=38.4
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEeee
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIE 149 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiE 149 (384)
..+|++.. |+........++...+...+.+..+++.++.+|++|+++++-.
T Consensus 106 g~~i~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~ 156 (219)
T smart00062 106 GKKVAVVA--GTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADAP 156 (219)
T ss_pred CCEEEEec--CccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEeccH
Confidence 35788753 6555555444455677888999999999999999999998644
No 161
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=66.76 E-value=12 Score=34.95 Aligned_cols=49 Identities=12% Similarity=0.048 Sum_probs=38.1
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..+|++ ..|+..+.-..+.++..+++.+++.++++.+|.+|++|+.+..
T Consensus 131 g~~I~v--~~g~~~~~~l~~~~~~~~i~~~~~~~~~~~~L~~grvDa~i~~ 179 (247)
T PRK09495 131 GKVVAV--KSGTGSVDYAKANIKTKDLRQFPNIDNAYLELGTGRADAVLHD 179 (247)
T ss_pred CCEEEE--ecCchHHHHHHhcCCCCceEEcCCHHHHHHHHHcCceeEEEeC
Confidence 347887 4477666655566666678889999999999999999988863
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=66.71 E-value=85 Score=27.12 Aligned_cols=140 Identities=11% Similarity=0.030 Sum_probs=71.2
Q ss_pred ceEEEEECCCCcHH-HHH---HHHHCCCCccc-CCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEE
Q 016702 97 KVRISFKGLPGSFS-EDA---ALKAYPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIV 171 (384)
Q Consensus 97 ~~~Va~LGP~GTfS-~~A---A~~~f~~~~~~-~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~ 171 (384)
..+||+-..-+++- -.+ -++.+++.++. ...+..++.+.+.+|++|+|++.-..-..|.. ...+.+.++.+
T Consensus 2 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~~~~~~---~~~l~~~~~~l- 77 (198)
T cd08486 2 ELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIE---IVNIAQEDLYL- 77 (198)
T ss_pred eEEEEEechhhHHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCCCCceE---EEEEeeccEEE-
Confidence 35777765544321 111 12345665443 23577899999999999999984321111111 11222333332
Q ss_pred EEEEEeeeeeeecCCCCCcCCc---cEEEecH----HHHHHHHHHHHhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEE
Q 016702 172 GEVQLAANFCLLALPGIKADQL---KRVLSHP----QALASSDIVLTQLGV--AR-ENVDDTASAAQYVASNGLRDAGAV 241 (384)
Q Consensus 172 gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp----qAl~QC~~fL~~~~~--~~-i~~~STA~AA~~v~~~~~~~~AAI 241 (384)
.++-+|-+......+++++ .-|.-.+ .-..+..+++.+.+. .. ..+++......+++.+ ...+|
T Consensus 78 ---v~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~ 151 (198)
T cd08486 78 ---AVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG---AASSI 151 (198)
T ss_pred ---EecCCCccccCCcccHHHHcCCCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---ceEEE
Confidence 2344555543333344444 3343222 234567777777653 22 3455555555566653 46677
Q ss_pred cCHHH
Q 016702 242 ASARA 246 (384)
Q Consensus 242 as~~a 246 (384)
.+..+
T Consensus 152 lp~~~ 156 (198)
T cd08486 152 VPASV 156 (198)
T ss_pred cchhh
Confidence 77654
No 163
>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=66.66 E-value=80 Score=26.79 Aligned_cols=122 Identities=14% Similarity=0.098 Sum_probs=61.3
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCc---CC
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---DQ 192 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l---~~ 192 (384)
.+++.++.-. .+..++.+.+.+|++|+|+.+-.....+... ..|.+..+.+ ..+-+|-+......++ .+
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 4566544322 3567888999999999999754322122111 1122333332 2333444432221222 33
Q ss_pred ccEEE-ecH---HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 193 LKRVL-SHP---QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 193 I~~Vy-SHp---qAl~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
..-|. .++ ....+...|+.+.+.. ...++|...+.++++.+ ...++.++..+.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (198)
T cd08446 99 EPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAG---FGVCIVPESVAA 158 (198)
T ss_pred CCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcC---CcEEEchhhhhc
Confidence 33443 121 1123445666665432 24566777777777764 456777765543
No 164
>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=66.50 E-value=57 Score=27.40 Aligned_cols=122 Identities=15% Similarity=0.114 Sum_probs=62.6
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCc---CC
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---DQ 192 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l---~~ 192 (384)
.+++.++.. ..+..++.+++.+|++|+|++.......+... ..|.+.++.++ .+-.|-+......++ .+
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 356554322 34668899999999999999865433222211 22333344332 233343432222223 33
Q ss_pred ccEEEecHH--HHHHHHHHHHhcC-----Ce-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 193 LKRVLSHPQ--ALASSDIVLTQLG-----VA-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 193 I~~VySHpq--Al~QC~~fL~~~~-----~~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
..-|.-.+. -..+..+|+.+.+ .. ...+.+...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08420 98 EPWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAG---LGISILSRLAVR 158 (201)
T ss_pred CCEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcC---CCEEEeeHHHHH
Confidence 333332221 1234556666432 12 34566777777777764 457777776554
No 165
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=66.27 E-value=16 Score=30.53 Aligned_cols=47 Identities=9% Similarity=0.009 Sum_probs=37.6
Q ss_pred eEEEEECCCCcHHHHHHHHHCCC-----------CcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 98 VRISFKGLPGSFSEDAALKAYPK-----------CETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 98 ~~Va~LGP~GTfS~~AA~~~f~~-----------~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
.+|+++ .||+.+..++++.+. .++..+++..+++.+|.+|+ |..+..
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 578885 899999888776543 25678999999999999999 866654
No 166
>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=64.88 E-value=41 Score=31.00 Aligned_cols=130 Identities=22% Similarity=0.247 Sum_probs=73.6
Q ss_pred cccCCCCHHHHHHHHHhCCCCeEEEeeecccccc--ccccccccccCCeEEEEEEEEeeeeeeecCCC-----CCcCCc-
Q 016702 122 ETVPCDEFEDTFKAVELWLADKAVLPIENSSSGS--IHRNYDLLLRHRLHIVGEVQLAANFCLLALPG-----IKADQL- 193 (384)
Q Consensus 122 ~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~--V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g-----~~l~~I- 193 (384)
...+..|. +-+.++..|++|.+.+-+-..-.|. +...-++|...++.++.=. .=...|+.+++ .+++|+
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 34444444 4467888999999998554332222 2222234444444443211 12245666666 234444
Q ss_pred --cEEEecHHHHHHHHHHHHhc----CC-----e--EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH-cCCceee
Q 016702 194 --KRVLSHPQALASSDIVLTQL----GV-----A--RENVDDTASAAQYVASNGLRDAGAVASARAAEI-YGLNILA 256 (384)
Q Consensus 194 --~~VySHpqAl~QC~~fL~~~----~~-----~--~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~-ygL~il~ 256 (384)
...+--.|+=+=.|.+|++. ++ . ...+.|..+.|..|+.+ ...++++.+.+|+. |||.++.
T Consensus 91 ~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G--~AD~G~g~~~~A~~~~gL~Fvp 165 (193)
T PF12727_consen 91 DPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASG--KADAGIGIRAAAEEFYGLDFVP 165 (193)
T ss_pred cCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcC--CCCEEeehHHHHHhhcCCCcEE
Confidence 22333444444466666552 22 1 23566777788888886 57899999999975 7998765
No 167
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=64.73 E-value=1.3e+02 Score=28.50 Aligned_cols=141 Identities=12% Similarity=0.016 Sum_probs=72.2
Q ss_pred CceEEEEECCCCcHHH--HH---HHHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeE
Q 016702 96 TKVRISFKGLPGSFSE--DA---ALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (384)
Q Consensus 96 ~~~~Va~LGP~GTfS~--~A---A~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~ 169 (384)
...+||.--.- +... .+ ..+.+++.++.. ..+.+++++.+.+|++|+|+++-.....+ -+...|.+.++.
T Consensus 90 ~~l~Ig~~~~~-~~~~l~~~~~~~~~~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~---l~~~~l~~~~~~ 165 (296)
T PRK09906 90 RQLTIGFVPSA-EVNLLPKVLPMFRLRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDE---IDYLELLDEPLV 165 (296)
T ss_pred CcEEEEEecch-hhhHHHHHHHHHHHHCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecCCCCCCC---ceEEEEecccEE
Confidence 34777765322 2222 11 233456665543 33578899999999999999865421111 112334444444
Q ss_pred EEEEEEEeeeeeeecCCCCC---cCCccEEEecH---HH-HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeE
Q 016702 170 IVGEVQLAANFCLLALPGIK---ADQLKRVLSHP---QA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAG 239 (384)
Q Consensus 170 I~gEi~l~I~h~Ll~~~g~~---l~~I~~VySHp---qA-l~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~A 239 (384)
++ .+-.|-|......+ +.+..-|.--+ .. ..+...|+...++. ...++|...+..+++.+ ...
T Consensus 166 ~v----~~~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g~ 238 (296)
T PRK09906 166 VV----LPVDHPLAHEKEITAAQLDGVNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG---LGC 238 (296)
T ss_pred EE----ecCCCccccCCCcCHHHHcCCCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcE
Confidence 43 33344444322222 23333343211 12 34456777766542 34566666667777764 345
Q ss_pred EEcCHHHH
Q 016702 240 AVASARAA 247 (384)
Q Consensus 240 AIas~~aA 247 (384)
++.+...+
T Consensus 239 ~~~p~~~~ 246 (296)
T PRK09906 239 TIIPGYMN 246 (296)
T ss_pred EEeeHHHh
Confidence 55565544
No 168
>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=64.40 E-value=89 Score=26.63 Aligned_cols=122 Identities=16% Similarity=0.134 Sum_probs=62.7
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc--
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (384)
.|++.++... .+..++.+.+.+|++|+|+.+......+. ....|.+.++.+ ..+-+|-+...+ .+++++
T Consensus 25 ~~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~l---~~~~l~~~~~~~----v~~~~~~l~~~~-i~~~~L~~ 96 (201)
T cd08459 25 VAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGF---FQQRLFRERYVC----LVRKDHPRIGST-LTLEQFLA 96 (201)
T ss_pred HCCCCeEEEEecCccCHHHHhhCCCceEEEEcCCCCcccc---eEEEeecCceEE----EEcCCCccccCC-cCHHHHhh
Confidence 3566554333 34568889999999999998643221111 111222333322 234445443322 333332
Q ss_pred -cEEEecHH--HHHHHHHHHHhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 194 -KRVLSHPQ--ALASSDIVLTQLGV--AR-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 194 -~~VySHpq--Al~QC~~fL~~~~~--~~-i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
.-|...+. ...+..+|+.+++. .. ..++|.....++++.+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (201)
T cd08459 97 ARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQT---DLVATVPERLARL 155 (201)
T ss_pred CCcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcC---CEEEecHHHHHHH
Confidence 23332221 12345677777654 22 3455555555666653 4688888877664
No 169
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=64.29 E-value=88 Score=26.55 Aligned_cols=110 Identities=18% Similarity=0.185 Sum_probs=60.1
Q ss_pred CcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCC---CcCCc--cE
Q 016702 121 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI---KADQL--KR 195 (384)
Q Consensus 121 ~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~---~l~~I--~~ 195 (384)
.++.+. +..++++++.+|++|+++.+.....+.. ..+. .........+.++.+++. +++|+ ++
T Consensus 41 ~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~~-----~~~~------~~~~~~~~~~~~~~~~~~~~~~~~dL~g~~ 108 (219)
T smart00062 41 VEFVEV-SFDNLLTALKSGKIDVVAAGMTITPERA-----KQVD------FSDPYYKSGQVILVRKDSPIKSLEDLKGKK 108 (219)
T ss_pred EEEEec-cHHHHHHHHHCCcccEEeccccCCHHHH-----hhee------eccceeeceeEEEEecCCCCCChHHhCCCE
Confidence 577787 8899999999999999997643221111 0010 011111222445544432 22333 23
Q ss_pred EEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHH
Q 016702 196 VLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARA 246 (384)
Q Consensus 196 VySHpqAl~QC~~fL~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~a 246 (384)
|..-+ . .-...++... +...+.+.+..++..++..+ ...|++.....
T Consensus 109 i~~~~-g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~~ 157 (219)
T smart00062 109 VAVVA-G-TTGEELLKKLYPEAKIVSYDSQAEALAALKAG--RADAAVADAPA 157 (219)
T ss_pred EEEec-C-ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcC--cccEEEeccHH
Confidence 33322 1 2234556554 56677788888888888765 34455555543
No 170
>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=64.12 E-value=70 Score=27.51 Aligned_cols=121 Identities=17% Similarity=0.108 Sum_probs=59.3
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCcc-
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (384)
.+++.++... .+. +.++.+.+|++|+|+++-.....+.. ...|.+.++.++ .+-+|-+.. ...+++++.
T Consensus 25 ~~P~i~l~i~~~~~-~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~hpl~~-~~~~~~~l~~ 95 (200)
T cd08462 25 EAPGVRFELLPPDD-QPHELLERGEVDLLIAPERFMSDGHP---SEPLFEEEFVCV----VWADNPLVG-GELTAEQYFS 95 (200)
T ss_pred HCCCCEEEEecCCh-hHHHHHhcCCeeEEEecCCCCCCCce---eeeeeccceEEE----EcCCCCccC-CCCCHHHHhh
Confidence 4566544333 244 99999999999999986432222211 111222222222 244455543 223444443
Q ss_pred --EEE-ecHHHH-HHHHH-HHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 195 --RVL-SHPQAL-ASSDI-VLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 195 --~Vy-SHpqAl-~QC~~-fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
-|. +.+... ..-.+ |+.+++.. ...++|......+++.+ ...||.++..++.
T Consensus 96 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~giailp~~~~~~ 155 (200)
T cd08462 96 AGHVVVRFGRNRRPSFEDWFLNEYGLKRRVEVVTPSFSSIPPLLVGT---NRIATLHRRLAEQ 155 (200)
T ss_pred CCCEEEecCCCCCccHHHHHHHHcCCcceEEEEeChHHHHHHHHHcC---chhhhhHHHHHHh
Confidence 121 111111 11222 33445543 23566666666777764 4677888776653
No 171
>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=63.37 E-value=94 Score=26.45 Aligned_cols=121 Identities=12% Similarity=0.056 Sum_probs=62.0
Q ss_pred CCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeecc---ccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc
Q 016702 118 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS---SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (384)
Q Consensus 118 f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS---~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (384)
|++.++... .+..++.+.+.+|++|+|+..-... -.|. ....|.+.++.+ ..+-.|-+...+..+++++
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~---~~~~l~~~~~~~----v~~~~hp~~~~~~i~~~~L 98 (200)
T cd08453 26 YPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAPPAL---AYRPLLSEPLVL----AVPAAWAAEGGAPLALAAV 98 (200)
T ss_pred CCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCcccCCCcce---eEEEeeeCceEE----EEECCCccccCCCCCHHHh
Confidence 566554333 3567889999999999999753211 0111 112233344433 2344454443322333333
Q ss_pred ---cEEEec-HH---HHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 194 ---KRVLSH-PQ---ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 194 ---~~VySH-pq---Al~QC~~fL~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
.-|... .. ....+..|+.+.+.. . ..++|...+.++++.+ ...++.+...++
T Consensus 99 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08453 99 AAEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAG---MGVALVPASLRN 160 (200)
T ss_pred ccCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcC---CcEEEeEhHHhh
Confidence 333322 11 234567788776542 2 3455555566666664 356666665543
No 172
>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=62.93 E-value=70 Score=24.81 Aligned_cols=36 Identities=14% Similarity=0.256 Sum_probs=29.1
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~ 324 (384)
+++..+|+||-+.++-..|+.+|+|+..=....++.
T Consensus 4 I~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~d 39 (68)
T cd04928 4 ITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDD 39 (68)
T ss_pred EEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCC
Confidence 566778999999999999999999999654444433
No 173
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=62.82 E-value=11 Score=32.76 Aligned_cols=28 Identities=21% Similarity=0.272 Sum_probs=23.8
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeee
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTKI 317 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtkI 317 (384)
.+-+.|+||-|.++++.++.+|||+.-+
T Consensus 7 SvFlENk~GRL~~~~~~L~eagINiRA~ 34 (142)
T COG4747 7 SVFLENKPGRLASVANKLKEAGINIRAF 34 (142)
T ss_pred EEEecCCcchHHHHHHHHHHcCCceEEE
Confidence 3346799999999999999999998743
No 174
>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=62.55 E-value=30 Score=27.43 Aligned_cols=58 Identities=14% Similarity=0.183 Sum_probs=40.3
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCC----CcHHHHHHHHHHHHh
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASM----ADPRAQNALGHLQEF 368 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~----~d~~v~~al~~L~~~ 368 (384)
.++.||.+.++++.|+++|||+-.|-+ + . ..+.|-|+-+-.. -+..++++..+|++.
T Consensus 11 ~~~~~g~~a~IF~~La~~~InVDmI~q-s--~----------------~sISftV~~sd~~~~~~~~~~l~~~~~~~~~~ 71 (78)
T cd04933 11 MLGQYGFLAKVFSIFETLGISVDVVAT-S--E----------------VSISLTLDPSKLWSRELIQQELDHVVEELEKD 71 (78)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe-c--C----------------CEEEEEEEhhhhhhhhhHHHHHHHHHHHHHHc
Confidence 357899999999999999999999965 1 1 2477888753211 013555666666665
Q ss_pred c
Q 016702 369 A 369 (384)
Q Consensus 369 ~ 369 (384)
+
T Consensus 72 ~ 72 (78)
T cd04933 72 A 72 (78)
T ss_pred C
Confidence 4
No 175
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=61.79 E-value=63 Score=31.44 Aligned_cols=110 Identities=17% Similarity=0.166 Sum_probs=63.8
Q ss_pred CceEEEEE-CCCCcHHHHHHHHHC---C-CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccc--cCCe
Q 016702 96 TKVRISFK-GLPGSFSEDAALKAY---P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL--RHRL 168 (384)
Q Consensus 96 ~~~~Va~L-GP~GTfS~~AA~~~f---~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~--~~~l 168 (384)
+.++||+. +|.....+.+...++ | +++++.+++..+.++++.+|++|.... ..+.... ..+. ..++
T Consensus 31 ~~I~IG~~~~~~~~~~~~~~~~l~~~~G~~Vel~~f~~~~~~~~ALa~GdID~~~~-----qh~~~l~--~~~~~~g~~l 103 (271)
T PRK11063 31 NHIKVGVIVGAEQQVAEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAF-----QHKPYLD--QQIKDRGYKL 103 (271)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHcCCcceecc-----cCHHHHH--HHHHHcCCcE
Confidence 35899997 566544454444443 3 478899999999999999999998762 1111100 0111 2456
Q ss_pred EEEEEEEE-eeeeeeecCCCCCcCCcc---EEEec--HHHHHHHHHHHHhcC
Q 016702 169 HIVGEVQL-AANFCLLALPGIKADQLK---RVLSH--PQALASSDIVLTQLG 214 (384)
Q Consensus 169 ~I~gEi~l-~I~h~Ll~~~g~~l~~I~---~VySH--pqAl~QC~~fL~~~~ 214 (384)
.++|-..+ |+ .+...+-.+++|++ +|.-. |--.+.+-.+|.+.|
T Consensus 104 ~~~~~~~vvp~--~~ys~~i~si~DL~~Gk~IAip~d~~n~~r~L~lL~~~G 153 (271)
T PRK11063 104 VAVGNTFVYPI--AGYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKVG 153 (271)
T ss_pred EEEeEEEEEEe--eccccCCCCHHHhcCCCEEEecCCCccHHHHHHHHHHCC
Confidence 66665433 43 22232223456664 56444 555566666777743
No 176
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=61.65 E-value=35 Score=31.68 Aligned_cols=37 Identities=19% Similarity=0.231 Sum_probs=30.6
Q ss_pred eEEEEEEe--CCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 016702 286 KTSIVFTL--DEGPGVLFKALAVFALREINLTKIESRPQRK 324 (384)
Q Consensus 286 Ktsl~f~~--~~~pGaL~~~L~~F~~~~INLtkIESRP~~~ 324 (384)
++.+++++ +|+||-+.++-+.++++|.|+. +||-+.-
T Consensus 6 ~~~lviTviG~DrpGIVa~vs~~l~~~g~NI~--ds~~t~l 44 (190)
T PRK11589 6 QHYLVITALGADRPGIVNTITRHVSSCGCNIE--DSRLAML 44 (190)
T ss_pred ccEEEEEEEcCCCChHHHHHHHHHHHcCCCee--ehhhHhh
Confidence 45677766 8999999999999999999987 6776543
No 177
>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=61.53 E-value=1.1e+02 Score=26.39 Aligned_cols=121 Identities=16% Similarity=0.046 Sum_probs=61.8
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeecc-ccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc-
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS-SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 193 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS-~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I- 193 (384)
.|++.++... .+-.++.+.+.+|++|+|+.+-... ..+.. ...|.+.++. +..+..|-|......+++++
T Consensus 25 ~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~~l~~~~~~----~v~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08413 25 RYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLV---TLPCYRWNHC----VIVPPGHPLADLGPLTLEDLA 97 (198)
T ss_pred hCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCcE---EEEeeeeeEE----EEecCCCcccccCCCCHHHHh
Confidence 3566554433 3467899999999999999853211 11111 1112222222 22344555544333333333
Q ss_pred --cEEEec-HH-HHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHH
Q 016702 194 --KRVLSH-PQ-ALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAA 247 (384)
Q Consensus 194 --~~VySH-pq-Al~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA 247 (384)
.-|.-. .. -..+-+.|+.+.+. . ...++|......+++.+ ...|+.++..+
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~ 155 (198)
T cd08413 98 QYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLG---LGVGIIAEMAY 155 (198)
T ss_pred cCCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhC---CCEEEcccccc
Confidence 233311 11 22445667776553 2 34566777777777764 34566666544
No 178
>cd08451 PBP2_BudR The C-terminal substrate binding domain of LysR-type transcrptional regulator BudR, which is responsible for activation of the expression of the butanediol operon genes; contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of BudR regulator, which is responsible for induction of the butanediol formation pathway under fermentative growth conditions. Three enzymes are involved in the production of 1 mol of 2,3 butanediol from the condensation of 2 mol of pyruvate with acetolactate and acetoin as intermediates: acetolactate synthetase, acetolactate decarboxylase, and acetoin reductase. In Klebsiella terrigena, BudR regulates the expression of the budABC operon genes, encoding these three enzymes of the butanediol pathway. In many bacterial species, the use of this pathway can prevent intracellular acidification by diverting metabolism from acid production to the formation of neutral compounds (acetoin and butanediol). This substra
Probab=61.39 E-value=99 Score=26.06 Aligned_cols=123 Identities=21% Similarity=0.216 Sum_probs=60.2
Q ss_pred HHCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeecc-ccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc
Q 016702 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS-SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (384)
Q Consensus 116 ~~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS-~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (384)
+.|++.++... .+-+++++.+.+|++|+|+++.... ..+.. ...|.+..+.++ .+-+|-+...+..+++|+
T Consensus 25 ~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~~l~~~~~~~~~dL 97 (199)
T cd08451 25 EAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLV---LELLLEEPMLVA----LPAGHPLARERSIPLAAL 97 (199)
T ss_pred HHCCCcEEEEecCChHHHHHHHHCCCccEEEEecCCCCCCcee---EEEeecccEEEE----ecCCCCCcccCccCHHHh
Confidence 34566544332 3567899999999999999864322 12211 122223333332 234454543322233333
Q ss_pred ---cEEE-ecHH---HHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 194 ---KRVL-SHPQ---ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 194 ---~~Vy-SHpq---Al~QC~~fL~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
.-|. +... ...+-.+|+.+.+.. . ..++|...+..++..+ ...++.+...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 159 (199)
T cd08451 98 ADEPFILFPRPVGPGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAG---LGVSIVPASMRQ 159 (199)
T ss_pred cCCCEEEecCCcChhHHHHHHHHHHHcCCceeeEEehhhHHHHHHHHHcC---CCEEEechHHHh
Confidence 2332 1111 112334455555432 2 3455555555666654 456677776554
No 179
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=61.16 E-value=1.6e+02 Score=28.43 Aligned_cols=142 Identities=9% Similarity=0.028 Sum_probs=70.5
Q ss_pred CCceEEEEECCCCcH-HHHH---HHHHCCCCccc-CCCCHHHHHHHHHhCCCCeEEEeeecc-ccccccccccccccCCe
Q 016702 95 GTKVRISFKGLPGSF-SEDA---ALKAYPKCETV-PCDEFEDTFKAVELWLADKAVLPIENS-SSGSIHRNYDLLLRHRL 168 (384)
Q Consensus 95 ~~~~~Va~LGP~GTf-S~~A---A~~~f~~~~~~-~~~s~~~Vf~aV~~g~~d~gVvPiENS-~~G~V~~tlDlL~~~~l 168 (384)
.+..+||.-..-+.+ --.. -.+.+++.++. ...+.+++.+.|.+|++|+|+.+-... ..+. ...-|.+.++
T Consensus 92 ~g~l~Ig~~~~~~~~~l~~~i~~f~~~~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~l---~~~~l~~~~~ 168 (309)
T PRK12683 92 SGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDL---VSFPYYSWHH 168 (309)
T ss_pred CceEEEEeccchHHHHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCCc---eEEEcccCeE
Confidence 456788774322211 1111 12235665543 335788999999999999999753211 1221 1122233333
Q ss_pred EEEEEEEEeeeeeeecCCCCCcCCc---cEEEecH--HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEE
Q 016702 169 HIVGEVQLAANFCLLALPGIKADQL---KRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGA 240 (384)
Q Consensus 169 ~I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp--qAl~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AA 240 (384)
. +..+..|-|...+..+++++ .-|.-.+ .--.+...|+.+.+.. ...++|......++..+ .+ .+
T Consensus 169 ~----~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~G-i~ 241 (309)
T PRK12683 169 V----VVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELG--MG-VG 241 (309)
T ss_pred E----EEecCCCCcccCCccCHHHHhcCCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhC--CC-eE
Confidence 2 33455666654333333333 3343211 1235577788776542 23455555555666654 23 44
Q ss_pred EcCHHH
Q 016702 241 VASARA 246 (384)
Q Consensus 241 Ias~~a 246 (384)
+.+...
T Consensus 242 ~lp~~~ 247 (309)
T PRK12683 242 IVAAMA 247 (309)
T ss_pred Eeehhh
Confidence 444443
No 180
>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=60.81 E-value=13 Score=36.01 Aligned_cols=135 Identities=16% Similarity=0.119 Sum_probs=74.5
Q ss_pred CCCceEEEEECCCCcHHHHHHHHHC---C-CCcccCCCCHHHHHHHHHhCCCCeEEEeeecc----cccccccc------
Q 016702 94 DGTKVRISFKGLPGSFSEDAALKAY---P-KCETVPCDEFEDTFKAVELWLADKAVLPIENS----SSGSIHRN------ 159 (384)
Q Consensus 94 ~~~~~~Va~LGP~GTfS~~AA~~~f---~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS----~~G~V~~t------ 159 (384)
...+.+++..|+ |+.+|.++..++ | +.+.+|+.+-.+...++..|++|.++...-+. -.|.+...
T Consensus 103 ~p~~~~~g~~g~-g~~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~~~~~~~~~~G~~k~Lav~~~~ 181 (274)
T PF03401_consen 103 NPGKLTFGSSGP-GSSDHLAAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSPGEALPYVEAGDLKPLAVFSDE 181 (274)
T ss_dssp SCCC-EEEESST-TSHHHHHHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHTTSEEEEEECSSS
T ss_pred CCCCeEEEecCC-CchHHHHHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecHHHHHHHHhCCCceEEEEecCc
Confidence 356688888885 889998877654 3 36789999999999999999999998865433 12333211
Q ss_pred -cccccc------CCeEEEEEEEEeeeeeeecCCCCCcCCccEEEecHHH---HHHHHHHHHhcCCeEEecCCHHHHHHH
Q 016702 160 -YDLLLR------HRLHIVGEVQLAANFCLLALPGIKADQLKRVLSHPQA---LASSDIVLTQLGVARENVDDTASAAQY 229 (384)
Q Consensus 160 -lDlL~~------~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~VySHpqA---l~QC~~fL~~~~~~~i~~~STA~AA~~ 229 (384)
++.|-+ ..+ -++.+...+.+++++|++.+-+.++..--+. ....++|+++.+.... ..+..+..+.
T Consensus 182 r~~~~pdvPT~~E~G~---~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~~g~~~~-~~~~~~~~~~ 257 (274)
T PF03401_consen 182 RSPALPDVPTFKEQGY---PDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEKMGLEPV-YMDGEEFDAF 257 (274)
T ss_dssp -BTTCTTS-BTTTTT----TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHHHTEEEE-CESHHHHHHH
T ss_pred cccccCCCCCHHHhCc---cceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHHCCCcCC-CCCHHHHHHH
Confidence 111111 111 0223455677888887653333322211111 1233455555555443 5566666666
Q ss_pred HHhc
Q 016702 230 VASN 233 (384)
Q Consensus 230 v~~~ 233 (384)
+.++
T Consensus 258 l~~~ 261 (274)
T PF03401_consen 258 LAEE 261 (274)
T ss_dssp HHHH
T ss_pred HHHH
Confidence 6553
No 181
>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=60.55 E-value=99 Score=25.78 Aligned_cols=122 Identities=20% Similarity=0.114 Sum_probs=60.7
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc--
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (384)
.+++.++.- ..+..++.+.+.+|++|+|+..-.....+.. ...|.+.++.++ .+-+|-+...+..+++++
T Consensus 25 ~~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~pl~~~~~~~~~~l~~ 97 (197)
T cd08440 25 RHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLE---FEPLLRDPFVLV----CPKDHPLARRRSVTWAELAG 97 (197)
T ss_pred hCCCcEEEEEeCChHHHHHHHHcCCccEEEEeCCCCCCCee---EEEeecccEEEE----ecCCCCcccCCccCHHHHcc
Confidence 356654432 2356889999999999999985332111111 112222333322 233343432222233333
Q ss_pred -cEE-EecHHH-HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 194 -KRV-LSHPQA-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 194 -~~V-ySHpqA-l~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
.-| +.+... .....+|+.+.+. + ...++|...+.++++.+ ...|+.++..+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (197)
T cd08440 98 YPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAG---LGVAVLPALALP 155 (197)
T ss_pred CCEEecCCCccHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEcchhHHH
Confidence 223 222221 2234456665543 2 34566777777777764 456777776554
No 182
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=59.81 E-value=1.6e+02 Score=28.61 Aligned_cols=142 Identities=15% Similarity=0.157 Sum_probs=74.6
Q ss_pred CceEEEEECCCCcHHH----HHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEE
Q 016702 96 TKVRISFKGLPGSFSE----DAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIV 171 (384)
Q Consensus 96 ~~~~Va~LGP~GTfS~----~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~ 171 (384)
+..+||+...-+.+-= .+..+.+++.++... +..++++.+.+|++|+|+.+-.....+... ..|.+.++.+
T Consensus 117 ~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~l- 191 (317)
T PRK11482 117 RTITIATTPSVGALVMPVIYQAIKTHYPQLLLRNI-PISDAENQLSQFQTDLIIDTHSCSNRTIQH---HVLFTDNVVL- 191 (317)
T ss_pred ceEEEEecHHHHHHHHHHHHHHHHHHCCCCEEEEe-cchhHHHHHHCCCcCEEEeccCCCCCceEE---EEEecCcEEE-
Confidence 4567776544333211 112334566654322 346789999999999999875543333332 2333444443
Q ss_pred EEEEEeeeeeeecCCCCCcCCccE----E-EecHHHHHHHHHHHHhc--CCe-EEecCCHHHHHHHHHhcCCCCeEEEcC
Q 016702 172 GEVQLAANFCLLALPGIKADQLKR----V-LSHPQALASSDIVLTQL--GVA-RENVDDTASAAQYVASNGLRDAGAVAS 243 (384)
Q Consensus 172 gEi~l~I~h~Ll~~~g~~l~~I~~----V-ySHpqAl~QC~~fL~~~--~~~-~i~~~STA~AA~~v~~~~~~~~AAIas 243 (384)
..+-.|-|... ..+++++.. + ...+......++++.+. ... ...+.|......+++.+ ...+|.+
T Consensus 192 ---v~~~~hpl~~~-~~~~~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~ilp 264 (317)
T PRK11482 192 ---VCRQGHPLLSL-EDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASS---DMLGIMP 264 (317)
T ss_pred ---EEeCCCCccCC-CCCHHHHhhCCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcC---CeeEEeH
Confidence 24556666543 345566552 2 22222222344555553 222 23455555566666653 4667877
Q ss_pred HHHHHH
Q 016702 244 ARAAEI 249 (384)
Q Consensus 244 ~~aA~~ 249 (384)
...+..
T Consensus 265 ~~~~~~ 270 (317)
T PRK11482 265 SRFYNL 270 (317)
T ss_pred HHHHHH
Confidence 776654
No 183
>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=58.79 E-value=1.1e+02 Score=25.87 Aligned_cols=122 Identities=19% Similarity=0.098 Sum_probs=62.7
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc--
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (384)
.+++.++.. ..+..++.+.+.+|++|+|++.-.....+.. ...|.+.++.++. +-.|-+... ..+++++
T Consensus 25 ~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~lv~----~~~~~~~~~-~~~~~~L~~ 96 (200)
T cd08466 25 LAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFK---SELLFEDELVCVA----RKDHPRIQG-SLSLEQYLA 96 (200)
T ss_pred HCCCCEEEEecCchHhHHHHHHcCCccEEEecccCCCCCce---eeeecccceEEEE----eCCCCCCCC-CcCHHHHhh
Confidence 356655543 3467789999999999999974221111111 1223334444332 333444322 2344444
Q ss_pred -cEEEecHHH-HHHHHHHHHhcCC---e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 194 -KRVLSHPQA-LASSDIVLTQLGV---A-RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 194 -~~VySHpqA-l~QC~~fL~~~~~---~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
..+.-.++. ..+-..|+.+.+. . ...+.|.....++++.+ ...|+.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08466 97 EKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQT---DLIAIAPRWLADQ 155 (200)
T ss_pred CCcEEecCCCCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCC---CeehhhHHHHHHH
Confidence 223322221 1234556655543 2 34456666666666654 4677778766654
No 184
>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=58.56 E-value=18 Score=38.64 Aligned_cols=105 Identities=13% Similarity=0.227 Sum_probs=66.0
Q ss_pred CHHHHHHcCCceeeccccC--CCCCeeEEEEEeeCCCC-------CCCC-------------CCceEEEEEEeCCCcchH
Q 016702 243 SARAAEIYGLNILADRIQD--EPDNITRFLVLARDPII-------PRTD-------------KLFKTSIVFTLDEGPGVL 300 (384)
Q Consensus 243 s~~aA~~ygL~il~~~I~D--~~~N~TRF~vi~~~~~~-------~~~~-------------~~~Ktsl~f~~~~~pGaL 300 (384)
+..-|+-.|+++....... .-.|+-++-+-+..... ..+. ...-..+++...|+||.+
T Consensus 386 A~~iA~e~GI~v~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~gGg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I 465 (525)
T TIGR01327 386 APAVAKERGITVEESKSESSPDYKNYLSVTVTGDSGTVSVAGTVFGGFSPRIVEIDGFHVDLEPEGIMLIILHLDKPGVI 465 (525)
T ss_pred HHHHHHHcCCEEEEEEccCCCCCCCEEEEEEEeCCcEEEEEEEEecCCcEEEEEECCEEEEEecCccEEEEEecCcCCcc
Confidence 3466888899986644332 23465566543322110 0000 112345677778999999
Q ss_pred HHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 301 FKALAVFALREINLTKIE-SRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 301 ~~~L~~F~~~~INLtkIE-SRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
.++.+.+.+++||+.... +|-.++ .+.+..|+++....+ +++++|++
T Consensus 466 ~~v~~~L~~~~iNIa~m~~~R~~~g----------------~~al~~i~~D~~v~~----~~l~~i~~ 513 (525)
T TIGR01327 466 GKVGTLLGTAGINIASMQLGRKEKG----------------GEALMLLSLDQPVPD----EVLEEIKA 513 (525)
T ss_pred hHHHhHHhhcCCChHHcEeecCCCC----------------CeEEEEEEcCCCCCH----HHHHHHhc
Confidence 999999999999998774 454433 357888999887754 34555554
No 185
>cd08461 PBP2_DntR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=58.32 E-value=84 Score=26.65 Aligned_cols=123 Identities=20% Similarity=0.167 Sum_probs=63.8
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCcc-
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (384)
.|+++++.-. .+-+++.+.+.+|++|+|++.......+... ..|.+.++.++. +-.|-+.. +..+++++.
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 3566554333 3456788999999999999864322222221 122333443332 22333322 222333322
Q ss_pred --EEEecHHH---HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHHc
Q 016702 195 --RVLSHPQA---LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEIY 250 (384)
Q Consensus 195 --~VySHpqA---l~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~y 250 (384)
-|.-++.. -.+-.+|+.+.+.. ...++|...+..+++.+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~ 157 (198)
T cd08461 97 LDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAAT---DMVAFVPSRLVPNL 157 (198)
T ss_pred CCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcC---CeEEEchHHHHHhh
Confidence 23322211 12356677766532 34566666666777664 56888888777654
No 186
>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=57.94 E-value=1.7e+02 Score=27.70 Aligned_cols=145 Identities=19% Similarity=0.200 Sum_probs=72.0
Q ss_pred CCCceEEEEECCCCc-HHHHH---HHHHCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccc--cccccccccccccC
Q 016702 94 DGTKVRISFKGLPGS-FSEDA---ALKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRH 166 (384)
Q Consensus 94 ~~~~~~Va~LGP~GT-fS~~A---A~~~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~--~G~V~~tlDlL~~~ 166 (384)
..+..+|+...+-+. +--.+ -.+.|++..+... .+..++.+++.+|++|+|++...+.. .+... .-|.+.
T Consensus 91 ~~~~l~I~~~~~~~~~~~~~~l~~~~~~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~---~~l~~~ 167 (300)
T TIGR02424 91 EGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGLSF---EHLYNE 167 (300)
T ss_pred CCceEEEecccHHHHhhhHHHHHHHHHhCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCcccccceee---eeecCC
Confidence 455678876533221 11111 1234566554333 36688999999999999997543221 11111 122233
Q ss_pred CeEEEEEEEEeeeeeeecCCCCCcCCccE--EEecHHH---HHHHHHHHHhcCCe----EEecCCHHHHHHHHHhcCCCC
Q 016702 167 RLHIVGEVQLAANFCLLALPGIKADQLKR--VLSHPQA---LASSDIVLTQLGVA----RENVDDTASAAQYVASNGLRD 237 (384)
Q Consensus 167 ~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~--VySHpqA---l~QC~~fL~~~~~~----~i~~~STA~AA~~v~~~~~~~ 237 (384)
++.++ .+-.|-|...+..+++|+.. .+..+.. ......|+.+++.. ...+.|......++..+ .
T Consensus 168 ~~~~~----~~~~hpl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~ 240 (300)
T TIGR02424 168 PVVFV----VRAGHPLLAAPSLPVASLADYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQES---D 240 (300)
T ss_pred ceEEE----EcCCCccccCCCCCHHHHhCCCEEecCCCCchHHHHHHHHHHCCCCCCCceEEeccHHHHHHHHHhC---C
Confidence 33322 23334444333223333321 2222221 13445677765432 35566766667777664 3
Q ss_pred eEEEcCHHHHH
Q 016702 238 AGAVASARAAE 248 (384)
Q Consensus 238 ~AAIas~~aA~ 248 (384)
..++.+...++
T Consensus 241 gi~~lp~~~~~ 251 (300)
T TIGR02424 241 AIWIISRGVVA 251 (300)
T ss_pred ceEeCcHHHHh
Confidence 46677776664
No 187
>PRK03381 PII uridylyl-transferase; Provisional
Probab=57.61 E-value=37 Score=38.13 Aligned_cols=53 Identities=11% Similarity=0.154 Sum_probs=39.7
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEE-EeecCC
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYI-DFEASM 353 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfI-D~eg~~ 353 (384)
-|-|.+..+|+||-|+++-.+|+.+|+|+..-..--..+ ...=.||| |-+|..
T Consensus 707 ~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~---------------~a~D~F~V~d~~g~~ 760 (774)
T PRK03381 707 ATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGA---------------DVVDVFYVTGAAGGP 760 (774)
T ss_pred eEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCC---------------eEEEEEEEECCCCCc
Confidence 477778889999999999999999999999655444322 13457888 555554
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=57.59 E-value=1.2e+02 Score=25.88 Aligned_cols=122 Identities=19% Similarity=0.107 Sum_probs=68.0
Q ss_pred HCCCCccc-CCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc--
Q 016702 117 AYPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (384)
Q Consensus 117 ~f~~~~~~-~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (384)
.+++.++. ...+..++.+.+.+|++|+|+.+......|... ..|.+..+. +..+-+|-|......+++++
T Consensus 31 ~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----~~~~~~~pl~~~~~i~~~dL~~ 103 (209)
T PF03466_consen 31 RHPNIRIEIREGDSDELIEALRSGELDLAITFGPPPPPGLES---EPLGEEPLV----LVVSPDHPLAQKKPITLEDLAD 103 (209)
T ss_dssp HSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSSSSTTEEE---EEEEEEEEE----EEEETTSGGGTTSSSSGGGGTT
T ss_pred HCCCcEEEEEeccchhhhHHHhcccccEEEEEeecccccccc---ccccceeee----eeeeccccccccccchhhhhhh
Confidence 45665442 335568999999999999999976642222221 111111121 12233343444333334444
Q ss_pred -cEEEec--HHHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 194 -KRVLSH--PQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 194 -~~VySH--pqAl~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
.-|.-. ..-..+..+|+.+++.. ...++|...+..++..+ ...+|.+...+.
T Consensus 104 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 161 (209)
T PF03466_consen 104 YPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASG---DGIAILPDSLAQ 161 (209)
T ss_dssp SEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTT---SEBEEEEHHHHH
T ss_pred ccccccccccccccccccccccccccccccccccchhhhccccccc---cceeecCccccc
Confidence 334322 12346666777776643 34577777777777764 577888877764
No 189
>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=57.33 E-value=1.2e+02 Score=25.63 Aligned_cols=122 Identities=17% Similarity=0.073 Sum_probs=61.1
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCcc-
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (384)
.+++.++.. ..+-.++.+.+.+|++|+|+++-.-...+. ....|.+.++.++ .+-.|-+...+..+++++.
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~ 97 (198)
T cd08421 25 AHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGL---ETRPYRTDRLVVV----VPRDHPLAGRASVAFADTLD 97 (198)
T ss_pred HCCCceEEEEecCcHHHHHHHhcCCceEEEEecCCCCCCc---EEEEeecCcEEEE----eCCCCCccccCCCCHHHhcC
Confidence 456655432 246688999999999999998532111111 1122333343332 2333434332223333332
Q ss_pred --EEEecH-H-HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 195 --RVLSHP-Q-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 195 --~VySHp-q-Al~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
-|.-.+ . ...++..++.+.+.+ ...++|...+..+++.+ ...|+.+...+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08421 98 HDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAG---LGIGIVPESAAR 155 (198)
T ss_pred CceEeecCCcchHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CCeEEccchhhh
Confidence 232111 1 112344555554432 24566776667777664 456777766555
No 190
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=57.24 E-value=1.5e+02 Score=28.65 Aligned_cols=143 Identities=9% Similarity=0.058 Sum_probs=69.9
Q ss_pred CCceEEEEECCCCcH-HHHH---HHHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeE
Q 016702 95 GTKVRISFKGLPGSF-SEDA---ALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (384)
Q Consensus 95 ~~~~~Va~LGP~GTf-S~~A---A~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~ 169 (384)
.+..+||+...-+.+ --.. -.+.+++..+.. ..+..++++.+.+|++|+|+.+-.......+ ....|.+.++.
T Consensus 92 ~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l--~~~~l~~~~~~ 169 (316)
T PRK12679 92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQL--VAFPWFRWHHS 169 (316)
T ss_pred CceEEEEechHhhhcchHHHHHHHHHHCCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCCCCc--eEEEccCCcEE
Confidence 456788875433322 1111 122356654432 3467789999999999999975321100001 11122222332
Q ss_pred EEEEEEEeeeeeeecCCCCCcCCc---cEEEecHH--HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEE
Q 016702 170 IVGEVQLAANFCLLALPGIKADQL---KRVLSHPQ--ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAV 241 (384)
Q Consensus 170 I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHpq--Al~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAI 241 (384)
+..+..|-|......+++++ +-|.-++. .......|+...+.. ...++|+..+..++..+ ...|+
T Consensus 170 ----~v~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g---~Gi~~ 242 (316)
T PRK12679 170 ----LLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALG---LGIGL 242 (316)
T ss_pred ----EEecCCCccccCCCCCHHHHhCCCeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcC---CcEEE
Confidence 23455666544332333333 33332221 223456677766542 23455666666666654 34556
Q ss_pred cCHHH
Q 016702 242 ASARA 246 (384)
Q Consensus 242 as~~a 246 (384)
.+..+
T Consensus 243 lp~~~ 247 (316)
T PRK12679 243 VAEQS 247 (316)
T ss_pred ecccc
Confidence 55543
No 191
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=57.05 E-value=97 Score=28.53 Aligned_cols=145 Identities=14% Similarity=0.093 Sum_probs=71.2
Q ss_pred CCceEEEEECCCCc--HHH--HHHHHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeE
Q 016702 95 GTKVRISFKGLPGS--FSE--DAALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (384)
Q Consensus 95 ~~~~~Va~LGP~GT--fS~--~AA~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~ 169 (384)
.+..+||+-..-+. ++. ....+.|++.++.. ..+.+++.+.+.+|++|+|++...+...+.+ ....|...++.
T Consensus 66 ~~~l~I~~~~~~~~~~~~~~l~~~~~~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~--~~~~l~~~~~~ 143 (269)
T PRK11716 66 SGELSLFCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASV--AFSPIDEIPLV 143 (269)
T ss_pred CceEEEEecchHHHHHHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcce--EEEEcccceEE
Confidence 45567775443322 122 11233456655433 3577899999999999999986443222211 11223333443
Q ss_pred EEEEEEEeeeeeeecCC----CCCcCCccEEEe-cHHHHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEE
Q 016702 170 IVGEVQLAANFCLLALP----GIKADQLKRVLS-HPQALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAV 241 (384)
Q Consensus 170 I~gEi~l~I~h~Ll~~~----g~~l~~I~~VyS-HpqAl~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAI 241 (384)
++ .+-+|.+.... -.++.+..-|.. .......-..|+..++. . ...++|......++..+ ...++
T Consensus 144 ~v----~~~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~ 216 (269)
T PRK11716 144 LI----APALPCPVRQQLSQEKPDWSRIPFILPEHGPARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALG---CGVGL 216 (269)
T ss_pred EE----EcCCcchhhhccccchhhHhhCCeeecCCCchHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcC---CCeEe
Confidence 33 23333332211 112333333331 11111223456665543 2 23456666666666654 45677
Q ss_pred cCHHHHH
Q 016702 242 ASARAAE 248 (384)
Q Consensus 242 as~~aA~ 248 (384)
.+...++
T Consensus 217 ~p~~~~~ 223 (269)
T PRK11716 217 LPEVVLE 223 (269)
T ss_pred ccHHHhh
Confidence 7776664
No 192
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=56.24 E-value=1.3e+02 Score=25.84 Aligned_cols=142 Identities=13% Similarity=0.039 Sum_probs=68.9
Q ss_pred ceEEEEECCCCcH--HHH--HHHHHCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEE
Q 016702 97 KVRISFKGLPGSF--SED--AALKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIV 171 (384)
Q Consensus 97 ~~~Va~LGP~GTf--S~~--AA~~~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~ 171 (384)
..+|++...-+.+ ... +..+.+++.++... .+.+++++++.+|++|+|+++-.....|.... .|.+.++.++
T Consensus 2 ~l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~l~~~---~l~~~~~~~~ 78 (198)
T cd08485 2 ELRVAYFGTVVLHTLPLLLRQLLSVAPSATVSLTQMSKNRQIEALDAGTIDIGFGRFYPYQEGVVVR---NVTNERLFLG 78 (198)
T ss_pred eEEEEEeccchhHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHcCCccEEEecCCCCCCCeEEE---EeeccceEEE
Confidence 3567766444432 221 12234566655443 36778999999999999998532222222221 1223333322
Q ss_pred EEEEEeeeeeeecCCCCCcCCc---cEEE-ecHH---HHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEE
Q 016702 172 GEVQLAANFCLLALPGIKADQL---KRVL-SHPQ---ALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAV 241 (384)
Q Consensus 172 gEi~l~I~h~Ll~~~g~~l~~I---~~Vy-SHpq---Al~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAI 241 (384)
.+-.|.+......+++++ .-|. .++. .-.+-.+|+.+.+. . ...++|.....++++.+ ...||
T Consensus 79 ----~~~~~~~~~~~~v~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~ 151 (198)
T cd08485 79 ----AQKSRARSFGEQVHCSALRNEPLILFPREGRPSFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAG---VGVTI 151 (198)
T ss_pred ----eCCCCccccCCCcCHHHHhcCCeEecCCCCCccHHHHHHHHHHHcCCCcceEEEcCcHHHHHHHHHcC---CceEE
Confidence 233344322222333333 3332 2211 12233346665543 2 23456666666677764 34667
Q ss_pred cCHHHHH
Q 016702 242 ASARAAE 248 (384)
Q Consensus 242 as~~aA~ 248 (384)
.++..++
T Consensus 152 ~p~~~~~ 158 (198)
T cd08485 152 VPETVAM 158 (198)
T ss_pred Ccchhhc
Confidence 7665443
No 193
>PRK04374 PII uridylyl-transferase; Provisional
Probab=56.09 E-value=53 Score=37.52 Aligned_cols=52 Identities=19% Similarity=0.284 Sum_probs=39.7
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeeeeeCCCCCCccccCCCCCCcccccEEEEE-EeecCC
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLT--KIESRPQRKRPLRVVDDSNNGTAKYFDYLFYI-DFEASM 353 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLt--kIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfI-D~eg~~ 353 (384)
+.|.|.+..+|+||-|+++-.+|+.+|+|+. ||.+. .+ ...=.||| |-+|..
T Consensus 795 ~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~--g~---------------~a~D~F~V~d~~g~~ 849 (869)
T PRK04374 795 RRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATF--GE---------------RAEDQFQITDEHDRP 849 (869)
T ss_pred CeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEec--CC---------------EEEEEEEEECCCCCc
Confidence 4677888889999999999999999999998 44444 22 13457888 666663
No 194
>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=55.35 E-value=1.3e+02 Score=25.51 Aligned_cols=121 Identities=12% Similarity=0.024 Sum_probs=61.4
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeecc--ccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS--~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (384)
.|++.++.-. .+.+++.+.+.+|++|+|+++-... ..+. ....|.+.++.++ .+-+|-|......+++++
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l---~~~~l~~~~~~~~----~~~~hpl~~~~~i~~~dL 97 (198)
T cd08437 25 TGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSAL---HSKIIKTQHFMII----VSKDHPLAKAKKVNFADL 97 (198)
T ss_pred hCCceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCcccc---eEEEeecceEEEE----ecCCCcccccCcccHHHH
Confidence 3566554432 4678899999999999999853211 1111 1122333333332 333444443322333333
Q ss_pred c---EEE-ecHH-HHHHHHHHHHhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcCHHHH
Q 016702 194 K---RVL-SHPQ-ALASSDIVLTQLGV--AR-ENVDDTASAAQYVASNGLRDAGAVASARAA 247 (384)
Q Consensus 194 ~---~Vy-SHpq-Al~QC~~fL~~~~~--~~-i~~~STA~AA~~v~~~~~~~~AAIas~~aA 247 (384)
. -|. .... --.+...|+.+.+. +. ..++|...+.++++.+ ...++.+...+
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 156 (198)
T cd08437 98 KKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVREN---VGIGFLTDIAV 156 (198)
T ss_pred cCCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CcEEEEEhhhc
Confidence 3 232 1111 12445666666543 22 3456666666666664 34677776544
No 195
>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=54.94 E-value=53 Score=28.32 Aligned_cols=121 Identities=15% Similarity=0.052 Sum_probs=61.0
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeecc---ccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCC
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS---SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ 192 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS---~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~ 192 (384)
.+++.++... .+-.++.+.+.+|++|+|++.-.+. ..+... ..|.+.++.++ .+-.|-|.. ..++++
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~---~~l~~~~~~~~----~~~~hpl~~--~~~~~~ 95 (202)
T cd08468 25 LAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEE---RDWWEDTYVVI----ASRDHPRLS--RLTLDA 95 (202)
T ss_pred hCCCCEEEEEECChHhHHHHHHCCCccEEEecccccccCCCCEEE---EEEecCcEEEE----EeCCCCCcC--CCCHHH
Confidence 3566554333 4678999999999999999854321 111111 11222233222 222333321 123333
Q ss_pred cc---EEEec--HHHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 193 LK---RVLSH--PQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 193 I~---~VySH--pqAl~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
+. .|.-. ...-.+..+++.+.+.. ...++|......+++.+ ...++.+..+++.
T Consensus 96 L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~---~~~~~~p~~~~~~ 157 (202)
T cd08468 96 FLAERHLVVTPWNEDRGVVDQVLEKQGLEREIALQLPNVLNAPFIVASS---DLLMTLPRQAARA 157 (202)
T ss_pred HhhCCCeEEecCCCCCchHHHHHHHcCCCceEEEEcChhHhHHHHHhcC---CeeeecHHHHHHH
Confidence 21 22111 11224456677665532 34566666666666543 5677888877654
No 196
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=54.81 E-value=1.8e+02 Score=28.04 Aligned_cols=144 Identities=14% Similarity=0.057 Sum_probs=70.4
Q ss_pred CCCceEEEEECCCCcH-HHHHHH---HHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeecccccccccccc--ccccC
Q 016702 94 DGTKVRISFKGLPGSF-SEDAAL---KAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYD--LLLRH 166 (384)
Q Consensus 94 ~~~~~~Va~LGP~GTf-S~~AA~---~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlD--lL~~~ 166 (384)
..+..+|+....-+.+ -..+.. +.+++.++.. ..+..++++.+.+|++|+|+.+-.+.. ...++ -|.+.
T Consensus 91 ~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~----~~~l~~~~l~~~ 166 (313)
T PRK12684 91 DQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIAD----YKELVSLPCYQW 166 (313)
T ss_pred CCCeEEEEechHHHHHHhHHHHHHHHHHCCCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCC----CCCceEEEeccc
Confidence 3456788875443332 112222 2345554433 346789999999999999998632111 11111 11122
Q ss_pred CeEEEEEEEEeeeeeeecCCCCCcC---CccEEEecH-HH-HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCe
Q 016702 167 RLHIVGEVQLAANFCLLALPGIKAD---QLKRVLSHP-QA-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDA 238 (384)
Q Consensus 167 ~l~I~gEi~l~I~h~Ll~~~g~~l~---~I~~VySHp-qA-l~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~ 238 (384)
.+.+ ..+..|-+......+++ +..-|.-.+ .. -.+...|+...+. . ...++|......+|..+ .+
T Consensus 167 ~~~~----v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~G- 239 (313)
T PRK12684 167 NHCV----VVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELG--LG- 239 (313)
T ss_pred eEEE----EeCCCCccccCCCcCHHHHhcCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhC--Cc-
Confidence 2322 23445555433222222 223222111 11 2345666766543 2 34566777777777764 23
Q ss_pred EEEcCHHHHH
Q 016702 239 GAVASARAAE 248 (384)
Q Consensus 239 AAIas~~aA~ 248 (384)
.|+.+..+++
T Consensus 240 v~~lp~~~~~ 249 (313)
T PRK12684 240 VGIVADMAFD 249 (313)
T ss_pred eEEeehhhcc
Confidence 4555554443
No 197
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=54.76 E-value=58 Score=31.53 Aligned_cols=53 Identities=13% Similarity=0.056 Sum_probs=34.8
Q ss_pred CCCCceEEEEECCCCcHHHHHHHH-H----CCC--CcccCCCCHHHHHHHHHhCCCCeEEE
Q 016702 93 NDGTKVRISFKGLPGSFSEDAALK-A----YPK--CETVPCDEFEDTFKAVELWLADKAVL 146 (384)
Q Consensus 93 ~~~~~~~Va~LGP~GTfS~~AA~~-~----f~~--~~~~~~~s~~~Vf~aV~~g~~d~gVv 146 (384)
......+|||+. .......+... + +++ .+++...+..++++++.+|++|+|+.
T Consensus 24 ~~~~~lrIg~~~-~~~~~~l~~~~~~~~~~~p~v~ie~~~~~~~~~~~~aL~~G~iDia~~ 83 (314)
T PRK11553 24 SSPEALRIGYQK-GSIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGST 83 (314)
T ss_pred CCCCeEEEEeCC-CchHHHHHHhhCHHHHhCCCCeeEEEECCCcHHHHHHHHcCCCCEEcc
Confidence 345689999963 22222222211 2 333 45677777789999999999999985
No 198
>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=54.64 E-value=59 Score=23.02 Aligned_cols=27 Identities=30% Similarity=0.428 Sum_probs=23.9
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
+++.||.+.++++.+++++|++-.|-+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04923 10 MRSHPGVAAKMFKALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEc
Confidence 557799999999999999999988864
No 199
>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=54.39 E-value=1.3e+02 Score=25.33 Aligned_cols=122 Identities=18% Similarity=0.114 Sum_probs=62.3
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc--
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (384)
.+++.++.. ..+.+++.+.+.+|++|+|+..-.....+.. ...|.+.++.++ .+-+|-+...+..+++++
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 345544433 2356889999999999999985432222211 122223333322 233444433222223332
Q ss_pred -cEEEecH--HHHHHHHHHHHhcCC---eEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 194 -KRVLSHP--QALASSDIVLTQLGV---ARENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 194 -~~VySHp--qAl~QC~~fL~~~~~---~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
..|.-.+ ........|+.+.+. ....++|...+.+++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (199)
T cd08426 98 YPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAG---GGISLLTELAVR 155 (199)
T ss_pred CCeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcC---CCEEEEchHhhh
Confidence 3333221 112345566666543 234566777777777764 456777766543
No 200
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=54.11 E-value=1.7e+02 Score=28.22 Aligned_cols=119 Identities=14% Similarity=0.106 Sum_probs=59.1
Q ss_pred CCCCccc-CCCCHHHHHHHHHhCCCCeEEEeeeccc--cccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc-
Q 016702 118 YPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 193 (384)
Q Consensus 118 f~~~~~~-~~~s~~~Vf~aV~~g~~d~gVvPiENS~--~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I- 193 (384)
+++.++. ...+.+++++++.+|++|+|+++..+.. .+.. ...|.+.++.++ .+-+|-+. . ..+++|+
T Consensus 123 ~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~---~~~l~~~~~~lv----~~~~~pl~-~-~i~~~dL~ 193 (312)
T PRK10341 123 FPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLH---VEPLFESEFVLV----ASKSRTCT-G-TTTLESLK 193 (312)
T ss_pred CCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCcccccCCee---EEEEecccEEEE----EcCCCchh-c-cCCHHHHh
Confidence 4555443 2345689999999999999998754421 1111 112222333322 12223321 1 1222222
Q ss_pred --cEEEecH--HHHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 194 --KRVLSHP--QALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 194 --~~VySHp--qAl~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
.-|.--+ ....+...|+.+++. . ...++|.....+++..+ ...++.+...++
T Consensus 194 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 252 (312)
T PRK10341 194 NEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA---DFLTVIPCDMTS 252 (312)
T ss_pred CCCeEccCCCCcHHHHHHHHHHHcCcCCCceEEecCHHHHHHHHHhC---CcEEEeeHHhcC
Confidence 2222111 122344566666543 2 34566677677777664 356677766543
No 201
>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=53.87 E-value=23 Score=33.79 Aligned_cols=49 Identities=20% Similarity=0.133 Sum_probs=37.8
Q ss_pred ceEEEEECCCCcHHHHHHHHH-CCCCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALKA-YPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~-f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..+|+. +.|++.+....+. +...+++.+++.++++++|.+|++|+.+..
T Consensus 144 g~~Igv--~~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d 193 (275)
T TIGR02995 144 DAKIAA--PGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGRADAYSLT 193 (275)
T ss_pred CceEEE--eCCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCCCCEEecC
Confidence 357886 6777777665542 344567788999999999999999988875
No 202
>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=53.56 E-value=24 Score=32.80 Aligned_cols=88 Identities=13% Similarity=-0.034 Sum_probs=49.7
Q ss_pred ceEEEEECCCCcHHHHH----HHHHCC-C-----CcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccC
Q 016702 97 KVRISFKGLPGSFSEDA----ALKAYP-K-----CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRH 166 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~A----A~~~f~-~-----~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~ 166 (384)
..+|++.+|.++..+.. ..+..+ + ..+....+..+++.+|.+|++|.++.+-. ...+...+..+ ...
T Consensus 141 gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~~Da~~~~~~-~~~~~~~~~~~--~~~ 217 (254)
T TIGR01098 141 GKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGKVDAATNNSS-AIGRLKKRGPS--DMK 217 (254)
T ss_pred CCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCCCCeEEecHH-HHHHHHHhCcc--chh
Confidence 46899988765433332 223333 1 35566778899999999999999998743 22222211110 012
Q ss_pred CeEEEEEEEEeeeeeeecCCC
Q 016702 167 RLHIVGEVQLAANFCLLALPG 187 (384)
Q Consensus 167 ~l~I~gEi~l~I~h~Ll~~~g 187 (384)
++.+.++-.....+.++.+++
T Consensus 218 ~~~~~~~~~~~~~~~~~~~~~ 238 (254)
T TIGR01098 218 KVRVIWKSPLIPNDPIAVRKD 238 (254)
T ss_pred heEEEEecCCCCCCCEEEECC
Confidence 567777543333344555543
No 203
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=53.51 E-value=39 Score=32.05 Aligned_cols=48 Identities=10% Similarity=0.030 Sum_probs=33.1
Q ss_pred ceEEEEECCCCcHHHHHHHHHC----CCCcccCCCCHHHHHHHHHhCCCCeEEE
Q 016702 97 KVRISFKGLPGSFSEDAALKAY----PKCETVPCDEFEDTFKAVELWLADKAVL 146 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f----~~~~~~~~~s~~~Vf~aV~~g~~d~gVv 146 (384)
..+||+ ..||..+....+.. ...+++.+++..+.+++|.+|++|..+.
T Consensus 148 g~~V~v--~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~ 199 (259)
T PRK11917 148 GANIGV--AQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSV 199 (259)
T ss_pred CCeEEE--ecCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEe
Confidence 357888 45555444322222 2345678899999999999999998765
No 204
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=52.58 E-value=13 Score=33.34 Aligned_cols=63 Identities=21% Similarity=0.402 Sum_probs=40.7
Q ss_pred HHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHH--HHH--hcCceEEEc
Q 016702 301 FKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH--LQE--FATFLRVLG 376 (384)
Q Consensus 301 ~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~--L~~--~~~~vkvLG 376 (384)
.+.+++.++|||.++|. .|+......+ .|+|+| .++|.+++++++. .+. .-..|..||
T Consensus 58 ~R~~s~lK~hGI~~~H~-aRqit~~DF~-----------~FDYI~------~MDesN~~dL~~~a~~~~~~~kakV~Llg 119 (159)
T KOG3217|consen 58 PRTLSILKKHGIKIDHL-ARQITTSDFR-----------EFDYIL------AMDESNLRDLLRKASNQPKGSKAKVLLLG 119 (159)
T ss_pred hHHHHHHHHcCCcchhh-cccccHhHhh-----------hcceeE------EecHHHHHHHHHHhccCCCCcceEEEEee
Confidence 58899999999997765 5777654311 144443 3567777777663 221 223599999
Q ss_pred cccCC
Q 016702 377 CYPMD 381 (384)
Q Consensus 377 sYp~~ 381 (384)
+|-..
T Consensus 120 sy~~~ 124 (159)
T KOG3217|consen 120 SYDKN 124 (159)
T ss_pred ccCCC
Confidence 99653
No 205
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=52.47 E-value=24 Score=34.53 Aligned_cols=52 Identities=29% Similarity=0.243 Sum_probs=38.7
Q ss_pred CceEEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEeee
Q 016702 96 TKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIE 149 (384)
Q Consensus 96 ~~~~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiE 149 (384)
+..+||+-|+--| ++.-.+-++++.+++++ -|+++..||.+|++|.||+--|
T Consensus 94 ~~~rvavpG~~TT-A~lL~rl~~p~~~~V~m-~fdeI~~Avl~G~VDaGvlIHE 145 (272)
T COG2107 94 KGKRVAVPGEMTT-AALLFRLAYPKAEIVYM-PFDEIIPAVLEGKVDAGVLIHE 145 (272)
T ss_pred ccceEecCCcccH-HHHHHHHhCCCceEEEe-eHHHHHHHHHcCCCccceEEee
Confidence 3567888776433 34444556677777765 4999999999999999999777
No 206
>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=52.46 E-value=39 Score=26.88 Aligned_cols=66 Identities=20% Similarity=0.142 Sum_probs=41.8
Q ss_pred CC-CcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCc-HHHHHHHHHHHH
Q 016702 294 DE-GPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMAD-PRAQNALGHLQE 367 (384)
Q Consensus 294 ~~-~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d-~~v~~al~~L~~ 367 (384)
++ .+|.++++=+.++.+|+|+..|...-.+. ++ .+......|..-+++++...| ..++.+|.++.+
T Consensus 7 ~~~~a~~ia~Vs~~lA~~~~NI~~I~~l~~~~-~~-------~~~~~~~~~~~e~~v~~~~~~~~~lr~~L~~la~ 74 (84)
T cd04871 7 RPLTAEQLAAVTRVVADQGLNIDRIRRLSGRV-PL-------EEQDDSPKACVEFSVRGQPADLEALRAALLELAS 74 (84)
T ss_pred CcCCHHHHHHHHHHHHHcCCCHHHHHHhhccc-cc-------cccCCCCcEEEEEEEeCCCCCHHHHHHHHHHHhc
Confidence 45 78999999999999999999887631110 00 000011356666666665433 567777777654
No 207
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=52.44 E-value=35 Score=36.41 Aligned_cols=59 Identities=19% Similarity=0.353 Sum_probs=44.4
Q ss_pred EEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh
Q 016702 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 368 (384)
Q Consensus 289 l~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~ 368 (384)
|-+...|+.|-..++|+.|..++|||..||=-|.. ..|+++. ..+....+.++.+++..
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 45667899999999999999999999999975531 3677776 34444566777777544
No 208
>cd04936 ACT_AKii-LysC-BS-like_2 ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive, aspartokinase (AK) isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis strain 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive AK isoenzymes. The B. subtilis strain 168 AKII is induced by methionine and repressed and inhibited by lysine. Although C. glutamicum is known to contain a single AK, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is feedback regu
Probab=50.93 E-value=73 Score=22.52 Aligned_cols=27 Identities=30% Similarity=0.433 Sum_probs=23.9
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
+++.||.+.++++.++++||++--|.+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04936 10 MRSHPGVAAKMFEALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 567799999999999999999988864
No 209
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=50.77 E-value=2.5e+02 Score=27.50 Aligned_cols=146 Identities=14% Similarity=0.072 Sum_probs=76.7
Q ss_pred CCCceEEEEECCCCcHH-HHH---HHHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCe
Q 016702 94 DGTKVRISFKGLPGSFS-EDA---ALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRL 168 (384)
Q Consensus 94 ~~~~~~Va~LGP~GTfS-~~A---A~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l 168 (384)
..+..+|++...-+++- -.+ -.+.++++++.. ..+.+++++++.+|++|+||++-.....+... .-.|.+..+
T Consensus 91 ~~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~ 168 (327)
T PRK12680 91 SQGQLTLTTTHTQARFVLPPAVAQIKQAYPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGI--AVPLYRWRR 168 (327)
T ss_pred CceEEEEEecchhHHHhhHHHHHHHHHHCCCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCCcce--EEEeeccce
Confidence 34578888876555432 122 123456655543 33568999999999999999863221111111 112223333
Q ss_pred EEEEEEEEeeeeeeecC-CCCCcCC---ccEEEecH-HHH-HHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeE
Q 016702 169 HIVGEVQLAANFCLLAL-PGIKADQ---LKRVLSHP-QAL-ASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAG 239 (384)
Q Consensus 169 ~I~gEi~l~I~h~Ll~~-~g~~l~~---I~~VySHp-qAl-~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~A 239 (384)
.+ .++..|-|... ...+++| ..-|..-+ ... ....+|+..++.. ...+.|.....++|..+ ...
T Consensus 169 ~l----~~~~~hpl~~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G---~Gi 241 (327)
T PRK12680 169 LV----VVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAG---LGV 241 (327)
T ss_pred EE----EEeCCChhhccCCCCCHHHHhcCCEEEecCCCchHHHHHHHHHHCCCCCcEEEEECCHHHHHHHHHcC---CCE
Confidence 32 35666666542 2233333 33333222 122 4466778776532 34566666667777764 345
Q ss_pred EEcCHHHHH
Q 016702 240 AVASARAAE 248 (384)
Q Consensus 240 AIas~~aA~ 248 (384)
|+.+..++.
T Consensus 242 a~lp~~~~~ 250 (327)
T PRK12680 242 GLLAEMAVN 250 (327)
T ss_pred EEeechhcc
Confidence 666655443
No 210
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=50.44 E-value=2.2e+02 Score=26.73 Aligned_cols=144 Identities=13% Similarity=0.071 Sum_probs=73.9
Q ss_pred CCceEEEEECCCCc-HHHH---HHHHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeec--cccccccccccccccCC
Q 016702 95 GTKVRISFKGLPGS-FSED---AALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIEN--SSSGSIHRNYDLLLRHR 167 (384)
Q Consensus 95 ~~~~~Va~LGP~GT-fS~~---AA~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiEN--S~~G~V~~tlDlL~~~~ 167 (384)
.+..+||+...-+. +-.. +..+.|+++++.- ..+.+++++.+.+|++|+|++.-.. ...+.. ...|.+.+
T Consensus 96 ~~~l~I~~~~~~~~~~l~~~l~~f~~~~p~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~l~---~~~l~~~~ 172 (294)
T PRK09986 96 AGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFT---SRRLHESA 172 (294)
T ss_pred cceEEEEEehHHhHHHHHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHcCCCCEEEecCCccCCCCCeE---EEEeeccc
Confidence 45688888644432 1121 2223456554432 3456889999999999999973210 011111 11222223
Q ss_pred eEEEEEEEEeeeeeeecCCCCCcCCcc---EEEecH--HHHH-HHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCe
Q 016702 168 LHIVGEVQLAANFCLLALPGIKADQLK---RVLSHP--QALA-SSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDA 238 (384)
Q Consensus 168 l~I~gEi~l~I~h~Ll~~~g~~l~~I~---~VySHp--qAl~-QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~ 238 (384)
+.+ ..+-.|-+...+..+++++. -|...+ ..+. +...|+.+.+.. ...++|......+++.+ ..
T Consensus 173 ~~~----v~~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g 245 (294)
T PRK09986 173 FAV----AVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG---IG 245 (294)
T ss_pred EEE----EEcCCCCcccCCccCHHHHcCCCEEecCCCchhHHHHHHHHHHHCCCCCceeeecCCHHHHHHHHHcC---Ce
Confidence 322 23444545443333444443 344322 2233 556666555432 34566777667777764 46
Q ss_pred EEEcCHHHHH
Q 016702 239 GAVASARAAE 248 (384)
Q Consensus 239 AAIas~~aA~ 248 (384)
.++.++..++
T Consensus 246 i~~l~~~~~~ 255 (294)
T PRK09986 246 ITLLPDSYAQ 255 (294)
T ss_pred EEEccHHHhh
Confidence 7777776654
No 211
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=49.51 E-value=65 Score=36.87 Aligned_cols=36 Identities=22% Similarity=0.293 Sum_probs=30.8
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeeee
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLT--KIESR 320 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLt--kIESR 320 (384)
+-|-|.+..+|+||-|+++-++|+..|+|+. +|.+.
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 3677888889999999999999999999997 55444
No 212
>PRK03059 PII uridylyl-transferase; Provisional
Probab=48.86 E-value=76 Score=36.18 Aligned_cols=36 Identities=19% Similarity=0.360 Sum_probs=30.7
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceee--eeeee
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLT--KIESR 320 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLt--kIESR 320 (384)
+.|-|.+..+|+||-|+++-++|+.+|+|+. ||.+.
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 4677888889999999999999999999998 44443
No 213
>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=48.55 E-value=1.7e+02 Score=24.98 Aligned_cols=122 Identities=11% Similarity=0.062 Sum_probs=62.8
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeee-ccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCc---C
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIE-NSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---D 191 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiE-NS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l---~ 191 (384)
.|+++++.- ..+.+++.+.+.+|++|+|+..-. +...+.. ...|...++. +..+..|-|......++ .
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 456654433 346778999999999999997421 0011111 1111122221 23445555543222232 3
Q ss_pred CccEEEecHH-H-HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 192 QLKRVLSHPQ-A-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 192 ~I~~VySHpq-A-l~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
+..-|.-++. . -.++..|+.+++. . ...++|...+.+++..+ ...++.+...+.
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08444 98 KWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLG---MGIGIVAEMAFE 156 (198)
T ss_pred CCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcC---CcEEeccHHHHh
Confidence 3444443332 2 2446777776653 2 34566666666777764 356666665544
No 214
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=48.49 E-value=83 Score=33.04 Aligned_cols=48 Identities=17% Similarity=0.178 Sum_probs=35.6
Q ss_pred eEEEEECCCCcHHHHHHHH---HCCCC--cccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 98 VRISFKGLPGSFSEDAALK---AYPKC--ETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 98 ~~Va~LGP~GTfS~~AA~~---~f~~~--~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
.+|++ +.||..+....+ .++.. ..+.+.+.++++++|.+|++|+.|+.
T Consensus 150 k~I~V--~~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d 202 (482)
T PRK10859 150 GTLTV--AAGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIAD 202 (482)
T ss_pred CeEEE--ECCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEEC
Confidence 57887 467766655443 34544 34677899999999999999999984
No 215
>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=48.01 E-value=1.7e+02 Score=24.68 Aligned_cols=120 Identities=17% Similarity=0.087 Sum_probs=60.5
Q ss_pred CCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCC-CCCcCCcc-
Q 016702 118 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALP-GIKADQLK- 194 (384)
Q Consensus 118 f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~-g~~l~~I~- 194 (384)
+++.++.-. .+..++++.+.+|++|+|+.+-.....+... ..|.+.++.++ .+-.|-+.... ..+++|+.
T Consensus 27 ~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~pl~~~~~~~~~~dL~~ 99 (197)
T cd08425 27 YPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDA---QPLFDERLALV----VGATHPLAQRRTALTLDDLAA 99 (197)
T ss_pred CCCcEEEEEECcHHHHHHHHHcCCccEEEEecCCCCCCcEE---EEeccccEEEE----ecCCCchhHhcccCCHHHHhc
Confidence 455544332 3567899999999999999864322222111 12223333222 23334443222 12333332
Q ss_pred --EEE-ec-HHHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHH
Q 016702 195 --RVL-SH-PQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAA 247 (384)
Q Consensus 195 --~Vy-SH-pqAl~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA 247 (384)
-|. .. ........+|+.+.+.. ...++|...+.++++.+ ...|+.+...+
T Consensus 100 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 156 (197)
T cd08425 100 EPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRG---RLATILPDAIA 156 (197)
T ss_pred CCcEecCCCccHHHHHHHHHHHcCCCeeeEEeeCcHHHHHHHHhcC---CcEEeechhhh
Confidence 222 11 12233456677766543 23456666666777764 35667776544
No 216
>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=47.70 E-value=41 Score=22.98 Aligned_cols=27 Identities=30% Similarity=0.370 Sum_probs=23.6
Q ss_pred CCcchHHHHHHHHHhCCceeeeeeeee
Q 016702 295 EGPGVLFKALAVFALREINLTKIESRP 321 (384)
Q Consensus 295 ~~pGaL~~~L~~F~~~~INLtkIESRP 321 (384)
+.||.+.++++.+++++|++.-+..-+
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~~~~ 38 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMISQSE 38 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEEcCC
Confidence 578999999999999999998886544
No 217
>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=47.52 E-value=1.8e+02 Score=24.92 Aligned_cols=123 Identities=14% Similarity=0.086 Sum_probs=60.7
Q ss_pred HHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCcc
Q 016702 116 KAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK 194 (384)
Q Consensus 116 ~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~ 194 (384)
+.+++.++.- ..+..++.+.+.+|++|+|+.+-.-.....+ ....|.+.++.++ .+-+|.+......+++++.
T Consensus 24 ~~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~--~~~~l~~~~~~~v----~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08443 24 ERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDL--ITLPCYHWNRCVV----VKRDHPLADKQSISIEELA 97 (198)
T ss_pred HHCCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccccccCCc--eEeeeeeceEEEE----EcCCCccccCCCCCHHHHh
Confidence 3466655433 3467889999999999999975210001111 0112223333322 3334545433223333333
Q ss_pred --EEEecHH--H-HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHH
Q 016702 195 --RVLSHPQ--A-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAA 247 (384)
Q Consensus 195 --~VySHpq--A-l~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA 247 (384)
...+++. . ...-..|+.+++.. ...+++.....++++.+ ...|+.+...+
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~~p~~~~ 155 (198)
T cd08443 98 TYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLG---LGVGVIASMAY 155 (198)
T ss_pred cCCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CcEEEeecccc
Confidence 1222222 2 22344566665542 34566777777777764 34556565444
No 218
>PRK09034 aspartate kinase; Reviewed
Probab=47.06 E-value=3.6e+02 Score=28.23 Aligned_cols=127 Identities=14% Similarity=0.062 Sum_probs=72.8
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHH---HHHcCCceeeccccCCCCCeeEEEEEeeCCCCC-C---C--CCC
Q 016702 214 GVARENVDDTASAAQYVASNGLRDAGAVASARA---AEIYGLNILADRIQDEPDNITRFLVLARDPIIP-R---T--DKL 284 (384)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~a---A~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~-~---~--~~~ 284 (384)
+++.+..-|-.+|.+++..+ |-+=.+.| |..++++|.-.|..+....-|..- ......+ . + ...
T Consensus 234 ~A~~l~~lsy~Ea~ela~~G-----akvlhp~ai~~a~~~~Ipi~v~~~~~p~~~GT~I~--~~~~~~~~~~Vk~It~~~ 306 (454)
T PRK09034 234 NPKSIKEITYREMRELSYAG-----FSVFHDEALIPAYRGGIPINIKNTNNPEDPGTLIV--PDRDNKNKNPITGIAGDK 306 (454)
T ss_pred CCeECCccCHHHHHHHHhCC-----cccCCHHHHHHHHHcCCCEEEEcCCCCCCCccEEE--eccccCccccceEEEecC
Confidence 34566677888888876532 23333333 345899999988876544455442 2211110 0 0 011
Q ss_pred ceEEEEEE---eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHH
Q 016702 285 FKTSIVFT---LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNA 361 (384)
Q Consensus 285 ~Ktsl~f~---~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~a 361 (384)
+-+.|.+. .++.||.+.++++.|+++|||.-.| |+ +. ....|+|+=+ ..+......+
T Consensus 307 ~i~~Itv~~~~~~~~~g~~a~if~~la~~~I~Vd~i---~s-s~---------------~sis~~v~~~-~~~~a~~~~l 366 (454)
T PRK09034 307 GFTSIYISKYLMNREVGFGRKVLQILEDHGISYEHM---PS-GI---------------DDLSIIIRER-QLTPKKEDEI 366 (454)
T ss_pred CEEEEEEccCCCCCCccHHHHHHHHHHHcCCeEEEE---cC-CC---------------cEEEEEEeHH-HhhHHHHHHH
Confidence 22333332 3457899999999999999999988 22 11 3578888742 2222222556
Q ss_pred HHHHHH
Q 016702 362 LGHLQE 367 (384)
Q Consensus 362 l~~L~~ 367 (384)
+++|+.
T Consensus 367 ~~el~~ 372 (454)
T PRK09034 367 LAEIKQ 372 (454)
T ss_pred HHHHHH
Confidence 666653
No 219
>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=46.87 E-value=93 Score=22.30 Aligned_cols=27 Identities=22% Similarity=0.349 Sum_probs=23.5
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
+++.||.+.++++.++++|||+--|-.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~q 37 (66)
T cd04924 11 MRGTPGVAGRVFGALGKAGINVIMISQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 467899999999999999999987754
No 220
>PRK09224 threonine dehydratase; Reviewed
Probab=46.64 E-value=47 Score=35.37 Aligned_cols=35 Identities=26% Similarity=0.381 Sum_probs=31.0
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeee
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESR 320 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESR 320 (384)
+..-+.|.+|.+||+|.+.|+.+. -+-|+|.++=|
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 356788999999999999999887 78899999998
No 221
>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=46.41 E-value=69 Score=28.14 Aligned_cols=122 Identities=19% Similarity=0.170 Sum_probs=69.0
Q ss_pred HHHHHHHCC-CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCC-
Q 016702 111 EDAALKAYP-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI- 188 (384)
Q Consensus 111 ~~AA~~~f~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~- 188 (384)
.+++.+. | +.+++++ ++.++++++++|++|.++-++..+.+-. ..+.... -+....+.++.+++.
T Consensus 30 ~~i~~~~-g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~r~----------~~~~~s~-p~~~~~~~~~~~~~~~ 96 (225)
T PF00497_consen 30 RAIAKRL-GIKIEFVPM-PWSRLLEMLENGKADIIIGGLSITPERA----------KKFDFSD-PYYSSPYVLVVRKGDA 96 (225)
T ss_dssp HHHHHHH-TCEEEEEEE-EGGGHHHHHHTTSSSEEESSEB-BHHHH----------TTEEEES-ESEEEEEEEEEETTST
T ss_pred HHHHhhc-ccccceeec-cccccccccccccccccccccccccccc----------ccccccc-cccchhheeeeccccc
Confidence 3444433 3 4678888 9999999999999999875554322210 0111111 122334455554331
Q ss_pred ----C---cCCc--cEEEecHHHHHHHHHHHHh-c--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 189 ----K---ADQL--KRVLSHPQALASSDIVLTQ-L--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 189 ----~---l~~I--~~VySHpqAl~QC~~fL~~-~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
. ++++ ++|..-.-.. -.+||.+ . +++.+.+.|..++.+++..+ ...|+|.....+..
T Consensus 97 ~~~~~~~~~~dl~~~~i~~~~g~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~i~~~~~~~~ 165 (225)
T PF00497_consen 97 PPIKTIKSLDDLKGKRIGVVRGSS--YADYLKQQYPSNINIVEVDSPEEALEALLSG--RIDAFIVDESTAEY 165 (225)
T ss_dssp CSTSSHSSGGGGTTSEEEEETTSH--HHHHHHHHTHHTSEEEEESSHHHHHHHHHTT--SSSEEEEEHHHHHH
T ss_pred cccccccchhhhcCcccccccchh--HHHHhhhhccchhhhcccccHHHHHHHHhcC--Ceeeeeccchhhhh
Confidence 1 2244 2343333222 1223433 1 67788899999999998886 45688877766653
No 222
>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=46.01 E-value=51 Score=28.34 Aligned_cols=121 Identities=19% Similarity=0.119 Sum_probs=62.3
Q ss_pred HCCCCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCcc--
Q 016702 117 AYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK-- 194 (384)
Q Consensus 117 ~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~-- 194 (384)
.|++.++.......++.+.+.+|++|+|++.......+.. ...|.+..+.+ ..+-.|-|...+ .+++|+.
T Consensus 25 ~~P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~----v~~~~hpl~~~~-~~l~dl~~~ 96 (200)
T cd08460 25 EAPGVRLRFVPESDKDVDALREGRIDLEIGVLGPTGPEIR---VQTLFRDRFVG----VVRAGHPLARGP-ITPERYAAA 96 (200)
T ss_pred HCCCCEEEEecCchhHHHHHHCCCccEEEecCCCCCcchh---eeeeeccceEE----EEeCCCCCCCCC-CCHHHHhcC
Confidence 3566554433222378899999999999984322111111 12222333322 234455544322 3333333
Q ss_pred -EEE-ecHH-HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 195 -RVL-SHPQ-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 195 -~Vy-SHpq-Al~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
-|. +... .-.+..+|+.+.+.. ...++|...+..+++.+ ...|+.+...++
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 153 (200)
T cd08460 97 PHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGS---DLIALVPERVTA 153 (200)
T ss_pred CCEEEecCCCCcchHHHHHHhcCCceeEEEEcCcHHHHHHHHhcC---CHHHHHHHHHHH
Confidence 222 2211 124567787776543 34566777777777764 346677766554
No 223
>cd08457 PBP2_OccR The C-terminal substrate-domain of LysR-type transcriptional regulator, OccR, involved in the catabolism of octopine, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator OccR, which is involved in the catabolism of octopine. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, OccR protein activates the occQ operon of the Ti plasmid in response to octopine. This operon encodes proteins required for the uptake and catabolism of octopine, an arginine derivative. The occ operon also encodes the TraR protein, which is a quorum-sensing transcriptional regulator of the Ti plasmid tra regulon. This substrate-binding domain shows significant h
Probab=45.90 E-value=1.9e+02 Score=24.55 Aligned_cols=120 Identities=12% Similarity=0.003 Sum_probs=60.5
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCC---
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ--- 192 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~--- 192 (384)
.+++.++... .+-+++++.+.+|++|+|++.......+... ..|.+..+.++ .+-.|.+...+..++++
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 4566544332 2357889999999999999864432222111 12223333322 34455554333233333
Q ss_pred ccEEE-ecHH-HHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHH
Q 016702 193 LKRVL-SHPQ-ALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARA 246 (384)
Q Consensus 193 I~~Vy-SHpq-Al~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~a 246 (384)
..-|. ++.. ......+|+.+++. . ...++|...+.++++.+ ...++.+...
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~ 153 (196)
T cd08457 98 ERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREG---LGIAIIDPAT 153 (196)
T ss_pred CceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcC---CeEEEEChHH
Confidence 33333 2222 22446667766543 2 34556666666666654 3455665443
No 224
>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=45.69 E-value=1e+02 Score=21.45 Aligned_cols=27 Identities=26% Similarity=0.408 Sum_probs=23.2
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
..+.+|.+.++++.|++++|++--+..
T Consensus 10 ~~~~~~~~~~i~~~l~~~~i~v~~i~~ 36 (65)
T cd04892 10 MRGTPGVAARIFSALAEAGINIIMISQ 36 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 346789999999999999999987754
No 225
>TIGR03871 ABC_peri_MoxJ_2 quinoprotein dehydrogenase-associated probable ABC transporter substrate-binding protein. This protein family, a sister family to TIGR03870, is found more broadly. It occurs a range of PQQ-biosynthesizing species, not just in known methanotrophs. Interpretation of evidence by homology and by direct experimental work suggest two different roles. By homology, this family appears to be the periplasmic substrate-binding protein of an ABC transport family. However, mutational studies and direct characterization for some sequences related to this family suggests this family may act as a maturation chaperone or additional subunit of a methanol dehydrogenase-like enzyme.
Probab=45.68 E-value=44 Score=30.42 Aligned_cols=49 Identities=16% Similarity=0.065 Sum_probs=33.5
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCCCccc---------CCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPKCETV---------PCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~~~~~---------~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..+||. +.|+..+....+........ ...|..+++.+|.+|++|.+++.
T Consensus 104 g~~V~v--~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~ 161 (232)
T TIGR03871 104 KLRIGV--FAGTPPAHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVW 161 (232)
T ss_pred CCeEEE--EcCChHHHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEec
Confidence 357887 55888777654422111111 23488999999999999999985
No 226
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=45.13 E-value=31 Score=33.53 Aligned_cols=52 Identities=19% Similarity=0.198 Sum_probs=40.1
Q ss_pred ceEEEEE----CCCCcHHHHHHHHHCC-----CCcccCCCCHHHHHHHHHhCCCCeEEEeee
Q 016702 97 KVRISFK----GLPGSFSEDAALKAYP-----KCETVPCDEFEDTFKAVELWLADKAVLPIE 149 (384)
Q Consensus 97 ~~~Va~L----GP~GTfS~~AA~~~f~-----~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiE 149 (384)
..++|+- -|-|-|++++-.+ .| ...++.-.+..+++..|+.|++|+|+|=.-
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 DVRLAIGDPKTVPAGKYAKEALEL-LGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYVS 195 (258)
T ss_pred CcEEEecCCCCCCchHHHHHHHHH-hchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEEE
Confidence 5667664 4789999988654 32 236678889999999999999999998543
No 227
>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=44.69 E-value=1.9e+02 Score=24.20 Aligned_cols=32 Identities=19% Similarity=-0.014 Sum_probs=23.3
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEee
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPI 148 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPi 148 (384)
.|++.++.- ..+-.++++.+.+|++|+|++.-
T Consensus 25 ~~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~~ 57 (197)
T cd08438 25 RYPNIELELVEYGGKKVEQAVLNGELDVGITVL 57 (197)
T ss_pred HCcCeEEEEEEcCcHHHHHHHHcCCCCEEEEec
Confidence 356554432 24678899999999999999853
No 228
>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=44.56 E-value=2.9e+02 Score=28.02 Aligned_cols=97 Identities=19% Similarity=0.107 Sum_probs=58.4
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHH---HHHHcCCceeeccccCCCCCeeEEEEEeeCCCC-CC--C--CCCc
Q 016702 214 GVARENVDDTASAAQYVASNGLRDAGAVASAR---AAEIYGLNILADRIQDEPDNITRFLVLARDPII-PR--T--DKLF 285 (384)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~---aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~-~~--~--~~~~ 285 (384)
+++.+..-|..+|.+++..+ |-+-.+. .|..++.++.-.|..+.. --|.. .+.... |. + ...+
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 34566667788888876642 2233333 345689999888766543 23333 222111 10 0 0122
Q ss_pred eEEEEEE---eCCCcchHHHHHHHHHhCCceeeeeee
Q 016702 286 KTSIVFT---LDEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 286 Ktsl~f~---~~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
.+-+.+. +.++||.+.++++.|++++||+-.|..
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 568899999999999999999987754
No 229
>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=44.13 E-value=2.4e+02 Score=25.25 Aligned_cols=105 Identities=16% Similarity=0.058 Sum_probs=65.5
Q ss_pred CcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc-----cE
Q 016702 121 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-----KR 195 (384)
Q Consensus 121 ~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-----~~ 195 (384)
++++...+..++++++.+|++|+|+......+ ...-...++++++...-.-...|+++++..+.++ |+
T Consensus 23 ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~-------~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DLkGK~ 95 (216)
T PF09084_consen 23 VEIVFFGGGGDVLEALASGKADIAVAGPDAVL-------FARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADLKGKK 95 (216)
T ss_dssp EEEEEESSHHHHHHHHHTTSHSEEEEECHHHH-------HHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGGTTSE
T ss_pred EEEEEecChhHHHHHHhcCCceEEeccchHHH-------HHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHhCCCE
Confidence 67888899999999999999999997654222 1111234688887766555567777665433333 36
Q ss_pred EEecH--HHHHHHHHHHHhcCC-----eEEecCCHHHHHHHHHhc
Q 016702 196 VLSHP--QALASSDIVLTQLGV-----ARENVDDTASAAQYVASN 233 (384)
Q Consensus 196 VySHp--qAl~QC~~fL~~~~~-----~~i~~~STA~AA~~v~~~ 233 (384)
|...+ .....-+.+|+++++ +.+.. +....+..+.++
T Consensus 96 i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~-~~~~~~~al~~g 139 (216)
T PF09084_consen 96 IGVSRGSSSEYFLRALLKKNGIDPDDVKIVNL-GPPELAQALLSG 139 (216)
T ss_dssp EEESTTSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTT
T ss_pred EEEecCcchhHHHHHHHHHhccccccceeeee-ehhhhhhhhhcC
Confidence 66555 344455678887753 34444 345555555554
No 230
>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=44.08 E-value=81 Score=27.35 Aligned_cols=51 Identities=12% Similarity=0.176 Sum_probs=38.9
Q ss_pred cchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHH
Q 016702 297 PGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 363 (384)
Q Consensus 297 pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~ 363 (384)
+..+..+++.+.++||.+|-|.+.-...+| -+||+-++|+-+-..+.+.++
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 345677888889999999999999887766 589999999764444444443
No 231
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=42.44 E-value=90 Score=32.77 Aligned_cols=28 Identities=29% Similarity=0.196 Sum_probs=23.4
Q ss_pred CCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 120 KCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 120 ~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..++++..++++++.++++|++|+++..
T Consensus 81 ~~e~v~~~~~~~ll~aL~~G~iDi~~~~ 108 (482)
T PRK10859 81 KLEIKVRDNISQLFDALDKGKADLAAAG 108 (482)
T ss_pred cEEEEecCCHHHHHHHHhCCCCCEEecc
Confidence 3577778999999999999999976543
No 232
>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=42.20 E-value=38 Score=25.61 Aligned_cols=28 Identities=14% Similarity=0.144 Sum_probs=24.3
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeee
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIESRP 321 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIESRP 321 (384)
+++.||.+.++++.++++|||+--| ++-
T Consensus 9 ~~~~~~~~a~if~~La~~~InvDmI-~~~ 36 (67)
T cd04914 9 KDNENDLQQRVFKALANAGISVDLI-NVS 36 (67)
T ss_pred CCCCccHHHHHHHHHHHcCCcEEEE-Eec
Confidence 3577999999999999999999999 443
No 233
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=41.65 E-value=85 Score=35.56 Aligned_cols=32 Identities=28% Similarity=0.242 Sum_probs=29.4
Q ss_pred CceEEEEEEeCCCcchHHHHHHHHHhCCceee
Q 016702 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLT 315 (384)
Q Consensus 284 ~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLt 315 (384)
+++|.|=+...|+||-|+.+.++|++.++++.
T Consensus 789 ~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~ 820 (867)
T COG2844 789 NDKTVLEVRALDRPGLLAALAGVFADLGLSLH 820 (867)
T ss_pred CCceEEEEEeCCcccHHHHHHHHHHhccccee
Confidence 35888889999999999999999999999987
No 234
>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=41.62 E-value=1.2e+02 Score=24.18 Aligned_cols=57 Identities=19% Similarity=0.223 Sum_probs=40.2
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhcC
Q 016702 294 DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFAT 370 (384)
Q Consensus 294 ~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~ 370 (384)
....|-+.++|++|.++||+.-++ |+.- -.....|+=. ...++..++++++|++.+.
T Consensus 12 n~evGF~rk~L~I~E~~~is~Eh~---PSGI----------------D~~Siii~~~-~~~~~~~~~i~~~i~~~~~ 68 (76)
T cd04911 12 NREVGFGRKLLSILEDNGISYEHM---PSGI----------------DDISIIIRDN-QLTDEKEQKILAEIKEELH 68 (76)
T ss_pred cchhcHHHHHHHHHHHcCCCEeee---cCCC----------------ccEEEEEEcc-ccchhhHHHHHHHHHHhcC
Confidence 457899999999999999987765 6532 2344444432 2334488899999998654
No 235
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=40.40 E-value=2.4e+02 Score=26.81 Aligned_cols=105 Identities=13% Similarity=-0.010 Sum_probs=53.2
Q ss_pred HHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc---cEEEecHHHHHHHHHH
Q 016702 133 FKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL---KRVLSHPQALASSDIV 209 (384)
Q Consensus 133 f~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHpqAl~QC~~f 209 (384)
.+.+.+|++|+|+++.+....+... ..|.+.++.++ .+-.|.+......+++|+ .-|...+ ....+.|
T Consensus 133 ~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~~----~~~~~~~~~~~~i~~~dL~~~p~i~~~~--~~~~~~~ 203 (297)
T PRK11139 133 LEDFLRDDVDVAIRYGRGNWPGLRV---EKLLDEYLLPV----CSPALLNGGKPLKTPEDLARHTLLHDDS--REDWRAW 203 (297)
T ss_pred hhhhccCCCCEEEEeCCCCCCCceE---EEeccceeEEE----eCHHHhcccCCCCCHHHhhcCceEeecC--cccHHHH
Confidence 4678889999999976543333222 12223333322 333444333332333333 3343222 2345678
Q ss_pred HHhcCC-----e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 210 LTQLGV-----A-RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 210 L~~~~~-----~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
+...+. . ...+++...+..++..+ ...|+.+...++.
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 246 (297)
T PRK11139 204 FRAAGLDDLNVQQGPIFSHSSMALQAAIHG---QGVALGNRVLAQP 246 (297)
T ss_pred HHHhCCCCcCcccceeeCCHHHHHHHHHhC---CCeEecchhhhHH
Confidence 776433 1 23455555555566653 4567777766553
No 236
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=40.25 E-value=2.2e+02 Score=23.75 Aligned_cols=32 Identities=16% Similarity=0.096 Sum_probs=23.2
Q ss_pred CCCCcccC-CCCHHHHHHHHHhCCCCeEEEeee
Q 016702 118 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIE 149 (384)
Q Consensus 118 f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiE 149 (384)
+++.++.- ..+..++.+.+.+|++|+|++.-+
T Consensus 26 ~p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (197)
T cd08414 26 YPDVELELREMTTAEQLEALRAGRLDVGFVRPP 58 (197)
T ss_pred CCCcEEEEecCChHHHHHHHHcCCccEEEEcCC
Confidence 45554432 235688999999999999998643
No 237
>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=40.16 E-value=3.8e+02 Score=26.79 Aligned_cols=130 Identities=15% Similarity=0.053 Sum_probs=66.8
Q ss_pred CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEE-EeeeeeeecCCCCCcCCc--cEE
Q 016702 120 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQ-LAANFCLLALPGIKADQL--KRV 196 (384)
Q Consensus 120 ~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~-l~I~h~Ll~~~g~~l~~I--~~V 196 (384)
+++++.+++..++++++.+|++|+|.+--.-++..... ...+++|+.-.. -+-...+++++..+++|. |+|
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 46788999999999999999999986521100000000 012333322111 111134555544456666 477
Q ss_pred EecHHHHHH--HHHHHHhcC-----CeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH---cCCceeec
Q 016702 197 LSHPQALAS--SDIVLTQLG-----VARENVDDTASAAQYVASNGLRDAGAVASARAAEI---YGLNILAD 257 (384)
Q Consensus 197 ySHpqAl~Q--C~~fL~~~~-----~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~---ygL~il~~ 257 (384)
..++-...+ ....|++.+ ++.+.... ++++..+..+ .-+++++-.+..+.+ .|.++|..
T Consensus 110 av~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~~-~d~~aAl~~G-~VDAa~~~eP~~s~~~~~~g~~~l~~ 178 (328)
T TIGR03427 110 NLVELSVSHYLLARALESVGLSEKDVKVVNTSD-ADIVAAFITK-DVTAVVTWNPQLSEIKAQPGANEVFD 178 (328)
T ss_pred eccCCChHHHHHHHHHHHcCCCHHHeEEEeCCh-HHHHHHHhcC-CCcEEEEcCchHHHHHhCCCcEEecc
Confidence 655543332 345566654 45555543 4555545543 345555555544322 35666543
No 238
>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=40.15 E-value=69 Score=23.06 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=23.7
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
+++.||.+.++++.|++.|||+--|..
T Consensus 11 ~~~~~~~~~~i~~~l~~~~I~v~~i~~ 37 (66)
T cd04922 11 MAGTPGVAATFFSALAKANVNIRAIAQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 467899999999999999999988753
No 239
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=40.10 E-value=3.4e+02 Score=25.92 Aligned_cols=142 Identities=13% Similarity=0.106 Sum_probs=72.0
Q ss_pred CCCceEEEEECCCCc-HHHHHH---HHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEee--eccc-ccccccccccccc
Q 016702 94 DGTKVRISFKGLPGS-FSEDAA---LKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPI--ENSS-SGSIHRNYDLLLR 165 (384)
Q Consensus 94 ~~~~~~Va~LGP~GT-fS~~AA---~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPi--ENS~-~G~V~~tlDlL~~ 165 (384)
..+..+|+...+-+. +-.... .+.++++++.. ..+..++.+.+.+|++|+|+.+- .+.. .+.. ...|.+
T Consensus 93 ~~g~l~ig~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~---~~~l~~ 169 (305)
T CHL00180 93 QRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKILE---ITPYVE 169 (305)
T ss_pred cCceEEEEEcCcchHhHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEEcCccCccccccee---EEEecc
Confidence 456789998877654 322221 23456655443 33578899999999999999842 1111 1111 122223
Q ss_pred CCeEEEEEEEEeeeeeeecCCCCCcCCc---cEEEecH-HHH-HHHHHHHHhcCCe------EEecCCHHHHHHHHHhcC
Q 016702 166 HRLHIVGEVQLAANFCLLALPGIKADQL---KRVLSHP-QAL-ASSDIVLTQLGVA------RENVDDTASAAQYVASNG 234 (384)
Q Consensus 166 ~~l~I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp-qAl-~QC~~fL~~~~~~------~i~~~STA~AA~~v~~~~ 234 (384)
.++.++ .+-+|-|..+...+++++ .-|.... ..+ .+-.+|+.+.+.+ ...++|...+..+++.+
T Consensus 170 ~~~~~v----~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g- 244 (305)
T CHL00180 170 DELALI----IPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAVQSG- 244 (305)
T ss_pred CcEEEE----ECCCCccccCCccCHHHHccCCceEecCCCcHHHHHHHHHHHcCCCcccceEEEEeCCHHHHHHHHHcC-
Confidence 333332 344455544333333333 3333222 222 2234556554432 34567777777777764
Q ss_pred CCCeEEEcCHH
Q 016702 235 LRDAGAVASAR 245 (384)
Q Consensus 235 ~~~~AAIas~~ 245 (384)
...++.+..
T Consensus 245 --~g~~~lp~~ 253 (305)
T CHL00180 245 --LGAAFVSVS 253 (305)
T ss_pred --CcEEEeEhH
Confidence 234554444
No 240
>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=40.02 E-value=1.2e+02 Score=22.28 Aligned_cols=33 Identities=18% Similarity=0.334 Sum_probs=25.5
Q ss_pred EEEEE-EeCCCcchHHHHHHHHHhCCceeeeeee
Q 016702 287 TSIVF-TLDEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 287 tsl~f-~~~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
.+++- .+.+.||.+.++++.+++.|||+..+-+
T Consensus 4 isvvG~~~~~~~gi~~~if~aL~~~~I~v~~~~~ 37 (64)
T cd04937 4 VTIIGSRIRGVPGVMAKIVGALSKEGIEILQTAD 37 (64)
T ss_pred EEEECCCccCCcCHHHHHHHHHHHCCCCEEEEEc
Confidence 34443 2457899999999999999999975553
No 241
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=39.62 E-value=40 Score=32.46 Aligned_cols=67 Identities=18% Similarity=0.041 Sum_probs=52.3
Q ss_pred cCceeccccCCCCCCCcccchhhHHHH-----------HHHHHHHHHHhhhccCCCC--CCchhHHHHHhhhhCCCCCCc
Q 016702 19 SGLVFNGVRNSNRTPRKCVCRGGFSGL-----------SGDSVIKSADNQNTGKSSN--VNDVPGKLCKDLISLPKPLTV 85 (384)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~il~L-----------Ln~Ra~~a~eig~~K~~~~--~~RE~~il~~~~~~n~GPL~~ 85 (384)
.+..|||--..-|-||.---+.||..| |-|||+||..+|-.-..-. |.-.+-.++|++..+.++..-
T Consensus 111 ~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~e~ 190 (245)
T KOG0850|consen 111 SERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPVEG 190 (245)
T ss_pred ceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCcccc
Confidence 345688888888999999888888877 6789999999997655434 456677899999977776653
No 242
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=38.90 E-value=3.7e+02 Score=26.06 Aligned_cols=143 Identities=21% Similarity=0.140 Sum_probs=69.8
Q ss_pred CCceEEEEECCCCcH-HHHHH---HHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeE
Q 016702 95 GTKVRISFKGLPGSF-SEDAA---LKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (384)
Q Consensus 95 ~~~~~Va~LGP~GTf-S~~AA---~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~ 169 (384)
.+.++|+...+.+++ -.... .+.|++..+.. ..+-.++.+.+.+|++|+|+++-.-...+.. ...|.+.++.
T Consensus 88 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~ 164 (317)
T PRK15421 88 QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLH---YSPMFDYEVR 164 (317)
T ss_pred ceeEEEEecccchHHHHHHHHHHHHHHCCCceEEEEeCccHHHHHHHHCCCcCEEEecCcccCCCce---EEEeccceEE
Confidence 345778775433321 11111 22356554432 3456788999999999999986321111111 1222233333
Q ss_pred EEEEEEEeeeeeeecCCCCCcCCcc---EEE--ecHHHHHHHHHHHHhcCCe--EEecCCHHHHHHHHHhcCCCCeEEEc
Q 016702 170 IVGEVQLAANFCLLALPGIKADQLK---RVL--SHPQALASSDIVLTQLGVA--RENVDDTASAAQYVASNGLRDAGAVA 242 (384)
Q Consensus 170 I~gEi~l~I~h~Ll~~~g~~l~~I~---~Vy--SHpqAl~QC~~fL~~~~~~--~i~~~STA~AA~~v~~~~~~~~AAIa 242 (384)
+ .++-.|-+......+++++. -|. .+.........|+.+.+.+ .+.++|.....+++..+ ...++.
T Consensus 165 l----v~~~~hpl~~~~~i~~~~L~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~i~ 237 (317)
T PRK15421 165 L----VLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAAR---MGIAAL 237 (317)
T ss_pred E----EEcCCCCccccCcCCHHHhCCCcEEecCCchhhHHHHHHHHHHhCCCCceeecCCHHHHHHHHHhC---CcEEEe
Confidence 2 23445545433333344433 222 1112234455566665543 33466767666666664 345566
Q ss_pred CHHHH
Q 016702 243 SARAA 247 (384)
Q Consensus 243 s~~aA 247 (384)
++..+
T Consensus 238 p~~~~ 242 (317)
T PRK15421 238 PHWVV 242 (317)
T ss_pred cchhc
Confidence 66543
No 243
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=38.78 E-value=72 Score=29.92 Aligned_cols=49 Identities=16% Similarity=0.161 Sum_probs=36.6
Q ss_pred ceEEEEECCCCcHHHHHHHHHCC--CCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALKAYP--KCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~--~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..+|++ +.|+..+.-..+.+. +.+.+.+.+.++.+++|.+|++|+.+..
T Consensus 133 g~~Igv--~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 133 GKHVGV--LQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred CCEEEE--ecCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeC
Confidence 357888 578766554444333 3567788999999999999999998865
No 244
>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=38.70 E-value=2.4e+02 Score=23.73 Aligned_cols=122 Identities=14% Similarity=0.036 Sum_probs=60.4
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCcc-
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (384)
.+++.++.-. .+-.++.+.+.+|++|+|+..-.....+. ....|.+.++.++ .+-+|-+.. ...+++++.
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 4566554333 34567889999999999997533211111 1112223333322 223332221 112333322
Q ss_pred --EE-EecHHH-HHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 195 --RV-LSHPQA-LASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 195 --~V-ySHpqA-l~QC~~fL~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
.| +.+... ......|+.+.+.. . ..++|......+++.+ ...||.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 155 (200)
T cd08464 97 RPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGT---PLIATVPARLARA 155 (200)
T ss_pred CCcEEecCCCCCcchHHHHHHHcCCCcceEEEcCchhhHHHHHcCC---CceeecHHHHHHH
Confidence 22 222111 13356677766542 2 3455555555555553 4688888887763
No 245
>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=38.00 E-value=1e+02 Score=28.57 Aligned_cols=108 Identities=21% Similarity=0.250 Sum_probs=61.8
Q ss_pred HHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeee---eecCCCCCc---CC--ccEEEe-c
Q 016702 129 FEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFC---LLALPGIKA---DQ--LKRVLS-H 199 (384)
Q Consensus 129 ~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~---Ll~~~g~~l---~~--I~~VyS-H 199 (384)
..||-..|+.|.+|+||+= .|.|.+++-.+.--..|+..+| +++.++.+. ++ -++|.+ .
T Consensus 49 ~~Dip~yV~~G~aDlGI~G------------~D~l~E~~~~v~~~~dL~fg~crl~vA~p~~~~~~~~~~l~~~rIATky 116 (182)
T TIGR00070 49 PQDIPTYVEHGAADLGITG------------YDVLLESGADVYELLDLGFGKCRLVLAVPQESDISSVEDLKGKRIATKY 116 (182)
T ss_pred cchhHHHHhCCCccEEEec------------chhhhhCCCCEEEEeecCcCceEEEEEEECCCCCCChHHhCCCEEEECC
Confidence 3578899999999999863 2444444433333334566655 334433221 22 135666 5
Q ss_pred HHHHHHHHHHHHhcCC--eEEecCCHHHHHHHHHhcCCCCeEEE----cCHHHHHHcCCceee
Q 016702 200 PQALASSDIVLTQLGV--ARENVDDTASAAQYVASNGLRDAGAV----ASARAAEIYGLNILA 256 (384)
Q Consensus 200 pqAl~QC~~fL~~~~~--~~i~~~STA~AA~~v~~~~~~~~AAI----as~~aA~~ygL~il~ 256 (384)
|. -.++||.++++ +.+....+.|+|-. ..-+-|| .+-..-+.+||++++
T Consensus 117 p~---i~~~~f~~~Gi~v~ii~l~GsvE~aP~-----~GlaD~IvDiv~TG~TL~~NgL~~ie 171 (182)
T TIGR00070 117 PN---LARRYFEKKGIDVEIIKLNGSVELAPL-----LGLADAIVDIVSTGTTLRENGLRIIE 171 (182)
T ss_pred HH---HHHHHHHHcCCeEEEEECcceeecccC-----CCceeEEEEEeCCHHHHHHCCCEEee
Confidence 65 45779999865 45555554444321 1123344 345556778999985
No 246
>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=37.72 E-value=2.5e+02 Score=23.69 Aligned_cols=141 Identities=21% Similarity=0.146 Sum_probs=69.6
Q ss_pred eEEEEECCCCcH-HHHH---HHHHCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEE
Q 016702 98 VRISFKGLPGSF-SEDA---ALKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVG 172 (384)
Q Consensus 98 ~~Va~LGP~GTf-S~~A---A~~~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~g 172 (384)
.+||+-.+-+++ --.+ ..+.|++.++.-. .+-.++.+.+.+|++|+|+.+-.....+. ....|.+.++.++
T Consensus 2 l~Ig~~~~~~~~~~~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~~- 77 (198)
T cd08441 2 LRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGI---AYEPLFDYEVVLV- 77 (198)
T ss_pred EEEEeeccchhhhhHHHHHHHHHhCCCeEEEEEeCCchhHHHHHHcCCceEEEecCCcCCCCc---EEEEccCCcEEEE-
Confidence 467765554432 1111 1234566554433 35578899999999999997422111111 1122233333322
Q ss_pred EEEEeeeeeeecCCCCCcCCcc--EEEecH--HH-HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCH
Q 016702 173 EVQLAANFCLLALPGIKADQLK--RVLSHP--QA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASA 244 (384)
Q Consensus 173 Ei~l~I~h~Ll~~~g~~l~~I~--~VySHp--qA-l~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~ 244 (384)
.+..|-+......+++++. ....++ .. ......|+.+.+.. ...++|...+..+++.+ ...++.+.
T Consensus 78 ---~~~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~ 151 (198)
T cd08441 78 ---VAPDHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASG---RGVAALPN 151 (198)
T ss_pred ---EcCCCChHHcccCCHHHhcCCceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhC---CcEEEeeH
Confidence 3444544433222333333 122222 11 23355677665432 34567777777777764 34566666
Q ss_pred HHHH
Q 016702 245 RAAE 248 (384)
Q Consensus 245 ~aA~ 248 (384)
..++
T Consensus 152 ~~~~ 155 (198)
T cd08441 152 WAVR 155 (198)
T ss_pred HHHH
Confidence 6554
No 247
>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=37.53 E-value=85 Score=22.75 Aligned_cols=26 Identities=19% Similarity=0.234 Sum_probs=23.0
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeee
Q 016702 294 DEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 294 ~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
++.||.+.++++.|+++|||+--|..
T Consensus 12 ~~~~~~~~~if~~L~~~~I~v~~i~q 37 (66)
T cd04919 12 KNMIGIAGRMFTTLADHRINIEMISQ 37 (66)
T ss_pred CCCcCHHHHHHHHHHHCCCCEEEEEe
Confidence 56899999999999999999987754
No 248
>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=37.48 E-value=2.4e+02 Score=23.42 Aligned_cols=122 Identities=19% Similarity=0.087 Sum_probs=59.1
Q ss_pred HHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeec-cccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCC-
Q 016702 116 KAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIEN-SSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ- 192 (384)
Q Consensus 116 ~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiEN-S~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~- 192 (384)
+.|++.++.- ..+..++.+.+.+|++|+|+..-.. ...+... ..|.+.++.+ ..+-+|-|...+..++++
T Consensus 24 ~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~~l~~~~~~~----~~~~~~~l~~~~~~~~~~L 96 (194)
T cd08436 24 RRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLPERRPPGLAS---RELAREPLVA----VVAPDHPLAGRRRVALADL 96 (194)
T ss_pred HHCCCcEEEEecCCHHHHHHHHHcCCccEEEEecCCCCCCCcEE---EEeecceEEE----EecCCCcccCCCccCHHHH
Confidence 3456654432 2357889999999999999986442 1122111 1222223222 233344443322222222
Q ss_pred --ccEEE-ecHHHH-HHHHHHHHhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcCHHHH
Q 016702 193 --LKRVL-SHPQAL-ASSDIVLTQLGV--AR-ENVDDTASAAQYVASNGLRDAGAVASARAA 247 (384)
Q Consensus 193 --I~~Vy-SHpqAl-~QC~~fL~~~~~--~~-i~~~STA~AA~~v~~~~~~~~AAIas~~aA 247 (384)
-+.|. ...... .....|+.+.+. +. ..++|...+.+++..+ ...++.+...+
T Consensus 97 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 155 (194)
T cd08436 97 ADEPFVDFPPGTGARRQVDRAFAAAGVRRRVAFEVSDVDLLLDLVARG---LGVALLPASVA 155 (194)
T ss_pred hCCCeEEecCcccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcC---CceEEecchhh
Confidence 22332 221112 234556666543 22 3456666666666654 35666666544
No 249
>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=37.47 E-value=3.6e+02 Score=25.74 Aligned_cols=137 Identities=14% Similarity=-0.022 Sum_probs=68.9
Q ss_pred EEEEECCCCcHHHHHHHH-HC----C-CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEE
Q 016702 99 RISFKGLPGSFSEDAALK-AY----P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVG 172 (384)
Q Consensus 99 ~Va~LGP~GTfS~~AA~~-~f----~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~g 172 (384)
+|+|+=. .+-...|-.+ +| | +++++++.+-.++++++.+|++|+++...... +.. .-...++.++.
T Consensus 2 ~~~~~~~-~~p~~va~~~G~~~k~~Gl~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~~~----~~a---~~~g~~~~~v~ 73 (300)
T TIGR01729 2 TVGYQTI-VEPFKVAQADGAAAKEAGATIDWRKFDSGADISTALASGNVPIGVIGSSPL----AAA---ASRGVPIELFW 73 (300)
T ss_pred EEEecCC-CCHHHHHHHcCchHHhcCCeeEEEecCcHHHHHHHHHcCCCCEeccCCCHH----HHH---HHCCCCeEEEE
Confidence 6888632 2333333322 22 3 46888999999999999999999997532211 000 00112344332
Q ss_pred EEE-EeeeeeeecCCCC---CcCCcc--EEEecHHH--HHHHHHHHHhcCC-----eEEecCCHHHHHHHHHhcCCCCeE
Q 016702 173 EVQ-LAANFCLLALPGI---KADQLK--RVLSHPQA--LASSDIVLTQLGV-----ARENVDDTASAAQYVASNGLRDAG 239 (384)
Q Consensus 173 Ei~-l~I~h~Ll~~~g~---~l~~I~--~VySHpqA--l~QC~~fL~~~~~-----~~i~~~STA~AA~~v~~~~~~~~A 239 (384)
-.. ..-.+.|+++++. +++|++ +|..++-. ...-..||++++. +.+.. +.++++..+..+ .-+++
T Consensus 74 ~~~~~~~~~~lv~~~~s~I~s~~DLkGK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~G-~vDa~ 151 (300)
T TIGR01729 74 ILDNIGKSEALVAREGSGIEKPEDLKGKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQRG-DIDAA 151 (300)
T ss_pred EeccCCccceEEecCCCCCCChhHcCCCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHcC-CcCEE
Confidence 111 1112467776652 233443 55544311 1223467876653 33333 345566656554 23444
Q ss_pred EEcCHH
Q 016702 240 AVASAR 245 (384)
Q Consensus 240 AIas~~ 245 (384)
++..+.
T Consensus 152 ~~~~p~ 157 (300)
T TIGR01729 152 YVWPPA 157 (300)
T ss_pred EEecHH
Confidence 444443
No 250
>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=37.03 E-value=2.5e+02 Score=23.55 Aligned_cols=122 Identities=18% Similarity=0.094 Sum_probs=61.3
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeecc--ccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcC--
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD-- 191 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS--~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~-- 191 (384)
.+++.++.-. .+-.++.+.+.+|++|+|+...... ..+... ..|.+.++.+ ..+-.|-+......+++
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 3566544332 3556788999999999999864321 111111 1122223322 23445555433222333
Q ss_pred -CccEEE-ecHHH-HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 192 -QLKRVL-SHPQA-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 192 -~I~~Vy-SHpqA-l~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
+..-|. +.... .....+++.+.+. . ...++|...+.++++.+ ...++++...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (199)
T cd08416 98 KDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGG---VGYALLPGRIAD 157 (199)
T ss_pred cCCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcC---CcEEEechhhhh
Confidence 333333 22221 2335566666543 2 23466666666777664 356677765554
No 251
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=36.19 E-value=46 Score=30.76 Aligned_cols=48 Identities=23% Similarity=0.264 Sum_probs=37.4
Q ss_pred eEEEEECCCCcH--HHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 98 VRISFKGLPGSF--SEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 98 ~~Va~LGP~GTf--S~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
.+|+.+ .||. .+..+....+..+.+.+++..+.+.++.+|++|+.+..
T Consensus 147 k~v~v~--~gt~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d 196 (275)
T COG0834 147 KKVGVQ--LGTTDEAEEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSD 196 (275)
T ss_pred CEEEEE--cCcchhHHHHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcc
Confidence 577774 5666 45544444456889999999999999999999999975
No 252
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=35.57 E-value=4e+02 Score=25.37 Aligned_cols=145 Identities=10% Similarity=-0.049 Sum_probs=68.7
Q ss_pred CCceEEEEECCCCcH--HHHHH--HHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeecc--c-cccccccccccccC
Q 016702 95 GTKVRISFKGLPGSF--SEDAA--LKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENS--S-SGSIHRNYDLLLRH 166 (384)
Q Consensus 95 ~~~~~Va~LGP~GTf--S~~AA--~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS--~-~G~V~~tlDlL~~~ 166 (384)
.+..+|+..-+.+.+ +...+ .+.+++.++.- ..+.+++.+.+.+|++|+|++..... . .+.. ...|.+.
T Consensus 92 ~g~l~i~~~~~~~~~~l~~~l~~f~~~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l~---~~~l~~~ 168 (296)
T PRK11062 92 NLLFDVGVADALSKRLVSRVLLTAVPEDESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEGLF---SKKLGEC 168 (296)
T ss_pred ceEEEEEecchhhHhhHHHHHHHHHhcCCceEEEEEeCCHHHHHHHHHcCCCCEEEecCCCccccccchh---hhhhhcc
Confidence 445677764333321 12111 12245555443 35788999999999999999743211 1 1111 1222333
Q ss_pred CeEEEEEEEEeeeeeeecCCCCCcCCccEEEec-HHH-HHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEE
Q 016702 167 RLHIVGEVQLAANFCLLALPGIKADQLKRVLSH-PQA-LASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAV 241 (384)
Q Consensus 167 ~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~VySH-pqA-l~QC~~fL~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAI 241 (384)
++.++ .+-.|-+.. .-..+.+..-|... ... ..+-..|+..++.. . ..++|.....+++..+ ...++
T Consensus 169 ~~~~~----~~~~~~~~~-~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~ 240 (296)
T PRK11062 169 GVSFF----CTNPLPEKP-FPACLEERRLLIPGRRTMLGRKLLNWFNSQGLNVEILGEFDDAALMKAFGAYH---DAIFV 240 (296)
T ss_pred CcceE----ecCCCcccc-ChHHHhcCCeeecCCCchHHHHHHHHHHHcCCCceeeeeeCcHHHHHHHHHcC---CceEE
Confidence 33222 111222111 10123333333211 111 22345677665532 2 3455666666666653 46788
Q ss_pred cCHHHHHHc
Q 016702 242 ASARAAEIY 250 (384)
Q Consensus 242 as~~aA~~y 250 (384)
.+...++.+
T Consensus 241 lp~~~~~~~ 249 (296)
T PRK11062 241 APSLYAQDF 249 (296)
T ss_pred CCHHHHHHH
Confidence 888777643
No 253
>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=35.40 E-value=1.5e+02 Score=22.31 Aligned_cols=63 Identities=24% Similarity=0.282 Sum_probs=45.9
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCc-HHHHHHHHHHHHh
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMAD-PRAQNALGHLQEF 368 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d-~~v~~al~~L~~~ 368 (384)
-|.+.+..-++.++|.-.-..++.-..|...|.. .+|.|.|+-.|..+- ..+.+|++.|.+.
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 3555666668889998888888888888884432 468999999998533 4567788877765
Q ss_pred c
Q 016702 369 A 369 (384)
Q Consensus 369 ~ 369 (384)
+
T Consensus 65 ~ 65 (66)
T PF01193_consen 65 L 65 (66)
T ss_dssp H
T ss_pred c
Confidence 3
No 254
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=35.18 E-value=2.7e+02 Score=23.34 Aligned_cols=121 Identities=17% Similarity=0.118 Sum_probs=59.5
Q ss_pred CCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcC---Cc
Q 016702 118 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD---QL 193 (384)
Q Consensus 118 f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~---~I 193 (384)
+++.++.. ..+..++.+.+.+|++|+|+..-.....+... ..|.+.++.++ .+-.|-|...+..+++ +-
T Consensus 26 ~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~~ 98 (198)
T cd08447 26 LPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLET---RPLVREPLVAA----VPAGHPLAGAERLTLEDLDGQ 98 (198)
T ss_pred CCCeEEEEEeCCHHHHHHHHHcCCceEEEecCCCCCCCeeE---EEeecCceEEE----ecCCCchhhcCcccHHHhCCC
Confidence 45554432 23678999999999999999753322111111 12223333221 2233333322212222 22
Q ss_pred cEEE-ecH--HHHHH-HHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 194 KRVL-SHP--QALAS-SDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 194 ~~Vy-SHp--qAl~Q-C~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
.-|. .+. ....+ -..|+.+.+. . ...++|...+.++++.+ ...|+.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (198)
T cd08447 99 PFIMYSPTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAG---LGVALVPASASR 157 (198)
T ss_pred eEEEeCCCCCchHHHHHHHHHHHcCCCCCceeecCCHHHHHHHHHcC---CCeEEhhHHHhh
Confidence 3333 211 11222 2456666543 2 34566777777777764 346677776554
No 255
>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=34.01 E-value=85 Score=23.56 Aligned_cols=33 Identities=36% Similarity=0.409 Sum_probs=25.6
Q ss_pred eEEEEEE-eC-CCcchHHHHHHHHHhCCceeeeee
Q 016702 286 KTSIVFT-LD-EGPGVLFKALAVFALREINLTKIE 318 (384)
Q Consensus 286 Ktsl~f~-~~-~~pGaL~~~L~~F~~~~INLtkIE 318 (384)
+.++.-. ++ +.||.+.++.+++++.|||+--|-
T Consensus 8 ~i~v~g~g~~~~~~Gv~a~i~~~La~~~I~i~~is 42 (65)
T PF13840_consen 8 KISVVGPGLRFDVPGVAAKIFSALAEAGINIFMIS 42 (65)
T ss_dssp EEEEEEECGTTTSHHHHHHHHHHHHHTTS-ECEEE
T ss_pred EEEEEccccCCCcccHHHHHHHHHHHCCCCEEEEE
Confidence 3444444 44 489999999999999999998887
No 256
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=33.98 E-value=51 Score=32.35 Aligned_cols=143 Identities=12% Similarity=0.029 Sum_probs=73.7
Q ss_pred CCCCceEEEEECCCCcHHHHHH-HHHC----C-CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccC
Q 016702 93 NDGTKVRISFKGLPGSFSEDAA-LKAY----P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRH 166 (384)
Q Consensus 93 ~~~~~~~Va~LGP~GTfS~~AA-~~~f----~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~ 166 (384)
....+.+|+|....+-| ..|- +.+| | +++++.+.+-.++.+++.+|++|+|+++....+... ....
T Consensus 20 ~~~~~v~~~y~~~~~~~-~vA~~~g~f~~~~Gl~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~~~a~-------~~g~ 91 (320)
T PRK11480 20 AQAVNVTVAYQTSAEPA-KVAQADNTFAKESGATVDWRKFDSGASIVRALASGDVQIGNLGSSPLAVAA-------SQQV 91 (320)
T ss_pred cCCCeEEEEecCCCcHH-HHHHHcCchHHHcCCeeEEEEeCCHHHHHHHHHCCCCCEECcCchHHHHHH-------HCCC
Confidence 35678999998432212 2221 2234 2 368889999999999999999999987543211110 1122
Q ss_pred CeEEEEEEEE-eeeeeeecCCCC-CcCCc--cEEEecHHH--HHHHHHHHHhcCC-----eEEecCCHHHHHHHHHhcCC
Q 016702 167 RLHIVGEVQL-AANFCLLALPGI-KADQL--KRVLSHPQA--LASSDIVLTQLGV-----ARENVDDTASAAQYVASNGL 235 (384)
Q Consensus 167 ~l~I~gEi~l-~I~h~Ll~~~g~-~l~~I--~~VySHpqA--l~QC~~fL~~~~~-----~~i~~~STA~AA~~v~~~~~ 235 (384)
++.+++-... .....++++++. +++|. |+|...+-. ...-..||++.|. +.+... .++++..+..+ .
T Consensus 92 ~~~~v~~~~~~~~~~~lv~~~~I~s~~DLkGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~-~~~~~~Al~~G-~ 169 (320)
T PRK11480 92 PIEVFLLASKLGNSEALVVKKTISKPEDLIGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQ-PPAIIAAWQRG-D 169 (320)
T ss_pred CeEEEEeeccCCcceEEEecCCCCChHHcCCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECC-cHHHHHHHHcC-C
Confidence 3444332211 122345555442 33444 356543211 1223567877653 333333 44555555554 2
Q ss_pred CCeEEEcCHH
Q 016702 236 RDAGAVASAR 245 (384)
Q Consensus 236 ~~~AAIas~~ 245 (384)
-+++++..+.
T Consensus 170 VDAa~~~~p~ 179 (320)
T PRK11480 170 IDGAYVWAPA 179 (320)
T ss_pred cCEEEEcchH
Confidence 3444554444
No 257
>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=32.45 E-value=2.1e+02 Score=21.15 Aligned_cols=34 Identities=18% Similarity=0.249 Sum_probs=27.1
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeee
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
+.|++=.....+|.+.++++.|++.|||+.-|-.
T Consensus 3 ~VsvVG~~~~~~~~~~~i~~aL~~~~I~v~~i~~ 36 (65)
T cd04918 3 IISLIGNVQRSSLILERAFHVLYTKGVNVQMISQ 36 (65)
T ss_pred EEEEECCCCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 4566655556789999999999999999976653
No 258
>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=32.12 E-value=1e+02 Score=24.63 Aligned_cols=38 Identities=24% Similarity=0.409 Sum_probs=29.6
Q ss_pred cccEEEEEEeecCCCcHHHHHHHHHHHHhcC-----ceEEEcc
Q 016702 340 YFDYLFYIDFEASMADPRAQNALGHLQEFAT-----FLRVLGC 377 (384)
Q Consensus 340 ~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~-----~vkvLGs 377 (384)
...|+|-||+.|+..-..=|++|+.|+.... -|+|-|.
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 3679999999998766777889999987544 3777776
No 259
>PRK05007 PII uridylyl-transferase; Provisional
Probab=32.10 E-value=1.8e+02 Score=33.23 Aligned_cols=32 Identities=16% Similarity=0.168 Sum_probs=28.6
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeee
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKI 317 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkI 317 (384)
-|.|.+..+|+||-|+++.+.|+.+|+|+..-
T Consensus 701 ~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A 732 (884)
T PRK05007 701 GTEIFIWSPDRPYLFAAVCAELDRRNLSVHDA 732 (884)
T ss_pred eEEEEEEecCCcCHHHHHHHHHHHCCCEEEEE
Confidence 57788888999999999999999999999844
No 260
>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=32.04 E-value=3.1e+02 Score=23.04 Aligned_cols=122 Identities=19% Similarity=0.091 Sum_probs=61.2
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCc---CC
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---DQ 192 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l---~~ 192 (384)
.+++.++... .+-.++.+.+.+|++|+|+..-.+...+.. ...|.+..+.++ .+-.|-+...+..++ .+
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 3565544332 456788999999999999985332222211 112222233222 333444433222222 23
Q ss_pred ccEEE-ecHHH-HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 193 LKRVL-SHPQA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 193 I~~Vy-SHpqA-l~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
..-|. .+... .....+|+.+++.. ...++|...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08433 98 LPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAG---LGYTILPASAVA 155 (198)
T ss_pred CceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcC---CcEEEcchhhhh
Confidence 33332 22222 23456666665432 34566777777777764 356666665443
No 261
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=30.95 E-value=1.1e+02 Score=28.62 Aligned_cols=49 Identities=14% Similarity=0.150 Sum_probs=35.7
Q ss_pred ceEEEEECCCCcHHHHHHHHHCC--CCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALKAYP--KCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~--~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..+|++. .|++.++-...++. +.+++...+.++++++|.+|++|+.+..
T Consensus 133 g~~Igv~--~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~ 183 (259)
T PRK15437 133 GKRVGVL--QGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQD 183 (259)
T ss_pred CCEEEEe--cCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEec
Confidence 4578884 57765544333332 3567888999999999999999998763
No 262
>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=30.75 E-value=3.4e+02 Score=23.19 Aligned_cols=118 Identities=18% Similarity=0.064 Sum_probs=58.3
Q ss_pred CCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCccE-
Q 016702 118 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR- 195 (384)
Q Consensus 118 f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~- 195 (384)
|+++++.. ..+..++.+.+.+|++|+|+...+....+... ..|.+.++. +.++-+| +......+++++..
T Consensus 26 ~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----lv~~~~h-~~~~~~i~~~~l~~~ 97 (200)
T cd08465 26 APGIDLAVSQASREAMLAQVADGEIDLALGVFPELPEELHA---ETLFEERFV----CLADRAT-LPASGGLSLDAWLAR 97 (200)
T ss_pred CCCcEEEEecCChHhHHHHHHCCCccEEEeccccCCcCeeE---EEeeeccEE----EEEeCCC-CccCCCcCHHHHhhC
Confidence 56655432 35778999999999999999754322111111 112223322 2334445 33332234444321
Q ss_pred --EEe--cHHHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcCHH
Q 016702 196 --VLS--HPQALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASAR 245 (384)
Q Consensus 196 --VyS--HpqAl~QC~~fL~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~ 245 (384)
|.- ...-......++.+++.+ . ..++|......+++.. ...+++....
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~--~~~~~~~~~~ 152 (200)
T cd08465 98 PHVLVAMRGDAANEIDRALAARGLRRRVALTLPHWGVAPELIAGT--DLILTVARRA 152 (200)
T ss_pred CcEEEecCCCcCChHHHHHHHcCCceEEEEEcCcHHHHHHHHHcC--ChhhHhHHHH
Confidence 221 111123455666666643 2 3466666666777653 1234444443
No 263
>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=30.27 E-value=79 Score=29.76 Aligned_cols=73 Identities=27% Similarity=0.187 Sum_probs=42.5
Q ss_pred CCceEEEEECCCCcHHHHHHHH---HCC-CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccc-cccccCCeE
Q 016702 95 GTKVRISFKGLPGSFSEDAALK---AYP-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNY-DLLLRHRLH 169 (384)
Q Consensus 95 ~~~~~Va~LGP~GTfS~~AA~~---~f~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tl-DlL~~~~l~ 169 (384)
.+..||++.= +||=.+.-++. ..+ ..+++..++.++++++.++|++|-+|||.+ +.. .+++ |+|.+.+++
T Consensus 66 ~~~~rI~vwR-kGsaADvl~Ral~d~~~~~~EvVytdD~~~i~~Ml~~g~vdsAVv~~~--~~~--G~~fEdl~~~~g~~ 140 (201)
T PF12916_consen 66 IGKPRIAVWR-KGSAADVLTRALLDLKGIKAEVVYTDDMSEIVKMLNEGEVDSAVVGSE--FSK--GETFEDLLGSLGLY 140 (201)
T ss_dssp TTSSEEEESS-TTSHHHHHHHHHHHHH--T-EEEE---HHHHHHHHHTT-E--EEEETT--T-----EEHHHHHHHTT--
T ss_pred CCCceEEEEe-cccHHHHHHHHHHhhccccceeEEecCHHHHHHHHhcCceeeeeecch--hcc--chhHHHHHhhcCCC
Confidence 3445899986 78877754443 334 589999999999999999999999999943 222 4555 466677777
Q ss_pred EEE
Q 016702 170 IVG 172 (384)
Q Consensus 170 I~g 172 (384)
+=|
T Consensus 141 ~Pg 143 (201)
T PF12916_consen 141 APG 143 (201)
T ss_dssp ---
T ss_pred CCh
Confidence 644
No 264
>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=30.25 E-value=2e+02 Score=32.68 Aligned_cols=32 Identities=16% Similarity=0.337 Sum_probs=28.7
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeee
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKI 317 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkI 317 (384)
-|-|.+..+|+||-|+++.++|+.+|+|+..=
T Consensus 668 ~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A 699 (850)
T TIGR01693 668 GTEVFIYAPDQPGLFAKVAGALAMLSLSVHDA 699 (850)
T ss_pred eEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEE
Confidence 57788888999999999999999999999843
No 265
>PRK02047 hypothetical protein; Provisional
Probab=29.83 E-value=3.1e+02 Score=22.32 Aligned_cols=60 Identities=23% Similarity=0.333 Sum_probs=40.5
Q ss_pred CCCcchHHHHHHHHHhC--CceeeeeeeeeCCCCCCccccCCCCCCcccccE-EEEEEeecCCCcHHHHHHHHHHHHhcC
Q 016702 294 DEGPGVLFKALAVFALR--EINLTKIESRPQRKRPLRVVDDSNNGTAKYFDY-LFYIDFEASMADPRAQNALGHLQEFAT 370 (384)
Q Consensus 294 ~~~pGaL~~~L~~F~~~--~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y-~FfID~eg~~~d~~v~~al~~L~~~~~ 370 (384)
++.++-...+.+++..+ +++...|.+||+++. .| .+=|.+... +.+.+.++.++|.+.-.
T Consensus 24 ~~~~~~~~~v~~iv~~~~~~~~~~~i~~k~Ss~G----------------kY~Svtv~v~v~-s~eq~~~iY~~L~~~~~ 86 (91)
T PRK02047 24 KAHPEFADTIFKVVSVHDPEFDLEKIEERPSSGG----------------NYTGLTITVRAT-SREQLDNIYRALTGHPM 86 (91)
T ss_pred eCcHhHHHHHHHHHHHhCCCCccCceEEccCCCC----------------eEEEEEEEEEEC-CHHHHHHHHHHHhhCCC
Confidence 45666666777777766 666788999999873 45 355555544 34667778888876543
No 266
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=29.58 E-value=2.7e+02 Score=26.92 Aligned_cols=146 Identities=14% Similarity=0.026 Sum_probs=70.1
Q ss_pred ceEEEEECCCCc-HHHHHH---HHHCCCCcccCCCCHHHHHHHHHhCCCCeEEEeeeccc---ccccc----cccccccc
Q 016702 97 KVRISFKGLPGS-FSEDAA---LKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSS---SGSIH----RNYDLLLR 165 (384)
Q Consensus 97 ~~~Va~LGP~GT-fS~~AA---~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~---~G~V~----~tlDlL~~ 165 (384)
..+|+...+.+. +--... .+.+++.++.....-.++.+.+.+|++|+|++.-.... .|... .....|..
T Consensus 98 ~l~I~~~~~~~~~~~~~~l~~f~~~~P~v~v~i~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~~~~~~~~~~~l~~ 177 (319)
T PRK10216 98 KFELAAESPLMMIMLNALSKRIYQRYPQATIKLRNWDYDSLDAITRGEVDIGFTGRESHPRSRELLSLLPLAIDFEVLFS 177 (319)
T ss_pred EEEEEecchhHHHHHHHHHHHHHHHCCCCEEEEEeCCcchHHHHhcCCccEEEecCCCCccccccccccccccceeeeee
Confidence 467776543332 222221 23456644322222224789999999999998421100 11110 11111222
Q ss_pred CCeEEEEEEEEeeeeeeecCCCCCcCCc---cEEEecH--HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCC
Q 016702 166 HRLHIVGEVQLAANFCLLALPGIKADQL---KRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRD 237 (384)
Q Consensus 166 ~~l~I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp--qAl~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~ 237 (384)
.++. +.++-+|-+.. ....++|+ .-|..-+ ....+...|+.+.+.+ ...++|...+.++++.++ ..
T Consensus 178 ~~~~----~v~~~~hp~~~-~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~-~~ 251 (319)
T PRK10216 178 DLPC----VWLRKDHPALH-EEWNLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPEFEQSLFMAAQPD-HL 251 (319)
T ss_pred cceE----EEEeCCCCccC-CCCCHHHHhhCCCeEecCCCCCcchHHHHHHHhCCccceEEECCcHHHHHHHHHcCC-cc
Confidence 2222 23455555432 22233332 2333211 1233567777776532 356777777788887631 23
Q ss_pred eEEEcCHHHHH
Q 016702 238 AGAVASARAAE 248 (384)
Q Consensus 238 ~AAIas~~aA~ 248 (384)
..+|.++.+++
T Consensus 252 gi~ilp~~~~~ 262 (319)
T PRK10216 252 LLATAPRYCQY 262 (319)
T ss_pred eEeccHHHHHH
Confidence 57888886543
No 267
>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=29.57 E-value=3.4e+02 Score=22.72 Aligned_cols=121 Identities=15% Similarity=0.106 Sum_probs=62.0
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccc--cccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~--~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (384)
.+++.++... .+..++.+.+.+|++|+|+....... .+.. ...|.+.++.++. +-+|-+.. . .+++++
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 3565544332 35679999999999999998532211 1111 1122233433332 22232221 1 123333
Q ss_pred c---EEEec--HHHHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 194 K---RVLSH--PQALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 194 ~---~VySH--pqAl~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
. .|... ........+|+.+.+. . ...++|...+..+++.+ ...||.+...++.
T Consensus 96 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 156 (201)
T cd08418 96 LDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKA---DFLTILSRDMGRG 156 (201)
T ss_pred cCCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhC---CEEEEeEHHHhhh
Confidence 2 23321 1223445667766543 2 34566777777777764 4677887766653
No 268
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=29.36 E-value=89 Score=30.51 Aligned_cols=48 Identities=17% Similarity=0.159 Sum_probs=37.1
Q ss_pred eEEEEECCCCcHHHHHHHHHCC----CCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 98 VRISFKGLPGSFSEDAALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 98 ~~Va~LGP~GTfS~~AA~~~f~----~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
.+||. ..||.++....++.. +.+++.+.+.++.+++|.+|++|+.+..
T Consensus 154 k~V~v--~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~d 205 (302)
T PRK10797 154 KAVVV--TSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMD 205 (302)
T ss_pred CEEEE--eCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEcc
Confidence 46776 577777766655443 3578899999999999999999998753
No 269
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=28.81 E-value=4.2e+02 Score=24.08 Aligned_cols=114 Identities=15% Similarity=0.164 Sum_probs=59.2
Q ss_pred CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCC----CcCCcc-
Q 016702 120 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI----KADQLK- 194 (384)
Q Consensus 120 ~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~----~l~~I~- 194 (384)
..++++. +..+++.++++|++|.++.++..+.+-. ..++ ...++. .....++.+.+. .+++++
T Consensus 64 ~~~~~~~-~~~~~~~~l~~G~~D~~~~~~~~~~~r~--~~~~--~s~p~~-------~~~~~~~~~~~~~~~~~~~dl~g 131 (250)
T TIGR01096 64 KCKFVEQ-NFDGLIPSLKAKKVDAIMATMSITPKRQ--KQID--FSDPYY-------ATGQGFVVKKGSDLAKTLEDLDG 131 (250)
T ss_pred eEEEEeC-CHHHHHHHHhCCCcCEEEecCccCHHHh--hccc--cccchh-------cCCeEEEEECCCCcCCChHHcCC
Confidence 4677774 6899999999999999875442221110 0011 001111 111222222211 122221
Q ss_pred -EEEecHHHHHHHHHHHHhc---CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 195 -RVLSHPQALASSDIVLTQL---GVARENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 195 -~VySHpqAl~QC~~fL~~~---~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
+|-. .....+. .++.+. +...+.+.|..++.+++..+ .-.++|.+...+..
T Consensus 132 ~~i~~-~~g~~~~-~~l~~~~~~~~~~~~~~s~~~~~~~L~~g--~vD~~v~~~~~~~~ 186 (250)
T TIGR01096 132 KTVGV-QSGTTHE-QYLKDYFKPGVDIVEYDSYDNANMDLKAG--RIDAVFTDASVLAE 186 (250)
T ss_pred CEEEE-ecCchHH-HHHHHhccCCcEEEEcCCHHHHHHHHHcC--CCCEEEeCHHHHHH
Confidence 2322 1222222 344442 56677888999999998886 45677777665554
No 270
>cd08483 PBP2_HvrB The C-terminal substrate-binding domain of LysR-type transcriptional regulator HvrB, an activator of S-adenosyl-L-homocysteine hydrolase expression, contains the type 2 periplasmic binding fold. The transcriptional regulator HvrB of the LysR family is required for the light-dependent activation of both ahcY, which encoding the enzyme S-adenosyl-L-homocysteine hydrolase (AdoHcyase) that responsible for the reversible hydrolysis of AdoHcy to adenosine and homocysteine, and orf5, a gene of unknown. The topology of this C-terminal domain of HvrB is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transp
Probab=28.74 E-value=1.1e+02 Score=25.73 Aligned_cols=116 Identities=12% Similarity=-0.004 Sum_probs=57.9
Q ss_pred CCCCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc---c
Q 016702 118 YPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL---K 194 (384)
Q Consensus 118 f~~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I---~ 194 (384)
|++.++.... .+..+.+.+|++|+|+..-.-...|. ....|.+.++.++ .+-+| +......+++++ .
T Consensus 26 ~P~i~l~~~~--~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~-~~~~~~~~~~~L~~~~ 95 (190)
T cd08483 26 HPEIELSLLP--SADLVDLRPDGIDVAIRYGNGDWPGL---ESEPLTAAPFVVV----AAPGL-LGDRKVDSLADLAGLP 95 (190)
T ss_pred CCCceEEEEe--cCCcCCCCCCCcCEEEEecCCCCCCc---EEEeecccceEee----eCHHH-HhhCCCCCHHHHhcCc
Confidence 5554433222 23457789999999998532112221 1233444555443 23344 333222333333 3
Q ss_pred EEEecHHHHHHHHHHHHhcCCe-----EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 195 RVLSHPQALASSDIVLTQLGVA-----RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 195 ~VySHpqAl~QC~~fL~~~~~~-----~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
-|. ++. ......|+.+.+.. ...++|.....++++.+ ...++.++..++
T Consensus 96 ~i~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~~ 149 (190)
T cd08483 96 WLQ-ERG-TNEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAG---LGLSIQARALVE 149 (190)
T ss_pred eec-cCC-chHHHHHHHHcCCCcccccCceeCcHHHHHHHHHcC---CcEEeecHHhhH
Confidence 332 221 12346777765532 24456666666667664 456777765544
No 271
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=28.25 E-value=5e+02 Score=24.24 Aligned_cols=55 Identities=18% Similarity=0.201 Sum_probs=34.3
Q ss_pred CCCceEEEEECCCCcHH-HH---HHHHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEee
Q 016702 94 DGTKVRISFKGLPGSFS-ED---AALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPI 148 (384)
Q Consensus 94 ~~~~~~Va~LGP~GTfS-~~---AA~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPi 148 (384)
..+..+|+....-+.+- -. ..++.+++.++.- ..+..++++.+.+|++|+|+++-
T Consensus 87 ~~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~~ 146 (290)
T PRK10837 87 DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEG 146 (290)
T ss_pred hCCeEEEEecchhHhhhhHHHHHHHHHHCCCceEEEEECCHHHHHHHHHhCCceEEEecC
Confidence 34567777765444321 11 1223356654432 34677899999999999999863
No 272
>PRK08210 aspartate kinase I; Reviewed
Probab=28.23 E-value=2.2e+02 Score=29.06 Aligned_cols=95 Identities=13% Similarity=-0.014 Sum_probs=53.1
Q ss_pred CeEEecCCHHHHHHHHHhcCCCCeEEEcCHHH---HHHcCCceeeccccCCCCCeeEEEEEeeCCC-------CC--CC-
Q 016702 215 VARENVDDTASAAQYVASNGLRDAGAVASARA---AEIYGLNILADRIQDEPDNITRFLVLARDPI-------IP--RT- 281 (384)
Q Consensus 215 ~~~i~~~STA~AA~~v~~~~~~~~AAIas~~a---A~~ygL~il~~~I~D~~~N~TRF~vi~~~~~-------~~--~~- 281 (384)
.+.++.-|..+|.+++..+ +-+-.+.| |..++.++.-.+..+.+. -|..- ...+. .+ ++
T Consensus 194 a~~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~~~~~~i~i~i~~~~~~~~-gT~I~--~~~~~~~~~~~~~~~v~~I 265 (403)
T PRK08210 194 ARLLDVVSYNEVFQMAYQG-----AKVIHPRAVEIAMQANIPLRIRSTYSDSP-GTLIT--SLGDAKGGIDVEERLITGI 265 (403)
T ss_pred CeECCccCHHHHHHHHHCC-----ccccCHHHHHHHHHCCCeEEEEecCCCcC-CcEEE--ecCccccccccccCceEEE
Confidence 4455555667777765442 22333333 346788888877765322 34331 11110 00 00
Q ss_pred -CCCceEEEEEE-eCCCcchHHHHHHHHHhCCceeeee
Q 016702 282 -DKLFKTSIVFT-LDEGPGVLFKALAVFALREINLTKI 317 (384)
Q Consensus 282 -~~~~Ktsl~f~-~~~~pGaL~~~L~~F~~~~INLtkI 317 (384)
...+-+.+.+. .++.||.+.++++.|+++|||+-.|
T Consensus 266 t~~~~i~~isv~~~~~~~g~la~If~~L~~~~I~i~~i 303 (403)
T PRK08210 266 AHVSNVTQIKVKAKENAYDLQQEVFKALAEAGISVDFI 303 (403)
T ss_pred EEcCCcEEEEEecCCCcchHHHHHHHHHHHcCCeEEEE
Confidence 01123333333 3445999999999999999999988
No 273
>TIGR00149 TIGR00149_YbjQ secondary thiamine-phosphate synthase enzyme. Members of this protein family have been studied extensively by crystallography. Members from several different species have been shown to have sufficient thiamin phosphate synthase activity (EC 2.5.1.3) to complement thiE mutants. However, it is presumed that this is a secondary activity, and the primary function of this enzyme remains unknown.
Probab=27.97 E-value=38 Score=29.73 Aligned_cols=18 Identities=22% Similarity=0.573 Sum_probs=14.5
Q ss_pred CCCCCcccccEEEEEEeecCC
Q 016702 333 SNNGTAKYFDYLFYIDFEASM 353 (384)
Q Consensus 333 ~~~~~~~~~~Y~FfID~eg~~ 353 (384)
..+|+ |+.+||+|++|..
T Consensus 104 L~LGt---wQ~I~l~E~Dg~r 121 (132)
T TIGR00149 104 LQLGT---WQGIFFAEFDGPR 121 (132)
T ss_pred EcccC---ccEEEEEECCCCC
Confidence 45664 9999999999864
No 274
>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=27.74 E-value=3.7e+02 Score=22.66 Aligned_cols=114 Identities=16% Similarity=0.191 Sum_probs=60.5
Q ss_pred CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCC---cCCcc--
Q 016702 120 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIK---ADQLK-- 194 (384)
Q Consensus 120 ~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~---l~~I~-- 194 (384)
+.++++.+ ..++.+++.+|++|+++.+...+.+.. ..+. ...........++.+++.. ++|++
T Consensus 39 ~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~~~--~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~dl~g~ 106 (218)
T cd00134 39 KVKFVEVD-WDGLITALKSGKVDLIAAGMTITPERA--KQVD---------FSDPYYKSGQVILVKKGSPIKSVKDLKGK 106 (218)
T ss_pred eEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHHHH--hhcc---------CcccceeccEEEEEECCCCCCChHHhCCC
Confidence 35677777 889999999999999998762111110 0000 0001111233444444322 23322
Q ss_pred EEEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 195 RVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 195 ~VySHpqAl~QC~~fL~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
+|..-+ . .-...++.+. ......+.+..++.+++..+ ...|++.....+..
T Consensus 107 ~i~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~~~~~ 159 (218)
T cd00134 107 KVAVQK-G-STAEKYLKKALPEAKVVSYDDNAEALAALENG--RADAVIVDEIALAA 159 (218)
T ss_pred EEEEEc-C-chHHHHHHHhCCcccEEEeCCHHHHHHHHHcC--CccEEEeccHHHHH
Confidence 222111 1 1123455543 35667788888999998876 34566666555543
No 275
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=27.12 E-value=2e+02 Score=32.79 Aligned_cols=31 Identities=10% Similarity=0.319 Sum_probs=28.4
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeee
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTK 316 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtk 316 (384)
-|.|.+..+|+||-|+++-++|+.+|+|+..
T Consensus 677 ~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~ 707 (854)
T PRK01759 677 GTEIFIYCQDQANLFLKVVSTIGAKKLSIHD 707 (854)
T ss_pred eEEEEEEecCCccHHHHHHHHHHHCCCeEEE
Confidence 5788888899999999999999999999973
No 276
>PRK05092 PII uridylyl-transferase; Provisional
Probab=27.09 E-value=2.9e+02 Score=31.79 Aligned_cols=34 Identities=15% Similarity=0.187 Sum_probs=29.5
Q ss_pred ceEEEEEEeCCCcchHHHHHHHHHhCCceeeeee
Q 016702 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIE 318 (384)
Q Consensus 285 ~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIE 318 (384)
+-|.+.+..+|+||-+.++.++|+.+|+|+..-.
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 3578888889999999999999999999998433
No 277
>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=27.08 E-value=3.7e+02 Score=22.35 Aligned_cols=121 Identities=15% Similarity=0.040 Sum_probs=59.7
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeecc--ccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS--~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (384)
.+++.++.. ..+.+++.+.+.+|++|+|+.+-... ..+.. ...|.+.++.++. +-+|-+.... ..+.+-
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~---~~~l~~~~~~~v~----~~~~p~~~~~-~~l~~~ 96 (195)
T cd08427 25 RHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLPKDLV---WTPLVREPLVLIA----PAELAGDDPR-ELLATQ 96 (195)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCCCEEEEcCCCCccccCce---EEEcccCcEEEEE----CCCCCcchHH-HHhcCC
Confidence 356655433 23568899999999999999853221 12211 1223333333321 1122221110 012222
Q ss_pred cEEEe-cHHH-HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 194 KRVLS-HPQA-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 194 ~~VyS-HpqA-l~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
.-|.. +... -.+...|+.+++. . ...++|...+.++++.+ ...|+.+...++
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 153 (195)
T cd08427 97 PFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQG---LGVAIVPDIAVP 153 (195)
T ss_pred CeEEecCCchHHHHHHHHHHHcCCCCCeEEEeccHHHHHHHHHhC---CcEEEccHHHHh
Confidence 22321 2111 2344667766643 2 24456666666677664 457777776655
No 278
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=27.05 E-value=7.8e+02 Score=28.09 Aligned_cols=128 Identities=12% Similarity=0.062 Sum_probs=74.5
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH---HcCCceeeccccCCCCCeeEEEEEeeCCCCCC--C--CCCce
Q 016702 214 GVARENVDDTASAAQYVASNGLRDAGAVASARAAE---IYGLNILADRIQDEPDNITRFLVLARDPIIPR--T--DKLFK 286 (384)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~---~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~--~--~~~~K 286 (384)
+++.+..-|..+|.+++..+ |.+-.+.|++ .+|.++.-.+..+....-|..- ......+. + ...+-
T Consensus 250 ~a~~i~~ls~~e~~el~~~g-----~~v~~~~a~~~a~~~~i~i~v~~~~~~~~~gT~I~--~~~~~~~~v~~It~~~~v 322 (861)
T PRK08961 250 DARLLTRLDYDEAQEIATTG-----AKVLHPRSIKPCRDAGIPMAILDTERPDLSGTSID--GDAEPVPGVKAISRKNGI 322 (861)
T ss_pred CceEecccCHHHHHHHHHCC-----CeEECHHHHHHHHHCCCCEEEEeCCCCCCCccEEe--CCCCCCCcceeEEEECCE
Confidence 34566667778877766542 4555555554 4799998887765444445432 11111111 0 11223
Q ss_pred EEEEEE---eCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCC-CcHHHHHHH
Q 016702 287 TSIVFT---LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASM-ADPRAQNAL 362 (384)
Q Consensus 287 tsl~f~---~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~-~d~~v~~al 362 (384)
+.+.+. ..+.||.+.++++.|++++||+-.|.|-. ....|.||-.... .+..++.++
T Consensus 323 ~lItv~~~~~~~~~g~~a~if~~la~~~I~Vd~I~sse-------------------~sis~~i~~~~~~~~~~~~~~l~ 383 (861)
T PRK08961 323 VLVSMETIGMWQQVGFLADVFTLFKKHGLSVDLISSSE-------------------TNVTVSLDPSENLVNTDVLAALS 383 (861)
T ss_pred EEEEEecCCccccccHHHHHHHHHHHcCCeEEEEEcCC-------------------CEEEEEEccccccchHHHHHHHH
Confidence 333342 24689999999999999999999994321 2467777654321 234455566
Q ss_pred HHHHH
Q 016702 363 GHLQE 367 (384)
Q Consensus 363 ~~L~~ 367 (384)
++|+.
T Consensus 384 ~~l~~ 388 (861)
T PRK08961 384 ADLSQ 388 (861)
T ss_pred HHHhh
Confidence 66653
No 279
>PRK04998 hypothetical protein; Provisional
Probab=27.00 E-value=3.3e+02 Score=21.83 Aligned_cols=60 Identities=13% Similarity=0.144 Sum_probs=40.7
Q ss_pred CCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccE-EEEEEeecCCCcHHHHHHHHHHHHhcC
Q 016702 294 DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDY-LFYIDFEASMADPRAQNALGHLQEFAT 370 (384)
Q Consensus 294 ~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y-~FfID~eg~~~d~~v~~al~~L~~~~~ 370 (384)
+..+..+..+.++|..+--.-..+.+||+++. .| .+-|.+..+ +.+.+.++.++|.++-.
T Consensus 23 ~~~~~~~~~v~~v~~~~~~~~~~~~~r~S~~G----------------kY~Svtv~v~v~-s~eq~~~iY~~L~~~~~ 83 (88)
T PRK04998 23 LARPELVDQVVEVVQRHAPGDYTPTVKPSSKG----------------NYHSVSITITAT-SIEQVETLYEELAKIEG 83 (88)
T ss_pred eCcHhHHHHHHHHHHHhCCCCCCceEccCCCC----------------EEEEEEEEEEEC-CHHHHHHHHHHHhcCCC
Confidence 45677888888999777444445889998763 46 466676654 34667777778776543
No 280
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=26.87 E-value=3.7e+02 Score=22.35 Aligned_cols=121 Identities=20% Similarity=0.081 Sum_probs=59.5
Q ss_pred CCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeec-----cccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcC
Q 016702 118 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIEN-----SSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD 191 (384)
Q Consensus 118 f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiEN-----S~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~ 191 (384)
+++.++.- ..+-.++.+.+.+|++|+|+++-.. ...+.. ..-|.+.++.++ .+-+|-+...+..+++
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~p~~~~~~~~~~ 98 (200)
T cd08423 26 HPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGLT---RVPLLDDPLDLV----LPADHPLAGREEVALA 98 (200)
T ss_pred CCCCeEEEEeCCHHHHHHHHhcCCccEEEEeccccccCCCCCCcE---EEEeccCcEEEE----ecCCCCccccCCCCHH
Confidence 45554432 2356788999999999999986421 011111 112222333322 2333433332222333
Q ss_pred Cc---cEEE-ecHHHH-HHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 192 QL---KRVL-SHPQAL-ASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 192 ~I---~~Vy-SHpqAl-~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
++ .-|. +++... ....+|+.+++. + ...++|...+.++++.+ ...||.++..+.
T Consensus 99 ~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08423 99 DLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAG---LGVALVPRLALG 160 (200)
T ss_pred HhcCCceEEecCCchHHHHHHHHHHHcCCCCCeeeeeccHHHHHHHHHcC---CCHhhhhhHHHH
Confidence 33 2232 222222 334566666543 2 34466666666777664 456676765543
No 281
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=26.38 E-value=4.4e+02 Score=24.46 Aligned_cols=28 Identities=11% Similarity=0.210 Sum_probs=22.7
Q ss_pred CCcccCCCCHHHHHHHHHhCCCCeEEEee
Q 016702 120 KCETVPCDEFEDTFKAVELWLADKAVLPI 148 (384)
Q Consensus 120 ~~~~~~~~s~~~Vf~aV~~g~~d~gVvPi 148 (384)
+.++++. ++..++.++++|++|..+-|+
T Consensus 66 ~i~~~~~-pw~~~~~~l~~g~~D~~~~~~ 93 (259)
T PRK15437 66 QCTFVEN-PLDALIPSLKAKKIDAIMSSL 93 (259)
T ss_pred ceEEEeC-CHHHHHHHHHCCCCCEEEecC
Confidence 4677775 499999999999999776555
No 282
>PRK06635 aspartate kinase; Reviewed
Probab=26.19 E-value=2.2e+02 Score=28.98 Aligned_cols=29 Identities=21% Similarity=0.354 Sum_probs=25.5
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeeeee
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIESRP 321 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIESRP 321 (384)
..++||.|.++++.|+++|||+-.|.+-.
T Consensus 270 ~~~~~g~l~~i~~~L~~~~I~i~~is~s~ 298 (404)
T PRK06635 270 VPDKPGIAAQIFGALAEANINVDMIVQNV 298 (404)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEecC
Confidence 57899999999999999999999885543
No 283
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=26.12 E-value=3.8e+02 Score=22.22 Aligned_cols=122 Identities=15% Similarity=0.126 Sum_probs=61.0
Q ss_pred HCCCCcccCC-CCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCC---
Q 016702 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ--- 192 (384)
Q Consensus 117 ~f~~~~~~~~-~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~--- 192 (384)
.+++.++.-. .+..++.+.+.+|++|+|+..-.....+.. ...|.+.++.++ .+-.|-+...+..++++
T Consensus 24 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~~l~~~~~~~~~~l~~ 96 (197)
T cd08419 24 RHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLV---AEPFLDNPLVVI----APPDHPLAGQKRIPLERLAR 96 (197)
T ss_pred HCCCceEEEEECCHHHHHHHHhcCCccEEEecCCCCCCCeE---EEEeccCCEEEE----ecCCCCCcCCCCcCHHHHhC
Confidence 3565544322 467888999999999999974332111111 112223333322 22233332222222222
Q ss_pred ccEEEecH-H-HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 193 LKRVLSHP-Q-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 193 I~~VySHp-q-Al~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
..-|.-.+ . ...+-..|+.+++.+ ...++|...+.++++.+ ...++.+...++
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (197)
T cd08419 97 EPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAG---LGLSVLSLHTLA 154 (197)
T ss_pred CCcEEecCCCcHHHHHHHHHHHCCCCcceEEEECCHHHHHHHHHhC---CceEeecHHHHH
Confidence 22332111 1 123455666665432 34567777777788775 346777776554
No 284
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=25.54 E-value=1.1e+02 Score=29.33 Aligned_cols=50 Identities=22% Similarity=0.198 Sum_probs=36.6
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCC-------CcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPK-------CETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~-------~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
..+|++ |+.|+.++....+++.. ...+++.+..+++.++.+|++|.++..
T Consensus 141 gk~v~~-~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 141 GKRVAV-GAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred CCEEec-CCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEEe
Confidence 356765 56677777666555421 224678899999999999999999875
No 285
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=25.51 E-value=4.1e+02 Score=22.43 Aligned_cols=121 Identities=15% Similarity=0.096 Sum_probs=60.6
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCc--
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (384)
.+++.++.. ..+..++.+.+.+|++|+|+..-.....|.. ...|.+..+.++ .+-+|-+...+..+++|+
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~hpl~~~~~i~~~dL~~ 97 (196)
T cd08458 25 DRPDVSVYLDTVPSQTVLELVSLQHYDLGISILAGDYPGLT---TEPVPSFRAVCL----LPPGHRLEDKETVHATDLEG 97 (196)
T ss_pred HCCCcEEEEeccChHHHHHHHHcCCCCEEEEeccCCCCCce---EEEeccCceEEE----ecCCCccccCCccCHHHhCC
Confidence 456655433 3467789999999999999984321111211 112223333222 344454443322333333
Q ss_pred -cEEE-ecHH-HHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcCHHHH
Q 016702 194 -KRVL-SHPQ-ALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAA 247 (384)
Q Consensus 194 -~~Vy-SHpq-Al~QC~~fL~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~aA 247 (384)
.-|. +... ...+...|+.+.+. . ...++|...+.+++..+ ...|+.+...+
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~l~~~~~ 154 (196)
T cd08458 98 ESLICLSPVSLLRMQTDAALDSCGVHCNRRIESSLALNLCDLVSRG---MGVGIVDPFTA 154 (196)
T ss_pred CccEEecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcEEEECchhh
Confidence 2232 1111 22455677777653 3 23455666566666664 34556665544
No 286
>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=25.10 E-value=82 Score=31.55 Aligned_cols=48 Identities=13% Similarity=-0.039 Sum_probs=35.9
Q ss_pred ceEEEEECCCCcHHHHHHHH---HCC----CCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 97 KVRISFKGLPGSFSEDAALK---AYP----KCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~---~f~----~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
-.|||+ +.||.+|....+ ..| ++++++++ ..+...++.+|++|.++++
T Consensus 106 GKkIav--~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~-~~d~~aAl~~G~VDAa~~~ 160 (328)
T TIGR03427 106 GQKVNL--VELSVSHYLLARALESVGLSEKDVKVVNTS-DADIVAAFITKDVTAVVTW 160 (328)
T ss_pred CCEEec--cCCChHHHHHHHHHHHcCCCHHHeEEEeCC-hHHHHHHHhcCCCcEEEEc
Confidence 358998 778988854433 333 36778875 4788999999999999874
No 287
>cd08448 PBP2_LTTR_aromatics_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=25.08 E-value=4e+02 Score=22.09 Aligned_cols=122 Identities=20% Similarity=0.104 Sum_probs=59.3
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCcc-
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (384)
.+++.++.- ..+-.++.+.+.+|++|+|+..-.....+.. ...|.+.++.++ .+-.|-|...+..+++++.
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~---~~~l~~~~~~~~----~~~~hpl~~~~~~~~~~L~~ 97 (197)
T cd08448 25 EYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLS---ARLLHREPFVCC----LPAGHPLAARRRIDLRELAG 97 (197)
T ss_pred HCCCCeEEEEeCCHHHHHHHHHcCCcceEEEeCCCCCcCce---EEEEecCcEEEE----eeCCCCCcCCCCcCHHHhCC
Confidence 456654432 2357889999999999999975332212211 122333343332 3334444333222333322
Q ss_pred --EEE-ecH---HHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 195 --RVL-SHP---QALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 195 --~Vy-SHp---qAl~QC~~fL~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
-|. +.. ....+-..|+.+.+.. . ..++|...+.+++..+ ...+|.+...+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08448 98 EPFVLFSREVSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAG---MGVALVPRSLAR 157 (197)
T ss_pred CcEEeeCcccChHHHHHHHHHHHHcCCceeeeeccccHHHHHHHHHcC---CceEecchhhhh
Confidence 232 111 1122333455554432 2 3455555566666654 456777765544
No 288
>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]
Probab=24.65 E-value=4.3e+02 Score=26.24 Aligned_cols=35 Identities=11% Similarity=0.187 Sum_probs=30.7
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeee
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESR 320 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESR 320 (384)
+..|.++.||.||-...+-+.+.++|.|++.-..-
T Consensus 7 ~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf 41 (287)
T COG0788 7 TFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQF 41 (287)
T ss_pred ceEEEEecCCCCCcHHHHHHHHHHcCCceeecccc
Confidence 56788899999999999999999999999976655
No 289
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=24.65 E-value=3.4e+02 Score=25.56 Aligned_cols=151 Identities=12% Similarity=0.041 Sum_probs=79.1
Q ss_pred EECCCCcHHHHHHHHHC--------CCC--cccCC---CCHHHHHHHHHhCCCCeEEEeeecccc-----c------c--
Q 016702 102 FKGLPGSFSEDAALKAY--------PKC--ETVPC---DEFEDTFKAVELWLADKAVLPIENSSS-----G------S-- 155 (384)
Q Consensus 102 ~LGP~GTfS~~AA~~~f--------~~~--~~~~~---~s~~~Vf~aV~~g~~d~gVvPiENS~~-----G------~-- 155 (384)
..-|+|+...+++..+. |.. ++.|- -.-.+++++|..|.+|+++++.-+... + .
T Consensus 3 ~~~p~~~~~~~~~~~f~~~v~e~t~G~v~v~~~~~g~Lg~~~e~~~~v~~G~~d~~~~~~~~~~~~~p~~~~~~lP~~~~ 82 (257)
T TIGR00787 3 HNAARSSPKHKAAEKFAKLVNEKTNGEIKISVFPSSQLGSDRAMLEALQGGALDMTAPSSSKFGPLVPELAVFDLPFLFR 82 (257)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHcCCeEEEEEcCCCCCCChHHHHHHHhCCCccEEecccccccccCcchhhccCCeecC
Confidence 34588888888776543 222 33332 346899999999999999865322110 0 0
Q ss_pred ----ccccc---------cccccCCeEEEEEEEEeeeeeeec--CCCCCcCCcc--EEEecHHHHHHHHHHHHhcCCeEE
Q 016702 156 ----IHRNY---------DLLLRHRLHIVGEVQLAANFCLLA--LPGIKADQLK--RVLSHPQALASSDIVLTQLGVARE 218 (384)
Q Consensus 156 ----V~~tl---------DlL~~~~l~I~gEi~l~I~h~Ll~--~~g~~l~~I~--~VySHpqAl~QC~~fL~~~~~~~i 218 (384)
....+ +.+.+.++++.+-...... .+.. .+-.+++|++ +|...+-.. -.++++..++..+
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~~g~~-~~~~~~~~i~s~~Dl~G~kir~~~~~~--~~~~~~~~Ga~~v 159 (257)
T TIGR00787 83 DYNHVHKVLDGEVGKALKKSLEKKGLKGLAYWDNGFR-QFTSSKKPITKPEDLKGLKIRIPNSPM--NEAQFKALGANPE 159 (257)
T ss_pred CHHHHHHHHcCHHHHHHHHHHHHcCcEEEeecCCcee-EeeeCCCccCChHHhCCCEEecCCCHH--HHHHHHHcCCccc
Confidence 00001 1122345666553332222 2222 2323456654 454433221 3566777676655
Q ss_pred ecCCHHHHHHHHHhcCCCCeEEEcCHHHHHHcCCceeecc
Q 016702 219 NVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADR 258 (384)
Q Consensus 219 ~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ygL~il~~~ 258 (384)
.-+.++.-..+..+ .-.+++.+......+++.=+.+.
T Consensus 160 -~~~~~e~~~aL~~G--~vDg~~~~~~~~~~~~~~ev~~y 196 (257)
T TIGR00787 160 -PMAFSEVYTALQTG--VVDGQENPLSNVYSSKFYEVQKY 196 (257)
T ss_pred -ccCHHHHHHHHHcC--CcccccCCHHHHhhcchhhhcch
Confidence 44556666666654 24567777666655566443333
No 290
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=24.59 E-value=4.6e+02 Score=22.65 Aligned_cols=32 Identities=13% Similarity=-0.070 Sum_probs=22.8
Q ss_pred HCCCCccc-CCCCHHHHHHHHHhCCCCeEEEee
Q 016702 117 AYPKCETV-PCDEFEDTFKAVELWLADKAVLPI 148 (384)
Q Consensus 117 ~f~~~~~~-~~~s~~~Vf~aV~~g~~d~gVvPi 148 (384)
.++++++. ...+-.++.+.+.+|++|+|+...
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 25 EAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred HCCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 35554432 234667889999999999999854
No 291
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=24.34 E-value=2.2e+02 Score=27.09 Aligned_cols=138 Identities=18% Similarity=0.189 Sum_probs=75.5
Q ss_pred ceEEEEECCCCcHHHHHHHHHCCC-------C-----ccc----------CCCCHHHHHHHHHhCCCCeEEEeeeccccc
Q 016702 97 KVRISFKGLPGSFSEDAALKAYPK-------C-----ETV----------PCDEFEDTFKAVELWLADKAVLPIENSSSG 154 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~AA~~~f~~-------~-----~~~----------~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G 154 (384)
+++||. |+|.-.+.+.. +|.. . ++. .+--..|+-..|+.|.+|+||+=
T Consensus 3 ~l~iAl--pKGRL~e~t~~-ll~~aG~~~~~~~~~~R~L~~~~~~~~i~~~~~r~~DIp~yV~~G~~DlGItG------- 72 (215)
T PRK01686 3 MLTIAL--PKGRILEETLP-LLAKAGIDPSEDPDKSRKLIFPTPEPDVRFLLVRATDVPTYVEHGAADLGIVG------- 72 (215)
T ss_pred cEEEEe--cCcccHHHHHH-HHHHcCCCcccCCCCCcceEeecCCCCEEEEEECHHHHHHHHhCCCccEEEee-------
Confidence 467777 69988877754 3311 0 111 11234689999999999999974
Q ss_pred cccccccccccCCeEEEEEEEEeeeee---eecCCCCCc------CCccEEEecHHHHHHHHHHHHhcCC--eEEecCCH
Q 016702 155 SIHRNYDLLLRHRLHIVGEVQLAANFC---LLALPGIKA------DQLKRVLSHPQALASSDIVLTQLGV--ARENVDDT 223 (384)
Q Consensus 155 ~V~~tlDlL~~~~l~I~gEi~l~I~h~---Ll~~~g~~l------~~I~~VySHpqAl~QC~~fL~~~~~--~~i~~~ST 223 (384)
.|.|.+..-.+.--..|...+| +++.++... ..-++|.+..--+. ++|+.++++ +.+..+-.
T Consensus 73 -----~D~l~E~~~~v~~l~dLgfG~crl~vAvp~~~~~~~~~~~~~~~rIATkYp~it--~~yf~~~gv~~~iv~l~Gs 145 (215)
T PRK01686 73 -----KDVLLEHGKDLYEPLDLGIGKCRMSVAVPPGFDYAPAVKQGPRLRVATKYPNIA--RRYFAEKGEQVEIIKLYGS 145 (215)
T ss_pred -----eeEeeecCCCeEEEecCCccCEEEEEEEECcccccchhhccCCCEEEeCCHHHH--HHHHHHcCCeEEEEECcCc
Confidence 3444443322222334555555 333433221 12246666555444 569998865 44544433
Q ss_pred HHHHHHHHhcCCCCeE-EE----cCHHHHHHcCCceeec
Q 016702 224 ASAAQYVASNGLRDAG-AV----ASARAAEIYGLNILAD 257 (384)
Q Consensus 224 A~AA~~v~~~~~~~~A-AI----as~~aA~~ygL~il~~ 257 (384)
.|+|=. -+.| || .+-..-+.+||+++.+
T Consensus 146 vE~aP~------~GlAD~IvDivsTG~TLr~NgL~~ie~ 178 (215)
T PRK01686 146 VELAPL------VGLADAIVDIVETGNTLRANGLVEVEE 178 (215)
T ss_pred eeeccc------cCCccEEEEeecChHHHHHCcCEEeeE
Confidence 333321 1222 33 3556678899999863
No 292
>PRK00341 hypothetical protein; Provisional
Probab=24.22 E-value=3.9e+02 Score=21.73 Aligned_cols=60 Identities=15% Similarity=0.293 Sum_probs=41.0
Q ss_pred CCCcchHHHHHHHHHhC-CceeeeeeeeeCCCCCCccccCCCCCCcccccE-EEEEEeecCCCcHHHHHHHHHHHHhcC
Q 016702 294 DEGPGVLFKALAVFALR-EINLTKIESRPQRKRPLRVVDDSNNGTAKYFDY-LFYIDFEASMADPRAQNALGHLQEFAT 370 (384)
Q Consensus 294 ~~~pGaL~~~L~~F~~~-~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y-~FfID~eg~~~d~~v~~al~~L~~~~~ 370 (384)
.+.++-...+++++.++ .++...+.+||+++. .| .+=|.+... +.+.+.++.++|+.+-.
T Consensus 25 ~~~~~~~~~V~~iv~~~~~~~~~~~~~k~Ss~G----------------kY~S~tv~i~~~-s~~q~~~iy~~L~~~~~ 86 (91)
T PRK00341 25 DTGVGFKDLVIEILQKHADVDLSTLAERQSSNG----------------KYTTVQLHIVAT-DEDQLQDINSALRATGR 86 (91)
T ss_pred cCchhHHHHHHHHHHHhCCCcccceeeccCCCC----------------EEEEEEEEEEEC-CHHHHHHHHHHHhhCCC
Confidence 45677777777777655 455778999999873 45 355666554 35677788888876644
No 293
>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=24.20 E-value=4.5e+02 Score=22.37 Aligned_cols=122 Identities=20% Similarity=0.122 Sum_probs=61.5
Q ss_pred HCCCCcccCCC-CHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCcc-
Q 016702 117 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (384)
Q Consensus 117 ~f~~~~~~~~~-s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (384)
.+++.++.... +..++.+.+.+|++|+|+.....- .+.+. ...|.+.++.++ .+-.|-|...+ .+++++.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~-~~~~~--~~~l~~~~~~~v----~~~~h~l~~~~-~~~~dL~~ 96 (200)
T cd08467 25 RAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVP-PDGLV--VRRLYDDGFACL----VRHGHPALAQE-WTLDDFAT 96 (200)
T ss_pred hCCCCEEEEecCCcccHHHHhhCCCcCEEEecCCCC-Cccce--eEEeeeccEEEE----EcCCCccccCC-CCHHHHhC
Confidence 35666554333 455889999999999999753211 11111 112223333322 24445444322 3333322
Q ss_pred --EEEec-HHH-HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHHH
Q 016702 195 --RVLSH-PQA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (384)
Q Consensus 195 --~VySH-pqA-l~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~~ 249 (384)
-|.-. ... ...-.+|+.+.+.. ...++|.....++++.+ ...|+.+...+..
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08467 97 LRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAAT---DLIATVPRRVATQ 155 (200)
T ss_pred CCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcC---CeEEeeHHHHHHH
Confidence 22211 111 12344566665532 34566777777777764 4577777766653
No 294
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=24.19 E-value=3.8e+02 Score=25.46 Aligned_cols=147 Identities=13% Similarity=0.086 Sum_probs=71.9
Q ss_pred CCCceEEEEECCCCcHH-HHHH---HHHCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCe
Q 016702 94 DGTKVRISFKGLPGSFS-EDAA---LKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRL 168 (384)
Q Consensus 94 ~~~~~~Va~LGP~GTfS-~~AA---~~~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l 168 (384)
..+..+||+..+-+.+- -.+. .+.|++.++.- ..+-.+..+.+.+|++|+||++..+..... .-....|.+.++
T Consensus 90 ~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~-~l~~~~l~~~~~ 168 (300)
T PRK11074 90 WRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGG-RFAFRDMGMLSW 168 (300)
T ss_pred CCceEEEEEcCccchhHHHHHHHHHHHhCCCceEEEEehhhhHHHHHHHCCCCCEEEecCccCCccc-ccceeecccceE
Confidence 35678899765544322 2221 22355544422 245677899999999999998643211110 011112334444
Q ss_pred EEEEEEEEeeeeeeecCCC-CCcCC---ccEEEe-cHHH-HHHHHHHHHhcCCeEEecCCHHHHHHHHHhcCCCCeEEEc
Q 016702 169 HIVGEVQLAANFCLLALPG-IKADQ---LKRVLS-HPQA-LASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAVA 242 (384)
Q Consensus 169 ~I~gEi~l~I~h~Ll~~~g-~~l~~---I~~VyS-HpqA-l~QC~~fL~~~~~~~i~~~STA~AA~~v~~~~~~~~AAIa 242 (384)
.++ .+-.|-|...++ .+++| -.-|.. +... ..+...|+..... ...++|.....++|+.+ ...++.
T Consensus 169 ~~v----~~~~hpl~~~~~~~~~~dl~~~p~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g---~gi~~l 240 (300)
T PRK11074 169 ACV----VSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQR-RLVVPDWESAINCLSAG---LCVGMV 240 (300)
T ss_pred EEE----EcCCCcccccCCCCCHHHHhhCCEEEecCCCcccccCccceecCCc-eEEECCHHHHHHHHHcC---CeEEeC
Confidence 433 344555543322 23333 233322 2111 2223334432222 34466666667777654 456777
Q ss_pred CHHHHHH
Q 016702 243 SARAAEI 249 (384)
Q Consensus 243 s~~aA~~ 249 (384)
+....+.
T Consensus 241 p~~~~~~ 247 (300)
T PRK11074 241 PTHFAKP 247 (300)
T ss_pred CHHHhHH
Confidence 7766553
No 295
>PRK09084 aspartate kinase III; Validated
Probab=24.03 E-value=8.4e+02 Score=25.48 Aligned_cols=100 Identities=15% Similarity=0.104 Sum_probs=60.1
Q ss_pred CCeEEecCCHHHHHHHHHhcCCCCeEEEcCH--HHHHHcCCceeeccccCCCCCeeEEEEEeeCCCCCC--C--CCCceE
Q 016702 214 GVARENVDDTASAAQYVASNGLRDAGAVASA--RAAEIYGLNILADRIQDEPDNITRFLVLARDPIIPR--T--DKLFKT 287 (384)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~--~aA~~ygL~il~~~I~D~~~N~TRF~vi~~~~~~~~--~--~~~~Kt 287 (384)
+++.+..-|-.+|.+++..+ +-.+-+. ..|..++.++.-.+..|...--|.+- ......+. + ...+-+
T Consensus 234 ~a~~i~~is~~ea~ela~~G----a~vlh~~~~~~~~~~~i~i~i~~~~~~~~~GT~I~--~~~~~~~~v~~it~~~~i~ 307 (448)
T PRK09084 234 AAKRIDEISFEEAAEMATFG----AKVLHPATLLPAVRSNIPVFVGSSKDPEAGGTWIC--NDTENPPLFRAIALRRNQT 307 (448)
T ss_pred CCeEcccCCHHHHHHHHhCC----CcccCHHHHHHHHHcCCcEEEEeCCCCCCCceEEe--cCCCCCCeeEEEEeeCCEE
Confidence 45667777888888876542 2223322 22567899998888776544455542 11111110 0 111223
Q ss_pred EEEEEe---CCCcchHHHHHHHHHhCCceeeeeee
Q 016702 288 SIVFTL---DEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 288 sl~f~~---~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
.+.+.- .+.||.+.++++.|++++||+-.|.|
T Consensus 308 lItv~~~~~~~~~g~~a~if~~l~~~~I~Vd~I~s 342 (448)
T PRK09084 308 LLTLHSLNMLHARGFLAEVFGILARHKISVDLITT 342 (448)
T ss_pred EEEEecCCCCccccHHHHHHHHHHHcCCeEEEEec
Confidence 333332 35789999999999999999999964
No 296
>KOG4028 consensus Uncharacterized conserved protein [Function unknown]
Probab=23.84 E-value=59 Score=28.79 Aligned_cols=34 Identities=21% Similarity=0.151 Sum_probs=25.5
Q ss_pred eEEEEECCCCcHHHHHHHHHCCC-CcccCCCCHHH
Q 016702 98 VRISFKGLPGSFSEDAALKAYPK-CETVPCDEFED 131 (384)
Q Consensus 98 ~~Va~LGP~GTfS~~AA~~~f~~-~~~~~~~s~~~ 131 (384)
+.-++--|+||+-|+-|+++.|. .++..-+++++
T Consensus 108 la~~~wrp~gswreel~~~~vggg~ql~~~~ai~~ 142 (175)
T KOG4028|consen 108 LACGCWRPKGSWREELAHAFVGGGLQLLHGDAIED 142 (175)
T ss_pred ecccccCCCCcHHHHHHHHHhcCCceeeccccccC
Confidence 44566779999999999998875 56666655544
No 297
>PF06153 DUF970: Protein of unknown function (DUF970); InterPro: IPR010375 This is a family of uncharacterised bacterial proteins.; PDB: 3M05_A.
Probab=23.41 E-value=2.3e+02 Score=24.15 Aligned_cols=53 Identities=15% Similarity=0.052 Sum_probs=36.1
Q ss_pred HHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHhcCc
Q 016702 301 FKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATF 371 (384)
Q Consensus 301 ~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~~~~ 371 (384)
.++.+.|.++|+-.|||-|.=- ++. ..+-.|.|-++ |++++++|+-+++.|..
T Consensus 14 ~~l~~~L~~~g~~~TkLsstGG-----------FLr---~GNtTlliGve----de~v~~vl~iIk~~c~~ 66 (109)
T PF06153_consen 14 DDLSDALNENGFRVTKLSSTGG-----------FLR---EGNTTLLIGVE----DEKVDEVLEIIKENCKK 66 (109)
T ss_dssp HHHHHHHHHTT--EEEEEEEET-----------TTT---EEEEEEEEEEE----GGGHHHHHHHHHHHH--
T ss_pred HHHHHHHHHCCceEEEEecccc-----------eec---cCCEEEEEEec----HHHHHHHHHHHHHhhcC
Confidence 3456667999999999998742 111 24668888775 57899999999988874
No 298
>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=23.37 E-value=4.3e+02 Score=21.86 Aligned_cols=121 Identities=12% Similarity=0.003 Sum_probs=61.4
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccccCCeEEEEEEEEeeeeeeecCCCCCcCCccE
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR 195 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~ 195 (384)
.|++.++.- ..+-+++.+.+.+|++|+|++.-.....+... ..|.+.++.++ .+-.|-+... -.++.+..-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~~~~~~-~~~l~~~~~ 96 (193)
T cd08442 25 RYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQ---EPVFQEELVLV----SPKGHPPVSR-AEDLAGSTL 96 (193)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEEeCCCCCCCcEE---EEeecCcEEEE----ecCCCccccc-HHHhCCCce
Confidence 356655433 24667899999999999999853221111111 12222233222 1222322210 012233333
Q ss_pred EEec-H-HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcCHHHHH
Q 016702 196 VLSH-P-QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (384)
Q Consensus 196 VySH-p-qAl~QC~~fL~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~aA~ 248 (384)
|.-. . ....+...|+.+.+.. ...++|...+..++.++ ...++.+...++
T Consensus 97 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 151 (193)
T cd08442 97 LAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAG---MGIALLPRSVLD 151 (193)
T ss_pred EEecCCCcHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHhC---CcEEEcCHHHHh
Confidence 3211 1 1234567788776532 24566777777777764 457777777665
No 299
>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=23.16 E-value=4.4e+02 Score=21.90 Aligned_cols=33 Identities=15% Similarity=-0.028 Sum_probs=23.7
Q ss_pred HCCCCcccC-CCCHHHHHHHHHhCCCCeEEEeee
Q 016702 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIE 149 (384)
Q Consensus 117 ~f~~~~~~~-~~s~~~Vf~aV~~g~~d~gVvPiE 149 (384)
.|++.++.- ..+..+..+.+.+|++|+|++...
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (197)
T cd08449 25 QYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFA 58 (197)
T ss_pred HCCCeEEEEEECCHHHHHHHHhCCCccEEEeccc
Confidence 356654432 235788999999999999997543
No 300
>PLN02550 threonine dehydratase
Probab=22.88 E-value=3.3e+02 Score=29.90 Aligned_cols=67 Identities=18% Similarity=0.213 Sum_probs=44.7
Q ss_pred EEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHH
Q 016702 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 367 (384)
Q Consensus 288 sl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~ 367 (384)
.+.|++|.+||+|.+.|+.|.. .-|+|.++=|-.... .-. -||=++-. +..++.+++.|++
T Consensus 512 l~~v~fPErpGAl~~Fl~~lg~-~~nITeF~YR~~~~~---------------~a~-vlvGi~v~--~~e~~~l~~~l~~ 572 (591)
T PLN02550 512 LYRFVFPERPGALMKFLDAFSP-RWNISLFHYRGQGET---------------GAN-VLVGIQVP--PEEMQEFKSRANA 572 (591)
T ss_pred EEEEEecCcCCHHHHHHHhhCC-CCceeeEEeecCCCC---------------Ccc-EEEEEeeC--HHHHHHHHHHHHH
Confidence 4678899999999999998864 357788888854332 112 44555432 3566777788877
Q ss_pred hcCceE
Q 016702 368 FATFLR 373 (384)
Q Consensus 368 ~~~~vk 373 (384)
..-.+.
T Consensus 573 ~gy~~~ 578 (591)
T PLN02550 573 LGYEYQ 578 (591)
T ss_pred cCCCeE
Confidence 654443
No 301
>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=22.64 E-value=1e+02 Score=22.11 Aligned_cols=26 Identities=31% Similarity=0.360 Sum_probs=23.0
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeee
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIE 318 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIE 318 (384)
+++.||.+.++++.+++.|||+--|.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~i~v~~i~ 36 (66)
T cd04916 11 MKNTVGVSARATAALAKAGINIRMIN 36 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 45689999999999999999998774
No 302
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=22.63 E-value=3e+02 Score=26.43 Aligned_cols=84 Identities=18% Similarity=0.160 Sum_probs=52.3
Q ss_pred eEEEEE-CCCCcHHHHHHHHHC---C-CCcccCCCCHHHHHHHHHhCCCCeEEEeeeccccccccccccccc------cC
Q 016702 98 VRISFK-GLPGSFSEDAALKAY---P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL------RH 166 (384)
Q Consensus 98 ~~Va~L-GP~GTfS~~AA~~~f---~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~------~~ 166 (384)
.|||+. ||....-+ ++.+.+ | ..+++.++++.+.=.|+.+|++|.-+. ++.-.|. .+
T Consensus 1 ikIG~~~~~~~~i~~-~v~~~~~~~Gi~vevv~f~D~~~~N~AL~~G~iDaN~f-----------Qh~~yl~~~n~~~~~ 68 (237)
T PF03180_consen 1 IKIGVTPGPDAEILE-AVKEKLKKKGIDVEVVEFSDYVQPNEALADGEIDANFF-----------QHIPYLEQFNKENGY 68 (237)
T ss_dssp EEEEEETTCHHHHHH-HHHHHHHHTTEEEEEEEESSTTHHHHHHHTTSSSEEEE-----------EEHHHHHHHHHHHT-
T ss_pred CEEEEeCCCHHHHHH-HHHHHHHhcCCeEEEEEecchhhcChHHHCCCcceecc-----------CCHHHHHHHHHHCCC
Confidence 478888 56444444 333333 2 367899999999999999999997664 3333332 25
Q ss_pred CeEEEEEEEEeeeeeeecCCCCCcCCcc
Q 016702 167 RLHIVGEVQLAANFCLLALPGIKADQLK 194 (384)
Q Consensus 167 ~l~I~gEi~l~I~h~Ll~~~g~~l~~I~ 194 (384)
+|..++.+++. ...|.+.+-.++++|.
T Consensus 69 ~L~~v~~~~~~-p~glYS~k~~sl~~lp 95 (237)
T PF03180_consen 69 NLVPVGPTYIE-PMGLYSKKYKSLDDLP 95 (237)
T ss_dssp -EEEEEEEEE----EEEESSSSSGGGS-
T ss_pred cEEEecceeEE-eEEEeecccCchhhcC
Confidence 78888876665 3778777655566553
No 303
>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=22.58 E-value=2.5e+02 Score=25.11 Aligned_cols=51 Identities=24% Similarity=0.079 Sum_probs=34.4
Q ss_pred ceEEEEECCCCcHHHHH---HHHHCC----CCcccCCCCHHHHHHHHHhCCCCeEEEeeec
Q 016702 97 KVRISFKGLPGSFSEDA---ALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLPIEN 150 (384)
Q Consensus 97 ~~~Va~LGP~GTfS~~A---A~~~f~----~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiEN 150 (384)
-.||++.+ |+.++.. +.+.+| +++++... ..+...++.+|++|.+++..++
T Consensus 93 GK~i~v~~--~s~~~~~~~~~l~~~g~~~~~v~~v~~~-~~~~~~al~~g~vDa~~~~~~~ 150 (216)
T PF09084_consen 93 GKKIGVSR--GSSSEYFLRALLKKNGIDPDDVKIVNLG-PPELAQALLSGQVDAAILWYPP 150 (216)
T ss_dssp TSEEEEST--TSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTTSSSEEEEEEEC
T ss_pred CCEEEEec--CcchhHHHHHHHHHhccccccceeeeee-hhhhhhhhhcCCCCEEEEccCC
Confidence 46999865 7766643 334444 24555554 5667779999999999977776
No 304
>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=22.52 E-value=3.4e+02 Score=20.35 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=23.5
Q ss_pred eCCCcchHHHHHHHHHhCCceeeeeee
Q 016702 293 LDEGPGVLFKALAVFALREINLTKIES 319 (384)
Q Consensus 293 ~~~~pGaL~~~L~~F~~~~INLtkIES 319 (384)
..+.+|.+.++++.|++++|++--|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~~ 37 (80)
T cd04921 11 MVGVPGIAARIFSALARAGINVILISQ 37 (80)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEe
Confidence 457899999999999999999987754
No 305
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=22.45 E-value=1.9e+02 Score=27.03 Aligned_cols=50 Identities=20% Similarity=0.111 Sum_probs=35.4
Q ss_pred CceEEEEECCCCcHHHHHHHHHC---C-----CCcccCCCCHHHHHHHHHhCCCCeEEEe
Q 016702 96 TKVRISFKGLPGSFSEDAALKAY---P-----KCETVPCDEFEDTFKAVELWLADKAVLP 147 (384)
Q Consensus 96 ~~~~Va~LGP~GTfS~~AA~~~f---~-----~~~~~~~~s~~~Vf~aV~~g~~d~gVvP 147 (384)
+..+|+. .+.|+-+|...+.++ | +++++.++. .+...++.+|++|.++++
T Consensus 120 kGk~i~~-~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~iDa~~~~ 177 (252)
T PF13379_consen 120 KGKKIAV-PFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGEIDAAVLW 177 (252)
T ss_dssp STEEEEE-SSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-SEEEEE
T ss_pred CCcEEEE-cCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCCcCEEEec
Confidence 5567775 456777777665544 2 357788888 999999999999999985
No 306
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=21.99 E-value=1.3e+02 Score=27.51 Aligned_cols=35 Identities=26% Similarity=0.266 Sum_probs=29.5
Q ss_pred EEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeee
Q 016702 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRP 321 (384)
Q Consensus 287 tsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP 321 (384)
..+..+..+.||-|..+++..++|||++..+-|+-
T Consensus 96 iei~~~~~~~pgi~A~V~~~iak~gi~Irqi~~~d 130 (167)
T COG2150 96 IEIYPEDARYPGILAGVASLIAKRGISIRQIISED 130 (167)
T ss_pred EEEEeccCCCccHHHHHHHHHHHcCceEEEEecCC
Confidence 34455567899999999999999999999998873
No 307
>COG3978 Acetolactate synthase (isozyme II), small (regulatory) subunit [Function unknown]
Probab=21.79 E-value=4.3e+02 Score=21.48 Aligned_cols=50 Identities=14% Similarity=0.113 Sum_probs=36.6
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecC
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEAS 352 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~ 352 (384)
-+....+|+.|.++|.+-..||.-...+.--+.-.. ..|+-.|-||=+-.
T Consensus 7 dl~ar~~pe~leRVLrvtrhRGF~vcamnmt~~~da-------------~~~nie~tV~s~R~ 56 (86)
T COG3978 7 DLSARFNPETLERVLRVTRHRGFRVCAMNMTAAVDA-------------GNANIELTVDSDRS 56 (86)
T ss_pred eeeccCChHHHHHHHHHhhhcCeEEEEeeccccccc-------------ccceEEEEEcCCCC
Confidence 345678999999999999999988887766565322 14777777765443
No 308
>COG3482 Uncharacterized conserved protein [Function unknown]
Probab=21.72 E-value=1.3e+02 Score=29.03 Aligned_cols=45 Identities=22% Similarity=0.229 Sum_probs=34.8
Q ss_pred EEEEECCCCcHHHHHHHHHCCCCcccCCCCHHHHHHHHHhCCCCeEEE
Q 016702 99 RISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVL 146 (384)
Q Consensus 99 ~Va~LGP~GTfS~~AA~~~f~~~~~~~~~s~~~Vf~aV~~g~~d~gVv 146 (384)
+|.|.|| |-||..+++.. +..+.|=.-..+++.+|..|-...|+|
T Consensus 3 ~vvf~Gp--ti~~~~~~~v~-~~~~~~Pa~~g~~~~av~~~~~~i~ii 47 (237)
T COG3482 3 PVVFAGP--TISHADAEKVL-DAIYLPPAAQGDVLSAVQRGPAAIGII 47 (237)
T ss_pred ceeecCC--CccHHHHHhhh-cccccCchhhhhHHHHHHhcCceEEEe
Confidence 4899999 67787777654 667777788899999999995555554
No 309
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=21.65 E-value=2e+02 Score=27.55 Aligned_cols=55 Identities=20% Similarity=0.093 Sum_probs=39.2
Q ss_pred CCCceEEEEECCCCcHHHHH---HHHH---CCC--CcccCCCCHHHHHHHHHhCCCCeEEEee
Q 016702 94 DGTKVRISFKGLPGSFSEDA---ALKA---YPK--CETVPCDEFEDTFKAVELWLADKAVLPI 148 (384)
Q Consensus 94 ~~~~~~Va~LGP~GTfS~~A---A~~~---f~~--~~~~~~~s~~~Vf~aV~~g~~d~gVvPi 148 (384)
....++|+...+.|+|.-.+ +..+ +++ +++++..+..+.+++|.+|++|++++..
T Consensus 28 ~~~~l~Ig~~~~~~~~~~~~~~la~~~~~~~~~i~v~~~~~~~~~~~~~~l~~G~~D~~~~~~ 90 (320)
T TIGR02122 28 EPTFVTIGTGGTGGVYYPIGGAIAQLINKKSGKLRVRVQSTGGSVENVNLLEAGEADLAIVQS 90 (320)
T ss_pred CCceEEEEeCCCCCChHHHHHHHHHHHhccCCCeeEEEEeCcchHHHHHHHhCCCCcEEEEcc
Confidence 34578999998988865432 2222 243 3456666778899999999999999864
No 310
>PF01894 UPF0047: Uncharacterised protein family UPF0047; InterPro: IPR001602 This family contains small uncharacterised proteins of 14 to 16 kDa mainly from bacteria although the signatures also occur in a hypothetical protein from archaea and from yeast.; PDB: 1VPH_E 2P6C_A 2CU5_A 1VMJ_A 1XBF_B 1VMH_A 1VE0_A 2P6H_B 1VMF_C.
Probab=21.63 E-value=44 Score=28.74 Aligned_cols=17 Identities=18% Similarity=0.559 Sum_probs=11.0
Q ss_pred CCCCCcccccEEEEEEeecC
Q 016702 333 SNNGTAKYFDYLFYIDFEAS 352 (384)
Q Consensus 333 ~~~~~~~~~~Y~FfID~eg~ 352 (384)
..+|+ |+.+||+|++|.
T Consensus 92 L~LGt---wQ~I~l~E~dgp 108 (118)
T PF01894_consen 92 LALGT---WQGIYLVEFDGP 108 (118)
T ss_dssp E---T---TEEEEEEESS-S
T ss_pred EccCC---cCEEEEEECCCC
Confidence 34564 999999999983
No 311
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.43 E-value=97 Score=31.27 Aligned_cols=97 Identities=19% Similarity=0.065 Sum_probs=63.6
Q ss_pred EEEEECC-CCcHHHHHHHHHCC----CCcccCCCCHHHHHHHHHhCCCCeEEEeeecccccccccccccccc---CCeEE
Q 016702 99 RISFKGL-PGSFSEDAALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLR---HRLHI 170 (384)
Q Consensus 99 ~Va~LGP-~GTfS~~AA~~~f~----~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiENS~~G~V~~tlDlL~~---~~l~I 170 (384)
.|-+-|+ .||+.|.++..++. +..++|++.-.++..++..|++|.++.=+-++....=.-++.+|.- ..+..
T Consensus 150 ~v~~~~~g~Gs~dhl~~~~~~k~~Gi~~~~Vpy~g~gea~taLlgg~v~a~~~~~se~~~~vksG~lr~Lav~s~eRl~~ 229 (319)
T COG3181 150 SVIGGGSGLGSADHLAGALFAKAAGIKITYVPYKGGGEALTALLGGHVDAGSTNLSELLSQVKSGTLRLLAVFSEERLPG 229 (319)
T ss_pred eEEecCCCCCcHHHHHHHHHHHHhCCceeEEeecCccHHHHHHhcCceeeeecChhhhhhhhccCceEEEEeechhhcCC
Confidence 4555544 58999998877653 4678999999999999999999999876654444444445555542 11111
Q ss_pred ------EEE----EEEeeeeeeecCCCCCcCCccE
Q 016702 171 ------VGE----VQLAANFCLLALPGIKADQLKR 195 (384)
Q Consensus 171 ------~gE----i~l~I~h~Ll~~~g~~l~~I~~ 195 (384)
+.| +..++.+.+.+.+|++-+.|.+
T Consensus 230 ~pdvPT~~E~G~~~~~~~wrgvfap~g~~~e~~~~ 264 (319)
T COG3181 230 LPDVPTLKEQGYDVVMSIWRGVFAPAGTPDEIIAK 264 (319)
T ss_pred CCCCCChHhcCCceeeeeeeEEEeCCCCCHHHHHH
Confidence 111 2256777888888876555444
No 312
>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=21.36 E-value=4e+02 Score=21.15 Aligned_cols=74 Identities=15% Similarity=0.216 Sum_probs=40.0
Q ss_pred eEEEEEEeCCCcchHHHHHHHHHhC-Cceeeeeee-eeCCCCCCccccCCCCCCcccccEEEEEEeecCCC-cHHHHHHH
Q 016702 286 KTSIVFTLDEGPGVLFKALAVFALR-EINLTKIES-RPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMA-DPRAQNAL 362 (384)
Q Consensus 286 Ktsl~f~~~~~pGaL~~~L~~F~~~-~INLtkIES-RP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~-d~~v~~al 362 (384)
+..+.|.+.+..-.|.++|..--.+ .|....-.- -|..+.. +....+.|.|+-.|..+ ...+.+|+
T Consensus 8 ~~~~~~~~~~edhTl~n~L~~~l~~~pV~~a~Y~v~hp~~~~~-----------~~~d~~~~~VeT~Gs~~P~~al~~Ai 76 (86)
T cd00460 8 KNYVDFVLENEDHTLGNSLRRILLKSPVEFAAYYVEHPVKLQR-----------TDEDKFILRIETVGSIPPEEALRRAV 76 (86)
T ss_pred CCEEEEEEeCCCchHHHHHHHHHhCCCceEEEEEeCCCccCCC-----------CCCCeEEEEEEECCCCCHHHHHHHHH
Confidence 5667777776666677766654433 111111110 0111110 01235788888888643 35677888
Q ss_pred HHHHHhcC
Q 016702 363 GHLQEFAT 370 (384)
Q Consensus 363 ~~L~~~~~ 370 (384)
+.|.+.+.
T Consensus 77 ~~L~~~~~ 84 (86)
T cd00460 77 EILRKKLE 84 (86)
T ss_pred HHHHHHHh
Confidence 88887654
No 313
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=21.35 E-value=2.8e+02 Score=29.05 Aligned_cols=71 Identities=20% Similarity=0.331 Sum_probs=52.3
Q ss_pred EEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHHHHHHHHh-
Q 016702 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF- 368 (384)
Q Consensus 290 ~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~al~~L~~~- 368 (384)
-+...|+-|-.-++|..+..++|||..||--|.. ..|++|-. ++-+.++.++.+|+..
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 3455799999999999999999999999986642 35667632 4456777888888754
Q ss_pred -cCceEEEccccCC
Q 016702 369 -ATFLRVLGCYPMD 381 (384)
Q Consensus 369 -~~~vkvLGsYp~~ 381 (384)
...||..+--|..
T Consensus 63 GV~~vr~V~~mPse 76 (511)
T COG3283 63 GVTDVRTVPWMPSE 76 (511)
T ss_pred CccceeeecCCcch
Confidence 3457777766643
No 314
>PRK15385 magnesium transport protein MgtC; Provisional
Probab=20.93 E-value=6.3e+02 Score=24.23 Aligned_cols=66 Identities=11% Similarity=0.014 Sum_probs=43.3
Q ss_pred EEEEEeCCCcc--hHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecC-CCcHHHHHHHHH
Q 016702 288 SIVFTLDEGPG--VLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEAS-MADPRAQNALGH 364 (384)
Q Consensus 288 sl~f~~~~~pG--aL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~-~~d~~v~~al~~ 364 (384)
.+.+...++++ .+..+++.+...++.+..+++.|..+. .+..-..++..+ .++..+.+++.+
T Consensus 144 ~~~v~~~~~~~~~vr~~L~~~l~~~~~~~~~l~~~~~~~~---------------~~~ei~a~l~~~~~~~~~le~iv~~ 208 (225)
T PRK15385 144 ILKVTCNKEDESAVRQWLLNIVKEAAICLQGLGSVPAQEQ---------------GYKEIRAELVGHADYRKTRELIISR 208 (225)
T ss_pred EEEEEEcCcchhHHHHHHHHHHHhCCCceEEeEeeecCCC---------------CeEEEEEEEEecCCchhhHHHHHHH
Confidence 34444555444 478888999999999999999987542 123333444433 255778888888
Q ss_pred HHHh
Q 016702 365 LQEF 368 (384)
Q Consensus 365 L~~~ 368 (384)
|...
T Consensus 209 L~~~ 212 (225)
T PRK15385 209 IGDN 212 (225)
T ss_pred HhCC
Confidence 7643
No 315
>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=20.91 E-value=2.4e+02 Score=25.92 Aligned_cols=55 Identities=7% Similarity=0.003 Sum_probs=37.7
Q ss_pred CCceEEEEECCCCcHHHH----HHHHHC----C-CCcccCCCCHHHHHHHHHhCCCCeEEEeee
Q 016702 95 GTKVRISFKGLPGSFSED----AALKAY----P-KCETVPCDEFEDTFKAVELWLADKAVLPIE 149 (384)
Q Consensus 95 ~~~~~Va~LGP~GTfS~~----AA~~~f----~-~~~~~~~~s~~~Vf~aV~~g~~d~gVvPiE 149 (384)
..+++||+.+....+... ...+.| | .+++++..++.+.+.++.+|++|+++.+..
T Consensus 31 ~~~l~vg~~~~~~~~~~~~~~~~l~~~l~~~~g~~v~~~~~~~~~~~~~~l~~g~~Di~~~~~~ 94 (254)
T TIGR01098 31 PKELNFGILPGENASNLTRRWEPLADYLEKKLGIKVQLFVATDYSAVIEAMRFGRVDIAWFGPS 94 (254)
T ss_pred CCceEEEECCCCCHHHHHHHHHHHHHHHHHHhCCcEEEEeCCCHHHHHHHHHcCCccEEEECcH
Confidence 457899998754433221 111222 2 357778889999999999999999987643
No 316
>PHA03169 hypothetical protein; Provisional
Probab=20.18 E-value=4e+02 Score=27.60 Aligned_cols=66 Identities=8% Similarity=0.049 Sum_probs=46.5
Q ss_pred CCceEEEEEEeCCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCcccccEEEEEEeecCCCcHHHHHH
Q 016702 283 KLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNA 361 (384)
Q Consensus 283 ~~~Ktsl~f~~~~~pGaL~~~L~~F~~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~~Y~FfID~eg~~~d~~v~~a 361 (384)
...|--++|.- .|-+||++-..|.--||--+-+..-|-.... ...|.|+.||=|.-...-..|+.+
T Consensus 320 ~~W~~~v~fWg--dP~~LyrLsraLqfpG~~ssgvq~lP~~p~~-----------p~~~~y~ItVyCqsk~TaK~V~ka 385 (413)
T PHA03169 320 GPWCWVVFCWG--DPYSLYRLSRCLQFPGAVSSGVQTFPDAPGS-----------PVIWAYCITVFCQSRGTAKAVIKA 385 (413)
T ss_pred CceeEEEEecC--CcHHHHHHHHHhccCCeeccceeecCCCCCC-----------CCCceeEEEEEecCcccHHHHHHH
Confidence 35677677765 7889999999999999988888877764322 125888888888654433444443
Done!