Query 018090
Match_columns 361
No_of_seqs 213 out of 1130
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 06:03:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018090.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018090hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN02317 arogenate dehydratase 100.0 1.1E-84 2.3E-89 647.5 32.1 322 28-361 15-336 (382)
2 COG0077 PheA Prephenate dehydr 100.0 1.4E-79 3.1E-84 588.6 27.5 233 119-352 2-238 (279)
3 PRK11899 prephenate dehydratas 100.0 1.9E-78 4E-83 583.4 29.4 235 118-352 3-238 (279)
4 KOG2797 Prephenate dehydratase 100.0 7.2E-76 1.6E-80 562.1 21.7 324 6-355 3-328 (377)
5 PRK10622 pheA bifunctional cho 100.0 5.2E-73 1.1E-77 567.0 28.1 235 118-352 102-341 (386)
6 PRK11898 prephenate dehydratas 100.0 4.3E-72 9.2E-77 540.0 29.3 233 119-352 1-241 (283)
7 PF00800 PDT: Prephenate dehyd 100.0 1.6E-56 3.5E-61 405.3 18.8 177 122-298 1-181 (181)
8 cd04904 ACT_AAAH ACT domain of 99.5 1.6E-14 3.6E-19 113.2 5.2 44 309-352 1-44 (74)
9 cd04931 ACT_PAH ACT domain of 99.5 5E-14 1.1E-18 115.3 6.1 48 305-352 11-58 (90)
10 cd04930 ACT_TH ACT domain of t 99.4 1.8E-13 3.9E-18 116.7 5.7 47 306-352 39-85 (115)
11 PRK06034 hypothetical protein; 99.4 4.1E-14 8.9E-19 136.9 1.7 117 63-195 50-169 (279)
12 cd04929 ACT_TPH ACT domain of 99.4 2.5E-13 5.5E-18 107.3 5.1 44 309-352 1-44 (74)
13 cd04880 ACT_AAAH-PDT-like ACT 99.2 2.9E-11 6.4E-16 93.9 4.7 43 310-352 1-43 (75)
14 TIGR01268 Phe4hydrox_tetr phen 99.0 2.1E-10 4.6E-15 117.0 5.5 46 307-352 15-60 (436)
15 cd04905 ACT_CM-PDT C-terminal 99.0 7.6E-10 1.6E-14 87.3 5.7 45 308-352 1-45 (80)
16 TIGR01270 Trp_5_monoox tryptop 99.0 6.2E-10 1.3E-14 114.1 5.9 47 305-351 28-75 (464)
17 PRK08818 prephenate dehydrogen 98.2 1.5E-06 3.3E-11 87.7 5.0 44 307-352 294-338 (370)
18 PF01842 ACT: ACT domain; Int 97.6 0.00011 2.5E-09 54.1 5.0 43 309-351 1-43 (66)
19 TIGR01269 Tyr_3_monoox tyrosin 97.2 0.00052 1.1E-08 70.7 5.5 47 308-354 37-89 (457)
20 cd04886 ACT_ThrD-II-like C-ter 96.9 0.0017 3.7E-08 48.0 4.6 34 312-345 2-35 (73)
21 cd04908 ACT_Bt0572_1 N-termina 96.5 0.0046 1E-07 46.8 4.4 37 310-346 3-39 (66)
22 cd04882 ACT_Bt0572_2 C-termina 96.4 0.0066 1.4E-07 44.7 4.8 35 311-345 2-36 (65)
23 KOG3820 Aromatic amino acid hy 96.1 0.0058 1.2E-07 62.3 4.4 41 307-347 35-75 (461)
24 cd04884 ACT_CBS C-terminal ACT 95.7 0.017 3.7E-07 44.2 4.4 34 311-344 2-35 (72)
25 PRK06737 acetolactate synthase 95.5 0.024 5.2E-07 45.4 4.6 39 309-347 3-41 (76)
26 cd04909 ACT_PDH-BS C-terminal 95.4 0.023 5E-07 42.8 4.3 36 310-345 3-38 (69)
27 cd04883 ACT_AcuB C-terminal AC 95.4 0.028 6.2E-07 42.4 4.6 36 309-344 2-37 (72)
28 cd04878 ACT_AHAS N-terminal AC 95.2 0.043 9.4E-07 40.3 5.1 35 310-344 2-36 (72)
29 PRK11152 ilvM acetolactate syn 95.2 0.035 7.7E-07 44.4 4.6 39 308-346 3-41 (76)
30 cd04874 ACT_Af1403 N-terminal 95.1 0.046 9.9E-07 40.3 5.0 42 310-351 2-43 (72)
31 cd04903 ACT_LSD C-terminal ACT 94.9 0.05 1.1E-06 39.9 4.5 34 311-344 2-35 (71)
32 PF13291 ACT_4: ACT domain; PD 94.7 0.045 9.7E-07 42.6 4.0 41 305-345 3-43 (80)
33 cd04889 ACT_PDH-BS-like C-term 94.6 0.049 1.1E-06 39.5 3.9 34 312-345 2-35 (56)
34 cd04902 ACT_3PGDH-xct C-termin 94.5 0.08 1.7E-06 39.7 4.9 34 311-344 2-35 (73)
35 cd04879 ACT_3PGDH-like ACT_3PG 94.5 0.081 1.8E-06 38.6 4.8 35 311-345 2-36 (71)
36 cd02116 ACT ACT domains are co 94.2 0.094 2E-06 34.9 4.4 34 312-345 2-35 (60)
37 cd04887 ACT_MalLac-Enz ACT_Mal 93.7 0.098 2.1E-06 39.7 4.1 36 310-345 1-36 (74)
38 cd04881 ACT_HSDH-Hom ACT_HSDH_ 93.6 0.16 3.5E-06 37.8 5.1 41 311-351 3-44 (79)
39 cd04885 ACT_ThrD-I Tandem C-te 93.5 0.059 1.3E-06 41.1 2.5 33 312-345 2-34 (68)
40 cd04926 ACT_ACR_4 C-terminal 93.3 0.18 3.8E-06 39.0 4.9 38 309-346 2-39 (72)
41 cd04899 ACT_ACR-UUR-like_2 C-t 93.2 0.16 3.4E-06 38.0 4.5 38 309-346 1-38 (70)
42 cd04888 ACT_PheB-BS C-terminal 93.1 0.19 4.1E-06 38.1 4.8 33 310-342 2-34 (76)
43 PRK13562 acetolactate synthase 93.1 0.14 3.1E-06 41.8 4.2 39 308-346 2-40 (84)
44 cd04901 ACT_3PGDH C-terminal A 93.0 0.11 2.4E-06 38.7 3.3 35 311-345 2-36 (69)
45 PRK11895 ilvH acetolactate syn 93.0 0.18 4E-06 45.7 5.2 37 309-345 3-39 (161)
46 cd04873 ACT_UUR-ACR-like ACT d 92.6 0.22 4.8E-06 36.8 4.5 37 310-346 2-38 (70)
47 PRK08178 acetolactate synthase 92.5 0.25 5.4E-06 41.4 5.1 40 307-346 7-46 (96)
48 TIGR00119 acolac_sm acetolacta 92.3 0.24 5.1E-06 44.8 5.0 36 310-345 3-38 (157)
49 PRK08526 threonine dehydratase 92.3 2.3 4.9E-05 43.7 12.7 179 161-349 167-368 (403)
50 PF13710 ACT_5: ACT domain; PD 91.7 0.18 4E-06 38.4 3.0 29 317-345 1-29 (63)
51 PF12974 Phosphonate-bd: ABC t 91.6 0.5 1.1E-05 43.8 6.5 84 118-210 104-202 (243)
52 cd04895 ACT_ACR_1 ACT domain-c 91.3 0.3 6.5E-06 38.6 4.0 30 309-338 2-31 (72)
53 PRK00194 hypothetical protein; 91.3 0.26 5.7E-06 39.2 3.7 36 308-343 3-38 (90)
54 cd04906 ACT_ThrD-I_1 First of 90.9 0.19 4.1E-06 40.2 2.5 26 310-335 3-28 (85)
55 cd04896 ACT_ACR-like_3 ACT dom 90.4 0.33 7.1E-06 38.8 3.5 28 310-337 2-29 (75)
56 cd04877 ACT_TyrR N-terminal AC 90.4 0.44 9.4E-06 36.7 4.1 35 310-344 2-36 (74)
57 PRK08639 threonine dehydratase 90.2 2.8 6.1E-05 43.0 11.0 36 307-343 335-371 (420)
58 cd04876 ACT_RelA-SpoT ACT dom 90.0 0.53 1.1E-05 33.0 4.1 34 312-345 2-35 (71)
59 PRK04435 hypothetical protein; 89.9 0.56 1.2E-05 41.6 4.9 37 306-342 67-103 (147)
60 cd04872 ACT_1ZPV ACT domain pr 89.9 0.38 8.3E-06 38.3 3.6 36 308-343 1-36 (88)
61 COG4747 ACT domain-containing 89.6 0.44 9.5E-06 41.7 3.9 39 308-346 69-107 (142)
62 cd04875 ACT_F4HF-DF N-terminal 89.5 0.5 1.1E-05 36.3 3.8 32 311-342 2-33 (74)
63 TIGR01127 ilvA_1Cterm threonin 89.3 0.61 1.3E-05 46.9 5.3 35 308-342 305-339 (380)
64 TIGR01728 SsuA_fam ABC transpo 88.9 5.3 0.00011 36.9 10.9 138 120-268 1-158 (288)
65 PRK06382 threonine dehydratase 88.1 0.86 1.9E-05 46.5 5.5 35 307-341 329-363 (406)
66 PRK08577 hypothetical protein; 88.1 1.2 2.6E-05 38.6 5.6 38 308-345 56-93 (136)
67 PRK08198 threonine dehydratase 88.0 1 2.2E-05 45.7 6.0 37 307-343 326-362 (404)
68 cd04870 ACT_PSP_1 CT domains f 86.9 0.82 1.8E-05 35.3 3.5 33 313-345 4-36 (75)
69 cd04900 ACT_UUR-like_1 ACT dom 86.2 1.1 2.5E-05 34.4 4.0 36 309-344 2-37 (73)
70 smart00079 PBPe Eukaryotic hom 86.0 3.5 7.6E-05 34.2 7.2 78 120-209 14-104 (134)
71 cd08417 PBP2_Nitroaromatics_li 86.0 19 0.00042 30.2 13.4 121 140-271 26-155 (200)
72 PRK06545 prephenate dehydrogen 84.7 1.1 2.4E-05 44.9 4.1 41 308-348 290-330 (359)
73 cd08445 PBP2_BenM_CatM_CatR Th 84.4 24 0.00053 30.0 12.4 119 140-269 27-158 (203)
74 TIGR00363 lipoprotein, YaeC fa 84.3 41 0.00089 32.5 16.1 148 118-277 18-201 (258)
75 COG4492 PheB ACT domain-contai 84.1 1.4 3E-05 39.3 3.9 42 306-347 70-112 (150)
76 PRK09959 hybrid sensory histid 84.0 3.6 7.8E-05 46.9 8.3 49 119-169 164-212 (1197)
77 cd04897 ACT_ACR_3 ACT domain-c 83.9 1.5 3.3E-05 34.9 3.8 29 309-337 2-30 (75)
78 cd04869 ACT_GcvR_2 ACT domains 83.7 1.7 3.8E-05 33.4 4.0 34 311-344 2-35 (81)
79 cd08452 PBP2_AlsR The C-termin 83.2 27 0.00059 29.6 12.3 123 139-271 25-158 (197)
80 PRK15007 putative ABC transpor 83.1 3.9 8.4E-05 37.3 6.7 49 119-169 126-174 (243)
81 COG2061 ACT-domain-containing 82.7 1.1 2.5E-05 40.6 2.9 38 308-345 5-43 (170)
82 PF00497 SBP_bac_3: Bacterial 82.5 21 0.00046 31.0 11.0 48 120-169 111-159 (225)
83 PRK07334 threonine dehydratase 82.2 2.3 5.1E-05 43.3 5.4 39 306-344 324-362 (403)
84 smart00062 PBPb Bacterial peri 81.8 15 0.00033 30.8 9.5 48 120-169 107-154 (219)
85 TIGR01096 3A0103s03R lysine-ar 81.6 4.4 9.5E-05 36.9 6.5 49 119-169 131-180 (250)
86 PLN02550 threonine dehydratase 81.1 9.6 0.00021 41.4 9.7 171 162-343 258-450 (591)
87 PRK11151 DNA-binding transcrip 81.1 22 0.00047 33.8 11.3 144 117-270 90-246 (305)
88 PF13740 ACT_6: ACT domain; PD 81.0 2.1 4.6E-05 33.3 3.6 33 313-345 7-39 (76)
89 PRK09224 threonine dehydratase 80.8 13 0.00028 39.4 10.4 36 307-344 327-362 (504)
90 PF03401 TctC: Tripartite tric 79.5 11 0.00024 36.4 8.8 132 114-255 101-261 (274)
91 COG4747 ACT domain-containing 79.5 2.1 4.6E-05 37.5 3.4 29 311-339 6-34 (142)
92 PRK13397 3-deoxy-7-phosphohept 79.4 0.4 8.6E-06 46.5 -1.2 32 60-91 217-248 (250)
93 cd00134 PBPb Bacterial peripla 79.2 6.9 0.00015 33.1 6.5 48 120-169 106-153 (218)
94 PF13379 NMT1_2: NMT1-like fam 79.2 14 0.00031 34.4 9.3 146 116-267 4-180 (252)
95 PRK09959 hybrid sensory histid 78.6 3.5 7.6E-05 47.0 5.8 49 119-169 407-455 (1197)
96 PRK11553 alkanesulfonate trans 78.5 23 0.0005 34.0 10.7 139 116-265 25-183 (314)
97 PRK11589 gcvR glycine cleavage 78.2 2.9 6.4E-05 38.8 4.2 36 310-345 97-132 (190)
98 smart00062 PBPb Bacterial peri 77.9 13 0.00028 31.3 7.8 112 142-269 40-158 (219)
99 cd08486 PBP2_CbnR The C-termin 77.5 39 0.00084 28.9 10.9 139 119-269 2-157 (198)
100 PRK11260 cystine transporter s 77.3 6.4 0.00014 36.8 6.3 48 120-169 150-197 (266)
101 cd04925 ACT_ACR_2 ACT domain-c 77.2 3.4 7.3E-05 32.0 3.6 33 310-342 2-34 (74)
102 PRK11480 tauA taurine transpor 76.8 39 0.00085 32.8 11.9 141 116-266 21-178 (320)
103 cd04891 ACT_AK-LysC-DapG-like_ 76.8 3.7 8E-05 28.8 3.5 31 313-343 6-36 (61)
104 TIGR01098 3A0109s03R phosphate 76.1 7.9 0.00017 35.6 6.4 88 119-209 141-238 (254)
105 cd08453 PBP2_IlvR The C-termin 75.5 48 0.001 27.9 12.0 122 140-270 26-160 (200)
106 cd04913 ACT_AKii-LysC-BS-like_ 74.8 3.4 7.3E-05 30.4 3.0 28 314-341 8-35 (75)
107 PRK11917 bifunctional adhesin/ 74.7 20 0.00044 33.7 9.0 94 119-234 148-245 (259)
108 PRK09495 glnH glutamine ABC tr 74.6 8.4 0.00018 35.5 6.2 48 119-168 131-178 (247)
109 cd04927 ACT_ACR-like_2 Second 74.5 4.1 8.9E-05 31.9 3.5 30 311-340 3-32 (76)
110 cd08411 PBP2_OxyR The C-termin 74.2 51 0.0011 27.6 13.3 123 139-271 26-157 (200)
111 COG0440 IlvH Acetolactate synt 72.6 3 6.5E-05 38.1 2.6 39 308-346 4-42 (163)
112 PRK08673 3-deoxy-7-phosphohept 71.6 0.57 1.2E-05 47.2 -2.5 32 62-93 297-328 (335)
113 TIGR01124 ilvA_2Cterm threonin 71.4 13 0.00029 39.2 7.5 178 153-344 158-359 (499)
114 PRK05198 2-dehydro-3-deoxyphos 71.3 0.61 1.3E-05 45.6 -2.3 29 65-93 232-260 (264)
115 PRK13396 3-deoxy-7-phosphohept 70.9 0.62 1.4E-05 47.3 -2.4 34 60-93 304-337 (352)
116 cd04893 ACT_GcvR_1 ACT domains 70.9 6.7 0.00014 30.6 4.0 33 311-343 4-36 (77)
117 cd04907 ACT_ThrD-I_2 Second of 70.8 9.2 0.0002 30.6 4.8 40 309-349 2-41 (81)
118 COG2716 GcvR Glycine cleavage 70.8 12 0.00027 34.6 6.1 35 309-343 91-127 (176)
119 TIGR03339 phn_lysR aminoethylp 70.7 87 0.0019 28.7 13.0 140 117-268 86-237 (279)
120 PF12727 PBP_like: PBP superfa 70.5 44 0.00096 30.7 9.9 128 145-278 15-165 (193)
121 TIGR01362 KDO8P_synth 3-deoxy- 70.1 0.66 1.4E-05 45.2 -2.3 29 65-93 224-252 (258)
122 cd08446 PBP2_Chlorocatechol Th 69.2 67 0.0015 26.8 12.1 122 139-270 26-158 (198)
123 cd08450 PBP2_HcaR The C-termin 69.1 66 0.0014 26.7 10.8 32 139-170 25-57 (196)
124 cd04932 ACT_AKiii-LysC-EC_1 AC 68.4 6.5 0.00014 30.9 3.4 27 315-341 11-37 (75)
125 cd08437 PBP2_MleR The substrat 67.7 73 0.0016 26.7 10.6 121 139-269 25-156 (198)
126 cd08435 PBP2_GbpR The C-termin 67.4 71 0.0015 26.5 12.7 122 139-270 25-158 (201)
127 PRK12457 2-dehydro-3-deoxyphos 67.4 0.82 1.8E-05 45.1 -2.3 29 65-93 240-268 (281)
128 PRK11063 metQ DL-methionine tr 67.3 1.3E+02 0.0027 29.3 13.1 108 118-235 31-152 (271)
129 PRK09508 leuO leucine transcri 67.3 26 0.00056 33.6 8.0 122 139-271 137-266 (314)
130 cd08462 PBP2_NodD The C-termin 67.0 54 0.0012 27.8 9.2 122 139-271 25-155 (200)
131 cd08420 PBP2_CysL_like C-termi 65.9 58 0.0013 26.9 9.0 121 140-270 26-158 (201)
132 COG2876 AroA 3-deoxy-D-arabino 64.1 1.2 2.5E-05 43.9 -2.0 29 65-93 252-280 (286)
133 PRK10859 membrane-bound lytic 63.9 57 0.0012 34.0 10.3 48 120-169 150-202 (482)
134 cd08412 PBP2_PAO1_like The C-t 63.7 85 0.0018 26.0 11.9 122 139-270 25-154 (198)
135 cd08440 PBP2_LTTR_like_4 TThe 62.6 86 0.0019 25.7 12.3 121 140-270 26-155 (197)
136 PRK06349 homoserine dehydrogen 62.5 12 0.00025 38.7 4.9 37 310-346 350-386 (426)
137 cd08468 PBP2_Pa0477 The C-term 62.1 73 0.0016 27.0 9.2 118 140-272 26-158 (202)
138 cd04935 ACT_AKiii-DAPDC_1 ACT 62.0 7.9 0.00017 30.3 2.8 27 315-341 11-37 (75)
139 cd04914 ACT_AKi-DapG-BS_1 ACT 61.9 9.2 0.0002 29.1 3.1 28 315-343 9-36 (67)
140 COG2107 Predicted periplasmic 61.8 18 0.00039 35.6 5.7 51 119-171 95-145 (272)
141 TIGR02995 ectoine_ehuB ectoine 60.6 19 0.00041 34.0 5.6 49 119-169 144-193 (275)
142 PRK12683 transcriptional regul 60.4 1.4E+02 0.0031 28.6 11.7 144 116-269 91-248 (309)
143 TIGR02079 THD1 threonine dehyd 60.4 13 0.00027 38.2 4.7 37 307-343 324-360 (409)
144 cd08459 PBP2_DntR_NahR_LinR_li 60.4 1E+02 0.0022 25.9 9.9 119 140-271 26-155 (201)
145 PRK12684 transcriptional regul 60.0 1.4E+02 0.0029 28.7 11.5 144 116-270 91-249 (313)
146 PRK12680 transcriptional regul 59.1 1.7E+02 0.0036 28.6 12.1 146 116-270 91-250 (327)
147 PRK10341 DNA-binding transcrip 58.2 1.7E+02 0.0038 27.8 13.1 115 140-270 123-252 (312)
148 TIGR01693 UTase_glnD [Protein- 58.1 13 0.00029 41.6 4.7 40 306-345 777-816 (850)
149 PF00497 SBP_bac_3: Bacterial 57.6 69 0.0015 27.7 8.3 133 125-272 22-166 (225)
150 PLN03033 2-dehydro-3-deoxyphos 57.3 1.6 3.4E-05 43.3 -2.4 32 62-93 240-271 (290)
151 cd08456 PBP2_LysR The C-termin 57.2 1.1E+02 0.0023 25.4 9.2 122 139-270 25-155 (196)
152 COG3830 ACT domain-containing 57.0 12 0.00025 31.2 3.0 28 313-340 8-35 (90)
153 cd04933 ACT_AK1-AT_1 ACT domai 56.8 11 0.00024 30.1 2.8 27 315-341 11-37 (78)
154 cd08443 PBP2_CysB The C-termin 55.8 1.3E+02 0.0028 25.6 12.2 121 139-270 25-156 (198)
155 PRK11242 DNA-binding transcrip 54.9 1.4E+02 0.003 27.9 10.4 146 117-272 90-249 (296)
156 TIGR02122 TRAP_TAXI TRAP trans 54.5 1.9E+02 0.0042 27.3 11.5 56 115-170 27-90 (320)
157 PRK11716 DNA-binding transcrip 54.4 95 0.0021 28.2 9.0 146 116-270 65-223 (269)
158 cd08436 PBP2_LTTR_like_3 The C 53.8 1.2E+02 0.0027 24.8 10.9 32 139-170 25-57 (194)
159 cd08461 PBP2_DntR_like_3 The C 52.9 1E+02 0.0022 25.7 8.4 123 139-272 25-157 (198)
160 PRK10859 membrane-bound lytic 52.4 77 0.0017 33.0 9.0 113 142-270 81-207 (482)
161 cd04934 ACT_AK-Hom3_1 CT domai 52.0 26 0.00056 27.3 4.1 26 316-341 12-37 (73)
162 cd08460 PBP2_DntR_like_1 The C 51.8 32 0.00069 29.2 5.1 121 139-270 25-153 (200)
163 PRK12679 cbl transcriptional r 51.3 1.9E+02 0.0041 27.7 11.0 142 117-269 92-248 (316)
164 cd04928 ACT_TyrKc Uncharacteri 51.1 21 0.00047 27.9 3.5 36 310-345 3-38 (68)
165 cd08444 PBP2_Cbl The C-termina 51.0 1.5E+02 0.0033 25.0 12.2 122 139-270 25-156 (198)
166 PRK12483 threonine dehydratase 50.9 19 0.00042 38.4 4.3 179 153-343 178-378 (521)
167 PRK13011 formyltetrahydrofolat 50.5 28 0.0006 34.3 5.0 35 308-342 7-41 (286)
168 cd08466 PBP2_LeuO The C-termin 50.2 1.5E+02 0.0033 24.7 9.6 123 139-272 25-156 (200)
169 PRK09906 DNA-binding transcrip 50.2 2.2E+02 0.0048 26.6 11.5 122 139-270 115-247 (296)
170 TIGR00719 sda_beta L-serine de 50.1 20 0.00044 33.4 3.9 38 308-345 148-186 (208)
171 cd08415 PBP2_LysR_opines_like 50.1 1.5E+02 0.0032 24.5 11.3 123 138-270 24-155 (196)
172 PRK05007 PII uridylyl-transfer 49.2 19 0.00041 40.8 4.1 32 307-338 807-838 (884)
173 cd00134 PBPb Bacterial peripla 49.2 74 0.0016 26.7 7.0 114 142-271 39-159 (218)
174 PRK11092 bifunctional (p)ppGpp 49.0 46 0.001 36.9 7.0 41 306-346 624-664 (702)
175 PRK09986 DNA-binding transcrip 48.7 2.3E+02 0.0049 26.4 12.1 144 117-270 96-255 (294)
176 COG0317 SpoT Guanosine polypho 48.4 53 0.0011 36.6 7.2 45 305-349 624-668 (701)
177 cd04868 ACT_AK-like ACT domain 48.3 18 0.0004 24.7 2.6 27 317-343 12-38 (60)
178 PF00585 Thr_dehydrat_C: C-ter 48.1 13 0.00028 30.3 2.0 41 306-347 8-48 (91)
179 PF13840 ACT_7: ACT domain ; P 48.0 34 0.00073 25.9 4.1 24 317-340 19-42 (65)
180 TIGR01729 taurine_ABC_bnd taur 47.9 2.5E+02 0.0054 26.6 13.5 135 120-265 1-155 (300)
181 PRK15010 ABC transporter lysin 47.9 56 0.0012 30.3 6.5 49 119-169 133-183 (260)
182 PF09084 NMT1: NMT1/THI5 like; 47.8 2E+02 0.0044 25.5 17.8 104 143-255 23-139 (216)
183 COG0834 HisJ ABC-type amino ac 47.3 32 0.00068 31.4 4.7 48 120-169 147-196 (275)
184 cd08421 PBP2_LTTR_like_1 The C 46.8 1.7E+02 0.0036 24.3 12.9 122 139-270 25-155 (198)
185 TIGR03871 ABC_peri_MoxJ_2 quin 46.5 43 0.00093 30.1 5.4 48 120-169 105-161 (232)
186 cd04922 ACT_AKi-HSDH-ThrA_2 AC 46.3 20 0.00043 26.0 2.6 27 315-341 11-37 (66)
187 cd08451 PBP2_BudR The C-termin 46.1 1.7E+02 0.0037 24.2 13.2 32 139-170 26-58 (199)
188 cd04936 ACT_AKii-LysC-BS-like_ 45.8 23 0.0005 25.1 2.8 28 315-342 10-37 (63)
189 cd04924 ACT_AK-Arch_2 ACT doma 45.7 21 0.00045 25.8 2.6 27 315-341 11-37 (66)
190 PRK10797 glutamate and asparta 45.6 44 0.00096 32.4 5.6 47 120-168 154-204 (302)
191 PRK01759 glnD PII uridylyl-tra 45.3 26 0.00055 39.6 4.4 32 306-337 781-812 (854)
192 TIGR00691 spoT_relA (p)ppGpp s 45.3 28 0.00061 38.4 4.6 39 306-344 608-646 (683)
193 cd04912 ACT_AKiii-LysC-EC-like 44.8 29 0.00064 26.7 3.5 27 315-341 11-37 (75)
194 PRK11482 putative DNA-binding 44.6 3E+02 0.0065 26.6 11.3 144 117-272 116-271 (317)
195 TIGR01361 DAHP_synth_Bsub phos 44.4 4.4 9.6E-05 39.2 -1.5 32 61-92 228-259 (260)
196 COG0725 ModA ABC-type molybdat 44.3 41 0.0009 32.6 5.1 51 120-170 136-194 (258)
197 cd04890 ACT_AK-like_1 ACT doma 44.3 22 0.00049 25.8 2.6 26 316-341 11-36 (62)
198 PRK13398 3-deoxy-7-phosphohept 44.0 4.8 0.0001 39.2 -1.4 34 60-93 229-262 (266)
199 PF03466 LysR_substrate: LysR 44.0 1.9E+02 0.0042 24.2 13.8 115 139-271 31-162 (209)
200 cd08441 PBP2_MetR The C-termin 43.7 1.9E+02 0.0042 24.1 9.4 140 120-271 2-156 (198)
201 PRK03601 transcriptional regul 43.6 2.8E+02 0.0061 25.9 12.3 115 139-271 114-232 (275)
202 KOG2663 Acetolactate synthase, 43.4 34 0.00074 33.8 4.3 35 305-339 74-108 (309)
203 cd08423 PBP2_LTTR_like_6 The C 43.0 1.9E+02 0.0041 23.8 10.7 31 140-170 26-57 (200)
204 PRK05092 PII uridylyl-transfer 42.9 29 0.00064 39.4 4.4 35 308-342 843-877 (931)
205 PRK10872 relA (p)ppGpp synthet 42.7 33 0.00072 38.4 4.6 39 307-345 665-703 (743)
206 cd04919 ACT_AK-Hom3_2 ACT doma 42.4 25 0.00053 25.7 2.6 26 316-341 12-37 (66)
207 cd08457 PBP2_OccR The C-termin 42.3 2E+02 0.0044 24.0 12.3 120 139-268 25-153 (196)
208 cd08416 PBP2_MdcR The C-termin 42.3 2E+02 0.0043 23.9 12.3 123 139-271 25-158 (199)
209 cd08419 PBP2_CbbR_RubisCO_like 41.2 2E+02 0.0044 23.6 15.1 114 140-271 25-155 (197)
210 cd04923 ACT_AK-LysC-DapG-like_ 41.2 27 0.00058 24.8 2.6 27 315-341 10-36 (63)
211 TIGR00070 hisG ATP phosphoribo 41.0 1E+02 0.0022 28.6 6.9 107 152-278 50-171 (182)
212 PRK13010 purU formyltetrahydro 41.0 43 0.00093 33.1 4.7 35 308-342 9-43 (289)
213 PRK11790 D-3-phosphoglycerate 40.7 29 0.00063 35.7 3.6 37 307-343 337-373 (409)
214 cd08438 PBP2_CidR The C-termin 40.5 2.1E+02 0.0045 23.6 12.1 30 140-169 26-56 (197)
215 cd08413 PBP2_CysB_like The C-t 40.5 2.3E+02 0.0049 24.0 12.1 121 139-270 25-156 (198)
216 cd08418 PBP2_TdcA The C-termin 40.2 2.1E+02 0.0046 23.6 10.5 120 140-271 26-156 (201)
217 cd08433 PBP2_Nac The C-teminal 40.2 2.2E+02 0.0047 23.7 11.7 121 140-270 26-155 (198)
218 cd08426 PBP2_LTTR_like_5 The C 40.1 2.2E+02 0.0047 23.6 15.4 121 140-270 26-155 (199)
219 cd04916 ACT_AKiii-YclM-BS_2 AC 39.5 29 0.00063 25.1 2.6 26 315-340 11-36 (66)
220 PF12916 DUF3834: Protein of u 39.2 1.3E+02 0.0029 28.5 7.3 73 117-194 66-143 (201)
221 cd08485 PBP2_ClcR The C-termin 38.2 2.5E+02 0.0054 23.8 13.1 141 120-270 3-158 (198)
222 TIGR02424 TF_pcaQ pca operon t 37.9 3.4E+02 0.0074 25.3 13.6 145 116-270 91-251 (300)
223 cd08427 PBP2_LTTR_like_2 The C 37.7 2.3E+02 0.005 23.3 13.9 116 139-270 25-153 (195)
224 cd08465 PBP2_ToxR The C-termin 37.7 2.5E+02 0.0055 23.7 9.5 117 140-268 26-153 (200)
225 cd04937 ACT_AKi-DapG-BS_2 ACT 37.3 33 0.00072 25.4 2.6 27 315-341 11-37 (64)
226 PRK15437 histidine ABC transpo 37.0 99 0.0021 28.7 6.3 49 119-169 133-183 (259)
227 PRK11139 DNA-binding transcrip 36.3 2.1E+02 0.0045 26.9 8.5 118 140-271 120-246 (297)
228 PRK15010 ABC transporter lysin 35.8 2.8E+02 0.0061 25.6 9.2 129 126-270 50-188 (260)
229 CHL00180 rbcR LysR transcripti 35.4 3.9E+02 0.0085 25.3 13.1 53 117-169 94-151 (305)
230 cd04921 ACT_AKi-HSDH-ThrA-like 35.3 53 0.0011 24.9 3.5 26 315-340 11-36 (80)
231 cd08464 PBP2_DntR_like_2 The C 34.5 2.6E+02 0.0057 23.1 8.1 120 139-271 25-155 (200)
232 PRK12682 transcriptional regul 34.0 4.2E+02 0.009 25.1 14.6 53 117-169 92-149 (309)
233 cd04892 ACT_AK-like_2 ACT doma 33.8 42 0.00091 23.4 2.6 27 315-341 10-36 (65)
234 PRK03059 PII uridylyl-transfer 33.7 50 0.0011 37.4 4.4 32 307-338 785-816 (856)
235 PRK15437 histidine ABC transpo 33.5 2.8E+02 0.0062 25.6 8.8 45 125-170 49-93 (259)
236 TIGR03427 ABC_peri_uca ABC tra 33.4 64 0.0014 32.2 4.7 48 119-169 106-160 (328)
237 PRK10216 DNA-binding transcrip 33.2 3.6E+02 0.0078 25.7 9.7 145 119-270 98-262 (319)
238 PRK03381 PII uridylyl-transfer 33.2 54 0.0012 36.7 4.5 40 308-347 707-746 (774)
239 TIGR01096 3A0103s03R lysine-ar 33.0 3.7E+02 0.0079 24.2 9.3 115 142-272 64-187 (250)
240 TIGR00787 dctP tripartite ATP- 32.8 4.2E+02 0.0091 24.8 12.2 152 124-282 3-198 (257)
241 cd08469 PBP2_PnbR The C-termin 32.7 3.2E+02 0.0069 23.4 10.2 31 140-170 26-57 (221)
242 COG2150 Predicted regulator of 32.5 52 0.0011 30.3 3.5 32 311-342 98-129 (167)
243 TIGR01098 3A0109s03R phosphate 32.5 3.9E+02 0.0084 24.3 15.7 54 117-170 31-93 (254)
244 cd08432 PBP2_GcdR_TrpI_HvrB_Am 32.2 72 0.0016 26.4 4.2 119 140-271 26-152 (194)
245 cd08425 PBP2_CynR The C-termin 32.2 2.9E+02 0.0064 22.8 13.9 121 140-270 27-157 (197)
246 TIGR03427 ABC_peri_uca ABC tra 31.8 5.3E+02 0.011 25.7 16.5 143 142-295 36-193 (328)
247 PF12974 Phosphonate-bd: ABC t 31.6 4.1E+02 0.0088 24.3 12.1 113 143-265 31-165 (243)
248 cd08448 PBP2_LTTR_aromatics_li 31.4 2.9E+02 0.0064 22.6 12.0 31 139-169 25-56 (197)
249 PRK04374 PII uridylyl-transfer 31.4 63 0.0014 36.7 4.7 34 307-340 795-828 (869)
250 PRK13581 D-3-phosphoglycerate 30.9 51 0.0011 35.0 3.7 77 266-342 388-487 (526)
251 KOG4028 Uncharacterized conser 30.4 40 0.00087 30.2 2.4 61 120-183 108-169 (175)
252 PF09084 NMT1: NMT1/THI5 like; 29.0 1.7E+02 0.0037 25.9 6.3 51 119-172 93-150 (216)
253 PRK09224 threonine dehydratase 28.7 68 0.0015 34.0 4.1 36 307-343 422-457 (504)
254 PRK00275 glnD PII uridylyl-tra 28.2 72 0.0016 36.3 4.5 33 307-339 813-845 (895)
255 PRK10837 putative DNA-binding 27.9 4.9E+02 0.011 24.1 11.6 54 116-169 87-145 (290)
256 cd08481 PBP2_GcdR_like The C-t 27.8 1.7E+02 0.0038 24.0 5.8 120 140-272 26-153 (194)
257 TIGR02122 TRAP_TAXI TRAP trans 27.0 97 0.0021 29.3 4.5 49 120-169 142-197 (320)
258 cd08483 PBP2_HvrB The C-termin 26.0 95 0.0021 25.7 3.9 116 140-270 26-149 (190)
259 TIGR01693 UTase_glnD [Protein- 25.1 77 0.0017 35.7 4.0 40 307-346 667-706 (850)
260 PF00072 Response_reg: Respons 23.7 81 0.0018 24.5 2.9 77 218-298 4-81 (112)
261 TIGR01327 PGDH D-3-phosphoglyc 23.5 78 0.0017 33.7 3.4 81 266-346 387-490 (525)
262 PF13379 NMT1_2: NMT1-like fam 23.1 2.2E+02 0.0047 26.4 6.0 50 118-169 120-177 (252)
263 COG3181 Uncharacterized protei 23.0 1.1E+02 0.0024 30.8 4.3 98 120-218 151-265 (319)
264 PRK15421 DNA-binding transcrip 23.0 6.8E+02 0.015 24.0 11.0 142 117-270 88-243 (317)
265 cd08414 PBP2_LTTR_aromatics_li 22.9 4.2E+02 0.0092 21.6 15.2 31 140-170 26-57 (197)
266 cd08430 PBP2_IlvY The C-termin 22.6 4.4E+02 0.0095 21.7 13.4 126 138-272 24-158 (199)
267 PRK11553 alkanesulfonate trans 22.5 1.5E+02 0.0032 28.4 4.9 47 120-169 130-183 (314)
268 cd04915 ACT_AK-Ectoine_2 ACT d 21.4 67 0.0015 24.2 1.9 37 317-353 13-49 (66)
269 PF01634 HisG: ATP phosphoribo 21.3 4.9E+02 0.011 23.6 7.7 110 152-278 4-129 (163)
270 cd04918 ACT_AK1-AT_2 ACT domai 21.2 1.2E+02 0.0026 22.5 3.2 26 315-340 10-35 (65)
271 PRK12595 bifunctional 3-deoxy- 21.1 20 0.00044 36.5 -1.4 32 62-93 322-353 (360)
272 PRK01686 hisG ATP phosphoribos 20.9 2E+02 0.0043 27.4 5.3 142 119-279 3-178 (215)
273 COG2844 GlnD UTP:GlnB (protein 20.8 1.2E+02 0.0026 34.5 4.3 34 306-339 789-822 (867)
No 1
>PLN02317 arogenate dehydratase
Probab=100.00 E-value=1.1e-84 Score=647.50 Aligned_cols=322 Identities=72% Similarity=1.085 Sum_probs=297.9
Q ss_pred ccCCccccccccccchhhhhhhhccccccccccCCCCCCCcccchhhhhcccccccccccccCCcccccccccccccccc
Q 018090 28 RCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDDRPYTPDVQSSEANERSQDSQSSGFHKDLNLLPTLVYGQIAEPLSI 107 (361)
Q Consensus 28 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~d~~~lp~~~~~~~~~~~~~ 107 (361)
.+..+|.. +.+.|+|+|.. +.+ +...+..+..+..+.+..+++.......+...+++|...+| +|++.
T Consensus 15 ~~~~~~~~-~~~~~~~~~~~-~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~ 82 (382)
T PLN02317 15 SFPARWAS-RRAAWQSSCAI-LSS--KVRSPEGDAPPSRPAVESSGGAGLVVATQSVSFHRDLSGLP--------RPLSI 82 (382)
T ss_pred ccCCCccc-cchhhhhhcch-hhc--ccccccccccccccccccccccccccccccccccccccccc--------ccccH
Confidence 34444544 33567766654 445 56778888888889999999999999999999999998888 99999
Q ss_pred cccCCCCCCCCccEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhc
Q 018090 108 MELSSSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLR 187 (361)
Q Consensus 108 ~~~~~~~~~~~~~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~ 187 (361)
.+++..++.+.++|||||||+|||||+||+++|++.+++||++|++||++|++|++||||||||||++|+|++|||+|.+
T Consensus 83 ~~~~~~~~~~~~~rVaylGp~GtfSe~AA~~~f~~~e~vp~~sf~~vf~AVe~g~ad~gVvPIENS~~GsV~~t~DlL~~ 162 (382)
T PLN02317 83 TDLSPSPMHGSKLRVAYQGVPGAYSEAAARKAYPNCEAVPCEQFEAAFQAVELWLADRAVLPIENSLGGSIHRNYDLLLR 162 (382)
T ss_pred hhhcccccCCCCcEEEEECCCcCHHHHHHHHhhCcCceeecCCHHHHHHHHHCCCCCEEEEEEeccCccchHHHHHHHhc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeEEEEEEEEeeeeEeeeCCCCCccCccEEEechHHHHHHHHHHHhcCCeEEeccCHHHHHHHHHhcCCCCeEEecCHh
Q 018090 188 HRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQ 267 (361)
Q Consensus 188 ~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik~VySHPqALaQC~~fL~~~~~~~i~~~STA~AA~~va~~~~~~~AAIas~~ 267 (361)
++++|+||+++||+|||++++|+++++|++||||||||+||++||++++++++++.|||+||++|++.+.++.|||||+.
T Consensus 163 ~~l~IvgEv~l~I~h~Ll~~~g~~l~~Ik~VySHPQALaQC~~~L~~~~~~~~~~~sTA~AA~~Va~~~~~~~AAIaS~~ 242 (382)
T PLN02317 163 HRLHIVGEVQLPVHHCLLALPGVRKEELKRVISHPQALAQCENTLTKLGVVREAVDDTAGAAKMVAANGLRDTAAIASAR 242 (382)
T ss_pred CCCEEEEEEEEEeeeEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHcCCeEEEcCCHHHHHHHHHhcCCCCceeecCHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999987777899999999
Q ss_pred hHHHcCCceeeccccCCCCCceEEEEEeeCCCCCCCCCCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCC
Q 018090 268 AAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347 (361)
Q Consensus 268 AA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~ 347 (361)
||++|||+||+++|||+++|+|||+||+|++..+..++.+||||+|+++|+||+|+++|++|+.+|||||||||||.+++
T Consensus 243 aA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KTSivfsl~~~pG~L~k~L~~Fa~~~INLtkIESRP~~~~ 322 (382)
T PLN02317 243 AAELYGLDILAEGIQDDSDNVTRFLMLAREPIIPRTDRPFKTSIVFSLEEGPGVLFKALAVFALRDINLTKIESRPQRKR 322 (382)
T ss_pred HHHHcCCcchhhhhcCCCCCeeeEEEEecCCcCCCCCCCccEEEEEEcCCCCchHHHHHHHHHHCCCCEEEEEeeecCCC
Confidence 99999999999999999999999999999976555556679999999999999999999999999999999999999999
Q ss_pred CCeeeecCCCCCCC
Q 018090 348 PLRVVDDSNKGSAK 361 (361)
Q Consensus 348 pw~y~~~~~~~~~~ 361 (361)
|-+.+||+|+|++|
T Consensus 323 ~~~~~~~~~~~~~~ 336 (382)
T PLN02317 323 PLRVVDDSNSGTAK 336 (382)
T ss_pred Cccccccccccccc
Confidence 99999999999875
No 2
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=1.4e-79 Score=588.55 Aligned_cols=233 Identities=49% Similarity=0.725 Sum_probs=221.4
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCCC-CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEE
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYPK-CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQ 197 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~~-~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~ 197 (361)
.++|+||||+|||||+||+++|++ .+..||+||+|||++|++|++||||||||||++|+|++|+|+|...+|+|+||+.
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 478999999999999999999998 8999999999999999999999999999999999999999999999999999999
Q ss_pred EeeeeEeeeCCCCCccCccEEEechHHHHHHHHHHHhc--CCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCc
Q 018090 198 LVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLD 275 (361)
Q Consensus 198 lpI~h~Lla~~g~~l~~Ik~VySHPqALaQC~~fL~~~--~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~ 275 (361)
|||+|||++++|.++++|++|||||||++||++||+++ ++++++++|||+||+++++..+...|||||+.||++|||+
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 99999999998899999999999999999999999997 5999999999999999999878899999999999999999
Q ss_pred eeeccccCCCCCceEEEEEeeC-CCCCCCCCCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 276 ILAEKIQDDDDNVTRFLILARE-PIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 276 iLa~~IqD~~~N~TRFlvl~r~-~~~~~~~~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
||++||||.++|+|||+||+|+ +... .+...||||+|+++|+||+|+++|++|++||||||||||||+++++|+|+
T Consensus 162 il~~~I~D~~~N~TRF~vl~r~~~~~~-~~~~~kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~~~~~Y~ 238 (279)
T COG0077 162 ILAENIEDEPNNRTRFLVLSRRKPPSV-SDGPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTGLGEYL 238 (279)
T ss_pred hHhhcccCCCCCeEEEEEEeccCCCCc-CCCCceEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCCCCeeEE
Confidence 9999999999999999999985 2211 12457999999999999999999999999999999999999999999986
No 3
>PRK11899 prephenate dehydratase; Provisional
Probab=100.00 E-value=1.9e-78 Score=583.44 Aligned_cols=235 Identities=46% Similarity=0.674 Sum_probs=223.4
Q ss_pred CccEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEE
Q 018090 118 TKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQ 197 (361)
Q Consensus 118 ~~~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~ 197 (361)
++++||||||+|||||+||+++|++.+++||.||++||++|++|++||||||||||++|+|.+|||+|.+++++|+||+.
T Consensus 3 ~~~kvaylGp~GsfS~~Aa~~~~~~~~~v~~~s~~~vf~av~~g~~d~gVvPiENS~~G~V~~~~Dll~~~~l~Iv~E~~ 82 (279)
T PRK11899 3 KTNRIAFQGEPGANSHLACRDAFPDMEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVADIHHLLPESGLHIVGEYF 82 (279)
T ss_pred CCCEEEEECCCCCHHHHHHHHhcCcCceeecCCHHHHHHHHHCCCCCEEEEEeeccCCccHHHHHHHHhcCCCEEEEEEE
Confidence 45789999999999999999999988999999999999999999999999999999999999999999999999999999
Q ss_pred EeeeeEeeeCCCCCccCccEEEechHHHHHHHHHHHhcCCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCcee
Q 018090 198 LVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDIL 277 (361)
Q Consensus 198 lpI~h~Lla~~g~~l~~Ik~VySHPqALaQC~~fL~~~~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iL 277 (361)
+||+|||++.+|.++++|++||||||||+||++||++++++.+++.|||+||++|++.++++.|||||+.||++|||+||
T Consensus 83 l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAIas~~aa~~YgL~il 162 (279)
T PRK11899 83 LPIRHQLMALPGATLEEIKTVHSHPHALGQCRKIIRALGLKPVVAADTAGAARLVAERGDPSMAALASRLAAELYGLDIL 162 (279)
T ss_pred EEeeEEEecCCCCCHHHCeEEEEeHHHHHHHHHHHHHcCCeEEEcCChHHHHHHHHhcCCCCeeEeCCHHHHHHcCCcch
Confidence 99999999999999999999999999999999999999999999999999999999877778999999999999999999
Q ss_pred eccccCCCCCceEEEEEeeCCCC-CCCCCCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 278 AEKIQDDDDNVTRFLILAREPII-AGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 278 a~~IqD~~~N~TRFlvl~r~~~~-~~~~~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
+++|||+++|+|||+||++++.. +.....+||||+|+++|+||+|+++|++|+++|||||||||||+++++|+|+
T Consensus 163 ~~~IqD~~~N~TRF~vi~~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~~~Y~ 238 (279)
T PRK11899 163 AENIEDADHNTTRFVVLSREADWAARGDGPIVTTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSFTATQ 238 (279)
T ss_pred hhcccCCcccceeEEEEecCCCCCCCCCCCceEEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCCceEE
Confidence 99999999999999999998642 2223356999999999999999999999999999999999999999999997
No 4
>KOG2797 consensus Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=7.2e-76 Score=562.10 Aligned_cols=324 Identities=58% Similarity=0.907 Sum_probs=288.7
Q ss_pred CCccccCCCCccCCCCCCCCCCccCCccccccccccchhhhhhhhccccccccccCCCCCCCcccchhhhhccccccccc
Q 018090 6 NPVWGCAKTPHFHKGLPDLVPNRCGFGLDLRVLNKWECTCVGVLAQTHRAITPVEDDRPYTPDVQSSEANERSQDSQSSG 85 (361)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~ 85 (361)
.++|.++.+.++.-+.. +.-.|+-| +.|+|.|.... |+.+.+|.... .--.-..++. .++-+|.++
T Consensus 3 ~~~~~~~~~~~~~~~~~--~~~~~~~~------~~w~~s~~~~~----~~v~~~e~~~~-~~~~~~~~~~-~~~~~~~~~ 68 (377)
T KOG2797|consen 3 FPSSVPPATTSHAAPKR--VLVECSYR------SDWQSSCAILS----SKVTSQENSES-MKVNGHVNGY-NTQLVQAKK 68 (377)
T ss_pred CccCCCCcccccccccc--eeeccCcc------cccccchHHHH----HHHHhhhcccc-cceecccchh-hhhhhhhhh
Confidence 67899987755543322 22334322 79999998754 44666666542 1111122221 277778888
Q ss_pred ccccCCcccccccccccccccccccCCCCCCCCccEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCe
Q 018090 86 FHKDLNLLPTLVYGQIAEPLSIMELSSSPDDGTKVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDK 165 (361)
Q Consensus 86 ~~~d~~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~ 165 (361)
.++| | +|+...+++++++.+...||+|||++|+|||.||.+.|++++.+||+.|+.+|+||+.+.+||
T Consensus 69 ~~~~----~--------~pl~~~~l~psp~~~s~lRva~qg~pgaysesaa~ka~pn~~avpc~~f~~afqave~w~vD~ 136 (377)
T KOG2797|consen 69 VRKA----P--------QPLTSTDLSPSPMHGSTLRVAYQGVPGAYSESAALKAYPNCEAVPCDQFEAAFQAVELWIVDY 136 (377)
T ss_pred hhcC----C--------CcchhhhcccCCCCCceEEEEeecCCchhhhhhhhhhcCCcccccHhHHHHHHHHHHHhhccc
Confidence 8888 3 899999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCccEEEechHHHHHHHHHHHhcC--CeEEecc
Q 018090 166 AVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNLG--IVRISAD 243 (361)
Q Consensus 166 gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik~VySHPqALaQC~~fL~~~~--~~~i~~~ 243 (361)
+|||||||+.|+|+++||||++++++|+||+++||+|||++++|+..+++++|.||||||+||+.||++++ +.++.++
T Consensus 137 AVLPiENS~gGsIhrnYDLLlrh~lhiVgEv~vPvhHCLi~~~gv~~e~~~~VlSHPQal~Qce~~L~~l~~~~~r~a~~ 216 (377)
T KOG2797|consen 137 AVLPIENSTGGSIHRNYDLLLRHRLHIVGEVQVPVHHCLIALPGVRKEEVVRVLSHPQALGQCECSLTKLGPNAAREAVS 216 (377)
T ss_pred eeeeeeccCCceeeechHHHhhcchheeeEEecceeeeEecCCCCChhheeeeecCcHHHHHHHHHHHhcccceeeeecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999975 8999999
Q ss_pred CHHHHHHHHHhcCCCCeEEecCHhhHHHcCCceeeccccCCCCCceEEEEEeeCCCCCCCCCCceEEEEEEecCCcchHH
Q 018090 244 DTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLF 323 (361)
Q Consensus 244 STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KtSi~f~~~~~PGaL~ 323 (361)
|||+||+.++.++..+++||+|+.||++|||+||+++|||+.+|.|||++|.|++.+|..++..||||+|...+.||+|+
T Consensus 217 dTa~Aa~~~s~~~~~d~~AIASe~aA~ly~l~Il~~~IqDd~~NvTRFLmLar~p~ip~t~rl~ktsivf~~~~gp~vLf 296 (377)
T KOG2797|consen 217 DTAGAAEQISASNTADTAAIASERAAELYGLNILEKNIQDDLGNVTRFLMLAREPIIPDTDRLFKTSIVFFREKGPGVLF 296 (377)
T ss_pred chHHHHHHHHhcccccHHHHHHHHHHHHhcchhhhhhcccccCCeeEEEEEeccCCCCCCCccceeeEEEEeecCCchHH
Confidence 99999999999888899999999999999999999999999999999999999999999889999999999999999999
Q ss_pred HHHHHHHHCCccccceeeecCCCCCCeeeecC
Q 018090 324 KALAVFALRDINLTKIESRPQRKRPLRVVDDS 355 (361)
Q Consensus 324 ~iL~~Fa~~~INLtkIESRP~~~~pw~y~~~~ 355 (361)
++|++|+.|+||||||||||....|.|.|||+
T Consensus 297 kvl~vfa~r~inltkIesRP~h~~p~r~v~~~ 328 (377)
T KOG2797|consen 297 KVLSVFAFRSINLTKIESRPFHNRPLRVVDDS 328 (377)
T ss_pred HHHHHHHhhhceeeeeecccccCCCccccccc
Confidence 99999999999999999999999999999985
No 5
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=100.00 E-value=5.2e-73 Score=567.02 Aligned_cols=235 Identities=34% Similarity=0.539 Sum_probs=219.7
Q ss_pred CccEEEEeCCCCcHHHHHHHHHCCC----CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEE
Q 018090 118 TKVRVAYQGLPGAYSEAAARKAYPK----CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIV 193 (361)
Q Consensus 118 ~~~rIAyLGP~GTySe~AA~~~f~~----~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Iv 193 (361)
..++||||||+|||||+||+++|+. ...+||+||++||++|++|++||||||||||++|+|.+|||+|.+++++|+
T Consensus 102 ~~~~va~lGp~GtfSh~Aa~~~~~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~DlL~~~~l~I~ 181 (386)
T PRK10622 102 HSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVLPIENTSSGAINDVYDLLQHTSLSIV 181 (386)
T ss_pred ccceEEEECCCCcHHHHHHHHhhccccccccccCCCCHHHHHHHHHCCCCCEEEEEEecCCceehHHHHHHHhcCCCEEE
Confidence 4578999999999999999998753 234589999999999999999999999999999999999999999999999
Q ss_pred EEEEEeeeeEeeeCCCCCccCccEEEechHHHHHHHHHHHhc-CCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHc
Q 018090 194 GEVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL-GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (361)
Q Consensus 194 gEi~lpI~h~Lla~~g~~l~~Ik~VySHPqALaQC~~fL~~~-~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~Y 272 (361)
||+.+||+|||++++|.++++|++||||||||+||++||+++ +++.++++|||+||++|++.++++.|||||+.||++|
T Consensus 182 ~E~~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~aa~~y 261 (386)
T PRK10622 182 GEMTLPIDHCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRYPHWKIEYTESTAAAMEKVAQANSPHVAALGSEAGGALY 261 (386)
T ss_pred EEEEEEEEEEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHCCCceEEEcCChHHHHHHHHhcCCCCEEEECCHHHHHHc
Confidence 999999999999999999999999999999999999999997 6999999999999999998877788999999999999
Q ss_pred CCceeeccccCCCCCceEEEEEeeCCCCCCCCCCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 273 GLDILAEKIQDDDDNVTRFLILAREPIIAGTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 273 gL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
||+||+++|||.++|+|||+||++++..+.....+||||+|.++|+||+|+++|++|+.+|||||||||||+++++|+|+
T Consensus 262 gL~vl~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~~L~~Fa~~giNLtkIeSRP~~~~~~~Y~ 341 (386)
T PRK10622 262 GLQVLERNLANQQQNITRFIVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTKLESRPIHGNPWEEM 341 (386)
T ss_pred CCcChhhcCcCCccccceEEEEecCCCCCCCCCCCcEEEEEEcCCCCcHHHHHHHHHHHcCCCeeEEEeeecCCCCceEE
Confidence 99999999999999999999999986433323347999999999999999999999999999999999999999999997
No 6
>PRK11898 prephenate dehydratase; Provisional
Probab=100.00 E-value=4.3e-72 Score=540.03 Aligned_cols=233 Identities=45% Similarity=0.604 Sum_probs=217.5
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCCC---CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcC-CeEEEE
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYPK---CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRH-RLHIVG 194 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~~---~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~-~L~Ivg 194 (361)
+++||||||+|||||+||.++|++ .++++|+||++||++|++|++||||||||||++|+|.+|||+|.++ +++|+|
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 468999999999999999999976 7999999999999999999999999999999999999999999875 899999
Q ss_pred EEEEeeeeEeeeCCCCCccCccEEEechHHHHHHHHHHHhc--CCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHc
Q 018090 195 EVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (361)
Q Consensus 195 Ei~lpI~h~Lla~~g~~l~~Ik~VySHPqALaQC~~fL~~~--~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~Y 272 (361)
|+.+||+|||++++|.. ++|++||||||||+||++||+++ +++.+.++|||+||+++++++..+.|||+|+.||++|
T Consensus 81 E~~l~I~~~L~~~~~~~-~~i~~V~SHpqal~QC~~~l~~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y 159 (283)
T PRK11898 81 EIVLPIAQHLLVHPGHA-AKIRTVYSHPQALAQCRKWLAEHLPGAELEPANSTAAAAQYVAEHPDEPIAAIASELAAELY 159 (283)
T ss_pred EEEeeeeEEEeCCCCCh-hcCeEEEEeHHHHHHHHHHHHhcCCCCEEEEcCchHHHHHHHhcCCCCCeEEECCHHHHHHc
Confidence 99999999999999866 99999999999999999999987 6999999999999999998776678999999999999
Q ss_pred CCceeeccccCCCCCceEEEEEeeCCC-CCCCCCCceEEEEEEecC-CcchHHHHHHHHHHCCccccceeeecCCCCCCe
Q 018090 273 GLDILAEKIQDDDDNVTRFLILAREPI-IAGTDRPYKTSIVFTLEE-GPGMLFKALAVFALRDINLTKIESRPQRKRPLR 350 (361)
Q Consensus 273 gL~iLa~~IqD~~~N~TRFlvl~r~~~-~~~~~~~~KtSi~f~~~~-~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~ 350 (361)
||+||++||||.++|+|||+||++++. .+.....+||||+|+++| +||+|+++|++|+++|||||+|||||.++++|+
T Consensus 160 gL~il~~~I~d~~~N~TRF~vi~~~~~~~~~~~~~~ktslif~l~~~~pGsL~~~L~~F~~~~INLt~IeSRP~~~~~~~ 239 (283)
T PRK11898 160 GLEILAEDIQDYPNNRTRFWLLGRKKPPPPLRTGGDKTSLVLTLPNNLPGALYKALSEFAWRGINLTRIESRPTKTGLGT 239 (283)
T ss_pred CCcEehhcCCCCCccceEEEEEEcCcccCCCCCCCCeEEEEEEeCCCCccHHHHHHHHHHHCCCCeeeEecccCCCCCcc
Confidence 999999999999999999999999864 222345679999999986 599999999999999999999999999999998
Q ss_pred ee
Q 018090 351 VV 352 (361)
Q Consensus 351 y~ 352 (361)
|.
T Consensus 240 y~ 241 (283)
T PRK11898 240 YF 241 (283)
T ss_pred EE
Confidence 75
No 7
>PF00800 PDT: Prephenate dehydratase Caution this is only a partial structure.; InterPro: IPR001086 Prephenate dehydratase (4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate to phenylpyruvate. In microorganisms it is part of the terminal pathway of phenylalanine biosynthesis. In some bacteria such as Escherichia coli PDT is part of a bifunctional enzyme (P-protein) that also catalyses the transformation of chorismate into prephenate (chorismate mutase, IPR002701 from INTERPRO, 5.4.99.5 from EC) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional PDT aligns well with the C-terminal part of P-proteins [].; GO: 0004664 prephenate dehydratase activity, 0009094 L-phenylalanine biosynthetic process; PDB: 3MWB_B 2QMX_A 2QMW_A 3LUY_A.
Probab=100.00 E-value=1.6e-56 Score=405.26 Aligned_cols=177 Identities=48% Similarity=0.768 Sum_probs=164.4
Q ss_pred EEEeCCCCcHHHHHHHHHC--CCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEe
Q 018090 122 VAYQGLPGAYSEAAARKAY--PKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLV 199 (361)
Q Consensus 122 IAyLGP~GTySe~AA~~~f--~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lp 199 (361)
||||||+|||||+||++|| ++.++++|+||++||++|++|++||||||||||++|+|.+|+|+|.+.++.|+||+.+|
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 8999999999999999999 57899999999999999999999999999999999999999999999899999999999
Q ss_pred eeeEeeeCCCCCccCccEEEechHHHHHHHHHHHhc--CCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCcee
Q 018090 200 VNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDIL 277 (361)
Q Consensus 200 I~h~Lla~~g~~l~~Ik~VySHPqALaQC~~fL~~~--~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iL 277 (361)
|+|||+++++.++++|++|||||||++||++||+++ +++++.+.||++||++|+..+.++.|||+|+.||++|||+||
T Consensus 81 i~~~L~~~~~~~l~~i~~V~SHp~al~Qc~~~l~~~~p~~~~~~~~Sta~Aa~~v~~~~~~~~aAI~s~~aa~~y~L~il 160 (181)
T PF00800_consen 81 IHHCLLAKPGTSLSDIKTVYSHPQALAQCREFLEKHLPGAEIVEASSTAEAAEKVAASEGPGDAAIASEEAAELYGLEIL 160 (181)
T ss_dssp --EEEEECTT--GGG-SEEEEEHHHHHHTHHHHHHT-TTSEEEEESSHHHHHHHCCCCTBTTEEEEEECCHHHHTTEEEE
T ss_pred cccEEeccCCCchhcceEEEEchHHHHHHHHHHHhcCCceEEEeCCCHHHHHHHHHhccCCCeEEECCHHHHHHcCccCh
Confidence 999999999999999999999999999999999997 699999999999999988777788999999999999999999
Q ss_pred eccccCCCCCceEEEEEeeCC
Q 018090 278 AEKIQDDDDNVTRFLILAREP 298 (361)
Q Consensus 278 a~~IqD~~~N~TRFlvl~r~~ 298 (361)
+++|||+++|+|||+||++++
T Consensus 161 ~~~I~d~~~N~TRF~vi~~~~ 181 (181)
T PF00800_consen 161 ARNIQDNPNNYTRFLVIGKEP 181 (181)
T ss_dssp ECS-SSSTT-EEEEEEEECCT
T ss_pred hhcCCCCCCCeEeEEEEecCC
Confidence 999999999999999999874
No 8
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=99.51 E-value=1.6e-14 Score=113.20 Aligned_cols=44 Identities=43% Similarity=0.623 Sum_probs=42.7
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
|||+|+++|+||+|+++|+.|+.+|||||+|||||.++++|+|.
T Consensus 1 tsl~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~ 44 (74)
T cd04904 1 TSLIFSLKEEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYE 44 (74)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEE
Confidence 68999999999999999999999999999999999999999986
No 9
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.48 E-value=5e-14 Score=115.31 Aligned_cols=48 Identities=42% Similarity=0.549 Sum_probs=45.6
Q ss_pred CCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 305 RPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 305 ~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
..+||||+|+++|+||+|+++|++|+++||||++|||||.++++|+|.
T Consensus 11 ~~~ktslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~ 58 (90)
T cd04931 11 KNGVISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYE 58 (90)
T ss_pred CCCcEEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEE
Confidence 456899999999999999999999999999999999999999999876
No 10
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.42 E-value=1.8e-13 Score=116.75 Aligned_cols=47 Identities=34% Similarity=0.542 Sum_probs=44.6
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
.+||||+|+++|+||+|+++|++|+.+|||||+|||||+++.+|+|.
T Consensus 39 ~~ktSlifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~~~~~eY~ 85 (115)
T cd04930 39 PQKATLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSRKEGGDLE 85 (115)
T ss_pred cccEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCCCCCceEE
Confidence 35999999999999999999999999999999999999999999875
No 11
>PRK06034 hypothetical protein; Provisional
Probab=99.42 E-value=4.1e-14 Score=136.85 Aligned_cols=117 Identities=15% Similarity=0.075 Sum_probs=89.2
Q ss_pred CCCCCcccchhhhhcccccccccccccCCcccccccccccccccccccCCCCCCCCccEE-EEeCCCCcHHHHHHHHHCC
Q 018090 63 RPYTPDVQSSEANERSQDSQSSGFHKDLNLLPTLVYGQIAEPLSIMELSSSPDDGTKVRV-AYQGLPGAYSEAAARKAYP 141 (361)
Q Consensus 63 ~~~~p~~~~~~~~~~~~~~~~~~~~~d~~~lp~~~~~~~~~~~~~~~~~~~~~~~~~~rI-AyLGP~GTySe~AA~~~f~ 141 (361)
.-|+|+++.+ ..+++.....+.|..|. + +.||...|+.|+..+...+| +||||+|||||+||++||+
T Consensus 50 pv~dP~RE~e-vl~rl~~~~~g~L~~~~--i---------e~Ifr~Iis~Sr~lQ~~~~V~a~lG~~gs~s~~AA~~~FG 117 (279)
T PRK06034 50 SAFRPGREAD-MMRRLVSRHRGILPLDT--V---------ESIWRVIIATFTYVQAPFSVHADGSGGEAAMRDSARFHFG 117 (279)
T ss_pred CccChHHHHH-HHHHHHHhccCCCCHHH--H---------HHHHHHHHHHHHHhcCCceEEEEeCCccHHHHHHHHHHhc
Confidence 4577887655 44555444434444333 3 67888899999888888999 9999999999999999998
Q ss_pred C-CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHh-cCCeEEEEE
Q 018090 142 K-CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL-RHRLHIVGE 195 (361)
Q Consensus 142 ~-~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~-~~~L~IvgE 195 (361)
. .++++|.||++||++|++|++|||||||+++ . ..=+-.|. ....+|+.-
T Consensus 118 ~s~~~~~~~s~~dVf~AV~~g~adyGVVPI~~~-~---~~WW~~L~~~~~~~iiar 169 (279)
T PRK06034 118 FTVPYVPHFSAQAVVEAVARSKGDLGLVSLTSS-D---TPWWGRLEAEGAPKIIAR 169 (279)
T ss_pred cccCCccCCCHHHHHHHHHcCCCCEEEEECCCC-C---CcHHHHhccCCCCeEEEe
Confidence 4 6889999999999999999999999999544 2 34455454 344777654
No 12
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.40 E-value=2.5e-13 Score=107.28 Aligned_cols=44 Identities=39% Similarity=0.545 Sum_probs=42.4
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
|||+|+++|+||+|+++|++|+++||||++|||||.++.+|+|.
T Consensus 1 tsl~~~l~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~ 44 (74)
T cd04929 1 TSVIFSLKNEVGGLAKALKLFQELGINVVHIESRKSKRRSSEFE 44 (74)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEE
Confidence 68999999999999999999999999999999999999999975
No 13
>cd04880 ACT_AAAH-PDT-like ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. Eukaryotic AAAHs have an N-terminal ACT (regulatory) domain, a middle catalytic domain and a C-terminal domain which is responsible for the oligomeric state of the enzyme forming a domain-swapped tetrameric coiled-coil. The PAH, TH, and TPH enzymes contain highly conserved catalytic domains but distinct N-terminal ACT domains and differ in their mech
Probab=99.17 E-value=2.9e-11 Score=93.94 Aligned_cols=43 Identities=60% Similarity=0.792 Sum_probs=41.0
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
|++|+++|+||+|+++|+.|+++|+||++|||||.++.+|+|.
T Consensus 1 sl~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~ 43 (75)
T cd04880 1 SLVFSLKNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYE 43 (75)
T ss_pred CEEEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEE
Confidence 5889999999999999999999999999999999999999875
No 14
>TIGR01268 Phe4hydrox_tetr phenylalanine-4-hydroxylase, tetrameric form. The member of this family from Drosophila has been described as having both phenylalanine-4-hydroxylase and tryptophan 5-monoxygenase activity (PubMed:1371286). However, a Drosophila member of the tryptophan 5-monoxygenase clade has subsequently been discovered.
Probab=99.03 E-value=2.1e-10 Score=117.01 Aligned_cols=46 Identities=43% Similarity=0.684 Sum_probs=44.6
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
+||||+|+++|+||+|+++|++|+.+||||++|||||+++++|+|.
T Consensus 15 ~KTSLiFsL~d~pGaL~~vL~vFa~~gINLthIESRPsk~~~~eY~ 60 (436)
T TIGR01268 15 AKTSLIFSLKEEAGALAETLKLFQAHDVNLTHIESRPSKTHPGEYE 60 (436)
T ss_pred CeEEEEEEcCCCCcHHHHHHHHHHHCCCCeeEEecccCCCCCccEE
Confidence 5999999999999999999999999999999999999999999985
No 15
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=98.98 E-value=7.6e-10 Score=87.27 Aligned_cols=45 Identities=60% Similarity=0.820 Sum_probs=42.8
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
|+|+.|.++|+||+|+++|+.|+++||||++|+|||.+...|.|+
T Consensus 1 ~~sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~ 45 (80)
T cd04905 1 KTSIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYV 45 (80)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEE
Confidence 589999999999999999999999999999999999999999875
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=98.97 E-value=6.2e-10 Score=114.13 Aligned_cols=47 Identities=34% Similarity=0.487 Sum_probs=45.0
Q ss_pred CCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCe-e
Q 018090 305 RPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLR-V 351 (361)
Q Consensus 305 ~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~-y 351 (361)
+..||||+|+++|+||+|+++|++|+.+||||++|||||+++++|+ |
T Consensus 28 ~~~ktSLIFsL~d~pGaL~~vL~vFa~~gINLThIESRPsk~~~~e~Y 75 (464)
T TIGR01270 28 GVQRLSIIFSLSNVVGDLSKAIAIFQDRHINILHLESRDSKDGTSKTM 75 (464)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHCCCCEEEEECCcCCCCCCccE
Confidence 4579999999999999999999999999999999999999999999 5
No 17
>PRK08818 prephenate dehydrogenase; Provisional
Probab=98.19 E-value=1.5e-06 Score=87.73 Aligned_cols=44 Identities=27% Similarity=0.354 Sum_probs=41.3
Q ss_pred ceEEEEEEec-CCcchHHHHHHHHHHCCccccceeeecCCCCCCeee
Q 018090 307 YKTSIVFTLE-EGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVV 352 (361)
Q Consensus 307 ~KtSi~f~~~-~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~ 352 (361)
.-++|+|.++ |+||+|+++|++|+++|||||+||| .+.++|+|+
T Consensus 294 ~~~~l~~~v~~d~pG~L~~vl~~la~~~INit~Ies--~~~r~~~y~ 338 (370)
T PRK08818 294 EPLTLSVYLPEDRPGSLRTLLHVFEQHGVNLSSIHS--SRTPAGELH 338 (370)
T ss_pred cceEEEEECCCCCCChHHHHHHHHHHcCcccceEEE--ecccCceEE
Confidence 4689999997 9999999999999999999999999 999999975
No 18
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=97.60 E-value=0.00011 Score=54.14 Aligned_cols=43 Identities=19% Similarity=0.285 Sum_probs=37.8
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCee
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRV 351 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y 351 (361)
+.|.|.++|+||.|.++++.|+++|||+..+++++.+.+.|.+
T Consensus 1 ~~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~ 43 (66)
T PF01842_consen 1 YRVRVIVPDRPGILADVTEILADHGINIDSISQSSDKDGVGIV 43 (66)
T ss_dssp EEEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEE
T ss_pred CEEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEE
Confidence 4677888999999999999999999999999999998864333
No 19
>TIGR01269 Tyr_3_monoox tyrosine 3-monooxygenase, tetrameric. This model describes tyrosine 3-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tryptophan 5-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=97.18 E-value=0.00052 Score=70.73 Aligned_cols=47 Identities=19% Similarity=0.246 Sum_probs=39.5
Q ss_pred eEEEEEEecCC-cchHHHHHHHHHHCCccccceeeecCCCCC-----Ceeeec
Q 018090 308 KTSIVFTLEEG-PGMLFKALAVFALRDINLTKIESRPQRKRP-----LRVVDD 354 (361)
Q Consensus 308 KtSi~f~~~~~-PGaL~~iL~~Fa~~~INLtkIESRP~~~~p-----w~y~~~ 354 (361)
.++++|++.++ +|+|.++|++|..++|||+.|||||.+... .+++.|
T Consensus 37 ~~~~~~~~~~~~~g~L~~~l~~f~~~~inl~hiEsr~~~~~~~~~~~~~~~v~ 89 (457)
T TIGR01269 37 MQNNQFYIRTKEISSLHRILKYIETFKLNLVHFETRPTRTLSNADVDYSCLIT 89 (457)
T ss_pred ceeEEEEeccCcchhHHHHHHHHHHcCCcEEEeecCCccccCCCCCceEEEEE
Confidence 57788888744 999999999999999999999999987554 566554
No 20
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.87 E-value=0.0017 Score=48.03 Aligned_cols=34 Identities=29% Similarity=0.344 Sum_probs=31.4
Q ss_pred EEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 312 ~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
.+.++|+||.|.++++.|+..|+|+++|.+++.+
T Consensus 2 ~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~ 35 (73)
T cd04886 2 RVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAF 35 (73)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEEEEEEEecc
Confidence 4678999999999999999999999999999875
No 21
>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=96.46 E-value=0.0046 Score=46.76 Aligned_cols=37 Identities=19% Similarity=0.305 Sum_probs=32.3
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
-|.+.++|+||.|.++++.|+++|||+..+..-+..+
T Consensus 3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~ 39 (66)
T cd04908 3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTSE 39 (66)
T ss_pred EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCC
Confidence 3566889999999999999999999999998866644
No 22
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.37 E-value=0.0066 Score=44.68 Aligned_cols=35 Identities=17% Similarity=0.356 Sum_probs=30.9
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
+.+.++|+||.|.++++.|+++|+|+.++...+..
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~ 36 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEK 36 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccC
Confidence 45688999999999999999999999999876654
No 23
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=96.15 E-value=0.0058 Score=62.27 Aligned_cols=41 Identities=39% Similarity=0.626 Sum_probs=38.3
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCC
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~ 347 (361)
-.++++|++.+++|+|.++|++|...++|+..|||||.+..
T Consensus 35 ~~~~~if~~r~~~~~l~~~Lk~f~~~~vnl~HiEsR~s~~~ 75 (461)
T KOG3820|consen 35 ARISLIFSLRNKVGALARALKAFEEFHVNLLHIESRPSERR 75 (461)
T ss_pred ceEEEEEEecccchHHHHHHHHhhhcCceEEEeeccccccc
Confidence 47889999999999999999999999999999999999654
No 24
>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=95.70 E-value=0.017 Score=44.18 Aligned_cols=34 Identities=21% Similarity=0.301 Sum_probs=29.9
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
+.+.++|+||+|.++++.|+++|+|+..+...+.
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~ 35 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFE 35 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccc
Confidence 4568899999999999999999999998866554
No 25
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=95.48 E-value=0.024 Score=45.38 Aligned_cols=39 Identities=13% Similarity=0.370 Sum_probs=34.2
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCC
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~ 347 (361)
-+|.+-+.|+||.|.++++.|+.||+|+.+|.--|+...
T Consensus 3 ~tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te~~ 41 (76)
T PRK06737 3 HTFSLVIHNDPSVLLRISGIFARRGYYISSLNLNERDTS 41 (76)
T ss_pred EEEEEEEecCCCHHHHHHHHHhccCcceEEEEecccCCC
Confidence 457777889999999999999999999999998887643
No 26
>cd04909 ACT_PDH-BS C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH). The C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback-inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.44 E-value=0.023 Score=42.77 Aligned_cols=36 Identities=17% Similarity=0.346 Sum_probs=31.5
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
.+.+.++|+||.|.++++.|+++|+|+..+...+.+
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~ 38 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIR 38 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEee
Confidence 456778899999999999999999999999876654
No 27
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.38 E-value=0.028 Score=42.37 Aligned_cols=36 Identities=25% Similarity=0.446 Sum_probs=31.7
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
+.+.+.++|+||.|.++++.|+++|+|+.++...+.
T Consensus 2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~ 37 (72)
T cd04883 2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPS 37 (72)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEecc
Confidence 457788999999999999999999999999976554
No 28
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=95.24 E-value=0.043 Score=40.26 Aligned_cols=35 Identities=26% Similarity=0.518 Sum_probs=31.8
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
+|.+...|+||.|.++++.|+++|+|+.++...+.
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~ 36 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPT 36 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeec
Confidence 46778889999999999999999999999998765
No 29
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=95.16 E-value=0.035 Score=44.37 Aligned_cols=39 Identities=13% Similarity=0.222 Sum_probs=34.3
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
|-+|.+.+.|+||+|..+++.|+.||.|+.+|.--|+..
T Consensus 3 ~~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~ 41 (76)
T PRK11152 3 QHQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTD 41 (76)
T ss_pred eEEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCC
Confidence 456777888999999999999999999999998888653
No 30
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.14 E-value=0.046 Score=40.35 Aligned_cols=42 Identities=24% Similarity=0.301 Sum_probs=34.0
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCCee
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPLRV 351 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y 351 (361)
.|.+..+|+||.|.++++.|+++++|+.++...+..+..+.+
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~ 43 (72)
T cd04874 2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIEREGKARI 43 (72)
T ss_pred eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccCCCeEEE
Confidence 466778899999999999999999999999877654333333
No 31
>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=94.86 E-value=0.05 Score=39.93 Aligned_cols=34 Identities=21% Similarity=0.406 Sum_probs=30.7
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
|.+..+|+||.|.++++.|+++|+|+.++...+.
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~ 35 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRK 35 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEec
Confidence 5667789999999999999999999999988774
No 32
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=94.66 E-value=0.045 Score=42.65 Aligned_cols=41 Identities=20% Similarity=0.475 Sum_probs=33.8
Q ss_pred CCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 305 RPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 305 ~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
+.+.+.|.+...|+||.|.++++.+++.|+|+..+..+..+
T Consensus 3 ~~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~ 43 (80)
T PF13291_consen 3 KSFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNK 43 (80)
T ss_dssp --EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--
T ss_pred cEEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEec
Confidence 35789999999999999999999999999999999999875
No 33
>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=94.65 E-value=0.049 Score=39.50 Aligned_cols=34 Identities=26% Similarity=0.362 Sum_probs=30.4
Q ss_pred EEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 312 ~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
.+.++|+||.|.++++.|.++|+|+..+...+..
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 34
>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=94.48 E-value=0.08 Score=39.72 Aligned_cols=34 Identities=18% Similarity=0.317 Sum_probs=30.6
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
+++..+|+||.|.++++.|+++|+|+..+.+.+.
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~ 35 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRD 35 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeecc
Confidence 4567889999999999999999999999987665
No 35
>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=94.46 E-value=0.081 Score=38.56 Aligned_cols=35 Identities=14% Similarity=0.332 Sum_probs=31.9
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
+.+..+|+||.|.++++.|+++|+|+.++++.+..
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~ 36 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKE 36 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccC
Confidence 56778899999999999999999999999998764
No 36
>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=94.24 E-value=0.094 Score=34.94 Aligned_cols=34 Identities=38% Similarity=0.540 Sum_probs=30.4
Q ss_pred EEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 312 ~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
.+..+++||.|.++++.|+.+|+|+.++.+++..
T Consensus 2 ~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~ 35 (60)
T cd02116 2 TVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSG 35 (60)
T ss_pred EEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence 4667889999999999999999999999987764
No 37
>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=93.73 E-value=0.098 Score=39.69 Aligned_cols=36 Identities=19% Similarity=0.262 Sum_probs=31.8
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
+|.+..+|+||.|.++.+.+++.|+|+..++++..+
T Consensus 1 ~l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~ 36 (74)
T cd04887 1 TLRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQG 36 (74)
T ss_pred CEEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEec
Confidence 356778899999999999999999999999987644
No 38
>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=93.60 E-value=0.16 Score=37.83 Aligned_cols=41 Identities=20% Similarity=0.368 Sum_probs=33.4
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeeecCCC-CCCee
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK-RPLRV 351 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~-~pw~y 351 (361)
|.+...|+||.|.++++.|++.|+|+.++.+++... ....+
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~ 44 (79)
T cd04881 3 LRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGGETAPV 44 (79)
T ss_pred EEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeE
Confidence 456677999999999999999999999998877643 44444
No 39
>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=93.51 E-value=0.059 Score=41.10 Aligned_cols=33 Identities=33% Similarity=0.406 Sum_probs=28.6
Q ss_pred EEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 312 ~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
.+.+|++||+|.++++.++. |.|++.|.=|-..
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~ 34 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQG 34 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCC
Confidence 57789999999999999999 9999998765543
No 40
>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=93.32 E-value=0.18 Score=39.02 Aligned_cols=38 Identities=21% Similarity=0.307 Sum_probs=32.5
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
|.+.+..+|+||.|+++.++|+.+|+|+.+....+..+
T Consensus 2 tri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~ 39 (72)
T cd04926 2 VRLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGD 39 (72)
T ss_pred eEEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCC
Confidence 45777889999999999999999999998887766533
No 41
>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=93.24 E-value=0.16 Score=38.03 Aligned_cols=38 Identities=21% Similarity=0.272 Sum_probs=33.3
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
|-|.+..+|+||.|.++.+.|+.+|+|+.++..++..+
T Consensus 1 ~~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~ 38 (70)
T cd04899 1 TVLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGE 38 (70)
T ss_pred CEEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCC
Confidence 34667788999999999999999999999999987754
No 42
>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=93.14 E-value=0.19 Score=38.13 Aligned_cols=33 Identities=30% Similarity=0.403 Sum_probs=30.2
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeee
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
+|.+..+|+||.|.++++.+++.|+|+..|.+.
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~ 34 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQN 34 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeC
Confidence 567788899999999999999999999999875
No 43
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=93.07 E-value=0.14 Score=41.81 Aligned_cols=39 Identities=8% Similarity=0.156 Sum_probs=33.7
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
|-+|.+-+.|+||.|.++-+.|+.||+|+.+|.-=|+..
T Consensus 2 k~~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~ 40 (84)
T PRK13562 2 TRILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQ 40 (84)
T ss_pred cEEEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCC
Confidence 345777788999999999999999999999998777754
No 44
>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=93.03 E-value=0.11 Score=38.68 Aligned_cols=35 Identities=20% Similarity=0.274 Sum_probs=30.6
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
+++...|+||.|.++++.|+++|+|+..+.+++..
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~ 36 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRG 36 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCC
Confidence 45667799999999999999999999999887654
No 45
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=92.95 E-value=0.18 Score=45.69 Aligned_cols=37 Identities=22% Similarity=0.483 Sum_probs=33.3
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
-+|.+.++|+||.|.++.+.|+++|+|+.++-.-|..
T Consensus 3 ~~IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te 39 (161)
T PRK11895 3 HTLSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTE 39 (161)
T ss_pred EEEEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecC
Confidence 4577788999999999999999999999999888875
No 46
>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD. This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t
Probab=92.63 E-value=0.22 Score=36.77 Aligned_cols=37 Identities=16% Similarity=0.219 Sum_probs=32.6
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
.|.+..+|+||.|.++.+.|+.+|+|+..+......+
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~ 38 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGE 38 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCC
Confidence 4667888999999999999999999999998877654
No 47
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=92.55 E-value=0.25 Score=41.37 Aligned_cols=40 Identities=23% Similarity=0.371 Sum_probs=34.1
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
.+-+|.+-+.|+||.|.++-+.|+.||.|+.+|-.=|+..
T Consensus 7 ~~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~ 46 (96)
T PRK08178 7 DNVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQD 46 (96)
T ss_pred CCEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCC
Confidence 3566777888999999999999999999999997666654
No 48
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=92.34 E-value=0.24 Score=44.79 Aligned_cols=36 Identities=22% Similarity=0.480 Sum_probs=32.9
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
+|.+.++|+||.|.++.+.|+++|+|+.++-.-|..
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~ 38 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTE 38 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecC
Confidence 567788999999999999999999999999888885
No 49
>PRK08526 threonine dehydratase; Provisional
Probab=92.28 E-value=2.3 Score=43.66 Aligned_cols=179 Identities=18% Similarity=0.159 Sum_probs=94.0
Q ss_pred CCcCeEEEeeecccccchHHhHHHHh--cCCeEEEEEEEEeee---eEeeeCCCCCccCccEE----Ee---chHHHHHH
Q 018090 161 WLVDKAVLPIENSVGGSIHRNYDLLL--RHRLHIVGEVQLVVN---HCLLGLPGVLKEELKRV----FS---HPQALAQC 228 (361)
Q Consensus 161 g~~d~gVVPIENS~~G~V~~tlDlL~--~~~L~IvgEi~lpI~---h~Lla~~g~~l~~Ik~V----yS---HPqALaQC 228 (361)
+..|+-|+|+- .+|.+.-....+. ..+.+|+|--.-.-. ..+-..+-.....+.++ .. -|..+..|
T Consensus 167 ~~~D~vvvpvG--gGGl~aGia~~~k~~~p~~kvigVep~~~~~~~~s~~~g~~~~~~~~~tiadgiav~~~~~~~~~~~ 244 (403)
T PRK08526 167 SDLDMVVVPVG--GGGLISGIASAAKQINPNIKIIGVGAKGAPAMYESFHAKKIINSKSVRTIADGIAVRDASPINLAII 244 (403)
T ss_pred CCCCEEEEecC--hHHHHHHHHHHHHHhCCCCEEEEEEECCCChHHHHHHcCCcccCCCCCceeccccCCCCCHHHHHHH
Confidence 35899999985 4666666666654 345777764332110 11111100111222222 11 16777777
Q ss_pred HHHHHhcCCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCceeeccccCCCCCceEEEEEeeCCCCCC------
Q 018090 229 EMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIAG------ 302 (361)
Q Consensus 229 ~~fL~~~~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~------ 302 (361)
++++++ +..+.-.....|.+.+++.. + -.+.+..|+-+-+|.--...+ ..+.+=-++++-...-..
T Consensus 245 ~~~vd~--~v~V~d~ei~~A~~~l~~~~--g-i~ve~aga~~lAall~~~~~~---~~~~~Vv~ilsGGnid~~~~~~i~ 316 (403)
T PRK08526 245 LECVDD--FVQVDDEEIANAILFLLEKQ--K-IVVEGAGAASVAALLHQKIDL---KKGKKIGVVLSGGNIDVQMLNIII 316 (403)
T ss_pred HHhCCE--EEEECHHHHHHHHHHHHHhc--C-cEeeHHHHHHHHHHHhCcccc---ccCCeEEEEECCCCCCHHHHHHHH
Confidence 766652 22233344455666666542 1 223444444444443111112 122232333332211100
Q ss_pred ----CCCCceEEEEEEecCCcchHHHHHHHHHHCCccccceee-ecCCCCCC
Q 018090 303 ----TDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIES-RPQRKRPL 349 (361)
Q Consensus 303 ----~~~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIES-RP~~~~pw 349 (361)
.....+..+.+.++|+||+|.++++.++..+.|++.|+= |.....++
T Consensus 317 ~~~l~~~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~~~~~~ 368 (403)
T PRK08526 317 EKGLIKSYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFSTKLDY 368 (403)
T ss_pred HHHHHhcCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEeccCCCCC
Confidence 012347888899999999999999999999999999865 65544333
No 50
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=91.65 E-value=0.18 Score=38.45 Aligned_cols=29 Identities=28% Similarity=0.538 Sum_probs=25.3
Q ss_pred CCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 317 EGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 317 ~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
|+||+|..+++.|..+|+|+.+|..-|+.
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~ 29 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTE 29 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-S
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecC
Confidence 68999999999999999999999988844
No 51
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=91.64 E-value=0.5 Score=43.81 Aligned_cols=84 Identities=18% Similarity=0.185 Sum_probs=59.4
Q ss_pred CccEEEEeCCCCcHHHHHHHHHC-CC--------CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHh--
Q 018090 118 TKVRVAYQGLPGAYSEAAARKAY-PK--------CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL-- 186 (361)
Q Consensus 118 ~~~rIAyLGP~GTySe~AA~~~f-~~--------~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~-- 186 (361)
+..+|++-.|..+.++.+....+ .+ .+.+...+.+.++.+|.+|++|.|+++ ..+++.+.
T Consensus 104 ~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~~Da~~~~---------~~~~~~~~~~ 174 (243)
T PF12974_consen 104 KGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGKADAAAIP---------SDAFERLEAE 174 (243)
T ss_dssp GGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTSSSEEEEE---------HHHHHHHHHH
T ss_pred CCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCCccEEEEe---------chhHHHHHHc
Confidence 34689998776555578777755 32 245678899999999999999999988 34555443
Q ss_pred ----cCCeEEEEEEEEeeeeEeeeCCCC
Q 018090 187 ----RHRLHIVGEVQLVVNHCLLGLPGV 210 (361)
Q Consensus 187 ----~~~L~IvgEi~lpI~h~Lla~~g~ 210 (361)
..+++|+++...-..+.+++.++.
T Consensus 175 ~~~~~~~~rvl~~s~~~p~~~~~~~~~~ 202 (243)
T PF12974_consen 175 GPDIPSQLRVLWTSPPYPNWPLVASPDL 202 (243)
T ss_dssp -HHHHTTEEEEEEEEEEE--EEEEETTS
T ss_pred cCcccccEEEEEEeCCCCCcEEEEeCCC
Confidence 357999999887777888888764
No 52
>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=91.27 E-value=0.3 Score=38.63 Aligned_cols=30 Identities=30% Similarity=0.457 Sum_probs=26.1
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccc
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTK 338 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtk 338 (361)
|.|-+..+|+||.|+++.++|++.|+++.+
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~~ 31 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCITK 31 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEEE
Confidence 455677889999999999999999999864
No 53
>PRK00194 hypothetical protein; Validated
Probab=91.27 E-value=0.26 Score=39.20 Aligned_cols=36 Identities=19% Similarity=0.230 Sum_probs=31.7
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
+-.+.+.-+|+||.+.++.+.|+++|+|+..+++.=
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~ 38 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTI 38 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHh
Confidence 456667778999999999999999999999998874
No 54
>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=90.86 E-value=0.19 Score=40.16 Aligned_cols=26 Identities=27% Similarity=0.406 Sum_probs=22.1
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCcc
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDIN 335 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~IN 335 (361)
.+.+.+||+||+|.++|+.++..|||
T Consensus 3 vl~v~ipD~PG~L~~ll~~l~~anI~ 28 (85)
T cd04906 3 LLAVTIPERPGSFKKFCELIGPRNIT 28 (85)
T ss_pred EEEEecCCCCcHHHHHHHHhCCCcee
Confidence 36678899999999999999966666
No 55
>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=90.38 E-value=0.33 Score=38.75 Aligned_cols=28 Identities=14% Similarity=0.253 Sum_probs=24.7
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCcccc
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLT 337 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLt 337 (361)
.|-+..+|+||.||++...|++.|+++.
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~ 29 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQIS 29 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEE
Confidence 4556778999999999999999999985
No 56
>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=90.38 E-value=0.44 Score=36.74 Aligned_cols=35 Identities=26% Similarity=0.414 Sum_probs=31.1
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
.|.+...|++|.|.++++.+++.|+|+..+++++.
T Consensus 2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~ 36 (74)
T cd04877 2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK 36 (74)
T ss_pred EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC
Confidence 35566779999999999999999999999999874
No 57
>PRK08639 threonine dehydratase; Validated
Probab=90.23 E-value=2.8 Score=43.03 Aligned_cols=36 Identities=25% Similarity=0.404 Sum_probs=29.9
Q ss_pred ceEEEEEEecCCcchHHHHHH-HHHHCCccccceeeec
Q 018090 307 YKTSIVFTLEEGPGMLFKALA-VFALRDINLTKIESRP 343 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~-~Fa~~~INLtkIESRP 343 (361)
.+..+.|.+|++||+|.++|+ ++.... |++.|+-|.
T Consensus 335 r~~~~~v~ipdrPGaL~~~l~~i~~~~~-NI~~~~~~~ 371 (420)
T PRK08639 335 LKHYFIVNFPQRPGALREFLDDVLGPND-DITRFEYLK 371 (420)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCC-cEEEEEEee
Confidence 478899999999999999999 555444 999997664
No 58
>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=90.04 E-value=0.53 Score=33.00 Aligned_cols=34 Identities=24% Similarity=0.381 Sum_probs=29.8
Q ss_pred EEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 312 VFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 312 ~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
.+..+|+||.|.++++.|+++++|+.+++.....
T Consensus 2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~ 35 (71)
T cd04876 2 RVEAIDRPGLLADITTVIAEEKINILSVNTRTDD 35 (71)
T ss_pred EEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECC
Confidence 4567899999999999999999999999887643
No 59
>PRK04435 hypothetical protein; Provisional
Probab=89.92 E-value=0.56 Score=41.63 Aligned_cols=37 Identities=27% Similarity=0.279 Sum_probs=33.9
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCccccceeee
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
..+++|.+.++|+||.|.++++.+++.|+|+..|...
T Consensus 67 ~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~ 103 (147)
T PRK04435 67 GKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQS 103 (147)
T ss_pred CcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEE
Confidence 3579999999999999999999999999999999864
No 60
>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=89.92 E-value=0.38 Score=38.30 Aligned_cols=36 Identities=17% Similarity=0.188 Sum_probs=31.5
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
|-.+.+.-+|+||.+.++.+.|+++|+|+..++..=
T Consensus 1 ~~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~ 36 (88)
T cd04872 1 KAVITVVGKDRVGIVAGVSTKLAELNVNILDISQTI 36 (88)
T ss_pred CEEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHh
Confidence 345677788999999999999999999999998764
No 61
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=89.64 E-value=0.44 Score=41.71 Aligned_cols=39 Identities=28% Similarity=0.319 Sum_probs=32.6
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
+.-+.+.++|+||.|..++.+|.+++||+.-|.-.-.++
T Consensus 69 ~dVlaVEmeD~PG~l~~I~~vl~d~diNldYiYAFv~ek 107 (142)
T COG4747 69 TDVLAVEMEDVPGGLSRIAEVLGDADINLDYIYAFVTEK 107 (142)
T ss_pred eeEEEEEecCCCCcHHHHHHHHhhcCcCceeeeeeeecC
Confidence 344667889999999999999999999999887665544
No 62
>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=89.51 E-value=0.5 Score=36.27 Aligned_cols=32 Identities=13% Similarity=0.251 Sum_probs=29.0
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeee
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
|.+.-+|+||.+.++-+.|+++|+|+..++++
T Consensus 2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~ 33 (74)
T cd04875 2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQF 33 (74)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeee
Confidence 44566899999999999999999999999887
No 63
>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=89.29 E-value=0.61 Score=46.86 Aligned_cols=35 Identities=31% Similarity=0.458 Sum_probs=31.4
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeee
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
+.+|.+.++|+||.|.++++.+++.|.|++.|.-+
T Consensus 305 ~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~ 339 (380)
T TIGR01127 305 KVRIETVLPDRPGALYHLLESIAEARANIVKIDHD 339 (380)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEee
Confidence 45888899999999999999999999999999553
No 64
>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=88.92 E-value=5.3 Score=36.88 Aligned_cols=138 Identities=18% Similarity=0.052 Sum_probs=74.9
Q ss_pred cEEEEeCCCCcHHHH-HH-HHHCC------CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhc-CCe
Q 018090 120 VRVAYQGLPGAYSEA-AA-RKAYP------KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLR-HRL 190 (361)
Q Consensus 120 ~rIAyLGP~GTySe~-AA-~~~f~------~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~-~~L 190 (361)
+||||+.. +..... |. ..+|. +.+++...+..+++++|.+|++|+|++... ..+....+ .++
T Consensus 1 l~vg~~~~-~~~~~~~a~~~g~f~~~g~~l~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~--------~~~~~~~~g~~~ 71 (288)
T TIGR01728 1 VRIGYQKN-GHSALALAKEKGLLEKELGKTKVEWVEFPAGPPALEALGAGSLDFGYIGPG--------PALFAYAAGADI 71 (288)
T ss_pred CeEEecCC-CchHHHHHHHhCHHHHhhCCceEEEEecCCCcHHHHHHhcCCccccccCCc--------HHHHHHhcCCCE
Confidence 47899975 333323 32 23442 356788888889999999999999986432 11111122 367
Q ss_pred EEEEEEEEeeeeEeeeCCCC---CccCcc--EEEechH--HHHHHHHHHHhcCCe---E-EeccCHHHHHHHHHhcCCCC
Q 018090 191 HIVGEVQLVVNHCLLGLPGV---LKEELK--RVFSHPQ--ALAQCEMTLSNLGIV---R-ISADDTAGAAQMVASIGERD 259 (361)
Q Consensus 191 ~IvgEi~lpI~h~Lla~~g~---~l~~Ik--~VySHPq--ALaQC~~fL~~~~~~---~-i~~~STA~AA~~va~~~~~~ 259 (361)
.+++-..-.-..+++++++. +++|++ +|...+- .......+|.+.|+. . ....+.+++.+.+..+. -
T Consensus 72 ~~i~~~~~~~~~~~v~~~~~~i~s~~dL~Gk~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~--v 149 (288)
T TIGR01728 72 KAVGLVSDNKATAIVVIKGSPIRTVADLKGKRIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQ--V 149 (288)
T ss_pred EEEEEecCCCceEEEECCCCCCCCHHHcCCCEEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCC--C
Confidence 76665443224566665543 333442 5553211 123444566665432 1 22245566777776653 3
Q ss_pred eEEecCHhh
Q 018090 260 TGAVASAQA 268 (361)
Q Consensus 260 ~AAIas~~A 268 (361)
.|++.++..
T Consensus 150 da~~~~~p~ 158 (288)
T TIGR01728 150 DAWAIWEPW 158 (288)
T ss_pred CEEEeccch
Confidence 455555443
No 65
>PRK06382 threonine dehydratase; Provisional
Probab=88.11 E-value=0.86 Score=46.53 Aligned_cols=35 Identities=20% Similarity=0.265 Sum_probs=32.7
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceee
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
.++.|.+.++|+||.|.++++.|++.|+|+++|+-
T Consensus 329 ~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~ 363 (406)
T PRK06382 329 QLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEV 363 (406)
T ss_pred CEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEE
Confidence 47888899999999999999999999999999986
No 66
>PRK08577 hypothetical protein; Provisional
Probab=88.06 E-value=1.2 Score=38.62 Aligned_cols=38 Identities=21% Similarity=0.378 Sum_probs=34.3
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
...|.+...|+||.|.++++.|+++|+|+..+.++...
T Consensus 56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~ 93 (136)
T PRK08577 56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELK 93 (136)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEec
Confidence 56777888899999999999999999999999888765
No 67
>PRK08198 threonine dehydratase; Provisional
Probab=88.04 E-value=1 Score=45.67 Aligned_cols=37 Identities=22% Similarity=0.303 Sum_probs=32.9
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
...++.+.++|+||.|.++|+.+++.|.|+..|.-+.
T Consensus 326 r~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~ 362 (404)
T PRK08198 326 RYLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDR 362 (404)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEE
Confidence 4578889999999999999999999999999986643
No 68
>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=86.86 E-value=0.82 Score=35.34 Aligned_cols=33 Identities=15% Similarity=0.213 Sum_probs=28.1
Q ss_pred EEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 313 FTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 313 f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
+.=+|+||-++++-+.|+++|+|+..++++=..
T Consensus 4 v~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~ 36 (75)
T cd04870 4 VTGPDRPGLTSALTEVLAAHGVRILDVGQAVIH 36 (75)
T ss_pred EEcCCCCCHHHHHHHHHHHCCCCEEecccEEEc
Confidence 444799999999999999999999999765544
No 69
>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=86.23 E-value=1.1 Score=34.37 Aligned_cols=36 Identities=11% Similarity=0.226 Sum_probs=29.2
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
+.|.+..+|+||.|+++-++|+.+|+|+..-...-.
T Consensus 2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~ 37 (73)
T cd04900 2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTT 37 (73)
T ss_pred EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEe
Confidence 356677789999999999999999999986544333
No 70
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=86.02 E-value=3.5 Score=34.17 Aligned_cols=78 Identities=14% Similarity=0.054 Sum_probs=52.6
Q ss_pred cEEEEeCCCCcHHHHHHHHHCCC-----------CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHh--
Q 018090 120 VRVAYQGLPGAYSEAAARKAYPK-----------CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL-- 186 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~~-----------~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~-- 186 (361)
.+|+++ .||+.+..+++..+. .+++.+++..+++.+|.+|+ |..+.. ++ ++..+.
T Consensus 14 ~~vgv~--~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d--~~-------~~~~~~~~ 81 (134)
T smart00079 14 IEYGTI--RGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLME--ST-------YLDYELSQ 81 (134)
T ss_pred ccceEe--cCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEee--hH-------hHHHHHhC
Confidence 578886 799999998876543 25678999999999999999 866654 22 222222
Q ss_pred cCCeEEEEEEEEeeeeEeeeCCC
Q 018090 187 RHRLHIVGEVQLVVNHCLLGLPG 209 (361)
Q Consensus 187 ~~~L~IvgEi~lpI~h~Lla~~g 209 (361)
..++.++++..-+-..+++.++|
T Consensus 82 ~~~~~~~~~~~~~~~~~ia~~k~ 104 (134)
T smart00079 82 NCDLMTVGENFGRKGYGIAFPKG 104 (134)
T ss_pred CCCeEEcCcccCCCceEEEecCC
Confidence 23467777654444556655554
No 71
>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=85.99 E-value=19 Score=30.16 Aligned_cols=121 Identities=20% Similarity=0.138 Sum_probs=67.3
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCccE-
Q 018090 140 YPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR- 217 (361)
Q Consensus 140 f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik~- 217 (361)
+|+.++... .+-.++.+.+.+|++|+|++.-.+...+. ....|.+.++.++. +-.|-+.. +..+++++..
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~~~~~-~~~~~~~L~~~ 97 (200)
T cd08417 26 APGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGL---RSQPLFEDRFVCVA----RKDHPLAG-GPLTLEDYLAA 97 (200)
T ss_pred CCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccCCCcc---chhhhhcCceEEEe----cCCCcccc-cccCHHHHhCC
Confidence 466555433 35678899999999999998654332221 12334445555443 33444433 3344455432
Q ss_pred ---EEechH-HHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 218 ---VFSHPQ-ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 218 ---VySHPq-ALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
++.+.. ......+|+.+.+. + ...+++...+.+++..+ ...+|.+...++.
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08417 98 PHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGT---DLIATVPRRLAEA 155 (200)
T ss_pred CeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcC---CeeeeccHHHHHh
Confidence 233322 23345666766553 2 34556666666777664 3577778776654
No 72
>PRK06545 prephenate dehydrogenase; Validated
Probab=84.66 E-value=1.1 Score=44.86 Aligned_cols=41 Identities=12% Similarity=0.276 Sum_probs=35.3
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCC
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRP 348 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~p 348 (361)
-..+.+.++|+||.|..++..++..|||++.|+-.-.+...
T Consensus 290 ~~~~~v~v~d~pg~~~~~~~~~~~~~i~i~~~~i~~~~~~~ 330 (359)
T PRK06545 290 FYDLYVDVPDEPGVIARVTAILGEEGISIENLRILEAREDI 330 (359)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHcCCCeecceeeeccCCc
Confidence 46788899999999999999999999999999876655443
No 73
>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=84.42 E-value=24 Score=29.97 Aligned_cols=119 Identities=14% Similarity=0.072 Sum_probs=60.0
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCC-CCCccCcc-
Q 018090 140 YPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLP-GVLKEELK- 216 (361)
Q Consensus 140 f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~-g~~l~~Ik- 216 (361)
+|+.++.... +-.++.+.+.+|++|+|+........|... ..|.+..+.+ ..+-+|-|.... ..+++++.
T Consensus 27 ~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----v~~~~hpl~~~~~~i~~~dL~~ 99 (203)
T cd08445 27 APDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRR---IVLREEPLVV----ALPAGHPLAQEKAPLTLAQLAD 99 (203)
T ss_pred CCCeEEEEEeCChHHHHHHHHcCCCcEEEecCCCCCCCcee---EEEEeccEEE----EeeCCCCCccCCCCcCHHHhcC
Confidence 5776655443 468999999999999999642211111100 0111122221 223344443332 23344432
Q ss_pred --EEEechH----H-HHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhH
Q 018090 217 --RVFSHPQ----A-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAA 269 (361)
Q Consensus 217 --~VySHPq----A-LaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA 269 (361)
-|. ++. . ..+..+++.+.+. + ...++|...+.++++.+ ...+|.+...+
T Consensus 100 ~~~i~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 158 (203)
T cd08445 100 EPLIL-YPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAG---EGVTLVPASVQ 158 (203)
T ss_pred CCEEe-cCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcC---CCeEEehHHhh
Confidence 233 221 1 2345556665542 2 34566767777777764 34677777654
No 74
>TIGR00363 lipoprotein, YaeC family. This family of putative lipoproteins contains a consensus site for lipoprotein signal sequence cleavage. Included in this family is the E. coli hypothetical protein yaeC. About half of the proteins between the noise and trusted cutoffs contain the consensus lipoprotein signature and may belong to this family.
Probab=84.30 E-value=41 Score=32.49 Aligned_cols=148 Identities=18% Similarity=0.132 Sum_probs=82.3
Q ss_pred CccEEEEe-CCCCcHHHHHHHHHCC----CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHH-Hhc--CC
Q 018090 118 TKVRVAYQ-GLPGAYSEAAARKAYP----KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDL-LLR--HR 189 (361)
Q Consensus 118 ~~~rIAyL-GP~GTySe~AA~~~f~----~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDl-L~~--~~ 189 (361)
...|||++ ||....=+.|...++. +.+++.+++..+..+|+.+|++|.+.. +... .+.. ... .+
T Consensus 18 ~~l~vG~~~~~~~~~~~~~~~~~~~~~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~-------q~~~-~l~~~~~~~g~~ 89 (258)
T TIGR00363 18 LHIKVGVISGAEQQVAEVAAKVAKEKYGLDVELVEFNDYALPNEAVSKGDLDANAF-------QHKP-YLDQDAKAKGYK 89 (258)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCEEEEEEeCCcHHHHHHHHcCCCCeEec-------CCHH-HHHHHHHhCCCc
Confidence 46999998 4544444455555553 368899999999999999999998653 2112 2222 222 35
Q ss_pred eEEEEEEEEeeeeEeeeCCCCCccCcc---EEEec--hHHHHHHHHHHHhcC-----------------------CeEEe
Q 018090 190 LHIVGEVQLVVNHCLLGLPGVLKEELK---RVFSH--PQALAQCEMTLSNLG-----------------------IVRIS 241 (361)
Q Consensus 190 L~IvgEi~lpI~h~Lla~~g~~l~~Ik---~VySH--PqALaQC~~fL~~~~-----------------------~~~i~ 241 (361)
+.+++...+- ...+...+=.+++|++ +|.-. |.-.++.-..|.+.| ++++.
T Consensus 90 lv~v~~~~~~-p~~~ys~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~ve 168 (258)
T TIGR00363 90 LVAVGNTFVY-PLAGYSKKIKNVNELQDGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITE 168 (258)
T ss_pred EEEEeeeEEe-cccccCcCCCCHHHcCCCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEE
Confidence 6666643221 1233333334667774 55433 444444445666533 44555
Q ss_pred ccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCcee
Q 018090 242 ADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDIL 277 (361)
Q Consensus 242 ~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iL 277 (361)
.... ..++.+.++ .-.||+....-+...||...
T Consensus 169 l~~~-~~~~al~~g--~vDaa~v~~~~~~~agl~~~ 201 (258)
T TIGR00363 169 LETS-QLPRALDDP--KVDLAVINTTYAGQVGLNPQ 201 (258)
T ss_pred cCHH-HHHHHhhcc--cccEEEEChHHHHHcCCCcC
Confidence 5443 333433332 13466666666667777643
No 75
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=84.15 E-value=1.4 Score=39.28 Aligned_cols=42 Identities=29% Similarity=0.445 Sum_probs=36.2
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCccccce-eeecCCCC
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKI-ESRPQRKR 347 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkI-ESRP~~~~ 347 (361)
....+|.+.+.|+.|.|.++|++.++.++|...| ++-|..++
T Consensus 70 ~ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~ 112 (150)
T COG4492 70 ERIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGR 112 (150)
T ss_pred ceEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCce
Confidence 3578999999999999999999999999998888 45676553
No 76
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=84.00 E-value=3.6 Score=46.92 Aligned_cols=49 Identities=14% Similarity=0.162 Sum_probs=42.8
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
..+||.. .|++.+..+++.||+.+++.++|..+++++|.+|++|+.|..
T Consensus 164 ~~~i~~~--~g~~~~~~~~~~~p~~~i~~~~s~~~al~av~~G~~Da~i~~ 212 (1197)
T PRK09959 164 PVNIARV--ANYPPDEVIHQSFPKATIISFTNLYQALASVSAGQNDYFIGS 212 (1197)
T ss_pred CeEEEEe--CCCCCHHHHHHhCCCCEEEeCCCHHHHHHHHHcCCCCEEEcc
Confidence 4567764 488888888889999999999999999999999999988864
No 77
>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=83.95 E-value=1.5 Score=34.92 Aligned_cols=29 Identities=14% Similarity=0.298 Sum_probs=25.3
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCcccc
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLT 337 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLt 337 (361)
|-|=+..+|+||.||++...|++.|+++.
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~ 30 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVF 30 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEE
Confidence 44557778999999999999999999985
No 78
>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=83.69 E-value=1.7 Score=33.38 Aligned_cols=34 Identities=18% Similarity=0.411 Sum_probs=29.4
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
+.+..+|+||.+.++-+.|+++|+|+..+++.-.
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~ 35 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETY 35 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeee
Confidence 3466789999999999999999999999977443
No 79
>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=83.19 E-value=27 Score=29.59 Aligned_cols=123 Identities=10% Similarity=-0.009 Sum_probs=60.4
Q ss_pred HCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc--
Q 018090 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (361)
Q Consensus 139 ~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I-- 215 (361)
.||+.++.-. .+..++.+.+.+|++|+|++.-.....|.. ...|.+..+. +..+-.|-+......+++++
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~----lv~~~~hpl~~~~~~~~~~L~~ 97 (197)
T cd08452 25 KFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALH---IETVQSSPCV----LALPKQHPLASKEEITIEDLRD 97 (197)
T ss_pred HCCCcEEEEEecChHHHHHHHHCCCccEEEeeCCCCCCCee---EEEeeeccEE----EEEeCCCccccCCCCCHHHhcC
Confidence 3677665433 367889999999999999974211111100 0011111221 22233454433222333333
Q ss_pred -cEEEe-ch---HHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 216 -KRVFS-HP---QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 216 -k~VyS-HP---qALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
.-|.. .+ ....+-.+|+.+.+. . ...+++...+.+.++.+ ...|+.+...+..
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~~ 158 (197)
T cd08452 98 EPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAG---IGVTFVPSSAKKL 158 (197)
T ss_pred CCEEeccCCcchhHHHHHHHHHHHcCCCccceeecccHHHHHHHHHcC---CCEEEchHHHhhc
Confidence 22332 21 123344456666542 2 24466666677777754 2466777765543
No 80
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=83.11 E-value=3.9 Score=37.29 Aligned_cols=49 Identities=20% Similarity=0.203 Sum_probs=40.7
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
..+||.. .|++.+....+.+++.+.+++++.++++.+|.+|++|+.+.+
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 3578885 577777666666788889999999999999999999999864
No 81
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=82.67 E-value=1.1 Score=40.65 Aligned_cols=38 Identities=26% Similarity=0.498 Sum_probs=33.1
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccce-eeecCC
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKI-ESRPQR 345 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkI-ESRP~~ 345 (361)
+.++.+.++|+||-|.++|+.++..|-|+-.| +||--+
T Consensus 5 ritldIEL~D~PGQLl~vLqPls~~g~NiItIiH~r~kk 43 (170)
T COG2061 5 RITLDIELKDKPGQLLKVLQPLSKTGANIITIIHSRDKK 43 (170)
T ss_pred EEEEEEEecCCCcchhhhhcchhhcCccEEEEEeecCcc
Confidence 67888899999999999999999999998765 777644
No 82
>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=82.46 E-value=21 Score=30.98 Aligned_cols=48 Identities=21% Similarity=0.268 Sum_probs=38.9
Q ss_pred cEEEEeCCCCcHHHHHHHHHCC-CCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 120 VRVAYQGLPGAYSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~-~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+|++. .|++......+.++ +.+++.+.+.++++++|.+|++|+.++.
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 478875 46666656556565 7889999999999999999999999886
No 83
>PRK07334 threonine dehydratase; Provisional
Probab=82.16 E-value=2.3 Score=43.27 Aligned_cols=39 Identities=13% Similarity=0.244 Sum_probs=36.0
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
.+.+.|.+...|+||.|.++++.+++.++|+.++.++..
T Consensus 324 ~y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~ 362 (403)
T PRK07334 324 GRLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRL 362 (403)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEec
Confidence 467999999999999999999999999999999998854
No 84
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=81.80 E-value=15 Score=30.81 Aligned_cols=48 Identities=29% Similarity=0.348 Sum_probs=38.0
Q ss_pred cEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 120 VRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+|++.. |+........++++.+.+.+.+..+++.+|.+|++|+++++
T Consensus 107 ~~i~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 154 (219)
T smart00062 107 KKVAVVA--GTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVAD 154 (219)
T ss_pred CEEEEec--CccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEec
Confidence 5788764 65555555555566788999999999999999999999986
No 85
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=81.59 E-value=4.4 Score=36.94 Aligned_cols=49 Identities=16% Similarity=0.193 Sum_probs=41.3
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCC-CCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYP-KCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~-~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
..+|++. .|+..+.....+++ +.+++.+.+.++++++|.+|++|+.|+.
T Consensus 131 g~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~ 180 (250)
T TIGR01096 131 GKTVGVQ--SGTTHEQYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTD 180 (250)
T ss_pred CCEEEEe--cCchHHHHHHHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 3578874 68887777777777 7888999999999999999999999974
No 86
>PLN02550 threonine dehydratase
Probab=81.08 E-value=9.6 Score=41.37 Aligned_cols=171 Identities=15% Similarity=0.156 Sum_probs=86.3
Q ss_pred CcCeEEEeeecccccchHHhHHHHh--cCCeEEEEEEEEee---eeEeeeCCCCCccCccE----EEe---chHHHHHHH
Q 018090 162 LVDKAVLPIENSVGGSIHRNYDLLL--RHRLHIVGEVQLVV---NHCLLGLPGVLKEELKR----VFS---HPQALAQCE 229 (361)
Q Consensus 162 ~~d~gVVPIENS~~G~V~~tlDlL~--~~~L~IvgEi~lpI---~h~Lla~~g~~l~~Ik~----VyS---HPqALaQC~ 229 (361)
..|+-|+|+- .+|.+.-..-.+. ..+++|+|--.-.- ...+...+-+.+..+.+ +.. =++.+.-|+
T Consensus 258 ~~D~VvvpVG--gGGLiaGia~~lK~l~p~vkVIGVEp~~a~~~~~s~~~G~~v~~~~~~tiAdGiav~~~G~~t~~i~~ 335 (591)
T PLN02550 258 PLHAIFVPVG--GGGLIAGIAAYVKRVRPEVKIIGVEPSDANAMALSLHHGERVMLDQVGGFADGVAVKEVGEETFRLCR 335 (591)
T ss_pred CCCEEEEEeC--hhHHHHHHHHHHHHhCCCCEEEEEEECCChHHHHHHhcCCccccCCCCCccceeecCCCCHHHHHHHH
Confidence 4899999985 4666655555554 34678877444221 11111111111111111 111 145566666
Q ss_pred HHHHhcCCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCceeeccccCCCCCceEEEEEeeCCCCC--------
Q 018090 230 MTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPIIA-------- 301 (361)
Q Consensus 230 ~fL~~~~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~-------- 301 (361)
++++. +-.+......+|.+.+.+.. ...+-+..|+-+.+|.-..+... . .+.+=-+|++-...-.
T Consensus 336 ~~vD~--vV~Vsd~eI~~Ai~~l~e~~---givvEpAGA~alAall~~~~~~~-~-~g~~Vv~vlsGgNid~~~l~~v~~ 408 (591)
T PLN02550 336 ELVDG--VVLVSRDAICASIKDMFEEK---RSILEPAGALALAGAEAYCKYYG-L-KDENVVAITSGANMNFDRLRIVTE 408 (591)
T ss_pred hhCCE--EEEECHHHHHHHHHHHHHHC---CCEEeHHHHHHHHHHHHHHHhcC-C-CCCeEEEEecCCCCCHHHHHHHHH
Confidence 65442 22334444566777777642 12233334444445443322111 1 1222222333221110
Q ss_pred --CCCCCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 302 --GTDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 302 --~~~~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
......+..+.+.++++||+|.++++.+... |++.|+=|-
T Consensus 409 ~~~~~~~r~~~~~v~ipd~pG~l~~~~~~l~~~--ni~~~~~~~ 450 (591)
T PLN02550 409 LADVGRQQEAVLATFMPEEPGSFKRFCELVGPM--NITEFKYRY 450 (591)
T ss_pred HHHhccCCEEEEEEEcCCCCCHHHHHHHHhhhh--cceEEEEEe
Confidence 0112346778889999999999999999986 888887654
No 87
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=81.05 E-value=22 Score=33.76 Aligned_cols=144 Identities=15% Similarity=0.126 Sum_probs=76.2
Q ss_pred CCccEEEEeCCCCcH--HHH--HHHHHCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeE
Q 018090 117 GTKVRVAYQGLPGAY--SEA--AARKAYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLH 191 (361)
Q Consensus 117 ~~~~rIAyLGP~GTy--Se~--AA~~~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~ 191 (361)
.+..+|+....-+.+ .+. ...+.+|+.++.... +.+++++.+.+|++|+||+.......+... ..|.+.++.
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 356777776544421 111 123346777765554 589999999999999999876543333111 122222332
Q ss_pred EEEEEEEeeeeEeeeCCCCCccCcc--EEEechHH---HHHHHHHHHhcC--C-eEEeccCHHHHHHHHHhcCCCCeEEe
Q 018090 192 IVGEVQLVVNHCLLGLPGVLKEELK--RVFSHPQA---LAQCEMTLSNLG--I-VRISADDTAGAAQMVASIGERDTGAV 263 (361)
Q Consensus 192 IvgEi~lpI~h~Lla~~g~~l~~Ik--~VySHPqA---LaQC~~fL~~~~--~-~~i~~~STA~AA~~va~~~~~~~AAI 263 (361)
++ .+-+|-+...+..+++++. ..++++.. ..+..+++...+ . ....++|...+.+++..+ ...+|
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 22 2334444333223444432 23333222 234444554443 2 235577777777888764 35778
Q ss_pred cCHhhHH
Q 018090 264 ASAQAAE 270 (361)
Q Consensus 264 as~~AA~ 270 (361)
.+...+.
T Consensus 240 lp~~~~~ 246 (305)
T PRK11151 240 LPALAVP 246 (305)
T ss_pred eeHHhhh
Confidence 8887664
No 88
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=80.99 E-value=2.1 Score=33.27 Aligned_cols=33 Identities=15% Similarity=0.178 Sum_probs=24.3
Q ss_pred EEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 313 FTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 313 f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
+.=+|+||.++.+.+.++++|.|+..++-.-..
T Consensus 7 v~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~ 39 (76)
T PF13740_consen 7 VVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLG 39 (76)
T ss_dssp EEEE--TTHHHHHHHHHHCTT-EEEEEEEEEET
T ss_pred EEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEc
Confidence 334799999999999999999999887665443
No 89
>PRK09224 threonine dehydratase; Reviewed
Probab=80.81 E-value=13 Score=39.36 Aligned_cols=36 Identities=22% Similarity=0.348 Sum_probs=30.6
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
.+..+.|.+|++||+|.++++.+. +-|+|.++=|-.
T Consensus 327 re~~l~v~iPerPGaL~~f~~~l~--~~nItef~yr~~ 362 (504)
T PRK09224 327 REALLAVTIPEEPGSFLKFCELLG--GRNVTEFNYRYA 362 (504)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhc--cCcEEEEEEEec
Confidence 478889999999999999999999 678888776553
No 90
>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=79.54 E-value=11 Score=36.35 Aligned_cols=132 Identities=17% Similarity=0.099 Sum_probs=74.3
Q ss_pred CCCCCccEEEEeCCCCcHHHHHHHHHC---C-CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCC
Q 018090 114 PDDGTKVRVAYQGLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHR 189 (361)
Q Consensus 114 ~~~~~~~rIAyLGP~GTySe~AA~~~f---~-~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~ 189 (361)
....++.++|..|+ |+.+|.++..+. + +.+.+|+++-.++..++..|++|.++...- ...+++...+
T Consensus 101 k~~p~~~~~g~~g~-g~~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~~--------~~~~~~~~G~ 171 (274)
T PF03401_consen 101 KANPGKLTFGSSGP-GSSDHLAAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSPG--------EALPYVEAGD 171 (274)
T ss_dssp HCSCCC-EEEESST-TSHHHHHHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEHH--------HHHHHHHTTS
T ss_pred HhCCCCeEEEecCC-CchHHHHHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecHH--------HHHHHHhCCC
Confidence 33456788999886 899999887654 2 467899999999999999999999887533 2223322222
Q ss_pred eEEEE----------------------EEEEeeeeEeeeCCCCCccCccEEEechHH---HHHHHHHHHhcCCeEEeccC
Q 018090 190 LHIVG----------------------EVQLVVNHCLLGLPGVLKEELKRVFSHPQA---LAQCEMTLSNLGIVRISADD 244 (361)
Q Consensus 190 L~Ivg----------------------Ei~lpI~h~Lla~~g~~l~~Ik~VySHPqA---LaQC~~fL~~~~~~~i~~~S 244 (361)
+++.+ ++.+...+.+++.+|++.+-+.++..--+. ....++|+++.++... ..+
T Consensus 172 ~k~Lav~~~~r~~~~pdvPT~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~~g~~~~-~~~ 250 (274)
T PF03401_consen 172 LKPLAVFSDERSPALPDVPTFKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEKMGLEPV-YMD 250 (274)
T ss_dssp EEEEEECSSS-BTTCTTS-BTTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHHHTEEEE-CES
T ss_pred ceEEEEecCccccccCCCCCHHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHHCCCcCC-CCC
Confidence 22211 223445567777877654332222211111 1123345555554443 556
Q ss_pred HHHHHHHHHhc
Q 018090 245 TAGAAQMVASI 255 (361)
Q Consensus 245 TA~AA~~va~~ 255 (361)
..+..+++.+.
T Consensus 251 ~~~~~~~l~~~ 261 (274)
T PF03401_consen 251 GEEFDAFLAEE 261 (274)
T ss_dssp HHHHHHHHHHH
T ss_pred HHHHHHHHHHH
Confidence 66666666653
No 91
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=79.47 E-value=2.1 Score=37.54 Aligned_cols=29 Identities=28% Similarity=0.332 Sum_probs=25.1
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccce
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKI 339 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkI 339 (361)
|.+-+.|+||-|.++++.++++|||+.-+
T Consensus 6 ISvFlENk~GRL~~~~~~L~eagINiRA~ 34 (142)
T COG4747 6 ISVFLENKPGRLASVANKLKEAGINIRAF 34 (142)
T ss_pred EEEEecCCcchHHHHHHHHHHcCCceEEE
Confidence 55567899999999999999999998644
No 92
>PRK13397 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=79.41 E-value=0.4 Score=46.50 Aligned_cols=32 Identities=19% Similarity=0.118 Sum_probs=28.6
Q ss_pred cCCCCCCCcccchhhhhcccccccccccccCC
Q 018090 60 EDDRPYTPDVQSSEANERSQDSQSSGFHKDLN 91 (361)
Q Consensus 60 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~d~~ 91 (361)
.=|+-+.|++++|||+|+|.++++++|++++.
T Consensus 217 ~IE~H~~P~~A~sD~~q~l~~~~l~~l~~~~~ 248 (250)
T PRK13397 217 MMEVHPDPDHALSDAAQQIDYKQLEQLGQELW 248 (250)
T ss_pred EEEecCCcccccCchhhhCCHHHHHHHHHHhc
Confidence 33778899999999999999999999998873
No 93
>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=79.20 E-value=6.9 Score=33.15 Aligned_cols=48 Identities=29% Similarity=0.351 Sum_probs=39.3
Q ss_pred cEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 120 VRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+|++. .|+..+....+.++..+++++.+.++++++|.+|++|++++.
T Consensus 106 ~~i~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 153 (218)
T cd00134 106 KKVAVQ--KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVD 153 (218)
T ss_pred CEEEEE--cCchHHHHHHHhCCcccEEEeCCHHHHHHHHHcCCccEEEec
Confidence 578877 566666666666666788999999999999999999988875
No 94
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=79.19 E-value=14 Score=34.35 Aligned_cols=146 Identities=12% Similarity=0.071 Sum_probs=80.6
Q ss_pred CCCccEEEEeCCCCcHHHHHHHH--HCC----CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCC
Q 018090 116 DGTKVRVAYQGLPGAYSEAAARK--AYP----KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHR 189 (361)
Q Consensus 116 ~~~~~rIAyLGP~GTySe~AA~~--~f~----~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~ 189 (361)
.....||||+...+.+.-..|.. +|. +.+++.+.+-.++.+++.+|++|++.+ ...++.+.-... .-...+
T Consensus 4 ~~~~l~ig~~~~~~~~p~~~a~~~g~f~~~G~~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~--~~~~~~ 80 (252)
T PF13379_consen 4 EPTTLRIGYLPGPDYAPLYVAQEKGLFEKEGLDVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGA--GGPDVD 80 (252)
T ss_dssp SESEEEEEETSSGGGHHHHHHHHTTHHHHTTSCEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTT--TT----
T ss_pred CCcEEEEEeecchHHHHHHHHHHcChHHHcCCEEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCC--CCcccc
Confidence 34568999986555454444432 442 368899999999999999999999998 432221110000 000123
Q ss_pred eEEEEEEEEeeeeEeeeCCC-------CCccCc---------cEEEe-chHH--HHHHHHHHHhcC------CeEEeccC
Q 018090 190 LHIVGEVQLVVNHCLLGLPG-------VLKEEL---------KRVFS-HPQA--LAQCEMTLSNLG------IVRISADD 244 (361)
Q Consensus 190 L~IvgEi~lpI~h~Lla~~g-------~~l~~I---------k~VyS-HPqA--LaQC~~fL~~~~------~~~i~~~S 244 (361)
+.+++-...- ...++++.+ .+++|+ ++|.. ++-. .-..+.+|++.| ++++.+..
T Consensus 81 ~~~~~~~~~~-g~~lvv~~~~~~~~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~ 159 (252)
T PF13379_consen 81 IVVLAGLSQN-GNALVVRNDLKDASDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP 159 (252)
T ss_dssp EEEEEECSBS-SEEEEECGGGTTCSTTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G
T ss_pred eEEeeccCCC-ceEEEEcCccccCCCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH
Confidence 4444333222 135566532 245555 46665 5533 334577888753 46666666
Q ss_pred HHHHHHHHHhcCCCCeEEecCHh
Q 018090 245 TAGAAQMVASIGERDTGAVASAQ 267 (361)
Q Consensus 245 TA~AA~~va~~~~~~~AAIas~~ 267 (361)
.++...+..++ -+.+++....
T Consensus 160 -~~~~~al~~g~-iDa~~~~eP~ 180 (252)
T PF13379_consen 160 -PEMVAALRAGE-IDAAVLWEPF 180 (252)
T ss_dssp -HHHHHHHHTTS--SEEEEETTH
T ss_pred -HHHHHHHhCCC-cCEEEecCCH
Confidence 77777777653 3444444444
No 95
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=78.59 E-value=3.5 Score=47.03 Aligned_cols=49 Identities=24% Similarity=0.219 Sum_probs=43.2
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
..|||. +.|++.+....+.+++.+++.+++.++++++|.+|++|++|..
T Consensus 407 g~~vav--~~g~~~~~~~~~~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~ 455 (1197)
T PRK09959 407 GMKVAI--PYYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDALVAT 455 (1197)
T ss_pred CCEEEE--eCCcchHHHHHHHCCCcEEEEcCCHHHHHHHHHcCCCCEEehh
Confidence 467888 5688888888888999999999999999999999999998864
No 96
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=78.51 E-value=23 Score=34.00 Aligned_cols=139 Identities=14% Similarity=0.029 Sum_probs=71.8
Q ss_pred CCCccEEEEeCCCCcHHHHHHHH-H----CCC--CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcC
Q 018090 116 DGTKVRVAYQGLPGAYSEAAARK-A----YPK--CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRH 188 (361)
Q Consensus 116 ~~~~~rIAyLGP~GTySe~AA~~-~----f~~--~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~ 188 (361)
..+..||||+.. ......+-.. + +++ .+++...+-.++++++.+|++|+|+.. ........-...
T Consensus 25 ~~~~lrIg~~~~-~~~~~l~~~~~~~~~~~p~v~ie~~~~~~~~~~~~aL~~G~iDia~~~-------~~~~~~~~~~g~ 96 (314)
T PRK11553 25 SPEALRIGYQKG-SIGLVLAKSHQLLEKRFPQTKISWVEFPAGPQMLEALNVGSIDLGSTG-------DIPPIFAQAAGA 96 (314)
T ss_pred CCCeEEEEeCCC-chHHHHHHhhCHHHHhCCCCeeEEEECCCcHHHHHHHHcCCCCEEccC-------CHHHHHHHhCCC
Confidence 456789999742 2222222211 2 333 566777677899999999999999842 111111111123
Q ss_pred CeEEEEEEEE-eeeeEeeeCCCC---CccCc--cEEEech--HHHHHHHHHHHhcCC-----eEEeccCHHHHHHHHHhc
Q 018090 189 RLHIVGEVQL-VVNHCLLGLPGV---LKEEL--KRVFSHP--QALAQCEMTLSNLGI-----VRISADDTAGAAQMVASI 255 (361)
Q Consensus 189 ~L~IvgEi~l-pI~h~Lla~~g~---~l~~I--k~VySHP--qALaQC~~fL~~~~~-----~~i~~~STA~AA~~va~~ 255 (361)
++.+++.... .-..+++++++. +++|+ ++|...+ .......++|++.+. +.+.. +..++...+..+
T Consensus 97 ~~~~v~~~~~~~~~~~lvv~~~s~i~s~~dL~Gk~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~-~~~~~~~al~~G 175 (314)
T PRK11553 97 DLVYVGVEPPKPKAEVILVAENSPIKTVADLKGHKVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYL-TPADARAAFQQG 175 (314)
T ss_pred CEEEEEEecCCCcceEEEEeCCCCCCCHHHhCCCEEeecCCCcHHHHHHHHHHHcCCCHHHeEEEec-ChHHHHHHHHcC
Confidence 5666654322 223467776653 33444 2344322 123455666766553 23333 445555555554
Q ss_pred CCCCeEEecC
Q 018090 256 GERDTGAVAS 265 (361)
Q Consensus 256 ~~~~~AAIas 265 (361)
. -.|+++.
T Consensus 176 ~--vDa~~~~ 183 (314)
T PRK11553 176 N--VDAWAIW 183 (314)
T ss_pred C--CCEEEEc
Confidence 2 3455443
No 97
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=78.17 E-value=2.9 Score=38.82 Aligned_cols=36 Identities=19% Similarity=0.377 Sum_probs=30.0
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
.+.+.-+|+||-++++=+.|+.+|||+..+.++=.+
T Consensus 97 ~v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~ 132 (190)
T PRK11589 97 WVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQP 132 (190)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCChhheEEeeec
Confidence 344445699999999999999999999999997443
No 98
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=77.89 E-value=13 Score=31.30 Aligned_cols=112 Identities=21% Similarity=0.127 Sum_probs=62.5
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCC---CccCc--c
Q 018090 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV---LKEEL--K 216 (361)
Q Consensus 142 ~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~---~l~~I--k 216 (361)
+.++++. +..++++++.+|++|+++....+..+. ...+ ..........+.++.+++. +++|+ +
T Consensus 40 ~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~-----~~~~------~~~~~~~~~~~~~~~~~~~~~~~~~dL~g~ 107 (219)
T smart00062 40 KVEFVEV-SFDNLLTALKSGKIDVVAAGMTITPER-----AKQV------DFSDPYYKSGQVILVRKDSPIKSLEDLKGK 107 (219)
T ss_pred eEEEEec-cHHHHHHHHHCCcccEEeccccCCHHH-----Hhhe------eeccceeeceeEEEEecCCCCCChHHhCCC
Confidence 3677888 889999999999999998754321111 0011 1111122233556665553 23333 2
Q ss_pred EEEechHHHHHHHHHHHhc--CCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhH
Q 018090 217 RVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAA 269 (361)
Q Consensus 217 ~VySHPqALaQC~~fL~~~--~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA 269 (361)
+|..-. . .-...++... +.+.+.+.+..++.+++..+. ..|++.....+
T Consensus 108 ~i~~~~-g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~--~d~~~~~~~~~ 158 (219)
T smart00062 108 KVAVVA-G-TTGEELLKKLYPEAKIVSYDSQAEALAALKAGR--ADAAVADAPAL 158 (219)
T ss_pred EEEEec-C-ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCc--ccEEEeccHHH
Confidence 333322 1 1233455544 467778888888888887653 34666555543
No 99
>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=77.55 E-value=39 Score=28.94 Aligned_cols=139 Identities=11% Similarity=0.005 Sum_probs=70.9
Q ss_pred ccEEEEeCCCCcHHH-HHH---HHHCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCCeE
Q 018090 119 KVRVAYQGLPGAYSE-AAA---RKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLH 191 (361)
Q Consensus 119 ~~rIAyLGP~GTySe-~AA---~~~f~~~e~vp-~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~L~ 191 (361)
..+||+....+.+-= .+. ++.+|+.++.- ..+..++.+.+.+|++|+|++.-.. ..+.++ .|.+.++.
T Consensus 2 ~l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~-----~~~~~~~~~l~~~~~~ 76 (198)
T cd08486 2 ELSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFP-----RHPGIEIVNIAQEDLY 76 (198)
T ss_pred eEEEEEechhhHHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHcCCceEEEecCCC-----CCCceEEEEEeeccEE
Confidence 356777665553211 121 23357765543 2467899999999999999974211 111111 11122222
Q ss_pred EEEEEEEeeeeEeeeCCCCCccCcc---EEEech----HHHHHHHHHHHhcC--CeE-EeccCHHHHHHHHHhcCCCCeE
Q 018090 192 IVGEVQLVVNHCLLGLPGVLKEELK---RVFSHP----QALAQCEMTLSNLG--IVR-ISADDTAGAAQMVASIGERDTG 261 (361)
Q Consensus 192 IvgEi~lpI~h~Lla~~g~~l~~Ik---~VySHP----qALaQC~~fL~~~~--~~~-i~~~STA~AA~~va~~~~~~~A 261 (361)
+ .++-+|-+.....++++++. -|.-.+ ....+..+++.+.+ .+. ..+++......+++.+ ...
T Consensus 77 l----v~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi 149 (198)
T cd08486 77 L----AVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG---AAS 149 (198)
T ss_pred E----EecCCCccccCCcccHHHHcCCCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---ceE
Confidence 1 23444544333334455443 332121 23456677777655 233 4455555566666653 356
Q ss_pred EecCHhhH
Q 018090 262 AVASAQAA 269 (361)
Q Consensus 262 AIas~~AA 269 (361)
+|.+..++
T Consensus 150 ~~lp~~~~ 157 (198)
T cd08486 150 SIVPASVA 157 (198)
T ss_pred EEcchhhc
Confidence 77776543
No 100
>PRK11260 cystine transporter subunit; Provisional
Probab=77.28 E-value=6.4 Score=36.84 Aligned_cols=48 Identities=13% Similarity=0.126 Sum_probs=40.5
Q ss_pred cEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 120 VRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+|+. ..|+..+....+.++..++..+++..+++++|.+|++|+.+.+
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 46776 6788777777777888889999999999999999999998874
No 101
>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=77.16 E-value=3.4 Score=32.03 Aligned_cols=33 Identities=27% Similarity=0.361 Sum_probs=27.6
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeee
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
.|-+..+|+||-|+++-+.|+.+|+|+..-...
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~ 34 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAW 34 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEE
Confidence 355667899999999999999999999875544
No 102
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=76.85 E-value=39 Score=32.85 Aligned_cols=141 Identities=14% Similarity=0.042 Sum_probs=74.8
Q ss_pred CCCccEEEEeCCCCcHHHHHH-HHHC-C----CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCC
Q 018090 116 DGTKVRVAYQGLPGAYSEAAA-RKAY-P----KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHR 189 (361)
Q Consensus 116 ~~~~~rIAyLGP~GTySe~AA-~~~f-~----~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~ 189 (361)
.....||+|+...+-+ ..|- +.+| . +++++.+.+-.++++++..|++|+|++..... ..-.....+
T Consensus 21 ~~~~v~~~y~~~~~~~-~vA~~~g~f~~~~Gl~Ve~~~~~~~~~~~~al~~G~~D~a~~~~~~~-------~~a~~~g~~ 92 (320)
T PRK11480 21 QAVNVTVAYQTSAEPA-KVAQADNTFAKESGATVDWRKFDSGASIVRALASGDVQIGNLGSSPL-------AVAASQQVP 92 (320)
T ss_pred CCCeEEEEecCCCcHH-HHHHHcCchHHHcCCeeEEEEeCCHHHHHHHHHCCCCCEECcCchHH-------HHHHHCCCC
Confidence 4567899998532212 2222 2234 2 37889999999999999999999997653211 111112335
Q ss_pred eEEEEEEE-EeeeeEeeeCCCC-CccCc--cEEEechHH--HHHHHHHHHhcC-----CeEEeccCHHHHHHHHHhcCCC
Q 018090 190 LHIVGEVQ-LVVNHCLLGLPGV-LKEEL--KRVFSHPQA--LAQCEMTLSNLG-----IVRISADDTAGAAQMVASIGER 258 (361)
Q Consensus 190 L~IvgEi~-lpI~h~Lla~~g~-~l~~I--k~VySHPqA--LaQC~~fL~~~~-----~~~i~~~STA~AA~~va~~~~~ 258 (361)
+.+++-.. ......|++++++ +++|+ |+|...+-. ...-..+|++.| ++.+... .+.++..+..++ -
T Consensus 93 ~~~v~~~~~~~~~~~lv~~~~I~s~~DLkGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~-~~~~~~Al~~G~-V 170 (320)
T PRK11480 93 IEVFLLASKLGNSEALVVKKTISKPEDLIGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQ-PPAIIAAWQRGD-I 170 (320)
T ss_pred eEEEEeeccCCcceEEEecCCCCChHHcCCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECC-cHHHHHHHHcCC-c
Confidence 65554322 2223467776653 44555 466643221 122356677654 3334433 344555555442 3
Q ss_pred CeEEecCH
Q 018090 259 DTGAVASA 266 (361)
Q Consensus 259 ~~AAIas~ 266 (361)
+.+++...
T Consensus 171 DAa~~~~p 178 (320)
T PRK11480 171 DGAYVWAP 178 (320)
T ss_pred CEEEEcch
Confidence 44444443
No 103
>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=76.78 E-value=3.7 Score=28.81 Aligned_cols=31 Identities=23% Similarity=0.281 Sum_probs=26.4
Q ss_pred EEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 313 FTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 313 f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
+..++.||.+.++++.|+++|||+..|..-+
T Consensus 6 ~~~~~~~~~~~~i~~~L~~~~i~i~~i~~~~ 36 (61)
T cd04891 6 KGVPDKPGVAAKIFSALAEAGINVDMIVQSV 36 (61)
T ss_pred ecCCCCCcHHHHHHHHHHHcCCcEEEEEEcC
Confidence 3457889999999999999999998886544
No 104
>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=76.09 E-value=7.9 Score=35.58 Aligned_cols=88 Identities=16% Similarity=0.056 Sum_probs=50.7
Q ss_pred ccEEEEeCCCCcHHHHHH----HHHCC------CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcC
Q 018090 119 KVRVAYQGLPGAYSEAAA----RKAYP------KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRH 188 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA----~~~f~------~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~ 188 (361)
..+|++.++.++..+... .+..+ ..+++...++.+++++|.+|++|.++++-. ...+...+..+ ...
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 468999987654433322 22222 145677778999999999999999998722 11111111100 012
Q ss_pred CeEEEEEEEEeeeeEeeeCCC
Q 018090 189 RLHIVGEVQLVVNHCLLGLPG 209 (361)
Q Consensus 189 ~L~IvgEi~lpI~h~Lla~~g 209 (361)
++.+.++-.....+.++.+++
T Consensus 218 ~~~~~~~~~~~~~~~~~~~~~ 238 (254)
T TIGR01098 218 KVRVIWKSPLIPNDPIAVRKD 238 (254)
T ss_pred heEEEEecCCCCCCCEEEECC
Confidence 577887654434455655554
No 105
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=75.55 E-value=48 Score=27.90 Aligned_cols=122 Identities=13% Similarity=0.031 Sum_probs=62.0
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc
Q 018090 140 YPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK 216 (361)
Q Consensus 140 f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik 216 (361)
+|+.++.... +..+..+.+.+|++|+|++.-.... .....++ .|.+.++.+ .++-.|-+...+..+++++.
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~--~~~~~~~~~~l~~~~~~~----v~~~~hp~~~~~~i~~~~L~ 99 (200)
T cd08453 26 YPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGA--SAPPALAYRPLLSEPLVL----AVPAAWAAEGGAPLALAAVA 99 (200)
T ss_pred CCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCccc--CCCcceeEEEeeeCceEE----EEECCCccccCCCCCHHHhc
Confidence 5776655443 4678899999999999997422110 0011111 222233322 23334444333223444433
Q ss_pred ---EEE-ech---HHHHHHHHHHHhcCC--eE-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 217 ---RVF-SHP---QALAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 217 ---~Vy-SHP---qALaQC~~fL~~~~~--~~-i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
-|. +.. .....+.+++.+.+. +. ..+++...+.++++.+ ...++.+...++
T Consensus 100 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08453 100 AEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAG---MGVALVPASLRN 160 (200)
T ss_pred cCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcC---CcEEEeEhHHhh
Confidence 333 221 123456777777653 22 3455555666666654 346677776553
No 106
>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=74.79 E-value=3.4 Score=30.40 Aligned_cols=28 Identities=25% Similarity=0.392 Sum_probs=24.5
Q ss_pred EecCCcchHHHHHHHHHHCCccccceee
Q 018090 314 TLEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 314 ~~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
.+++.||.+.++++.|++.|||+..|..
T Consensus 8 ~~~~~~g~~~~i~~~L~~~~I~i~~i~~ 35 (75)
T cd04913 8 GVPDKPGVAAKIFGALAEANINVDMIVQ 35 (75)
T ss_pred CCCCCCcHHHHHHHHHHHcCCeEEEEEe
Confidence 4578999999999999999999987743
No 107
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=74.73 E-value=20 Score=33.74 Aligned_cols=94 Identities=11% Similarity=0.017 Sum_probs=53.9
Q ss_pred ccEEEEeCCCCcHHHHHHHHHC----CCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEE
Q 018090 119 KVRVAYQGLPGAYSEAAARKAY----PKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVG 194 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f----~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Ivg 194 (361)
..+||+ ..||..+....++. ...+++.+++..+++++|.+|++|..+.. ..+ +..+......+++
T Consensus 148 g~~V~v--~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~d------~~~---~~~~~~~~~~~~~ 216 (259)
T PRK11917 148 GANIGV--AQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVD------KSI---LLGYVDDKSEILP 216 (259)
T ss_pred CCeEEE--ecCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEec------HHH---HHHhhhcCCeecC
Confidence 357888 45665554433322 23567789999999999999999977642 111 1111222333444
Q ss_pred EEEEeeeeEeeeCCCCCccCccEEEechHHHHHHHHHHHh
Q 018090 195 EVQLVVNHCLLGLPGVLKEELKRVFSHPQALAQCEMTLSN 234 (361)
Q Consensus 195 Ei~lpI~h~Lla~~g~~l~~Ik~VySHPqALaQC~~fL~~ 234 (361)
+..-+..++++.+++ +++-..+...+|.+
T Consensus 217 ~~~~~~~~~~a~~k~-----------~~~l~~~ln~~l~~ 245 (259)
T PRK11917 217 DSFEPQSYGIVTKKD-----------DPAFAKYVDDFVKE 245 (259)
T ss_pred CcCCCCceEEEEeCC-----------CHHHHHHHHHHHHH
Confidence 333333345554443 35556666777765
No 108
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=74.56 E-value=8.4 Score=35.47 Aligned_cols=48 Identities=15% Similarity=0.060 Sum_probs=38.6
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEE
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVL 168 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVV 168 (361)
..+|++. .|+..+.-..+.+++.+++.+++.++++++|.+|++|+.+.
T Consensus 131 g~~I~v~--~g~~~~~~l~~~~~~~~i~~~~~~~~~~~~L~~grvDa~i~ 178 (247)
T PRK09495 131 GKVVAVK--SGTGSVDYAKANIKTKDLRQFPNIDNAYLELGTGRADAVLH 178 (247)
T ss_pred CCEEEEe--cCchHHHHHHhcCCCCceEEcCCHHHHHHHHHcCceeEEEe
Confidence 3478874 47776666666677778889999999999999999998885
No 109
>cd04927 ACT_ACR-like_2 Second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the second ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=74.55 E-value=4.1 Score=31.87 Aligned_cols=30 Identities=10% Similarity=0.304 Sum_probs=25.2
Q ss_pred EEEEecCCcchHHHHHHHHHHCCcccccee
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIE 340 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIE 340 (361)
+-+..+|+||.|+++.+.|+.+|+|+..=.
T Consensus 3 ~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~ 32 (76)
T cd04927 3 LKLFCSDRKGLLHDVTEVLYELELTIERVK 32 (76)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCCeEEEEE
Confidence 335567999999999999999999997543
No 110
>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=74.19 E-value=51 Score=27.62 Aligned_cols=123 Identities=20% Similarity=0.122 Sum_probs=62.5
Q ss_pred HCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc-
Q 018090 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (361)
Q Consensus 139 ~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik- 216 (361)
.+|+.++.-. .+..++++.+.+|++|+|+..-.....+. ....|.+..+.++ .+-+|-+......+++++.
T Consensus 26 ~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~ 98 (200)
T cd08411 26 AYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGL---EEEPLFDEPFLLA----VPKDHPLAKRKSVTPEDLAG 98 (200)
T ss_pred HCCCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCCCCCc---eEEEeeccceEEE----ecCCCCccccCccCHHHHcC
Confidence 3566665544 35788999999999999997533211110 0111222222221 1222323222222333322
Q ss_pred --EEE-ech-HHHHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 217 --RVF-SHP-QALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 217 --~Vy-SHP-qALaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
-|. +.. ....+..+++.+++. ....++|...+.+++..+ ...|+.+...++.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 157 (200)
T cd08411 99 ERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAG---LGITLLPELAVPS 157 (200)
T ss_pred CceEecCCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CCEEEeCHHHhcc
Confidence 222 111 123344555555442 245667777777888765 3578888887764
No 111
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=72.58 E-value=3 Score=38.13 Aligned_cols=39 Identities=21% Similarity=0.470 Sum_probs=32.2
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
+-.+.+-+.|+||.|..+.+.|+.+|.|.-+|--=|+-.
T Consensus 4 ~rilsvlv~ne~GvLsRv~glfsrRG~NIeSltv~~tE~ 42 (163)
T COG0440 4 RRILSLLVENEPGVLSRVTGLFSRRGYNIESLTVGPTET 42 (163)
T ss_pred eEEEEEEEECCCCeeehhhHHHHhcCcccceEEEEecCC
Confidence 445666778999999999999999999999887665543
No 112
>PRK08673 3-deoxy-7-phosphoheptulonate synthase; Reviewed
Probab=71.56 E-value=0.57 Score=47.19 Aligned_cols=32 Identities=13% Similarity=0.156 Sum_probs=29.4
Q ss_pred CCCCCCcccchhhhhcccccccccccccCCcc
Q 018090 62 DRPYTPDVQSSEANERSQDSQSSGFHKDLNLL 93 (361)
Q Consensus 62 ~~~~~p~~~~~~~~~~~~~~~~~~~~~d~~~l 93 (361)
|+-+.|++++||++|+|.|++|+.|++++..+
T Consensus 297 E~H~~pd~alsD~~~sl~p~e~~~lv~~i~~i 328 (335)
T PRK08673 297 EVHPDPEKALSDGPQSLTPEEFEELMKKLRAI 328 (335)
T ss_pred EecCCcccCCCcchhcCCHHHHHHHHHHHHHH
Confidence 77889999999999999999999999998654
No 113
>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=71.43 E-value=13 Score=39.25 Aligned_cols=178 Identities=19% Similarity=0.233 Sum_probs=91.6
Q ss_pred HHHHHHHcCCcCeEEEeeecccccchHHhHHHHhc--CCeEEEEEEEEeee---eEeeeCCCCCccC---------ccEE
Q 018090 153 AAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLR--HRLHIVGEVQLVVN---HCLLGLPGVLKEE---------LKRV 218 (361)
Q Consensus 153 eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~--~~L~IvgEi~lpI~---h~Lla~~g~~l~~---------Ik~V 218 (361)
|+++.+. +..|+-|+|+- .+|.+.-..-.|.. .+.+|+|--...-. ..+-+..-..+.. ++.+
T Consensus 158 EI~~q~~-~~~D~vvvpvG--gGGliaGia~~lk~~~p~~kVIgVep~~~~~~~~s~~~g~~~~~~~~~t~adgiav~~~ 234 (499)
T TIGR01124 158 EILRQVA-NPLDAVFVPVG--GGGLAAGVAALIKQLMPEIKVIGVEPTDSDCMKQALDAGEPVDLDQVGLFADGVAVKRV 234 (499)
T ss_pred HHHHhCC-CCCCEEEEccC--ccHHHHHHHHHHHHhCCCCEEEEEEECCChHHHHHHhcCCceeCCCCCCccCcccCCCc
Confidence 4444442 36899999975 46666666555543 45777774442211 1111100001111 1222
Q ss_pred EechHHHHHHHHHHHhcCCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCceeeccccCCCCCceEEEEEeeCC
Q 018090 219 FSHPQALAQCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREP 298 (361)
Q Consensus 219 ySHPqALaQC~~fL~~~~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~ 298 (361)
=+..+.-|+++++. +-.+.......|.+.+.+.. -.-+.+..|+-+.+|.-+.+...- .+.|=-+|++-..
T Consensus 235 --g~~~~~~~~~~vd~--vv~V~d~ei~~ai~~l~~~~---gii~EpagA~~lAal~~~~~~~~~--~~~~vv~i~sG~n 305 (499)
T TIGR01124 235 --GDETFRLCQQYLDD--IVTVDTDEVCAAIKDLFEDT---RAVAEPAGALALAGLKKYVALHGI--RGQTLVAILSGAN 305 (499)
T ss_pred --cHHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhc---CcEEechHHHHHHHHHHhhhhcCC--CCCeEEEEECCCC
Confidence 14566666666542 22233333455666666542 123344455556665544332211 1333223333221
Q ss_pred CCC--------C--CCCCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 299 IIA--------G--TDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 299 ~~~--------~--~~~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
... . ........+.|.+|++||+|.++++.++.+ |+|.++=|-.
T Consensus 306 ~~~~~l~~~~~r~~~~~~re~~l~V~iPerPGal~~f~~~i~~~--nItef~yr~~ 359 (499)
T TIGR01124 306 MNFHRLRYVSERCELGEQREALLAVTIPEQPGSFLKFCELLGNR--NITEFNYRYA 359 (499)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhhc--ceEEEEEEec
Confidence 110 0 112357888899999999999999999974 8888776643
No 114
>PRK05198 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=71.32 E-value=0.61 Score=45.60 Aligned_cols=29 Identities=14% Similarity=0.108 Sum_probs=25.7
Q ss_pred CCCcccchhhhhcccccccccccccCCcc
Q 018090 65 YTPDVQSSEANERSQDSQSSGFHKDLNLL 93 (361)
Q Consensus 65 ~~p~~~~~~~~~~~~~~~~~~~~~d~~~l 93 (361)
-.|++++|||+|+|.+++|+.||+++..+
T Consensus 232 pdP~~AlsDg~q~l~~~~~~~ll~~l~~i 260 (264)
T PRK05198 232 PDPDNALSDGPNMLPLDKLEPLLEQLKAI 260 (264)
T ss_pred CCccccCCCccccCCHHHHHHHHHHHHHH
Confidence 47889999999999999999999987443
No 115
>PRK13396 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=70.88 E-value=0.62 Score=47.27 Aligned_cols=34 Identities=9% Similarity=0.096 Sum_probs=30.3
Q ss_pred cCCCCCCCcccchhhhhcccccccccccccCCcc
Q 018090 60 EDDRPYTPDVQSSEANERSQDSQSSGFHKDLNLL 93 (361)
Q Consensus 60 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~d~~~l 93 (361)
.=|+-+.|++++||++|+|.|++|++|++++..+
T Consensus 304 iIE~H~~pd~AlsD~~qsl~p~~~~~l~~~i~~i 337 (352)
T PRK13396 304 MIEVHPNPAKALSDGPQSLTPDRFDRLMQELAVI 337 (352)
T ss_pred EEEecCCcccCCChhhhcCCHHHHHHHHHHHHHH
Confidence 3467789999999999999999999999999766
No 116
>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=70.86 E-value=6.7 Score=30.58 Aligned_cols=33 Identities=15% Similarity=0.097 Sum_probs=27.9
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
|.+.-+|+||-.+++-+.++++|.|+..+...=
T Consensus 4 ltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~ 36 (77)
T cd04893 4 ISALGTDRPGILNELTRAVSESGCNILDSRMAI 36 (77)
T ss_pred EEEEeCCCChHHHHHHHHHHHcCCCEEEceeeE
Confidence 445668999999999999999999998776543
No 117
>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=70.82 E-value=9.2 Score=30.58 Aligned_cols=40 Identities=28% Similarity=0.231 Sum_probs=31.0
Q ss_pred EEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCC
Q 018090 309 TSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPL 349 (361)
Q Consensus 309 tSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw 349 (361)
..+.|+.|.+||+|.+.|+.+. -+-|+|.++=|-.....+
T Consensus 2 ~~~~v~iPErpGal~~Fl~~l~-p~~~ITeF~YR~~~~~~a 41 (81)
T cd04907 2 RLFRFEFPERPGALKKFLNELL-PKWNITLFHYRNQGSDYG 41 (81)
T ss_pred eEEEEEcCCCCCHHHHHHHHhC-CCCeEeEEEEecCCCCce
Confidence 3567889999999999999994 378888888776544433
No 118
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=70.80 E-value=12 Score=34.57 Aligned_cols=35 Identities=23% Similarity=0.408 Sum_probs=29.6
Q ss_pred EEEEEEe--cCCcchHHHHHHHHHHCCccccceeeec
Q 018090 309 TSIVFTL--EEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 309 tSi~f~~--~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
..+.|.+ .||||-+.++=+-|..+||||-.++||-
T Consensus 91 ~~v~v~v~a~DrpgIv~~~T~lf~~~~inie~L~~~~ 127 (176)
T COG2716 91 APVWVYVDANDRPGIVEEFTALFDGHGINIENLVSRT 127 (176)
T ss_pred ceEEEEEEecCCccHHHHHHHHHHhcCCchhhceeee
Confidence 4455554 5999999999999999999999999864
No 119
>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=70.74 E-value=87 Score=28.75 Aligned_cols=140 Identities=19% Similarity=0.134 Sum_probs=70.3
Q ss_pred CCccEEEEeCCCCcHHHHHHHH---HCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEE
Q 018090 117 GTKVRVAYQGLPGAYSEAAARK---AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHI 192 (361)
Q Consensus 117 ~~~~rIAyLGP~GTySe~AA~~---~f~~~e~vp-~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 192 (361)
.+..+|++.++ + +--.+..+ .+|+.++.- ..+..++++.+.+|++|.|++.......+. ....|.+..+.+
T Consensus 86 ~~~l~ig~~~~-~-~~~~~l~~~~~~~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~l 160 (279)
T TIGR03339 86 EGSLRIAATAP-Y-YVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRL---DRVVLGNDPLVA 160 (279)
T ss_pred ceEEEEeCchH-H-HHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEecccCCCce---EEEEcCCceEEE
Confidence 35678887643 1 22222222 256666543 357889999999999999997533221110 001111112221
Q ss_pred EEEEEEeeeeEeeeCCCCCccCcc---EEEech--HHHHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEec
Q 018090 193 VGEVQLVVNHCLLGLPGVLKEELK---RVFSHP--QALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVA 264 (361)
Q Consensus 193 vgEi~lpI~h~Lla~~g~~l~~Ik---~VySHP--qALaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIa 264 (361)
..+-+|-|...+..+++++. -|...+ .......+|+.+.+. ....++|...+.+++..+ ...++.
T Consensus 161 ----v~s~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~l 233 (279)
T TIGR03339 161 ----VVHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAG---LGVSVV 233 (279)
T ss_pred ----EECCCCccccCCCcCHHHHhCCCeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcC---CCEEEc
Confidence 11223333322223333333 333221 123456777776542 334567777777777764 235666
Q ss_pred CHhh
Q 018090 265 SAQA 268 (361)
Q Consensus 265 s~~A 268 (361)
+...
T Consensus 234 p~~~ 237 (279)
T TIGR03339 234 SAAE 237 (279)
T ss_pred chhh
Confidence 6643
No 120
>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=70.51 E-value=44 Score=30.69 Aligned_cols=128 Identities=22% Similarity=0.194 Sum_probs=72.5
Q ss_pred eeecCCHHHHHHHHHcCCcCeEEEeeecc--cccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCC-----CCccCc--
Q 018090 145 TVPCDQFEAAFKAVELWLVDKAVLPIENS--VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG-----VLKEEL-- 215 (361)
Q Consensus 145 ~vp~~sf~eVf~aV~~g~~d~gVVPIENS--~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g-----~~l~~I-- 215 (361)
..+..| .+.+.++.+|.+|.|.+=+-.. -+-.+...-++|...++.++.-. .=...|+.++| .+++|+
T Consensus 15 ~~~~gS-~~gl~~L~~g~~~iAg~h~~~~~~~~~n~~~~~~~l~g~~~v~v~~~--~r~~Gl~v~~~np~~i~~~~dL~~ 91 (193)
T PF12727_consen 15 VQYTGS-RAGLSALARGEADIAGIHLPDPESGEYNIPFVRRLLPGIEVVLVRLA--RREQGLIVRPGNPKGITSLEDLAD 91 (193)
T ss_pred EEecCC-HHHHHHHHCCCceEEEecCCCCcccccchHHHHHhcCCCcEEEEeee--EEeeeEEEeCCCCccCCCHHHhcc
Confidence 344444 4557899999999998843322 22222222334444454443222 22356777777 344555
Q ss_pred -c-EEEechHHHHHHHHHHHh----cCC-----e--EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH-cCCceee
Q 018090 216 -K-RVFSHPQALAQCEMTLSN----LGI-----V--RISADDTAGAAQMVASIGERDTGAVASAQAAEI-YGLDILA 278 (361)
Q Consensus 216 -k-~VySHPqALaQC~~fL~~----~~~-----~--~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~-YgL~iLa 278 (361)
. +++.-+.. .=.+.+|++ .++ . -..+.|..+.|..|+.+ ...++++.+.+|+. |||.++-
T Consensus 92 ~~~r~vnR~~G-SGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G--~AD~G~g~~~~A~~~~gL~Fvp 165 (193)
T PF12727_consen 92 PGLRFVNRQPG-SGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASG--KADAGIGIRAAAEEFYGLDFVP 165 (193)
T ss_pred CCcEEEECCCC-CHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcC--CCCEEeehHHHHHhhcCCCcEE
Confidence 2 23333333 335555554 221 1 13456667778888876 46789999999975 7999874
No 121
>TIGR01362 KDO8P_synth 3-deoxy-8-phosphooctulonate synthase. In Gram-negative bacteria, this is the first step in the biosynthesis of 3-deoxy-D-manno-octulosonate, part of the oligosaccharide core of lipopolysaccharide.
Probab=70.14 E-value=0.66 Score=45.19 Aligned_cols=29 Identities=17% Similarity=0.153 Sum_probs=26.0
Q ss_pred CCCcccchhhhhcccccccccccccCCcc
Q 018090 65 YTPDVQSSEANERSQDSQSSGFHKDLNLL 93 (361)
Q Consensus 65 ~~p~~~~~~~~~~~~~~~~~~~~~d~~~l 93 (361)
-.|++++|||+|.+.+++|+.||+++..+
T Consensus 224 pdP~~AlsDg~q~l~~~~~~~ll~~l~~i 252 (258)
T TIGR01362 224 PDPKNAKSDGPNMLPLSELEGLLEKLLAI 252 (258)
T ss_pred CCccccCCCccccCCHHHHHHHHHHHHHH
Confidence 47899999999999999999999988544
No 122
>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=69.16 E-value=67 Score=26.85 Aligned_cols=122 Identities=13% Similarity=0.079 Sum_probs=59.4
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc--
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I-- 215 (361)
.+|+.++.-.. +..++.+.+.+|++|+|+.+-.....+... ..|.+..+. +..+-+|-+...+..+++++
T Consensus 26 ~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----~v~~~~~pl~~~~~~~~~~l~~ 98 (198)
T cd08446 26 ARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAV---ENVAQERLY----LAVPKSHPLAARPAVSLADLRN 98 (198)
T ss_pred HCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecCCCCCCcee---EEeeeccEE----EEEeCCCCcccCCccCHHHHcC
Confidence 36776554433 567788999999999999753211111000 011122222 22233343332221233332
Q ss_pred -cEEE-ech---HHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 -KRVF-SHP---QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 -k~Vy-SHP---qALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
.-|. ... ....+..+|+.+.+. + ...++|...+.+++..+ ...++.++..+.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (198)
T cd08446 99 EPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAG---FGVCIVPESVAA 158 (198)
T ss_pred CCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcC---CcEEEchhhhhc
Confidence 3332 121 112334456665442 2 24567777777777764 356777776554
No 123
>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=69.07 E-value=66 Score=26.75 Aligned_cols=32 Identities=13% Similarity=-0.043 Sum_probs=24.4
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEee
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPI 170 (361)
.+|+.++.-.. +-.++++.+.+|++|+|++..
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08450 25 EHPDLDVELSSLFSPQLAEALMRGKLDVAFMRP 57 (196)
T ss_pred hCCCcEEEEEecChHHHHHHHhcCCccEEEEeC
Confidence 35776665544 467889999999999999753
No 124
>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=68.43 E-value=6.5 Score=30.85 Aligned_cols=27 Identities=22% Similarity=0.428 Sum_probs=24.8
Q ss_pred ecCCcchHHHHHHHHHHCCccccceee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
+++.||.+.++++.|+++|||.-.|-+
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~VDmI~~ 37 (75)
T cd04932 11 MLHAQGFLAKVFGILAKHNISVDLITT 37 (75)
T ss_pred CCCCcCHHHHHHHHHHHcCCcEEEEee
Confidence 468899999999999999999999965
No 125
>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=67.68 E-value=73 Score=26.71 Aligned_cols=121 Identities=11% Similarity=-0.015 Sum_probs=60.0
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhH--HHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNY--DLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tl--DlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I 215 (361)
.+|+.++.-.. +-.++.+.+.+|++|+|++.-..... ...+ ..|.+.++.+ ..+-+|-|......+++++
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~~~l~~~~l~~~~~~~----~~~~~hpl~~~~~i~~~dL 97 (198)
T cd08437 25 TGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLE---NSALHSKIIKTQHFMI----IVSKDHPLAKAKKVNFADL 97 (198)
T ss_pred hCCceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCC---cccceEEEeecceEEE----EecCCCcccccCcccHHHH
Confidence 35776655443 57889999999999999975321000 0011 1122222222 2233344433322344444
Q ss_pred c---EEE-echH-HHHHHHHHHHhcCC--eE-EeccCHHHHHHHHHhcCCCCeEEecCHhhH
Q 018090 216 K---RVF-SHPQ-ALAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAA 269 (361)
Q Consensus 216 k---~Vy-SHPq-ALaQC~~fL~~~~~--~~-i~~~STA~AA~~va~~~~~~~AAIas~~AA 269 (361)
. -|. .... --.+..+++.+.+. +. ..++|...+.++++.+ ...++.+...+
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 156 (198)
T cd08437 98 KKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVREN---VGIGFLTDIAV 156 (198)
T ss_pred cCCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CcEEEEEhhhc
Confidence 3 222 1111 12345556665542 33 4456666666677664 24677776654
No 126
>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=67.44 E-value=71 Score=26.50 Aligned_cols=122 Identities=14% Similarity=0.091 Sum_probs=60.8
Q ss_pred HCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecc--cccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc
Q 018090 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENS--VGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (361)
Q Consensus 139 ~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS--~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I 215 (361)
.+|+.++... .+..++.+.+.+|++|+|++..... ..|.. ...|.+..+.+ ..+-+|-+...+..+++++
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~~l~~~~~~~~~dL 97 (201)
T cd08435 25 RHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLA---SEELADEPLVV----VARPGHPLARRARLTLADL 97 (201)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCCCCcE---EEEcccCcEEE----EEeCCCcCcccCCcCHHHH
Confidence 3576655443 3578899999999999999753211 11110 11222233332 2233344433322333333
Q ss_pred c---EEEe-chH-HHHHHHHHHHhcCCe----EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 K---RVFS-HPQ-ALAQCEMTLSNLGIV----RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 k---~VyS-HPq-ALaQC~~fL~~~~~~----~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
. -|.. ... -.....+++.+.+.+ ...+++...+.+++..+ ...|+.+...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08435 98 ADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARS---DMLAVLPRSVAE 158 (201)
T ss_pred hcCCEEecCCCCcHHHHHHHHHHHcCCCCCCceEEEccHHHHHHHHhcC---CeEEEeEHHHhh
Confidence 2 2221 111 122345555554432 23456666666667654 356788888775
No 127
>PRK12457 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=67.37 E-value=0.82 Score=45.07 Aligned_cols=29 Identities=17% Similarity=0.159 Sum_probs=26.5
Q ss_pred CCCcccchhhhhcccccccccccccCCcc
Q 018090 65 YTPDVQSSEANERSQDSQSSGFHKDLNLL 93 (361)
Q Consensus 65 ~~p~~~~~~~~~~~~~~~~~~~~~d~~~l 93 (361)
-.|++++|||+|.|.+++|++|++++..+
T Consensus 240 pdP~~AlsDg~q~l~~~~~~~l~~~l~~i 268 (281)
T PRK12457 240 PDPDRARCDGPSALPLDQLEPFLSQVKAL 268 (281)
T ss_pred CCccccCCCcccccCHHHHHHHHHHHHHH
Confidence 47899999999999999999999998665
No 128
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=67.33 E-value=1.3e+02 Score=29.28 Aligned_cols=108 Identities=18% Similarity=0.176 Sum_probs=63.6
Q ss_pred CccEEEEe-CCCCcHHHHHHHHHC---C-CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH-HHh--cCC
Q 018090 118 TKVRVAYQ-GLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD-LLL--RHR 189 (361)
Q Consensus 118 ~~~rIAyL-GP~GTySe~AA~~~f---~-~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD-lL~--~~~ 189 (361)
..++|||. +|.....+.+...++ + +++++.+.+..+.++++.+|++|.... +. ...++ .+. ..+
T Consensus 31 ~~I~IG~~~~~~~~~~~~~~~~l~~~~G~~Vel~~f~~~~~~~~ALa~GdID~~~~-------qh-~~~l~~~~~~~g~~ 102 (271)
T PRK11063 31 NHIKVGVIVGAEQQVAEVAQKVAKEKYGLDVELVTFNDYVLPNEALSKGDIDANAF-------QH-KPYLDQQIKDRGYK 102 (271)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCeEEEEEecCcHHHHHHHHcCCcceecc-------cC-HHHHHHHHHHcCCc
Confidence 35899998 555544444444433 2 478999999999999999999998651 11 11222 222 245
Q ss_pred eEEEEEEEE-eeeeEeeeCCCCCccCcc---EEEec--hHHHHHHHHHHHhc
Q 018090 190 LHIVGEVQL-VVNHCLLGLPGVLKEELK---RVFSH--PQALAQCEMTLSNL 235 (361)
Q Consensus 190 L~IvgEi~l-pI~h~Lla~~g~~l~~Ik---~VySH--PqALaQC~~fL~~~ 235 (361)
+.+++-..+ |+. +....=.+++|++ +|... |.-.+.+-.+|.+.
T Consensus 103 l~~~~~~~vvp~~--~ys~~i~si~DL~~Gk~IAip~d~~n~~r~L~lL~~~ 152 (271)
T PRK11063 103 LVAVGNTFVYPIA--GYSKKIKSLDELQDGSQVAVPNDPTNLGRSLLLLQKV 152 (271)
T ss_pred EEEEeEEEEEEee--ccccCCCCHHHhcCCCEEEecCCCccHHHHHHHHHHC
Confidence 777665433 432 2222123556664 66544 65666666677763
No 129
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=67.27 E-value=26 Score=33.62 Aligned_cols=122 Identities=13% Similarity=-0.008 Sum_probs=66.8
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCccE
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR 217 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik~ 217 (361)
.+|+.++.... +-.++++.|.+|++|+|+++-+-...+.. ...|.+.++.+ +.+..|-|. ....+++++..
T Consensus 137 ~~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~l~---~~~l~~~~~~l----v~~~~hpl~-~~~~~~~~L~~ 208 (314)
T PRK09508 137 IAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFT---SVPLFKDELVL----VASKNHPRI-KGPITEEQLYN 208 (314)
T ss_pred hCCCcEEEEEeCcchhHHHHHhcCCccEEEecCCCCccccc---eeeeecCceEE----EEcCCCCcc-CCCCCHHHHhh
Confidence 35776655443 46888999999999999987542111111 11222333333 234445443 22234455431
Q ss_pred ----EEechHHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 218 ----VFSHPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 218 ----VySHPqALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
++.++....+..+|+.+.+. . ...++|......+|..+ ...++.+...++.
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 266 (314)
T PRK09508 209 EQHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQT---HLVAIAPRWLAEE 266 (314)
T ss_pred CCCEEecCCCCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhC---ChHHHHHHHHHHH
Confidence 23333333444667766542 2 35567777777777764 2467778877754
No 130
>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=67.02 E-value=54 Score=27.82 Aligned_cols=122 Identities=14% Similarity=0.101 Sum_probs=59.0
Q ss_pred HCCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc--
Q 018090 139 AYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK-- 216 (361)
Q Consensus 139 ~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik-- 216 (361)
.+|+.++.....-.+.++.|.+|++|+|+++-.....+.. ...|.+..+.+ ..+-+|-+.. ...+++++.
T Consensus 25 ~~P~i~l~i~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~----v~~~~hpl~~-~~~~~~~l~~~ 96 (200)
T cd08462 25 EAPGVRFELLPPDDQPHELLERGEVDLLIAPERFMSDGHP---SEPLFEEEFVC----VVWADNPLVG-GELTAEQYFSA 96 (200)
T ss_pred HCCCCEEEEecCChhHHHHHhcCCeeEEEecCCCCCCCce---eeeeeccceEE----EEcCCCCccC-CCCCHHHHhhC
Confidence 3576655444322399999999999999986332211110 00111112211 2244454432 233444443
Q ss_pred -EEE-echHHH-HHHH-HHHHhcCC--eE-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 217 -RVF-SHPQAL-AQCE-MTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 217 -~Vy-SHPqAL-aQC~-~fL~~~~~--~~-i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
-|. +..... .... .++.+.+. .. ..++|......+|+.+ ...||.++..++.
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~giailp~~~~~~ 155 (200)
T cd08462 97 GHVVVRFGRNRRPSFEDWFLNEYGLKRRVEVVTPSFSSIPPLLVGT---NRIATLHRRLAEQ 155 (200)
T ss_pred CCEEEecCCCCCccHHHHHHHHcCCcceEEEEeChHHHHHHHHHcC---chhhhhHHHHHHh
Confidence 121 121111 1122 23444443 22 4566666666777764 3578888877654
No 131
>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=65.94 E-value=58 Score=26.87 Aligned_cols=121 Identities=19% Similarity=0.165 Sum_probs=60.3
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc---
Q 018090 140 YPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL--- 215 (361)
Q Consensus 140 f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I--- 215 (361)
+|+.++... .+..++.+.+.+|++|+|++.......+... ..|.+..+.++ .+-.|-+......+++++
T Consensus 26 ~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~~~~~~~~i~~~~l~~~ 98 (201)
T cd08420 26 YPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIV---EPFAEDELVLV----VPPDHPLAGRKEVTAEELAAE 98 (201)
T ss_pred CCCceEEEEeCCcHHHHHHHHCCCccEEEecCCCCCcceEE---EeecCccEEEE----ecCCCCccccCccCHHHHhcC
Confidence 566554333 4567899999999999999854322111110 11122222222 222333332222333333
Q ss_pred cEEEechH--HHHHHHHHHHhcC-----C-eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 KRVFSHPQ--ALAQCEMTLSNLG-----I-VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 k~VySHPq--ALaQC~~fL~~~~-----~-~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
.-|.-.+. -..+..+++.+.+ . ....+++...+.++++.+ ...|+.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08420 99 PWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAG---LGISILSRLAVR 158 (201)
T ss_pred CEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcC---CCEEEeeHHHHH
Confidence 23322211 1234556665432 1 234566777777777764 357777877654
No 132
>COG2876 AroA 3-deoxy-D-arabino-heptulosonate 7-phosphate (DAHP) synthase [Amino acid transport and metabolism]
Probab=64.08 E-value=1.2 Score=43.89 Aligned_cols=29 Identities=21% Similarity=0.268 Sum_probs=25.5
Q ss_pred CCCcccchhhhhcccccccccccccCCcc
Q 018090 65 YTPDVQSSEANERSQDSQSSGFHKDLNLL 93 (361)
Q Consensus 65 ~~p~~~~~~~~~~~~~~~~~~~~~d~~~l 93 (361)
-+|++++||+.|++-+++|+.|+..+..+
T Consensus 252 p~P~~AlsD~~Qql~~~~f~~l~~~~~~~ 280 (286)
T COG2876 252 PDPEKALSDAKQQLTPEEFEELVKELRAL 280 (286)
T ss_pred CCcccccCcccccCCHHHHHHHHHHHHHH
Confidence 37899999999999999999999887443
No 133
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=63.94 E-value=57 Score=34.00 Aligned_cols=48 Identities=13% Similarity=0.138 Sum_probs=35.9
Q ss_pred cEEEEeCCCCcHHHHHHHH---HCCCCc--eeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 120 VRVAYQGLPGAYSEAAARK---AYPKCE--TVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~---~f~~~e--~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+|+.. .||..++...+ .+++.. .+.+.+.++++++|.+|++|+.|+.
T Consensus 150 k~I~V~--~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d 202 (482)
T PRK10859 150 GTLTVA--AGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIAD 202 (482)
T ss_pred CeEEEE--CCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEEC
Confidence 578874 67777766544 345543 4567899999999999999999874
No 134
>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=63.70 E-value=85 Score=26.05 Aligned_cols=122 Identities=16% Similarity=0.090 Sum_probs=61.2
Q ss_pred HCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc--
Q 018090 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (361)
Q Consensus 139 ~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I-- 215 (361)
.+|+.++... .+..++++.+.+|++|.|++.-.....|.. ...|.+..+. +..+-+|-|...+..+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~----~~~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08412 25 AYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIA---FEPLARLPPY----VWLPADHPLAGKDEVSLADLAA 97 (198)
T ss_pred HCCCcEEEEEECCHHHHHHHHHcCCCcEEEEcCCCCCcccc---eeeeeccceE----EEecCCCCCCCCCcCCHHHHcC
Confidence 3677655443 357889999999999999985332111100 0111112211 12333444433222333333
Q ss_pred -cEEE-echHHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 -KRVF-SHPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 -k~Vy-SHPqALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
.-|. .......+-.+++.+.+. + ...+++...+.+++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (198)
T cd08412 98 EPLILLDLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANG---LGYSLLNDRPYR 154 (198)
T ss_pred CcEEecCchhHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CCEEEeeccccc
Confidence 3333 222222333455655542 2 24456667777777654 346777777665
No 135
>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=62.61 E-value=86 Score=25.74 Aligned_cols=121 Identities=21% Similarity=0.087 Sum_probs=58.6
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc--
Q 018090 140 YPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK-- 216 (361)
Q Consensus 140 f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik-- 216 (361)
+|+.++.-. .+..++.+.+.+|++|.|+..-.....|.. ...|.+.++.+ ..+-+|-+...+..+++++.
T Consensus 26 ~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~pl~~~~~~~~~~l~~~ 98 (197)
T cd08440 26 HPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLE---FEPLLRDPFVL----VCPKDHPLARRRSVTWAELAGY 98 (197)
T ss_pred CCCcEEEEEeCChHHHHHHHHcCCccEEEEeCCCCCCCee---EEEeecccEEE----EecCCCCcccCCccCHHHHccC
Confidence 566655433 356889999999999999975321101100 00111112221 12223333222222333332
Q ss_pred -EE-EechHH-HHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 217 -RV-FSHPQA-LAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 217 -~V-ySHPqA-LaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
-| +.+... .....+++.+.+. ....++|...+.+++..+ ...|+.++..+.
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (197)
T cd08440 99 PLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAG---LGVAVLPALALP 155 (197)
T ss_pred CEEecCCCccHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEcchhHHH
Confidence 22 222211 2233455555442 234566777777777764 356777877654
No 136
>PRK06349 homoserine dehydrogenase; Provisional
Probab=62.49 E-value=12 Score=38.70 Aligned_cols=37 Identities=24% Similarity=0.380 Sum_probs=31.0
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
-|.+.+.|+||.|.++-+.|++++||+.++...+..+
T Consensus 350 ylRl~v~d~pGvLa~I~~~f~~~~vsI~si~q~~~~~ 386 (426)
T PRK06349 350 YLRLLVADKPGVLAKIAAIFAENGISIESILQKGAGG 386 (426)
T ss_pred EEEEEecCCcchHHHHHHHHhhcCccEEEEEeccCCC
Confidence 3445567999999999999999999999998777643
No 137
>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=62.09 E-value=73 Score=27.04 Aligned_cols=118 Identities=13% Similarity=0.033 Sum_probs=59.7
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCC------CCc
Q 018090 140 YPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG------VLK 212 (361)
Q Consensus 140 f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g------~~l 212 (361)
+|+.++.... +-.++.+.+.+|++|+|++.-.+.. . ...+ +..+.......++++.++ .++
T Consensus 26 ~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~--~--------~~~~--~~~~~l~~~~~~~~~~~~hpl~~~~~~ 93 (202)
T cd08468 26 APSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDG--A--------EPRL--IEERDWWEDTYVVIASRDHPRLSRLTL 93 (202)
T ss_pred CCCCEEEEEECChHhHHHHHHCCCccEEEecccccc--c--------CCCC--EEEEEEecCcEEEEEeCCCCCcCCCCH
Confidence 5766665443 5789999999999999997532210 0 0001 111111222223333222 333
Q ss_pred cCcc---EEE-e-chHHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHc
Q 018090 213 EELK---RVF-S-HPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (361)
Q Consensus 213 ~~Ik---~Vy-S-HPqALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~Y 272 (361)
+++. .|. . +...-.+..+++.+.+. + ...++|......+++.+ +..++.++.+++.+
T Consensus 94 ~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~---~~~~~~p~~~~~~~ 158 (202)
T cd08468 94 DAFLAERHLVVTPWNEDRGVVDQVLEKQGLEREIALQLPNVLNAPFIVASS---DLLMTLPRQAARAL 158 (202)
T ss_pred HHHhhCCCeEEecCCCCCchHHHHHHHcCCCceEEEEcChhHhHHHHHhcC---CeeeecHHHHHHHh
Confidence 3322 121 1 11122345666666543 2 34566666666666532 45778888877653
No 138
>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=62.05 E-value=7.9 Score=30.32 Aligned_cols=27 Identities=15% Similarity=0.300 Sum_probs=24.6
Q ss_pred ecCCcchHHHHHHHHHHCCccccceee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
+++.||.+.++++.|+++|||.-.|-+
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~vDmI~~ 37 (75)
T cd04935 11 MWQQVGFLADVFAPFKKHGVSVDLVST 37 (75)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe
Confidence 357899999999999999999999966
No 139
>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=61.92 E-value=9.2 Score=29.14 Aligned_cols=28 Identities=11% Similarity=0.143 Sum_probs=24.5
Q ss_pred ecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
.++.||.+.++++.++++|||+-.| ++-
T Consensus 9 ~~~~~~~~a~if~~La~~~InvDmI-~~~ 36 (67)
T cd04914 9 KDNENDLQQRVFKALANAGISVDLI-NVS 36 (67)
T ss_pred CCCCccHHHHHHHHHHHcCCcEEEE-Eec
Confidence 3577999999999999999999999 543
No 140
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=61.80 E-value=18 Score=35.64 Aligned_cols=51 Identities=37% Similarity=0.309 Sum_probs=39.5
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEeee
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIE 171 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIE 171 (361)
..|||.-|+- |-++.-.+-++++.++++. -|+++..||.+|++|.||+=.|
T Consensus 95 ~~rvavpG~~-TTA~lL~rl~~p~~~~V~m-~fdeI~~Avl~G~VDaGvlIHE 145 (272)
T COG2107 95 GKRVAVPGEM-TTAALLFRLAYPKAEIVYM-PFDEIIPAVLEGKVDAGVLIHE 145 (272)
T ss_pred cceEecCCcc-cHHHHHHHHhCCCceEEEe-eHHHHHHHHHcCCCccceEEee
Confidence 4578877763 3344445556788888877 5999999999999999999777
No 141
>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=60.59 E-value=19 Score=33.99 Aligned_cols=49 Identities=20% Similarity=0.167 Sum_probs=38.4
Q ss_pred ccEEEEeCCCCcHHHHHHHHH-CCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 119 KVRVAYQGLPGAYSEAAARKA-YPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~-f~~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
..+|+. +.|++.+...... ++..+++.+++.++++++|.+|++|+.+..
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 357885 5677777766553 455678899999999999999999988864
No 142
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=60.41 E-value=1.4e+02 Score=28.58 Aligned_cols=144 Identities=13% Similarity=0.033 Sum_probs=70.1
Q ss_pred CCCccEEEEeCCCCcH-HHHHH---HHHCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecc-cccchHHhHHHHhcCC
Q 018090 116 DGTKVRVAYQGLPGAY-SEAAA---RKAYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENS-VGGSIHRNYDLLLRHR 189 (361)
Q Consensus 116 ~~~~~rIAyLGP~GTy-Se~AA---~~~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS-~~G~V~~tlDlL~~~~ 189 (361)
..+..+||.-..-+.+ --... .+.+|+.++.-. .+..++.+.|.+|++|+|+.+-... ..+. ....|.+.+
T Consensus 91 ~~g~l~Ig~~~~~~~~~l~~~i~~f~~~~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~l---~~~~l~~~~ 167 (309)
T PRK12683 91 DSGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDL---VSFPYYSWH 167 (309)
T ss_pred CCceEEEEeccchHHHHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCCc---eEEEcccCe
Confidence 3456777774322221 11121 123577665433 4678999999999999999742211 1111 111122222
Q ss_pred eEEEEEEEEeeeeEeeeCCCCCccCcc---EEEech--HHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeE
Q 018090 190 LHIVGEVQLVVNHCLLGLPGVLKEELK---RVFSHP--QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTG 261 (361)
Q Consensus 190 L~IvgEi~lpI~h~Lla~~g~~l~~Ik---~VySHP--qALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~A 261 (361)
+. +..+..|-|...+..+++++. -|.-.+ .--.+...|+.+.+. . ...++|......+|..+ .+ .
T Consensus 168 ~~----~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~G-i 240 (309)
T PRK12683 168 HV----VVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELG--MG-V 240 (309)
T ss_pred EE----EEecCCCCcccCCccCHHHHhcCCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhC--CC-e
Confidence 22 334555555443334444432 332111 123456677776653 2 23455555555666654 23 4
Q ss_pred EecCHhhH
Q 018090 262 AVASAQAA 269 (361)
Q Consensus 262 AIas~~AA 269 (361)
++.+...+
T Consensus 241 ~~lp~~~~ 248 (309)
T PRK12683 241 GIVAAMAY 248 (309)
T ss_pred EEeehhhc
Confidence 45455444
No 143
>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=60.41 E-value=13 Score=38.23 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=29.9
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
.+..+.|.+|++||+|.++|+.....+-|++.++-|.
T Consensus 324 r~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~y~~ 360 (409)
T TIGR02079 324 LKHYFIVRFPQRPGALREFLNDVLGPNDDITRFEYTK 360 (409)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeee
Confidence 4778889999999999999994444555999887664
No 144
>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=60.39 E-value=1e+02 Score=25.87 Aligned_cols=119 Identities=18% Similarity=0.151 Sum_probs=60.8
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc
Q 018090 140 YPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK 216 (361)
Q Consensus 140 f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik 216 (361)
||+.++.... +..++.+.+.+|++|+|+...... ...+. .|.+..+.+ ..+-+|-+...+ .+++++.
T Consensus 26 ~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~~~-----~~~l~~~~l~~~~~~~----v~~~~~~l~~~~-i~~~~L~ 95 (201)
T cd08459 26 APGVRIETVRLPVDELEEALESGEIDLAIGYLPDL-----GAGFFQQRLFRERYVC----LVRKDHPRIGST-LTLEQFL 95 (201)
T ss_pred CCCCeEEEEecCccCHHHHhhCCCceEEEEcCCCC-----cccceEEEeecCceEE----EEcCCCccccCC-cCHHHHh
Confidence 5666655443 446888999999999999764321 11111 112222222 233344443222 3443332
Q ss_pred ---EEEechH--HHHHHHHHHHhcCC--eE-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 217 ---RVFSHPQ--ALAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 217 ---~VySHPq--ALaQC~~fL~~~~~--~~-i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
-|...+. ...+.++++.+++. .. ..++|.....++++.+ ...++.+...++.
T Consensus 96 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (201)
T cd08459 96 AARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQT---DLVATVPERLARL 155 (201)
T ss_pred hCCcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcC---CEEEecHHHHHHH
Confidence 2332221 22345667766553 33 3445555555666653 3578888877664
No 145
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=60.04 E-value=1.4e+02 Score=28.74 Aligned_cols=144 Identities=15% Similarity=0.042 Sum_probs=70.5
Q ss_pred CCCccEEEEeCCCCcH-HHHHHHH---HCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcC
Q 018090 116 DGTKVRVAYQGLPGAY-SEAAARK---AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRH 188 (361)
Q Consensus 116 ~~~~~rIAyLGP~GTy-Se~AA~~---~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~ 188 (361)
..+..+|+.....+.+ -..+... .+|+.++... .+..++++.+.+|++|+++.+-.+.. ...++ -|.+.
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 3456788875444432 1122222 2466655443 45788999999999999998622111 11111 11112
Q ss_pred CeEEEEEEEEeeeeEeeeCCCCCccCc---cEEEec-hH-HHHHHHHHHHhcC--Ce-EEeccCHHHHHHHHHhcCCCCe
Q 018090 189 RLHIVGEVQLVVNHCLLGLPGVLKEEL---KRVFSH-PQ-ALAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDT 260 (361)
Q Consensus 189 ~L~IvgEi~lpI~h~Lla~~g~~l~~I---k~VySH-Pq-ALaQC~~fL~~~~--~~-~i~~~STA~AA~~va~~~~~~~ 260 (361)
.+. +..+..|-+......+++++ .-|.-. .. -..+...++...+ .. ...++|......+|..+ -+
T Consensus 167 ~~~----~v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~G- 239 (313)
T PRK12684 167 NHC----VVVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELG--LG- 239 (313)
T ss_pred eEE----EEeCCCCccccCCCcCHHHHhcCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhC--Cc-
Confidence 222 23344455443322333332 222211 11 1233455665544 22 35566777777777764 23
Q ss_pred EEecCHhhHH
Q 018090 261 GAVASAQAAE 270 (361)
Q Consensus 261 AAIas~~AA~ 270 (361)
.++.+..+++
T Consensus 240 v~~lp~~~~~ 249 (313)
T PRK12684 240 VGIVADMAFD 249 (313)
T ss_pred eEEeehhhcc
Confidence 5555665554
No 146
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=59.07 E-value=1.7e+02 Score=28.56 Aligned_cols=146 Identities=14% Similarity=0.056 Sum_probs=76.6
Q ss_pred CCCccEEEEeCCCCcHH-HHHHH---HHCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCe
Q 018090 116 DGTKVRVAYQGLPGAYS-EAAAR---KAYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRL 190 (361)
Q Consensus 116 ~~~~~rIAyLGP~GTyS-e~AA~---~~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L 190 (361)
..+..+|+....-+++- -.+.. +.+|+.++.... +.+++++++.+|++|+|+++--+-..+... ...|.+..+
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 34567888876655542 12222 235776665544 468999999999999999863211111100 011222232
Q ss_pred EEEEEEEEeeeeEeeeC-CCCCccCcc---EEEech-HHH-HHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeE
Q 018090 191 HIVGEVQLVVNHCLLGL-PGVLKEELK---RVFSHP-QAL-AQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTG 261 (361)
Q Consensus 191 ~IvgEi~lpI~h~Lla~-~g~~l~~Ik---~VySHP-qAL-aQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~A 261 (361)
. +.++..|-|... ...+++|+. -|..-+ ... ....+++..++. . ...+++.....++|..+ ...
T Consensus 169 ~----l~~~~~hpl~~~~~~~~~~dl~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G---~Gi 241 (327)
T PRK12680 169 L----VVVPRGHALDTPRRAPDMAALAEHPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAG---LGV 241 (327)
T ss_pred E----EEEeCCChhhccCCCCCHHHHhcCCEEEecCCCchHHHHHHHHHHCCCCCcEEEEECCHHHHHHHHHcC---CCE
Confidence 2 234566666542 223444433 332221 122 445667776552 2 34566666777777764 235
Q ss_pred EecCHhhHH
Q 018090 262 AVASAQAAE 270 (361)
Q Consensus 262 AIas~~AA~ 270 (361)
|+.+..++.
T Consensus 242 a~lp~~~~~ 250 (327)
T PRK12680 242 GLLAEMAVN 250 (327)
T ss_pred EEeechhcc
Confidence 666666554
No 147
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=58.16 E-value=1.7e+02 Score=27.84 Aligned_cols=115 Identities=18% Similarity=0.161 Sum_probs=59.1
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCC------CCc
Q 018090 140 YPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG------VLK 212 (361)
Q Consensus 140 f~~~e~vp-~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g------~~l 212 (361)
+++.++.- ..+-.+++++|.+|++|+|+++..+... . . .+..+.......++++.++ .++
T Consensus 123 ~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~---~--------~--~l~~~~l~~~~~~lv~~~~~pl~~~i~~ 189 (312)
T PRK10341 123 FPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMK---L--------Q--DLHVEPLFESEFVLVASKSRTCTGTTTL 189 (312)
T ss_pred CCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCcccc---c--------C--CeeEEEEecccEEEEEcCCCchhccCCH
Confidence 56666543 3346899999999999999986543210 0 0 1222222223333333332 222
Q ss_pred cCcc---EEEe--chHHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 213 EELK---RVFS--HPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 213 ~~Ik---~VyS--HPqALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
+|+. -|.- ......+..+|+.+++. + ...++|.....+.+..+ ...++.+...++
T Consensus 190 ~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 252 (312)
T PRK10341 190 ESLKNEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA---DFLTVIPCDMTS 252 (312)
T ss_pred HHHhCCCeEccCCCCcHHHHHHHHHHHcCcCCCceEEecCHHHHHHHHHhC---CcEEEeeHHhcC
Confidence 3222 2211 11123344556665542 2 35566777777777664 346777776654
No 148
>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=58.13 E-value=13 Score=41.59 Aligned_cols=40 Identities=10% Similarity=0.091 Sum_probs=34.4
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
.+.|.|-+...|+||.|+++.++|+++|||+......-.+
T Consensus 777 ~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~ 816 (850)
T TIGR01693 777 RKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFG 816 (850)
T ss_pred CCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecC
Confidence 3578888889999999999999999999999887665544
No 149
>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=57.57 E-value=69 Score=27.72 Aligned_cols=133 Identities=16% Similarity=0.097 Sum_probs=77.2
Q ss_pred eCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEe
Q 018090 125 QGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCL 204 (361)
Q Consensus 125 LGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~L 204 (361)
.|...-+-.+++.+.--+.++++. ++..+++.+++|++|.++-++.. +.+.- ..+.... -.+...+.+
T Consensus 22 ~G~~~dl~~~i~~~~g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~--------~~~r~--~~~~~s~-p~~~~~~~~ 89 (225)
T PF00497_consen 22 SGIDVDLLRAIAKRLGIKIEFVPM-PWSRLLEMLENGKADIIIGGLSI--------TPERA--KKFDFSD-PYYSSPYVL 89 (225)
T ss_dssp ESHHHHHHHHHHHHHTCEEEEEEE-EGGGHHHHHHTTSSSEEESSEB---------BHHHH--TTEEEES-ESEEEEEEE
T ss_pred EEEhHHHHHHHHhhcccccceeec-ccccccccccccccccccccccc--------ccccc--ccccccc-cccchhhee
Confidence 344444445555544225788888 99999999999999987744432 33321 1233333 234445666
Q ss_pred eeCCCC-----C---ccCc--cEEEechHH--HHHHHHHHHhcCCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHc
Q 018090 205 LGLPGV-----L---KEEL--KRVFSHPQA--LAQCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (361)
Q Consensus 205 la~~g~-----~---l~~I--k~VySHPqA--LaQC~~fL~~~~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~Y 272 (361)
+.+++. . ++++ ++|..-.-. .....+...+ +++++.+.|..++.+++..+ .-.|+|+....+..+
T Consensus 90 ~~~~~~~~~~~~~~~~~dl~~~~i~~~~g~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~l~~g--~~d~~i~~~~~~~~~ 166 (225)
T PF00497_consen 90 VVRKGDAPPIKTIKSLDDLKGKRIGVVRGSSYADYLKQQYPS-NINIVEVDSPEEALEALLSG--RIDAFIVDESTAEYL 166 (225)
T ss_dssp EEETTSTCSTSSHSSGGGGTTSEEEEETTSHHHHHHHHHTHH-TSEEEEESSHHHHHHHHHTT--SSSEEEEEHHHHHHH
T ss_pred eeccccccccccccchhhhcCcccccccchhHHHHhhhhccc-hhhhcccccHHHHHHHHhcC--Ceeeeeccchhhhhh
Confidence 666541 2 2244 233333322 1122222222 67888899999999998876 356888877766543
No 150
>PLN03033 2-dehydro-3-deoxyphosphooctonate aldolase; Provisional
Probab=57.30 E-value=1.6 Score=43.26 Aligned_cols=32 Identities=6% Similarity=0.002 Sum_probs=27.7
Q ss_pred CCCCCCcccchhhhhcccccccccccccCCcc
Q 018090 62 DRPYTPDVQSSEANERSQDSQSSGFHKDLNLL 93 (361)
Q Consensus 62 ~~~~~p~~~~~~~~~~~~~~~~~~~~~d~~~l 93 (361)
|---.|++++|||+|.+.+++|+.|++.+..+
T Consensus 240 EvHpdP~~AlsDg~q~l~~~~l~~ll~~l~~i 271 (290)
T PLN03033 240 EVHDDPLSAPVDGPTQWPLRHLEELLEELIAI 271 (290)
T ss_pred EecCCccccCCCcccCcCHHHHHHHHHHHHHH
Confidence 33357999999999999999999999998655
No 151
>cd08456 PBP2_LysR The C-terminal substrate binding domain of LysR, transcriptional regulator for lysine biosynthesis, contains the type 2 periplasmic binding fold. LysR, the transcriptional activator of lysA encoding diaminopimelate decarboxylase, catalyses the decarboxylation of diaminopimelate to produce lysine. The LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational
Probab=57.17 E-value=1.1e+02 Score=25.43 Aligned_cols=122 Identities=13% Similarity=0.033 Sum_probs=57.7
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc-
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik- 216 (361)
.+|+.++.-.. +-.++.+.+.+|++|+|+..-.....+.. ...|.+..+.+ ..+-.|-+...+..+++++.
T Consensus 25 ~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08456 25 RHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIE---RERLLRIDGVC----VLPPGHRLAVKKVLTPSDLEG 97 (196)
T ss_pred HCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCee---EEEeeccCeEE----EecCCCchhccCccCHHHcCC
Confidence 35766554443 45678899999999999975322111100 01111122211 22333333322222333333
Q ss_pred --EEE-echHH-HHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 217 --RVF-SHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 217 --~Vy-SHPqA-LaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
-|. .+... ......++.+.+. . ...+++...+.+++..+ ...++.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (196)
T cd08456 98 EPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAG---VGVSVVNPLTAL 155 (196)
T ss_pred CcEEEecCCcchHHHHHHHHHHCCCCcceEEEEccHHHHHHHHHcC---CeEEEeChhhhc
Confidence 332 22222 2234556655442 2 24456666666777654 345666666554
No 152
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=56.97 E-value=12 Score=31.18 Aligned_cols=28 Identities=18% Similarity=0.247 Sum_probs=24.6
Q ss_pred EEecCCcchHHHHHHHHHHCCcccccee
Q 018090 313 FTLEEGPGMLFKALAVFALRDINLTKIE 340 (361)
Q Consensus 313 f~~~~~PGaL~~iL~~Fa~~~INLtkIE 340 (361)
+.=.|+||.-+.+-.+|+++|+|+..|+
T Consensus 8 V~GkDr~GIva~is~vLAe~~vNIldis 35 (90)
T COG3830 8 VIGKDRVGIVAAVSRVLAEHGVNILDIS 35 (90)
T ss_pred EEcCCCCchhHHHHHHHHHcCCcEEEHH
Confidence 3346999999999999999999998875
No 153
>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=56.77 E-value=11 Score=30.08 Aligned_cols=27 Identities=19% Similarity=0.343 Sum_probs=24.7
Q ss_pred ecCCcchHHHHHHHHHHCCccccceee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
.++.||.+.++++.|+++|||.-.|.+
T Consensus 11 ~~~~~g~~a~IF~~La~~~InVDmI~q 37 (78)
T cd04933 11 MLGQYGFLAKVFSIFETLGISVDVVAT 37 (78)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe
Confidence 357899999999999999999999965
No 154
>cd08443 PBP2_CysB The C-terminal substrate domain of LysR-type transcriptional regulator CysB contains type 2 periplasmic binding fold. CysB is a transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the regulation of transcription in response to sulfur source is attributed to two transcriptional regulators, CysB and Cbl. CysB, in association with Cbl, downregulates the expression of ssuEADCB operon which is required for the utilization of sulfur from aliphatic sulfonates, in the presence of cysteine. Also, Cbl and CysB together directly function as transcriptional activators of tauABCD genes, which are required for utilization of taurine as sulfur source for growth. Like many other members of the LTTR family, CysB is composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding speci
Probab=55.79 E-value=1.3e+02 Score=25.58 Aligned_cols=121 Identities=15% Similarity=0.057 Sum_probs=60.9
Q ss_pred HCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc
Q 018090 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (361)
Q Consensus 139 ~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I 215 (361)
.+|+.++.-. .+..++.+.+.+|++|+|+..-. .. ....++ .|.+.++.+ ..+-+|-+......+++++
T Consensus 25 ~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~-~~---~~~~~~~~~l~~~~~~~----v~~~~hpl~~~~~i~~~~l 96 (198)
T cd08443 25 RYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEA-LH---DYDDLITLPCYHWNRCV----VVKRDHPLADKQSISIEEL 96 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEEecc-cc---ccCCceEeeeeeceEEE----EEcCCCccccCCCCCHHHH
Confidence 4677665544 36788999999999999997421 00 011111 122222222 2233444433322344443
Q ss_pred c--EEEechH--H-HHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 K--RVFSHPQ--A-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 k--~VySHPq--A-LaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
. ...+++. . ......++.+.+. . ...+++.....++++.+ ...|+.+...++
T Consensus 97 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~~p~~~~~ 156 (198)
T cd08443 97 ATYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLG---LGVGVIASMAYD 156 (198)
T ss_pred hcCCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CcEEEeeccccc
Confidence 3 2333332 1 2233455555543 2 34567777777777764 235566665543
No 155
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=54.93 E-value=1.4e+02 Score=27.89 Aligned_cols=146 Identities=15% Similarity=0.045 Sum_probs=69.5
Q ss_pred CCccEEEEeCCCCcH-HHHHHHH---HCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeE
Q 018090 117 GTKVRVAYQGLPGAY-SEAAARK---AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLH 191 (361)
Q Consensus 117 ~~~~rIAyLGP~GTy-Se~AA~~---~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~ 191 (361)
.+..+|+....-+.+ --.+..+ .|++.++... .+..++.+.+.+|++|+|+++......+... ..|.+.++.
T Consensus 90 ~~~i~I~~~~~~~~~~l~~~l~~~~~~~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~ 166 (296)
T PRK11242 90 RGSLRLAMTPTFTAYLIGPLIDAFHARYPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA---QPLFTETLA 166 (296)
T ss_pred eeEEEEEeccchhhhhhHHHHHHHHHHCCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCCCCcceeE---EEeeeccEE
Confidence 345777764333322 1122222 2466666554 3568899999999999999864432221111 111122222
Q ss_pred EEEEEEEeeeeEeeeCCC-CCccCc---cEEEechHHH--HHHHHHHHhcCC--eE-EeccCHHHHHHHHHhcCCCCeEE
Q 018090 192 IVGEVQLVVNHCLLGLPG-VLKEEL---KRVFSHPQAL--AQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGA 262 (361)
Q Consensus 192 IvgEi~lpI~h~Lla~~g-~~l~~I---k~VySHPqAL--aQC~~fL~~~~~--~~-i~~~STA~AA~~va~~~~~~~AA 262 (361)
+ +.+-+|-|...+. .+++++ .-|.-.+... ..-.+|+.+.+. +. ..++|-..+.+++..+ ...+
T Consensus 167 ~----~~~~~~pl~~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~ 239 (296)
T PRK11242 167 L----VVGRHHPLAARRKALTLDELADEPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG---RLAT 239 (296)
T ss_pred E----EEcCCCcccccCCCcCHHHHhCCCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhC---CeEE
Confidence 2 2222333322211 233332 2343333321 223455655542 22 4455666666777764 2466
Q ss_pred ecCHhhHHHc
Q 018090 263 VASAQAAEIY 272 (361)
Q Consensus 263 Ias~~AA~~Y 272 (361)
+.++..++.+
T Consensus 240 ~~p~~~~~~~ 249 (296)
T PRK11242 240 LLPAAIAREH 249 (296)
T ss_pred EeehhhcccC
Confidence 7777665533
No 156
>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=54.52 E-value=1.9e+02 Score=27.27 Aligned_cols=56 Identities=18% Similarity=0.103 Sum_probs=40.2
Q ss_pred CCCCccEEEEeCCCCcHHHHH---HHHH---CCCC--ceeecCCHHHHHHHHHcCCcCeEEEee
Q 018090 115 DDGTKVRVAYQGLPGAYSEAA---ARKA---YPKC--ETVPCDQFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 115 ~~~~~~rIAyLGP~GTySe~A---A~~~---f~~~--e~vp~~sf~eVf~aV~~g~~d~gVVPI 170 (361)
...+..+|++..+.|+|--.+ +..+ +++. ++++..+-.+.+++|.+|++|++++..
T Consensus 27 ~~~~~l~Ig~~~~~~~~~~~~~~la~~~~~~~~~i~v~~~~~~~~~~~~~~l~~G~~D~~~~~~ 90 (320)
T TIGR02122 27 GEPTFVTIGTGGTGGVYYPIGGAIAQLINKKSGKLRVRVQSTGGSVENVNLLEAGEADLAIVQS 90 (320)
T ss_pred CCCceEEEEeCCCCCChHHHHHHHHHHHhccCCCeeEEEEeCcchHHHHHHHhCCCCcEEEEcc
Confidence 456679999999999875442 2222 2433 455556677899999999999999863
No 157
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=54.44 E-value=95 Score=28.23 Aligned_cols=146 Identities=12% Similarity=0.029 Sum_probs=69.8
Q ss_pred CCCccEEEEeCCCCcH--HHH--HHHHHCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCe
Q 018090 116 DGTKVRVAYQGLPGAY--SEA--AARKAYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRL 190 (361)
Q Consensus 116 ~~~~~rIAyLGP~GTy--Se~--AA~~~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L 190 (361)
..+..+||.-...+.. ... ...+.+++.++... .+.+++.+.+.+|++|+|++...+...+.+ ....|...++
T Consensus 65 ~~~~l~I~~~~~~~~~~~~~~l~~~~~~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~--~~~~l~~~~~ 142 (269)
T PRK11716 65 LSGELSLFCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASV--AFSPIDEIPL 142 (269)
T ss_pred cCceEEEEecchHHHHHHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcce--EEEEcccceE
Confidence 3455777755433321 221 11233577665443 467899999999999999985333221111 0112223333
Q ss_pred EEEEEEEEeeeeEeeeCC-C---CCccCccEEE-echHHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEE
Q 018090 191 HIVGEVQLVVNHCLLGLP-G---VLKEELKRVF-SHPQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGA 262 (361)
Q Consensus 191 ~IvgEi~lpI~h~Lla~~-g---~~l~~Ik~Vy-SHPqALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AA 262 (361)
.++ .+-+|.+.... . .++.+..-|. +.......-.+|+...+. . ...++|......++..+ ...+
T Consensus 143 ~~v----~~~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~ 215 (269)
T PRK11716 143 VLI----APALPCPVRQQLSQEKPDWSRIPFILPEHGPARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALG---CGVG 215 (269)
T ss_pred EEE----EcCCcchhhhccccchhhHhhCCeeecCCCchHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcC---CCeE
Confidence 332 23333322211 1 1222323332 111111223455655442 2 24456666666666654 3477
Q ss_pred ecCHhhHH
Q 018090 263 VASAQAAE 270 (361)
Q Consensus 263 Ias~~AA~ 270 (361)
+.+...++
T Consensus 216 ~~p~~~~~ 223 (269)
T PRK11716 216 LLPEVVLE 223 (269)
T ss_pred eccHHHhh
Confidence 88887765
No 158
>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=53.83 E-value=1.2e+02 Score=24.84 Aligned_cols=32 Identities=16% Similarity=0.068 Sum_probs=24.0
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEee
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPI 170 (361)
.+|+.++.-.. +-.++.+.+.+|++|+|+..-
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (194)
T cd08436 25 RHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGL 57 (194)
T ss_pred HCCCcEEEEecCCHHHHHHHHHcCCccEEEEec
Confidence 36766554433 567899999999999999854
No 159
>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=52.93 E-value=1e+02 Score=25.68 Aligned_cols=123 Identities=18% Similarity=0.143 Sum_probs=63.0
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc-
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik- 216 (361)
.||+.++.-.. +-.++.+.+.+|++|+|++.......+.. ...|.+.++.++. +-.|-+.. +..+++++.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~---~~~l~~~~~~lv~----~~~~p~~~-~~~~~~~L~~ 96 (198)
T cd08461 25 EAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLR---SRPLFEERYVCVT----RRGHPLLQ-GPLSLDQFCA 96 (198)
T ss_pred HCCCcEEEEeeCCcccHHHHHhcCCCcEEEecCccCCccce---eeeeecCcEEEEE----cCCChhhc-CCCCHHHHhh
Confidence 36776655443 35678899999999999975332111111 1122223333222 22333322 223333332
Q ss_pred --EEEechHH---HHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHc
Q 018090 217 --RVFSHPQA---LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (361)
Q Consensus 217 --~VySHPqA---LaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~Y 272 (361)
-|.-++.. ..+-.+|+.+.+. + ...++|...+..++..+ ...||.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~ 157 (198)
T cd08461 97 LDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAAT---DMVAFVPSRLVPNL 157 (198)
T ss_pred CCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcC---CeEEEchHHHHHhh
Confidence 23322211 1234566666542 2 34466666677777764 46788888877655
No 160
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=52.42 E-value=77 Score=33.03 Aligned_cols=113 Identities=17% Similarity=0.096 Sum_probs=59.6
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCC----CccCcc-
Q 018090 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV----LKEELK- 216 (361)
Q Consensus 142 ~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~----~l~~Ik- 216 (361)
+.+++...+++++++++++|++|.++..+- +.+.-.. .+.. ..-++.+...|+.+++. ++++++
T Consensus 81 ~~e~v~~~~~~~ll~aL~~G~iDi~~~~lt------~T~eR~~----~~~F-S~Py~~~~~~lv~r~~~~~i~~l~dL~G 149 (482)
T PRK10859 81 KLEIKVRDNISQLFDALDKGKADLAAAGLT------YTPERLK----QFRF-GPPYYSVSQQLVYRKGQPRPRSLGDLKG 149 (482)
T ss_pred cEEEEecCCHHHHHHHHhCCCCCEEeccCc------CChhhhc----cCcc-cCCceeeeEEEEEeCCCCCCCCHHHhCC
Confidence 467888899999999999999997653321 1111111 1111 11223345555555442 223332
Q ss_pred -EEEe-----chHHHHHHHHHHHhc-CCeE--EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 217 -RVFS-----HPQALAQCEMTLSNL-GIVR--ISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 217 -~VyS-----HPqALaQC~~fL~~~-~~~~--i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
+|.. +-+.+ +++..++ ++.. +...|+.++.+.|..+. -.++|+....+.
T Consensus 150 k~I~V~~gS~~~~~L---~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~--iDa~v~d~~~~~ 207 (482)
T PRK10859 150 GTLTVAAGSSHVETL---QELKKKYPELSWEESDDKDSEELLEQVAEGK--IDYTIADSVEIS 207 (482)
T ss_pred CeEEEECCCcHHHHH---HHHHHhCCCceEEecCCCCHHHHHHHHHCCC--CCEEEECcHHHH
Confidence 3322 22222 1222223 2333 44568888999988763 456776665544
No 161
>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=51.99 E-value=26 Score=27.34 Aligned_cols=26 Identities=15% Similarity=0.291 Sum_probs=23.8
Q ss_pred cCCcchHHHHHHHHHHCCccccceee
Q 018090 316 EEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 316 ~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
...||.+.++++.|+++|||.-.|-+
T Consensus 12 ~~~~g~~~~If~~la~~~I~vd~I~~ 37 (73)
T cd04934 12 SLSHGFLARIFAILDKYRLSVDLIST 37 (73)
T ss_pred ccccCHHHHHHHHHHHcCCcEEEEEe
Confidence 35799999999999999999999976
No 162
>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=51.82 E-value=32 Score=29.18 Aligned_cols=121 Identities=16% Similarity=0.072 Sum_probs=63.0
Q ss_pred HCCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc--
Q 018090 139 AYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK-- 216 (361)
Q Consensus 139 ~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik-- 216 (361)
.||+.++.......++.+.+.+|++|+|++.......+ -....|.+..+.+ ..+-+|-|... ..+++|+.
T Consensus 25 ~~P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~~~~~---~~~~~l~~~~~~~----v~~~~hpl~~~-~~~l~dl~~~ 96 (200)
T cd08460 25 EAPGVRLRFVPESDKDVDALREGRIDLEIGVLGPTGPE---IRVQTLFRDRFVG----VVRAGHPLARG-PITPERYAAA 96 (200)
T ss_pred HCCCCEEEEecCchhHHHHHHCCCccEEEecCCCCCcc---hheeeeeccceEE----EEeCCCCCCCC-CCCHHHHhcC
Confidence 35766655544333889999999999999743211011 0111222223322 23444544332 23444443
Q ss_pred -EEE-echH-HHHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 217 -RVF-SHPQ-ALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 217 -~Vy-SHPq-ALaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
-|. +... ...+..+++.+.+. ....++|...+..+++.+ ...|+.+...++
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 12446777776653 234567777777777764 346777776654
No 163
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=51.28 E-value=1.9e+02 Score=27.75 Aligned_cols=142 Identities=11% Similarity=0.052 Sum_probs=69.4
Q ss_pred CCccEEEEeCCCCcH-HHHHHH---HHCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCC
Q 018090 117 GTKVRVAYQGLPGAY-SEAAAR---KAYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHR 189 (361)
Q Consensus 117 ~~~~rIAyLGP~GTy-Se~AA~---~~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~ 189 (361)
.+..+||+...-+.+ --.... +.+|+.++... .+-.++++.+.+|++|+|+..-.... ...++ .|.+..
T Consensus 92 ~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~----~~~l~~~~l~~~~ 167 (316)
T PRK12679 92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSN----DPQLVAFPWFRWH 167 (316)
T ss_pred CceEEEEechHhhhcchHHHHHHHHHHCCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCC----CCCceEEEccCCc
Confidence 456788885433322 111111 23566655443 35678999999999999997422100 11111 112222
Q ss_pred eEEEEEEEEeeeeEeeeCCCCCccCcc---EEEechH--HHHHHHHHHHhcCC--eE-EeccCHHHHHHHHHhcCCCCeE
Q 018090 190 LHIVGEVQLVVNHCLLGLPGVLKEELK---RVFSHPQ--ALAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTG 261 (361)
Q Consensus 190 L~IvgEi~lpI~h~Lla~~g~~l~~Ik---~VySHPq--ALaQC~~fL~~~~~--~~-i~~~STA~AA~~va~~~~~~~A 261 (361)
+. +..+.+|-|......+++++. -|.-++. ......+|+...+. .. ..++|+..+..++..+ ...
T Consensus 168 ~~----~v~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g---~Gi 240 (316)
T PRK12679 168 HS----LLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALG---LGI 240 (316)
T ss_pred EE----EEecCCCccccCCCCCHHHHhCCCeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcC---CcE
Confidence 22 234555555433223444433 2322221 22235556666553 22 4456666666666654 235
Q ss_pred EecCHhhH
Q 018090 262 AVASAQAA 269 (361)
Q Consensus 262 AIas~~AA 269 (361)
|+.+..++
T Consensus 241 ~~lp~~~~ 248 (316)
T PRK12679 241 GLVAEQSS 248 (316)
T ss_pred EEeccccc
Confidence 66666544
No 164
>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=51.08 E-value=21 Score=27.88 Aligned_cols=36 Identities=14% Similarity=0.263 Sum_probs=28.7
Q ss_pred EEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 310 SIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 310 Si~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
.|.+..+|+||.+.++-++|+.+|+|+-.=...-++
T Consensus 3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~ 38 (68)
T cd04928 3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTD 38 (68)
T ss_pred EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcC
Confidence 356667899999999999999999999865444443
No 165
>cd08444 PBP2_Cbl The C-terminal substrate binding domain of LysR-type transcriptional regulator Cbl, which is required for expression of sulfate starvation-inducible (ssi) genes, contains the type 2 periplasmic binding fold. Cbl is a member of the LysR transcriptional regulators that comprise the largest family of prokaryotic transcription factor. Cbl shows high sequence similarity to CysB, the LysR-type transcriptional activator of genes involved in sulfate and thiosulfate transport, sulfate reduction, and cysteine synthesis. In Escherichia coli, the function of Cbl is required for expression of sulfate starvation-inducible (ssi) genes, coupled with the biosynthesis of cysteine from the organic sulfur sources (sulfonates). The ssi genes include the ssuEADCB and tauABCD operons encoding uptake systems for organosulfur compounds, aliphatic sulfonates, and taurine. The genes in these operons encode an ABC-type transport system required for uptake of aliphatic sulfonates and a desulfonati
Probab=51.05 E-value=1.5e+02 Score=25.03 Aligned_cols=122 Identities=13% Similarity=0.030 Sum_probs=62.5
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeee-cccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc-
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIE-NSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL- 215 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIE-NS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I- 215 (361)
.||+.++.-.. +-.++.+.+.+|++|+|+..-. +...+. ....|.+..+ .+..+..|-|...+..+++++
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~~l~~~~~----~~~~~~~hpl~~~~~~~~~~l~ 97 (198)
T cd08444 25 QFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPEL---VSFPYYDWHH----HIIVPVGHPLESITPLTIETIA 97 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEeccccCCCcCc---EEeeccccce----eEEecCCCccccCCCcCHHHHh
Confidence 36776655443 5678899999999999997411 000110 0011111111 133444555543322333333
Q ss_pred --cEEEechH-H-HHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 --KRVFSHPQ-A-LAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 --k~VySHPq-A-LaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
.-|.-++. . -.++..|+.+.+. ....+++...+.+++..+ ...+|.+...++
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08444 98 KWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLG---MGIGIVAEMAFE 156 (198)
T ss_pred CCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcC---CcEEeccHHHHh
Confidence 33432322 1 2345667766543 234567777777777764 246677776554
No 166
>PRK12483 threonine dehydratase; Reviewed
Probab=50.89 E-value=19 Score=38.43 Aligned_cols=179 Identities=17% Similarity=0.180 Sum_probs=87.9
Q ss_pred HHHHHHHcCCcCeEEEeeecccccchHHhHHHHh--cCCeEEEEEEEEee---eeEeeeCCCCCccCccEEEe-----c-
Q 018090 153 AAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL--RHRLHIVGEVQLVV---NHCLLGLPGVLKEELKRVFS-----H- 221 (361)
Q Consensus 153 eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~--~~~L~IvgEi~lpI---~h~Lla~~g~~l~~Ik~VyS-----H- 221 (361)
|+++.+. +..|+-|+|+- .+|.+.-..-.+. ..+.+|+|--.-.- ...+-..+-+.+..+.++.. .
T Consensus 178 EI~eQ~~-~~~D~VvvpvG--gGGliaGia~~~K~~~p~vkVIGVep~~a~~~~~sl~~g~~~~~~~~~t~adGiav~~~ 254 (521)
T PRK12483 178 EILRQHP-GPLDAIFVPVG--GGGLIAGIAAYVKYVRPEIKVIGVEPDDSNCLQAALAAGERVVLGQVGLFADGVAVAQI 254 (521)
T ss_pred HHHHHhC-CCCCEEEEecC--ccHHHHHHHHHHHHhCCCCEEEEEEeCCCchhhHHHhcCCcccCCCCCceeceeccCCC
Confidence 4444442 25899999986 4666665555543 34578877443211 11111111111111111110 1
Q ss_pred -hHHHHHHHHHHHhcCCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCceeeccccCCCCCceEEEEEeeCCCC
Q 018090 222 -PQALAQCEMTLSNLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAREPII 300 (361)
Q Consensus 222 -PqALaQC~~fL~~~~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~ 300 (361)
+..+.-|++++.. +-.+.-.....|.+.+.+.. ..-+.+.-|+-+.+|.-+.....- .+.+=-+|++-..+-
T Consensus 255 g~~~~~~~~~~vd~--vv~Vse~ei~~ai~~l~~~~---~i~vEpagAaalAal~~~~~~~~~--~g~~VV~IlsGgNid 327 (521)
T PRK12483 255 GEHTFELCRHYVDE--VVTVSTDELCAAIKDIYDDT---RSITEPAGALAVAGIKKYAEREGI--EGQTLVAIDSGANVN 327 (521)
T ss_pred CHHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhC---CcEEeHHHHHHHHHHHHHHHhcCC--CCCEEEEEeCCCCCC
Confidence 2345444444331 22233333455666666532 122344445555554432211110 122323333332221
Q ss_pred C--------C--CCCCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 301 A--------G--TDRPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 301 ~--------~--~~~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
. . .....+..+.+.+|++||+|.++++.+... |++.|+=|-
T Consensus 328 ~~~l~~i~~r~l~~~~r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~~ 378 (521)
T PRK12483 328 FDRLRHVAERAELGEQREAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYRY 378 (521)
T ss_pred HHHHHHHHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEEe
Confidence 0 0 012347888999999999999999999988 888887653
No 167
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=50.46 E-value=28 Score=34.31 Aligned_cols=35 Identities=11% Similarity=0.176 Sum_probs=30.9
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeee
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
+..+.+.-+|+||-..++=+.|+++|+|+..+.+.
T Consensus 7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~ 41 (286)
T PRK13011 7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSF 41 (286)
T ss_pred eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeee
Confidence 44566666899999999999999999999999996
No 168
>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=50.18 E-value=1.5e+02 Score=24.72 Aligned_cols=123 Identities=16% Similarity=0.071 Sum_probs=61.8
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc-
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik- 216 (361)
.+|+.++.... +..++.+.+.+|++|+|++--.....+. ....|.+.++.++. +-.|-+.. ...+++++.
T Consensus 25 ~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~lv~----~~~~~~~~-~~~~~~~L~~ 96 (200)
T cd08466 25 LAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSF---KSELLFEDELVCVA----RKDHPRIQ-GSLSLEQYLA 96 (200)
T ss_pred HCCCCEEEEecCchHhHHHHHHcCCccEEEecccCCCCCc---eeeeecccceEEEE----eCCCCCCC-CCcCHHHHhh
Confidence 35777665544 5678999999999999997321111110 11122233333322 23343322 223455542
Q ss_pred --EEEechHH-HHHHHHHHHhcCC---e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHc
Q 018090 217 --RVFSHPQA-LAQCEMTLSNLGI---V-RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (361)
Q Consensus 217 --~VySHPqA-LaQC~~fL~~~~~---~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~Y 272 (361)
.+.-.+.. ..+-.+|+.+.+. + ...++|.....++++.+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~~ 156 (200)
T cd08466 97 EKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQT---DLIAIAPRWLADQY 156 (200)
T ss_pred CCcEEecCCCCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCC---CeehhhHHHHHHHh
Confidence 23322221 1233455555433 2 34456666666666654 35678887776643
No 169
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=50.18 E-value=2.2e+02 Score=26.62 Aligned_cols=122 Identities=12% Similarity=0.005 Sum_probs=61.0
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc--
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL-- 215 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I-- 215 (361)
.+|+.++.... +.+++++.+.+|++|+|++.-.....+ -....|.+.++.++ .+-.|-|......+++++
T Consensus 115 ~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~---l~~~~l~~~~~~~v----~~~~~pl~~~~~i~~~~L~~ 187 (296)
T PRK09906 115 RHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDE---IDYLELLDEPLVVV----LPVDHPLAHEKEITAAQLDG 187 (296)
T ss_pred HCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecCCCCCCC---ceEEEEecccEEEE----ecCCCccccCCCcCHHHHcC
Confidence 45776665443 468899999999999999854321111 00112222233222 233343432222233332
Q ss_pred -cEEEech---H-HHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 -KRVFSHP---Q-ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 -k~VySHP---q-ALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
.-|.--+ . ...+...|+...++ + ...++|...+..+|..+ ...++.+...++
T Consensus 188 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g~~~~p~~~~~ 247 (296)
T PRK09906 188 VNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG---LGCTIIPGYMNN 247 (296)
T ss_pred CCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcEEEeeHHHhh
Confidence 3332211 1 13445667766543 2 34566666677777754 235556665554
No 170
>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=50.13 E-value=20 Score=33.41 Aligned_cols=38 Identities=13% Similarity=0.239 Sum_probs=31.0
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccce-eeecCC
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKI-ESRPQR 345 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkI-ESRP~~ 345 (361)
-..|++.-.|+||.+.++-+.|.++|||+..+ -+|-.+
T Consensus 148 g~~L~~~~~D~PG~Ig~vg~~Lg~~~iNIa~m~v~r~~~ 186 (208)
T TIGR00719 148 HPAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDI 186 (208)
T ss_pred ccEEEEEeCCCCChHHHHHHHHHhCCccEEEEEEEecCC
Confidence 45677777899999999999999999999766 445433
No 171
>cd08415 PBP2_LysR_opines_like The C-terminal substrate-domain of LysR-type transcriptional regulators involved in the catabolism of opines and that of related regulators, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulators, OccR and NocR, involved in the catabolism of opines and that of LysR for lysine biosynthesis which clustered together in phylogenetic trees. Opines, such as octopine and nopaline, are low molecular weight compounds found in plant crown gall tumors that are produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. NocR and OccR belong to the family of LysR-type transcriptional regulators that positively regulates the catabolism of nopaline and octopine, respectively. Both nopaline and octopalin are arginine derivatives. In Agrobacterium tumefa
Probab=50.06 E-value=1.5e+02 Score=24.54 Aligned_cols=123 Identities=16% Similarity=0.054 Sum_probs=60.3
Q ss_pred HHCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc-
Q 018090 138 KAYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL- 215 (361)
Q Consensus 138 ~~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I- 215 (361)
+.+|+.++.-.. +..+.++.+.+|++|+|++.-.....+ -....|.+..+.++ .+-+|-+...+..+++++
T Consensus 24 ~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~---~~~~~l~~~~~~~v----~~~~~~l~~~~~~~~~~l~ 96 (196)
T cd08415 24 ARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPG---LESEPLASGRAVCV----LPPGHPLARKDVVTPADLA 96 (196)
T ss_pred HHCCCcEEEEEecchHHHHHHHHcCCccEEEEeCCCCCCc---ceeeeecccceEEE----EcCCCChHhcCccCHHHhc
Confidence 346776654433 567899999999999999863311000 01111222222221 122233322222233332
Q ss_pred --cEEE-ech-HHHHHHHHHHHhcC--Ce-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 --KRVF-SHP-QALAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 --k~Vy-SHP-qALaQC~~fL~~~~--~~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
.-|. ++. ....+..+++.+.+ .+ ...++|...+.+++..+ ...++.+...++
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 155 (196)
T cd08415 97 GEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAG---LGVAIVDPLTAA 155 (196)
T ss_pred CCcEEEeCCCccHHHHHHHHHHHcCCCceEEEEEeHHHHHHHHHHcC---CCeEEechhhhh
Confidence 2333 222 22345566666654 22 24566666666667654 346677776554
No 172
>PRK05007 PII uridylyl-transferase; Provisional
Probab=49.22 E-value=19 Score=40.81 Aligned_cols=32 Identities=22% Similarity=0.322 Sum_probs=28.2
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccc
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTK 338 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtk 338 (361)
+.|.|=+..+|+||.|+++..+|++.|||+..
T Consensus 807 ~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~ 838 (884)
T PRK05007 807 RRSYMELIALDQPGLLARVGKIFADLGISLHG 838 (884)
T ss_pred CeEEEEEEeCCchHHHHHHHHHHHHCCcEEEE
Confidence 46777788899999999999999999999853
No 173
>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=49.17 E-value=74 Score=26.73 Aligned_cols=114 Identities=17% Similarity=0.129 Sum_probs=62.8
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCC---ccCcc--
Q 018090 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVL---KEELK-- 216 (361)
Q Consensus 142 ~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~---l~~Ik-- 216 (361)
+.++++.. ..++++++.+|++|+++.+...+-+. .+. +.+ ........+.++++++.. +++++
T Consensus 39 ~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~~-----~~~-----~~~-~~~~~~~~~~~~~~~~~~~~~~~dl~g~ 106 (218)
T cd00134 39 KVKFVEVD-WDGLITALKSGKVDLIAAGMTITPER-----AKQ-----VDF-SDPYYKSGQVILVKKGSPIKSVKDLKGK 106 (218)
T ss_pred eEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHHH-----Hhh-----ccC-cccceeccEEEEEECCCCCCChHHhCCC
Confidence 46778887 88999999999999998775211110 011 001 112222344556555432 23332
Q ss_pred EEEechHHHHHHHHHHHhc--CCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 217 RVFSHPQALAQCEMTLSNL--GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 217 ~VySHPqALaQC~~fL~~~--~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
+|..- ... -...++.+. ......+.+...+++++..+. ..|++.....+..
T Consensus 107 ~i~~~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~--~d~~~~~~~~~~~ 159 (218)
T cd00134 107 KVAVQ-KGS-TAEKYLKKALPEAKVVSYDDNAEALAALENGR--ADAVIVDEIALAA 159 (218)
T ss_pred EEEEE-cCc-hHHHHHHHhCCcccEEEeCCHHHHHHHHHcCC--ccEEEeccHHHHH
Confidence 22221 111 123444443 256778888888999988763 4567766665543
No 174
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=48.95 E-value=46 Score=36.94 Aligned_cols=41 Identities=12% Similarity=0.178 Sum_probs=36.2
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
.+.+.|.+...|++|.|.++...++..++|+.++.++..++
T Consensus 624 ~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~ 664 (702)
T PRK11092 624 EFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDG 664 (702)
T ss_pred eeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCC
Confidence 46788888899999999999999999999999999875543
No 175
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=48.71 E-value=2.3e+02 Score=26.36 Aligned_cols=144 Identities=13% Similarity=0.025 Sum_probs=72.2
Q ss_pred CCccEEEEeCCCCcH-HHHH---HHHHCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCC
Q 018090 117 GTKVRVAYQGLPGAY-SEAA---ARKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHR 189 (361)
Q Consensus 117 ~~~~rIAyLGP~GTy-Se~A---A~~~f~~~e~vp-~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~ 189 (361)
.+..+||+...-+.+ -... ..+.+|++++.- ..+-.++++.+.+|++|+|++.-.... ....++ .|.+..
T Consensus 96 ~~~l~I~~~~~~~~~~l~~~l~~f~~~~p~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~---~~~~l~~~~l~~~~ 172 (294)
T PRK09986 96 AGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLE---PNPGFTSRRLHESA 172 (294)
T ss_pred cceEEEEEehHHhHHHHHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHcCCCCEEEecCCccC---CCCCeEEEEeeccc
Confidence 456889886544421 1211 222356655433 335688999999999999997311000 011111 111111
Q ss_pred eEEEEEEEEeeeeEeeeCCCCCccCcc---EEEech--HHHH-HHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCe
Q 018090 190 LHIVGEVQLVVNHCLLGLPGVLKEELK---RVFSHP--QALA-QCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDT 260 (361)
Q Consensus 190 L~IvgEi~lpI~h~Lla~~g~~l~~Ik---~VySHP--qALa-QC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~ 260 (361)
+. +..+-+|-|...+..+++++. -|...+ .... +..+++.+.+. . ...++|......+|+.+ ..
T Consensus 173 ~~----~v~~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g 245 (294)
T PRK09986 173 FA----VAVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG---IG 245 (294)
T ss_pred EE----EEEcCCCCcccCCccCHHHHcCCCEEecCCCchhHHHHHHHHHHHCCCCCceeeecCCHHHHHHHHHcC---Ce
Confidence 11 122334444433334445543 343222 1233 55555555442 2 34567777777777764 35
Q ss_pred EEecCHhhHH
Q 018090 261 GAVASAQAAE 270 (361)
Q Consensus 261 AAIas~~AA~ 270 (361)
.++.++..++
T Consensus 246 i~~l~~~~~~ 255 (294)
T PRK09986 246 ITLLPDSYAQ 255 (294)
T ss_pred EEEccHHHhh
Confidence 7777877654
No 176
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=48.36 E-value=53 Score=36.58 Aligned_cols=45 Identities=20% Similarity=0.306 Sum_probs=39.1
Q ss_pred CCceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCCCC
Q 018090 305 RPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKRPL 349 (361)
Q Consensus 305 ~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw 349 (361)
..+.+.|.+...|++|.|.+++++++..++|+.++.++...++..
T Consensus 624 ~~f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~~~~ 668 (701)
T COG0317 624 QVYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQFA 668 (701)
T ss_pred cceEEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCCceE
Confidence 357888888889999999999999999999999999988755443
No 177
>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=48.32 E-value=18 Score=24.69 Aligned_cols=27 Identities=26% Similarity=0.359 Sum_probs=23.9
Q ss_pred CCcchHHHHHHHHHHCCccccceeeec
Q 018090 317 EGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 317 ~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
+.||.+.++|+.|++++||+..|..-.
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~~~~ 38 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMISQSE 38 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEEcCC
Confidence 579999999999999999998886644
No 178
>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=48.14 E-value=13 Score=30.34 Aligned_cols=41 Identities=22% Similarity=0.309 Sum_probs=28.3
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCC
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~ 347 (361)
..+..+.|..|.+||+|.+.|+.+..++ |+|.++=|-....
T Consensus 8 ~~E~~~~v~~PE~pGal~~F~~~l~~~~-nITeF~YR~~~~~ 48 (91)
T PF00585_consen 8 GREALFAVEFPERPGALKRFLDALGPRN-NITEFHYRYSGDD 48 (91)
T ss_dssp --EEEEEEE--BSTTHCHHHHHCCSSSE--EEEEEEE-TTTS
T ss_pred CCEEEEEEECCCCccHHHHHHHHhCCCc-eEEEEEEcCCCCC
Confidence 3578888999999999999999886655 4887776655543
No 179
>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=47.97 E-value=34 Score=25.89 Aligned_cols=24 Identities=29% Similarity=0.412 Sum_probs=21.4
Q ss_pred CCcchHHHHHHHHHHCCcccccee
Q 018090 317 EGPGMLFKALAVFALRDINLTKIE 340 (361)
Q Consensus 317 ~~PGaL~~iL~~Fa~~~INLtkIE 340 (361)
+.||.+.++.+.+++.|||+-.|-
T Consensus 19 ~~~Gv~a~i~~~La~~~I~i~~is 42 (65)
T PF13840_consen 19 DVPGVAAKIFSALAEAGINIFMIS 42 (65)
T ss_dssp TSHHHHHHHHHHHHHTTS-ECEEE
T ss_pred CcccHHHHHHHHHHHCCCCEEEEE
Confidence 599999999999999999998876
No 180
>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=47.94 E-value=2.5e+02 Score=26.64 Aligned_cols=135 Identities=14% Similarity=-0.012 Sum_probs=70.9
Q ss_pred cEEEEeCCCCcHHHHHHHH-HC----C-CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHH-hcCCeEE
Q 018090 120 VRVAYQGLPGAYSEAAARK-AY----P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLL-LRHRLHI 192 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~-~f----~-~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL-~~~~L~I 192 (361)
.+|+|+=.. +--..|-.+ +| + +++++++.+-.++++++..|++|++++... ..+... ...++.+
T Consensus 1 ~~~~~~~~~-~p~~va~~~G~~~k~~Gl~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~--------~~~~a~~~g~~~~~ 71 (300)
T TIGR01729 1 VTVGYQTIV-EPFKVAQADGAAAKEAGATIDWRKFDSGADISTALASGNVPIGVIGSS--------PLAAAASRGVPIEL 71 (300)
T ss_pred CEEEecCCC-CHHHHHHHcCchHHhcCCeeEEEecCcHHHHHHHHHcCCCCEeccCCC--------HHHHHHHCCCCeEE
Confidence 368886433 323333322 33 2 468899999999999999999999875321 111111 1234555
Q ss_pred EEEEE-EeeeeEeeeCCCC---CccCcc--EEEechHH--HHHHHHHHHhcC-----CeEEeccCHHHHHHHHHhcCCCC
Q 018090 193 VGEVQ-LVVNHCLLGLPGV---LKEELK--RVFSHPQA--LAQCEMTLSNLG-----IVRISADDTAGAAQMVASIGERD 259 (361)
Q Consensus 193 vgEi~-lpI~h~Lla~~g~---~l~~Ik--~VySHPqA--LaQC~~fL~~~~-----~~~i~~~STA~AA~~va~~~~~~ 259 (361)
+.-.. ..-.+.|+++++. +++|++ +|..++-. ...-..+|++.+ ++.+.. +.+.++..+..+. -+
T Consensus 72 v~~~~~~~~~~~lv~~~~s~I~s~~DLkGK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~G~-vD 149 (300)
T TIGR01729 72 FWILDNIGKSEALVAREGSGIEKPEDLKGKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQRGD-ID 149 (300)
T ss_pred EEEeccCCccceEEecCCCCCCChhHcCCCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHcCC-cC
Confidence 43221 1223578887763 344443 56554322 122345777654 334444 3445555555543 33
Q ss_pred eEEecC
Q 018090 260 TGAVAS 265 (361)
Q Consensus 260 ~AAIas 265 (361)
.+++..
T Consensus 150 a~~~~~ 155 (300)
T TIGR01729 150 AAYVWP 155 (300)
T ss_pred EEEEec
Confidence 444433
No 181
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=47.89 E-value=56 Score=30.35 Aligned_cols=49 Identities=16% Similarity=0.191 Sum_probs=37.4
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCC--CCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYP--KCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~--~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
..+||+. .|+..+.-....+. +.+.+..++.++.+++|.+|++|+.+..
T Consensus 133 g~~Igv~--~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 133 GKHVGVL--QGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred CCEEEEe--cCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeC
Confidence 3578884 78876655544443 3678889999999999999999998764
No 182
>PF09084 NMT1: NMT1/THI5 like; InterPro: IPR015168 This entry is found in the NMT1 and THI5 proteins. These proteins are proposed to be required for the biosynthesis of the pyrimidine moiety of thiamine [, , ]. They are regulated by thiamine []. ; PDB: 2X26_A 3E4R_A 3KSJ_A 3KSX_A 3UIF_A 4DDD_A 1US4_A 1US5_A 3IX1_B 2X7P_A ....
Probab=47.79 E-value=2e+02 Score=25.48 Aligned_cols=104 Identities=14% Similarity=-0.020 Sum_probs=67.2
Q ss_pred CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHH-hcCCeEEEEEEEEeeeeEeeeCCCCCc---cCc--c
Q 018090 143 CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLL-LRHRLHIVGEVQLVVNHCLLGLPGVLK---EEL--K 216 (361)
Q Consensus 143 ~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL-~~~~L~IvgEi~lpI~h~Lla~~g~~l---~~I--k 216 (361)
++++...+-.++++++..|++|+|+.... ..+-.. ...++++++...-.-...|+++++..+ .|+ |
T Consensus 23 ve~~~~~~~~~~~~~l~~G~~D~~~~~~~--------~~~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DLkGK 94 (216)
T PF09084_consen 23 VEIVFFGGGGDVLEALASGKADIAVAGPD--------AVLFARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADLKGK 94 (216)
T ss_dssp EEEEEESSHHHHHHHHHTTSHSEEEEECH--------HHHHHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGGTTS
T ss_pred EEEEEecChhHHHHHHhcCCceEEeccch--------HHHHHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHhCCC
Confidence 68899999999999999999999997543 122211 235788888777555677888776533 344 3
Q ss_pred EEEech--HHHHHHHHHHHhcC-----CeEEeccCHHHHHHHHHhc
Q 018090 217 RVFSHP--QALAQCEMTLSNLG-----IVRISADDTAGAAQMVASI 255 (361)
Q Consensus 217 ~VySHP--qALaQC~~fL~~~~-----~~~i~~~STA~AA~~va~~ 255 (361)
+|...+ .....-..+|++++ ++.+... ....+..+..+
T Consensus 95 ~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~-~~~~~~al~~g 139 (216)
T PF09084_consen 95 KIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLG-PPELAQALLSG 139 (216)
T ss_dssp EEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTT
T ss_pred EEEEecCcchhHHHHHHHHHhccccccceeeeee-hhhhhhhhhcC
Confidence 666665 34445567777764 4555553 44454455554
No 183
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=47.25 E-value=32 Score=31.45 Aligned_cols=48 Identities=27% Similarity=0.255 Sum_probs=37.7
Q ss_pred cEEEEeCCCCcH--HHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 120 VRVAYQGLPGAY--SEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 120 ~rIAyLGP~GTy--Se~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+|+.+ .||. .+..+....+..+.+.+++..+++.++.+|++|..+..
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 567665 4666 55555454566899999999999999999999999864
No 184
>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=46.79 E-value=1.7e+02 Score=24.30 Aligned_cols=122 Identities=18% Similarity=0.069 Sum_probs=59.9
Q ss_pred HCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc-
Q 018090 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (361)
Q Consensus 139 ~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik- 216 (361)
.+|+.++... .+-.++.+.+.+|++|+|++.-.-...+. ....|.+.++.++ .+-.|-+...+..+++++.
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 3677665443 35688999999999999998532100110 0011222222221 2223333322223333332
Q ss_pred --EEEechH--HHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 217 --RVFSHPQ--ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 217 --~VySHPq--ALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
-|.-.+. ...++.+++.+.+. . ...++|...+..++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08421 98 HDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAG---LGIGIVPESAAR 155 (198)
T ss_pred CceEeecCCcchHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CCeEEccchhhh
Confidence 2221111 12234455555443 2 34566767777777764 347777777665
No 185
>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=46.45 E-value=43 Score=30.13 Aligned_cols=48 Identities=13% Similarity=0.051 Sum_probs=33.2
Q ss_pred cEEEEeCCCCcHHHHHHHHHCCCCcee---------ecCCHHHHHHHHHcCCcCeEEEe
Q 018090 120 VRVAYQGLPGAYSEAAARKAYPKCETV---------PCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~~~e~v---------p~~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+||. +.|+..++...+.....++. ...+..+++.+|.+|++|.+++.
T Consensus 105 ~~V~v--~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~ 161 (232)
T TIGR03871 105 LRIGV--FAGTPPAHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVW 161 (232)
T ss_pred CeEEE--EcCChHHHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEec
Confidence 57887 45888877665432111211 13478999999999999999975
No 186
>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=46.26 E-value=20 Score=25.98 Aligned_cols=27 Identities=19% Similarity=0.389 Sum_probs=23.8
Q ss_pred ecCCcchHHHHHHHHHHCCccccceee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
+++.||.+.++++.|++.|||+-.|..
T Consensus 11 ~~~~~~~~~~i~~~l~~~~I~v~~i~~ 37 (66)
T cd04922 11 MAGTPGVAATFFSALAKANVNIRAIAQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 457899999999999999999988853
No 187
>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=46.07 E-value=1.7e+02 Score=24.19 Aligned_cols=32 Identities=22% Similarity=0.221 Sum_probs=24.1
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEee
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPI 170 (361)
.+|+.++.... +-+++++.+.+|++|+|++..
T Consensus 26 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~ 58 (199)
T cd08451 26 AYPDVELTLEEANTAELLEALREGRLDAAFVRP 58 (199)
T ss_pred HCCCcEEEEecCChHHHHHHHHCCCccEEEEec
Confidence 46776655443 467889999999999999753
No 188
>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=45.79 E-value=23 Score=25.14 Aligned_cols=28 Identities=25% Similarity=0.413 Sum_probs=24.6
Q ss_pred ecCCcchHHHHHHHHHHCCccccceeee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
+++.||.+.++++.++++|||+-.|.+.
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~s 37 (63)
T cd04936 10 MRSHPGVAAKMFEALAEAGINIEMISTS 37 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEcc
Confidence 5577999999999999999999888743
No 189
>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=45.67 E-value=21 Score=25.81 Aligned_cols=27 Identities=19% Similarity=0.347 Sum_probs=23.6
Q ss_pred ecCCcchHHHHHHHHHHCCccccceee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
+++.||.+.++++.|+++|||+-.|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~q 37 (66)
T cd04924 11 MRGTPGVAGRVFGALGKAGINVIMISQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 457899999999999999999988753
No 190
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=45.64 E-value=44 Score=32.42 Aligned_cols=47 Identities=15% Similarity=0.142 Sum_probs=38.0
Q ss_pred cEEEEeCCCCcHHHHHHHHHCC----CCceeecCCHHHHHHHHHcCCcCeEEE
Q 018090 120 VRVAYQGLPGAYSEAAARKAYP----KCETVPCDQFEAAFKAVELWLVDKAVL 168 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~----~~e~vp~~sf~eVf~aV~~g~~d~gVV 168 (361)
.+||. ..||.+++.+.++.+ +.+++.+++.++++++|.+|++|+.+.
T Consensus 154 k~V~v--~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~ 204 (302)
T PRK10797 154 KAVVV--TSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMM 204 (302)
T ss_pred CEEEE--eCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEc
Confidence 57886 478888777666543 367899999999999999999998874
No 191
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=45.30 E-value=26 Score=39.63 Aligned_cols=32 Identities=22% Similarity=0.294 Sum_probs=28.7
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCcccc
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLT 337 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLt 337 (361)
.+.|.|=+..+|+||-|+++-++|.+.||++.
T Consensus 781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~ 812 (854)
T PRK01759 781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLL 812 (854)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEE
Confidence 35688888899999999999999999999985
No 192
>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=45.29 E-value=28 Score=38.38 Aligned_cols=39 Identities=15% Similarity=0.236 Sum_probs=34.7
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecC
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQ 344 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~ 344 (361)
.+.+.|.+...|++|.|.++.+.++..++|+.++..+-.
T Consensus 608 ~f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~ 646 (683)
T TIGR00691 608 RFIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTY 646 (683)
T ss_pred eeEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEc
Confidence 467788888899999999999999999999999988644
No 193
>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=44.76 E-value=29 Score=26.65 Aligned_cols=27 Identities=22% Similarity=0.421 Sum_probs=24.1
Q ss_pred ecCCcchHHHHHHHHHHCCccccceee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
+.+.||.+.++++.|+++|||+-.+-+
T Consensus 11 l~~~~g~~~~if~~L~~~~I~v~~i~~ 37 (75)
T cd04912 11 MLGAHGFLAKVFEIFAKHGLSVDLIST 37 (75)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEc
Confidence 457899999999999999999988865
No 194
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=44.55 E-value=3e+02 Score=26.56 Aligned_cols=144 Identities=17% Similarity=0.156 Sum_probs=73.3
Q ss_pred CCccEEEEeCCCCcHHHH----HHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEE
Q 018090 117 GTKVRVAYQGLPGAYSEA----AARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHI 192 (361)
Q Consensus 117 ~~~~rIAyLGP~GTySe~----AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~I 192 (361)
.+..+||....-+.+-=. +..+.+|+.++... ...++++.|.+|++|.|+.+-.....|... ..|.+..+.+
T Consensus 116 ~~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~l 191 (317)
T PRK11482 116 QRTITIATTPSVGALVMPVIYQAIKTHYPQLLLRNI-PISDAENQLSQFQTDLIIDTHSCSNRTIQH---HVLFTDNVVL 191 (317)
T ss_pred CceEEEEecHHHHHHHHHHHHHHHHHHCCCCEEEEe-cchhHHHHHHCCCcCEEEeccCCCCCceEE---EEEecCcEEE
Confidence 345677766544432111 12234577665433 346789999999999999864432222111 1222223332
Q ss_pred EEEEEEeeeeEeeeCCCCCccCccE----E-EechHHHHHHHHHHHhc--CCeE-EeccCHHHHHHHHHhcCCCCeEEec
Q 018090 193 VGEVQLVVNHCLLGLPGVLKEELKR----V-FSHPQALAQCEMTLSNL--GIVR-ISADDTAGAAQMVASIGERDTGAVA 264 (361)
Q Consensus 193 vgEi~lpI~h~Lla~~g~~l~~Ik~----V-ySHPqALaQC~~fL~~~--~~~~-i~~~STA~AA~~va~~~~~~~AAIa 264 (361)
..+-+|-|... ..+++++.. + ..........++++.+. .... ..+++.......|+.+ ...+|.
T Consensus 192 ----v~~~~hpl~~~-~~~~~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~il 263 (317)
T PRK11482 192 ----VCRQGHPLLSL-EDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASS---DMLGIM 263 (317)
T ss_pred ----EEeCCCCccCC-CCCHHHHhhCCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcC---CeeEEe
Confidence 24555655432 345666542 2 22222112234455543 2232 3455555566667653 456788
Q ss_pred CHhhHHHc
Q 018090 265 SAQAAEIY 272 (361)
Q Consensus 265 s~~AA~~Y 272 (361)
+...+..+
T Consensus 264 p~~~~~~~ 271 (317)
T PRK11482 264 PSRFYNLF 271 (317)
T ss_pred HHHHHHHH
Confidence 88776543
No 195
>TIGR01361 DAHP_synth_Bsub phospho-2-dehydro-3-deoxyheptonate aldolase. The member of this family from Synechocystis PCC 6803, CcmA, was shown to be essential for carboxysome formation. However, no other candidate for this enzyme is present in that species, chorismate biosynthesis does occur, other species having this protein lack carboxysomes but appear to make chorismate, and a requirement of CcmA for carboxysome formation does not prohibit a role in chorismate biosynthesis.
Probab=44.44 E-value=4.4 Score=39.23 Aligned_cols=32 Identities=13% Similarity=0.142 Sum_probs=28.8
Q ss_pred CCCCCCCcccchhhhhcccccccccccccCCc
Q 018090 61 DDRPYTPDVQSSEANERSQDSQSSGFHKDLNL 92 (361)
Q Consensus 61 ~~~~~~p~~~~~~~~~~~~~~~~~~~~~d~~~ 92 (361)
=|+-|.|+++++|+++++.|++++.|.+++..
T Consensus 228 iE~H~t~d~a~~D~~~sl~p~~l~~lv~~i~~ 259 (260)
T TIGR01361 228 IEVHPDPEKALSDSKQQLTPEEFKRLVKELRA 259 (260)
T ss_pred EEeCCCccccCCcchhcCCHHHHHHHHHHHhh
Confidence 47889999999999999999999999998754
No 196
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=44.33 E-value=41 Score=32.56 Aligned_cols=51 Identities=24% Similarity=0.210 Sum_probs=39.9
Q ss_pred cEEEE----eCCCCcHHHHHHHHH--CC--CCceeecCCHHHHHHHHHcCCcCeEEEee
Q 018090 120 VRVAY----QGLPGAYSEAAARKA--YP--KCETVPCDQFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 120 ~rIAy----LGP~GTySe~AA~~~--f~--~~e~vp~~sf~eVf~aV~~g~~d~gVVPI 170 (361)
.|+|+ .-|.|-|++++-.+. .. ...++.-.+.++++..|+.|++|+|+|=.
T Consensus 136 ~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~ 194 (258)
T COG0725 136 VRLAIGDPKTVPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYV 194 (258)
T ss_pred cEEEecCCCCCCchHHHHHHHHHhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEE
Confidence 45554 348999999997653 11 24678899999999999999999999854
No 197
>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=44.32 E-value=22 Score=25.80 Aligned_cols=26 Identities=19% Similarity=0.312 Sum_probs=23.6
Q ss_pred cCCcchHHHHHHHHHHCCccccceee
Q 018090 316 EEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 316 ~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
.++||...++++.|+++|||.-.|.+
T Consensus 11 ~~~~~~~~~if~~l~~~~i~v~~i~t 36 (62)
T cd04890 11 NGEVGFLRKIFEILEKHGISVDLIPT 36 (62)
T ss_pred CcccCHHHHHHHHHHHcCCeEEEEec
Confidence 47799999999999999999999965
No 198
>PRK13398 3-deoxy-7-phosphoheptulonate synthase; Provisional
Probab=44.05 E-value=4.8 Score=39.24 Aligned_cols=34 Identities=12% Similarity=0.085 Sum_probs=29.8
Q ss_pred cCCCCCCCcccchhhhhcccccccccccccCCcc
Q 018090 60 EDDRPYTPDVQSSEANERSQDSQSSGFHKDLNLL 93 (361)
Q Consensus 60 ~~~~~~~p~~~~~~~~~~~~~~~~~~~~~d~~~l 93 (361)
.=|+-+.|+++++|+++++.|++|+.|++++..+
T Consensus 229 ~iE~H~~pd~a~~D~~~sl~p~~l~~l~~~i~~~ 262 (266)
T PRK13398 229 MIEVHPEPEKALSDARQTLNFEEMKELVDELKPM 262 (266)
T ss_pred EEeccCCccccCCchhhcCCHHHHHHHHHHHHHH
Confidence 4478889999999999999999999999987443
No 199
>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=43.96 E-value=1.9e+02 Score=24.23 Aligned_cols=115 Identities=17% Similarity=0.048 Sum_probs=67.7
Q ss_pred HCCCCceee-cCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCC--------
Q 018090 139 AYPKCETVP-CDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG-------- 209 (361)
Q Consensus 139 ~f~~~e~vp-~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g-------- 209 (361)
.+|+.++.. ..+..++++.+.+|++|+|+..... ... .+..+.......++++.++
T Consensus 31 ~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~-------------~~~--~~~~~~l~~~~~~~~~~~~~pl~~~~~ 95 (209)
T PF03466_consen 31 RHPNIRIEIREGDSDELIEALRSGELDLAITFGPP-------------PPP--GLESEPLGEEPLVLVVSPDHPLAQKKP 95 (209)
T ss_dssp HSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSS-------------SST--TEEEEEEEEEEEEEEEETTSGGGTTSS
T ss_pred HCCCcEEEEEeccchhhhHHHhcccccEEEEEeec-------------ccc--ccccccccceeeeeeeecccccccccc
Confidence 357755533 3455899999999999999987553 111 1233333344455554433
Q ss_pred CCccCcc---EEEe--chHHHHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 210 VLKEELK---RVFS--HPQALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 210 ~~l~~Ik---~VyS--HPqALaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
++++++. -|.- ...-..+..+++.+.+. ....++|...+..++..+ ...+|.+...+..
T Consensus 96 i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 162 (209)
T PF03466_consen 96 ITLEDLADYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASG---DGIAILPDSLAQD 162 (209)
T ss_dssp SSGGGGTTSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTT---SEBEEEEHHHHHH
T ss_pred chhhhhhhccccccccccccccccccccccccccccccccccchhhhccccccc---cceeecCcccccc
Confidence 3344443 3331 12245556666666653 235577777777777764 4678888888743
No 200
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=43.73 E-value=1.9e+02 Score=24.09 Aligned_cols=140 Identities=18% Similarity=0.068 Sum_probs=69.0
Q ss_pred cEEEEeCCCCcHH-HHHH---HHHCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCCeEE
Q 018090 120 VRVAYQGLPGAYS-EAAA---RKAYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLHI 192 (361)
Q Consensus 120 ~rIAyLGP~GTyS-e~AA---~~~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~L~I 192 (361)
.+||+-..-+++- -.+. .+.+|+.++.-.. +-.++.+.+.+|++|+|+..-... ...+. .|.+..+.+
T Consensus 2 l~Ig~~~~~~~~~~~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~-----~~~~~~~~l~~~~~~~ 76 (198)
T cd08441 2 LRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLP-----LPGIAYEPLFDYEVVL 76 (198)
T ss_pred EEEEeeccchhhhhHHHHHHHHHhCCCeEEEEEeCCchhHHHHHHcCCceEEEecCCcC-----CCCcEEEEccCCcEEE
Confidence 4677765554321 1121 2235766655443 457889999999999999642110 11111 122222222
Q ss_pred EEEEEEeeeeEeeeCCCCCccCcc--EEEechH--H-HHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEec
Q 018090 193 VGEVQLVVNHCLLGLPGVLKEELK--RVFSHPQ--A-LAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVA 264 (361)
Q Consensus 193 vgEi~lpI~h~Lla~~g~~l~~Ik--~VySHPq--A-LaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIa 264 (361)
..+..|-|......+++++. ..+.++. . .....+|+.+.+. ....++|...+.++++.+ ...++.
T Consensus 77 ----~~~~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~l 149 (198)
T cd08441 77 ----VVAPDHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASG---RGVAAL 149 (198)
T ss_pred ----EEcCCCChHHcccCCHHHhcCCceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhC---CcEEEe
Confidence 23334444322223333333 2222221 1 2334556666542 234567777777777764 245677
Q ss_pred CHhhHHH
Q 018090 265 SAQAAEI 271 (361)
Q Consensus 265 s~~AA~~ 271 (361)
+...++.
T Consensus 150 p~~~~~~ 156 (198)
T cd08441 150 PNWAVRE 156 (198)
T ss_pred eHHHHHH
Confidence 7765543
No 201
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=43.62 E-value=2.8e+02 Score=25.94 Aligned_cols=115 Identities=12% Similarity=0.034 Sum_probs=58.8
Q ss_pred HCCCCcee-ecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCccE
Q 018090 139 AYPKCETV-PCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR 217 (361)
Q Consensus 139 ~f~~~e~v-p~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik~ 217 (361)
.||+.++. -.....++++.+.+|++|+|+....... + . +..+......+++++.++-.+..-..
T Consensus 114 ~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~--------~-----~--l~~~~l~~~~~~~v~~~~~~~~~~~~ 178 (275)
T PRK03601 114 NQEALQFEARIAQRQSLVKQLHERQLDLLITTEAPKM--------D-----E--FSSQLLGHFTLALYTSAPSKKKSELN 178 (275)
T ss_pred hCCCcEEEEEECChHHHHHHHHcCCCCEEEEcCCCcc--------C-----C--ccEEEecceeEEEEecCchhhcccCC
Confidence 46776654 3556778999999999999997533211 1 1 11222223334444444321111111
Q ss_pred EE--echHHHHHHHHHHHhcC-CeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 218 VF--SHPQALAQCEMTLSNLG-IVRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 218 Vy--SHPqALaQC~~fL~~~~-~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
.+ .++..+.+-..++...+ -....++|.....++|+.+ ...++.+...++.
T Consensus 179 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~~~p~~~~~~ 232 (275)
T PRK03601 179 YIRLEWGADFQQHEAGLIGADEVPILTTSSAELARQLLATL---NGCAFLPVHWAKE 232 (275)
T ss_pred eEEccCCccHhHHHHHhcccCCcceEEeCcHHHHHHHHHhC---CCEEEEcHHHHhh
Confidence 11 12222322222222222 2245667777777777764 3477888876653
No 202
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=43.43 E-value=34 Score=33.78 Aligned_cols=35 Identities=26% Similarity=0.427 Sum_probs=29.6
Q ss_pred CCceEEEEEEecCCcchHHHHHHHHHHCCccccce
Q 018090 305 RPYKTSIVFTLEEGPGMLFKALAVFALRDINLTKI 339 (361)
Q Consensus 305 ~~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkI 339 (361)
+..|-.|-+-+-|+||.|.++=++|+.||.|+.++
T Consensus 74 r~krHvinclVqnEpGvlsRisGvlAaRGfNIdSL 108 (309)
T KOG2663|consen 74 RVKRHVINCLVQNEPGVLSRISGVLAARGFNIDSL 108 (309)
T ss_pred cccceeEEEEecCCchHHHHHHHHHHhccCCchhe
Confidence 34466777778899999999999999999998665
No 203
>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=43.01 E-value=1.9e+02 Score=23.85 Aligned_cols=31 Identities=19% Similarity=0.052 Sum_probs=23.2
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcCeEEEee
Q 018090 140 YPKCETVPCD-QFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 140 f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPI 170 (361)
+|+.++.-.. +-.++.+.+.+|++|+|++.-
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (200)
T cd08423 26 HPGLEVRLREAEPPESLDALRAGELDLAVVFD 57 (200)
T ss_pred CCCCeEEEEeCCHHHHHHHHhcCCccEEEEec
Confidence 4666554433 467889999999999999853
No 204
>PRK05092 PII uridylyl-transferase; Provisional
Probab=42.93 E-value=29 Score=39.44 Aligned_cols=35 Identities=17% Similarity=0.274 Sum_probs=31.0
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeee
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
.|.|.+..+|+||.|+++.++|+..|||+..-...
T Consensus 843 ~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~ 877 (931)
T PRK05092 843 FTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIA 877 (931)
T ss_pred eEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEE
Confidence 46777788899999999999999999999877666
No 205
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=42.68 E-value=33 Score=38.36 Aligned_cols=39 Identities=21% Similarity=0.370 Sum_probs=34.5
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCC
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQR 345 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~ 345 (361)
+.+.|.+...|++|.|.++.+.++..++|+..+.++..+
T Consensus 665 ~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~ 703 (743)
T PRK10872 665 YSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDT 703 (743)
T ss_pred eEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcC
Confidence 567788888899999999999999999999999987544
No 206
>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=42.43 E-value=25 Score=25.67 Aligned_cols=26 Identities=19% Similarity=0.226 Sum_probs=23.2
Q ss_pred cCCcchHHHHHHHHHHCCccccceee
Q 018090 316 EEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 316 ~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
.+.||.+.++++.|++.|||+-.|..
T Consensus 12 ~~~~~~~~~if~~L~~~~I~v~~i~q 37 (66)
T cd04919 12 KNMIGIAGRMFTTLADHRINIEMISQ 37 (66)
T ss_pred CCCcCHHHHHHHHHHHCCCCEEEEEe
Confidence 46899999999999999999988853
No 207
>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=42.28 E-value=2e+02 Score=23.97 Aligned_cols=120 Identities=13% Similarity=0.015 Sum_probs=59.5
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc-
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK- 216 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik- 216 (361)
.+|+.++.... +-+++++.+.+|++|+|++.......+... ..|.+..+.+ ..+-.|.+...+..+++++.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08457 25 LRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFL---IETRSLPAVV----AVPMGHPLAQLDVVSPQDLAG 97 (196)
T ss_pred HCCCeEEEEEecCcHHHHHHHHcCCccEEEeccCCCCCCcEE---EEeccCCeEE----EeeCCCccccCCccCHHHhCC
Confidence 35766655443 347889999999999999864321111110 1112222222 22334545433333444433
Q ss_pred --EEE-echH-HHHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhh
Q 018090 217 --RVF-SHPQ-ALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQA 268 (361)
Q Consensus 217 --~Vy-SHPq-ALaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~A 268 (361)
-|. ++.. ......+++.+++. ....++|...+.++++.+ ...++.+...
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~ 153 (196)
T cd08457 98 ERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREG---LGIAIIDPAT 153 (196)
T ss_pred CceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcC---CeEEEEChHH
Confidence 333 2222 23445666666542 234566666666666654 2355665443
No 208
>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=42.27 E-value=2e+02 Score=23.86 Aligned_cols=123 Identities=12% Similarity=0.122 Sum_probs=60.9
Q ss_pred HCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc
Q 018090 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (361)
Q Consensus 139 ~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I 215 (361)
.+|++++.-. .+-.++.+.+.+|++|+|+........ ...++ .|.+.++.+ ..+-.|-+...+..+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~---~~~l~~~~l~~~~~~~----v~~~~hp~~~~~~~~~~~L 97 (199)
T cd08416 25 RRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLN---DPDFEVVPLFEDDIFL----AVPATSPLAASSEIDLRDL 97 (199)
T ss_pred hCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCC---CCCeEEEEeecceEEE----EECCCCcccccCccCHHHh
Confidence 3577665544 345678899999999999986432100 01111 111112211 2344444433222333333
Q ss_pred ---cEEE-echH-HHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 216 ---KRVF-SHPQ-ALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 216 ---k~Vy-SHPq-ALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
.-|. +... ......+++.+.+. + ...++|...+.++++.+ ...++++...++.
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 158 (199)
T cd08416 98 KDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGG---VGYALLPGRIADV 158 (199)
T ss_pred cCCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcC---CcEEEechhhhhh
Confidence 2332 2221 12234556665542 2 24466666677777764 3466777765543
No 209
>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=41.18 E-value=2e+02 Score=23.62 Aligned_cols=114 Identities=18% Similarity=0.110 Sum_probs=59.4
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCC--------C
Q 018090 140 YPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPG--------V 210 (361)
Q Consensus 140 f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g--------~ 210 (361)
+|+.++.-. .+..++++.+.+|++|+|+..-..... + +..+.......++++.++ .
T Consensus 25 ~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~-------------~--~~~~~l~~~~~~~~~~~~~~l~~~~~~ 89 (197)
T cd08419 25 HPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDL-------------D--LVAEPFLDNPLVVIAPPDHPLAGQKRI 89 (197)
T ss_pred CCCceEEEEECCHHHHHHHHhcCCccEEEecCCCCCC-------------C--eEEEEeccCCEEEEecCCCCCcCCCCc
Confidence 566655443 367788999999999999964321111 1 122222223333333322 2
Q ss_pred CccCc---cEEEech-H-HHHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 211 LKEEL---KRVFSHP-Q-ALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 211 ~l~~I---k~VySHP-q-ALaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
+++++ .-|.-.+ . ...+-.+++.+.+. ....++|...+.++++.+ ...++.+...++.
T Consensus 90 ~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 155 (197)
T cd08419 90 PLERLAREPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAG---LGLSVLSLHTLAL 155 (197)
T ss_pred CHHHHhCCCcEEecCCCcHHHHHHHHHHHCCCCcceEEEECCHHHHHHHHHhC---CceEeecHHHHHH
Confidence 23332 2222111 1 12334556665542 234567777777788765 2467777776643
No 210
>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=41.15 E-value=27 Score=24.77 Aligned_cols=27 Identities=26% Similarity=0.426 Sum_probs=24.1
Q ss_pred ecCCcchHHHHHHHHHHCCccccceee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
+.+.||.+.++++.++++|||+-.|-+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04923 10 MRSHPGVAAKMFKALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEc
Confidence 457799999999999999999998864
No 211
>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=40.98 E-value=1e+02 Score=28.58 Aligned_cols=107 Identities=20% Similarity=0.236 Sum_probs=64.9
Q ss_pred HHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEe---eeCCCCCc---cCc--cEEEe-ch
Q 018090 152 EAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCL---LGLPGVLK---EEL--KRVFS-HP 222 (361)
Q Consensus 152 ~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~L---la~~g~~l---~~I--k~VyS-HP 222 (361)
.|+-.-|+.|.+|+||+ -.|.|.+++-.+..-..|...+|= ++.++.+. ++. ++|.+ .|
T Consensus 50 ~Dip~yV~~G~aDlGI~------------G~D~l~E~~~~v~~~~dL~fg~crl~vA~p~~~~~~~~~~l~~~rIATkyp 117 (182)
T TIGR00070 50 QDIPTYVEHGAADLGIT------------GYDVLLESGADVYELLDLGFGKCRLVLAVPQESDISSVEDLKGKRIATKYP 117 (182)
T ss_pred chhHHHHhCCCccEEEe------------cchhhhhCCCCEEEEeecCcCceEEEEEEECCCCCCChHHhCCCEEEECCH
Confidence 57888999999999985 356666655444444456776663 34443322 221 46776 55
Q ss_pred HHHHHHHHHHHhcC--CeEEeccCHHHHHHHHHhcCCCCeEEe----cCHhhHHHcCCceee
Q 018090 223 QALAQCEMTLSNLG--IVRISADDTAGAAQMVASIGERDTGAV----ASAQAAEIYGLDILA 278 (361)
Q Consensus 223 qALaQC~~fL~~~~--~~~i~~~STA~AA~~va~~~~~~~AAI----as~~AA~~YgL~iLa 278 (361)
. -.++|+++++ ++++..+.+.|+|-.+ .-+-|| .+-..-+.+||++++
T Consensus 118 ~---i~~~~f~~~Gi~v~ii~l~GsvE~aP~~-----GlaD~IvDiv~TG~TL~~NgL~~ie 171 (182)
T TIGR00070 118 N---LARRYFEKKGIDVEIIKLNGSVELAPLL-----GLADAIVDIVSTGTTLRENGLRIIE 171 (182)
T ss_pred H---HHHHHHHHcCCeEEEEECcceeecccCC-----CceeEEEEEeCCHHHHHHCCCEEee
Confidence 5 4477999987 5556666555543321 112244 355556789999995
No 212
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=40.97 E-value=43 Score=33.08 Aligned_cols=35 Identities=9% Similarity=0.205 Sum_probs=30.4
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeee
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
+.-|.+.-+|+||-.+++=+.++++|+|+..+...
T Consensus 9 ~~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~ 43 (289)
T PRK13010 9 SYVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQF 43 (289)
T ss_pred CEEEEEECCCCCCcHHHHHHHHHHCCCCEEecccc
Confidence 34555666899999999999999999999999886
No 213
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=40.72 E-value=29 Score=35.74 Aligned_cols=37 Identities=22% Similarity=0.272 Sum_probs=30.8
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
..-+|++.-.|+||.+.+++++++++|||+-.+..+.
T Consensus 337 ~~~rlii~h~d~pG~ia~it~~l~~~~iNI~~m~~~~ 373 (409)
T PRK11790 337 GGHRLLHIHENRPGVLAAINQIFAEQGINIAAQYLQT 373 (409)
T ss_pred CCceEEEEeCCCCCHHHHHHHHHHhcCCCHHHheecc
Confidence 3456777777999999999999999999998776543
No 214
>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=40.49 E-value=2.1e+02 Score=23.55 Aligned_cols=30 Identities=20% Similarity=0.016 Sum_probs=23.0
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEe
Q 018090 140 YPKCETVPC-DQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 140 f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVP 169 (361)
+|+.++.-. .+-.++++.+.+|++|+|++.
T Consensus 26 ~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~ 56 (197)
T cd08438 26 YPNIELELVEYGGKKVEQAVLNGELDVGITV 56 (197)
T ss_pred CcCeEEEEEEcCcHHHHHHHHcCCCCEEEEe
Confidence 566555433 366888999999999999975
No 215
>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=40.46 E-value=2.3e+02 Score=23.96 Aligned_cols=121 Identities=16% Similarity=0.051 Sum_probs=61.3
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I 215 (361)
.+|+.++.... +-.++.+.+.+|++|+|+.+-.... .+.+. .|.+.++. +..+.+|-|......+++++
T Consensus 25 ~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~----~~~~~~~~l~~~~~~----~v~~~~hpl~~~~~i~~~~l 96 (198)
T cd08413 25 RYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDD----HPDLVTLPCYRWNHC----VIVPPGHPLADLGPLTLEDL 96 (198)
T ss_pred hCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCC----CCCcEEEEeeeeeEE----EEecCCCcccccCCCCHHHH
Confidence 35766655444 3567899999999999997521100 01111 11111111 22344555543333344443
Q ss_pred c---EEEec-hH-HHHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 K---RVFSH-PQ-ALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 k---~VySH-Pq-ALaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
. -|.-. .. -..+-+.++.+.+. ....++|......++..+ ...|+.++..++
T Consensus 97 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08413 97 AQYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLG---LGVGIIAEMAYD 156 (198)
T ss_pred hcCCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhC---CCEEEccccccC
Confidence 2 23211 11 23345566666542 234566777777777764 235666765543
No 216
>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=40.22 E-value=2.1e+02 Score=23.64 Aligned_cols=120 Identities=16% Similarity=0.125 Sum_probs=60.4
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcCeEEEeeeccc--ccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc
Q 018090 140 YPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSV--GGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK 216 (361)
Q Consensus 140 f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~--~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik 216 (361)
+|+.++.... +..++++.+.+|++|+|+....... .+. ....|.+..+.++. +-+|-+. .+ .+++++.
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~~~~-~~-~~~~~l~ 96 (201)
T cd08418 26 FPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKEL---ISEPLFESDFVVVA----RKDHPLQ-GA-RSLEELL 96 (201)
T ss_pred CCCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCCCCcce---eEEeecCCceEEEe----CCCCccc-cC-CCHHHHc
Confidence 5666554443 4678999999999999997432110 110 00112222332222 1222221 11 1233332
Q ss_pred ---EEEec--hHHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 217 ---RVFSH--PQALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 217 ---~VySH--PqALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
.|... ........+++.+.+. + ...++|...+..+|+.+ ...||.+...++.
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 156 (201)
T cd08418 97 DASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKA---DFLTILSRDMGRG 156 (201)
T ss_pred CCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhC---CEEEEeEHHHhhh
Confidence 23221 1223445566665542 2 34567777777777764 3578888776654
No 217
>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=40.16 E-value=2.2e+02 Score=23.69 Aligned_cols=121 Identities=18% Similarity=0.085 Sum_probs=60.0
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc---
Q 018090 140 YPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL--- 215 (361)
Q Consensus 140 f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I--- 215 (361)
+|+.++... .+-.++.+.+.+|++|+|+..-.+...+. ....|.+..+.+ ..+-+|-+...+..+++++
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~---~~~~l~~~~~~~----~~~~~~~~~~~~~~~~~~l~~~ 98 (198)
T cd08433 26 YPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGL---STEPLLEEDLFL----VGPADAPLPRGAPVPLAELARL 98 (198)
T ss_pred CCCcEEEEEecCcHHHHHHHhCCCCcEEEEeCCCCCCCe---eEEEeccccEEE----EecCCCccccCCCCCHHHhCCC
Confidence 566655444 35678899999999999997432211110 001111222221 2233343332222333333
Q ss_pred cEEE-echHH-HHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 KRVF-SHPQA-LAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 k~Vy-SHPqA-LaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
.-|. .+... .....+++.+++. ....+++...+.++++.+ ...||.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08433 99 PLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAG---LGYTILPASAVA 155 (198)
T ss_pred ceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcC---CcEEEcchhhhh
Confidence 2232 22222 2345566666543 235567777777777764 346666766553
No 218
>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=40.14 E-value=2.2e+02 Score=23.65 Aligned_cols=121 Identities=14% Similarity=0.045 Sum_probs=60.6
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc---
Q 018090 140 YPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL--- 215 (361)
Q Consensus 140 f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I--- 215 (361)
+|+.++.... +.+++.+.+.+|++|+|+..-.....+.. ...|.+.++.+ ..+-+|-+...+..+++++
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~----v~~~~hpl~~~~~~~~~~l~~~ 98 (199)
T cd08426 26 YPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIR---VHSRQPAPIGA----VVPPGHPLARQPSVTLAQLAGY 98 (199)
T ss_pred CCCeEEEEEeCCcHHHHHHHHCCCccEEEecCCCCCCCeE---EEeeccCcEEE----EecCCCCcccCCccCHHHHhCC
Confidence 5666554443 56889999999999999975332211100 11112222221 1233333332222233333
Q ss_pred cEEEech--HHHHHHHHHHHhcCC---eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 216 KRVFSHP--QALAQCEMTLSNLGI---VRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 216 k~VySHP--qALaQC~~fL~~~~~---~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
..|.-.+ ........++.+.+. ....++|...+.+++..+ ...|+.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (199)
T cd08426 99 PLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAG---GGISLLTELAVR 155 (199)
T ss_pred CeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcC---CCEEEEchHhhh
Confidence 2333221 112344566665542 234567777777777764 346777876554
No 219
>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=39.52 E-value=29 Score=25.06 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=23.2
Q ss_pred ecCCcchHHHHHHHHHHCCcccccee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIE 340 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIE 340 (361)
+++.||.+.++++.+++.|||+-.|.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~i~v~~i~ 36 (66)
T cd04916 11 MKNTVGVSARATAALAKAGINIRMIN 36 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 45789999999999999999998884
No 220
>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=39.18 E-value=1.3e+02 Score=28.51 Aligned_cols=73 Identities=27% Similarity=0.236 Sum_probs=44.4
Q ss_pred CCccEEEEeCCCCcHHHHHHHHHC---C-CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhH-HHHhcCCeE
Q 018090 117 GTKVRVAYQGLPGAYSEAAARKAY---P-KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNY-DLLLRHRLH 191 (361)
Q Consensus 117 ~~~~rIAyLGP~GTySe~AA~~~f---~-~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tl-DlL~~~~L~ 191 (361)
.+..|||+.= +||=.+.-++.+. + ..|++..++..++++.+++|++|-|||+.| +.. .+++ |+|.+.++.
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 3456899997 7998887666543 3 589999999999999999999999999944 322 4555 466677777
Q ss_pred EEE
Q 018090 192 IVG 194 (361)
Q Consensus 192 Ivg 194 (361)
+=|
T Consensus 141 ~Pg 143 (201)
T PF12916_consen 141 APG 143 (201)
T ss_dssp ---
T ss_pred CCh
Confidence 644
No 221
>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=38.16 E-value=2.5e+02 Score=23.77 Aligned_cols=141 Identities=13% Similarity=0.016 Sum_probs=67.9
Q ss_pred cEEEEeCCCCcH--HHH--HHHHHCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEE
Q 018090 120 VRVAYQGLPGAY--SEA--AARKAYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVG 194 (361)
Q Consensus 120 ~rIAyLGP~GTy--Se~--AA~~~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~Ivg 194 (361)
.+|++....+.+ ... +.++.+|+.++.... +.+++++.+.+|++|.|+++-.....|.... .|.+.++.+
T Consensus 3 l~ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~l~~~---~l~~~~~~~-- 77 (198)
T cd08485 3 LRVAYFGTVVLHTLPLLLRQLLSVAPSATVSLTQMSKNRQIEALDAGTIDIGFGRFYPYQEGVVVR---NVTNERLFL-- 77 (198)
T ss_pred EEEEEeccchhHHHHHHHHHHHHhCCCcEEEEEECCHHHHHHHHHcCCccEEEecCCCCCCCeEEE---EeeccceEE--
Confidence 566666554432 221 112336777665544 5778999999999999998522111121111 111222222
Q ss_pred EEEEeeeeEeeeCCCCCccCcc---EEE-echH---HHHHHHHHHHhcC--Ce-EEeccCHHHHHHHHHhcCCCCeEEec
Q 018090 195 EVQLVVNHCLLGLPGVLKEELK---RVF-SHPQ---ALAQCEMTLSNLG--IV-RISADDTAGAAQMVASIGERDTGAVA 264 (361)
Q Consensus 195 Ei~lpI~h~Lla~~g~~l~~Ik---~Vy-SHPq---ALaQC~~fL~~~~--~~-~i~~~STA~AA~~va~~~~~~~AAIa 264 (361)
..+-.|.+.....++++++. -|. .+.. .-.+-.+++.+.+ .. ...++|.....++|+.+ ...+|.
T Consensus 78 --~~~~~~~~~~~~~v~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~ 152 (198)
T cd08485 78 --GAQKSRARSFGEQVHCSALRNEPLILFPREGRPSFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAG---VGVTIV 152 (198)
T ss_pred --EeCCCCccccCCCcCHHHHhcCCeEecCCCCCccHHHHHHHHHHHcCCCcceEEEcCcHHHHHHHHHcC---CceEEC
Confidence 12233333222223444432 232 2211 1223334555444 22 24456666677777764 346777
Q ss_pred CHhhHH
Q 018090 265 SAQAAE 270 (361)
Q Consensus 265 s~~AA~ 270 (361)
++..++
T Consensus 153 p~~~~~ 158 (198)
T cd08485 153 PETVAM 158 (198)
T ss_pred cchhhc
Confidence 776554
No 222
>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=37.93 E-value=3.4e+02 Score=25.35 Aligned_cols=145 Identities=17% Similarity=0.128 Sum_probs=70.5
Q ss_pred CCCccEEEEeCCCCcH-HHHHH---HHHCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcC
Q 018090 116 DGTKVRVAYQGLPGAY-SEAAA---RKAYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRH 188 (361)
Q Consensus 116 ~~~~~rIAyLGP~GTy-Se~AA---~~~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~ 188 (361)
..+..+|+.....+.+ --.+. .+.||+.++.... +-.++++.+.+|++|+|++...+... ...++ -|.+.
T Consensus 91 ~~~~l~I~~~~~~~~~~~~~~l~~~~~~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~---~~~~~~~~l~~~ 167 (300)
T TIGR02424 91 EGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPET---MQGLSFEHLYNE 167 (300)
T ss_pred CCceEEEecccHHHHhhhHHHHHHHHHhCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCccc---ccceeeeeecCC
Confidence 3556777765322111 11111 1235776655443 56788999999999999974432211 01111 12222
Q ss_pred CeEEEEEEEEeeeeEeeeCCCCCccCcc--EEEechHH---HHHHHHHHHhcCC---e-EEeccCHHHHHHHHHhcCCCC
Q 018090 189 RLHIVGEVQLVVNHCLLGLPGVLKEELK--RVFSHPQA---LAQCEMTLSNLGI---V-RISADDTAGAAQMVASIGERD 259 (361)
Q Consensus 189 ~L~IvgEi~lpI~h~Lla~~g~~l~~Ik--~VySHPqA---LaQC~~fL~~~~~---~-~i~~~STA~AA~~va~~~~~~ 259 (361)
++.++ .+-.|-|...+..+++|+. ..+..+.. ......|+.+++. . ...+++......++..+ .
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 32221 2223434333222334333 12233222 1334566665542 2 35566766677777664 3
Q ss_pred eEEecCHhhHH
Q 018090 260 TGAVASAQAAE 270 (361)
Q Consensus 260 ~AAIas~~AA~ 270 (361)
..++.+...++
T Consensus 241 gi~~lp~~~~~ 251 (300)
T TIGR02424 241 AIWIISRGVVA 251 (300)
T ss_pred ceEeCcHHHHh
Confidence 46677777664
No 223
>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=37.71 E-value=2.3e+02 Score=23.29 Aligned_cols=116 Identities=15% Similarity=0.012 Sum_probs=58.9
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCC------
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVL------ 211 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~------ 211 (361)
.+++.++.... +.+++.+.+.+|++|+|+..-.... ... + +..+.......++++.++-.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~---~~~--------~--~~~~~l~~~~~~~v~~~~~p~~~~~~ 91 (195)
T cd08427 25 RHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFP---LPK--------D--LVWTPLVREPLVLIAPAELAGDDPRE 91 (195)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCCCEEEEcCCCCc---ccc--------C--ceEEEcccCcEEEEECCCCCcchHHH
Confidence 35776655433 5688899999999999998532110 000 1 11222222333333333211
Q ss_pred -ccCccEEE-echHH-HHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 212 -KEELKRVF-SHPQA-LAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 212 -l~~Ik~Vy-SHPqA-LaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
+.+-.-|. .+... -.+..+++.+.+. + ...++|...+.+++..+ ...||.+...++
T Consensus 92 ~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 153 (195)
T cd08427 92 LLATQPFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQG---LGVAIVPDIAVP 153 (195)
T ss_pred HhcCCCeEEecCCchHHHHHHHHHHHcCCCCCeEEEeccHHHHHHHHHhC---CcEEEccHHHHh
Confidence 22222222 12111 2334566666542 2 34456666666777764 357777877665
No 224
>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=37.67 E-value=2.5e+02 Score=23.75 Aligned_cols=117 Identities=15% Similarity=0.075 Sum_probs=58.2
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc
Q 018090 140 YPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK 216 (361)
Q Consensus 140 f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik 216 (361)
+|+.++... .+..++++.+.+|++|+|+...+... +.++ .|.+..+. +.++-+| +...+..+++++.
T Consensus 26 ~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~~~~-----~~~~~~~l~~~~~~----lv~~~~h-~~~~~~i~~~~l~ 95 (200)
T cd08465 26 APGIDLAVSQASREAMLAQVADGEIDLALGVFPELP-----EELHAETLFEERFV----CLADRAT-LPASGGLSLDAWL 95 (200)
T ss_pred CCCcEEEEecCChHhHHHHHHCCCccEEEeccccCC-----cCeeEEEeeeccEE----EEEeCCC-CccCCCcCHHHHh
Confidence 577665433 46789999999999999997433211 1111 11122221 2334445 3333234444443
Q ss_pred E---EEe--chHHHHHHHHHHHhcCCe--E-EeccCHHHHHHHHHhcCCCCeEEecCHhh
Q 018090 217 R---VFS--HPQALAQCEMTLSNLGIV--R-ISADDTAGAAQMVASIGERDTGAVASAQA 268 (361)
Q Consensus 217 ~---VyS--HPqALaQC~~fL~~~~~~--~-i~~~STA~AA~~va~~~~~~~AAIas~~A 268 (361)
. |.- ...-......++.+++.+ . ..++|......+|+.++ ..+++.+..+
T Consensus 96 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~--~~~~~~~~~~ 153 (200)
T cd08465 96 ARPHVLVAMRGDAANEIDRALAARGLRRRVALTLPHWGVAPELIAGTD--LILTVARRAL 153 (200)
T ss_pred hCCcEEEecCCCcCChHHHHHHHcCCceEEEEEcCcHHHHHHHHHcCC--hhhHhHHHHH
Confidence 2 221 111123445566666543 2 44566666777776532 2344444433
No 225
>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=37.33 E-value=33 Score=25.41 Aligned_cols=27 Identities=15% Similarity=0.365 Sum_probs=23.2
Q ss_pred ecCCcchHHHHHHHHHHCCccccceee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
+.+.||.+.++++.|++.|||+..+-.
T Consensus 11 ~~~~~gi~~~if~aL~~~~I~v~~~~~ 37 (64)
T cd04937 11 IRGVPGVMAKIVGALSKEGIEILQTAD 37 (64)
T ss_pred ccCCcCHHHHHHHHHHHCCCCEEEEEc
Confidence 347899999999999999999976653
No 226
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=36.96 E-value=99 Score=28.66 Aligned_cols=49 Identities=16% Similarity=0.177 Sum_probs=36.3
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCC--CCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYP--KCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~--~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
..+||+. .|++.++-...++. +.+++...+.++++++|.+|++|+.+..
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 57766554444332 4678899999999999999999988753
No 227
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=36.25 E-value=2.1e+02 Score=26.93 Aligned_cols=118 Identities=14% Similarity=-0.052 Sum_probs=56.9
Q ss_pred CCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCcc---
Q 018090 140 YPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELK--- 216 (361)
Q Consensus 140 f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik--- 216 (361)
+|+.++.-..+ +..+.+.+|++|+|++..+....|.... .|.+..+.+ ..+-.|.+......+++++.
T Consensus 120 ~p~i~i~l~~~--~~~~~l~~g~~Dl~i~~~~~~~~~l~~~---~l~~~~~~~----~~~~~~~~~~~~~i~~~dL~~~p 190 (297)
T PRK11139 120 HPDIDVRLKAV--DRLEDFLRDDVDVAIRYGRGNWPGLRVE---KLLDEYLLP----VCSPALLNGGKPLKTPEDLARHT 190 (297)
T ss_pred CCCceEEEEeC--CChhhhccCCCCEEEEeCCCCCCCceEE---EeccceeEE----EeCHHHhcccCCCCCHHHhhcCc
Confidence 56654433322 3347788999999998754332221111 111222222 22333433333333444432
Q ss_pred EEEechHHHHHHHHHHHhcCC-----e-EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 217 RVFSHPQALAQCEMTLSNLGI-----V-RISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 217 ~VySHPqALaQC~~fL~~~~~-----~-~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
-|...+ .....+|+...+. . ...+++...+..+|..+ ...||.+...++.
T Consensus 191 ~i~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 246 (297)
T PRK11139 191 LLHDDS--REDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG---QGVALGNRVLAQP 246 (297)
T ss_pred eEeecC--cccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhC---CCeEecchhhhHH
Confidence 343222 2345567765432 1 23456666566666654 3467777776654
No 228
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=35.81 E-value=2.8e+02 Score=25.64 Aligned_cols=129 Identities=15% Similarity=0.174 Sum_probs=67.6
Q ss_pred CCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEee
Q 018090 126 GLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLL 205 (361)
Q Consensus 126 GP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Ll 205 (361)
|..--.-++.|++.--+.++++. ++++++++++.|++|.++-++.-+ +--. ..+.....+ +.....++
T Consensus 50 G~~vdl~~~ia~~lg~~~~~~~~-~~~~~~~~l~~g~~Di~~~~~~~t------~eR~----~~~~fs~p~-~~~~~~~~ 117 (260)
T PRK15010 50 GFDIDLGNEMCKRMQVKCTWVAS-DFDALIPSLKAKKIDAIISSLSIT------DKRQ----QEIAFSDKL-YAADSRLI 117 (260)
T ss_pred eeeHHHHHHHHHHhCCceEEEeC-CHHHHHHHHHCCCCCEEEecCcCC------HHHH----hhcccccce-EeccEEEE
Confidence 33334444445443224677764 699999999999999776433211 1111 111112221 22345566
Q ss_pred eCCCC----CccCcc--EEEechHHHHHHHHHHH----hcCCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 206 GLPGV----LKEELK--RVFSHPQALAQCEMTLS----NLGIVRISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 206 a~~g~----~l~~Ik--~VySHPqALaQC~~fL~----~~~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
++++. +++++. +|--..-... ..|+. ..++..+.+.+...+.+++..+ +-.|.|++...+.
T Consensus 118 ~~~~~~~~~~~~dl~g~~Igv~~gs~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--riDa~i~d~~~~~ 188 (260)
T PRK15010 118 AAKGSPIQPTLDSLKGKHVGVLQGSTQ--EAYANETWRSKGVDVVAYANQDLVYSDLAAG--RLDAALQDEVAAS 188 (260)
T ss_pred EECCCCCCCChhHcCCCEEEEecCchH--HHHHHHhcccCCceEEecCCHHHHHHHHHcC--CccEEEeCcHHHH
Confidence 65542 223332 3332221111 12443 2346777778888888888876 3467777766554
No 229
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=35.36 E-value=3.9e+02 Score=25.26 Aligned_cols=53 Identities=11% Similarity=0.028 Sum_probs=36.3
Q ss_pred CCccEEEEeCCCCc-HHHHHHH---HHCCCCceeecC-CHHHHHHHHHcCCcCeEEEe
Q 018090 117 GTKVRVAYQGLPGA-YSEAAAR---KAYPKCETVPCD-QFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 117 ~~~~rIAyLGP~GT-ySe~AA~---~~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVP 169 (361)
.+..+|+..+..+. +-..... +.+|+.++.... +..++.+.+.+|++|+|+..
T Consensus 94 ~g~l~ig~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 94 RGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred CceEEEEEcCcchHhHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEEc
Confidence 46688999877664 3222222 335766655443 57888999999999999974
No 230
>cd04921 ACT_AKi-HSDH-ThrA-like_1 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the first of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pat
Probab=35.27 E-value=53 Score=24.92 Aligned_cols=26 Identities=23% Similarity=0.359 Sum_probs=23.2
Q ss_pred ecCCcchHHHHHHHHHHCCcccccee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIE 340 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIE 340 (361)
+.+.+|.+.++++.|++++||+..|.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~ 36 (80)
T cd04921 11 MVGVPGIAARIFSALARAGINVILIS 36 (80)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEE
Confidence 45789999999999999999998775
No 231
>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=34.54 E-value=2.6e+02 Score=23.11 Aligned_cols=120 Identities=13% Similarity=0.007 Sum_probs=60.3
Q ss_pred HCCCCceeecC-CHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc
Q 018090 139 AYPKCETVPCD-QFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL 215 (361)
Q Consensus 139 ~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I 215 (361)
.+|+.++.-.. +-.++.+.+.+|++|.|++.-... .+.++ .|.+..+.++ .+-+|-+. ....+++++
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~-----~~~~~~~~l~~~~~~~v----~~~~~~~~-~~~~~~~~l 94 (200)
T cd08464 25 EAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGEL-----PAWLKREVLYTEGYACL----FDPQQLSL-SAPLTLEDY 94 (200)
T ss_pred HCCCcEEEEecCCcccHHHHHhcCcccEEEecCCCC-----cccceeeeecccceEEE----EeCCCccc-cCCCCHHHH
Confidence 35776665443 355778999999999999753211 11111 2222333222 22233222 112333433
Q ss_pred c---E-EEechHH-HHHHHHHHHhcCC--eE-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 216 K---R-VFSHPQA-LAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 216 k---~-VySHPqA-LaQC~~fL~~~~~--~~-i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
. . ++.+... .....+|+.+.+. .. ..++|......++..+ ...||.+...++.
T Consensus 95 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 155 (200)
T cd08464 95 VARPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGT---PLIATVPARLARA 155 (200)
T ss_pred hcCCcEEecCCCCCcchHHHHHHHcCCCcceEEEcCchhhHHHHHcCC---CceeecHHHHHHH
Confidence 2 1 2222111 2234566666553 22 3455555555566553 3578889888764
No 232
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=34.00 E-value=4.2e+02 Score=25.14 Aligned_cols=53 Identities=15% Similarity=0.115 Sum_probs=34.1
Q ss_pred CCccEEEEeCCCCcH-HHHHHH---HHCCCCceeecC-CHHHHHHHHHcCCcCeEEEe
Q 018090 117 GTKVRVAYQGLPGAY-SEAAAR---KAYPKCETVPCD-QFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 117 ~~~~rIAyLGP~GTy-Se~AA~---~~f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVP 169 (361)
.+..+||.....+++ --.... +.+|+.++.-.. +.+++++.+.+|++|+|+.+
T Consensus 92 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~ 149 (309)
T PRK12682 92 SGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIAT 149 (309)
T ss_pred CCeEEEeeCchHHHHHHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHcCCccEEEec
Confidence 456788777544432 112222 235666655433 57899999999999999975
No 233
>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=33.78 E-value=42 Score=23.39 Aligned_cols=27 Identities=22% Similarity=0.406 Sum_probs=23.4
Q ss_pred ecCCcchHHHHHHHHHHCCccccceee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIES 341 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIES 341 (361)
..+.+|.+.++++.|++++|++-.+..
T Consensus 10 ~~~~~~~~~~i~~~l~~~~i~v~~i~~ 36 (65)
T cd04892 10 MRGTPGVAARIFSALAEAGINIIMISQ 36 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 347799999999999999999988853
No 234
>PRK03059 PII uridylyl-transferase; Provisional
Probab=33.75 E-value=50 Score=37.41 Aligned_cols=32 Identities=16% Similarity=0.327 Sum_probs=28.4
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccc
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTK 338 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtk 338 (361)
+.|.|.+..+|+||.|+++-++|+..|+|+..
T Consensus 785 ~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~ 816 (856)
T PRK03059 785 QYYILSVSANDRPGLLYAIARVLAEHRVSVHT 816 (856)
T ss_pred CEEEEEEEeCCcchHHHHHHHHHHHCCCeEEE
Confidence 45777778889999999999999999999975
No 235
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=33.51 E-value=2.8e+02 Score=25.58 Aligned_cols=45 Identities=11% Similarity=0.231 Sum_probs=32.1
Q ss_pred eCCCCcHHHHHHHHHCCCCceeecCCHHHHHHHHHcCCcCeEEEee
Q 018090 125 QGLPGAYSEAAARKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 125 LGP~GTySe~AA~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPI 170 (361)
.|..--.-++++.+.--+.++++. .+..+++++++|++|.++-++
T Consensus 49 ~G~~vdi~~~ia~~lg~~i~~~~~-pw~~~~~~l~~g~~D~~~~~~ 93 (259)
T PRK15437 49 VGFDIDLAKELCKRINTQCTFVEN-PLDALIPSLKAKKIDAIMSSL 93 (259)
T ss_pred EeeeHHHHHHHHHHcCCceEEEeC-CHHHHHHHHHCCCCCEEEecC
Confidence 355555555666554346788876 499999999999999776554
No 236
>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=33.36 E-value=64 Score=32.19 Aligned_cols=48 Identities=15% Similarity=-0.056 Sum_probs=37.1
Q ss_pred ccEEEEeCCCCcHHHHHHHHHCC-------CCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 119 KVRVAYQGLPGAYSEAAARKAYP-------KCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f~-------~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
-+|||+ +.||.+|....+... ++++++.. ..+...|+.+|++|.++++
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 679999976655432 36788885 4889999999999999874
No 237
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=33.18 E-value=3.6e+02 Score=25.75 Aligned_cols=145 Identities=15% Similarity=0.014 Sum_probs=71.1
Q ss_pred ccEEEEeCCCCc-HHHHHH---HHHCCCCceeecCCHHHHHHHHHcCCcCeEEEeeeccc----ccchH----HhHHHHh
Q 018090 119 KVRVAYQGLPGA-YSEAAA---RKAYPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSV----GGSIH----RNYDLLL 186 (361)
Q Consensus 119 ~~rIAyLGP~GT-ySe~AA---~~~f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~----~G~V~----~tlDlL~ 186 (361)
..+|+...+.+. |--... .+.+|+.++.....-.++.+.+.+|++|+|++. .+.. .|... .....|.
T Consensus 98 ~l~I~~~~~~~~~~~~~~l~~f~~~~P~v~v~i~~~~~~~~~~l~~g~~D~~i~~-~~~~~~~~~~~~~~~~~~~~~~l~ 176 (319)
T PRK10216 98 KFELAAESPLMMIMLNALSKRIYQRYPQATIKLRNWDYDSLDAITRGEVDIGFTG-RESHPRSRELLSLLPLAIDFEVLF 176 (319)
T ss_pred EEEEEecchhHHHHHHHHHHHHHHHCCCCEEEEEeCCcchHHHHhcCCccEEEec-CCCCccccccccccccccceeeee
Confidence 467776644332 222222 223576554433322357899999999999984 2111 11100 0111111
Q ss_pred cCCeEEEEEEEEeeeeEeeeCCCCCccCcc---EEEec-h-HHHHHHHHHHHhcCC--e-EEeccCHHHHHHHHHhcCCC
Q 018090 187 RHRLHIVGEVQLVVNHCLLGLPGVLKEELK---RVFSH-P-QALAQCEMTLSNLGI--V-RISADDTAGAAQMVASIGER 258 (361)
Q Consensus 187 ~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik---~VySH-P-qALaQC~~fL~~~~~--~-~i~~~STA~AA~~va~~~~~ 258 (361)
...+. +.++-+|-+. ....+++++. -|..- . ....+..+++.+.+. . ...++|...+.++|+.++ .
T Consensus 177 ~~~~~----~v~~~~hp~~-~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~-~ 250 (319)
T PRK10216 177 SDLPC----VWLRKDHPAL-HEEWNLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPEFEQSLFMAAQPD-H 250 (319)
T ss_pred ecceE----EEEeCCCCcc-CCCCCHHHHhhCCCeEecCCCCCcchHHHHHHHhCCccceEEECCcHHHHHHHHHcCC-c
Confidence 22222 2345555542 2223344333 23311 1 123356677776553 2 356777777888887632 1
Q ss_pred CeEEecCHhhHH
Q 018090 259 DTGAVASAQAAE 270 (361)
Q Consensus 259 ~~AAIas~~AA~ 270 (361)
...+|.++.+++
T Consensus 251 ~gi~ilp~~~~~ 262 (319)
T PRK10216 251 LLLATAPRYCQY 262 (319)
T ss_pred ceEeccHHHHHH
Confidence 247888887554
No 238
>PRK03381 PII uridylyl-transferase; Provisional
Probab=33.17 E-value=54 Score=36.68 Aligned_cols=40 Identities=10% Similarity=0.155 Sum_probs=32.6
Q ss_pred eEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCCC
Q 018090 308 KTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRKR 347 (361)
Q Consensus 308 KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~ 347 (361)
-|.|.+..+|+||.|+++-++|+..|+|+..-...-..+.
T Consensus 707 ~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~ 746 (774)
T PRK03381 707 ATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGAD 746 (774)
T ss_pred eEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCe
Confidence 4677778889999999999999999999987665544333
No 239
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=33.00 E-value=3.7e+02 Score=24.21 Aligned_cols=115 Identities=15% Similarity=0.127 Sum_probs=60.5
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCC----CccCcc-
Q 018090 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGV----LKEELK- 216 (361)
Q Consensus 142 ~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~----~l~~Ik- 216 (361)
+.++++. +..++++++++|++|.++.++..+.+- ...++ ... -.......++++.+. .+++++
T Consensus 64 ~~~~~~~-~~~~~~~~l~~G~~D~~~~~~~~~~~r--~~~~~--------~s~-p~~~~~~~~~~~~~~~~~~~~~dl~g 131 (250)
T TIGR01096 64 KCKFVEQ-NFDGLIPSLKAKKVDAIMATMSITPKR--QKQID--------FSD-PYYATGQGFVVKKGSDLAKTLEDLDG 131 (250)
T ss_pred eEEEEeC-CHHHHHHHHhCCCcCEEEecCccCHHH--hhccc--------ccc-chhcCCeEEEEECCCCcCCChHHcCC
Confidence 4678884 689999999999999887543211111 00111 100 011112233333321 122221
Q ss_pred -EEEechHHHHHHHHHHHhc---CCeEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHc
Q 018090 217 -RVFSHPQALAQCEMTLSNL---GIVRISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (361)
Q Consensus 217 -~VySHPqALaQC~~fL~~~---~~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~Y 272 (361)
+|-. .....+. .++.+. ++.++.+.|..++.+++..+ +-.++|++...+..+
T Consensus 132 ~~i~~-~~g~~~~-~~l~~~~~~~~~~~~~~s~~~~~~~L~~g--~vD~~v~~~~~~~~~ 187 (250)
T TIGR01096 132 KTVGV-QSGTTHE-QYLKDYFKPGVDIVEYDSYDNANMDLKAG--RIDAVFTDASVLAEG 187 (250)
T ss_pred CEEEE-ecCchHH-HHHHHhccCCcEEEEcCCHHHHHHHHHcC--CCCEEEeCHHHHHHH
Confidence 2221 1222222 344432 56778888999999988876 356777777765543
No 240
>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=32.83 E-value=4.2e+02 Score=24.83 Aligned_cols=152 Identities=12% Similarity=0.003 Sum_probs=83.3
Q ss_pred EeCCCCcHHHHHHHHHCC--------CC--ceeecC---CHHHHHHHHHcCCcCeEEEeeecccc-----------cc--
Q 018090 124 YQGLPGAYSEAAARKAYP--------KC--ETVPCD---QFEAAFKAVELWLVDKAVLPIENSVG-----------GS-- 177 (361)
Q Consensus 124 yLGP~GTySe~AA~~~f~--------~~--e~vp~~---sf~eVf~aV~~g~~d~gVVPIENS~~-----------G~-- 177 (361)
..-|+|+...++...|.. +. ++.|-. .-.+++++|..|.+|.++++.-+... +.
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 345888888888776531 22 333332 35899999999999998865321110 00
Q ss_pred ----hHHhH---------HHHhcCCeEEEEEEEEeeeeEeee---CCCCCccCcc--EEEechHHHHHHHHHHHhcCCeE
Q 018090 178 ----IHRNY---------DLLLRHRLHIVGEVQLVVNHCLLG---LPGVLKEELK--RVFSHPQALAQCEMTLSNLGIVR 239 (361)
Q Consensus 178 ----V~~tl---------DlL~~~~L~IvgEi~lpI~h~Lla---~~g~~l~~Ik--~VySHPqALaQC~~fL~~~~~~~ 239 (361)
....+ +.+.+.++++.+-.. ....++. .+-.+++|++ +|...+-.. -.++++..++..
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~--~g~~~~~~~~~~i~s~~Dl~G~kir~~~~~~--~~~~~~~~Ga~~ 158 (257)
T TIGR00787 83 DYNHVHKVLDGEVGKALKKSLEKKGLKGLAYWD--NGFRQFTSSKKPITKPEDLKGLKIRIPNSPM--NEAQFKALGANP 158 (257)
T ss_pred CHHHHHHHHcCHHHHHHHHHHHHcCcEEEeecC--CceeEeeeCCCccCChHHhCCCEEecCCCHH--HHHHHHHcCCcc
Confidence 00011 112334666665333 2333333 2333566664 565543222 356777777665
Q ss_pred EeccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCceeecccc
Q 018090 240 ISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQ 282 (361)
Q Consensus 240 i~~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iLa~~Iq 282 (361)
+ .-+.++.-.-+..+ .-.+++.+......++|.=+.+.+.
T Consensus 159 v-~~~~~e~~~aL~~G--~vDg~~~~~~~~~~~~~~ev~~y~~ 198 (257)
T TIGR00787 159 E-PMAFSEVYTALQTG--VVDGQENPLSNVYSSKFYEVQKYLS 198 (257)
T ss_pred c-ccCHHHHHHHHHcC--CcccccCCHHHHhhcchhhhcchhe
Confidence 5 45556666655554 3457777777666667665555443
No 241
>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=32.68 E-value=3.2e+02 Score=23.41 Aligned_cols=31 Identities=10% Similarity=-0.091 Sum_probs=22.6
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEee
Q 018090 140 YPKCETVPC-DQFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 140 f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPI 170 (361)
+|+.++.-. .+-.++.+.+.+|++|+|+...
T Consensus 26 ~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 26 APGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred CCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 566554332 3566889999999999999853
No 242
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=32.51 E-value=52 Score=30.28 Aligned_cols=32 Identities=28% Similarity=0.309 Sum_probs=27.1
Q ss_pred EEEEecCCcchHHHHHHHHHHCCccccceeee
Q 018090 311 IVFTLEEGPGMLFKALAVFALRDINLTKIESR 342 (361)
Q Consensus 311 i~f~~~~~PGaL~~iL~~Fa~~~INLtkIESR 342 (361)
+..+..+.||.|..+++.++++||+..-+-|+
T Consensus 98 i~~~~~~~pgi~A~V~~~iak~gi~Irqi~~~ 129 (167)
T COG2150 98 IYPEDARYPGILAGVASLIAKRGISIRQIISE 129 (167)
T ss_pred EEeccCCCccHHHHHHHHHHHcCceEEEEecC
Confidence 34445589999999999999999999988775
No 243
>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=32.46 E-value=3.9e+02 Score=24.31 Aligned_cols=54 Identities=13% Similarity=0.036 Sum_probs=36.9
Q ss_pred CCccEEEEeCCCCcHHHH----HHHHHC----C-CCceeecCCHHHHHHHHHcCCcCeEEEee
Q 018090 117 GTKVRVAYQGLPGAYSEA----AARKAY----P-KCETVPCDQFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 117 ~~~~rIAyLGP~GTySe~----AA~~~f----~-~~e~vp~~sf~eVf~aV~~g~~d~gVVPI 170 (361)
...++||+.+....+.-. ...+++ + ++++++..++.+.++++.+|++|+++...
T Consensus 31 ~~~l~vg~~~~~~~~~~~~~~~~l~~~l~~~~g~~v~~~~~~~~~~~~~~l~~g~~Di~~~~~ 93 (254)
T TIGR01098 31 PKELNFGILPGENASNLTRRWEPLADYLEKKLGIKVQLFVATDYSAVIEAMRFGRVDIAWFGP 93 (254)
T ss_pred CCceEEEECCCCCHHHHHHHHHHHHHHHHHHhCCcEEEEeCCCHHHHHHHHHcCCccEEEECc
Confidence 346889998754433221 111222 1 36778888999999999999999998653
No 244
>cd08432 PBP2_GcdR_TrpI_HvrB_AmpR_like The C-terminal substrate domain of LysR-type GcdR, TrPI, HvR and beta-lactamase regulators, and that of other closely related homologs; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate domain of LysR-type transcriptional regulators involved in controlling the expression of glutaryl-CoA dehydrogenase (GcdH), S-adenosyl-L-homocysteine hydrolase, cell division protein FtsW, tryptophan synthase, and beta-lactamase. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex compris
Probab=32.23 E-value=72 Score=26.38 Aligned_cols=119 Identities=16% Similarity=-0.005 Sum_probs=55.8
Q ss_pred CCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCccE--
Q 018090 140 YPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR-- 217 (361)
Q Consensus 140 f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik~-- 217 (361)
+++.++....+- ..+.+.+|++|+|++..+....+.. ...|.+.++.++ .+-.|- ..++..+++++..
T Consensus 26 ~P~v~i~~~~~~--~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~~-~~~~~i~~~~l~~~~ 95 (194)
T cd08432 26 HPDIDLRLSTSD--RLVDFAREGIDLAIRYGDGDWPGLE---AERLMDEELVPV----CSPALL-AGLPLLSPADLARHT 95 (194)
T ss_pred CCCeEEEEEecC--CccccccccccEEEEecCCCCCCcc---eEEccCCcEEEe----cCHHHH-HhcCCCCHHHhhcCc
Confidence 565554433322 4677899999999986442222211 112223333222 222232 2222344444432
Q ss_pred -EE-ech-HHHHHHHHHHHhcC--C-eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHH
Q 018090 218 -VF-SHP-QALAQCEMTLSNLG--I-VRISADDTAGAAQMVASIGERDTGAVASAQAAEI 271 (361)
Q Consensus 218 -Vy-SHP-qALaQC~~fL~~~~--~-~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~ 271 (361)
|. +.. .......+++...+ . ....++|.....++++.+ ...||.++..++.
T Consensus 96 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 152 (194)
T cd08432 96 LLHDATRPEAWQWWLWAAGVADVDARRGPRFDDSSLALQAAVAG---LGVALAPRALVAD 152 (194)
T ss_pred eEEecCcccccHHHHhcCCeeccccCCeEEECCHHHHHHHHHhC---CCeEEeeHHHhhh
Confidence 32 211 11122222222222 1 234567777777777765 3477888876653
No 245
>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=32.20 E-value=2.9e+02 Score=22.85 Aligned_cols=121 Identities=15% Similarity=0.055 Sum_probs=59.0
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCC-CCCccCcc-
Q 018090 140 YPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLP-GVLKEELK- 216 (361)
Q Consensus 140 f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~-g~~l~~Ik- 216 (361)
+++.++.-. .+..++++.+.+|++|+|+..-.....+.. ...|.+..+.+ ..+-.|-+.... ..+++|+.
T Consensus 27 ~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~----v~~~~~pl~~~~~~~~~~dL~~ 99 (197)
T cd08425 27 YPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDID---AQPLFDERLAL----VVGATHPLAQRRTALTLDDLAA 99 (197)
T ss_pred CCCcEEEEEECcHHHHHHHHHcCCccEEEEecCCCCCCcE---EEEeccccEEE----EecCCCchhHhcccCCHHHHhc
Confidence 566555443 356789999999999999975331111100 01111122221 122233332221 13333333
Q ss_pred --EEE-ec-hHHHHHHHHHHHhcCCe--E-EeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 217 --RVF-SH-PQALAQCEMTLSNLGIV--R-ISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 217 --~Vy-SH-PqALaQC~~fL~~~~~~--~-i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
-|. .. ........+|+.+.+.. . ..++|...+..+++++ ...|+.+...++
T Consensus 100 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08425 100 EPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRG---RLATILPDAIAR 157 (197)
T ss_pred CCcEecCCCccHHHHHHHHHHHcCCCeeeEEeeCcHHHHHHHHhcC---CcEEeechhhhc
Confidence 222 11 12233456677665532 2 3456666666777764 346677776553
No 246
>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=31.82 E-value=5.3e+02 Score=25.69 Aligned_cols=143 Identities=9% Similarity=0.078 Sum_probs=76.7
Q ss_pred CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHh--cCCeEEEEEEE-EeeeeEeeeCCCCCccCc--c
Q 018090 142 KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL--RHRLHIVGEVQ-LVVNHCLLGLPGVLKEEL--K 216 (361)
Q Consensus 142 ~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~--~~~L~IvgEi~-lpI~h~Lla~~g~~l~~I--k 216 (361)
+++++.+++..++++++.+|.+|+|.+- .. +.+-+.. ..+++|+.-.. -.-...+++++..+++|+ |
T Consensus 36 ~Ve~~~f~~~~~~l~Al~aG~iD~~~~g-------~~-~~~~~~~a~g~~~~iv~v~~~~~g~~~ivv~~i~svaDLKGK 107 (328)
T TIGR03427 36 TIEVVQINDYVESINQYTAGKFDGCTMT-------NM-DALTIPAAGGVDTTALIVGDFSNGNDGIVLKGGKSLADLKGQ 107 (328)
T ss_pred eEEEEECCChHHHHHHHHcCCCCEEeec-------CH-HHHHHHHhCCCCeEEEEEEccCCCceEEEECCCCCHHHcCCC
Confidence 4788999999999999999999998652 11 1111111 23444432221 122245666665567777 4
Q ss_pred EEEechHHHHH--HHHHHHhcC-----CeEEeccCHHHHHHHHHhcCCCCeEEecCHhhH---HHcCCceeeccccCCCC
Q 018090 217 RVFSHPQALAQ--CEMTLSNLG-----IVRISADDTAGAAQMVASIGERDTGAVASAQAA---EIYGLDILAEKIQDDDD 286 (361)
Q Consensus 217 ~VySHPqALaQ--C~~fL~~~~-----~~~i~~~STA~AA~~va~~~~~~~AAIas~~AA---~~YgL~iLa~~IqD~~~ 286 (361)
+|..+.-...+ ..+.|++.| ++++.... +.+...+..+ .-+.+++-....+ +..|.++|... .+.++
T Consensus 108 kIav~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~~-~d~~aAl~~G-~VDAa~~~eP~~s~~~~~~g~~~l~~~-~~~~~ 184 (328)
T TIGR03427 108 KVNLVELSVSHYLLARALESVGLSEKDVKVVNTSD-ADIVAAFITK-DVTAVVTWNPQLSEIKAQPGANEVFDS-SQIPG 184 (328)
T ss_pred EEeccCCChHHHHHHHHHHHcCCCHHHeEEEeCCh-HHHHHHHhcC-CCcEEEEcCchHHHHHhCCCcEEeccc-ccCCC
Confidence 78665544433 334555543 56666654 4444444443 3344555444432 22477777654 23333
Q ss_pred CceEEEEEe
Q 018090 287 NVTRFLILA 295 (361)
Q Consensus 287 N~TRFlvl~ 295 (361)
..+-+++..
T Consensus 185 ~~~~~lv~~ 193 (328)
T TIGR03427 185 EILDLMVVN 193 (328)
T ss_pred cceEEEEEC
Confidence 333444444
No 247
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=31.58 E-value=4.1e+02 Score=24.31 Aligned_cols=113 Identities=16% Similarity=0.157 Sum_probs=65.5
Q ss_pred CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHh-cCCeEEEEEEEE----eeeeE-eeeCCCC---Ccc
Q 018090 143 CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL-RHRLHIVGEVQL----VVNHC-LLGLPGV---LKE 213 (361)
Q Consensus 143 ~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~-~~~L~IvgEi~l----pI~h~-Lla~~g~---~l~ 213 (361)
.++++..++.+..+++.+|++|+++++ ...+-.+. +.++..+....- +..++ ++++++. +++
T Consensus 31 v~~~~~~~~~~~~~~l~~g~~D~~~~~---------~~~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds~i~~l~ 101 (243)
T PF12974_consen 31 VELVPADDYAEFIEALRSGEIDLAFMG---------PLPYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADSPITSLA 101 (243)
T ss_dssp EEEE--SSHHHHHHHHHTTS-SEEE-----------HHHHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTSS--SHH
T ss_pred EEEEEcCCHHHHHHHHHcCCccEEEEC---------cHHHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCCCCCChh
Confidence 688999999999999999999999976 22333333 356766666655 33344 5566654 344
Q ss_pred Ccc---EEEechHH---HHHHHHHH-HhcC------CeEEeccCHHHHHHHHHhcCCCCeEEecC
Q 018090 214 ELK---RVFSHPQA---LAQCEMTL-SNLG------IVRISADDTAGAAQMVASIGERDTGAVAS 265 (361)
Q Consensus 214 ~Ik---~VySHPqA---LaQC~~fL-~~~~------~~~i~~~STA~AA~~va~~~~~~~AAIas 265 (361)
|++ -.+..|.. .--.+.+| +++| .+.+.+.+-..+++.|..+. -+.|++.+
T Consensus 102 dL~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~-~Da~~~~~ 165 (243)
T PF12974_consen 102 DLKGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGK-ADAAAIPS 165 (243)
T ss_dssp HHGGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTS-SSEEEEEH
T ss_pred hcCCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCC-ccEEEEec
Confidence 552 34445553 33456667 5654 34566777777888888753 44555544
No 248
>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=31.42 E-value=2.9e+02 Score=22.62 Aligned_cols=31 Identities=16% Similarity=0.086 Sum_probs=23.3
Q ss_pred HCCCCceeec-CCHHHHHHHHHcCCcCeEEEe
Q 018090 139 AYPKCETVPC-DQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 139 ~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+|+.++.-. .+-.++.+.+.+|++|+|+..
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~ 56 (197)
T cd08448 25 EYPGIEVALHEMSSAEQIEALLRGELDLGFVH 56 (197)
T ss_pred HCCCCeEEEEeCCHHHHHHHHHcCCcceEEEe
Confidence 3576655432 357889999999999999974
No 249
>PRK04374 PII uridylyl-transferase; Provisional
Probab=31.40 E-value=63 Score=36.74 Aligned_cols=34 Identities=18% Similarity=0.390 Sum_probs=29.1
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCcccccee
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIE 340 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIE 340 (361)
+.|.|-+...|+||.|+++-.+|+..|+|+..=.
T Consensus 795 ~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~Ak 828 (869)
T PRK04374 795 RRTRISLVAPDRPGLLADVAHVLRMQHLRVHDAR 828 (869)
T ss_pred CeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeE
Confidence 4567777788999999999999999999997543
No 250
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=30.93 E-value=51 Score=35.02 Aligned_cols=77 Identities=17% Similarity=0.264 Sum_probs=50.3
Q ss_pred HhhHHHcCCceeecc--ccCCCCCceEEEEEeeCCCC-----------CC---CC------CCceEEEEEEecCCcchHH
Q 018090 266 AQAAEIYGLDILAEK--IQDDDDNVTRFLILAREPII-----------AG---TD------RPYKTSIVFTLEEGPGMLF 323 (361)
Q Consensus 266 ~~AA~~YgL~iLa~~--IqD~~~N~TRFlvl~r~~~~-----------~~---~~------~~~KtSi~f~~~~~PGaL~ 323 (361)
..-|+..|+++-... ..+...|.-++.+-+..... +. -+ ..+..+++|.-.|+||.+.
T Consensus 388 ~~iA~e~GI~~~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~ggg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I~ 467 (526)
T PRK13581 388 PLLAKERGIEVEESKSEESPDYSNLITVTVTTDDGERSVAGTVFGDGEPRIVEIDGYRVDAKPEGHMLIIRNRDRPGVIG 467 (526)
T ss_pred HHHHHHcCCEEEEEEecCCCCCCCEEEEEEEeCCeEEEEEEEEecCCceEEEEECCEEEEeeCCceEEEEEeCCcCChhH
Confidence 355888888875433 33345677677665432110 00 00 1235667777789999999
Q ss_pred HHHHHHHHCCcccccee-ee
Q 018090 324 KALAVFALRDINLTKIE-SR 342 (361)
Q Consensus 324 ~iL~~Fa~~~INLtkIE-SR 342 (361)
.+.+.|++++||+.... +|
T Consensus 468 ~v~~~L~~~~iNIa~m~~~r 487 (526)
T PRK13581 468 KVGTLLGEAGINIAGMQLGR 487 (526)
T ss_pred HHHHHHhhcCCCchhcEecc
Confidence 99999999999998775 45
No 251
>KOG4028 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.43 E-value=40 Score=30.23 Aligned_cols=61 Identities=16% Similarity=0.181 Sum_probs=36.5
Q ss_pred cEEEEeCCCCcHHHHHHHHHCCC-CceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH
Q 018090 120 VRVAYQGLPGAYSEAAARKAYPK-CETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD 183 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~~-~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD 183 (361)
...+.--|+||+.|+-|+++.+. .++..-+++++--+.-.--.+..|+|-.| -|.+..|+|
T Consensus 108 la~~~wrp~gswreel~~~~vggg~ql~~~~ai~~~a~r~ki~s~a~g~v~~e---i~ii~knf~ 169 (175)
T KOG4028|consen 108 LACGCWRPKGSWREELAHAFVGGGLQLLHGDAIEDGADREKIHSAAAGTVHFE---IGIILKNFD 169 (175)
T ss_pred ecccccCCCCcHHHHHHHHHhcCCceeeccccccCchhhheeeeeccceEEEE---Eeeeehhhh
Confidence 34556679999999999998864 67776665554333222223444555555 344444443
No 252
>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=29.04 E-value=1.7e+02 Score=25.92 Aligned_cols=51 Identities=20% Similarity=0.059 Sum_probs=35.7
Q ss_pred ccEEEEeCCCCcHHHHHHHHHC---C----CCceeecCCHHHHHHHHHcCCcCeEEEeeec
Q 018090 119 KVRVAYQGLPGAYSEAAARKAY---P----KCETVPCDQFEAAFKAVELWLVDKAVLPIEN 172 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f---~----~~e~vp~~sf~eVf~aV~~g~~d~gVVPIEN 172 (361)
.+||++.+ |+.++.....+. + +.+++... ..+...++.+|++|.+++..++
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 36899876 777775554432 2 25677665 5677779999999999977765
No 253
>PRK09224 threonine dehydratase; Reviewed
Probab=28.69 E-value=68 Score=33.99 Aligned_cols=36 Identities=25% Similarity=0.372 Sum_probs=31.0
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeec
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRP 343 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP 343 (361)
+...+.|..|.+||+|.+.|+.+. -+-|+|.++=|-
T Consensus 422 ~e~~~~~~fPerpGal~~Fl~~l~-~~~~It~f~Yr~ 457 (504)
T PRK09224 422 DERLYRFEFPERPGALLKFLSTLG-THWNISLFHYRN 457 (504)
T ss_pred ceEEEEEeCCCCCCHHHHHHHhcC-CCCeeEEEEEcc
Confidence 456677889999999999999887 789999999873
No 254
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=28.19 E-value=72 Score=36.33 Aligned_cols=33 Identities=21% Similarity=0.293 Sum_probs=28.1
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccce
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKI 339 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkI 339 (361)
+-|.|.+..+|+||.|+++-++|+..|+|+..=
T Consensus 813 ~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~A 845 (895)
T PRK00275 813 PVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNA 845 (895)
T ss_pred CeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEe
Confidence 356677778899999999999999999998643
No 255
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=27.93 E-value=4.9e+02 Score=24.06 Aligned_cols=54 Identities=22% Similarity=0.283 Sum_probs=34.5
Q ss_pred CCCccEEEEeCCCCcHH-HHH---HHHHCCCCceee-cCCHHHHHHHHHcCCcCeEEEe
Q 018090 116 DGTKVRVAYQGLPGAYS-EAA---ARKAYPKCETVP-CDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 116 ~~~~~rIAyLGP~GTyS-e~A---A~~~f~~~e~vp-~~sf~eVf~aV~~g~~d~gVVP 169 (361)
..+..+|+.....+.+= -.+ .++.+|++++.- ..+-.++++.+.+|++|+|+++
T Consensus 87 ~~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~ 145 (290)
T PRK10837 87 DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIE 145 (290)
T ss_pred hCCeEEEEecchhHhhhhHHHHHHHHHHCCCceEEEEECCHHHHHHHHHhCCceEEEec
Confidence 34567777776544321 111 123367765543 3467789999999999999985
No 256
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=27.75 E-value=1.7e+02 Score=24.02 Aligned_cols=120 Identities=12% Similarity=-0.022 Sum_probs=55.9
Q ss_pred CCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCccE--
Q 018090 140 YPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEELKR-- 217 (361)
Q Consensus 140 f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~Ik~-- 217 (361)
+|+.++.-...- ..+.+.+|++|+|++...+...+. ....|.+.++.++ .+-+| +...+..+++++..
T Consensus 26 ~P~i~i~i~~~~--~~~~l~~~~~Dl~l~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~-~~~~~~~~~~dl~~~~ 95 (194)
T cd08481 26 HPDITVNLVTRD--EPFDFSQGSFDAAIHFGDPVWPGA---ESEYLMDEEVVPV----CSPAL-LAGRALAAPADLAHLP 95 (194)
T ss_pred CCCceEEEEecc--cccCcccCCCCEEEEcCCCCCCCc---cceecccCeeeec----CCHHH-HhcCCCCcHHHHhhCc
Confidence 566554433221 123688999999998644322221 1122333333322 23333 22222234444421
Q ss_pred EEechHHHHHHHHHHHhcCCe------EEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHc
Q 018090 218 VFSHPQALAQCEMTLSNLGIV------RISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (361)
Q Consensus 218 VySHPqALaQC~~fL~~~~~~------~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~Y 272 (361)
.+........-.+|+.+.+.+ ...+++...+.++|..+ ...|+.++..++.+
T Consensus 96 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~~~~ 153 (194)
T cd08481 96 LLQQTTRPEAWRDWFEEVGLEVPTAYRGMRFEQFSMLAQAAVAG---LGVALLPRFLIEEE 153 (194)
T ss_pred eEecCCCCcCHHHHHHHcCCCCCCccCceEeccHHHHHHHHHhC---CCeEEecHHHHHHH
Confidence 111110011234566654432 13445666667777664 34778888776644
No 257
>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=26.98 E-value=97 Score=29.34 Aligned_cols=49 Identities=29% Similarity=0.297 Sum_probs=36.7
Q ss_pred cEEEEeCCCCcHHHHHHHHHCCC-------CceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 120 VRVAYQGLPGAYSEAAARKAYPK-------CETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~~-------~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+|++ |+.|+.++....+++.. ...+++.+..+++.+|.+|++|.++..
T Consensus 142 k~v~~-~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 142 KRVAV-GAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred CEEec-CCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEEe
Confidence 46766 56678778776665431 224688899999999999999999875
No 258
>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=26.02 E-value=95 Score=25.72 Aligned_cols=116 Identities=12% Similarity=-0.021 Sum_probs=57.3
Q ss_pred CCCCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCCCCCccCc---c
Q 018090 140 YPKCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLPGVLKEEL---K 216 (361)
Q Consensus 140 f~~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~g~~l~~I---k 216 (361)
||+.++.... .+..+.+.+|++|.|++...-...|. ....|.+.++.++ .+-+| +......+++++ .
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 5665544332 23467799999999998532111111 1122333444333 23334 332222344443 2
Q ss_pred EEEechHHHHHHHHHHHhcCCe-----EEeccCHHHHHHHHHhcCCCCeEEecCHhhHH
Q 018090 217 RVFSHPQALAQCEMTLSNLGIV-----RISADDTAGAAQMVASIGERDTGAVASAQAAE 270 (361)
Q Consensus 217 ~VySHPqALaQC~~fL~~~~~~-----~i~~~STA~AA~~va~~~~~~~AAIas~~AA~ 270 (361)
-|. +.. ......|+.+.+.. ...++|.....+++..+ ...++.++..++
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 12345677665432 24456666677777764 346777776554
No 259
>TIGR01693 UTase_glnD [Protein-PII] uridylyltransferase. This model describes GlnD, the uridylyltransferase/uridylyl-removing enzyme for the nitrogen regulatory protein PII. Not all homologs of PII share the property of uridylyltransferase modification on the characteristic Tyr residue (see Prosite pattern PS00496 and document PDOC00439), but the modification site is preserved in the PII homolog of all species with a member of this family.
Probab=25.13 E-value=77 Score=35.69 Aligned_cols=40 Identities=13% Similarity=0.285 Sum_probs=31.7
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHHCCccccceeeecCCC
Q 018090 307 YKTSIVFTLEEGPGMLFKALAVFALRDINLTKIESRPQRK 346 (361)
Q Consensus 307 ~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkIESRP~~~ 346 (361)
.-|.|.+..+|+||.|+++.++|+..|+|+..=.---+.+
T Consensus 667 ~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~ 706 (850)
T TIGR01693 667 GGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKD 706 (850)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecC
Confidence 4577888889999999999999999999987654333333
No 260
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=23.67 E-value=81 Score=24.48 Aligned_cols=77 Identities=17% Similarity=0.200 Sum_probs=50.8
Q ss_pred EEechHHHHHHHHHHHhcCC-eEEeccCHHHHHHHHHhcCCCCeEEecCHhhHHHcCCceeeccccCCCCCceEEEEEee
Q 018090 218 VFSHPQALAQCEMTLSNLGI-VRISADDTAGAAQMVASIGERDTGAVASAQAAEIYGLDILAEKIQDDDDNVTRFLILAR 296 (361)
Q Consensus 218 VySHPqALaQC~~fL~~~~~-~~i~~~STA~AA~~va~~~~~~~AAIas~~AA~~YgL~iLa~~IqD~~~N~TRFlvl~r 296 (361)
|=.||.-..-.+++|...+. +...+.|..+|.+.+.... ++..-| .-......|+.++. .|.... ..+++++++.
T Consensus 4 vd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~~-~d~iii-d~~~~~~~~~~~~~-~i~~~~-~~~~ii~~t~ 79 (112)
T PF00072_consen 4 VDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLKKHP-PDLIII-DLELPDGDGLELLE-QIRQIN-PSIPIIVVTD 79 (112)
T ss_dssp EESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHST-ESEEEE-ESSSSSSBHHHHHH-HHHHHT-TTSEEEEEES
T ss_pred EECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhcccC-ceEEEE-Eeeecccccccccc-cccccc-ccccEEEecC
Confidence 44577788888889987787 7788888888888887653 444444 32223345555544 343333 7889999986
Q ss_pred CC
Q 018090 297 EP 298 (361)
Q Consensus 297 ~~ 298 (361)
+.
T Consensus 80 ~~ 81 (112)
T PF00072_consen 80 ED 81 (112)
T ss_dssp ST
T ss_pred CC
Confidence 54
No 261
>TIGR01327 PGDH D-3-phosphoglycerate dehydrogenase. This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli.
Probab=23.45 E-value=78 Score=33.67 Aligned_cols=81 Identities=16% Similarity=0.245 Sum_probs=50.8
Q ss_pred HhhHHHcCCceeecccc--CCCCCceEEEEEeeCCCC------CCCC--------------CCceEEEEEEecCCcchHH
Q 018090 266 AQAAEIYGLDILAEKIQ--DDDDNVTRFLILAREPII------AGTD--------------RPYKTSIVFTLEEGPGMLF 323 (361)
Q Consensus 266 ~~AA~~YgL~iLa~~Iq--D~~~N~TRFlvl~r~~~~------~~~~--------------~~~KtSi~f~~~~~PGaL~ 323 (361)
...|+..|+++...... +...|.-++-+-+..... -..+ ...-.++++.-.|+||.+.
T Consensus 387 ~~iA~e~GI~v~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~gGg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I~ 466 (525)
T TIGR01327 387 PAVAKERGITVEESKSESSPDYKNYLSVTVTGDSGTVSVAGTVFGGFSPRIVEIDGFHVDLEPEGIMLIILHLDKPGVIG 466 (525)
T ss_pred HHHHHHcCCEEEEEEccCCCCCCCEEEEEEEeCCcEEEEEEEEecCCcEEEEEECCEEEEEecCccEEEEEecCcCCcch
Confidence 35688899998665433 223466566544322110 0000 0123456666689999999
Q ss_pred HHHHHHHHCCcccccee-eecCCC
Q 018090 324 KALAVFALRDINLTKIE-SRPQRK 346 (361)
Q Consensus 324 ~iL~~Fa~~~INLtkIE-SRP~~~ 346 (361)
++.+.+.+++||+..+. +|-.++
T Consensus 467 ~v~~~L~~~~iNIa~m~~~R~~~g 490 (525)
T TIGR01327 467 KVGTLLGTAGINIASMQLGRKEKG 490 (525)
T ss_pred HHHhHHhhcCCChHHcEeecCCCC
Confidence 99999999999998874 565444
No 262
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=23.12 E-value=2.2e+02 Score=26.45 Aligned_cols=50 Identities=20% Similarity=0.187 Sum_probs=35.9
Q ss_pred CccEEEEeCCCCcHHHHHHHHHC--------CCCceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 118 TKVRVAYQGLPGAYSEAAARKAY--------PKCETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 118 ~~~rIAyLGP~GTySe~AA~~~f--------~~~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
+.++|+.- +.|+-++...+.++ .+.+++..+. .+...++.+|++|.++++
T Consensus 120 kGk~i~~~-~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~iDa~~~~ 177 (252)
T PF13379_consen 120 KGKKIAVP-FPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGEIDAAVLW 177 (252)
T ss_dssp STEEEEES-STTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-SEEEEE
T ss_pred CCcEEEEc-CCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCCcCEEEec
Confidence 45567764 55887787766554 1367888888 999999999999999985
No 263
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.99 E-value=1.1e+02 Score=30.84 Aligned_cols=98 Identities=18% Similarity=0.116 Sum_probs=61.1
Q ss_pred cEEEEeCCCCcHHHHHHHHHCC----CCceeecCCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHh---cCCeEE
Q 018090 120 VRVAYQGLPGAYSEAAARKAYP----KCETVPCDQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLL---RHRLHI 192 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~----~~e~vp~~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~---~~~L~I 192 (361)
.+++-.| .|+..|.+...++. +...+|++...++..++..|++|.++.=+-++....=.-++.+|. ++++..
T Consensus 151 v~~~~~g-~Gs~dhl~~~~~~k~~Gi~~~~Vpy~g~gea~taLlgg~v~a~~~~~se~~~~vksG~lr~Lav~s~eRl~~ 229 (319)
T COG3181 151 VIGGGSG-LGSADHLAGALFAKAAGIKITYVPYKGGGEALTALLGGHVDAGSTNLSELLSQVKSGTLRLLAVFSEERLPG 229 (319)
T ss_pred EEecCCC-CCcHHHHHHHHHHHHhCCceeEEeecCccHHHHHHhcCceeeeecChhhhhhhhccCceEEEEeechhhcCC
Confidence 4444444 48999999887653 478999999999999999999998885443322222222333332 111111
Q ss_pred ------EE----EEEEeeeeEeeeCCCCCccCccEE
Q 018090 193 ------VG----EVQLVVNHCLLGLPGVLKEELKRV 218 (361)
Q Consensus 193 ------vg----Ei~lpI~h~Lla~~g~~l~~Ik~V 218 (361)
.. .+.+++.+.+.+.+|++.+.|.++
T Consensus 230 ~pdvPT~~E~G~~~~~~~wrgvfap~g~~~e~~~~~ 265 (319)
T COG3181 230 LPDVPTLKEQGYDVVMSIWRGVFAPAGTPDEIIAKL 265 (319)
T ss_pred CCCCCChHhcCCceeeeeeeEEEeCCCCCHHHHHHH
Confidence 11 123677788888888766554443
No 264
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=22.98 E-value=6.8e+02 Score=24.05 Aligned_cols=142 Identities=19% Similarity=0.105 Sum_probs=69.7
Q ss_pred CCccEEEEeCCCCcH-HHHHHH---HHCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHH--HHhcCC
Q 018090 117 GTKVRVAYQGLPGAY-SEAAAR---KAYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYD--LLLRHR 189 (361)
Q Consensus 117 ~~~~rIAyLGP~GTy-Se~AA~---~~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlD--lL~~~~ 189 (361)
.+..+|+.....+++ =..... +.+++.++... .+-.++.+.+.+|++|+|+++-. . . ...++ .|.+.+
T Consensus 88 ~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~L~~g~~Dl~i~~~~-~-~---~~~~~~~~l~~~~ 162 (317)
T PRK15421 88 QTRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDI-L-P---RSGLHYSPMFDYE 162 (317)
T ss_pred ceeEEEEecccchHHHHHHHHHHHHHHCCCceEEEEeCccHHHHHHHHCCCcCEEEecCc-c-c---CCCceEEEeccce
Confidence 356788876443332 111111 22566655433 34678899999999999997521 0 0 11111 111222
Q ss_pred eEEEEEEEEeeeeEeeeCCCCCccCcc--EEEech---HHHHHHHHHHHhcCC--eEEeccCHHHHHHHHHhcCCCCeEE
Q 018090 190 LHIVGEVQLVVNHCLLGLPGVLKEELK--RVFSHP---QALAQCEMTLSNLGI--VRISADDTAGAAQMVASIGERDTGA 262 (361)
Q Consensus 190 L~IvgEi~lpI~h~Lla~~g~~l~~Ik--~VySHP---qALaQC~~fL~~~~~--~~i~~~STA~AA~~va~~~~~~~AA 262 (361)
+. +.++..|-+......+++++. ..+..+ ........|+.+.+. +...++|.....++|..+ ...+
T Consensus 163 ~~----lv~~~~hpl~~~~~i~~~~L~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~ 235 (317)
T PRK15421 163 VR----LVLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAAR---MGIA 235 (317)
T ss_pred EE----EEEcCCCCccccCcCCHHHhCCCcEEecCCchhhHHHHHHHHHHhCCCCceeecCCHHHHHHHHHhC---CcEE
Confidence 22 223444444333333444443 222222 223445556665553 334566777666777664 2355
Q ss_pred ecCHhhHH
Q 018090 263 VASAQAAE 270 (361)
Q Consensus 263 Ias~~AA~ 270 (361)
|.+...++
T Consensus 236 i~p~~~~~ 243 (317)
T PRK15421 236 ALPHWVVE 243 (317)
T ss_pred Eecchhcc
Confidence 66665443
No 265
>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=22.94 E-value=4.2e+02 Score=21.63 Aligned_cols=31 Identities=16% Similarity=0.176 Sum_probs=23.3
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCcCeEEEee
Q 018090 140 YPKCETVPCD-QFEAAFKAVELWLVDKAVLPI 170 (361)
Q Consensus 140 f~~~e~vp~~-sf~eVf~aV~~g~~d~gVVPI 170 (361)
+|+.++.-.. +..++.+.+.+|++|+|++.-
T Consensus 26 ~p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08414 26 YPDVELELREMTTAEQLEALRAGRLDVGFVRP 57 (197)
T ss_pred CCCcEEEEecCChHHHHHHHHcCCccEEEEcC
Confidence 4665554433 468899999999999999753
No 266
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=22.56 E-value=4.4e+02 Score=21.66 Aligned_cols=126 Identities=13% Similarity=0.007 Sum_probs=62.1
Q ss_pred HHCCCCceeec-CCHHHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCCeEEEEEEEEeeeeEeeeCC-CCCcc--
Q 018090 138 KAYPKCETVPC-DQFEAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHRLHIVGEVQLVVNHCLLGLP-GVLKE-- 213 (361)
Q Consensus 138 ~~f~~~e~vp~-~sf~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~L~IvgEi~lpI~h~Lla~~-g~~l~-- 213 (361)
+.+|+.++.-. .+..++++.+.+|++|+|++.-.......+ ....|.+..+.+ ..+-+|-+...+ ..+++
T Consensus 24 ~~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l--~~~~l~~~~~~~----~~~~~~~~~~~~~~~~~~~l 97 (199)
T cd08430 24 AQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARL--AFLPLATSPLVF----IAPNIACAVTQQLSQGEIDW 97 (199)
T ss_pred HHCCCceEEEEeCCHHHHHHHHHCCCCCEEEEecCCCCCccc--EEEeeccceEEE----EEeCCchhhhhhcccccccc
Confidence 34677665544 467788999999999999975221111000 011122222222 234445443221 12222
Q ss_pred -CccEEEec-hHHHHHHHHHHHhcCC--eE-EeccCHHHHHHHHHhcCCCCeEEecCHhhHHHc
Q 018090 214 -ELKRVFSH-PQALAQCEMTLSNLGI--VR-ISADDTAGAAQMVASIGERDTGAVASAQAAEIY 272 (361)
Q Consensus 214 -~Ik~VySH-PqALaQC~~fL~~~~~--~~-i~~~STA~AA~~va~~~~~~~AAIas~~AA~~Y 272 (361)
+..-|... ......-.+|+.+.+. +. ..+++.....+.++.+ ...|+.+...++.+
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~lp~~~~~~~ 158 (199)
T cd08430 98 SRLPFILPERGLARERLDQWFRRRGIKPNIYAQVAGHEAIVSMVALG---CGVGIVPELVLDNS 158 (199)
T ss_pred ccCCeEEccCChHHHHHHHHHHHcCCCCCeeEEEccHHHHHHHHHhC---CeEEEccHHHhhhh
Confidence 22333321 1112234566666542 32 3455555555666654 35778888766543
No 267
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=22.47 E-value=1.5e+02 Score=28.44 Aligned_cols=47 Identities=21% Similarity=0.064 Sum_probs=33.8
Q ss_pred cEEEEeCCCCcHHHHHHHHHCCC-------CceeecCCHHHHHHHHHcCCcCeEEEe
Q 018090 120 VRVAYQGLPGAYSEAAARKAYPK-------CETVPCDQFEAAFKAVELWLVDKAVLP 169 (361)
Q Consensus 120 ~rIAyLGP~GTySe~AA~~~f~~-------~e~vp~~sf~eVf~aV~~g~~d~gVVP 169 (361)
.+|++ +.||.+|....+++.+ .+++.. +..+.+.++.+|++|.+++.
T Consensus 130 k~I~~--~~gs~~~~~l~~~l~~~g~~~~dv~~v~~-~~~~~~~al~~G~vDa~~~~ 183 (314)
T PRK11553 130 HKVAF--QKGSSSHNLLLRALRKAGLKFTDIQPTYL-TPADARAAFQQGNVDAWAIW 183 (314)
T ss_pred CEEee--cCCCcHHHHHHHHHHHcCCCHHHeEEEec-ChHHHHHHHHcCCCCEEEEc
Confidence 46887 5688888776665532 233444 77888999999999988863
No 268
>cd04915 ACT_AK-Ectoine_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinas
Probab=21.40 E-value=67 Score=24.18 Aligned_cols=37 Identities=27% Similarity=0.280 Sum_probs=27.1
Q ss_pred CCcchHHHHHHHHHHCCccccceeeecCCCCCCeeee
Q 018090 317 EGPGMLFKALAVFALRDINLTKIESRPQRKRPLRVVD 353 (361)
Q Consensus 317 ~~PGaL~~iL~~Fa~~~INLtkIESRP~~~~pw~y~~ 353 (361)
..||.+.++++.+++.|||+-.|-.=+...+-+=+++
T Consensus 13 ~~~gv~~ki~~~L~~~~I~v~~i~~~~s~~~is~~V~ 49 (66)
T cd04915 13 STPGVLARGLAALAEAGIEPIAAHQSMRNVDVQFVVD 49 (66)
T ss_pred CcchHHHHHHHHHHHCCCCEEEEEecCCeeEEEEEEE
Confidence 3789999999999999999977765554433333333
No 269
>PF01634 HisG: ATP phosphoribosyltransferase; InterPro: IPR013820 ATP phosphoribosyltransferase (2.4.2.17 from EC) is the enzyme that catalyzes the first step in the biosynthesis of histidine in bacteria, fungi and plants as shown below. It is a member of the larger phosphoribosyltransferase superfamily of enzymes which catalyse the condensation of 5-phospho-alpha-D-ribose 1-diphosphate with nitrogenous bases in the presence of divalent metal ions []. ATP + 5-phospho-alpha-D-ribose 1-diphosphate = 1-(5-phospho-D-ribosyl)-ATP + diphosphate Histidine biosynthesis is an energetically expensive process and ATP phosphoribosyltransferase activity is subject to control at several levels. Transcriptional regulation is based primarily on nutrient conditions and determines the amount of enzyme present in the cell, while feedback inihibition rapidly modulates activity in response to cellular conditions. The enzyme has been shown to be inhibited by 1-(5-phospho-D-ribosyl)-ATP, histidine, ppGpp (a signal associated with adverse environmental conditions) and ADP and AMP (which reflect the overall energy status of the cell). As this pathway of histidine biosynthesis is present only in prokayrotes, plants and fungi, this enzyme is a promising target for the development of novel antimicrobial compounds and herbicides. ATP phosphoribosyltransferase is found in two distinct forms: a long form containing two catalytic domains and a C-terminal regulatory domain, and a short form in which the regulatory domain is missing. The long form is catalytically competent, but in organisms with the short form, a histidyl-tRNA synthetase paralogue, HisZ, is required for enzyme activity []. This entry represents the catalytic region of this enzyme. The structures of the long form enzymes from Escherichia coli (P60757 from SWISSPROT) and Mycobacterium tuberculosis (P60759 from SWISSPROT) have been determined [, ]. The enzyme itself exists in equilibrium between an active dimeric form, an inactive hexameric form and higher aggregates. Interconversion between the various forms is largely reversible and is influenced by the binding of the natural substrates and inhibitors of the enzyme. The two catalytic domains are linked by a two-stranded beta-sheet and togther form a "periplasmic binding protein fold". A crevice between these domains contains the active site. The C-terminal domain is not directly involved in catalysis but appears to be involved the formation of hexamers, induced by the binding of inhibitors such as histidine to the enzyme, thus regulating activity.; GO: 0003879 ATP phosphoribosyltransferase activity, 0000105 histidine biosynthetic process, 0005737 cytoplasm; PDB: 1VE4_A 2VD3_B 1NH7_A 1NH8_A 1Z7N_G 1Z7M_E 1O64_A 1O63_A 1USY_F 1Q1K_A ....
Probab=21.31 E-value=4.9e+02 Score=23.63 Aligned_cols=110 Identities=19% Similarity=0.181 Sum_probs=67.9
Q ss_pred HHHHHHHHcCCcCeEEEeeecccccchHHhHHHHhcCC---eEEEEEEEEeeeeEee---eCCCC---CccCcc---EEE
Q 018090 152 EAAFKAVELWLVDKAVLPIENSVGGSIHRNYDLLLRHR---LHIVGEVQLVVNHCLL---GLPGV---LKEELK---RVF 219 (361)
Q Consensus 152 ~eVf~aV~~g~~d~gVVPIENS~~G~V~~tlDlL~~~~---L~IvgEi~lpI~h~Ll---a~~g~---~l~~Ik---~Vy 219 (361)
.|+-.-|+.|.+|.||+ -.|.|.++. -.+.--..|+..+|=+ +..+. ++++++ +|.
T Consensus 4 ~DIp~yV~~G~~DlGI~------------G~D~l~E~~~~~~~v~~~~dL~fg~crl~vAvp~~~~~~~~~~l~~~~rIA 71 (163)
T PF01634_consen 4 QDIPTYVEDGIADLGIT------------GKDVLLESGLGRADVEELLDLGFGKCRLVVAVPEDWPYKSVEDLKAGLRIA 71 (163)
T ss_dssp GHHHHHHHTTSSSEEEE------------EHHHHHHHTHH-SSEEEEEEESCSEEEEEEEEETTSCGCCGGGGSSTEEEE
T ss_pred HHHHHHHHCCCCcEEEe------------ehheeccCCCCccceEEEeecccccEEEEEEEECCcCCCCHHHhccCCEEE
Confidence 46777899999999996 356665544 2355556777776633 33332 234444 788
Q ss_pred echHHHHHHHHHHHhcC--CeEEeccCHHHHHHHHHhcCCCCe-E-EecCHhhHHHcCCceee
Q 018090 220 SHPQALAQCEMTLSNLG--IVRISADDTAGAAQMVASIGERDT-G-AVASAQAAEIYGLDILA 278 (361)
Q Consensus 220 SHPqALaQC~~fL~~~~--~~~i~~~STA~AA~~va~~~~~~~-A-AIas~~AA~~YgL~iLa 278 (361)
+-..-+. ++|+++++ ++++..+...|+|=.+- ..+. . -..+-...+.+||+++.
T Consensus 72 Tkyp~l~--~~yf~~~g~~~~ii~l~GsvE~ap~~g---lAD~IvDiv~TG~TLr~NgL~~i~ 129 (163)
T PF01634_consen 72 TKYPNLT--RRYFAEKGINVEIIKLSGSVELAPPLG---LADAIVDIVETGTTLRANGLKEIE 129 (163)
T ss_dssp ES-HHHH--HHHHHHCT-EEEEEE-SS-TTHHHHTT---SSSEEEEEESSSHHHHHTTEEEEE
T ss_pred ECCHHHH--HHHHHHcCCcEEEEEccCCccccCCCC---CCCEEEEeccCcHHHHHCCCEEeE
Confidence 7776664 89999986 66777777777665421 1111 1 23556667899999984
No 270
>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=21.21 E-value=1.2e+02 Score=22.54 Aligned_cols=26 Identities=19% Similarity=0.327 Sum_probs=22.4
Q ss_pred ecCCcchHHHHHHHHHHCCcccccee
Q 018090 315 LEEGPGMLFKALAVFALRDINLTKIE 340 (361)
Q Consensus 315 ~~~~PGaL~~iL~~Fa~~~INLtkIE 340 (361)
+...+|.+.++++.|++.|||+..|-
T Consensus 10 ~~~~~~~~~~i~~aL~~~~I~v~~i~ 35 (65)
T cd04918 10 VQRSSLILERAFHVLYTKGVNVQMIS 35 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 34568999999999999999997775
No 271
>PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed
Probab=21.09 E-value=20 Score=36.46 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=28.7
Q ss_pred CCCCCCcccchhhhhcccccccccccccCCcc
Q 018090 62 DRPYTPDVQSSEANERSQDSQSSGFHKDLNLL 93 (361)
Q Consensus 62 ~~~~~p~~~~~~~~~~~~~~~~~~~~~d~~~l 93 (361)
|+-|.|+.+.+|+++++.|++|+.|++++..+
T Consensus 322 E~H~dp~~a~~D~~~sl~p~el~~l~~~i~~~ 353 (360)
T PRK12595 322 EVHPDPAVALSDSAQQMDIPEFDRFLDELKPL 353 (360)
T ss_pred EecCCCCCCCCchhhhCCHHHHHHHHHHHHHH
Confidence 66779999999999999999999999988554
No 272
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=20.94 E-value=2e+02 Score=27.38 Aligned_cols=142 Identities=18% Similarity=0.159 Sum_probs=78.4
Q ss_pred ccEEEEeCCCCcHHHHHHHHHC--C---------CCcee----------ecCCHHHHHHHHHcCCcCeEEEeeecccccc
Q 018090 119 KVRVAYQGLPGAYSEAAARKAY--P---------KCETV----------PCDQFEAAFKAVELWLVDKAVLPIENSVGGS 177 (361)
Q Consensus 119 ~~rIAyLGP~GTySe~AA~~~f--~---------~~e~v----------p~~sf~eVf~aV~~g~~d~gVVPIENS~~G~ 177 (361)
+++||. |+|.-.+.+...+- + +-+++ .+---.|+-.-|+.|.+|.||+=
T Consensus 3 ~l~iAl--pKGRL~e~t~~ll~~aG~~~~~~~~~~R~L~~~~~~~~i~~~~~r~~DIp~yV~~G~~DlGItG-------- 72 (215)
T PRK01686 3 MLTIAL--PKGRILEETLPLLAKAGIDPSEDPDKSRKLIFPTPEPDVRFLLVRATDVPTYVEHGAADLGIVG-------- 72 (215)
T ss_pred cEEEEe--cCcccHHHHHHHHHHcCCCcccCCCCCcceEeecCCCCEEEEEECHHHHHHHHhCCCccEEEee--------
Confidence 457777 58888887765331 0 00111 11234688899999999999963
Q ss_pred hHHhHHHHhcCCeEEEEEEEEeeeeE---eeeCCCCCc------cCccEEEechHHHHHHHHHHHhcC--CeEEeccCHH
Q 018090 178 IHRNYDLLLRHRLHIVGEVQLVVNHC---LLGLPGVLK------EELKRVFSHPQALAQCEMTLSNLG--IVRISADDTA 246 (361)
Q Consensus 178 V~~tlDlL~~~~L~IvgEi~lpI~h~---Lla~~g~~l------~~Ik~VySHPqALaQC~~fL~~~~--~~~i~~~STA 246 (361)
+|.|.+..-.+.-=..|...+| +++.++... ..-++|.+-.--+. ++|+++++ ++++..+...
T Consensus 73 ----~D~l~E~~~~v~~l~dLgfG~crl~vAvp~~~~~~~~~~~~~~~rIATkYp~it--~~yf~~~gv~~~iv~l~Gsv 146 (215)
T PRK01686 73 ----KDVLLEHGKDLYEPLDLGIGKCRMSVAVPPGFDYAPAVKQGPRLRVATKYPNIA--RRYFAEKGEQVEIIKLYGSV 146 (215)
T ss_pred ----eeEeeecCCCeEEEecCCccCEEEEEEEECcccccchhhccCCCEEEeCCHHHH--HHHHHHcCCeEEEEECcCce
Confidence 4555544322333344666655 333433221 11246766655554 57999887 4555555544
Q ss_pred HHHHHHHhcCCCC-eEEe-cCHhhHHHcCCceeec
Q 018090 247 GAAQMVASIGERD-TGAV-ASAQAAEIYGLDILAE 279 (361)
Q Consensus 247 ~AA~~va~~~~~~-~AAI-as~~AA~~YgL~iLa~ 279 (361)
|+|=.+ +..+ .+=| .+-...+.+||+++++
T Consensus 147 E~aP~~---GlAD~IvDivsTG~TLr~NgL~~ie~ 178 (215)
T PRK01686 147 ELAPLV---GLADAIVDIVETGNTLRANGLVEVEE 178 (215)
T ss_pred eecccc---CCccEEEEeecChHHHHHCcCEEeeE
Confidence 443221 1111 1112 3556678999999963
No 273
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=20.82 E-value=1.2e+02 Score=34.50 Aligned_cols=34 Identities=26% Similarity=0.289 Sum_probs=29.3
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHHCCccccce
Q 018090 306 PYKTSIVFTLEEGPGMLFKALAVFALRDINLTKI 339 (361)
Q Consensus 306 ~~KtSi~f~~~~~PGaL~~iL~~Fa~~~INLtkI 339 (361)
..+|.|=+.-.|+||.|+.+.++|++.|+++-..
T Consensus 789 ~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~A 822 (867)
T COG2844 789 NDKTVLEVRALDRPGLLAALAGVFADLGLSLHSA 822 (867)
T ss_pred CCceEEEEEeCCcccHHHHHHHHHHhcccceeee
Confidence 3578888888899999999999999999998643
Done!