Query 019548
Match_columns 339
No_of_seqs 271 out of 1268
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 02:38:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019548.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019548hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK10622 pheA bifunctional cho 100.0 4.7E-85 1E-89 647.3 28.3 299 37-335 16-348 (386)
2 COG0077 PheA Prephenate dehydr 100.0 4.2E-82 9.1E-87 597.7 27.5 236 97-333 2-243 (279)
3 PRK11899 prephenate dehydratas 100.0 4.5E-80 9.9E-85 588.1 29.3 241 95-335 2-245 (279)
4 PLN02317 arogenate dehydratase 100.0 2E-78 4.4E-83 594.9 28.8 250 77-326 74-323 (382)
5 PRK11898 prephenate dehydratas 100.0 3.9E-73 8.4E-78 542.1 29.1 237 97-334 1-247 (283)
6 KOG2797 Prephenate dehydratase 100.0 7.9E-66 1.7E-70 484.2 20.9 253 80-332 73-338 (377)
7 PF00800 PDT: Prephenate dehyd 100.0 3.5E-57 7.6E-62 406.1 17.9 177 100-276 1-181 (181)
8 PRK06034 hypothetical protein; 99.9 1.5E-25 3.3E-30 212.6 9.5 134 37-174 20-170 (279)
9 cd04904 ACT_AAAH ACT domain of 99.6 2.3E-15 5.1E-20 116.5 5.4 49 287-335 1-51 (74)
10 cd04931 ACT_PAH ACT domain of 99.6 3.6E-15 7.9E-20 120.1 6.6 52 284-335 12-65 (90)
11 cd04930 ACT_TH ACT domain of t 99.5 1.7E-14 3.6E-19 121.2 5.9 51 285-335 40-92 (115)
12 cd04929 ACT_TPH ACT domain of 99.5 2.5E-14 5.5E-19 111.2 5.5 48 287-334 1-50 (74)
13 cd04880 ACT_AAAH-PDT-like ACT 99.2 1.2E-11 2.6E-16 95.1 5.6 48 288-335 1-50 (75)
14 TIGR01268 Phe4hydrox_tetr phen 99.1 5E-11 1.1E-15 119.8 6.4 51 285-335 15-67 (436)
15 TIGR01270 Trp_5_monoox tryptop 99.1 5.7E-11 1.2E-15 119.8 6.2 52 283-334 28-82 (464)
16 cd04905 ACT_CM-PDT C-terminal 99.1 2.4E-10 5.3E-15 89.1 6.6 50 286-335 1-52 (80)
17 TIGR01807 CM_P2 chorismate mut 98.5 5.8E-08 1.3E-12 75.6 2.4 51 37-87 10-67 (76)
18 TIGR01801 CM_A chorismate muta 98.4 8.3E-08 1.8E-12 79.1 2.0 51 37-87 15-70 (102)
19 TIGR01805 CM_mono_grmpos monof 98.4 6.4E-08 1.4E-12 76.3 1.1 51 37-87 10-65 (81)
20 TIGR01797 CM_P_1 chorismate mu 98.4 7E-08 1.5E-12 76.5 0.7 51 37-87 10-66 (83)
21 PRK07248 hypothetical protein; 98.4 1.7E-07 3.6E-12 74.8 2.0 51 37-87 12-67 (87)
22 TIGR01803 CM-like chorismate m 98.2 5.3E-07 1.2E-11 71.2 1.9 51 37-87 10-66 (82)
23 PRK08818 prephenate dehydrogen 98.2 1.7E-06 3.6E-11 86.3 5.1 48 285-334 294-344 (370)
24 PRK07857 hypothetical protein; 98.2 1.1E-06 2.3E-11 72.9 2.5 42 37-78 39-85 (106)
25 TIGR01799 CM_T chorismate muta 98.1 8.7E-07 1.9E-11 70.2 1.7 51 37-87 10-66 (83)
26 PRK06443 chorismate mutase; Va 98.1 4.9E-07 1.1E-11 80.8 -0.2 71 37-113 16-96 (177)
27 TIGR01808 CM_M_hiGC-arch monof 98.1 1.4E-06 3.1E-11 67.7 2.2 44 37-80 11-59 (74)
28 TIGR01791 CM_archaeal chorisma 98.1 7.6E-07 1.6E-11 70.3 0.3 50 37-86 10-65 (83)
29 PRK07075 isochorismate-pyruvat 98.1 2.3E-06 5.1E-11 70.4 2.8 51 37-87 19-74 (101)
30 PRK06285 chorismate mutase; Pr 98.1 1.5E-06 3.3E-11 70.7 1.6 51 37-87 18-74 (96)
31 PRK11199 tyrA bifunctional cho 98.1 5.6E-06 1.2E-10 82.5 5.9 81 37-117 14-118 (374)
32 COG1605 PheA Chorismate mutase 98.0 3.4E-06 7.4E-11 69.3 2.7 50 38-87 20-76 (101)
33 PF01817 CM_2: Chorismate muta 98.0 9.9E-07 2.2E-11 69.0 -0.8 51 37-87 6-62 (81)
34 PRK12595 bifunctional 3-deoxy- 97.9 4E-06 8.7E-11 83.4 2.3 51 37-87 15-70 (360)
35 TIGR01269 Tyr_3_monoox tyrosin 97.9 1.5E-05 3.3E-10 80.4 5.9 50 286-335 37-92 (457)
36 PF01842 ACT: ACT domain; Int 97.9 3.5E-05 7.6E-10 56.4 6.2 46 287-332 1-46 (66)
37 TIGR01795 CM_mono_cladeE monof 97.8 9.9E-06 2.2E-10 65.9 1.3 44 37-80 14-62 (94)
38 PRK09239 chorismate mutase; Pr 97.7 1.2E-05 2.7E-10 66.5 1.6 50 37-86 21-76 (104)
39 smart00830 CM_2 Chorismate mut 97.7 3.2E-05 6.9E-10 59.9 3.1 47 37-83 6-57 (79)
40 TIGR01806 CM_mono2 chorismate 97.7 2.7E-05 5.9E-10 65.4 2.9 48 40-87 7-60 (114)
41 cd04886 ACT_ThrD-II-like C-ter 97.3 0.00056 1.2E-08 50.3 5.4 34 290-323 2-35 (73)
42 PRK09269 chorismate mutase; Pr 97.2 0.00024 5.3E-09 64.9 3.3 48 40-87 35-88 (193)
43 PRK08055 chorismate mutase; Pr 97.2 0.00026 5.6E-09 64.2 3.1 47 40-87 28-81 (181)
44 KOG3820 Aromatic amino acid hy 97.0 0.001 2.2E-08 66.3 5.7 50 285-334 35-86 (461)
45 cd04882 ACT_Bt0572_2 C-termina 97.0 0.0016 3.5E-08 47.4 5.2 46 289-334 2-48 (65)
46 cd04908 ACT_Bt0572_1 N-termina 96.9 0.0034 7.4E-08 46.8 6.2 37 288-324 3-39 (66)
47 cd04884 ACT_CBS C-terminal ACT 96.6 0.0057 1.2E-07 46.2 5.9 44 289-332 2-47 (72)
48 cd04874 ACT_Af1403 N-terminal 96.4 0.0085 1.8E-07 44.0 5.7 47 288-334 2-48 (72)
49 cd04878 ACT_AHAS N-terminal AC 96.2 0.017 3.7E-07 42.1 6.0 45 288-332 2-47 (72)
50 cd04903 ACT_LSD C-terminal ACT 96.0 0.017 3.8E-07 42.0 5.5 46 289-334 2-48 (71)
51 cd04883 ACT_AcuB C-terminal AC 96.0 0.022 4.8E-07 42.4 5.9 37 287-323 2-38 (72)
52 cd04909 ACT_PDH-BS C-terminal 95.9 0.022 4.8E-07 42.3 5.5 36 288-323 3-38 (69)
53 cd02116 ACT ACT domains are co 95.8 0.027 5.8E-07 37.5 5.1 44 290-333 2-46 (60)
54 cd04879 ACT_3PGDH-like ACT_3PG 95.8 0.03 6.5E-07 40.6 5.7 45 289-333 2-47 (71)
55 cd04889 ACT_PDH-BS-like C-term 95.7 0.031 6.7E-07 40.0 5.6 36 290-325 2-37 (56)
56 cd04902 ACT_3PGDH-xct C-termin 95.7 0.024 5.2E-07 42.1 5.2 46 289-334 2-48 (73)
57 PRK11152 ilvM acetolactate syn 95.6 0.023 5E-07 44.5 5.0 45 286-330 3-48 (76)
58 PRK06737 acetolactate synthase 95.6 0.022 4.8E-07 44.6 4.8 39 287-325 3-41 (76)
59 cd04885 ACT_ThrD-I Tandem C-te 95.5 0.026 5.5E-07 42.5 4.6 42 290-332 2-43 (68)
60 PF13291 ACT_4: ACT domain; PD 95.3 0.046 1E-06 42.0 5.6 47 284-330 4-51 (80)
61 cd04887 ACT_MalLac-Enz ACT_Mal 95.0 0.06 1.3E-06 40.4 5.3 38 289-326 2-39 (74)
62 cd04881 ACT_HSDH-Hom ACT_HSDH_ 95.0 0.074 1.6E-06 39.4 5.8 43 289-331 3-46 (79)
63 cd04873 ACT_UUR-ACR-like ACT d 94.8 0.086 1.9E-06 38.6 5.6 49 288-336 2-51 (70)
64 PRK11895 ilvH acetolactate syn 94.7 0.078 1.7E-06 47.3 6.2 47 287-333 3-50 (161)
65 cd04888 ACT_PheB-BS C-terminal 94.3 0.13 2.8E-06 38.6 5.8 34 288-321 2-35 (76)
66 TIGR00119 acolac_sm acetolacta 94.3 0.11 2.4E-06 46.1 6.1 45 288-332 3-48 (157)
67 cd04901 ACT_3PGDH C-terminal A 94.1 0.071 1.5E-06 39.3 3.9 43 289-332 2-44 (69)
68 cd04926 ACT_ACR_4 C-terminal 94.0 0.16 3.5E-06 38.6 5.7 38 287-324 2-39 (72)
69 cd04899 ACT_ACR-UUR-like_2 C-t 93.9 0.18 3.8E-06 37.3 5.6 38 287-324 1-38 (70)
70 cd04876 ACT_RelA-SpoT ACT dom 93.8 0.16 3.4E-06 35.6 5.0 34 290-323 2-35 (71)
71 PRK08526 threonine dehydratase 93.4 1.4 3.1E-05 44.6 13.0 182 131-324 161-365 (403)
72 PRK08178 acetolactate synthase 93.2 0.24 5.1E-06 40.6 5.7 39 286-324 8-46 (96)
73 PRK13562 acetolactate synthase 93.2 0.19 4.2E-06 40.2 5.0 38 287-324 3-40 (84)
74 COG4747 ACT domain-containing 93.1 0.2 4.3E-06 42.7 5.2 47 287-333 70-116 (142)
75 PF13710 ACT_5: ACT domain; PD 93.0 0.12 2.7E-06 38.6 3.6 38 295-332 1-39 (63)
76 PRK08198 threonine dehydratase 92.7 0.87 1.9E-05 45.7 10.2 47 286-332 327-377 (404)
77 PRK08639 threonine dehydratase 92.6 2.1 4.5E-05 43.5 12.8 37 285-321 335-371 (420)
78 PRK06382 threonine dehydratase 92.4 0.23 5E-06 50.1 5.7 49 285-333 329-381 (406)
79 cd04895 ACT_ACR_1 ACT domain-c 92.4 0.23 5.1E-06 38.4 4.4 49 287-336 2-52 (72)
80 PRK00194 hypothetical protein; 92.1 0.21 4.6E-06 39.2 4.0 36 286-321 3-38 (90)
81 TIGR01127 ilvA_1Cterm threonin 91.7 0.37 7.9E-06 48.0 6.1 47 286-332 305-355 (380)
82 cd04906 ACT_ThrD-I_1 First of 91.5 0.16 3.5E-06 39.9 2.7 25 289-313 4-28 (85)
83 cd04896 ACT_ACR-like_3 ACT dom 91.4 0.28 6E-06 38.3 3.8 48 288-335 2-52 (75)
84 cd04900 ACT_UUR-like_1 ACT dom 91.3 0.7 1.5E-05 35.0 6.0 50 287-336 2-53 (73)
85 PRK04435 hypothetical protein; 91.2 0.58 1.3E-05 40.9 6.1 36 285-320 68-103 (147)
86 cd04872 ACT_1ZPV ACT domain pr 91.1 0.29 6.3E-06 38.4 3.8 36 287-322 2-37 (88)
87 cd04875 ACT_F4HF-DF N-terminal 90.9 0.37 7.9E-06 36.5 4.1 32 289-320 2-33 (74)
88 cd04877 ACT_TyrR N-terminal AC 90.6 0.44 9.6E-06 36.1 4.3 35 288-322 2-36 (74)
89 PRK08577 hypothetical protein; 90.6 1.6 3.4E-05 37.3 8.1 38 286-323 56-93 (136)
90 cd08417 PBP2_Nitroaromatics_li 89.3 12 0.00026 31.3 13.5 121 118-249 26-155 (200)
91 COG2061 ACT-domain-containing 89.3 0.39 8.5E-06 42.6 3.3 47 286-332 5-55 (170)
92 cd04870 ACT_PSP_1 CT domains f 88.3 0.69 1.5E-05 35.2 3.8 33 291-323 4-36 (75)
93 PF12974 Phosphonate-bd: ABC t 88.1 0.87 1.9E-05 41.8 5.1 83 96-187 104-201 (243)
94 TIGR00363 lipoprotein, YaeC fa 87.7 22 0.00047 33.9 14.5 148 96-254 18-200 (258)
95 PRK06545 prephenate dehydrogen 87.4 0.72 1.6E-05 45.7 4.3 41 286-326 290-330 (359)
96 PF13740 ACT_6: ACT domain; PD 87.2 0.96 2.1E-05 34.7 4.0 36 289-324 3-40 (76)
97 cd04907 ACT_ThrD-I_2 Second of 87.1 1.8 3.8E-05 34.1 5.5 44 288-332 3-46 (81)
98 cd04869 ACT_GcvR_2 ACT domains 86.7 2.1 4.5E-05 32.5 5.7 35 289-323 2-36 (81)
99 cd04897 ACT_ACR_3 ACT domain-c 86.5 1.2 2.6E-05 34.7 4.3 50 287-337 2-53 (75)
100 PRK07334 threonine dehydratase 86.4 1.8 3.8E-05 43.7 6.6 38 285-322 325-362 (403)
101 PRK09224 threonine dehydratase 86.0 10 0.00022 39.6 12.1 44 285-330 327-370 (504)
102 cd08445 PBP2_BenM_CatM_CatR Th 85.5 21 0.00046 30.2 12.4 121 117-247 26-158 (203)
103 cd08411 PBP2_OxyR The C-termin 85.4 21 0.00044 29.9 12.0 123 117-249 26-157 (200)
104 cd04891 ACT_AK-LysC-DapG-like_ 85.1 2.3 4.9E-05 29.6 4.9 33 291-323 6-38 (61)
105 PRK11151 DNA-binding transcrip 84.9 16 0.00035 34.4 12.0 144 95-248 90-246 (305)
106 TIGR01728 SsuA_fam ABC transpo 84.5 8.1 0.00018 35.4 9.6 137 98-245 1-157 (288)
107 cd04927 ACT_ACR-like_2 Second 82.4 3.8 8.2E-05 31.5 5.5 46 290-335 4-51 (76)
108 PF00497 SBP_bac_3: Bacterial 82.1 21 0.00045 30.9 10.8 48 98-147 111-159 (225)
109 PLN02550 threonine dehydratase 82.0 11 0.00023 40.4 10.4 172 140-322 258-451 (591)
110 cd08435 PBP2_GbpR The C-termin 81.7 29 0.00062 28.8 11.4 123 116-248 24-158 (201)
111 PRK15007 putative ABC transpor 81.4 3.8 8.2E-05 37.1 6.0 49 97-147 126-174 (243)
112 PRK12483 threonine dehydratase 81.3 20 0.00043 37.8 11.9 35 285-321 344-378 (521)
113 COG4492 PheB ACT domain-contai 80.8 2.5 5.4E-05 36.8 4.2 42 284-325 70-112 (150)
114 cd08452 PBP2_AlsR The C-termin 80.5 34 0.00073 28.8 12.5 123 116-248 24-157 (197)
115 PRK11589 gcvR glycine cleavage 80.3 2.1 4.5E-05 39.1 3.9 36 288-323 97-132 (190)
116 cd08453 PBP2_IlvR The C-termin 79.6 35 0.00077 28.5 11.2 123 117-248 25-160 (200)
117 cd04893 ACT_GcvR_1 ACT domains 79.5 3.3 7.2E-05 31.8 4.2 33 289-321 4-36 (77)
118 COG2716 GcvR Glycine cleavage 79.5 5 0.00011 36.3 5.8 31 291-321 97-127 (176)
119 cd08450 PBP2_HcaR The C-termin 78.2 34 0.00073 28.4 10.5 122 117-248 25-156 (196)
120 cd00134 PBPb Bacterial peripla 78.1 6.4 0.00014 33.2 6.1 49 97-147 105-153 (218)
121 cd08446 PBP2_Chlorocatechol Th 78.1 39 0.00084 28.2 11.3 123 116-248 25-158 (198)
122 cd04925 ACT_ACR_2 ACT domain-c 77.6 3.6 7.9E-05 31.3 3.9 35 288-322 2-36 (74)
123 TIGR01096 3A0103s03R lysine-ar 77.4 5.9 0.00013 35.8 6.0 49 97-147 131-180 (250)
124 PRK09508 leuO leucine transcri 76.6 9.6 0.00021 36.2 7.4 122 117-249 137-266 (314)
125 cd04913 ACT_AKii-LysC-BS-like_ 76.4 3.4 7.4E-05 30.0 3.4 29 291-319 7-35 (75)
126 COG4747 ACT domain-containing 76.3 3.6 7.8E-05 35.2 3.8 29 289-317 6-34 (142)
127 TIGR01124 ilvA_2Cterm threonin 75.8 13 0.00029 38.8 8.7 186 131-330 158-367 (499)
128 TIGR03339 phn_lysR aminoethylp 75.4 52 0.0011 30.0 11.8 139 95-245 86-236 (279)
129 PRK09959 hybrid sensory histid 75.4 4 8.6E-05 46.3 5.1 50 96-147 406-455 (1197)
130 cd08486 PBP2_CbnR The C-termin 75.3 44 0.00095 28.4 10.6 140 98-247 3-157 (198)
131 PF12727 PBP_like: PBP superfa 74.5 29 0.00062 31.5 9.6 130 122-256 14-165 (193)
132 PRK11063 metQ DL-methionine tr 74.3 49 0.0011 31.6 11.6 108 96-213 31-152 (271)
133 PRK11260 cystine transporter s 73.9 7.7 0.00017 36.0 5.9 48 98-147 150-197 (266)
134 COG3830 ACT domain-containing 73.0 4.6 0.0001 32.7 3.5 31 289-319 4-36 (90)
135 PRK09959 hybrid sensory histid 72.5 5.6 0.00012 45.1 5.4 49 97-147 164-212 (1197)
136 TIGR01693 UTase_glnD [Protein- 72.4 9.2 0.0002 42.4 6.9 53 285-337 778-831 (850)
137 PRK11480 tauA taurine transpor 72.3 65 0.0014 30.9 12.1 142 94-245 21-179 (320)
138 PRK09906 DNA-binding transcrip 71.9 52 0.0011 30.6 11.0 123 116-248 114-247 (296)
139 PRK09495 glnH glutamine ABC tr 71.7 8.8 0.00019 35.0 5.6 48 97-146 131-178 (247)
140 COG0440 IlvH Acetolactate synt 71.5 4.3 9.4E-05 36.4 3.3 39 286-324 4-42 (163)
141 smart00062 PBPb Bacterial peri 71.3 11 0.00024 31.6 5.7 50 97-148 106-155 (219)
142 PRK11242 DNA-binding transcrip 71.1 56 0.0012 30.2 11.0 121 118-248 117-247 (296)
143 TIGR02079 THD1 threonine dehyd 71.0 9.6 0.00021 38.6 6.2 36 286-321 325-360 (409)
144 TIGR01098 3A0109s03R phosphate 70.8 14 0.00029 33.7 6.7 51 97-147 141-201 (254)
145 PF00585 Thr_dehydrat_C: C-ter 70.7 4.6 0.0001 32.4 3.1 46 285-331 9-54 (91)
146 PF13379 NMT1_2: NMT1-like fam 70.5 15 0.00033 33.8 7.0 144 96-245 6-180 (252)
147 cd04932 ACT_AKiii-LysC-EC_1 AC 70.3 11 0.00024 28.9 5.0 39 293-334 11-49 (75)
148 PRK06349 homoserine dehydrogen 69.7 8.1 0.00018 39.3 5.3 44 288-331 350-393 (426)
149 cd08412 PBP2_PAO1_like The C-t 69.6 63 0.0014 26.7 12.7 123 116-248 24-154 (198)
150 PRK11553 alkanesulfonate trans 69.5 40 0.00087 32.0 9.8 139 94-243 25-183 (314)
151 PF03401 TctC: Tripartite tric 69.0 19 0.00042 34.2 7.5 53 95-148 104-160 (274)
152 cd08462 PBP2_NodD The C-termin 67.6 51 0.0011 27.8 9.2 122 116-249 24-155 (200)
153 smart00079 PBPe Eukaryotic hom 67.3 14 0.0003 30.2 5.4 47 98-147 14-71 (134)
154 cd08466 PBP2_LeuO The C-termin 66.9 74 0.0016 26.5 10.3 123 117-250 25-156 (200)
155 cd08425 PBP2_CynR The C-termin 66.8 70 0.0015 26.5 9.8 122 117-248 26-157 (197)
156 cd08451 PBP2_BudR The C-termin 66.4 74 0.0016 26.3 12.4 123 116-248 25-159 (199)
157 smart00062 PBPb Bacterial peri 66.1 76 0.0017 26.3 10.0 111 121-247 41-158 (219)
158 cd04914 ACT_AKi-DapG-BS_1 ACT 65.9 13 0.00027 27.8 4.5 38 293-333 9-46 (67)
159 cd08485 PBP2_ClcR The C-termin 65.3 83 0.0018 26.5 10.7 141 98-248 3-158 (198)
160 cd04935 ACT_AKiii-DAPDC_1 ACT 65.2 13 0.00028 28.5 4.5 40 293-335 11-50 (75)
161 cd08426 PBP2_LTTR_like_5 The C 64.7 81 0.0017 26.1 12.2 122 117-248 25-155 (199)
162 cd08459 PBP2_DntR_NahR_LinR_li 63.6 67 0.0015 26.8 9.2 123 117-250 25-156 (201)
163 cd08461 PBP2_DntR_like_3 The C 63.1 42 0.0009 28.0 7.7 123 117-250 25-157 (198)
164 cd04933 ACT_AK1-AT_1 ACT domai 63.1 12 0.00027 29.2 4.0 40 293-335 11-50 (78)
165 COG2107 Predicted periplasmic 62.8 14 0.0003 35.6 5.1 52 96-149 94-145 (272)
166 PRK11917 bifunctional adhesin/ 62.6 39 0.00084 31.5 8.1 48 97-146 148-199 (259)
167 cd04912 ACT_AKiii-LysC-EC-like 62.4 16 0.00034 27.7 4.5 40 293-335 11-50 (75)
168 cd08421 PBP2_LTTR_like_1 The C 62.0 90 0.002 25.8 10.8 122 117-248 25-155 (198)
169 PRK12683 transcriptional regul 62.0 1.5E+02 0.0032 28.2 12.2 143 95-247 92-248 (309)
170 cd08444 PBP2_Cbl The C-termina 61.6 98 0.0021 26.0 12.3 122 117-248 25-156 (198)
171 PRK10859 membrane-bound lytic 61.2 58 0.0013 33.5 9.7 48 98-147 150-202 (482)
172 TIGR02424 TF_pcaQ pca operon t 61.2 1.2E+02 0.0026 28.2 11.2 145 94-248 91-251 (300)
173 PRK11482 putative DNA-binding 60.9 1.2E+02 0.0026 29.0 11.4 142 96-249 117-270 (317)
174 cd04919 ACT_AK-Hom3_2 ACT doma 60.0 12 0.00025 27.0 3.3 41 293-334 11-51 (66)
175 PRK11092 bifunctional (p)ppGpp 59.8 36 0.00077 37.3 8.2 43 284-326 624-666 (702)
176 PF03466 LysR_substrate: LysR 59.1 1.1E+02 0.0023 25.7 13.0 124 116-249 30-162 (209)
177 PF00497 SBP_bac_3: Bacterial 59.1 29 0.00064 29.9 6.2 122 111-249 30-165 (225)
178 cd04922 ACT_AKi-HSDH-ThrA_2 AC 59.1 18 0.00039 25.8 4.1 41 293-334 11-51 (66)
179 cd04936 ACT_AKii-LysC-BS-like_ 58.7 12 0.00025 26.3 3.0 38 293-333 10-47 (63)
180 TIGR02995 ectoine_ehuB ectoine 58.6 19 0.00041 33.6 5.2 49 97-147 144-193 (275)
181 PRK12680 transcriptional regul 58.4 1.2E+02 0.0025 29.3 10.8 146 94-248 91-250 (327)
182 PRK11716 DNA-binding transcrip 58.3 69 0.0015 28.9 8.8 145 95-248 66-223 (269)
183 cd08443 PBP2_CysB The C-termin 58.2 1.1E+02 0.0025 25.7 11.7 123 116-247 24-155 (198)
184 cd04937 ACT_AKi-DapG-BS_2 ACT 57.0 12 0.00027 27.3 3.0 40 293-335 11-50 (64)
185 cd04868 ACT_AK-like ACT domain 57.0 19 0.00042 24.2 3.9 38 295-333 12-49 (60)
186 cd08420 PBP2_CysL_like C-termi 56.9 88 0.0019 25.6 8.6 122 117-248 25-158 (201)
187 cd04928 ACT_TyrKc Uncharacteri 56.8 32 0.00069 26.3 5.2 36 289-324 4-39 (68)
188 PRK10341 DNA-binding transcrip 56.5 1.8E+02 0.0039 27.5 13.2 119 118-248 123-252 (312)
189 cd04924 ACT_AK-Arch_2 ACT doma 56.4 14 0.0003 26.3 3.1 40 293-333 11-50 (66)
190 PRK13011 formyltetrahydrofolat 56.3 19 0.00041 34.9 4.9 35 286-320 7-41 (286)
191 PRK12679 cbl transcriptional r 56.2 1.2E+02 0.0026 28.8 10.5 144 95-247 92-248 (316)
192 cd04934 ACT_AK-Hom3_1 CT domai 55.8 35 0.00076 26.0 5.4 38 294-334 12-49 (73)
193 COG0725 ModA ABC-type molybdat 55.2 18 0.00039 34.5 4.5 53 97-149 135-195 (258)
194 PRK13010 purU formyltetrahydro 53.9 26 0.00056 34.1 5.4 45 286-331 9-53 (289)
195 COG0317 SpoT Guanosine polypho 53.9 50 0.0011 36.2 7.9 47 284-330 625-671 (701)
196 PRK03381 PII uridylyl-transfer 53.5 35 0.00076 37.6 6.9 52 286-337 707-759 (774)
197 cd04923 ACT_AK-LysC-DapG-like_ 53.0 17 0.00037 25.4 3.1 38 293-333 10-47 (63)
198 PRK05092 PII uridylyl-transfer 52.8 36 0.00078 38.3 7.0 52 285-336 842-894 (931)
199 cd08457 PBP2_OccR The C-termin 52.5 1.4E+02 0.0029 24.9 12.1 121 117-247 25-154 (196)
200 PF12916 DUF3834: Protein of u 52.1 40 0.00086 31.2 5.9 73 95-172 66-143 (201)
201 COG2150 Predicted regulator of 51.9 32 0.0007 30.9 5.1 45 289-333 98-144 (167)
202 cd08440 PBP2_LTTR_like_4 TThe 51.9 1.3E+02 0.0028 24.5 12.9 122 117-248 25-155 (197)
203 PRK09986 DNA-binding transcrip 51.7 2E+02 0.0043 26.5 11.3 144 95-248 96-255 (294)
204 PRK09224 threonine dehydratase 51.6 22 0.00048 37.1 4.8 46 285-331 422-467 (504)
205 cd08437 PBP2_MleR The substrat 51.5 1.4E+02 0.003 24.8 11.4 121 117-247 25-156 (198)
206 PRK12684 transcriptional regul 51.5 1.7E+02 0.0037 27.7 10.7 144 94-248 91-249 (313)
207 cd08460 PBP2_DntR_like_1 The C 51.1 33 0.00072 28.9 5.1 121 117-248 25-153 (200)
208 TIGR00691 spoT_relA (p)ppGpp s 51.0 33 0.00072 37.3 6.2 42 285-326 609-650 (683)
209 PRK05007 PII uridylyl-transfer 50.6 18 0.0004 40.4 4.3 52 285-337 807-860 (884)
210 cd08413 PBP2_CysB_like The C-t 50.3 1.5E+02 0.0033 24.8 11.9 122 117-248 25-156 (198)
211 cd08449 PBP2_XapR The C-termin 50.1 1.4E+02 0.0031 24.4 10.9 33 117-149 25-58 (197)
212 PF13840 ACT_7: ACT domain ; P 49.8 31 0.00067 25.5 4.1 24 295-318 19-42 (65)
213 TIGR00070 hisG ATP phosphoribo 49.4 53 0.0012 29.9 6.4 108 129-256 49-171 (182)
214 cd04890 ACT_AK-like_1 ACT doma 49.1 32 0.00069 24.5 4.1 37 294-333 11-47 (62)
215 TIGR00656 asp_kin_monofn aspar 48.6 1E+02 0.0022 30.8 8.9 110 214-333 189-309 (401)
216 TIGR03871 ABC_peri_MoxJ_2 quin 47.9 40 0.00086 30.1 5.4 49 97-147 104-161 (232)
217 TIGR03427 ABC_peri_uca ABC tra 47.6 2.8E+02 0.0062 27.2 13.0 143 120-273 36-193 (328)
218 cd08438 PBP2_CidR The C-termin 47.3 1.6E+02 0.0034 24.1 12.6 32 117-148 25-57 (197)
219 PRK10872 relA (p)ppGpp synthet 46.9 43 0.00093 36.9 6.2 39 285-323 665-703 (743)
220 TIGR02122 TRAP_TAXI TRAP trans 46.7 2.5E+02 0.0054 26.2 10.9 54 95-148 29-90 (320)
221 KOG0850 Transcription factor D 46.6 29 0.00063 32.9 4.2 67 19-85 111-190 (245)
222 KOG2663 Acetolactate synthase, 46.0 27 0.00058 33.7 3.9 34 285-318 76-109 (309)
223 PRK11062 nhaR transcriptional 45.9 2.6E+02 0.0055 26.2 11.6 145 118-276 119-275 (296)
224 PRK01759 glnD PII uridylyl-tra 45.4 25 0.00054 39.2 4.3 52 285-337 782-835 (854)
225 PRK15010 ABC transporter lysin 45.0 55 0.0012 30.1 6.0 49 97-147 133-183 (260)
226 PRK09034 aspartate kinase; Rev 44.9 2.1E+02 0.0045 29.4 10.7 111 214-334 234-356 (454)
227 cd08441 PBP2_MetR The C-termin 44.8 1.8E+02 0.0039 24.1 11.2 142 98-249 2-156 (198)
228 cd08465 PBP2_ToxR The C-termin 44.0 1.9E+02 0.0042 24.2 9.5 108 117-232 25-141 (200)
229 TIGR00719 sda_beta L-serine de 43.9 33 0.00072 31.5 4.2 38 287-324 149-187 (208)
230 cd04921 ACT_AKi-HSDH-ThrA-like 43.5 46 0.00099 24.9 4.3 40 293-333 11-50 (80)
231 cd04916 ACT_AKiii-YclM-BS_2 AC 43.1 29 0.00063 24.7 3.0 41 293-334 11-51 (66)
232 COG0834 HisJ ABC-type amino ac 42.6 34 0.00074 31.0 4.1 48 98-147 147-196 (275)
233 cd08468 PBP2_Pa0477 The C-term 42.4 2E+02 0.0044 24.0 9.5 121 117-249 25-157 (202)
234 cd08464 PBP2_DntR_like_2 The C 42.4 1.7E+02 0.0038 24.1 8.2 122 117-249 25-155 (200)
235 cd08418 PBP2_TdcA The C-termin 42.2 1.9E+02 0.0042 23.7 10.5 121 117-249 25-156 (201)
236 PRK15421 DNA-binding transcrip 41.6 3.2E+02 0.0068 26.1 10.8 142 96-247 89-242 (317)
237 PRK06635 aspartate kinase; Rev 40.6 1.2E+02 0.0026 30.2 8.0 42 293-334 270-313 (404)
238 cd08436 PBP2_LTTR_like_3 The C 39.9 2E+02 0.0044 23.3 11.6 34 116-149 24-58 (194)
239 PRK03601 transcriptional regul 39.7 3.1E+02 0.0067 25.3 11.4 34 116-149 113-147 (275)
240 PF09084 NMT1: NMT1/THI5 like; 39.7 2.6E+02 0.0056 24.5 16.3 105 121-233 23-139 (216)
241 cd04892 ACT_AK-like_2 ACT doma 39.2 37 0.00081 23.3 3.0 40 293-333 10-49 (65)
242 cd00134 PBPb Bacterial peripla 38.9 1.7E+02 0.0037 24.3 7.7 114 120-249 39-159 (218)
243 PF03180 Lipoprotein_9: NLPA l 37.9 2.1E+02 0.0046 26.9 8.7 87 98-194 1-95 (237)
244 cd08433 PBP2_Nac The C-teminal 37.9 2.3E+02 0.005 23.3 12.0 122 117-248 25-155 (198)
245 TIGR00787 dctP tripartite ATP- 37.5 3.4E+02 0.0073 25.1 10.0 152 102-259 3-197 (257)
246 cd08469 PBP2_PnbR The C-termin 37.5 2.5E+02 0.0055 23.8 8.7 32 117-148 25-57 (221)
247 PRK10859 membrane-bound lytic 37.2 1.3E+02 0.0029 30.9 7.9 27 121-147 82-108 (482)
248 PRK04374 PII uridylyl-transfer 37.1 95 0.0021 34.9 7.2 53 285-337 795-848 (869)
249 PRK11139 DNA-binding transcrip 36.9 2.3E+02 0.0049 26.4 8.8 105 133-249 133-246 (297)
250 PF12974 Phosphonate-bd: ABC t 36.6 3.1E+02 0.0068 24.8 9.6 115 121-245 31-167 (243)
251 PRK05007 PII uridylyl-transfer 36.3 68 0.0015 36.0 5.9 52 286-337 701-754 (884)
252 cd08448 PBP2_LTTR_aromatics_li 35.8 2.4E+02 0.0052 23.0 13.1 122 117-248 25-157 (197)
253 COG1484 DnaC DNA replication p 35.4 80 0.0017 29.9 5.5 72 94-176 102-178 (254)
254 cd08416 PBP2_MdcR The C-termin 34.7 2.6E+02 0.0056 23.0 12.3 123 117-249 25-158 (199)
255 cd08423 PBP2_LTTR_like_6 The C 34.4 2.6E+02 0.0056 22.9 11.1 122 117-248 25-160 (200)
256 PRK15437 histidine ABC transpo 33.9 1E+02 0.0022 28.3 5.8 49 97-147 133-183 (259)
257 PRK10797 glutamate and asparta 33.8 73 0.0016 30.5 5.0 47 98-146 154-204 (302)
258 TIGR00656 asp_kin_monofn aspar 33.7 50 0.0011 33.0 4.0 41 292-335 346-386 (401)
259 PRK03059 PII uridylyl-transfer 33.1 52 0.0011 36.8 4.3 34 285-318 785-818 (856)
260 TIGR01098 3A0109s03R phosphate 32.9 3.7E+02 0.0079 24.2 14.4 54 95-148 31-93 (254)
261 CHL00180 rbcR LysR transcripti 32.7 4.2E+02 0.009 24.8 13.7 144 94-247 93-255 (305)
262 PRK10837 putative DNA-binding 32.7 3.9E+02 0.0085 24.4 11.3 56 94-149 87-147 (290)
263 PRK00275 glnD PII uridylyl-tra 32.2 97 0.0021 34.9 6.3 53 285-337 813-866 (895)
264 cd08415 PBP2_LysR_opines_like 31.7 2.9E+02 0.0062 22.6 11.9 123 116-248 24-155 (196)
265 PRK06291 aspartate kinase; Pro 31.4 4.6E+02 0.01 26.9 10.7 112 214-333 248-370 (465)
266 cd08483 PBP2_HvrB The C-termin 31.3 76 0.0017 26.1 4.2 117 117-248 25-149 (190)
267 PRK01759 glnD PII uridylyl-tra 31.0 95 0.002 34.7 5.9 52 286-337 677-730 (854)
268 PRK09084 aspartate kinase III; 30.3 3.1E+02 0.0068 28.1 9.2 112 214-334 234-354 (448)
269 PRK11790 D-3-phosphoglycerate 30.2 70 0.0015 32.5 4.4 38 286-323 338-375 (409)
270 cd08419 PBP2_CbbR_RubisCO_like 30.1 3E+02 0.0066 22.3 12.2 123 117-249 24-155 (197)
271 cd08432 PBP2_GcdR_TrpI_HvrB_Am 30.1 69 0.0015 26.3 3.7 107 132-249 38-152 (194)
272 cd08456 PBP2_LysR The C-termin 30.0 3.1E+02 0.0067 22.4 12.3 123 116-248 24-155 (196)
273 cd08467 PBP2_SyrM The C-termin 29.7 3.3E+02 0.0072 22.7 8.7 122 117-249 25-155 (200)
274 TIGR01693 UTase_glnD [Protein- 29.6 1.1E+02 0.0023 34.1 6.1 52 286-337 668-721 (850)
275 PF01634 HisG: ATP phosphoribo 29.5 2E+02 0.0044 25.6 6.7 112 130-256 4-129 (163)
276 PRK06635 aspartate kinase; Rev 29.3 57 0.0012 32.6 3.6 40 292-334 349-388 (404)
277 PRK12682 transcriptional regul 29.2 4.8E+02 0.01 24.4 12.9 145 94-248 91-249 (309)
278 PRK08961 bifunctional aspartat 29.1 4.5E+02 0.0098 29.4 10.8 111 214-334 250-370 (861)
279 TIGR01729 taurine_ABC_bnd taur 28.9 4.8E+02 0.011 24.3 12.6 136 99-245 2-157 (300)
280 PRK15437 histidine ABC transpo 28.7 3.6E+02 0.0078 24.6 8.6 37 111-148 57-93 (259)
281 cd04920 ACT_AKiii-DAPDC_2 ACT 28.4 71 0.0015 23.3 3.1 40 293-335 10-49 (63)
282 PRK02228 V-type ATP synthase s 28.1 2.8E+02 0.0061 22.4 6.9 64 98-165 1-67 (100)
283 PRK11074 putative DNA-binding 27.9 2.8E+02 0.0061 25.9 7.9 146 94-249 90-247 (300)
284 TIGR02122 TRAP_TAXI TRAP trans 27.6 97 0.0021 29.1 4.7 50 97-147 141-197 (320)
285 PRK01686 hisG ATP phosphoribos 27.4 1.1E+02 0.0024 28.5 4.9 110 128-256 53-177 (215)
286 PRK06526 transposase; Provisio 26.7 2.6E+02 0.0056 26.4 7.4 71 94-175 95-169 (254)
287 COG2844 GlnD UTP:GlnB (protein 26.7 80 0.0017 35.2 4.3 35 284-318 789-823 (867)
288 cd08442 PBP2_YofA_SoxR_like Th 26.3 3.5E+02 0.0077 21.9 12.7 122 117-249 25-152 (193)
289 cd08414 PBP2_LTTR_aromatics_li 26.3 3.6E+02 0.0077 21.9 14.5 32 118-149 26-58 (197)
290 cd08458 PBP2_NocR The C-termin 26.1 3.8E+02 0.0082 22.2 13.3 121 117-247 25-154 (196)
291 PLN02551 aspartokinase 25.8 5.2E+02 0.011 27.3 10.0 112 214-334 293-414 (521)
292 PRK11013 DNA-binding transcrip 25.7 5.6E+02 0.012 24.0 12.3 122 117-248 119-249 (309)
293 TIGR00657 asp_kinases aspartat 25.4 4.7E+02 0.01 26.5 9.4 119 214-335 228-352 (441)
294 PRK13581 D-3-phosphoglycerate 25.2 1.3E+02 0.0027 31.7 5.3 78 243-320 387-487 (526)
295 PRK10216 DNA-binding transcrip 24.9 5.9E+02 0.013 24.0 10.1 145 97-248 98-262 (319)
296 COG3482 Uncharacterized conser 24.9 99 0.0021 29.3 4.0 45 99-146 3-47 (237)
297 PF09084 NMT1: NMT1/THI5 like; 24.8 2.4E+02 0.0052 24.7 6.5 51 97-150 93-150 (216)
298 TIGR03427 ABC_peri_uca ABC tra 24.3 95 0.0021 30.5 4.0 48 97-147 106-160 (328)
299 PRK08181 transposase; Validate 23.3 1.9E+02 0.0042 27.6 5.9 71 94-175 103-177 (269)
300 cd08430 PBP2_IlvY The C-termin 23.1 4.2E+02 0.009 21.6 13.4 126 116-250 24-158 (199)
301 cd08447 PBP2_LTTR_aromatics_li 22.9 4.2E+02 0.0091 21.6 12.8 122 117-248 25-157 (198)
302 PF00072 Response_reg: Respons 22.4 72 0.0016 24.5 2.3 77 196-276 4-81 (112)
303 PRK13584 hisG ATP phosphoribos 22.2 1.9E+02 0.0041 26.9 5.3 108 129-257 52-168 (204)
304 PRK03957 V-type ATP synthase s 22.1 2.7E+02 0.0059 22.5 5.7 60 98-161 1-63 (100)
305 PRK09861 cytoplasmic membrane 20.7 7.4E+02 0.016 23.6 13.8 109 96-212 32-152 (272)
306 PF01695 IstB_IS21: IstB-like 20.4 1.3E+02 0.0028 26.7 3.8 70 94-174 44-117 (178)
307 PRK11553 alkanesulfonate trans 20.0 1.6E+02 0.0034 27.9 4.5 47 98-147 130-183 (314)
No 1
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=100.00 E-value=4.7e-85 Score=647.31 Aligned_cols=299 Identities=29% Similarity=0.376 Sum_probs=272.3
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCccc-------cc-cccCCCCc-----
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD-------FT-VTPNDGTK----- 97 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~-------i~-~s~~l~~~----- 97 (339)
-+|.+|++||+||++++.+||++|++.| + | ||+++|+++...+. ++++.+. || .|+..|..
T Consensus 16 ~ID~~ii~Ll~~R~~~~~~I~~~K~~~~~pi~dp~RE~~vl~~~~~~a~~~~l~~~~i~~if~~ii~~S~~~Q~~~~~~~ 95 (386)
T PRK10622 16 ALDEKLLALLAERRELAVEVAKAKLLSHRPVRDIDRERDLLERLITLGKAHHLDAHYITRLFQLIIEDSVLTQQALLQQH 95 (386)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCcChHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHHHHHHhhhhhhcc
Confidence 7899999999999999999999999988 3 5 99999999998886 7787764 34 35544433
Q ss_pred --------eEEEEECCCCcHHHHHHHHhCCC----CccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhc
Q 019548 98 --------VRISFKGLPGSFSEDAALKAYPK----CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLR 165 (339)
Q Consensus 98 --------~~VayLGP~GTfS~~AA~~~fg~----~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~ 165 (339)
++||||||+|||||+||+++|+. ...+||+||++||++|++|++||||||||||++|.|.+|||+|.+
T Consensus 96 ~~~~~~~~~~va~lGp~GtfSh~Aa~~~~~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~DlL~~ 175 (386)
T PRK10622 96 LNKTNPHSARIAFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVLPIENTSSGAINDVYDLLQH 175 (386)
T ss_pred ccccccccceEEEECCCCcHHHHHHHHhhccccccccccCCCCHHHHHHHHHCCCCCEEEEEEecCCceehHHHHHHHhc
Confidence 78999999999999999999863 234589999999999999999999999999999999999999999
Q ss_pred CCeEEEEEEEEeeeeeeccCCCCCcCCccEEEecHHHHHHHHHHHHhc-CCeeEecCCHHHHHHHHHhcCCCCeEEecCH
Q 019548 166 HRLHIVGEVQLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL-GVARENVDDTASAAQYVASNGLRDAGAVASA 244 (339)
Q Consensus 166 ~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~VySHpqal~QC~~~L~~~-~~~~i~~~STA~AA~~v~~~~~~~~AAIas~ 244 (339)
++++|+||+.+||+|||++.++.++++|++||||||||+||++||+++ +++.++++|||+||+++++.++++.|||||+
T Consensus 176 ~~l~I~~E~~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~ 255 (386)
T PRK10622 176 TSLSIVGEMTLPIDHCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRYPHWKIEYTESTAAAMEKVAQANSPHVAALGSE 255 (386)
T ss_pred CCCEEEEEEEEEEEEEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHCCCceEEEcCChHHHHHHHHhcCCCCEEEECCH
Confidence 999999999999999999999999999999999999999999999997 7899999999999999998777788999999
Q ss_pred HHHHHcCCceeeccccCCCCCeeeEEEEeeCCCCCCCCCCceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 019548 245 RAAEIYGLNILADRIQDEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (339)
Q Consensus 245 ~AA~~ygL~il~~~IeD~~~N~TRF~vi~~~~~~p~~~~~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~ 324 (339)
.||++|||++|+++|||.++|+|||+||++.+..+.....+||||+|+++|+||+|+++|++|+.+|||||||||||+++
T Consensus 256 ~aa~~ygL~vl~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~~L~~Fa~~giNLtkIeSRP~~~ 335 (386)
T PRK10622 256 AGGALYGLQVLERNLANQQQNITRFIVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTKLESRPIHG 335 (386)
T ss_pred HHHHHcCCcChhhcCcCCccccceEEEEecCCCCCCCCCCCcEEEEEEcCCCCcHHHHHHHHHHHcCCCeeEEEeeecCC
Confidence 99999999999999999999999999999987534333346999999999999999999999999999999999999999
Q ss_pred CCceEE--EecCC
Q 019548 325 RPLRVV--DDSNN 335 (339)
Q Consensus 325 ~~w~~~--~~~~~ 335 (339)
++|+|+ +|...
T Consensus 336 ~~~~Y~Ffid~eg 348 (386)
T PRK10622 336 NPWEEMFYLDVQA 348 (386)
T ss_pred CCceEEEEEEEeC
Confidence 999997 77654
No 2
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=4.2e-82 Score=597.67 Aligned_cols=236 Identities=47% Similarity=0.666 Sum_probs=222.9
Q ss_pred ceEEEEECCCCcHHHHHHHHhCCC-CccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEE
Q 019548 97 KVRISFKGLPGSFSEDAALKAYPK-CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQ 175 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg~-~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~ 175 (339)
+++||||||+|||||+||+++|++ .+..||+||+|||++|++|++||||||||||++|+|++|+|+|..++|+|+||+.
T Consensus 2 ~~~iayLGP~Gtfs~~Aa~~~f~~~~~~~p~~ti~evf~ave~g~aD~gVVPIENS~eG~V~~tlDlL~~~~l~IvgE~~ 81 (279)
T COG0077 2 TMKIAYLGPEGTFSEQAARKLFGSGAELLPCSTIEDVFKAVENGEADYGVVPIENSIEGSVNETLDLLAETDLQIVGEIV 81 (279)
T ss_pred CceeEEeCCCccHHHHHHHHhccccceeccCCCHHHHHHHHHcCCCceEEEEeeecCCcchHHHHHhhccCCcEEEEEEE
Confidence 689999999999999999999998 7999999999999999999999999999999999999999999999999999999
Q ss_pred EeeeeeeccCCCCCcCCccEEEecHHHHHHHHHHHHhc--CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCc
Q 019548 176 LAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLN 253 (339)
Q Consensus 176 l~I~h~Ll~~~g~~l~~I~~VySHpqal~QC~~~L~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~ 253 (339)
+||+|||+++.+.++++|++|||||||++||++||+++ ++++++++|||+||+++++.++...|||||+.||++|||+
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 99999999998889999999999999999999999997 6999999999999999999877899999999999999999
Q ss_pred eeeccccCCCCCeeeEEEEeeC-CCCCCCCCCceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE--
Q 019548 254 ILADRIQDEPDNITRFLVLARD-PIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV-- 330 (339)
Q Consensus 254 il~~~IeD~~~N~TRF~vi~~~-~~~p~~~~~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~-- 330 (339)
+|++||||.++|+|||+||+|. +....+ ...||||+|+++|+||+|+++|++|+.+|||||||||||+++++|+|+
T Consensus 162 il~~~I~D~~~N~TRF~vl~r~~~~~~~~-~~~kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~~~~~Y~F~ 240 (279)
T COG0077 162 ILAENIEDEPNNRTRFLVLSRRKPPSVSD-GPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTGLGEYLFF 240 (279)
T ss_pred hHhhcccCCCCCeEEEEEEeccCCCCcCC-CCceEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCCCCeeEEEE
Confidence 9999999999999999999985 222122 346999999999999999999999999999999999999999999985
Q ss_pred Eec
Q 019548 331 DDS 333 (339)
Q Consensus 331 ~~~ 333 (339)
||.
T Consensus 241 iD~ 243 (279)
T COG0077 241 IDI 243 (279)
T ss_pred EEE
Confidence 444
No 3
>PRK11899 prephenate dehydratase; Provisional
Probab=100.00 E-value=4.5e-80 Score=588.09 Aligned_cols=241 Identities=41% Similarity=0.569 Sum_probs=226.7
Q ss_pred CCceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEE
Q 019548 95 GTKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEV 174 (339)
Q Consensus 95 ~~~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi 174 (339)
.++++||||||+|||||+||+++|++.+++||.||++||++|++|++||||||||||++|+|.+|+|+|.+++++|+||+
T Consensus 2 ~~~~kvaylGp~GsfS~~Aa~~~~~~~~~v~~~s~~~vf~av~~g~~d~gVvPiENS~~G~V~~~~Dll~~~~l~Iv~E~ 81 (279)
T PRK11899 2 SKTNRIAFQGEPGANSHLACRDAFPDMEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVADIHHLLPESGLHIVGEY 81 (279)
T ss_pred CCCCEEEEECCCCCHHHHHHHHhcCcCceeecCCHHHHHHHHHCCCCCEEEEEeeccCCccHHHHHHHHhcCCCEEEEEE
Confidence 46789999999999999999999998899999999999999999999999999999999999999999999999999999
Q ss_pred EEeeeeeeccCCCCCcCCccEEEecHHHHHHHHHHHHhcCCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCce
Q 019548 175 QLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNI 254 (339)
Q Consensus 175 ~l~I~h~Ll~~~g~~l~~I~~VySHpqal~QC~~~L~~~~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~i 254 (339)
.+||+|||++.++.++++|++||||||||+||++||++++++.+++.|||+||+++++.++++.|||||+.||++|||+|
T Consensus 82 ~l~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAIas~~aa~~YgL~i 161 (279)
T PRK11899 82 FLPIRHQLMALPGATLEEIKTVHSHPHALGQCRKIIRALGLKPVVAADTAGAARLVAERGDPSMAALASRLAAELYGLDI 161 (279)
T ss_pred EEEeeEEEecCCCCCHHHCeEEEEeHHHHHHHHHHHHHcCCeEEEcCChHHHHHHHHhcCCCCeeEeCCHHHHHHcCCcc
Confidence 99999999999998999999999999999999999999999999999999999999987777899999999999999999
Q ss_pred eeccccCCCCCeeeEEEEeeCCCC-CCCCCCceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE--E
Q 019548 255 LADRIQDEPDNITRFLVLARDPII-PRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV--D 331 (339)
Q Consensus 255 l~~~IeD~~~N~TRF~vi~~~~~~-p~~~~~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~--~ 331 (339)
|+++|||.++|+|||+||++++.. +...+.+||||+|+++|+||+|+++|++|+++|||||||||||+++++|+|+ +
T Consensus 162 l~~~IqD~~~N~TRF~vi~~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~~~Y~F~i 241 (279)
T PRK11899 162 LAENIEDADHNTTRFVVLSREADWAARGDGPIVTTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSFTATQFYA 241 (279)
T ss_pred hhhcccCCcccceeEEEEecCCCCCCCCCCCceEEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCCceEEEEE
Confidence 999999999999999999998642 2233356999999999999999999999999999999999999999999997 6
Q ss_pred ecCC
Q 019548 332 DSNN 335 (339)
Q Consensus 332 ~~~~ 335 (339)
|...
T Consensus 242 d~eg 245 (279)
T PRK11899 242 DIEG 245 (279)
T ss_pred EEEC
Confidence 6543
No 4
>PLN02317 arogenate dehydratase
Probab=100.00 E-value=2e-78 Score=594.88 Aligned_cols=250 Identities=71% Similarity=1.175 Sum_probs=232.7
Q ss_pred hhCCCCCCccccccccCCCCceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccch
Q 019548 77 ISLPKPLTVADFTVTPNDGTKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSI 156 (339)
Q Consensus 77 ~~n~GPL~~e~i~~s~~l~~~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V 156 (339)
...+.||+...++.+.....+++||||||+|||||+||.++|++.+++||+||++||++|++|++||||||||||++|+|
T Consensus 74 ~~~~~~~~~~~~~~~~~~~~~~rVaylGp~GtfSe~AA~~~f~~~e~vp~~sf~~vf~AVe~g~ad~gVvPIENS~~GsV 153 (382)
T PLN02317 74 SGLPRPLSITDLSPSPMHGSKLRVAYQGVPGAYSEAAARKAYPNCEAVPCEQFEAAFQAVELWLADRAVLPIENSLGGSI 153 (382)
T ss_pred ccccccccHhhhcccccCCCCcEEEEECCCcCHHHHHHHHhhCcCceeecCCHHHHHHHHHCCCCCEEEEEEeccCccch
Confidence 35566776655665455566789999999999999999999998899999999999999999999999999999999999
Q ss_pred hhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCccEEEecHHHHHHHHHHHHhcCCeeEecCCHHHHHHHHHhcCCC
Q 019548 157 HRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLR 236 (339)
Q Consensus 157 ~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~VySHpqal~QC~~~L~~~~~~~i~~~STA~AA~~v~~~~~~ 236 (339)
.+|||+|.+++++|+||+++||+|||++++|.++++|++||||||||+||++||++++++++++.|||+||+++++.++.
T Consensus 154 ~~t~DlL~~~~l~IvgEv~l~I~h~Ll~~~g~~l~~Ik~VySHPQALaQC~~~L~~~~~~~~~~~sTA~AA~~Va~~~~~ 233 (382)
T PLN02317 154 HRNYDLLLRHRLHIVGEVQLPVHHCLLALPGVRKEELKRVISHPQALAQCENTLTKLGVVREAVDDTAGAAKMVAANGLR 233 (382)
T ss_pred HHHHHHHhcCCCEEEEEEEEEeeeEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHcCCeEEEcCCHHHHHHHHHhcCCC
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999987667
Q ss_pred CeEEecCHHHHHHcCCceeeccccCCCCCeeeEEEEeeCCCCCCCCCCceEEEEEEecCCcchHHHHHHHHHhCCceeee
Q 019548 237 DAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTK 316 (339)
Q Consensus 237 ~~AAIas~~AA~~ygL~il~~~IeD~~~N~TRF~vi~~~~~~p~~~~~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtk 316 (339)
+.|||||+.||++|||+||+++|||+++|+|||+||++++..|.....+||||+|+++|+||+|+++|+.|+.+||||||
T Consensus 234 ~~AAIaS~~aA~~YgL~iLa~~IqD~~~N~TRFlvl~r~~~~~~~~~~~KTSivfsl~~~pG~L~k~L~~Fa~~~INLtk 313 (382)
T PLN02317 234 DTAAIASARAAELYGLDILAEGIQDDSDNVTRFLMLAREPIIPRTDRPFKTSIVFSLEEGPGVLFKALAVFALRDINLTK 313 (382)
T ss_pred CceeecCHHHHHHcCCcchhhhhcCCCCCeeeEEEEecCCcCCCCCCCccEEEEEEcCCCCchHHHHHHHHHHCCCCEEE
Confidence 89999999999999999999999999999999999999876554445669999999999999999999999999999999
Q ss_pred eeeeeCCCCC
Q 019548 317 IESRPQRKRP 326 (339)
Q Consensus 317 IeSRP~~~~~ 326 (339)
|||||.++++
T Consensus 314 IESRP~~~~~ 323 (382)
T PLN02317 314 IESRPQRKRP 323 (382)
T ss_pred EEeeecCCCC
Confidence 9999999986
No 5
>PRK11898 prephenate dehydratase; Provisional
Probab=100.00 E-value=3.9e-73 Score=542.11 Aligned_cols=237 Identities=45% Similarity=0.591 Sum_probs=219.2
Q ss_pred ceEEEEECCCCcHHHHHHHHhCCC---CccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcC-CeEEEE
Q 019548 97 KVRISFKGLPGSFSEDAALKAYPK---CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRH-RLHIVG 172 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg~---~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~-~l~I~g 172 (339)
+++||||||+|||||+||.++|+. .+++||+||++||++|++|++||||||||||++|.|.+|||+|.++ +++|+|
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 358999999999999999999976 6899999999999999999999999999999999999999999875 899999
Q ss_pred EEEEeeeeeeccCCCCCcCCccEEEecHHHHHHHHHHHHhc--CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHc
Q 019548 173 EVQLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIY 250 (339)
Q Consensus 173 Ei~l~I~h~Ll~~~g~~l~~I~~VySHpqal~QC~~~L~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~y 250 (339)
|+.+||+|||+++++.. ++|++||||||||+||++||+++ +++.+++.|||+||+++++++..+.|||+|+.||++|
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 99999999999998755 99999999999999999999997 8999999999999999998766678999999999999
Q ss_pred CCceeeccccCCCCCeeeEEEEeeCCC-CCCCCCCceEEEEEEecC-CcchHHHHHHHHHhCCceeeeeeeeeCCCCCce
Q 019548 251 GLNILADRIQDEPDNITRFLVLARDPI-IPRTDKLFKTSIVFTLDE-GPGVLFKALAVFALREINLTKIESRPQRKRPLR 328 (339)
Q Consensus 251 gL~il~~~IeD~~~N~TRF~vi~~~~~-~p~~~~~~Ktsi~~~~~~-~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~ 328 (339)
||++|++||||.++|+|||+||+++.. .|...+.+||||+|+++| +||+|+++|++|+++|||||+|||||.++++|+
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 222334679999999987 599999999999999999999999999999996
Q ss_pred EE--EecC
Q 019548 329 VV--DDSN 334 (339)
Q Consensus 329 ~~--~~~~ 334 (339)
|. +|+.
T Consensus 240 y~F~vd~e 247 (283)
T PRK11898 240 YFFFIDVE 247 (283)
T ss_pred EEEEEEEE
Confidence 65 7765
No 6
>KOG2797 consensus Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=7.9e-66 Score=484.21 Aligned_cols=253 Identities=61% Similarity=1.031 Sum_probs=235.3
Q ss_pred CCCCCccccccccCCCCceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhh
Q 019548 80 PKPLTVADFTVTPNDGTKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRN 159 (339)
Q Consensus 80 ~GPL~~e~i~~s~~l~~~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~t 159 (339)
+.|+....+..+..-....+||||||+|+|||.||.+.|++.+-+||+.|+.+|++|+...+||+|+|||||+.|+|...
T Consensus 73 ~~pl~~~~l~psp~~~s~lRva~qg~pgaysesaa~ka~pn~~avpc~~f~~afqave~w~vD~AVLPiENS~gGsIhrn 152 (377)
T KOG2797|consen 73 PQPLTSTDLSPSPMHGSTLRVAYQGVPGAYSESAALKAYPNCEAVPCDQFEAAFQAVELWIVDYAVLPIENSTGGSIHRN 152 (377)
T ss_pred CCcchhhhcccCCCCCceEEEEeecCCchhhhhhhhhhcCCcccccHhHHHHHHHHHHHhhccceeeeeeccCCceeeec
Confidence 34554444555666677889999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCccEEEecHHHHHHHHHHHHhcC--CeeEecCCHHHHHHHHHhcCCCC
Q 019548 160 YDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQLG--VARENVDDTASAAQYVASNGLRD 237 (339)
Q Consensus 160 lDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~VySHpqal~QC~~~L~~~~--~~~i~~~STA~AA~~v~~~~~~~ 237 (339)
||||.++++.|+||+.+||||||++.+|.+.+++++|.||||||+||..||.+++ +.++.++|||+||+.++.+...+
T Consensus 153 YDLLlrh~lhiVgEv~vPvhHCLi~~~gv~~e~~~~VlSHPQal~Qce~~L~~l~~~~~r~a~~dTa~Aa~~~s~~~~~d 232 (377)
T KOG2797|consen 153 YDLLLRHRLHIVGEVQVPVHHCLIALPGVRKEEVVRVLSHPQALGQCECSLTKLGPNAAREAVSDTAGAAEQISASNTAD 232 (377)
T ss_pred hHHHhhcchheeeEEecceeeeEecCCCCChhheeeeecCcHHHHHHHHHHHhcccceeeeeccchHHHHHHHHhccccc
Confidence 9999999999999999999999999999999999999999999999999999974 88999999999999999988889
Q ss_pred eEEecCHHHHHHcCCceeeccccCCCCCeeeEEEEeeCCCCCCCCCCceEEEEEEecCCcchHHHHHHHHHhCCceeeee
Q 019548 238 AGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKI 317 (339)
Q Consensus 238 ~AAIas~~AA~~ygL~il~~~IeD~~~N~TRF~vi~~~~~~p~~~~~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkI 317 (339)
.+||+|+.||++|||.||+++|||+.+|.|||++|.+++.+|..+...||||+|...+.||.|+++|++|+-+.||||+|
T Consensus 233 ~~AIASe~aA~ly~l~Il~~~IqDd~~NvTRFLmLar~p~ip~t~rl~ktsivf~~~~gp~vLfkvl~vfa~r~inltkI 312 (377)
T KOG2797|consen 233 TAAIASERAAELYGLNILEKNIQDDLGNVTRFLMLAREPIIPDTDRLFKTSIVFFREKGPGVLFKVLSVFAFRSINLTKI 312 (377)
T ss_pred HHHHHHHHHHHHhcchhhhhhcccccCCeeEEEEEeccCCCCCCCccceeeEEEEeecCCchHHHHHHHHHhhhceeeee
Confidence 99999999999999999999999999999999999999999988778899999999999999999999999999999999
Q ss_pred eeee-----------CCCCCceEEEe
Q 019548 318 ESRP-----------QRKRPLRVVDD 332 (339)
Q Consensus 318 eSRP-----------~~~~~w~~~~~ 332 (339)
|||| .+.-+|-||||
T Consensus 313 esRP~h~~p~r~v~~~k~f~ylFyid 338 (377)
T KOG2797|consen 313 ESRPFHNRPLRVVDDSKNFEYLFYID 338 (377)
T ss_pred ecccccCCCcccccccccccEEEEEE
Confidence 9999 45555666665
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=3.5e-57 Score=406.08 Aligned_cols=177 Identities=47% Similarity=0.723 Sum_probs=163.8
Q ss_pred EEEECCCCcHHHHHHHHhC--CCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEe
Q 019548 100 ISFKGLPGSFSEDAALKAY--PKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLA 177 (339)
Q Consensus 100 VayLGP~GTfS~~AA~~~f--g~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~ 177 (339)
||||||+|||||+||+++| ++.+++||+||++||++|++|++||||||||||++|.|.+|+|+|.+.+++|+||+.+|
T Consensus 1 Ia~LGP~GT~S~~Aa~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~~vvPiENs~~G~V~~t~d~L~~~~l~i~~e~~l~ 80 (181)
T PF00800_consen 1 IAYLGPEGTFSHEAAQQYFGGPDAEIVPCDSFEEVFDAVEEGEADYGVVPIENSLEGSVSETLDLLIDSDLYIVGEIVLP 80 (181)
T ss_dssp EEEESSTTSHHHHHHCCCCTTTCSEEEEESSHHHHHHHHHCTSSSEEEEEEECTTTCECHHHHHHHHTSSCEEEEEEEEE
T ss_pred CEEeCCCCCHHHHHHHHHHHhhccceEecCCHHHHHHHHHcCCCceEEEeEeeecCCEeHHHHHHHhcCCceEEEEEEec
Confidence 7999999999999999999 45899999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeeccCCCCCcCCccEEEecHHHHHHHHHHHHhc--CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCcee
Q 019548 178 ANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNIL 255 (339)
Q Consensus 178 I~h~Ll~~~g~~l~~I~~VySHpqal~QC~~~L~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~il 255 (339)
|+|||+++++.++++|++|||||||++||++||+++ +++++.+.||++||++++..+.+..|||+|+.||++|||++|
T Consensus 81 i~~~L~~~~~~~l~~i~~V~SHp~al~Qc~~~l~~~~p~~~~~~~~Sta~Aa~~v~~~~~~~~aAI~s~~aa~~y~L~il 160 (181)
T PF00800_consen 81 IHHCLLAKPGTSLSDIKTVYSHPQALAQCREFLEKHLPGAEIVEASSTAEAAEKVAASEGPGDAAIASEEAAELYGLEIL 160 (181)
T ss_dssp --EEEEECTT--GGG-SEEEEEHHHHHHTHHHHHHT-TTSEEEEESSHHHHHHHCCCCTBTTEEEEEECCHHHHTTEEEE
T ss_pred cccEEeccCCCchhcceEEEEchHHHHHHHHHHHhcCCceEEEeCCCHHHHHHHHHhccCCCeEEECCHHHHHHcCccCh
Confidence 999999999988999999999999999999999997 799999999999999977766788999999999999999999
Q ss_pred eccccCCCCCeeeEEEEeeCC
Q 019548 256 ADRIQDEPDNITRFLVLARDP 276 (339)
Q Consensus 256 ~~~IeD~~~N~TRF~vi~~~~ 276 (339)
+++|||.++|+|||+||++++
T Consensus 161 ~~~I~d~~~N~TRF~vi~~~~ 181 (181)
T PF00800_consen 161 ARNIQDNPNNYTRFLVIGKEP 181 (181)
T ss_dssp ECS-SSSTT-EEEEEEEECCT
T ss_pred hhcCCCCCCCeEeEEEEecCC
Confidence 999999999999999999864
No 8
>PRK06034 hypothetical protein; Provisional
Probab=99.92 E-value=1.5e-25 Score=212.65 Aligned_cols=134 Identities=9% Similarity=-0.035 Sum_probs=115.1
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCC-C--C--C-chhHHHHHhhhhCCCCCCccc-------cc-cccCCCCceEE-E
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSS-N--V--N-DVPGKLCKDLISLPKPLTVAD-------FT-VTPNDGTKVRI-S 101 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~-~--~--~-RE~~il~~~~~~n~GPL~~e~-------i~-~s~~l~~~~~V-a 101 (339)
-+|.||++||+||++++.+||++|++. + + | ||++||+++...++|+|+.+. || .++.+|.+.+| +
T Consensus 20 ~ID~eLl~LL~eR~~lv~~Va~~K~~~~~~pv~dP~RE~evl~rl~~~~~g~L~~~~ie~Ifr~Iis~Sr~lQ~~~~V~a 99 (279)
T PRK06034 20 AIDEELHQLLMERGDIIDRLIAVKRTQEVGSAFRPGREADMMRRLVSRHRGILPLDTVESIWRVIIATFTYVQAPFSVHA 99 (279)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhccCCCCccChHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHHHhcCCceEEE
Confidence 789999999999999999999999986 3 3 5 999999999999999999875 45 57779999999 9
Q ss_pred EECCCCcHHHHHHHHhCCC-CccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhh-cCCeEEEEEE
Q 019548 102 FKGLPGSFSEDAALKAYPK-CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL-RHRLHIVGEV 174 (339)
Q Consensus 102 yLGP~GTfS~~AA~~~fg~-~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~-~~~l~I~gEi 174 (339)
||||+|||||+||++|||. .++++|.||++||++|++|++|||||||+++ .+.- +-.|. +...+|++-.
T Consensus 100 ~lG~~gs~s~~AA~~~FG~s~~~~~~~s~~dVf~AV~~g~adyGVVPI~~~-~~~W---W~~L~~~~~~~iiarl 170 (279)
T PRK06034 100 DGSGGEAAMRDSARFHFGFTVPYVPHFSAQAVVEAVARSKGDLGLVSLTSS-DTPW---WGRLEAEGAPKIIARL 170 (279)
T ss_pred EeCCccHHHHHHHHHHhccccCCccCCCHHHHHHHHHcCCCCEEEEECCCC-CCcH---HHHhccCCCCeEEEeC
Confidence 9999999999999999995 6899999999999999999999999999544 3433 34444 4557787653
No 9
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=99.57 E-value=2.3e-15 Score=116.46 Aligned_cols=49 Identities=41% Similarity=0.558 Sum_probs=45.8
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE--EecCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV--DDSNN 335 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~--~~~~~ 335 (339)
|||+|+++|+||+|+++|+.|+.+|||||+|||||.++++|+|+ +|+..
T Consensus 1 tsl~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~~~ 51 (74)
T cd04904 1 TSLIFSLKEEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDCEV 51 (74)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEEEc
Confidence 68999999999999999999999999999999999999999876 77753
No 10
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.57 E-value=3.6e-15 Score=120.10 Aligned_cols=52 Identities=37% Similarity=0.452 Sum_probs=48.2
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE--EecCC
Q 019548 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV--DDSNN 335 (339)
Q Consensus 284 ~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~--~~~~~ 335 (339)
.+||||+|+++|+||+|+++|++|+++|||||+|||||+++.+|+|. ||++.
T Consensus 12 ~~ktslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVDieg 65 (90)
T cd04931 12 NGVISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFINLDK 65 (90)
T ss_pred CCcEEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEEc
Confidence 45899999999999999999999999999999999999999999665 88864
No 11
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.51 E-value=1.7e-14 Score=121.22 Aligned_cols=51 Identities=33% Similarity=0.454 Sum_probs=46.7
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCce--EEEecCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLR--VVDDSNN 335 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~--~~~~~~~ 335 (339)
+||||+|+++|+||+|+++|++|+.+|||||+|||||++..+|+ ||||++.
T Consensus 40 ~ktSlifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~~~~~eY~FfIdieg 92 (115)
T cd04930 40 QKATLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSRKEGGDLEVLVRCEV 92 (115)
T ss_pred ccEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCCCCCceEEEEEEEEe
Confidence 48999999999999999999999999999999999999988875 5588863
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=99.50 E-value=2.5e-14 Score=111.17 Aligned_cols=48 Identities=38% Similarity=0.510 Sum_probs=45.1
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE--EecC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV--DDSN 334 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~--~~~~ 334 (339)
|||+|+++|+||+|+++|+.|+++||||++|||||.+..+|+|. ||++
T Consensus 1 tsl~~~l~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id~e 50 (74)
T cd04929 1 TSVIFSLKNEVGGLAKALKLFQELGINVVHIESRKSKRRSSEFEIFVDCE 50 (74)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEEEE
Confidence 68999999999999999999999999999999999999999765 8876
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=99.23 E-value=1.2e-11 Score=95.08 Aligned_cols=48 Identities=56% Similarity=0.706 Sum_probs=43.4
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE--EecCC
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV--DDSNN 335 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~--~~~~~ 335 (339)
|++|+++|+||+|+++|+.|+++|+||++|||||.++.+|+|. +++..
T Consensus 1 sl~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~ 50 (75)
T cd04880 1 SLVFSLKNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEG 50 (75)
T ss_pred CEEEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEEC
Confidence 5789999999999999999999999999999999999888665 77653
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=99.14 E-value=5e-11 Score=119.82 Aligned_cols=51 Identities=37% Similarity=0.605 Sum_probs=47.3
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE--EecCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV--DDSNN 335 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~--~~~~~ 335 (339)
+||||+|+++|+||+|+++|+.|+++|||||+|||||++..+|+|. ||++.
T Consensus 15 ~KTSLiFsL~d~pGaL~~vL~vFa~~gINLthIESRPsk~~~~eY~FFVD~eg 67 (436)
T TIGR01268 15 AKTSLIFSLKEEAGALAETLKLFQAHDVNLTHIESRPSKTHPGEYEFFVEFDE 67 (436)
T ss_pred CeEEEEEEcCCCCcHHHHHHHHHHHCCCCeeEEecccCCCCCccEEEEEEEec
Confidence 4899999999999999999999999999999999999999999765 88863
No 15
>TIGR01270 Trp_5_monoox tryptophan 5-monooxygenase, tetrameric. This model describes tryptophan 5-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tyrosine 3-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=99.13 E-value=5.7e-11 Score=119.83 Aligned_cols=52 Identities=35% Similarity=0.493 Sum_probs=48.8
Q ss_pred CCceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCce---EEEecC
Q 019548 283 KLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLR---VVDDSN 334 (339)
Q Consensus 283 ~~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~---~~~~~~ 334 (339)
+.+||||+|+++|+||+|+++|+.|+++|||||+|||||+++.+|+ ||||+.
T Consensus 28 ~~~ktSLIFsL~d~pGaL~~vL~vFa~~gINLThIESRPsk~~~~e~Y~FfVD~E 82 (464)
T TIGR01270 28 GVQRLSIIFSLSNVVGDLSKAIAIFQDRHINILHLESRDSKDGTSKTMDVLVDVE 82 (464)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHCCCCEEEEECCcCCCCCCccEEEEEEEE
Confidence 3569999999999999999999999999999999999999999998 779986
No 16
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=99.08 E-value=2.4e-10 Score=89.08 Aligned_cols=50 Identities=56% Similarity=0.732 Sum_probs=45.1
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE--EecCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV--DDSNN 335 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~--~~~~~ 335 (339)
||||.|.++|+||+|+++|+.|+++||||++|+|||.+...|+|. +++..
T Consensus 1 ~~sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~~ 52 (80)
T cd04905 1 KTSIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFEG 52 (80)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEEC
Confidence 589999999999999999999999999999999999998888665 66653
No 17
>TIGR01807 CM_P2 chorismate mutase domain of proteobacterial P-protein, clade 2. This model represents one of two separate clades of the chorismate mutase domain of the gamma and beta and epsilon proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain. It is also found in Aquifex aolicus.
Probab=98.50 E-value=5.8e-08 Score=75.61 Aligned_cols=51 Identities=10% Similarity=-0.055 Sum_probs=46.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCC--CC--C--C-chhHHHHHhhhhCCCCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKS--SN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~--~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (339)
.+|.||++||++|+.++.+||++|+. .| + | ||+++|.++...++|+++.+.
T Consensus 10 ~iD~~iv~Ll~~R~~~~~~i~~~K~~~~~~~~i~d~~Re~~vl~~~~~~~~~~l~~~~ 67 (76)
T TIGR01807 10 AIDDRILDLLSERATYAQAVGELKGSGASGASFYRPEREAQVIRRLQNLNKGPLDQEA 67 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcCChHHHHHHHHHHHHhccCCCCHHH
Confidence 78999999999999999999999998 66 3 5 999999999999999988764
No 18
>TIGR01801 CM_A chorismate mutase domain of gram positive AroA protein. This model represents a small clade of chorismate mutase domains N-terminally fused to the first enzyme in the chorismate pathway, 2-dehydro-3-deoxyphosphoheptanoate aldolase (DAHP synthetase, AroA) which are found in some gram positive species and Deinococcus. Only in Deinococcus, where this domain is the sole CM domain in the genome can a trusted assignment of function be made. In the other species there is at least one other trusted CM domain present. The similarity between the Deinococcus gene and the others in this clade is sufficiently strong (~44% identity), that the whole clade can be trusted to be functional. The possibility exists, however, that in the gram positive species the fusion to the first enzyme in the pathway has evolved a separate, regulatory role.
Probab=98.44 E-value=8.3e-08 Score=79.14 Aligned_cols=51 Identities=12% Similarity=-0.024 Sum_probs=47.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCCCCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (339)
-+|.+|++||++|+.++.+||++|++.| + | ||++||+++...++||++.+.
T Consensus 15 ~ID~eIl~LL~eR~~~~~~Ig~~K~~~~~~i~dp~RE~~vl~~~~~~~~g~l~~~~ 70 (102)
T TIGR01801 15 QLNRQILALISRRGEVVAQIGHAKSAQGPNHYDPAREEQMLNELIKINPGPFPTAT 70 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCChHHHHHHHHHHHHhcCCCCCHHH
Confidence 6899999999999999999999999887 3 5 999999999999999999875
No 19
>TIGR01805 CM_mono_grmpos monofunctional chorismate mutase, gram positive-type, clade 2. This model represents a clade of chorismate mutase proteins/domains from gram positive species. The sequence from Enterococcus is fused to the C-terminus of an aparrent acetyltransferase, and the seuence from Clostridium acetobutylicum (but not perfringens) is fused to the N-terminus of shikimate-5-dehydrogenase, another enzyme of the chorismate pathway. All the other members of this clade are mono-functional. Members of this clade from Streptococcus and Lactococcus have been found which represent the sole chorismate mutase domain in their respective genomes which also exhibit evidence of the enzymes of both the upstream and downstream branches of the chorismate pathways.
Probab=98.43 E-value=6.4e-08 Score=76.28 Aligned_cols=51 Identities=6% Similarity=-0.104 Sum_probs=46.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCCCCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (339)
-+|.+|++||++|+.++.+||++|.+.| + | ||++++.++...++++++.+.
T Consensus 10 ~iD~~i~~Ll~~R~~~~~~i~~~K~~~~~~i~d~~RE~~vl~~~~~~~~~~~~~~~ 65 (81)
T TIGR01805 10 EIDDKLVVLFEERMEVVKEIAAYKKKNGIPIFDSKREQEIIDKCTKNVENKEYRET 65 (81)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcccCCCHHH
Confidence 6899999999999999999999999987 3 5 999999999999999887654
No 20
>TIGR01797 CM_P_1 chorismate mutase domain of proteobacterial P-protein, clade 1. This model represents the chorismate mutase domain of the gamma and beta proteobacterial "P-protein" which contains an N-terminal chorismate mutase domain and a C-terminal prephenate dehydratase domain.
Probab=98.40 E-value=7e-08 Score=76.48 Aligned_cols=51 Identities=10% Similarity=-0.124 Sum_probs=46.2
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (339)
-.|.+|++||++|+.++.+||++|++.| + | ||+++|+++...+. ++|+.+.
T Consensus 10 ~ID~~lv~Ll~~R~~~~~~i~~~K~~~~~~v~dp~RE~~vl~~~~~~~~~~~l~~~~ 66 (83)
T TIGR01797 10 AIDEKLLKLLAERRELAFEVGKSKLLSHRPVRDIERERDLLQRLITLGKAYHLDAHY 66 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhhhCCCCHHH
Confidence 6799999999999999999999999887 3 5 99999999999886 8888764
No 21
>PRK07248 hypothetical protein; Provisional
Probab=98.36 E-value=1.7e-07 Score=74.84 Aligned_cols=51 Identities=10% Similarity=-0.095 Sum_probs=46.6
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCCCCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (339)
-+|.+|++||++|+.++.+||++|++.| + | ||+++|.++...++++++++.
T Consensus 12 ~iD~~i~~Ll~~R~~l~~~I~~~K~~~~~~v~d~~RE~~vl~~~~~~~~~~~~~~~ 67 (87)
T PRK07248 12 QIDDQLVALLEKRMALVEQVVAYKKATGKPVLDTKREQVILDKVSSLVENKAYQET 67 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHcccCCCHHH
Confidence 6899999999999999999999999988 3 5 999999999999999887664
No 22
>TIGR01803 CM-like chorismate mutase related enzymes. This subfamily includes two enzymes which are variants on the mechanism of chorismate mutase and are likely to have evolved from an ancestral chorismate mutase enzyme. 4-amino-4-deoxy-chorismate mutase produces amino-deoxy-prephenate which is subsequently converted to para-dimethylamino-phenylalanine, a component of the natural product pristinamycin. Isochorismate-pyruvate lyase presumably catalyzes the same type of 2+2+2 cyclo-rearrangement as chorismate mutase, but acting on isochorismate, this results in two broken bonds instead of one broken and one made. The product of this reaction is salicylate (2-hydroxy-benzoate) which is also incorporated into various natural products.
Probab=98.22 E-value=5.3e-07 Score=71.25 Aligned_cols=51 Identities=10% Similarity=-0.082 Sum_probs=45.3
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (339)
.+|.+|++||++|+.++.+||++|+..+ + | ||++++.++...+. ++++.+.
T Consensus 10 ~ID~~lv~Ll~~R~~~~~~ia~~K~~~~~~v~d~~Re~~vl~~~~~~a~~~gl~~~~ 66 (82)
T TIGR01803 10 RIDLALVQALGRRMDYVKRASEFKRSHEAAIPAPERVAAVLPNAARWAEENGLDPPF 66 (82)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhcCCCCCCChHHHHHHHHHHHHHHHHcCCCHHH
Confidence 7899999999999999999999999877 3 5 99999999988775 7787764
No 23
>PRK08818 prephenate dehydrogenase; Provisional
Probab=98.19 E-value=1.7e-06 Score=86.35 Aligned_cols=48 Identities=25% Similarity=0.273 Sum_probs=42.2
Q ss_pred ceEEEEEEec-CCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceE--EEecC
Q 019548 285 FKTSIVFTLD-EGPGVLFKALAVFALREINLTKIESRPQRKRPLRV--VDDSN 334 (339)
Q Consensus 285 ~Ktsi~~~~~-~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~--~~~~~ 334 (339)
.-++|+|.++ |+||+|+++|+.|+++|||||+||| .+.++|+| |++..
T Consensus 294 ~~~~l~~~v~~d~pG~L~~vl~~la~~~INit~Ies--~~~r~~~y~f~i~~~ 344 (370)
T PRK08818 294 EPLTLSVYLPEDRPGSLRTLLHVFEQHGVNLSSIHS--SRTPAGELHFRIGFE 344 (370)
T ss_pred cceEEEEECCCCCCChHHHHHHHHHHcCcccceEEE--ecccCceEEEEEEEe
Confidence 3689999997 9999999999999999999999999 88888886 44444
No 24
>PRK07857 hypothetical protein; Provisional
Probab=98.15 E-value=1.1e-06 Score=72.93 Aligned_cols=42 Identities=7% Similarity=-0.158 Sum_probs=38.7
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhh
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLIS 78 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~ 78 (339)
-+|.||++||++|+.++.+||++|++.| + + ||+++|+++.+.
T Consensus 39 ~ID~eIl~LL~eR~~la~eIg~~K~~~g~pI~dp~RE~eVl~rl~~~ 85 (106)
T PRK07857 39 RLDAEILALVKRRTEVSQAIGKARMASGGTRLVHSREMKVIERYREE 85 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhccCCCccChHHHHHHHHHHHHH
Confidence 7899999999999999999999999988 3 4 999999999874
No 25
>TIGR01799 CM_T chorismate mutase domain of T-protein. This model represents the chorismate mutase domain of the gamma proteobacterial "T-protein" which consists of an N-terminal chorismate mutase domain and a C-terminal prephenate dehydrogenase domain.
Probab=98.14 E-value=8.7e-07 Score=70.19 Aligned_cols=51 Identities=6% Similarity=-0.083 Sum_probs=44.6
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (339)
-+|.+|++||++|+.++.+||++|++.| + | ||++++.++...+. ++++.+.
T Consensus 10 ~ID~~il~Ll~~R~~~~~~ia~~K~~~~~~v~d~~RE~~vl~~~~~~a~~~gl~~~~ 66 (83)
T TIGR01799 10 GVDQELLHLLAKRLELVAQVGKVKHAAGLPIYAPEREAAMLAARREEAEKAGIAPDL 66 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHhhcCCCCHHH
Confidence 6899999999999999999999999988 3 5 99999999888665 6677654
No 26
>PRK06443 chorismate mutase; Validated
Probab=98.12 E-value=4.9e-07 Score=80.78 Aligned_cols=71 Identities=8% Similarity=-0.122 Sum_probs=53.2
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCCCCCCccccc-cccCCC----CceEEEEECCC
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVADFT-VTPNDG----TKVRISFKGLP 106 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~i~-~s~~l~----~~~~VayLGP~ 106 (339)
-.|.||++||+||++++.+||++|++.| + | ||+++++++.+.|+ +-. .|| .|+.+| .+..|-..|
T Consensus 16 ~ID~eIL~LL~kRm~la~eIg~~K~~~g~pI~Dp~RE~eVLerl~~~n~--If~-eIms~Sr~~Q~~~~~~~~i~~sg-- 90 (177)
T PRK06443 16 ENTMDIIELIEKRRELARMIGIIKMRNGLSIRDSERENYVKNNLKSDNP--LLN-MIFEATIHYQKNISLNINIEVSG-- 90 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCChHHHHHHHHHHHHhCH--HHH-HHHHHHHHHHhcccccceeeeec--
Confidence 6899999999999999999999999988 3 5 99999999999885 333 244 455544 344555554
Q ss_pred CcHHHHH
Q 019548 107 GSFSEDA 113 (339)
Q Consensus 107 GTfS~~A 113 (339)
.|-..|
T Consensus 91 -~y~~~~ 96 (177)
T PRK06443 91 -DYDSLI 96 (177)
T ss_pred -chHHHH
Confidence 454444
No 27
>TIGR01808 CM_M_hiGC-arch monofunctional chorismate mutase, high GC gram positive type. This model represents the monofunctional chorismate mutase from high GC gram-positive bacteria and archaea. Trusted annotations from Corynebacterium and Pyrococcus are aparrently the sole chorismate mutase enzymes in their respective genomes. This is coupled with the presence in those genomes of the enzymes of the chorismate pathways both up- and downstream of chorismate mutase.
Probab=98.11 E-value=1.4e-06 Score=67.72 Aligned_cols=44 Identities=9% Similarity=-0.145 Sum_probs=39.9
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP 80 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~ 80 (339)
-+|.||++||++|+.++.+||++|+..| + | ||++++.++...+|
T Consensus 11 ~ID~~ii~LL~~R~~~~~~i~~~K~~~~~~i~d~~RE~~vl~~~~~~~~ 59 (74)
T TIGR01808 11 RLDAEILALVKRRAEISQAIGKARMASGGTRLVHSREMKVIERYSELGP 59 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhCC
Confidence 6899999999999999999999999888 3 5 99999999987664
No 28
>TIGR01791 CM_archaeal chorismate mutase, archaeal type. This model represents a clade of archaeal chorismate mutases. Chorismate mutase catalyzes the conversion of chorismate into prephenate which is subsequently converted into either phenylalanine or tyrosine. In Sulfolobus this gene is found as a fusion with prephenate dehydrogenase (although the non-TIGR annotation contains a typographical error indicating it as a dehydratase) which is the next enzyme in the tyrosine biosynthesis pathway. The Archaeoglobus gene contains an N-terminal prephenate dehydrogenase domain and a C-terminal prephenate dehydratase domain followed by a regulatory amino acid-binding ACT domain. The Thermoplasma volcanium gene is adjacent to prephenate dehydratase.
Probab=98.09 E-value=7.6e-07 Score=70.32 Aligned_cols=50 Identities=6% Similarity=-0.072 Sum_probs=42.5
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCcc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVA 86 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e 86 (339)
-+|.||++||++|+.++.+||++|++.| + | ||++++.++..... ..++.+
T Consensus 10 ~iD~~i~~Ll~~R~~l~~~i~~~K~~~g~~i~d~~RE~~v~~~~~~~~~~~~l~~~ 65 (83)
T TIGR01791 10 EIDKSILDLIEKRIKIARKIGEIKHNNGLPITDEEREERVIERLRNTARNLGLDVL 65 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHHHhcCCCHH
Confidence 7899999999999999999999999988 3 5 99999999875443 346654
No 29
>PRK07075 isochorismate-pyruvate lyase; Reviewed
Probab=98.07 E-value=2.3e-06 Score=70.37 Aligned_cols=51 Identities=10% Similarity=-0.087 Sum_probs=44.9
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC-C--C-chhHHHHHhhhhCC-CCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN-V--N-DVPGKLCKDLISLP-KPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~-~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (339)
.+|.+|++||++|+.++.+||++|+... + | ||+++|.++...+. ++++.+.
T Consensus 19 ~ID~~iv~LL~eR~~~~~~ia~~K~~~~~i~d~~Re~~vl~~~~~~a~~~gl~~~~ 74 (101)
T PRK07075 19 RLDRDIIAALGRRMQYVKAASRFKPSEASIPAPERVAAMLPERRRWAEQAGLDADF 74 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcCcCCCCCChHHHHHHHHHHHHHhhcCCCCHHH
Confidence 7899999999999999999999999755 3 5 99999999988776 7887764
No 30
>PRK06285 chorismate mutase; Provisional
Probab=98.06 E-value=1.5e-06 Score=70.70 Aligned_cols=51 Identities=8% Similarity=-0.167 Sum_probs=45.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (339)
.+|.+|++||++|+.++.+||++|+..| + | ||++++.++...++ ++++.+.
T Consensus 18 ~ID~~iv~Ll~~R~~l~~~I~~~K~~~~~~v~dp~RE~~vl~~~~~~a~~~~l~~~~ 74 (96)
T PRK06285 18 EIDEQIIDLIAERTSLAKEIAELKKSLGMPIFDPEREDYIHEKIRKLCEEHNIDENI 74 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCChHHHHHHHHHHHHHhhhCCCCHHH
Confidence 7899999999999999999999999987 3 5 99999999988775 8887754
No 31
>PRK11199 tyrA bifunctional chorismate mutase/prephenate dehydrogenase; Provisional
Probab=98.06 E-value=5.6e-06 Score=82.48 Aligned_cols=81 Identities=7% Similarity=-0.078 Sum_probs=62.6
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCccc-------cc-cccCCC-------
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD-------FT-VTPNDG------- 95 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~-------i~-~s~~l~------- 95 (339)
.+|.||++||++|++++.+||++|++.+ + | ||++++.++...++ +.++.+. || .|+..|
T Consensus 14 ~iD~~iv~Ll~~R~~~~~~ia~~K~~~~~~v~d~~Re~~vl~~~~~~~~~~~l~~~~~~~i~~~i~~~s~~~q~~~~~~~ 93 (374)
T PRK11199 14 EVDKQLLELLAKRLELVAQVGEVKSRHGLPIYVPEREAAMLASRRAEAEALGVPPDLIEDVLRRVMRESYSSENDKGFKT 93 (374)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHhHHhcccc
Confidence 7899999999999999999999999988 3 5 99999999988775 6676653 34 334311
Q ss_pred ---CceEEEEECCCCcHHHHHHHHh
Q 019548 96 ---TKVRISFKGLPGSFSEDAALKA 117 (339)
Q Consensus 96 ---~~~~VayLGP~GTfS~~AA~~~ 117 (339)
..++|++.|-.|....--|..+
T Consensus 94 ~~~~~~~I~IiGG~GlmG~slA~~l 118 (374)
T PRK11199 94 LNPDLRPVVIVGGKGQLGRLFAKML 118 (374)
T ss_pred cCcccceEEEEcCCChhhHHHHHHH
Confidence 3478999995577776555544
No 32
>COG1605 PheA Chorismate mutase [Amino acid transport and metabolism]
Probab=98.01 E-value=3.4e-06 Score=69.30 Aligned_cols=50 Identities=8% Similarity=-0.090 Sum_probs=44.8
Q ss_pred chhhHHHHHHHHHHHHHHhhhcCCCCC-C----C-chhHHHHHhh-hhCCCCCCccc
Q 019548 38 CRGGFSGLSGDSVIKSADNQNTGKSSN-V----N-DVPGKLCKDL-ISLPKPLTVAD 87 (339)
Q Consensus 38 ~~~~Il~LlneRa~la~eIg~~K~~~~-~----~-RE~~il~~~~-~~n~GPL~~e~ 87 (339)
+|.+|++||++|+.++++||++|.++| . | ||++||+++. ..+.++++++.
T Consensus 20 iD~~ll~Ll~eR~~l~~~Va~~K~~~g~~pi~d~~RE~~vl~~~~~~~~~~~l~~~~ 76 (101)
T COG1605 20 IDRELLDLLAERLELAKEVGEAKAASGKLPIYDPEREEQVLERLRAEAEKGGLDPEL 76 (101)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCChHHHHHHHHHHHHHHHhCCCCHHH
Confidence 789999999999999999999999887 2 5 9999999998 57778888775
No 33
>PF01817 CM_2: Chorismate mutase type II; InterPro: IPR020822 Chorismate mutase, 5.4.99.5 from EC, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine [, ]. Prephenate dehydratase (IPR001086 from INTERPRO, 4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate into phenylpyruvate. In microorganisms PDT is involved in the terminal pathway of the biosynthesis of phenylalanine. In some bacteria, such as Escherichia coli, PDT is part of a bifunctional enzyme (P-protein) that also catalyzes the transformation of chorismate into prephenate (chorismate mutase) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional chorismate mutase aligns well with the N-terminal part of P-proteins [].; GO: 0046417 chorismate metabolic process; PDB: 1YBZ_A 2GTV_X 2FP1_B 2F6L_B 2FP2_B 2AO2_A 3HGW_C 3HGX_B 2H9C_A 3RET_B ....
Probab=97.98 E-value=9.9e-07 Score=69.01 Aligned_cols=51 Identities=8% Similarity=-0.147 Sum_probs=45.7
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (339)
-+|.+|++||.+|+.++.+||++|.+.| + | ||++++.++..... ++++.+.
T Consensus 6 ~iD~~i~~Ll~~R~~l~~~i~~~K~~~~~~i~d~~RE~~v~~~~~~~~~~~~l~~~~ 62 (81)
T PF01817_consen 6 EIDREIVDLLAERMDLVRKIAEYKKENGLPIFDPDREEEVLERLRELAEEGGLDPEF 62 (81)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHTTCCSSTHHHHHHHHHHHHHHHHHTTSEHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCcHHHHHHHHHHHHHhHhCCCCHHH
Confidence 5799999999999999999999999998 3 5 99999999998877 8888664
No 34
>PRK12595 bifunctional 3-deoxy-7-phosphoheptulonate synthase/chorismate mutase; Reviewed
Probab=97.94 E-value=4e-06 Score=83.36 Aligned_cols=51 Identities=6% Similarity=-0.185 Sum_probs=47.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCCCCCCccc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPLTVAD 87 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~GPL~~e~ 87 (339)
-+|.||++||+||++++.+||++|++.| + | ||+++|+++...+.|+|+.+.
T Consensus 15 ~ID~eIl~LL~~R~~~~~~I~~~K~~~g~pi~dp~RE~~vl~~~~~~~~g~l~~~~ 70 (360)
T PRK12595 15 EINLQLLELLSKRGELVQEIGEEKTKQGTKRYDPVREREMLDMIAENNEGPFEDST 70 (360)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHhccCCCCHHH
Confidence 7899999999999999999999999988 3 5 999999999999999999874
No 35
>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=97.91 E-value=1.5e-05 Score=80.41 Aligned_cols=50 Identities=18% Similarity=0.216 Sum_probs=44.0
Q ss_pred eEEEEEEecCC-cchHHHHHHHHHhCCceeeeeeeeeCCCC-----CceEEEecCC
Q 019548 286 KTSIVFTLDEG-PGVLFKALAVFALREINLTKIESRPQRKR-----PLRVVDDSNN 335 (339)
Q Consensus 286 Ktsi~~~~~~~-pGaL~~iL~~Fa~~gINLtkIeSRP~~~~-----~w~~~~~~~~ 335 (339)
.++++|++.++ +|+|.++|+.|.+++|||+.|||||++.. .++||++|+-
T Consensus 37 ~~~~~~~~~~~~~g~L~~~l~~f~~~~inl~hiEsr~~~~~~~~~~~~~~~v~~~~ 92 (457)
T TIGR01269 37 MQNNQFYIRTKEISSLHRILKYIETFKLNLVHFETRPTRTLSNADVDYSCLITLEA 92 (457)
T ss_pred ceeEEEEeccCcchhHHHHHHHHHHcCCcEEEeecCCccccCCCCCceEEEEEEec
Confidence 57888888754 99999999999999999999999998754 4999999974
No 36
>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=97.89 E-value=3.5e-05 Score=56.42 Aligned_cols=46 Identities=17% Similarity=0.216 Sum_probs=40.0
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEe
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDD 332 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~ 332 (339)
+.|.+.++|+||.|.++++.|+++|||+..+.+++.+.+.|.+++.
T Consensus 1 ~~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~ 46 (66)
T PF01842_consen 1 YRVRVIVPDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIV 46 (66)
T ss_dssp EEEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEE
T ss_pred CEEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEE
Confidence 4677888999999999999999999999999999998875555543
No 37
>TIGR01795 CM_mono_cladeE monofunctional chorismate mutase, alpha proteobacterial type. The alpha proteobacterial members are trusted because the pathways of CM are evident and there is only one plausible CM in the genome. In S. coelicolor, however, there is another aparrent monofunctional CM.
Probab=97.75 E-value=9.9e-06 Score=65.86 Aligned_cols=44 Identities=0% Similarity=-0.191 Sum_probs=39.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP 80 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~ 80 (339)
-+|.||++||++|+.++.+||++|+..| + | ||++++.++.....
T Consensus 14 ~ID~qLv~LL~~R~~~~~~ia~~K~~~~~~v~dp~Re~~vl~~~~~~a~ 62 (94)
T TIGR01795 14 NIDAAVIHMLAERFKCTSQVGVLKANAGLAPADPAREDYQIARLRRLAI 62 (94)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHHHHHH
Confidence 7899999999999999999999999988 3 5 99999999877444
No 38
>PRK09239 chorismate mutase; Provisional
Probab=97.73 E-value=1.2e-05 Score=66.49 Aligned_cols=50 Identities=2% Similarity=-0.182 Sum_probs=43.1
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCcc
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVA 86 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e 86 (339)
.+|.+|++||++|+.++.+||++|+..| + | ||++++.++...+. ..|+++
T Consensus 21 ~ID~eIv~LLa~R~~l~~~Ia~~K~~~~~~i~dp~RE~~vl~~~~~~a~~~gl~p~ 76 (104)
T PRK09239 21 NIDAALIHMLAERFKCTQAVGVLKAEHGLPPADPAREAYQIERLRQLAKDANLDPD 76 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHCCCCHH
Confidence 6899999999999999999999999888 3 5 99999999887665 445554
No 39
>smart00830 CM_2 Chorismate mutase type II. Chorismate mutase, catalyses the conversion of chorismate to prephenate in the pathway of tyrosine and phenylalanine biosynthesis. This enzyme is negatively regulated by tyrosine, tryptophan and phenylalanine PUBMED:9642265, PUBMED:9497350.
Probab=97.68 E-value=3.2e-05 Score=59.89 Aligned_cols=47 Identities=6% Similarity=-0.055 Sum_probs=41.4
Q ss_pred cchhhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCCCCC
Q 019548 37 VCRGGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLPKPL 83 (339)
Q Consensus 37 ~~~~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~GPL 83 (339)
.+|.+|++||.+|+.++.+||++|...| + | ||++++.++........
T Consensus 6 ~iD~~ii~Ll~~R~~l~~~i~~~K~~~~~~i~d~~Re~~vl~~~~~~a~~~~ 57 (79)
T smart00830 6 AIDDQILALLAERAALAREVARLKAKNGLPIYDPEREAEVLERLRALAEGPG 57 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCChHHHHHHHHHHHHHcccCC
Confidence 6789999999999999999999999876 3 5 99999999988776543
No 40
>TIGR01806 CM_mono2 chorismate mutase, putative. This model represents a clade of probable chorismate mutases from alpha, beta and gamma proteobacteria as well as Mycobacterium tuberculosis and a clade of nematodes. Although the most likely function for the enzymes represented by this model is as a chorismate mutase, in no species are these enzymes the sole chorismate mutase in the genome. Also, in no case are these enzymes located in a region of the genome proximal to any other enzymes involved in chorismate pathways. Although the Pantoea enzyme has been shown to complement a CM-free mutant of E. coli, this was also shown to be the case with isochorismate-pyruvate lyase which only has a secondary (non-physiologically relevant) chorismate mutase activity. This enzyme is believed to be a homodimer and be localized to the periplasm.
Probab=97.68 E-value=2.7e-05 Score=65.43 Aligned_cols=48 Identities=10% Similarity=0.005 Sum_probs=42.0
Q ss_pred hhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 019548 40 GGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (339)
Q Consensus 40 ~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (339)
.+|++||++|+.++.+||++|++.| + | ||++||+++...+. ++|+.+.
T Consensus 7 ~eLv~Ll~eR~~la~eVa~~K~~~~~pI~Dp~RE~~Vl~~~~~~a~~~gL~~~~ 60 (114)
T TIGR01806 7 GQLVDAANERLQLADDVAGYKARNNLPIEDSPREEQVLDSLRAQAQSAGLDPDY 60 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCChHHHHHHHHHHHHHhHcCCCCHHH
Confidence 5899999999999999999999888 4 5 99999999988776 6677654
No 41
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.30 E-value=0.00056 Score=50.30 Aligned_cols=34 Identities=29% Similarity=0.328 Sum_probs=31.6
Q ss_pred EEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 290 ~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
.+.++|+||.|.++++.|++.|+|++.|.++|.+
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 42
>PRK09269 chorismate mutase; Provisional
Probab=97.22 E-value=0.00024 Score=64.95 Aligned_cols=48 Identities=8% Similarity=-0.017 Sum_probs=42.4
Q ss_pred hhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC-CCCCccc
Q 019548 40 GGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP-KPLTVAD 87 (339)
Q Consensus 40 ~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~-GPL~~e~ 87 (339)
.+|++||+||+.++.+|+..|.+.| | + ||++||.++...++ ++++.+.
T Consensus 35 ~~Lv~Li~eRl~la~~VA~~K~~~~~pI~Dp~RE~~VL~~v~~~A~~~gLdp~~ 88 (193)
T PRK09269 35 TPLVDLAAQRLALADPVALSKWDSGKPIEDPPREAQVLANVEAQAPAHGVDPDY 88 (193)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHhhcCCCCHHH
Confidence 6899999999999999999999988 4 4 99999999988776 7777654
No 43
>PRK08055 chorismate mutase; Provisional
Probab=97.19 E-value=0.00026 Score=64.16 Aligned_cols=47 Identities=11% Similarity=0.057 Sum_probs=41.0
Q ss_pred hhHHHHHHHHHHHHHHhhhcCCCCC--C--C-chhHHHHHhhhhCC--CCCCccc
Q 019548 40 GGFSGLSGDSVIKSADNQNTGKSSN--V--N-DVPGKLCKDLISLP--KPLTVAD 87 (339)
Q Consensus 40 ~~Il~LlneRa~la~eIg~~K~~~~--~--~-RE~~il~~~~~~n~--GPL~~e~ 87 (339)
.+|++||+||+.++.+|++.|...| + | ||++||.++...++ | ++.+.
T Consensus 28 ~~Lv~Li~eRl~la~~VA~~K~~~~~PI~Dp~RE~~VL~~v~~~A~~~G-Ldp~~ 81 (181)
T PRK08055 28 GALATLINERLSYMKDVAGYKAEHHLPIEDLTQEQKVLAEAEEEAASNG-LDPES 81 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhCCCCCCChHHHHHHHHHHHHHhhhCC-CCHHH
Confidence 4799999999999999999999988 4 4 99999999988776 4 66654
No 44
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=97.03 E-value=0.001 Score=66.34 Aligned_cols=50 Identities=32% Similarity=0.507 Sum_probs=45.3
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC--CCceEEEecC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK--RPLRVVDDSN 334 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~--~~w~~~~~~~ 334 (339)
-.++++|++.+++|+|.++|+.|...++|+..|||||++. ...++|+++.
T Consensus 35 ~~~~~if~~r~~~~~l~~~Lk~f~~~~vnl~HiEsR~s~~~~~~~evlv~~~ 86 (461)
T KOG3820|consen 35 ARISLIFSLRNKVGALARALKAFEEFHVNLLHIESRPSERRSSGYEVLVELD 86 (461)
T ss_pred ceEEEEEEecccchHHHHHHHHhhhcCceEEEeecccccccCCCceEEEeec
Confidence 3788999999999999999999999999999999999954 4599999875
No 45
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.99 E-value=0.0016 Score=47.44 Aligned_cols=46 Identities=13% Similarity=0.239 Sum_probs=37.2
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC-CCCceEEEecC
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQR-KRPLRVVDDSN 334 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~-~~~w~~~~~~~ 334 (339)
+.+.++|+||.|.++++.|+++|+|+..+...|.. .+...++++.+
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve 48 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTE 48 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeC
Confidence 45678999999999999999999999999877765 35566666544
No 46
>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=96.87 E-value=0.0034 Score=46.80 Aligned_cols=37 Identities=16% Similarity=0.286 Sum_probs=32.8
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~ 324 (339)
-|.+.++|+||.|.++++.|+++|+|+..+..-|..+
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 3566889999999999999999999999999877655
No 47
>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=96.61 E-value=0.0057 Score=46.24 Aligned_cols=44 Identities=18% Similarity=0.207 Sum_probs=34.7
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC--CCCCceEEEe
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQ--RKRPLRVVDD 332 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~--~~~~w~~~~~ 332 (339)
+.+.++|+||+|.++++.|+++|+|+..+...+. .......+++
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~~~~~~~v~ 47 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPDGMRRVFIR 47 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCCCccEEEEE
Confidence 4568899999999999999999999999876665 3344555544
No 48
>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=96.45 E-value=0.0085 Score=43.96 Aligned_cols=47 Identities=21% Similarity=0.251 Sum_probs=38.5
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
+|.+..+|+||.|.++++.|+++++|+.++...|..++.+.++++-+
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~ 48 (72)
T cd04874 2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIEREGKARIYMELE 48 (72)
T ss_pred eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccCCCeEEEEEEEe
Confidence 46677899999999999999999999999988776555566665544
No 49
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=96.15 E-value=0.017 Score=42.07 Aligned_cols=45 Identities=22% Similarity=0.363 Sum_probs=36.8
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC-CCCCceEEEe
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ-RKRPLRVVDD 332 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~-~~~~w~~~~~ 332 (339)
+|.+..+|+||.|.+++..|+++|+|+.++...+. .++.+.++++
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~ 47 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIV 47 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEE
Confidence 46778899999999999999999999999998876 4454555543
No 50
>cd04903 ACT_LSD C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit. The C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillis, and Treponema species. These enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in Escherichia coli, and other enterobacterials, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.03 E-value=0.017 Score=42.03 Aligned_cols=46 Identities=20% Similarity=0.328 Sum_probs=36.9
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC-CCCCceEEEecC
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQ-RKRPLRVVDDSN 334 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~-~~~~w~~~~~~~ 334 (339)
|.+..+|+||.|.++++.|+++|+|+.++...+. .++.+.+.+.-+
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~v~ 48 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEVD 48 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEEeC
Confidence 5567899999999999999999999999998874 345555555543
No 51
>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=95.96 E-value=0.022 Score=42.45 Aligned_cols=37 Identities=24% Similarity=0.444 Sum_probs=32.4
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
+.+.+.++|+||.|.++++.|+++|+|+.++..-|..
T Consensus 2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~ 38 (72)
T cd04883 2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSK 38 (72)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccC
Confidence 4577889999999999999999999999999766653
No 52
>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=95.86 E-value=0.022 Score=42.34 Aligned_cols=36 Identities=19% Similarity=0.352 Sum_probs=31.6
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
.+.+.++|+||.|.++++.|+++|+|+..+...+.+
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~ 38 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIR 38 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEee
Confidence 456778999999999999999999999999877653
No 53
>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-p
Probab=95.76 E-value=0.027 Score=37.54 Aligned_cols=44 Identities=30% Similarity=0.349 Sum_probs=34.7
Q ss_pred EEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC-CCceEEEec
Q 019548 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRK-RPLRVVDDS 333 (339)
Q Consensus 290 ~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~-~~w~~~~~~ 333 (339)
.+..+++||.|.++++.|+++|+|+.++.+.+... ....+++..
T Consensus 2 ~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~ 46 (60)
T cd02116 2 TVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGDGGEADIFIVV 46 (60)
T ss_pred EEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcCCCCeEEEEEEE
Confidence 46678999999999999999999999999877642 334444443
No 54
>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=95.75 E-value=0.03 Score=40.57 Aligned_cols=45 Identities=18% Similarity=0.238 Sum_probs=37.0
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC-CCCceEEEec
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQR-KRPLRVVDDS 333 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~-~~~w~~~~~~ 333 (339)
|.+..+|+||.|.++++.|+++|+|+..+.+.+.. .+.+.+.++-
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v 47 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDV 47 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEc
Confidence 56778999999999999999999999999998875 3455555554
No 55
>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=95.71 E-value=0.031 Score=39.97 Aligned_cols=36 Identities=22% Similarity=0.316 Sum_probs=31.5
Q ss_pred EEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCC
Q 019548 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR 325 (339)
Q Consensus 290 ~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~ 325 (339)
.+.++|+||.|.++++.|.++|+|+..+...+..+.
T Consensus 2 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~ 37 (56)
T cd04889 2 SVFVENKPGRLAEVTEILAEAGINIKAISIAETRGE 37 (56)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEccCC
Confidence 457899999999999999999999999988877633
No 56
>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=95.71 E-value=0.024 Score=42.13 Aligned_cols=46 Identities=17% Similarity=0.212 Sum_probs=36.8
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC-CCCCceEEEecC
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQ-RKRPLRVVDDSN 334 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~-~~~~w~~~~~~~ 334 (339)
+++..+|+||.|.++++.|+++|+|+..+.+.+. ......++++-+
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~ 48 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVD 48 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeC
Confidence 4567899999999999999999999999988776 344555555543
No 57
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=95.64 E-value=0.023 Score=44.49 Aligned_cols=45 Identities=13% Similarity=0.231 Sum_probs=37.2
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC-CCceEE
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK-RPLRVV 330 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~-~~w~~~ 330 (339)
|-+|.+.+.|+||.|.++++.|+.+|.|+..|.--|+.. ..++..
T Consensus 3 ~~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~~~srit 48 (76)
T PRK11152 3 QHQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDAQNINIE 48 (76)
T ss_pred eEEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCCCEEEEE
Confidence 456778889999999999999999999999999999753 334443
No 58
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=95.63 E-value=0.022 Score=44.62 Aligned_cols=39 Identities=15% Similarity=0.378 Sum_probs=34.6
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR 325 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~ 325 (339)
-+|.+-+.|+||.|.+++..|+++|.|+..|.--|+...
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 357777899999999999999999999999999988653
No 59
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.47 E-value=0.026 Score=42.46 Aligned_cols=42 Identities=31% Similarity=0.358 Sum_probs=34.2
Q ss_pred EEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEe
Q 019548 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDD 332 (339)
Q Consensus 290 ~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~ 332 (339)
.+.+|++||+|.++++.++. |.|.+.+.=|-...+.+++++.
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~~~~~v~v~ 43 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGGDEARVLVG 43 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCCCceEEEEE
Confidence 46789999999999999999 9999999776655555666543
No 60
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=95.28 E-value=0.046 Score=41.99 Aligned_cols=47 Identities=19% Similarity=0.415 Sum_probs=36.3
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC-CCCceEE
Q 019548 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR-KRPLRVV 330 (339)
Q Consensus 284 ~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~-~~~w~~~ 330 (339)
.+.+.|-+...|+||.|.++.+.+++.|+|+..+...+.+ .+.....
T Consensus 4 ~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~ 51 (80)
T PF13291_consen 4 SFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARIT 51 (80)
T ss_dssp -EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEE
T ss_pred EEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEE
Confidence 4578899999999999999999999999999999999985 4444433
No 61
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.00 E-value=0.06 Score=40.39 Aligned_cols=38 Identities=16% Similarity=0.196 Sum_probs=33.0
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCC
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRP 326 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~ 326 (339)
|.+..+|+||.|.++.+.+++.|+|+..++++..+.+.
T Consensus 2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~ 39 (74)
T cd04887 2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDY 39 (74)
T ss_pred EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCE
Confidence 56778999999999999999999999999998755333
No 62
>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=94.97 E-value=0.074 Score=39.39 Aligned_cols=43 Identities=23% Similarity=0.349 Sum_probs=35.6
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC-CCceEEE
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK-RPLRVVD 331 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~-~~w~~~~ 331 (339)
|.+...|+||.|.++++.|+++|+|+.++.+.|... +.+.+.+
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i 46 (79)
T cd04881 3 LRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGGETAPVVI 46 (79)
T ss_pred EEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEE
Confidence 456678999999999999999999999999887654 5555554
No 63
>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD. This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t
Probab=94.77 E-value=0.086 Score=38.59 Aligned_cols=49 Identities=16% Similarity=0.170 Sum_probs=38.0
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCC-CceEEEecCCC
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR-PLRVVDDSNNG 336 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~-~w~~~~~~~~~ 336 (339)
-|.+..+|+||.|+++.+.|+++|+|+..+...+..+. .-.|.++..++
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~~~~ 51 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDSDG 51 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEECCCC
Confidence 46678899999999999999999999999998877542 23344555543
No 64
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=94.73 E-value=0.078 Score=47.27 Aligned_cols=47 Identities=19% Similarity=0.346 Sum_probs=39.3
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC-CCCceEEEec
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR-KRPLRVVDDS 333 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~-~~~w~~~~~~ 333 (339)
-.|.+.++|+||.|.++.+.|+++|+|+..+-.-|+. ...+++.+..
T Consensus 3 ~~IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V 50 (161)
T PRK11895 3 HTLSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVT 50 (161)
T ss_pred EEEEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEE
Confidence 4567788999999999999999999999999988986 4556665554
No 65
>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=94.32 E-value=0.13 Score=38.56 Aligned_cols=34 Identities=29% Similarity=0.382 Sum_probs=30.8
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeee
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRP 321 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP 321 (339)
+|.+..+|+||.|.++++.+++.|+|+..+.+..
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~ 35 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNI 35 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCC
Confidence 5677889999999999999999999999998753
No 66
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=94.29 E-value=0.11 Score=46.09 Aligned_cols=45 Identities=20% Similarity=0.342 Sum_probs=37.6
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC-CCCceEEEe
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR-KRPLRVVDD 332 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~-~~~w~~~~~ 332 (339)
.|.+.++|+||.|.++.+.|+++|+|+..+-.-|+. .+..++.+.
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~ 48 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIV 48 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEE
Confidence 466788999999999999999999999999999986 455555443
No 67
>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=94.12 E-value=0.071 Score=39.27 Aligned_cols=43 Identities=26% Similarity=0.217 Sum_probs=34.9
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEe
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDD 332 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~ 332 (339)
|++...|+||.|.++++.|++.|+|+..+.+++.. +.+...++
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~-~~a~~~~~ 44 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRG-EIGYVVID 44 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCC-CEEEEEEE
Confidence 45677899999999999999999999999887754 55544444
No 68
>cd04926 ACT_ACR_4 C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the C-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=94.01 E-value=0.16 Score=38.60 Aligned_cols=38 Identities=18% Similarity=0.282 Sum_probs=32.9
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~ 324 (339)
|-|.+..+|+||.|+++.+.|+++|+|+......|..+
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 56777889999999999999999999998887776633
No 69
>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=93.87 E-value=0.18 Score=37.29 Aligned_cols=38 Identities=21% Similarity=0.245 Sum_probs=33.7
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~ 324 (339)
|-|.+..+|+||.|.++.+.|+++|+|+.++...+..+
T Consensus 1 ~~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~ 38 (70)
T cd04899 1 TVLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGE 38 (70)
T ss_pred CEEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCC
Confidence 44667789999999999999999999999999988764
No 70
>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=93.77 E-value=0.16 Score=35.57 Aligned_cols=34 Identities=24% Similarity=0.367 Sum_probs=30.3
Q ss_pred EEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 290 VFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 290 ~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
.+..+|+||.|.++++.|+++++|+..++..+..
T Consensus 2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~ 35 (71)
T cd04876 2 RVEAIDRPGLLADITTVIAEEKINILSVNTRTDD 35 (71)
T ss_pred EEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECC
Confidence 4567899999999999999999999999887654
No 71
>PRK08526 threonine dehydratase; Provisional
Probab=93.44 E-value=1.4 Score=44.60 Aligned_cols=182 Identities=19% Similarity=0.172 Sum_probs=93.0
Q ss_pred HHHHHHHhCCCCeEEEeeeccCccchhhhHHHhh--cCCeEEEEEEEEeee---eeeccCCCCCcCCccEEE----e---
Q 019548 131 DTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL--RHRLHIVGEVQLAAN---FCLLALPGIKADQLKRVL----S--- 198 (339)
Q Consensus 131 ~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~--~~~l~I~gEi~l~I~---h~Ll~~~g~~l~~I~~Vy----S--- 198 (339)
|+++.+ ++.|+-|+|+ ...|.+.-+...|. ..+.+|+|--.-.-. ..+-.........+.++. .
T Consensus 161 EI~eq~--~~~D~vvvpv--GgGGl~aGia~~~k~~~p~~kvigVep~~~~~~~~s~~~g~~~~~~~~~tiadgiav~~~ 236 (403)
T PRK08526 161 EMLDEI--SDLDMVVVPV--GGGGLISGIASAAKQINPNIKIIGVGAKGAPAMYESFHAKKIINSKSVRTIADGIAVRDA 236 (403)
T ss_pred HHHHhc--CCCCEEEEec--ChHHHHHHHHHHHHHhCCCCEEEEEEECCCChHHHHHHcCCcccCCCCCceeccccCCCC
Confidence 444444 3589999998 45677766666664 356777665432111 111111101122222221 1
Q ss_pred cHHHHHHHHHHHHhcCCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCceeeccccCCCCCeeeEEEEeeCCCC
Q 019548 199 HPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDPII 278 (339)
Q Consensus 199 Hpqal~QC~~~L~~~~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~il~~~IeD~~~N~TRF~vi~~~~~~ 278 (339)
-|..+..|++++++ +..++-....+|.+.+.+.. + -.+.+..|+-+-+|.--...+ ..+.+=-+|++-....
T Consensus 237 ~~~~~~~~~~~vd~--~v~V~d~ei~~A~~~l~~~~--g-i~ve~aga~~lAall~~~~~~---~~~~~Vv~ilsGGnid 308 (403)
T PRK08526 237 SPINLAIILECVDD--FVQVDDEEIANAILFLLEKQ--K-IVVEGAGAASVAALLHQKIDL---KKGKKIGVVLSGGNID 308 (403)
T ss_pred CHHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhc--C-cEeeHHHHHHHHHHHhCcccc---ccCCeEEEEECCCCCC
Confidence 16666666655442 22233344455566666531 1 222344444444442111111 1222222333322211
Q ss_pred CC--------C--CCCceEEEEEEecCCcchHHHHHHHHHhCCceeeeeee-eeCCC
Q 019548 279 PR--------T--DKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIES-RPQRK 324 (339)
Q Consensus 279 p~--------~--~~~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeS-RP~~~ 324 (339)
+. + ...-+..+.+.+||+||+|.++++.++..+.|++.|+= |....
T Consensus 309 ~~~~~~i~~~~l~~~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~~~ 365 (403)
T PRK08526 309 VQMLNIIIEKGLIKSYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFSTK 365 (403)
T ss_pred HHHHHHHHHHHHHhcCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEeccCC
Confidence 00 0 12236778889999999999999999999999999876 65444
No 72
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=93.22 E-value=0.24 Score=40.61 Aligned_cols=39 Identities=26% Similarity=0.416 Sum_probs=34.6
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~ 324 (339)
+-.|.+-+.|+||.|.++-+.|++||.|+..|-.=|+..
T Consensus 8 ~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~ 46 (96)
T PRK08178 8 NVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQD 46 (96)
T ss_pred CEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCC
Confidence 566778889999999999999999999999998777754
No 73
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=93.17 E-value=0.19 Score=40.17 Aligned_cols=38 Identities=8% Similarity=0.169 Sum_probs=33.8
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~ 324 (339)
-.|.+-+.|+||.|.++-+.|+++|+|+..|.-=|+-.
T Consensus 3 ~~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~ 40 (84)
T PRK13562 3 RILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQ 40 (84)
T ss_pred EEEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCC
Confidence 45667789999999999999999999999999888864
No 74
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=93.09 E-value=0.2 Score=42.71 Aligned_cols=47 Identities=19% Similarity=0.232 Sum_probs=37.7
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
.-+.+.++|+||+|.++++.|.+++||+-.|.-.-.+++.-=.+++.
T Consensus 70 dVlaVEmeD~PG~l~~I~~vl~d~diNldYiYAFv~ek~KAlli~r~ 116 (142)
T COG4747 70 DVLAVEMEDVPGGLSRIAEVLGDADINLDYIYAFVTEKQKALLIVRV 116 (142)
T ss_pred eEEEEEecCCCCcHHHHHHHHhhcCcCceeeeeeeecCceEEEEEEh
Confidence 34567889999999999999999999999998877766544444443
No 75
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=93.05 E-value=0.12 Score=38.64 Aligned_cols=38 Identities=26% Similarity=0.383 Sum_probs=29.4
Q ss_pred CCcchHHHHHHHHHhCCceeeeeeeeeCCC-CCceEEEe
Q 019548 295 EGPGVLFKALAVFALREINLTKIESRPQRK-RPLRVVDD 332 (339)
Q Consensus 295 ~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~-~~w~~~~~ 332 (339)
|+||.|.+++..|..+|+|+..|..-|+.. +.+++.+.
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~ 39 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDPGISRITIV 39 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEE
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEE
Confidence 689999999999999999999999999543 33444443
No 76
>PRK08198 threonine dehydratase; Provisional
Probab=92.67 E-value=0.87 Score=45.73 Aligned_cols=47 Identities=19% Similarity=0.208 Sum_probs=37.2
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeee-CC---CCCceEEEe
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP-QR---KRPLRVVDD 332 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP-~~---~~~w~~~~~ 332 (339)
...|.+.++|+||.|.++|+.+++.|.|++.|.-.+ .+ ...+++.+.
T Consensus 327 ~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~~~~~~~~~~~~v~v~ 377 (404)
T PRK08198 327 YLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDRFSPDLRLGEVEVELT 377 (404)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEEccCCCCCceEEEEEE
Confidence 568888999999999999999999999999987654 32 234555544
No 77
>PRK08639 threonine dehydratase; Validated
Probab=92.57 E-value=2.1 Score=43.48 Aligned_cols=37 Identities=19% Similarity=0.230 Sum_probs=29.8
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeee
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP 321 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP 321 (339)
-+..+.|.+|++||+|.++|+.....+-|++.|+-|.
T Consensus 335 r~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~~~~ 371 (420)
T PRK08639 335 LKHYFIVNFPQRPGALREFLDDVLGPNDDITRFEYLK 371 (420)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEEee
Confidence 3678889999999999999994444444999997765
No 78
>PRK06382 threonine dehydratase; Provisional
Probab=92.40 E-value=0.23 Score=50.08 Aligned_cols=49 Identities=16% Similarity=0.102 Sum_probs=40.1
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeee----eCCCCCceEEEec
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESR----PQRKRPLRVVDDS 333 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSR----P~~~~~w~~~~~~ 333 (339)
-++.|.+.++|+||.|.++++.|++.|+|+++|+-. |...+...++++.
T Consensus 329 ~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~~~~~~~~~~~~~~v~i~v 381 (406)
T PRK06382 329 QLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEVDNLRKETPPGFQSVTFTV 381 (406)
T ss_pred CEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEEeeccccCCCCcEEEEEEE
Confidence 377888899999999999999999999999999874 5555555665554
No 79
>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=92.39 E-value=0.23 Score=38.43 Aligned_cols=49 Identities=20% Similarity=0.158 Sum_probs=35.2
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeee--eeeeCCCCCceEEEecCCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKI--ESRPQRKRPLRVVDDSNNG 336 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkI--eSRP~~~~~w~~~~~~~~~ 336 (339)
|.|=+..+|+||-|+++.+.|++.|+++.+= .+.= ..-.--|||+..+|
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~G-erv~DvFyV~d~~g 52 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDG-GWFMDVFHVTDQLG 52 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecC-CeEEEEEEEECCCC
Confidence 4566778999999999999999999998653 2211 12335677766665
No 80
>PRK00194 hypothetical protein; Validated
Probab=92.10 E-value=0.21 Score=39.22 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=31.9
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeee
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP 321 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP 321 (339)
+-.+.+.-+|+||.+.++.+.|+++|+|+..+++.=
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~ 38 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTI 38 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHh
Confidence 456667779999999999999999999999998874
No 81
>TIGR01127 ilvA_1Cterm threonine dehydratase, medium form. A form of threonine dehydratase with two copies of the C-terminal domain Pfam:PF00585 is described by TIGR01124. This model describes a phylogenetically distinct form with a single copy of pfam00585. This form branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any pfam00585 domain. Many members of this model are found in species with other Ile biosynthetic enzymes.
Probab=91.72 E-value=0.37 Score=47.97 Aligned_cols=47 Identities=26% Similarity=0.278 Sum_probs=36.5
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeee---eC-CCCCceEEEe
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESR---PQ-RKRPLRVVDD 332 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSR---P~-~~~~w~~~~~ 332 (339)
+..|.+.++|+||.|.++++.+++.|.|.+.|.-+ +. ..+.+.+.+.
T Consensus 305 ~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~r~~~~~~~~~~~v~v~ 355 (380)
T TIGR01127 305 KVRIETVLPDRPGALYHLLESIAEARANIVKIDHDRLSKEIPPGFAMVEIT 355 (380)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeccccCCCCceEEEEEE
Confidence 34788899999999999999999999999999554 32 2345555554
No 82
>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=91.48 E-value=0.16 Score=39.93 Aligned_cols=25 Identities=28% Similarity=0.436 Sum_probs=21.6
Q ss_pred EEEEecCCcchHHHHHHHHHhCCce
Q 019548 289 IVFTLDEGPGVLFKALAVFALREIN 313 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gIN 313 (339)
+.+.+||+||+|.++|+.++..+||
T Consensus 4 l~v~ipD~PG~L~~ll~~l~~anI~ 28 (85)
T cd04906 4 LAVTIPERPGSFKKFCELIGPRNIT 28 (85)
T ss_pred EEEecCCCCcHHHHHHHHhCCCcee
Confidence 5678899999999999999966666
No 83
>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=91.36 E-value=0.28 Score=38.34 Aligned_cols=48 Identities=13% Similarity=0.152 Sum_probs=34.5
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceee--eeeeeeCCC-CCceEEEecCC
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLT--KIESRPQRK-RPLRVVDDSNN 335 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLt--kIeSRP~~~-~~w~~~~~~~~ 335 (339)
.|-+..+|+||-||++...|++.|+++. ||.|--... -.--||+++++
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv~~~g 52 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIVQSDG 52 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEEeCCC
Confidence 4557789999999999999999999975 555433333 23556675544
No 84
>cd04900 ACT_UUR-like_1 ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_UUR-like_1, includes the first of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD is the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted tyrosine kinase. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=91.29 E-value=0.7 Score=34.97 Aligned_cols=50 Identities=12% Similarity=0.115 Sum_probs=35.8
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC--CCCCceEEEecCCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ--RKRPLRVVDDSNNG 336 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~--~~~~w~~~~~~~~~ 336 (339)
+-|.+..+|+||-|+++-..|+.+|+|+..-..... ..-.--|+|...+|
T Consensus 2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~~~~ 53 (73)
T cd04900 2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDPDG 53 (73)
T ss_pred EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECCCC
Confidence 356677899999999999999999999987544333 32334555554444
No 85
>PRK04435 hypothetical protein; Provisional
Probab=91.17 E-value=0.58 Score=40.87 Aligned_cols=36 Identities=25% Similarity=0.279 Sum_probs=33.3
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeee
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESR 320 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSR 320 (339)
.+++|.+..+|+||.|.++++.+++.|+|+..|...
T Consensus 68 r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~ 103 (147)
T PRK04435 68 KIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQS 103 (147)
T ss_pred cEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEE
Confidence 378899999999999999999999999999999864
No 86
>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=91.13 E-value=0.29 Score=38.43 Aligned_cols=36 Identities=14% Similarity=0.136 Sum_probs=31.7
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 322 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~ 322 (339)
-.+.+..+|+||-++++.+.|+++|+|+..++..=.
T Consensus 2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~ 37 (88)
T cd04872 2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIM 37 (88)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhh
Confidence 456777899999999999999999999999987653
No 87
>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=90.94 E-value=0.37 Score=36.48 Aligned_cols=32 Identities=13% Similarity=0.245 Sum_probs=29.3
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeee
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESR 320 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSR 320 (339)
|.+..+|+||-+.++-+.|+++|+|+..+++.
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 34567999999999999999999999999988
No 88
>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=90.60 E-value=0.44 Score=36.15 Aligned_cols=35 Identities=23% Similarity=0.398 Sum_probs=31.4
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 322 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~ 322 (339)
.|.+...|++|.|.++++.|++.|+|+..+++++.
T Consensus 2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~ 36 (74)
T cd04877 2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK 36 (74)
T ss_pred EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC
Confidence 35667789999999999999999999999999875
No 89
>PRK08577 hypothetical protein; Provisional
Probab=90.55 E-value=1.6 Score=37.33 Aligned_cols=38 Identities=21% Similarity=0.378 Sum_probs=34.5
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
...|.+...|+||.|.++++.|+++|+|+..+.++...
T Consensus 56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~ 93 (136)
T PRK08577 56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELK 93 (136)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEec
Confidence 56777888999999999999999999999999988766
No 90
>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=89.30 E-value=12 Score=31.34 Aligned_cols=121 Identities=21% Similarity=0.128 Sum_probs=68.0
Q ss_pred CCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCccE-
Q 019548 118 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR- 195 (339)
Q Consensus 118 fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~- 195 (339)
|++.++.. ..+-.++.+.+.+|++|+|+++-.+...+... ..|.+.++.++ .+-.|-+.. ...+++++..
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~~~~~-~~~~~~~L~~~ 97 (200)
T cd08417 26 APGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGLRS---QPLFEDRFVCV----ARKDHPLAG-GPLTLEDYLAA 97 (200)
T ss_pred CCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccCCCccch---hhhhcCceEEE----ecCCCcccc-cccCHHHHhCC
Confidence 45554432 34567899999999999999975544333222 23444455444 333454433 2234444432
Q ss_pred --E-EecHH-HHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 196 --V-LSHPQ-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 196 --V-ySHpq-al~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
| +.+.. .......|+..++.. ...++|...+.+++..+ ...|+.+...++.
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08417 98 PHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGT---DLIATVPRRLAEA 155 (200)
T ss_pred CeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcC---CeeeeccHHHHHh
Confidence 2 33322 224456777766543 34456666666777664 4578888776654
No 91
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=89.26 E-value=0.39 Score=42.56 Aligned_cols=47 Identities=26% Similarity=0.504 Sum_probs=37.1
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeee-eeeeeCC---CCCceEEEe
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTK-IESRPQR---KRPLRVVDD 332 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtk-IeSRP~~---~~~w~~~~~ 332 (339)
+.+|.+.++|+||.|.++|++++..|.|+.. |+||--+ ..|-+.+++
T Consensus 5 ritldIEL~D~PGQLl~vLqPls~~g~NiItIiH~r~kk~g~r~pV~i~~~ 55 (170)
T COG2061 5 RITLDIELKDKPGQLLKVLQPLSKTGANIITIIHSRDKKYGPRVPVQIVFE 55 (170)
T ss_pred EEEEEEEecCCCcchhhhhcchhhcCccEEEEEeecCcccCCceeEEEEEE
Confidence 6788889999999999999999999999865 5788744 344444443
No 92
>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=88.33 E-value=0.69 Score=35.23 Aligned_cols=33 Identities=15% Similarity=0.192 Sum_probs=28.6
Q ss_pred EEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 291 FTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 291 ~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
+.-+|+||-++++-+.|+++|+|+..++++=..
T Consensus 4 v~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~ 36 (75)
T cd04870 4 VTGPDRPGLTSALTEVLAAHGVRILDVGQAVIH 36 (75)
T ss_pred EEcCCCCCHHHHHHHHHHHCCCCEEecccEEEc
Confidence 344899999999999999999999999766554
No 93
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=88.09 E-value=0.87 Score=41.82 Aligned_cols=83 Identities=17% Similarity=0.168 Sum_probs=57.3
Q ss_pred CceEEEEECCCCcHHHHHHHHhC-CC--------CccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhh--
Q 019548 96 TKVRISFKGLPGSFSEDAALKAY-PK--------CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL-- 164 (339)
Q Consensus 96 ~~~~VayLGP~GTfS~~AA~~~f-g~--------~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~-- 164 (339)
+..+|++-.|..+.++.+....+ .. ...++..+.++++.+|.+|++|.|+++ ..+++.+.
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 45799998776555577766655 22 244577899999999999999999987 34555443
Q ss_pred ----cCCeEEEEEEEEeeeeeeccCCC
Q 019548 165 ----RHRLHIVGEVQLAANFCLLALPG 187 (339)
Q Consensus 165 ----~~~l~I~gEi~l~I~h~Ll~~~g 187 (339)
..+++|.++...-..+.+++.++
T Consensus 175 ~~~~~~~~rvl~~s~~~p~~~~~~~~~ 201 (243)
T PF12974_consen 175 GPDIPSQLRVLWTSPPYPNWPLVASPD 201 (243)
T ss_dssp -HHHHTTEEEEEEEEEEE--EEEEETT
T ss_pred cCcccccEEEEEEeCCCCCcEEEEeCC
Confidence 35799999987766777777765
No 94
>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=87.72 E-value=22 Score=33.89 Aligned_cols=148 Identities=17% Similarity=0.125 Sum_probs=81.7
Q ss_pred CceEEEEE-CCCCcHHHHHHHHhCC----CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhc--CCe
Q 019548 96 TKVRISFK-GLPGSFSEDAALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLR--HRL 168 (339)
Q Consensus 96 ~~~~VayL-GP~GTfS~~AA~~~fg----~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~--~~l 168 (339)
..++|+++ ||....-+.+...+|. +++++.+.+..+..+++.+|++|.+.. +........... .++
T Consensus 18 ~~l~vG~~~~~~~~~~~~~~~~~~~~~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~-------q~~~~l~~~~~~~g~~l 90 (258)
T TIGR00363 18 LHIKVGVISGAEQQVAEVAAKVAKEKYGLDVELVEFNDYALPNEAVSKGDLDANAF-------QHKPYLDQDAKAKGYKL 90 (258)
T ss_pred CcEEEEeCCCChHHHHHHHHHHHHHhcCCEEEEEEeCCcHHHHHHHHcCCCCeEec-------CCHHHHHHHHHhCCCcE
Confidence 46999998 5554444555555553 368899999999999999999998653 222211222223 345
Q ss_pred EEEEEEEEeeeeeeccCCCCCcCCcc---EEEec--HHHHHHHHHHHHhcC-----------------------CeeEec
Q 019548 169 HIVGEVQLAANFCLLALPGIKADQLK---RVLSH--PQALASSDIVLTQLG-----------------------VARENV 220 (339)
Q Consensus 169 ~I~gEi~l~I~h~Ll~~~g~~l~~I~---~VySH--pqal~QC~~~L~~~~-----------------------~~~i~~ 220 (339)
.+++-..+ ....+.+.+-.+++|++ +|.-. |.-.++.-..|++.| +++++.
T Consensus 91 v~v~~~~~-~p~~~ys~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel 169 (258)
T TIGR00363 91 VAVGNTFV-YPLAGYSKKIKNVNELQDGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITEL 169 (258)
T ss_pred EEEeeeEE-ecccccCcCCCCHHHcCCCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEc
Confidence 56654322 11233444444667774 55433 333344445666532 344555
Q ss_pred CCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCce
Q 019548 221 DDTASAAQYVASNGLRDAGAVASARAAEIYGLNI 254 (339)
Q Consensus 221 ~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~i 254 (339)
.... .++.+.++ .-.||+....-+...||..
T Consensus 170 ~~~~-~~~al~~g--~vDaa~v~~~~~~~agl~~ 200 (258)
T TIGR00363 170 ETSQ-LPRALDDP--KVDLAVINTTYAGQVGLNP 200 (258)
T ss_pred CHHH-HHHHhhcc--cccEEEEChHHHHHcCCCc
Confidence 4433 33333332 1346666666666777763
No 95
>PRK06545 prephenate dehydrogenase; Validated
Probab=87.36 E-value=0.72 Score=45.69 Aligned_cols=41 Identities=15% Similarity=0.281 Sum_probs=35.0
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRP 326 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~ 326 (339)
-..+.+.+||+||.|..++..++..|||++.|+-...++..
T Consensus 290 ~~~~~v~v~d~pg~~~~~~~~~~~~~i~i~~~~i~~~~~~~ 330 (359)
T PRK06545 290 FYDLYVDVPDEPGVIARVTAILGEEGISIENLRILEAREDI 330 (359)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHcCCCeecceeeeccCCc
Confidence 45678889999999999999999999999999876665443
No 96
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=87.17 E-value=0.96 Score=34.66 Aligned_cols=36 Identities=19% Similarity=0.294 Sum_probs=26.5
Q ss_pred EEEEe--cCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 019548 289 IVFTL--DEGPGVLFKALAVFALREINLTKIESRPQRK 324 (339)
Q Consensus 289 i~~~~--~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~ 324 (339)
+++++ +|+||-++.+.+.++++|.|+..++-.-..+
T Consensus 3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~ 40 (76)
T PF13740_consen 3 LVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGG 40 (76)
T ss_dssp EEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETT
T ss_pred EEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcC
Confidence 44444 8999999999999999999998887665543
No 97
>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=87.07 E-value=1.8 Score=34.07 Aligned_cols=44 Identities=30% Similarity=0.275 Sum_probs=35.8
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEe
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDD 332 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~ 332 (339)
.+.|++|.+||||.+.|+.+. -+.|+|.++=|-.....+..++-
T Consensus 3 ~~~v~iPErpGal~~Fl~~l~-p~~~ITeF~YR~~~~~~a~vlvG 46 (81)
T cd04907 3 LFRFEFPERPGALKKFLNELL-PKWNITLFHYRNQGSDYGRVLVG 46 (81)
T ss_pred EEEEEcCCCCCHHHHHHHHhC-CCCeEeEEEEecCCCCceeEEEE
Confidence 467888999999999999994 37899999988776666666653
No 98
>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=86.74 E-value=2.1 Score=32.50 Aligned_cols=35 Identities=17% Similarity=0.403 Sum_probs=30.1
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
+.+..+|+||-+.++-+.|+++|+|+..+.+.-..
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~ 36 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYS 36 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence 44667899999999999999999999999875443
No 99
>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=86.52 E-value=1.2 Score=34.73 Aligned_cols=50 Identities=10% Similarity=0.197 Sum_probs=36.5
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceee--eeeeeeCCCCCceEEEecCCCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLT--KIESRPQRKRPLRVVDDSNNGT 337 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLt--kIeSRP~~~~~w~~~~~~~~~~ 337 (339)
|-|=+..+|+||-|+++...|++.|+++. +|.+- --.-.-.|||+..+|.
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~-gera~D~FyV~d~~g~ 53 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTD-GDDAHQEYYIRHKDGR 53 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeec-CceEEEEEEEEcCCCC
Confidence 44557789999999999999999999986 34331 1123467888777663
No 100
>PRK07334 threonine dehydratase; Provisional
Probab=86.35 E-value=1.8 Score=43.68 Aligned_cols=38 Identities=13% Similarity=0.245 Sum_probs=35.3
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 322 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~ 322 (339)
..+.|.+...|+||.|.++++.+++.++|+..+.++..
T Consensus 325 y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~ 362 (403)
T PRK07334 325 RLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRL 362 (403)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEec
Confidence 46899999999999999999999999999999998864
No 101
>PRK09224 threonine dehydratase; Reviewed
Probab=86.01 E-value=10 Score=39.59 Aligned_cols=44 Identities=18% Similarity=0.300 Sum_probs=34.0
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV 330 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~ 330 (339)
.+..+.+.+|++||+|.++++.+. +-|+|.++=|-.....=+++
T Consensus 327 re~~l~v~iPerPGaL~~f~~~l~--~~nItef~yr~~~~~~a~V~ 370 (504)
T PRK09224 327 REALLAVTIPEEPGSFLKFCELLG--GRNVTEFNYRYADAKEAHIF 370 (504)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhc--cCcEEEEEEEecCCCeEEEE
Confidence 367788999999999999999999 67888887665444443444
No 102
>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=85.52 E-value=21 Score=30.18 Aligned_cols=121 Identities=16% Similarity=0.094 Sum_probs=61.8
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCC-CCCcCCc-
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALP-GIKADQL- 193 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~-g~~l~~I- 193 (339)
.+++.++... .+-.++.+.+.+|++|+|+........+.... .|.+.++.+ ..+-+|-|.... ..+++|+
T Consensus 26 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~l~~~~~~~----v~~~~hpl~~~~~~i~~~dL~ 98 (203)
T cd08445 26 AAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRRI---VLREEPLVV----ALPAGHPLAQEKAPLTLAQLA 98 (203)
T ss_pred HCCCeEEEEEeCChHHHHHHHHcCCCcEEEecCCCCCCCceeE---EEEeccEEE----EeeCCCCCccCCCCcCHHHhc
Confidence 3566555433 34689999999999999997432111221111 111222222 223445454332 2333333
Q ss_pred --cEEEecHH---H-HHHHHHHHHhcCC--e-eEecCCHHHHHHHHHhcCCCCeEEecCHHHH
Q 019548 194 --KRVLSHPQ---A-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAA 247 (339)
Q Consensus 194 --~~VySHpq---a-l~QC~~~L~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~AA 247 (339)
.-|.-... . ..+..+|+.+.+. . ...++|...+.++++.+ ...++.+...+
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 158 (203)
T cd08445 99 DEPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAG---EGVTLVPASVQ 158 (203)
T ss_pred CCCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcC---CCeEEehHHhh
Confidence 33331111 1 2345567766543 2 24466666677777764 45777777654
No 103
>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=85.43 E-value=21 Score=29.93 Aligned_cols=123 Identities=15% Similarity=0.116 Sum_probs=64.0
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc--
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (339)
.|++.++.-. .+..++.+.+.+|++|+|+..-.....+.. ...|.+.++.++ .+-.|-|......+++++
T Consensus 26 ~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~ 98 (200)
T cd08411 26 AYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGLE---EEPLFDEPFLLA----VPKDHPLAKRKSVTPEDLAG 98 (200)
T ss_pred HCCCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCCCCCce---EEEeeccceEEE----ecCCCCccccCccCHHHHcC
Confidence 4566555433 467899999999999999975432222111 112222233222 222333322222222222
Q ss_pred -cEEE-ecH-HHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 194 -KRVL-SHP-QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 194 -~~Vy-SHp-qal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
..|. +.. ....+..+|+.+++.. ...++|...+..++..+ ...|+.+...++.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 157 (200)
T cd08411 99 ERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAG---LGITLLPELAVPS 157 (200)
T ss_pred CceEecCCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CCEEEeCHHHhcc
Confidence 2232 111 1234455566665432 35667777777777764 4588888887764
No 104
>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=85.10 E-value=2.3 Score=29.55 Aligned_cols=33 Identities=27% Similarity=0.321 Sum_probs=27.4
Q ss_pred EEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 291 FTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 291 ~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
+..++.||.+.++++.|+++|||+..|..-+..
T Consensus 6 ~~~~~~~~~~~~i~~~L~~~~i~i~~i~~~~~~ 38 (61)
T cd04891 6 KGVPDKPGVAAKIFSALAEAGINVDMIVQSVSR 38 (61)
T ss_pred ecCCCCCcHHHHHHHHHHHcCCcEEEEEEcCCC
Confidence 345789999999999999999999888664433
No 105
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=84.94 E-value=16 Score=34.37 Aligned_cols=144 Identities=13% Similarity=0.090 Sum_probs=77.8
Q ss_pred CCceEEEEECCCCc--HHHH--HHHHhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeE
Q 019548 95 GTKVRISFKGLPGS--FSED--AALKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (339)
Q Consensus 95 ~~~~~VayLGP~GT--fS~~--AA~~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~ 169 (339)
....+|+...+-+. +.+. ...+.++++++... .+.+++++.+.+|++|+||++......+... ..|.+.++.
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 45567777544332 1111 22345677665444 3689999999999999999976554443222 222233333
Q ss_pred EEEEEEEeeeeeeccCCCCCcCCc---cEEEecH-H-HHHHHHHHHHhcCC---eeEecCCHHHHHHHHHhcCCCCeEEe
Q 019548 170 IVGEVQLAANFCLLALPGIKADQL---KRVLSHP-Q-ALASSDIVLTQLGV---ARENVDDTASAAQYVASNGLRDAGAV 241 (339)
Q Consensus 170 I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp-q-al~QC~~~L~~~~~---~~i~~~STA~AA~~v~~~~~~~~AAI 241 (339)
++ .+-+|-+...+..+++|+ ..|...+ . -..+...|+..++. ....++|...+.++++.+ ...+|
T Consensus 167 ~~----~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~i 239 (305)
T PRK11151 167 LA----VYEDHPWANRDRVPMSDLAGEKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAG---SGITL 239 (305)
T ss_pred EE----ecCCCCcccCCccCHHHhcCCCeEeecCCccHHHHHHHHHHHCCCCCCceEEeccHHHHHHHHHcC---CCEEE
Confidence 32 233454443322333333 2232211 1 12345556655443 234577777777877764 56788
Q ss_pred cCHHHHH
Q 019548 242 ASARAAE 248 (339)
Q Consensus 242 as~~AA~ 248 (339)
.+...+.
T Consensus 240 lp~~~~~ 246 (305)
T PRK11151 240 LPALAVP 246 (305)
T ss_pred eeHHhhh
Confidence 8887664
No 106
>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=84.48 E-value=8.1 Score=35.42 Aligned_cols=137 Identities=15% Similarity=0.022 Sum_probs=72.6
Q ss_pred eEEEEECCCCcHH-HHHH-HHhCC------CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhh-cCCe
Q 019548 98 VRISFKGLPGSFS-EDAA-LKAYP------KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL-RHRL 168 (339)
Q Consensus 98 ~~VayLGP~GTfS-~~AA-~~~fg------~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~-~~~l 168 (339)
++|+|+.. +... ..|. ..+|. ++++++..+..++++++.+|++|+|++... .++.... ..++
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 47899865 3322 2332 23442 356788888889999999999999986432 1111112 2366
Q ss_pred EEEEEEEEeeeeeeccCCCC---CcCCcc--EEEecHH--HHHHHHHHHHhcCCe---e-EecCCHHHHHHHHHhcCCCC
Q 019548 169 HIVGEVQLAANFCLLALPGI---KADQLK--RVLSHPQ--ALASSDIVLTQLGVA---R-ENVDDTASAAQYVASNGLRD 237 (339)
Q Consensus 169 ~I~gEi~l~I~h~Ll~~~g~---~l~~I~--~VySHpq--al~QC~~~L~~~~~~---~-i~~~STA~AA~~v~~~~~~~ 237 (339)
.+++-..-.-..+++++++. +++|++ +|...+- ....-..+|.++++. . ....+.+++...+..+. .
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 66654442224555554432 233332 4543221 123444577666542 1 22245566666666652 3
Q ss_pred eEEecCHH
Q 019548 238 AGAVASAR 245 (339)
Q Consensus 238 ~AAIas~~ 245 (339)
.|++..+.
T Consensus 150 da~~~~~p 157 (288)
T TIGR01728 150 DAWAIWEP 157 (288)
T ss_pred CEEEeccc
Confidence 45555543
No 107
>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=82.41 E-value=3.8 Score=31.48 Aligned_cols=46 Identities=11% Similarity=0.158 Sum_probs=32.7
Q ss_pred EEEecCCcchHHHHHHHHHhCCceeee--eeeeeCCCCCceEEEecCC
Q 019548 290 VFTLDEGPGVLFKALAVFALREINLTK--IESRPQRKRPLRVVDDSNN 335 (339)
Q Consensus 290 ~~~~~~~pGaL~~iL~~Fa~~gINLtk--IeSRP~~~~~w~~~~~~~~ 335 (339)
-+..+|+||-|+++...|+.+|+|+.. |.+.+-..-.--|+|...+
T Consensus 4 ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~~ 51 (76)
T cd04927 4 KLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDAR 51 (76)
T ss_pred EEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCCC
Confidence 356689999999999999999999975 4433333334456664433
No 108
>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=82.13 E-value=21 Score=30.88 Aligned_cols=48 Identities=25% Similarity=0.262 Sum_probs=38.6
Q ss_pred eEEEEECCCCcHHHHHHHHhCC-CCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 98 VRISFKGLPGSFSEDAALKAYP-KCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 98 ~~VayLGP~GTfS~~AA~~~fg-~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
.+|++. .|++......+.+. ..+++.+.+.++++++|.+|++|+.+++
T Consensus 111 ~~i~~~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~ 159 (225)
T PF00497_consen 111 KRIGVV--RGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVD 159 (225)
T ss_dssp SEEEEE--TTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEE
T ss_pred cccccc--cchhHHHHhhhhccchhhhcccccHHHHHHHHhcCCeeeeecc
Confidence 578874 56666655555565 6788899999999999999999999986
No 109
>PLN02550 threonine dehydratase
Probab=81.99 E-value=11 Score=40.36 Aligned_cols=172 Identities=14% Similarity=0.126 Sum_probs=84.4
Q ss_pred CCCeEEEeeeccCccchhhhHHHhh--cCCeEEEEEEEEeee---eeeccCCCCCcCCccE----EEe---cHHHHHHHH
Q 019548 140 LADKAVLPIENSSSGSIHRNYDLLL--RHRLHIVGEVQLAAN---FCLLALPGIKADQLKR----VLS---HPQALASSD 207 (339)
Q Consensus 140 ~ad~gVVPiENS~~G~V~~tlDlL~--~~~l~I~gEi~l~I~---h~Ll~~~g~~l~~I~~----VyS---Hpqal~QC~ 207 (339)
..|+-|||+= ..|.+.-..-.+. ..+++|+|--.-.-. ..+.......++.+.+ +.. =++++.-|+
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 5899999984 5666666665554 356888775543211 1111111011121111 111 134555555
Q ss_pred HHHHhcCCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCceeeccccCCCCCeeeEEEEeeCCCCCC-------
Q 019548 208 IVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDPIIPR------- 280 (339)
Q Consensus 208 ~~L~~~~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~il~~~IeD~~~N~TRF~vi~~~~~~p~------- 280 (339)
+++.. +-.+......+|.+.+.+.. + .-+-+..|+-+.+|.-..+... .+ +.+=-+|++-......
T Consensus 336 ~~vD~--vV~Vsd~eI~~Ai~~l~e~~-g--ivvEpAGA~alAall~~~~~~~-~~-g~~Vv~vlsGgNid~~~l~~v~~ 408 (591)
T PLN02550 336 ELVDG--VVLVSRDAICASIKDMFEEK-R--SILEPAGALALAGAEAYCKYYG-LK-DENVVAITSGANMNFDRLRIVTE 408 (591)
T ss_pred hhCCE--EEEECHHHHHHHHHHHHHHC-C--CEEeHHHHHHHHHHHHHHHhcC-CC-CCeEEEEecCCCCCHHHHHHHHH
Confidence 54332 22333344566666666642 1 1222233344444433222111 11 2222223322211100
Q ss_pred ---CCCCceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 019548 281 ---TDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 322 (339)
Q Consensus 281 ---~~~~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~ 322 (339)
-...-+..+.+.+|++||+|.++++.+... |++.|+=|-.
T Consensus 409 ~~~~~~~r~~~~~v~ipd~pG~l~~~~~~l~~~--ni~~~~~~~~ 451 (591)
T PLN02550 409 LADVGRQQEAVLATFMPEEPGSFKRFCELVGPM--NITEFKYRYS 451 (591)
T ss_pred HHHhccCCEEEEEEEcCCCCCHHHHHHHHhhhh--cceEEEEEec
Confidence 011225677888999999999999999986 8898876643
No 110
>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=81.74 E-value=29 Score=28.80 Aligned_cols=123 Identities=15% Similarity=0.122 Sum_probs=62.5
Q ss_pred HhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeecc--CccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCC
Q 019548 116 KAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ 192 (339)
Q Consensus 116 ~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS--~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~ 192 (339)
+.|++.++.. ..+..++.+.+.+|++|+|++..... ..|... ..|.+.++.++ .+-+|-|...+..+++|
T Consensus 24 ~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~---~~l~~~~~~~~----~~~~~~l~~~~~~~~~d 96 (201)
T cd08435 24 ARHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLAS---EELADEPLVVV----ARPGHPLARRARLTLAD 96 (201)
T ss_pred HHCCCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCCCCcEE---EEcccCcEEEE----EeCCCcCcccCCcCHHH
Confidence 3466655433 34678999999999999999853221 122111 12223333332 33344444332233333
Q ss_pred cc---EEEecH-H-HHHHHHHHHHhcCCe----eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 193 LK---RVLSHP-Q-ALASSDIVLTQLGVA----RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 193 I~---~VySHp-q-al~QC~~~L~~~~~~----~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
+. -|..-+ . ......+|+...+.. ...+++...+.+++..+ ...|+.++..++
T Consensus 97 L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08435 97 LADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARS---DMLAVLPRSVAE 158 (201)
T ss_pred HhcCCEEecCCCCcHHHHHHHHHHHcCCCCCCceEEEccHHHHHHHHhcC---CeEEEeEHHHhh
Confidence 32 222111 1 112345556555432 23456666666666654 457888887765
No 111
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=81.42 E-value=3.8 Score=37.08 Aligned_cols=49 Identities=14% Similarity=0.219 Sum_probs=40.0
Q ss_pred ceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+||+. .|++......+.+++.+.+++++.++.+.+|.+|++|+.+.+
T Consensus 126 g~~Igv~--~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~grvDa~i~~ 174 (243)
T PRK15007 126 GKKVGVQ--NGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGD 174 (243)
T ss_pred CCeEEEe--cCcHHHHHHHHhCCCCeEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 4588884 677766666666777888899999999999999999999874
No 112
>PRK12483 threonine dehydratase; Reviewed
Probab=81.32 E-value=20 Score=37.77 Aligned_cols=35 Identities=26% Similarity=0.309 Sum_probs=30.7
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeee
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP 321 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP 321 (339)
-+..+.+.+|++||+|.++++.+... |++.++=+-
T Consensus 344 r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~~ 378 (521)
T PRK12483 344 REAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYRY 378 (521)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEEe
Confidence 36788899999999999999999988 888887764
No 113
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=80.75 E-value=2.5 Score=36.77 Aligned_cols=42 Identities=29% Similarity=0.420 Sum_probs=35.9
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHhCCceeeee-eeeeCCCC
Q 019548 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKI-ESRPQRKR 325 (339)
Q Consensus 284 ~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkI-eSRP~~~~ 325 (339)
....+|.+.+.|+.|.|.++|+..|+.++|...| ++-|..+.
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 4478999999999999999999999999998777 45676554
No 114
>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=80.51 E-value=34 Score=28.83 Aligned_cols=123 Identities=10% Similarity=0.007 Sum_probs=61.6
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcC---
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD--- 191 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~--- 191 (339)
+.|++.++.-. .+..++.+.+.+|++|+|++.-.....|... ..|.+.++. +..+-+|-+......+++
T Consensus 24 ~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----lv~~~~hpl~~~~~~~~~~L~ 96 (197)
T cd08452 24 KKFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALHI---ETVQSSPCV----LALPKQHPLASKEEITIEDLR 96 (197)
T ss_pred HHCCCcEEEEEecChHHHHHHHHCCCccEEEeeCCCCCCCeeE---EEeeeccEE----EEEeCCCccccCCCCCHHHhc
Confidence 34676554332 4678899999999999999853211111111 111222222 223445555432222222
Q ss_pred CccEEEecHH----HHHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 192 QLKRVLSHPQ----ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 192 ~I~~VySHpq----al~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
+..-|...+. ...+-.+|+.+.+.. . ..++|...+..+++.+ ...|+.+...+.
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 157 (197)
T cd08452 97 DEPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAG---IGVTFVPSSAKK 157 (197)
T ss_pred CCCEEeccCCcchhHHHHHHHHHHHcCCCccceeecccHHHHHHHHHcC---CCEEEchHHHhh
Confidence 3333332111 233444567665432 2 3456666666667654 357777776544
No 115
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=80.34 E-value=2.1 Score=39.14 Aligned_cols=36 Identities=19% Similarity=0.365 Sum_probs=30.4
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
.+.+.-+|+||-++++=+.|+++|||+..+.++=.+
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 344455899999999999999999999999998443
No 116
>cd08453 PBP2_IlvR The C-terminal substrate binding domain of LysR-type transcriptional regulator, IlvR, involved in the biosynthesis of isoleucine, leucine and valine; contains type 2 periplasmic binding fold. The IlvR is an activator of the upstream and divergently transcribed ilvD gene, which encodes dihydroxy acid dehydratase that participates in isoleucine, leucine, and valine biosynthesis. As in the case of other members of the LysR family, the expression of ilvR gene is repressed in the presence of its own gene product. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport
Probab=79.60 E-value=35 Score=28.54 Aligned_cols=123 Identities=13% Similarity=0.057 Sum_probs=62.4
Q ss_pred hCCCCccccCC-CHHHHHHHHHhCCCCeEEEeeeccCccchhhhH--HHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc
Q 019548 117 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNY--DLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (339)
Q Consensus 117 ~fg~~~~~~~~-si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tl--DlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (339)
.|++.++.... +..++.+.+.+|++|+|++.-.... .....+ ..|.+.++.+ .++-.|-+...+..+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~--~~~~~~~~~~l~~~~~~~----v~~~~hp~~~~~~i~~~~L 98 (200)
T cd08453 25 AYPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGA--SAPPALAYRPLLSEPLVL----AVPAAWAAEGGAPLALAAV 98 (200)
T ss_pred hCCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCccc--CCCcceeEEEeeeCceEE----EEECCCccccCCCCCHHHh
Confidence 35665554332 5678899999999999997532110 001111 1222333332 2344454443322333333
Q ss_pred ---cEEEe-cHH---HHHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 194 ---KRVLS-HPQ---ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 194 ---~~VyS-Hpq---al~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
.-|.. ... .......|+.+.+.. . ..++|...+.++++.+ ...++.+...++
T Consensus 99 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08453 99 AAEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAG---MGVALVPASLRN 160 (200)
T ss_pred ccCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcC---CcEEEeEhHHhh
Confidence 33332 211 234567788776543 2 3455555566666654 456777776543
No 117
>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=79.51 E-value=3.3 Score=31.76 Aligned_cols=33 Identities=15% Similarity=0.095 Sum_probs=28.7
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeee
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRP 321 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP 321 (339)
|.+.-||+||-.+++-+.++++|.|+..+...=
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 456679999999999999999999999886654
No 118
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=79.50 E-value=5 Score=36.31 Aligned_cols=31 Identities=26% Similarity=0.443 Sum_probs=28.2
Q ss_pred EEecCCcchHHHHHHHHHhCCceeeeeeeee
Q 019548 291 FTLDEGPGVLFKALAVFALREINLTKIESRP 321 (339)
Q Consensus 291 ~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP 321 (339)
+...||||-+.++=+-|..+||||-.++||-
T Consensus 97 v~a~DrpgIv~~~T~lf~~~~inie~L~~~~ 127 (176)
T COG2716 97 VDANDRPGIVEEFTALFDGHGINIENLVSRT 127 (176)
T ss_pred EEecCCccHHHHHHHHHHhcCCchhhceeee
Confidence 4558999999999999999999999999983
No 119
>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=78.16 E-value=34 Score=28.39 Aligned_cols=122 Identities=20% Similarity=0.093 Sum_probs=59.1
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc-
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (339)
.|++.++.-. .+-.++++.+.+|++|+|+++......+... ..|.+.++.+ ..+-.|-|...+..+++|+.
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----~~~~~~pl~~~~~~~~~dl~~ 97 (196)
T cd08450 25 EHPDLDVELSSLFSPQLAEALMRGKLDVAFMRPEIQSDGIDY---QLLLKEPLIV----VLPADHRLAGREKIPPQDLAG 97 (196)
T ss_pred hCCCcEEEEEecChHHHHHHHhcCCccEEEEeCCCCCCCcEE---EEEEccceEE----EecCCCCcccCceECHHHhCC
Confidence 4566655443 3567899999999999999754321111110 1111112211 22334444332212333332
Q ss_pred --EEE-ecHH--HHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 195 --RVL-SHPQ--ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 195 --~Vy-SHpq--al~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
-|. ++.. ...+-..|+.+.+.. ...++|...+..+++.+ ...++.+...+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 156 (196)
T cd08450 98 ENFISPAPTAPVLQQVIENYAAQHNIQPNIIQEADNLLSAMSLVAST---LGCALLPLYANN 156 (196)
T ss_pred CCeEeecCCCchHHHHHHHHHHHCCCCcEeeeeechHHHHHHHHhcC---CcEEEeehhhhh
Confidence 222 2221 123456677766543 23456666666666654 346666765443
No 120
>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=78.14 E-value=6.4 Score=33.22 Aligned_cols=49 Identities=24% Similarity=0.339 Sum_probs=38.8
Q ss_pred ceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+|++. .|+..+....+.++.....++.+.++++++|.+|++|+++++
T Consensus 105 g~~i~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 153 (218)
T cd00134 105 GKKVAVQ--KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVD 153 (218)
T ss_pred CCEEEEE--cCchHHHHHHHhCCcccEEEeCCHHHHHHHHHcCCccEEEec
Confidence 3578876 555555566666666778899999999999999999988875
No 121
>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=78.11 E-value=39 Score=28.15 Aligned_cols=123 Identities=14% Similarity=0.098 Sum_probs=61.7
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcC---
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD--- 191 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~--- 191 (339)
+.+++.++.-. .+..++.+.+.+|++|+|+.+-.....+... ..|.+.++.+ ..+-+|-+......+++
T Consensus 25 ~~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----v~~~~~pl~~~~~~~~~~l~ 97 (198)
T cd08446 25 TARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAV---ENVAQERLYL----AVPKSHPLAARPAVSLADLR 97 (198)
T ss_pred HHCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecCCCCCCcee---EEeeeccEEE----EEeCCCCcccCCccCHHHHc
Confidence 34666554332 3567888999999999999754322111111 1112222222 23334444322212222
Q ss_pred CccEEE-ecH---HHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 192 QLKRVL-SHP---QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 192 ~I~~Vy-SHp---qal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
+...|. .++ ....+...|+.+.+.. ...++|...+.++++.+ ...++.++..+.
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (198)
T cd08446 98 NEPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAG---FGVCIVPESVAA 158 (198)
T ss_pred CCCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcC---CcEEEchhhhhc
Confidence 333443 121 1123445666665432 24567777677777764 457777776543
No 122
>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=77.59 E-value=3.6 Score=31.29 Aligned_cols=35 Identities=26% Similarity=0.344 Sum_probs=28.6
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeC
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 322 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~ 322 (339)
.|-+..+|+||-|+++-+.|+.+|+|+..-.....
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~ 36 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTH 36 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEE
Confidence 34566789999999999999999999987555533
No 123
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=77.41 E-value=5.9 Score=35.79 Aligned_cols=49 Identities=10% Similarity=0.127 Sum_probs=40.2
Q ss_pred ceEEEEECCCCcHHHHHHHHhCC-CCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALKAYP-KCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg-~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+|++ ..|+..++....+++ +.+++.+.+.++++++|.+|++|+.|+.
T Consensus 131 g~~i~~--~~g~~~~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~ 180 (250)
T TIGR01096 131 GKTVGV--QSGTTHEQYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTD 180 (250)
T ss_pred CCEEEE--ecCchHHHHHHHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 357887 467777776666777 6778889999999999999999999974
No 124
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=76.59 E-value=9.6 Score=36.23 Aligned_cols=122 Identities=16% Similarity=0.021 Sum_probs=68.2
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCccE
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR 195 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~ 195 (339)
.+++.++... .+-.++++.+.+|++|+|+++.+-...+... ..|.+.++.++ .+-+|-|. ....+++|+..
T Consensus 137 ~~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~l~~---~~l~~~~~~lv----~~~~hpl~-~~~~~~~~L~~ 208 (314)
T PRK09508 137 IAPNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFTS---VPLFKDELVLV----ASKNHPRI-KGPITEEQLYN 208 (314)
T ss_pred hCCCcEEEEEeCcchhHHHHHhcCCccEEEecCCCCccccce---eeeecCceEEE----EcCCCCcc-CCCCCHHHHhh
Confidence 4566555433 3568899999999999999975422222111 12223333332 34455553 22234444431
Q ss_pred ----EEecHHHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 196 ----VLSHPQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 196 ----VySHpqal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
++.++....+...|+.+.+.. ...++|......++..+ ...++.+...++.
T Consensus 209 ~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 266 (314)
T PRK09508 209 EQHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQT---HLVAIAPRWLAEE 266 (314)
T ss_pred CCCEEecCCCCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhC---ChHHHHHHHHHHH
Confidence 233333334456777766532 34567777777777764 4577888877754
No 125
>cd04913 ACT_AKii-LysC-BS-like_1 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related proteins. This CD includes the N-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, and related sequences. In B. subtilis 168, the regulation of the diaminopimelate (Dap)-lysine biosynthetic pathway involves dual control by Dap and lysine, effected through separate Dap- and lysine-sensitive aspartokinase isoenzymes. The B. subtilis 168 AKII is induced by methionine and repressed and inhibited by lysine. Although Corynebacterium glutamicum is known to contain a single aspartokinase, both the succinylase and dehydrogenase variant pathways of DAP-lysine synthesis operate simultaneously in this organism. In corynebacteria and other various Gram-positive bacteria, the DAP-lysine pathway is fee
Probab=76.41 E-value=3.4 Score=30.01 Aligned_cols=29 Identities=28% Similarity=0.345 Sum_probs=25.0
Q ss_pred EEecCCcchHHHHHHHHHhCCceeeeeee
Q 019548 291 FTLDEGPGVLFKALAVFALREINLTKIES 319 (339)
Q Consensus 291 ~~~~~~pGaL~~iL~~Fa~~gINLtkIeS 319 (339)
+.+++.||.+.++++.|++.|||+--+..
T Consensus 7 ~~~~~~~g~~~~i~~~L~~~~I~i~~i~~ 35 (75)
T cd04913 7 RGVPDKPGVAAKIFGALAEANINVDMIVQ 35 (75)
T ss_pred CCCCCCCcHHHHHHHHHHHcCCeEEEEEe
Confidence 34578999999999999999999987643
No 126
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=76.31 E-value=3.6 Score=35.22 Aligned_cols=29 Identities=24% Similarity=0.308 Sum_probs=25.0
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeee
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKI 317 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkI 317 (339)
|.+-+.|+||-|.++++.++++|||+.-+
T Consensus 6 ISvFlENk~GRL~~~~~~L~eagINiRA~ 34 (142)
T COG4747 6 ISVFLENKPGRLASVANKLKEAGINIRAF 34 (142)
T ss_pred EEEEecCCcchHHHHHHHHHHcCCceEEE
Confidence 44556899999999999999999998654
No 127
>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=75.77 E-value=13 Score=38.76 Aligned_cols=186 Identities=17% Similarity=0.220 Sum_probs=91.4
Q ss_pred HHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhc--CCeEEEEEEEEeeee---eeccCCCCCcCCc---------cEE
Q 019548 131 DTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLR--HRLHIVGEVQLAANF---CLLALPGIKADQL---------KRV 196 (339)
Q Consensus 131 ~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~--~~l~I~gEi~l~I~h---~Ll~~~g~~l~~I---------~~V 196 (339)
|+++.+. +..|+-|+|+= ..|.+.-+.-.|.. .+.+|+|--...-.. .+-+.....++.+ +.+
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 36899999974 46666666555543 457777655422111 1111000111111 111
Q ss_pred EecHHHHHHHHHHHHhcCCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCceeeccccCCCCCeeeEEEEeeCC
Q 019548 197 LSHPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDP 276 (339)
Q Consensus 197 ySHpqal~QC~~~L~~~~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~il~~~IeD~~~N~TRF~vi~~~~ 276 (339)
=+.++.-|++++.. +..+......+|.+.+.+.. -.-+.+..|+-+.+|.-+.+... . .+.|=-+|++-..
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---RAVAEPAGALALAGLKKYVALHG-I-RGQTLVAILSGAN 305 (499)
T ss_pred --cHHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhc---CcEEechHHHHHHHHHHhhhhcC-C-CCCeEEEEECCCC
Confidence 13555555555432 12222233445555566531 12234444555555544332211 1 1233222332221
Q ss_pred CCCC----------CCCCceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE
Q 019548 277 IIPR----------TDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV 330 (339)
Q Consensus 277 ~~p~----------~~~~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~ 330 (339)
.... -.......+.+++|++||+|.++++.++.+ |+|.++=|-.....=+++
T Consensus 306 ~~~~~l~~~~~r~~~~~~re~~l~V~iPerPGal~~f~~~i~~~--nItef~yr~~~~~~a~v~ 367 (499)
T TIGR01124 306 MNFHRLRYVSERCELGEQREALLAVTIPEQPGSFLKFCELLGNR--NITEFNYRYADRKDAHIF 367 (499)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhhc--ceEEEEEEecCCCeEEEE
Confidence 1100 012236778899999999999999999974 888887775443333333
No 128
>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=75.37 E-value=52 Score=29.99 Aligned_cols=139 Identities=17% Similarity=0.170 Sum_probs=72.2
Q ss_pred CCceEEEEECCCCcHHHHHH---HHhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEE
Q 019548 95 GTKVRISFKGLPGSFSEDAA---LKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHI 170 (339)
Q Consensus 95 ~~~~~VayLGP~GTfS~~AA---~~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I 170 (339)
....+|++.++ .+--.+. .+.+++.++.- ..+..++++.+.+|++|+|++.......+... ..|.+.++.+
T Consensus 86 ~~~l~ig~~~~--~~~~~~l~~~~~~~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~l 160 (279)
T TIGR03339 86 EGSLRIAATAP--YYVLDLVARFRQRYPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLDR---VVLGNDPLVA 160 (279)
T ss_pred ceEEEEeCchH--HHHHHHHHHHHHHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEecccCCCceEE---EEcCCceEEE
Confidence 45678887643 1222221 22356655433 35788999999999999999854433222111 1122222222
Q ss_pred EEEEEEeeeeeeccCCCCCcCCc---cEEEecH--HHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEec
Q 019548 171 VGEVQLAANFCLLALPGIKADQL---KRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVA 242 (339)
Q Consensus 171 ~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp--qal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIa 242 (339)
+ .+-+|-|......+++|+ ..|...+ ........|+.+.+.. ...++|...+.+++..+ ...++.
T Consensus 161 v----~s~~~pl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~l 233 (279)
T TIGR03339 161 V----VHRQHPLAERESVTLEELAGQPLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAG---LGVSVV 233 (279)
T ss_pred E----ECCCCccccCCCcCHHHHhCCCeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcC---CCEEEc
Confidence 2 222343433222333333 3443222 2235677788776532 34567777777777664 345676
Q ss_pred CHH
Q 019548 243 SAR 245 (339)
Q Consensus 243 s~~ 245 (339)
+..
T Consensus 234 p~~ 236 (279)
T TIGR03339 234 SAA 236 (279)
T ss_pred chh
Confidence 664
No 129
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=75.36 E-value=4 Score=46.26 Aligned_cols=50 Identities=16% Similarity=0.125 Sum_probs=43.4
Q ss_pred CceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 96 TKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 96 ~~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
...+||. +.|++.+....+.+++.+++.+++.++++.+|.+|++|+.|.+
T Consensus 406 ~g~~vav--~~g~~~~~~~~~~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~ 455 (1197)
T PRK09959 406 KGMKVAI--PYYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDALVAT 455 (1197)
T ss_pred cCCEEEE--eCCcchHHHHHHHCCCcEEEEcCCHHHHHHHHHcCCCCEEehh
Confidence 3568888 6788878877888998999999999999999999999998864
No 130
>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=75.30 E-value=44 Score=28.38 Aligned_cols=140 Identities=12% Similarity=0.029 Sum_probs=70.9
Q ss_pred eEEEEECCCCcHHH-HH---HHHhCCCCccc-cCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEE
Q 019548 98 VRISFKGLPGSFSE-DA---ALKAYPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVG 172 (339)
Q Consensus 98 ~~VayLGP~GTfS~-~A---A~~~fg~~~~~-~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~g 172 (339)
.+||+-..-+++-= .+ -++.+++.++. -..+-.++.+.+.+|++|+|++.-..-..|.. ...+.+.++.+
T Consensus 3 l~Ig~~~~~~~~~l~~~l~~f~~~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~~~~~~---~~~l~~~~~~l-- 77 (198)
T cd08486 3 LSVAYFGTPIYRSLPLLLRAFLTSTPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGIE---IVNIAQEDLYL-- 77 (198)
T ss_pred EEEEEechhhHHHHHHHHHHHHHhCCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCCCCceE---EEEEeeccEEE--
Confidence 56776655443211 11 12346665543 23567899999999999999974321111111 01112222222
Q ss_pred EEEEeeeeeeccCCCCCcCCc---cEEEecH----HHHHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEec
Q 019548 173 EVQLAANFCLLALPGIKADQL---KRVLSHP----QALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVA 242 (339)
Q Consensus 173 Ei~l~I~h~Ll~~~g~~l~~I---~~VySHp----qal~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIa 242 (339)
.++-+|-+......+++|+ .-|.-.+ .-..+..+++.+.+.. . ..+++......+++.+ ...+|.
T Consensus 78 --v~~~~h~l~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~l 152 (198)
T cd08486 78 --AVHRSQSGKFGKTCKLADLRAVELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG---AASSIV 152 (198)
T ss_pred --EecCCCccccCCcccHHHHcCCCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---ceEEEc
Confidence 2344555543333344444 3343222 2345677777776533 2 3455555555566653 567777
Q ss_pred CHHHH
Q 019548 243 SARAA 247 (339)
Q Consensus 243 s~~AA 247 (339)
+..++
T Consensus 153 p~~~~ 157 (198)
T cd08486 153 PASVA 157 (198)
T ss_pred chhhc
Confidence 76543
No 131
>PF12727 PBP_like: PBP superfamily domain; InterPro: IPR024370 This entry represents members of the periplasmic binding domain superfamily []. It is often associated with a helix-turn-helix domain.
Probab=74.48 E-value=29 Score=31.47 Aligned_cols=130 Identities=21% Similarity=0.222 Sum_probs=74.5
Q ss_pred ccccCCCHHHHHHHHHhCCCCeEEEeeecc--CccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCC-----CCcCCc-
Q 019548 122 ETVPCDEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPG-----IKADQL- 193 (339)
Q Consensus 122 ~~~~~~si~~Vf~aV~~g~ad~gVVPiENS--~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g-----~~l~~I- 193 (339)
.+.+..|. +.+.++.+|.+|.+.+=+-.. -+-.+....++|...++.++.-.. =..-|+.+++ ..++|+
T Consensus 14 ~~~~~gS~-~gl~~L~~g~~~iAg~h~~~~~~~~~n~~~~~~~l~g~~~v~v~~~~--r~~Gl~v~~~np~~i~~~~dL~ 90 (193)
T PF12727_consen 14 AVQYTGSR-AGLSALARGEADIAGIHLPDPESGEYNIPFVRRLLPGIEVVLVRLAR--REQGLIVRPGNPKGITSLEDLA 90 (193)
T ss_pred EEEecCCH-HHHHHHHCCCceEEEecCCCCcccccchHHHHHhcCCCcEEEEeeeE--EeeeEEEeCCCCccCCCHHHhc
Confidence 34444444 446788899999998844332 222233333445454554432222 2244666665 234444
Q ss_pred --cEEEecHHHHHHHHHHHHhc----CC-----e--eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH-cCCceee
Q 019548 194 --KRVLSHPQALASSDIVLTQL----GV-----A--RENVDDTASAAQYVASNGLRDAGAVASARAAEI-YGLNILA 256 (339)
Q Consensus 194 --~~VySHpqal~QC~~~L~~~----~~-----~--~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~-ygL~il~ 256 (339)
...+--.|+=.=.|.+|+.. ++ . ...+.|..+.|..|+.+ ...++++.+.+|+. |||.++-
T Consensus 91 ~~~~r~vnR~~GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G--~AD~G~g~~~~A~~~~gL~Fvp 165 (193)
T PF12727_consen 91 DPGLRFVNRQPGSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASG--KADAGIGIRAAAEEFYGLDFVP 165 (193)
T ss_pred cCCcEEEECCCCCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcC--CCCEEeehHHHHHhhcCCCcEE
Confidence 22333444444456666542 22 1 13567777788888876 56799999999975 7998776
No 132
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=74.30 E-value=49 Score=31.61 Aligned_cols=108 Identities=18% Similarity=0.160 Sum_probs=63.9
Q ss_pred CceEEEEE-CCCCcHHHHHHHHhC---C-CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHH-Hhh--cCC
Q 019548 96 TKVRISFK-GLPGSFSEDAALKAY---P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYD-LLL--RHR 167 (339)
Q Consensus 96 ~~~~VayL-GP~GTfS~~AA~~~f---g-~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlD-lL~--~~~ 167 (339)
..++|+|. +|.....+.+...++ | +++++.+.+..+.++++.+|++|.... +. .+.++ .+. ..+
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 35899997 565544444444333 3 478899999999999999999998661 11 11222 222 245
Q ss_pred eEEEEEEEE-eeeeeeccCCCCCcCCcc---EEEec--HHHHHHHHHHHHhc
Q 019548 168 LHIVGEVQL-AANFCLLALPGIKADQLK---RVLSH--PQALASSDIVLTQL 213 (339)
Q Consensus 168 l~I~gEi~l-~I~h~Ll~~~g~~l~~I~---~VySH--pqal~QC~~~L~~~ 213 (339)
+.+++-..+ |+. +.+..=.+++|++ +|... |--.+..-.+|++.
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 777665443 432 2222223456664 56544 55566666677763
No 133
>PRK11260 cystine transporter subunit; Provisional
Probab=73.93 E-value=7.7 Score=35.97 Aligned_cols=48 Identities=8% Similarity=0.070 Sum_probs=39.4
Q ss_pred eEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 98 VRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 98 ~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
.+|+. ..|+..+....+.++..++..+++..+.+++|.+|++|+.|.+
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 6677666666667777788889999999999999999999874
No 134
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=73.02 E-value=4.6 Score=32.74 Aligned_cols=31 Identities=23% Similarity=0.352 Sum_probs=26.3
Q ss_pred EEEEe--cCCcchHHHHHHHHHhCCceeeeeee
Q 019548 289 IVFTL--DEGPGVLFKALAVFALREINLTKIES 319 (339)
Q Consensus 289 i~~~~--~~~pGaL~~iL~~Fa~~gINLtkIeS 319 (339)
.++++ +||||-.+.+-..|+++|+|+-.|+-
T Consensus 4 avITV~GkDr~GIva~is~vLAe~~vNIldisQ 36 (90)
T COG3830 4 AVITVIGKDRVGIVAAVSRVLAEHGVNILDISQ 36 (90)
T ss_pred EEEEEEcCCCCchhHHHHHHHHHcCCcEEEHHH
Confidence 34444 79999999999999999999998864
No 135
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=72.49 E-value=5.6 Score=45.05 Aligned_cols=49 Identities=12% Similarity=0.181 Sum_probs=42.6
Q ss_pred ceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+|+. +.|++.+...+++|++.+++.++|..+++++|.+|++|+.|..
T Consensus 164 ~~~i~~--~~g~~~~~~~~~~~p~~~i~~~~s~~~al~av~~G~~Da~i~~ 212 (1197)
T PRK09959 164 PVNIAR--VANYPPDEVIHQSFPKATIISFTNLYQALASVSAGQNDYFIGS 212 (1197)
T ss_pred CeEEEE--eCCCCCHHHHHHhCCCCEEEeCCCHHHHHHHHHcCCCCEEEcc
Confidence 356776 5588888888889999999999999999999999999998864
No 136
>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=72.38 E-value=9.2 Score=42.39 Aligned_cols=53 Identities=9% Similarity=-0.016 Sum_probs=43.0
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC-CCceEEEecCCCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK-RPLRVVDDSNNGT 337 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~-~~w~~~~~~~~~~ 337 (339)
+.|.|-+..+|+||-|+++.+.|+++|||+......-... ..--|+++...|.
T Consensus 778 ~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~g~ 831 (850)
T TIGR01693 778 KATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFGL 831 (850)
T ss_pred CeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCCCC
Confidence 4788889999999999999999999999999887766543 3456777665553
No 137
>PRK11480 tauA taurine transporter substrate binding subunit; Provisional
Probab=72.25 E-value=65 Score=30.95 Aligned_cols=142 Identities=12% Similarity=0.019 Sum_probs=74.3
Q ss_pred CCCceEEEEECCCCcHHHHHH-HHhC----C-CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCC
Q 019548 94 DGTKVRISFKGLPGSFSEDAA-LKAY----P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHR 167 (339)
Q Consensus 94 l~~~~~VayLGP~GTfS~~AA-~~~f----g-~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~ 167 (339)
...+.+|+|....+-| ..|- +.+| | +++++.+.+-.++.+++.+|++|+|+++.... ..-.....+
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 5678999998432212 2221 2234 2 37889999999999999999999997653211 111112335
Q ss_pred eEEEEEEEE-eeeeeeccCCCC-CcCCc--cEEEecHHH--HHHHHHHHHhcCC-----eeEecCCHHHHHHHHHhcCCC
Q 019548 168 LHIVGEVQL-AANFCLLALPGI-KADQL--KRVLSHPQA--LASSDIVLTQLGV-----ARENVDDTASAAQYVASNGLR 236 (339)
Q Consensus 168 l~I~gEi~l-~I~h~Ll~~~g~-~l~~I--~~VySHpqa--l~QC~~~L~~~~~-----~~i~~~STA~AA~~v~~~~~~ 236 (339)
+.+++-... .....++++++. +++|+ |+|...+-. ...-..||++.|. +.+... .++++..+..+ .-
T Consensus 93 ~~~v~~~~~~~~~~~lv~~~~I~s~~DLkGK~Iav~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~~-~~~~~~Al~~G-~V 170 (320)
T PRK11480 93 IEVFLLASKLGNSEALVVKKTISKPEDLIGKRIAVPFISTTHYSLLAALKHWGIKPGQVEIVNLQ-PPAIIAAWQRG-DI 170 (320)
T ss_pred eEEEEeeccCCcceEEEecCCCCChHHcCCCEEecCCCCchHHHHHHHHHHcCCCHhheEEEECC-cHHHHHHHHcC-Cc
Confidence 555433222 222456665442 33444 356543211 1223567877653 334433 34444545544 34
Q ss_pred CeEEecCHH
Q 019548 237 DAGAVASAR 245 (339)
Q Consensus 237 ~~AAIas~~ 245 (339)
+++++..+.
T Consensus 171 DAa~~~~p~ 179 (320)
T PRK11480 171 DGAYVWAPA 179 (320)
T ss_pred CEEEEcchH
Confidence 445554443
No 138
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=71.93 E-value=52 Score=30.60 Aligned_cols=123 Identities=12% Similarity=-0.008 Sum_probs=64.2
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcC---
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD--- 191 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~--- 191 (339)
+.|+++++... .+.+++++.+.+|++|+|+++-.....+.. ...|.+.++.++ .+-.|-|......+++
T Consensus 114 ~~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~l~---~~~l~~~~~~~v----~~~~~pl~~~~~i~~~~L~ 186 (296)
T PRK09906 114 LRHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDEID---YLELLDEPLVVV----LPVDHPLAHEKEITAAQLD 186 (296)
T ss_pred HHCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecCCCCCCCce---EEEEecccEEEE----ecCCCccccCCCcCHHHHc
Confidence 34666655433 357889999999999999986542111111 122233333332 3334444332222223
Q ss_pred CccEEEecH---HH-HHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 192 QLKRVLSHP---QA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 192 ~I~~VySHp---qa-l~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
+..-|.--+ .. ..+...|+...++. ...++|...+..+++.+ ...++.+...++
T Consensus 187 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g~~~~p~~~~~ 247 (296)
T PRK09906 187 GVNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG---LGCTIIPGYMNN 247 (296)
T ss_pred CCCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcEEEeeHHHhh
Confidence 333343211 12 34456777776543 24456666666777654 346666665543
No 139
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=71.67 E-value=8.8 Score=35.02 Aligned_cols=48 Identities=13% Similarity=0.054 Sum_probs=37.8
Q ss_pred ceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEE
Q 019548 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVL 146 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVV 146 (339)
..+|++ ..|+..+.-..+.+++.+++.+++.++++.+|.+|++|+.+.
T Consensus 131 g~~I~v--~~g~~~~~~l~~~~~~~~i~~~~~~~~~~~~L~~grvDa~i~ 178 (247)
T PRK09495 131 GKVVAV--KSGTGSVDYAKANIKTKDLRQFPNIDNAYLELGTGRADAVLH 178 (247)
T ss_pred CCEEEE--ecCchHHHHHHhcCCCCceEEcCCHHHHHHHHHcCceeEEEe
Confidence 347887 447766666666666677888999999999999999998885
No 140
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=71.51 E-value=4.3 Score=36.36 Aligned_cols=39 Identities=21% Similarity=0.470 Sum_probs=32.7
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~ 324 (339)
+-.+.+-+.|+||.|..+.+.|+.+|.|.-.|---|+-.
T Consensus 4 ~rilsvlv~ne~GvLsRv~glfsrRG~NIeSltv~~tE~ 42 (163)
T COG0440 4 RRILSLLVENEPGVLSRVTGLFSRRGYNIESLTVGPTET 42 (163)
T ss_pred eEEEEEEEECCCCeeehhhHHHHhcCcccceEEEEecCC
Confidence 445667778999999999999999999999887776643
No 141
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=71.26 E-value=11 Score=31.61 Aligned_cols=50 Identities=24% Similarity=0.329 Sum_probs=37.8
Q ss_pred ceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEee
Q 019548 97 KVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPI 148 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPi 148 (339)
..+|++.. |+........++...+..++.+..+++.+|.+|++|+++++-
T Consensus 106 g~~i~~~~--g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~ 155 (219)
T smart00062 106 GKKVAVVA--GTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADA 155 (219)
T ss_pred CCEEEEec--CccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEecc
Confidence 35788753 655555444445567788899999999999999999999863
No 142
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=71.11 E-value=56 Score=30.24 Aligned_cols=121 Identities=15% Similarity=0.054 Sum_probs=62.4
Q ss_pred CCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCC-CCcCC---
Q 019548 118 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPG-IKADQ--- 192 (339)
Q Consensus 118 fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g-~~l~~--- 192 (339)
|++..+... .+..++.+.+.+|++|+|+++.....++... ..|.+.++.+ ..+-+|-|...+. .++++
T Consensus 117 ~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~----~~~~~~pl~~~~~~i~~~~L~~ 189 (296)
T PRK11242 117 YPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA---QPLFTETLAL----VVGRHHPLAARRKALTLDELAD 189 (296)
T ss_pred CCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCCCCcceeE---EEeeeccEEE----EEcCCCcccccCCCcCHHHHhC
Confidence 466555443 4568899999999999999875543333222 1122223322 2233333332221 22222
Q ss_pred ccEEEecHHHH--HHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 193 LKRVLSHPQAL--ASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 193 I~~VySHpqal--~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
-..|.-.+... ..-..|+...+.. ...++|-..+.+++..+ ...++.++..+.
T Consensus 190 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 247 (296)
T PRK11242 190 EPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG---RLATLLPAAIAR 247 (296)
T ss_pred CCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhC---CeEEEeehhhcc
Confidence 23343333321 2334566665433 23456666666777764 356777776554
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=71.05 E-value=9.6 Score=38.62 Aligned_cols=36 Identities=19% Similarity=0.229 Sum_probs=29.7
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeee
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP 321 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP 321 (339)
+..+.|.+|++||+|.++|+.....+-|++.++-|.
T Consensus 325 ~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~y~~ 360 (409)
T TIGR02079 325 KHYFIVRFPQRPGALREFLNDVLGPNDDITRFEYTK 360 (409)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeee
Confidence 677889999999999999995555555999888775
No 144
>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=70.82 E-value=14 Score=33.72 Aligned_cols=51 Identities=16% Similarity=-0.040 Sum_probs=35.8
Q ss_pred ceEEEEECCCCcHHHHH----HHHhCC-C-----CccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDA----ALKAYP-K-----CETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~A----A~~~fg-~-----~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+|++.+|.++..+.. ..+..+ + ..+....++.+++.+|.+|++|.++.+
T Consensus 141 gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G~~Da~~~~ 201 (254)
T TIGR01098 141 GKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANGKVDAATNN 201 (254)
T ss_pred CCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcCCCCeEEec
Confidence 46899988765433332 223333 1 355667789999999999999999987
No 145
>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=70.71 E-value=4.6 Score=32.35 Aligned_cols=46 Identities=24% Similarity=0.286 Sum_probs=31.6
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEE
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVD 331 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~ 331 (339)
.+..+.|.+|.+||||.+.|+.+..+. |+|.++=|-.....-..++
T Consensus 9 ~E~~~~v~~PE~pGal~~F~~~l~~~~-nITeF~YR~~~~~~a~vlv 54 (91)
T PF00585_consen 9 REALFAVEFPERPGALKRFLDALGPRN-NITEFHYRYSGDDFARVLV 54 (91)
T ss_dssp -EEEEEEE--BSTTHCHHHHHCCSSSE--EEEEEEE-TTTSCSEEEE
T ss_pred CEEEEEEECCCCccHHHHHHHHhCCCc-eEEEEEEcCCCCCeeeEEE
Confidence 467788999999999999999887665 5888887766654444443
No 146
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=70.50 E-value=15 Score=33.81 Aligned_cols=144 Identities=15% Similarity=0.079 Sum_probs=76.7
Q ss_pred CceEEEEECCCCcHHHHHHHH--hCC----CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeE
Q 019548 96 TKVRISFKGLPGSFSEDAALK--AYP----KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (339)
Q Consensus 96 ~~~~VayLGP~GTfS~~AA~~--~fg----~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~ 169 (339)
.+++|+|+...+.+....|.. +|. +++++.+.+-.++.+++.+|++|++.+ ...+..+.-... .-...++.
T Consensus 6 ~~l~ig~~~~~~~~p~~~a~~~g~f~~~G~~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~--~~~~~~~~ 82 (252)
T PF13379_consen 6 TTLRIGYLPGPDYAPLYVAQEKGLFEKEGLDVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGA--GGPDVDIV 82 (252)
T ss_dssp SEEEEEETSSGGGHHHHHHHHTTHHHHTTSCEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTT--TT----EE
T ss_pred cEEEEEeecchHHHHHHHHHHcChHHHcCCEEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCC--CCcccceE
Confidence 468999985444444333432 342 368899999999999999999999998 432221110000 00012344
Q ss_pred EEEEEEEeeeeeeccCC------C-CCcCCc---------cEEEe-cHHH--HHHHHHHHHhcC------CeeEecCCHH
Q 019548 170 IVGEVQLAANFCLLALP------G-IKADQL---------KRVLS-HPQA--LASSDIVLTQLG------VARENVDDTA 224 (339)
Q Consensus 170 I~gEi~l~I~h~Ll~~~------g-~~l~~I---------~~VyS-Hpqa--l~QC~~~L~~~~------~~~i~~~STA 224 (339)
+.+-...-- ..++.+. + .+++|+ ++|.. ++-. .-..+.+|++++ ++++.+.. .
T Consensus 83 ~~~~~~~~g-~~lvv~~~~~~~~~~~~~~dl~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~ 160 (252)
T PF13379_consen 83 VLAGLSQNG-NALVVRNDLKDASDIKSLADLIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-P 160 (252)
T ss_dssp EEEECSBSS-EEEEECGGGTTCSTTCCGHHHHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-H
T ss_pred EeeccCCCc-eEEEEcCccccCCCccCHHHHHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-H
Confidence 443322111 2344442 2 244555 45665 5533 334678898753 34565666 7
Q ss_pred HHHHHHHhcCCCCeEEecCHH
Q 019548 225 SAAQYVASNGLRDAGAVASAR 245 (339)
Q Consensus 225 ~AA~~v~~~~~~~~AAIas~~ 245 (339)
++...+..+ .-+++++..+.
T Consensus 161 ~~~~al~~g-~iDa~~~~eP~ 180 (252)
T PF13379_consen 161 EMVAALRAG-EIDAAVLWEPF 180 (252)
T ss_dssp HHHHHHHTT-S-SEEEEETTH
T ss_pred HHHHHHhCC-CcCEEEecCCH
Confidence 777766665 34455554444
No 147
>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=70.32 E-value=11 Score=28.94 Aligned_cols=39 Identities=18% Similarity=0.298 Sum_probs=31.7
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
.++.||.+.++++.|+++|||.-.|-+ ......|.++..
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~VDmI~~---s~~~iSftv~~~ 49 (75)
T cd04932 11 MLHAQGFLAKVFGILAKHNISVDLITT---SEISVALTLDNT 49 (75)
T ss_pred CCCCcCHHHHHHHHHHHcCCcEEEEee---cCCEEEEEEecc
Confidence 578899999999999999999999965 225566666654
No 148
>PRK06349 homoserine dehydrogenase; Provisional
Probab=69.68 E-value=8.1 Score=39.35 Aligned_cols=44 Identities=25% Similarity=0.330 Sum_probs=34.5
Q ss_pred EEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEE
Q 019548 288 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVD 331 (339)
Q Consensus 288 si~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~ 331 (339)
-|.+.+.|+||.|.++-+.|++++||+..+...+..+..-++++
T Consensus 350 ylRl~v~d~pGvLa~I~~~f~~~~vsI~si~q~~~~~~~~~ivi 393 (426)
T PRK06349 350 YLRLLVADKPGVLAKIAAIFAENGISIESILQKGAGGEGAEIVI 393 (426)
T ss_pred EEEEEecCCcchHHHHHHHHhhcCccEEEEEeccCCCCceeEEE
Confidence 34456689999999999999999999999988876543334443
No 149
>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=69.61 E-value=63 Score=26.69 Aligned_cols=123 Identities=15% Similarity=0.060 Sum_probs=62.5
Q ss_pred HhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCc---C
Q 019548 116 KAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---D 191 (339)
Q Consensus 116 ~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l---~ 191 (339)
+.+++.++.- ..+-.++++.+.+|++|+|++.-.....|... ..|.+..+. +..+-.|-|...+..++ .
T Consensus 24 ~~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~---~~l~~~~~~----~~~~~~~~l~~~~~~~~~~l~ 96 (198)
T cd08412 24 EAYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIAF---EPLARLPPY----VWLPADHPLAGKDEVSLADLA 96 (198)
T ss_pred HHCCCcEEEEEECCHHHHHHHHHcCCCcEEEEcCCCCCcccce---eeeeccceE----EEecCCCCCCCCCcCCHHHHc
Confidence 3466654433 34678899999999999999854322222111 111122221 12333454443222222 2
Q ss_pred CccEEE-ecHHHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 192 QLKRVL-SHPQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 192 ~I~~Vy-SHpqal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
+...|. .......+-.+|+.+.+.. ...++|...+.+++..+ ...|+.+...++
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (198)
T cd08412 97 AEPLILLDLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANG---LGYSLLNDRPYR 154 (198)
T ss_pred CCcEEecCchhHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CCEEEeeccccc
Confidence 333333 2222223344566665543 23456666677777654 457788776654
No 150
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=69.55 E-value=40 Score=32.01 Aligned_cols=139 Identities=14% Similarity=0.028 Sum_probs=69.0
Q ss_pred CCCceEEEEECCCCcHHHHHHH-----HhCCC--CccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcC
Q 019548 94 DGTKVRISFKGLPGSFSEDAAL-----KAYPK--CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRH 166 (339)
Q Consensus 94 l~~~~~VayLGP~GTfS~~AA~-----~~fg~--~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~ 166 (339)
.....+|+|+.. ......+.. +.+++ .++++..+-.++++++.+|++|+|+.. ........-...
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 456789999632 222222221 12333 466777777899999999999999852 111111001123
Q ss_pred CeEEEEEEEE-eeeeeeccCCCC---CcCCc--cEEEecH--HHHHHHHHHHHhcCCe-----eEecCCHHHHHHHHHhc
Q 019548 167 RLHIVGEVQL-AANFCLLALPGI---KADQL--KRVLSHP--QALASSDIVLTQLGVA-----RENVDDTASAAQYVASN 233 (339)
Q Consensus 167 ~l~I~gEi~l-~I~h~Ll~~~g~---~l~~I--~~VySHp--qal~QC~~~L~~~~~~-----~i~~~STA~AA~~v~~~ 233 (339)
++.+++.... +-..+++.+++. +++|+ ++|...+ ........||++.+.. .+.. +..++...+..+
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 4555544322 222355555432 23333 2344322 1235566677776542 2333 445555555554
Q ss_pred CCCCeEEecC
Q 019548 234 GLRDAGAVAS 243 (339)
Q Consensus 234 ~~~~~AAIas 243 (339)
.-.|+++.
T Consensus 176 --~vDa~~~~ 183 (314)
T PRK11553 176 --NVDAWAIW 183 (314)
T ss_pred --CCCEEEEc
Confidence 23344443
No 151
>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=68.96 E-value=19 Score=34.24 Aligned_cols=53 Identities=25% Similarity=0.081 Sum_probs=40.3
Q ss_pred CCceEEEEECCCCcHHHHHHHHhC---C-CCccccCCCHHHHHHHHHhCCCCeEEEee
Q 019548 95 GTKVRISFKGLPGSFSEDAALKAY---P-KCETVPCDEFEDTFKAVELWLADKAVLPI 148 (339)
Q Consensus 95 ~~~~~VayLGP~GTfS~~AA~~~f---g-~~~~~~~~si~~Vf~aV~~g~ad~gVVPi 148 (339)
..+.+++..|+ |+.+|.++..++ | +.+.+|+++-.+...++..|++|.++...
T Consensus 104 p~~~~~g~~g~-g~~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~ 160 (274)
T PF03401_consen 104 PGKLTFGSSGP-GSSDHLAAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSP 160 (274)
T ss_dssp CCC-EEEESST-TSHHHHHHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEH
T ss_pred CCCeEEEecCC-CchHHHHHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecH
Confidence 45578888875 889998876554 3 36789999999999999999999998753
No 152
>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=67.60 E-value=51 Score=27.77 Aligned_cols=122 Identities=16% Similarity=0.099 Sum_probs=60.0
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK 194 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~ 194 (339)
+.+++.++... .+. +.++.+.+|++|+|+++-.....+... ..|.+.++.+ ..+-+|-+.. ...+++++.
T Consensus 24 ~~~P~i~l~i~~~~~-~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~----v~~~~hpl~~-~~~~~~~l~ 94 (200)
T cd08462 24 REAPGVRFELLPPDD-QPHELLERGEVDLLIAPERFMSDGHPS---EPLFEEEFVC----VVWADNPLVG-GELTAEQYF 94 (200)
T ss_pred HHCCCCEEEEecCCh-hHHHHHhcCCeeEEEecCCCCCCCcee---eeeeccceEE----EEcCCCCccC-CCCCHHHHh
Confidence 34666544333 244 999999999999999864322222111 1111122211 1244555543 223444443
Q ss_pred ---EEE-ecHHHH-HHHHH-HHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 195 ---RVL-SHPQAL-ASSDI-VLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 195 ---~Vy-SHpqal-~QC~~-~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
.|. +.+... ..-.+ |+.+++.. . ..++|......+++.+ ...||.++..++.
T Consensus 95 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~giailp~~~~~~ 155 (200)
T cd08462 95 SAGHVVVRFGRNRRPSFEDWFLNEYGLKRRVEVVTPSFSSIPPLLVGT---NRIATLHRRLAEQ 155 (200)
T ss_pred hCCCEEEecCCCCCccHHHHHHHHcCCcceEEEEeChHHHHHHHHHcC---chhhhhHHHHHHh
Confidence 121 111111 11222 33444543 2 3466666666777764 4688888877654
No 153
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=67.26 E-value=14 Score=30.22 Aligned_cols=47 Identities=9% Similarity=0.009 Sum_probs=37.3
Q ss_pred eEEEEECCCCcHHHHHHHHhCCC-----------CccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 98 VRISFKGLPGSFSEDAALKAYPK-----------CETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 98 ~~VayLGP~GTfS~~AA~~~fg~-----------~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
.+|+++ .||+.+..++++.+. .++..+++..+++.+|.+|+ |..+..
T Consensus 14 ~~vgv~--~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d 71 (134)
T smart00079 14 IEYGTI--RGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLME 71 (134)
T ss_pred ccceEe--cCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEee
Confidence 578885 799999888776543 25678899999999999999 866654
No 154
>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=66.87 E-value=74 Score=26.46 Aligned_cols=123 Identities=20% Similarity=0.127 Sum_probs=63.3
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc--
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (339)
.+++.++... .+..++.+.+.+|++|+|++.-.....+... ..|.+.++.++ .+-.|-+... ..+++|+
T Consensus 25 ~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~lv----~~~~~~~~~~-~~~~~~L~~ 96 (200)
T cd08466 25 LAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSFKS---ELLFEDELVCV----ARKDHPRIQG-SLSLEQYLA 96 (200)
T ss_pred HCCCCEEEEecCchHhHHHHHHcCCccEEEecccCCCCCcee---eeecccceEEE----EeCCCCCCCC-CcCHHHHhh
Confidence 4566655433 4677899999999999999742211111111 12223343333 2334444322 2344544
Q ss_pred -cEEEecHHH-HHHHHHHHHhcCC---e-eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHc
Q 019548 194 -KRVLSHPQA-LASSDIVLTQLGV---A-RENVDDTASAAQYVASNGLRDAGAVASARAAEIY 250 (339)
Q Consensus 194 -~~VySHpqa-l~QC~~~L~~~~~---~-~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~y 250 (339)
..+.-.+.. ..+-..|+.+.+. . ...++|.....++++.+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~~ 156 (200)
T cd08466 97 EKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQT---DLIAIAPRWLADQY 156 (200)
T ss_pred CCcEEecCCCCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCC---CeehhhHHHHHHHh
Confidence 223322221 1234556655543 2 24456666566666653 56788888776543
No 155
>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=66.81 E-value=70 Score=26.52 Aligned_cols=122 Identities=16% Similarity=0.080 Sum_probs=61.2
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCC-CCCcCCcc
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALP-GIKADQLK 194 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~-g~~l~~I~ 194 (339)
.+++.++.-. .+..++++.+.+|++|+|+.+-.....+... ..|.+.++.++ .+-.|-+.... ..+++|+.
T Consensus 26 ~~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~pl~~~~~~~~~~dL~ 98 (197)
T cd08425 26 RYPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDIDA---QPLFDERLALV----VGATHPLAQRRTALTLDDLA 98 (197)
T ss_pred HCCCcEEEEEECcHHHHHHHHHcCCccEEEEecCCCCCCcEE---EEeccccEEEE----ecCCCchhHhcccCCHHHHh
Confidence 3565544332 3567899999999999999864322222111 11222222222 23334443221 12333332
Q ss_pred ---EEE-ec-HHHHHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 195 ---RVL-SH-PQALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 195 ---~Vy-SH-pqal~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
-|. .. ........+|+.+.+.. . ..++|...+..+++.+ ...|+.+...++
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08425 99 AEPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRG---RLATILPDAIAR 157 (197)
T ss_pred cCCcEecCCCccHHHHHHHHHHHcCCCeeeEEeeCcHHHHHHHHhcC---CcEEeechhhhc
Confidence 232 11 11234456677766543 2 3456666666667664 457777776543
No 156
>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=66.42 E-value=74 Score=26.28 Aligned_cols=123 Identities=21% Similarity=0.210 Sum_probs=60.0
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeecc-CccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS-SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS-~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (339)
+.|++.++... .+-+++++.+.+|++|+|+++.... ..+... ..|.+.++.+ ..+-+|-|......+++|+
T Consensus 25 ~~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~---~~l~~~~~~~----v~~~~~~l~~~~~~~~~dL 97 (199)
T cd08451 25 EAYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGLVL---ELLLEEPMLV----ALPAGHPLARERSIPLAAL 97 (199)
T ss_pred HHCCCcEEEEecCChHHHHHHHHCCCccEEEEecCCCCCCceeE---EEeecccEEE----EecCCCCCcccCccCHHHh
Confidence 34666554333 3567899999999999999864322 111111 1122223222 2233455543322233333
Q ss_pred ---cEEE-ecHH---HHHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 194 ---KRVL-SHPQ---ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 194 ---~~Vy-SHpq---al~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
..|. +... ...+-..|+.+.+.. . ..++|...+..++..+ ...++.+...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 159 (199)
T cd08451 98 ADEPFILFPRPVGPGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAG---LGVSIVPASMRQ 159 (199)
T ss_pred cCCCEEEecCCcChhHHHHHHHHHHHcCCceeeEEehhhHHHHHHHHHcC---CCEEEechHHHh
Confidence 2332 1111 112334455555432 2 3455555555666553 457777776665
No 157
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=66.08 E-value=76 Score=26.34 Aligned_cols=111 Identities=18% Similarity=0.158 Sum_probs=60.4
Q ss_pred CccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCC---CcCCc--cE
Q 019548 121 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI---KADQL--KR 195 (339)
Q Consensus 121 ~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~---~l~~I--~~ 195 (339)
.++++. +..++++++.+|++|+++.+.....+. ...+... .......+.++.+++. +++|+ ++
T Consensus 41 ~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~-----~~~~~~~------~~~~~~~~~~~~~~~~~~~~~~dL~g~~ 108 (219)
T smart00062 41 VEFVEV-SFDNLLTALKSGKIDVVAAGMTITPER-----AKQVDFS------DPYYKSGQVILVRKDSPIKSLEDLKGKK 108 (219)
T ss_pred EEEEec-cHHHHHHHHHCCcccEEeccccCCHHH-----Hhheeec------cceeeceeEEEEecCCCCCChHHhCCCE
Confidence 577788 889999999999999999764321111 0111111 1111222444444432 22333 23
Q ss_pred EEecHHHHHHHHHHHHhc--CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHH
Q 019548 196 VLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAA 247 (339)
Q Consensus 196 VySHpqal~QC~~~L~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA 247 (339)
|..-+ . .-...++... +...+.+.+..++..++..+ ...|++.....+
T Consensus 109 i~~~~-g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~~~ 158 (219)
T smart00062 109 VAVVA-G-TTGEELLKKLYPEAKIVSYDSQAEALAALKAG--RADAAVADAPAL 158 (219)
T ss_pred EEEec-C-ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcC--cccEEEeccHHH
Confidence 33322 1 1234556554 56677788888888888765 234566555433
No 158
>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=65.94 E-value=13 Score=27.81 Aligned_cols=38 Identities=13% Similarity=0.120 Sum_probs=29.5
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
.++.||.+.++++.++++|||+-.| ++- .. ...|.++.
T Consensus 9 ~~~~~~~~a~if~~La~~~InvDmI-~~~-~~-~isFtv~~ 46 (67)
T cd04914 9 KDNENDLQQRVFKALANAGISVDLI-NVS-PE-EVIFTVDG 46 (67)
T ss_pred CCCCccHHHHHHHHHHHcCCcEEEE-Eec-CC-CEEEEEch
Confidence 4677999999999999999999999 554 11 45565554
No 159
>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=65.32 E-value=83 Score=26.52 Aligned_cols=141 Identities=13% Similarity=0.043 Sum_probs=68.1
Q ss_pred eEEEEECCCCcH--HHH--HHHHhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEE
Q 019548 98 VRISFKGLPGSF--SED--AALKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVG 172 (339)
Q Consensus 98 ~~VayLGP~GTf--S~~--AA~~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~g 172 (339)
.+|++...-+.+ ... +-.+.+++.++... .+-+++++.+.+|++|+|+++-.....|.... .+.+.++.+
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 566665444432 221 12334666665443 36778999999999999998532212222221 111222222
Q ss_pred EEEEeeeeeeccCCCCCcCCc---cEEE-ecHH---HHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEec
Q 019548 173 EVQLAANFCLLALPGIKADQL---KRVL-SHPQ---ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVA 242 (339)
Q Consensus 173 Ei~l~I~h~Ll~~~g~~l~~I---~~Vy-SHpq---al~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIa 242 (339)
..+-.|.+......+++|+ .-|. .++. ...+-.+|+.+.+.. ...++|......+++.+ ...||.
T Consensus 78 --~~~~~~~~~~~~~v~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~ 152 (198)
T cd08485 78 --GAQKSRARSFGEQVHCSALRNEPLILFPREGRPSFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAG---VGVTIV 152 (198)
T ss_pred --EeCCCCccccCCCcCHHHHhcCCeEecCCCCCccHHHHHHHHHHHcCCCcceEEEcCcHHHHHHHHHcC---CceEEC
Confidence 1223333322222333333 2332 2211 122333466655432 23456666666677764 456777
Q ss_pred CHHHHH
Q 019548 243 SARAAE 248 (339)
Q Consensus 243 s~~AA~ 248 (339)
++..++
T Consensus 153 p~~~~~ 158 (198)
T cd08485 153 PETVAM 158 (198)
T ss_pred cchhhc
Confidence 776544
No 160
>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=65.18 E-value=13 Score=28.54 Aligned_cols=40 Identities=15% Similarity=0.228 Sum_probs=32.0
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecCC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNN 335 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~~ 335 (339)
.++.||.+.++++.|+++|||.-.|-+ ......|.++.+.
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~vDmI~~---s~~~isftv~~~~ 50 (75)
T cd04935 11 MWQQVGFLADVFAPFKKHGVSVDLVST---SETNVTVSLDPDP 50 (75)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe---CCCEEEEEEeCcc
Confidence 467899999999999999999999966 2355677666554
No 161
>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=64.66 E-value=81 Score=26.12 Aligned_cols=122 Identities=18% Similarity=0.104 Sum_probs=62.2
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc--
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (339)
.+++.++... .+.+++.+.+.+|++|+|+..-+....+.. ...|.+.++.++ .+-.|-+...+..+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~hpl~~~~~~~~~~l~~ 97 (199)
T cd08426 25 RYPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIR---VHSRQPAPIGAV----VPPGHPLARQPSVTLAQLAG 97 (199)
T ss_pred hCCCeEEEEEeCCcHHHHHHHHCCCccEEEecCCCCCCCeE---EEeeccCcEEEE----ecCCCCcccCCccCHHHHhC
Confidence 3565544333 356889999999999999985432222211 111222232222 233444433222223332
Q ss_pred -cEEEecH--HHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 194 -KRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 194 -~~VySHp--qal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
..|.-.+ ........|+.+.+.. ...++|...+..++..+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (199)
T cd08426 98 YPLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAG---GGISLLTELAVR 155 (199)
T ss_pred CCeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcC---CCEEEEchHhhh
Confidence 3333221 1123455666665432 34567777777777764 457787876554
No 162
>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=63.58 E-value=67 Score=26.81 Aligned_cols=123 Identities=16% Similarity=0.158 Sum_probs=62.7
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc--
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (339)
.|+++++... .+..++.+.+.+|++|+|+.+......+.. ...|.+.++.+ ..+-+|-+...+ .+++++
T Consensus 25 ~~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~l~---~~~l~~~~~~~----v~~~~~~l~~~~-i~~~~L~~ 96 (201)
T cd08459 25 VAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAGFF---QQRLFRERYVC----LVRKDHPRIGST-LTLEQFLA 96 (201)
T ss_pred HCCCCeEEEEecCccCHHHHhhCCCceEEEEcCCCCcccce---EEEeecCceEE----EEcCCCccccCC-cCHHHHhh
Confidence 4566554433 345688899999999999986432111111 11122222222 234445443322 333333
Q ss_pred -cEEEecHH--HHHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHHHc
Q 019548 194 -KRVLSHPQ--ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAEIY 250 (339)
Q Consensus 194 -~~VySHpq--al~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~y 250 (339)
..|...+. ...+..+|+.+++.. . ..++|......+++.+ ...++.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~~ 156 (201)
T cd08459 97 ARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQT---DLVATVPERLARLF 156 (201)
T ss_pred CCcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcC---CEEEecHHHHHHHH
Confidence 23332221 123456777766543 2 3445555555666553 56888888776643
No 163
>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=63.13 E-value=42 Score=27.95 Aligned_cols=123 Identities=20% Similarity=0.167 Sum_probs=63.9
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc-
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (339)
.|+++++.-. .+-+++.+.+.+|++|+|++.......+... ..|.+.++.++. +-+|-+.. +..+++++.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~---~~l~~~~~~lv~----~~~~p~~~-~~~~~~~L~~ 96 (198)
T cd08461 25 EAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLRS---RPLFEERYVCVT----RRGHPLLQ-GPLSLDQFCA 96 (198)
T ss_pred HCCCcEEEEeeCCcccHHHHHhcCCCcEEEecCccCCcccee---eeeecCcEEEEE----cCCChhhc-CCCCHHHHhh
Confidence 4666555433 3456789999999999999864322222111 122233333322 33333322 122333322
Q ss_pred --EEEecHHH---HHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHc
Q 019548 195 --RVLSHPQA---LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEIY 250 (339)
Q Consensus 195 --~VySHpqa---l~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~y 250 (339)
-|.-++.. ..+-.+|+.+.+.. ...++|...+..++..+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~ 157 (198)
T cd08461 97 LDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAAT---DMVAFVPSRLVPNL 157 (198)
T ss_pred CCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcC---CeEEEchHHHHHhh
Confidence 33322211 13456677765532 24466666666777664 56888888877654
No 164
>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=63.07 E-value=12 Score=29.16 Aligned_cols=40 Identities=15% Similarity=0.257 Sum_probs=32.1
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecCC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNN 335 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~~ 335 (339)
.++.||.+.++++.|+++|||.-.|-+ ......|.++...
T Consensus 11 ~~~~~g~~a~IF~~La~~~InVDmI~q---s~~sISftV~~sd 50 (78)
T cd04933 11 MLGQYGFLAKVFSIFETLGISVDVVAT---SEVSISLTLDPSK 50 (78)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe---cCCEEEEEEEhhh
Confidence 467899999999999999999999966 2255677766543
No 165
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=62.84 E-value=14 Score=35.63 Aligned_cols=52 Identities=29% Similarity=0.234 Sum_probs=39.1
Q ss_pred CceEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEeee
Q 019548 96 TKVRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIE 149 (339)
Q Consensus 96 ~~~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiE 149 (339)
+..+||.-|+- |-++.-.+-++++.++++++ |+++..||.+|++|.||+-.|
T Consensus 94 ~~~rvavpG~~-TTA~lL~rl~~p~~~~V~m~-fdeI~~Avl~G~VDaGvlIHE 145 (272)
T COG2107 94 KGKRVAVPGEM-TTAALLFRLAYPKAEIVYMP-FDEIIPAVLEGKVDAGVLIHE 145 (272)
T ss_pred ccceEecCCcc-cHHHHHHHHhCCCceEEEee-HHHHHHHHHcCCCccceEEee
Confidence 35678877663 33455555567787777654 999999999999999999887
No 166
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=62.57 E-value=39 Score=31.45 Aligned_cols=48 Identities=10% Similarity=0.030 Sum_probs=32.9
Q ss_pred ceEEEEECCCCcHHHHHHHHhC----CCCccccCCCHHHHHHHHHhCCCCeEEE
Q 019548 97 KVRISFKGLPGSFSEDAALKAY----PKCETVPCDEFEDTFKAVELWLADKAVL 146 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~f----g~~~~~~~~si~~Vf~aV~~g~ad~gVV 146 (339)
..+|++ ..||..+....++. ...+++..++..+.+++|.+|++|..+.
T Consensus 148 g~~V~v--~~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~ 199 (259)
T PRK11917 148 GANIGV--AQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSV 199 (259)
T ss_pred CCeEEE--ecCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEe
Confidence 357888 45555443322222 2346678899999999999999997765
No 167
>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=62.44 E-value=16 Score=27.71 Aligned_cols=40 Identities=18% Similarity=0.298 Sum_probs=32.1
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecCC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNN 335 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~~ 335 (339)
+++.||.+.++++.|+++|||+-.+-+ ......|+++..+
T Consensus 11 l~~~~g~~~~if~~L~~~~I~v~~i~~---s~~~is~~v~~~~ 50 (75)
T cd04912 11 MLGAHGFLAKVFEIFAKHGLSVDLIST---SEVSVSLTLDPTK 50 (75)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEc---CCcEEEEEEEchh
Confidence 467899999999999999999988864 3466777776543
No 168
>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=61.97 E-value=90 Score=25.78 Aligned_cols=122 Identities=17% Similarity=0.060 Sum_probs=61.0
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc-
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (339)
.+++.++... .+-.++.+.+.+|++|+|+++-.-...+.. ...|.+.++.++ .+-.|-+...+..+++++.
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~ 97 (198)
T cd08421 25 AHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGLE---TRPYRTDRLVVV----VPRDHPLAGRASVAFADTLD 97 (198)
T ss_pred HCCCceEEEEecCcHHHHHHHhcCCceEEEEecCCCCCCcE---EEEeecCcEEEE----eCCCCCccccCCCCHHHhcC
Confidence 4566554332 466889999999999999985321111111 111222333222 2233433332223333332
Q ss_pred --EEEecHH--HHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 195 --RVLSHPQ--ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 195 --~VySHpq--al~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
-|.-.+. ...++.+++...+.. ...++|...+..+++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08421 98 HDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAG---LGIGIVPESAAR 155 (198)
T ss_pred CceEeecCCcchHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CCeEEccchhhh
Confidence 2321111 122344555554433 24566766677777664 457787776665
No 169
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=61.97 E-value=1.5e+02 Score=28.17 Aligned_cols=143 Identities=9% Similarity=0.032 Sum_probs=71.3
Q ss_pred CCceEEEEECCCCcH-HHHH---HHHhCCCCccc-cCCCHHHHHHHHHhCCCCeEEEeeec-cCccchhhhHHHhhcCCe
Q 019548 95 GTKVRISFKGLPGSF-SEDA---ALKAYPKCETV-PCDEFEDTFKAVELWLADKAVLPIEN-SSSGSIHRNYDLLLRHRL 168 (339)
Q Consensus 95 ~~~~~VayLGP~GTf-S~~A---A~~~fg~~~~~-~~~si~~Vf~aV~~g~ad~gVVPiEN-S~~G~V~~tlDlL~~~~l 168 (339)
....+|+.-..-+.+ --.. -.+.|++.++. ...+..++.+.|.+|++|+|+.+-.. ...+.. ..-|.+.++
T Consensus 92 ~g~l~Ig~~~~~~~~~l~~~i~~f~~~~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~l~---~~~l~~~~~ 168 (309)
T PRK12683 92 SGHLTVATTHTQARYALPKVVRQFKEVFPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDLV---SFPYYSWHH 168 (309)
T ss_pred CceEEEEeccchHHHHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCCce---EEEcccCeE
Confidence 456777773322211 1111 12335665543 33577899999999999999975321 112211 111222233
Q ss_pred EEEEEEEEeeeeeeccCCCCCcCCc---cEEEecH--HHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEE
Q 019548 169 HIVGEVQLAANFCLLALPGIKADQL---KRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGA 240 (339)
Q Consensus 169 ~I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp--qal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AA 240 (339)
. +..+.+|-|...+..+++++ .-|.-.+ .-..+...|+.+.+.. ...++|......++..+ ...+
T Consensus 169 ~----~v~~~~hpl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~ 241 (309)
T PRK12683 169 V----VVVPKGHPLTGRENLTLEAIAEYPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELG---MGVG 241 (309)
T ss_pred E----EEecCCCCcccCCccCHHHHhcCCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhC---CCeE
Confidence 2 33555666654333333333 3343211 1235677788776543 23355555555666654 3355
Q ss_pred ecCHHHH
Q 019548 241 VASARAA 247 (339)
Q Consensus 241 Ias~~AA 247 (339)
+.+...+
T Consensus 242 ~lp~~~~ 248 (309)
T PRK12683 242 IVAAMAY 248 (309)
T ss_pred Eeehhhc
Confidence 5555443
No 170
>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=61.56 E-value=98 Score=26.02 Aligned_cols=122 Identities=11% Similarity=0.052 Sum_probs=63.5
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeee-ccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCc---C
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIE-NSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---D 191 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiE-NS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l---~ 191 (339)
.|+++++.-. .+-+++.+.+.+|++|+|+..-. ....+.. ...|.+.++ .+..+..|-|......++ .
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~~l~~~~~----~~~~~~~hpl~~~~~~~~~~l~ 97 (198)
T cd08444 25 QFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPELV---SFPYYDWHH----HIIVPVGHPLESITPLTIETIA 97 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEeccccCCCcCcE---Eeeccccce----eEEecCCCccccCCCcCHHHHh
Confidence 4676554333 46678999999999999997421 0011111 011111121 133455565543222233 3
Q ss_pred CccEEEecHH-H-HHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 192 QLKRVLSHPQ-A-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 192 ~I~~VySHpq-a-l~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
+..-|.-++. . -.++..|+.+.+.. ...++|...+.+++..+ ...++.+...++
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08444 98 KWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLG---MGIGIVAEMAFE 156 (198)
T ss_pred CCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcC---CcEEeccHHHHh
Confidence 3444543332 2 24567787776542 34566666666777664 457777776554
No 171
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=61.20 E-value=58 Score=33.54 Aligned_cols=48 Identities=17% Similarity=0.178 Sum_probs=35.3
Q ss_pred eEEEEECCCCcHHHHHHHH---hCCCC--ccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 98 VRISFKGLPGSFSEDAALK---AYPKC--ETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 98 ~~VayLGP~GTfS~~AA~~---~fg~~--~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
.+|++ +.||..++...+ .+++. ..+.+.+.++++++|.+|++|+.|+.
T Consensus 150 k~I~V--~~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d 202 (482)
T PRK10859 150 GTLTV--AAGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIAD 202 (482)
T ss_pred CeEEE--ECCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEEC
Confidence 57877 467766655443 34543 34567899999999999999999874
No 172
>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=61.16 E-value=1.2e+02 Score=28.21 Aligned_cols=145 Identities=19% Similarity=0.200 Sum_probs=71.7
Q ss_pred CCCceEEEEECCCCc-HHHHH---HHHhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccC--ccchhhhHHHhhcC
Q 019548 94 DGTKVRISFKGLPGS-FSEDA---ALKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRH 166 (339)
Q Consensus 94 l~~~~~VayLGP~GT-fS~~A---A~~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~--~G~V~~tlDlL~~~ 166 (339)
.....+|+...+-+. +--.. -.+.|++..+... .+-.++.+++.+|++|+|++...+.. .+... .-|.+.
T Consensus 91 ~~~~l~I~~~~~~~~~~~~~~l~~~~~~~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~~---~~l~~~ 167 (300)
T TIGR02424 91 EGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGLSF---EHLYNE 167 (300)
T ss_pred CCceEEEecccHHHHhhhHHHHHHHHHhCCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCcccccceee---eeecCC
Confidence 455677776533221 11111 1234666555433 36688999999999999997543321 11111 112222
Q ss_pred CeEEEEEEEEeeeeeeccCCCCCcCCccE--EEecHHH---HHHHHHHHHhcCCe----eEecCCHHHHHHHHHhcCCCC
Q 019548 167 RLHIVGEVQLAANFCLLALPGIKADQLKR--VLSHPQA---LASSDIVLTQLGVA----RENVDDTASAAQYVASNGLRD 237 (339)
Q Consensus 167 ~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~--VySHpqa---l~QC~~~L~~~~~~----~i~~~STA~AA~~v~~~~~~~ 237 (339)
++.++ .+-.|-|...+..+++|+.. .+..+.. ......|+.+++.. ...+.|......++..+ .
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 33222 23334444333223333321 2222221 13445677765432 24566666666777664 4
Q ss_pred eEEecCHHHHH
Q 019548 238 AGAVASARAAE 248 (339)
Q Consensus 238 ~AAIas~~AA~ 248 (339)
..++.+...++
T Consensus 241 gi~~lp~~~~~ 251 (300)
T TIGR02424 241 AIWIISRGVVA 251 (300)
T ss_pred ceEeCcHHHHh
Confidence 46777776664
No 173
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=60.94 E-value=1.2e+02 Score=28.98 Aligned_cols=142 Identities=15% Similarity=0.152 Sum_probs=73.7
Q ss_pred CceEEEEECCCCcHHH----HHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEE
Q 019548 96 TKVRISFKGLPGSFSE----DAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIV 171 (339)
Q Consensus 96 ~~~~VayLGP~GTfS~----~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~ 171 (339)
...+|++...-+.+-= .+..+.++++++... +..++++.+.+|++|+|+.+......+... ..|.+.++.+
T Consensus 117 ~~l~Ig~~~~~~~~~l~~~l~~f~~~~P~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~l- 191 (317)
T PRK11482 117 RTITIATTPSVGALVMPVIYQAIKTHYPQLLLRNI-PISDAENQLSQFQTDLIIDTHSCSNRTIQH---HVLFTDNVVL- 191 (317)
T ss_pred ceEEEEecHHHHHHHHHHHHHHHHHHCCCCEEEEe-cchhHHHHHHCCCcCEEEeccCCCCCceEE---EEEecCcEEE-
Confidence 3466666544333211 112334566655432 345789999999999999876543333322 1222333333
Q ss_pred EEEEEeeeeeeccCCCCCcCCccE----E-EecHHHHHHHHHHHHhc--CCee-EecCCHHHHHHHHHhcCCCCeEEecC
Q 019548 172 GEVQLAANFCLLALPGIKADQLKR----V-LSHPQALASSDIVLTQL--GVAR-ENVDDTASAAQYVASNGLRDAGAVAS 243 (339)
Q Consensus 172 gEi~l~I~h~Ll~~~g~~l~~I~~----V-ySHpqal~QC~~~L~~~--~~~~-i~~~STA~AA~~v~~~~~~~~AAIas 243 (339)
.++-.|-|... ..+++|+.. + ...+......++++... .... ..+.|......+++.+ ...+|.+
T Consensus 192 ---v~~~~hpl~~~-~~~~~dL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~ilp 264 (317)
T PRK11482 192 ---VCRQGHPLLSL-EDDEETLDNAEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASS---DMLGIMP 264 (317)
T ss_pred ---EEeCCCCccCC-CCCHHHHhhCCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcC---CeeEEeH
Confidence 24555666543 345566552 2 22222212344555553 2222 3455555566666653 5678888
Q ss_pred HHHHHH
Q 019548 244 ARAAEI 249 (339)
Q Consensus 244 ~~AA~~ 249 (339)
...+..
T Consensus 265 ~~~~~~ 270 (317)
T PRK11482 265 SRFYNL 270 (317)
T ss_pred HHHHHH
Confidence 877654
No 174
>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=59.97 E-value=12 Score=27.01 Aligned_cols=41 Identities=17% Similarity=0.212 Sum_probs=31.2
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
.++.||.+.++++.|++.|||+-.|..=+ ....-.|+++.+
T Consensus 11 ~~~~~~~~~~if~~L~~~~I~v~~i~q~~-s~~~isf~v~~~ 51 (66)
T cd04919 11 MKNMIGIAGRMFTTLADHRINIEMISQGA-SEINISCVIDEK 51 (66)
T ss_pred CCCCcCHHHHHHHHHHHCCCCEEEEEecC-ccceEEEEEeHH
Confidence 35689999999999999999998885422 345666666654
No 175
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=59.81 E-value=36 Score=37.26 Aligned_cols=43 Identities=16% Similarity=0.183 Sum_probs=36.7
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCC
Q 019548 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRP 326 (339)
Q Consensus 284 ~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~ 326 (339)
...+.|.+...|++|.|.++...+++.++|+..+.++..+++.
T Consensus 624 ~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~~ 666 (702)
T PRK11092 624 EFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGRV 666 (702)
T ss_pred eeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCCE
Confidence 3567788888999999999999999999999999987655433
No 176
>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=59.11 E-value=1.1e+02 Score=25.68 Aligned_cols=124 Identities=19% Similarity=0.098 Sum_probs=68.3
Q ss_pred HhCCCCccc-cCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc-
Q 019548 116 KAYPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 193 (339)
Q Consensus 116 ~~fg~~~~~-~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I- 193 (339)
+.+++.++. -..+..++.+.+.+|++|+|+.+..-...|... ..|.+..+ -+..+-+|-|......+++|+
T Consensus 30 ~~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~----~~~~~~~~pl~~~~~i~~~dL~ 102 (209)
T PF03466_consen 30 ERHPNIRIEIREGDSDELIEALRSGELDLAITFGPPPPPGLES---EPLGEEPL----VLVVSPDHPLAQKKPITLEDLA 102 (209)
T ss_dssp HHSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSSSSTTEEE---EEEEEEEE----EEEEETTSGGGTTSSSSGGGGT
T ss_pred HHCCCcEEEEEeccchhhhHHHhcccccEEEEEeecccccccc---ccccceee----eeeeeccccccccccchhhhhh
Confidence 346665442 335558999999999999999976642222111 00111111 112233333443333334444
Q ss_pred --cEEEec--HHHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 194 --KRVLSH--PQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 194 --~~VySH--pqal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
..|.-. ..-..+..+|+.+++.. ...++|...+..++..+ ...+|.+...+..
T Consensus 103 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 162 (209)
T PF03466_consen 103 DYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASG---DGIAILPDSLAQD 162 (209)
T ss_dssp TSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTT---SEBEEEEHHHHHH
T ss_pred hccccccccccccccccccccccccccccccccccchhhhccccccc---cceeecCcccccc
Confidence 334322 22346666777776653 24567777777777764 5788888887743
No 177
>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=59.09 E-value=29 Score=29.92 Aligned_cols=122 Identities=19% Similarity=0.155 Sum_probs=69.5
Q ss_pred HHHHHHhCC-CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCC-
Q 019548 111 EDAALKAYP-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI- 188 (339)
Q Consensus 111 ~~AA~~~fg-~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~- 188 (339)
.+++.+. | +.++++. ++..++.++++|++|.++-++.. |.+.- ..+.... -+....+.++.+++.
T Consensus 30 ~~i~~~~-g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~--------~~~r~--~~~~~s~-p~~~~~~~~~~~~~~~ 96 (225)
T PF00497_consen 30 RAIAKRL-GIKIEFVPM-PWSRLLEMLENGKADIIIGGLSI--------TPERA--KKFDFSD-PYYSSPYVLVVRKGDA 96 (225)
T ss_dssp HHHHHHH-TCEEEEEEE-EGGGHHHHHHTTSSSEEESSEB---------BHHHH--TTEEEES-ESEEEEEEEEEETTST
T ss_pred HHHHhhc-ccccceeec-ccccccccccccccccccccccc--------ccccc--ccccccc-cccchhheeeeccccc
Confidence 3444443 3 4678888 99999999999999987744443 22221 1222222 122334555554331
Q ss_pred ----C---cCCc--cEEEecHHHHHHHHHHHHh-c--CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 189 ----K---ADQL--KRVLSHPQALASSDIVLTQ-L--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 189 ----~---l~~I--~~VySHpqal~QC~~~L~~-~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
. ++++ ++|..-.-.. -.+||.+ . +++.+.+.|..++.+++..+ .-.|+|.....+..
T Consensus 97 ~~~~~~~~~~dl~~~~i~~~~g~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~i~~~~~~~~ 165 (225)
T PF00497_consen 97 PPIKTIKSLDDLKGKRIGVVRGSS--YADYLKQQYPSNINIVEVDSPEEALEALLSG--RIDAFIVDESTAEY 165 (225)
T ss_dssp CSTSSHSSGGGGTTSEEEEETTSH--HHHHHHHHTHHTSEEEEESSHHHHHHHHHTT--SSSEEEEEHHHHHH
T ss_pred cccccccchhhhcCcccccccchh--HHHHhhhhccchhhhcccccHHHHHHHHhcC--Ceeeeeccchhhhh
Confidence 1 2244 2343333222 1223433 1 67788899999999998876 35588877776654
No 178
>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=59.07 E-value=18 Score=25.82 Aligned_cols=41 Identities=22% Similarity=0.369 Sum_probs=31.5
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
.++.||.+.++++.|++.|||+-.|..=+ ......|+++.+
T Consensus 11 ~~~~~~~~~~i~~~l~~~~I~v~~i~~~~-s~~~is~~v~~~ 51 (66)
T cd04922 11 MAGTPGVAATFFSALAKANVNIRAIAQGS-SERNISAVIDED 51 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEecC-cccEEEEEEeHH
Confidence 46789999999999999999998885422 346666776653
No 179
>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=58.65 E-value=12 Score=26.33 Aligned_cols=38 Identities=24% Similarity=0.324 Sum_probs=30.0
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
.++.||.+.++++.+++.|||+-.|.+.+ ....|+++.
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~s~---~~is~~v~~ 47 (63)
T cd04936 10 MRSHPGVAAKMFEALAEAGINIEMISTSE---IKISCLIDE 47 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEccC---ceEEEEEeH
Confidence 56789999999999999999998887432 445566654
No 180
>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=58.63 E-value=19 Score=33.63 Aligned_cols=49 Identities=20% Similarity=0.133 Sum_probs=37.8
Q ss_pred ceEEEEECCCCcHHHHHHHHh-CCCCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALKA-YPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~-fg~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+|+. +.|++.+....+. +...+++.+++.++++++|.+|++|+.|..
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 357876 6677777665543 344577889999999999999999988874
No 181
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=58.36 E-value=1.2e+02 Score=29.30 Aligned_cols=146 Identities=15% Similarity=0.086 Sum_probs=77.0
Q ss_pred CCCceEEEEECCCCcHH-HHH---HHHhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCe
Q 019548 94 DGTKVRISFKGLPGSFS-EDA---ALKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRL 168 (339)
Q Consensus 94 l~~~~~VayLGP~GTfS-~~A---A~~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l 168 (339)
.....+|++...-+++- -.+ -.+.++++++... .+.+++++++.+|++|+||++-.....+... ...|.+.++
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 34567888866555432 111 1234566665443 3568999999999999999863221111100 011222333
Q ss_pred EEEEEEEEeeeeeeccC-CCCCcCCc---cEEEecH-HHH-HHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeE
Q 019548 169 HIVGEVQLAANFCLLAL-PGIKADQL---KRVLSHP-QAL-ASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAG 239 (339)
Q Consensus 169 ~I~gEi~l~I~h~Ll~~-~g~~l~~I---~~VySHp-qal-~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~A 239 (339)
. +.++..|-|... ....++|+ .-|..-+ ... ....+|+..++.. ...++|.....+++..+ ...
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 235666766542 22333333 3333222 222 4466778776543 24556666667777664 346
Q ss_pred EecCHHHHH
Q 019548 240 AVASARAAE 248 (339)
Q Consensus 240 AIas~~AA~ 248 (339)
|+.+..++.
T Consensus 242 a~lp~~~~~ 250 (327)
T PRK12680 242 GLLAEMAVN 250 (327)
T ss_pred EEeechhcc
Confidence 666665544
No 182
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=58.29 E-value=69 Score=28.90 Aligned_cols=145 Identities=14% Similarity=0.092 Sum_probs=71.4
Q ss_pred CCceEEEEECCCCc--HHH--HHHHHhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeE
Q 019548 95 GTKVRISFKGLPGS--FSE--DAALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (339)
Q Consensus 95 ~~~~~VayLGP~GT--fS~--~AA~~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~ 169 (339)
....+|++-..-+. ++. ....+.|+++++.. ..+.+++.+.+.+|++|+|++...+...+.+. ...|...++.
T Consensus 66 ~~~l~I~~~~~~~~~~~~~~l~~~~~~~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~--~~~l~~~~~~ 143 (269)
T PRK11716 66 SGELSLFCSVTAAYSHLPPILDRFRAEHPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVA--FSPIDEIPLV 143 (269)
T ss_pred CceEEEEecchHHHHHHHHHHHHHHHHCCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcceE--EEEcccceEE
Confidence 45567775443322 122 11233466655543 35778999999999999999864432222111 1122233433
Q ss_pred EEEEEEEeeeeeeccCC----CCCcCCccEEEe-cHHHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEe
Q 019548 170 IVGEVQLAANFCLLALP----GIKADQLKRVLS-HPQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAV 241 (339)
Q Consensus 170 I~gEi~l~I~h~Ll~~~----g~~l~~I~~VyS-Hpqal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAI 241 (339)
++ .+-+|.+.... -.++.+..-|.. .......-..|+..++.. ...++|......++..+ ...++
T Consensus 144 ~v----~~~~~~~~~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~ 216 (269)
T PRK11716 144 LI----APALPCPVRQQLSQEKPDWSRIPFILPEHGPARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALG---CGVGL 216 (269)
T ss_pred EE----EcCCcchhhhccccchhhHhhCCeeecCCCchHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcC---CCeEe
Confidence 32 23334332211 112333333331 111112234566665432 23456666566666654 45788
Q ss_pred cCHHHHH
Q 019548 242 ASARAAE 248 (339)
Q Consensus 242 as~~AA~ 248 (339)
.+...++
T Consensus 217 ~p~~~~~ 223 (269)
T PRK11716 217 LPEVVLE 223 (269)
T ss_pred ccHHHhh
Confidence 8887665
No 183
>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=58.16 E-value=1.1e+02 Score=25.69 Aligned_cols=123 Identities=14% Similarity=0.092 Sum_probs=60.5
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK 194 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~ 194 (339)
+.+++.++.-. .+..++.+.+.+|++|+|+.+-.-.....+. ...|.+.++.++ .+-+|-+......+++++.
T Consensus 24 ~~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~~~v----~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08443 24 ERYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLI--TLPCYHWNRCVV----VKRDHPLADKQSISIEELA 97 (198)
T ss_pred HHCCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccccccCCce--EeeeeeceEEEE----EcCCCccccCCCCCHHHHh
Confidence 34676554433 4678899999999999999742100011110 011222222222 3334544433223333333
Q ss_pred E--EEecHH--H-HHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHH
Q 019548 195 R--VLSHPQ--A-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAA 247 (339)
Q Consensus 195 ~--VySHpq--a-l~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA 247 (339)
. ..+++. . ...-..|+.+++.. ...++|.....++++.+ ...|+.+...+
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~~p~~~~ 155 (198)
T cd08443 98 TYPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLG---LGVGVIASMAY 155 (198)
T ss_pred cCCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CcEEEeecccc
Confidence 1 222222 2 23344566655543 34567777777777764 34666666544
No 184
>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=57.00 E-value=12 Score=27.27 Aligned_cols=40 Identities=13% Similarity=0.306 Sum_probs=31.2
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecCC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNN 335 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~~ 335 (339)
+.+.||.+.++++.|++.|||+..+-. ....-.++++.++
T Consensus 11 ~~~~~gi~~~if~aL~~~~I~v~~~~~---Se~~is~~v~~~~ 50 (64)
T cd04937 11 IRGVPGVMAKIVGALSKEGIEILQTAD---SHTTISCLVSEDD 50 (64)
T ss_pred ccCCcCHHHHHHHHHHHCCCCEEEEEc---CccEEEEEEcHHH
Confidence 457899999999999999999976553 4556667776554
No 185
>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=56.98 E-value=19 Score=24.24 Aligned_cols=38 Identities=24% Similarity=0.292 Sum_probs=29.1
Q ss_pred CCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 295 EGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 295 ~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
+.||.+.++++.|++++||+..+..-+. +....|+++.
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~~~~~-~~~~s~~v~~ 49 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMISQSES-EVNISFTVDE 49 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEEcCCC-cEEEEEEEeH
Confidence 5799999999999999999998876543 3344555543
No 186
>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=56.94 E-value=88 Score=25.60 Aligned_cols=122 Identities=15% Similarity=0.122 Sum_probs=62.5
Q ss_pred hCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcC---C
Q 019548 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD---Q 192 (339)
Q Consensus 117 ~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~---~ 192 (339)
.+++.++.. ..+..++.+.+.+|++|+|++.......+... ..|.+.++.++ .+-.|-+......+++ +
T Consensus 25 ~~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~~~~~~~~i~~~~l~~ 97 (201)
T cd08420 25 RYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIV---EPFAEDELVLV----VPPDHPLAGRKEVTAEELAA 97 (201)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEecCCCCCcceEE---EeecCccEEEE----ecCCCCccccCccCHHHHhc
Confidence 356654432 34667899999999999999865433222111 11222333322 2233434322222233 3
Q ss_pred ccEEEecHH--HHHHHHHHHHhcC-----Ce-eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 193 LKRVLSHPQ--ALASSDIVLTQLG-----VA-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 193 I~~VySHpq--al~QC~~~L~~~~-----~~-~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
...|.-.+. -..+...|+...+ .. ...+++...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08420 98 EPWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAG---LGISILSRLAVR 158 (201)
T ss_pred CCEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcC---CCEEEeeHHHHH
Confidence 333332221 1234556666432 12 34566777777777764 457888877654
No 187
>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=56.79 E-value=32 Score=26.29 Aligned_cols=36 Identities=14% Similarity=0.256 Sum_probs=29.3
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 324 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~ 324 (339)
|++..+|+||-+..+-+.|+.+|+|.-.=....+++
T Consensus 4 I~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~d 39 (68)
T cd04928 4 ITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDD 39 (68)
T ss_pred EEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCC
Confidence 566778999999999999999999998755544443
No 188
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=56.51 E-value=1.8e+02 Score=27.46 Aligned_cols=119 Identities=14% Similarity=0.108 Sum_probs=58.9
Q ss_pred CCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccC--ccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc-
Q 019548 118 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 193 (339)
Q Consensus 118 fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~--~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I- 193 (339)
+++.++.- ..+-++++++|.+|++|+|+++..+.. .+... ..|.+.++.++ .+-+|-+. . ..+++|+
T Consensus 123 ~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~~---~~l~~~~~~lv----~~~~~pl~-~-~i~~~dL~ 193 (312)
T PRK10341 123 FPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDLHV---EPLFESEFVLV----ASKSRTCT-G-TTTLESLK 193 (312)
T ss_pred CCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCcccccCCeeE---EEEecccEEEE----EcCCCchh-c-cCCHHHHh
Confidence 55555432 345689999999999999998754421 11110 11112222222 12223221 1 1222222
Q ss_pred --cEEEecH--HHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 194 --KRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 194 --~~VySHp--qal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
.-|.--+ ....+...|+..++.. ...++|......++..+ ...++.+...++
T Consensus 194 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 252 (312)
T PRK10341 194 NEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA---DFLTVIPCDMTS 252 (312)
T ss_pred CCCeEccCCCCcHHHHHHHHHHHcCcCCCceEEecCHHHHHHHHHhC---CcEEEeeHHhcC
Confidence 2222111 1233455667665432 34566777677777664 457777776553
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=56.39 E-value=14 Score=26.35 Aligned_cols=40 Identities=18% Similarity=0.243 Sum_probs=30.0
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
+++.||.+.++++.|+++|||+-.|..-+ ......|+++.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~q~~-s~~~isf~i~~ 50 (66)
T cd04924 11 MRGTPGVAGRVFGALGKAGINVIMISQGS-SEYNISFVVAE 50 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEecC-ccceEEEEEeH
Confidence 46789999999999999999998875333 22445566654
No 190
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=56.26 E-value=19 Score=34.93 Aligned_cols=35 Identities=11% Similarity=0.171 Sum_probs=31.6
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeee
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESR 320 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSR 320 (339)
+..+.+.-+|+||-..++=+.|+++|+|+..+.+.
T Consensus 7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~ 41 (286)
T PRK13011 7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSF 41 (286)
T ss_pred eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeee
Confidence 45666777999999999999999999999999997
No 191
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=56.23 E-value=1.2e+02 Score=28.79 Aligned_cols=144 Identities=9% Similarity=0.060 Sum_probs=70.2
Q ss_pred CCceEEEEECCCCcH-HHHH---HHHhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeE
Q 019548 95 GTKVRISFKGLPGSF-SEDA---ALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (339)
Q Consensus 95 ~~~~~VayLGP~GTf-S~~A---A~~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~ 169 (339)
....+|++...-+.+ --.. -.+.+++..+.. ..+..++++.+.+|++|+|+.+-.-.....+. ...|.+.++.
T Consensus 92 ~g~lrIg~~~~~~~~~l~~~l~~f~~~~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l~--~~~l~~~~~~ 169 (316)
T PRK12679 92 SGVLTIATTHTQARYSLPEVIKAFRELFPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQLV--AFPWFRWHHS 169 (316)
T ss_pred CceEEEEechHhhhcchHHHHHHHHHHCCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCCCCce--EEEccCCcEE
Confidence 456778875433322 1111 123356654433 34677899999999999999753211000010 0112222222
Q ss_pred EEEEEEEeeeeeeccCCCCCcCCcc---EEEecHH--HHHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEe
Q 019548 170 IVGEVQLAANFCLLALPGIKADQLK---RVLSHPQ--ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAV 241 (339)
Q Consensus 170 I~gEi~l~I~h~Ll~~~g~~l~~I~---~VySHpq--al~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAI 241 (339)
+.++.+|-|......+++++. -|.-++. ....-..|+...+.. . ..++|+..+..++..+ ...|+
T Consensus 170 ----~v~~~~hpl~~~~~i~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g---~Gi~~ 242 (316)
T PRK12679 170 ----LLVPHDHPLTQITPLTLESIAKWPLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALG---LGIGL 242 (316)
T ss_pred ----EEecCCCccccCCCCCHHHHhCCCeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcC---CcEEE
Confidence 234556665433223333333 3332221 223456677766543 2 3456666666666654 34666
Q ss_pred cCHHHH
Q 019548 242 ASARAA 247 (339)
Q Consensus 242 as~~AA 247 (339)
.+..++
T Consensus 243 lp~~~~ 248 (316)
T PRK12679 243 VAEQSS 248 (316)
T ss_pred eccccc
Confidence 666543
No 192
>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=55.82 E-value=35 Score=26.03 Aligned_cols=38 Identities=11% Similarity=0.170 Sum_probs=30.0
Q ss_pred cCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 294 DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 294 ~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
...||.+.++++.|+++|||.-.|-+ ......|.++.+
T Consensus 12 ~~~~g~~~~If~~la~~~I~vd~I~~---s~~~isftv~~~ 49 (73)
T cd04934 12 SLSHGFLARIFAILDKYRLSVDLIST---SEVHVSMALHME 49 (73)
T ss_pred ccccCHHHHHHHHHHHcCCcEEEEEe---CCCEEEEEEehh
Confidence 35799999999999999999999976 225566666543
No 193
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=55.23 E-value=18 Score=34.47 Aligned_cols=53 Identities=19% Similarity=0.203 Sum_probs=40.6
Q ss_pred ceEEEEE----CCCCcHHHHHHHHh--CC--CCccccCCCHHHHHHHHHhCCCCeEEEeee
Q 019548 97 KVRISFK----GLPGSFSEDAALKA--YP--KCETVPCDEFEDTFKAVELWLADKAVLPIE 149 (339)
Q Consensus 97 ~~~VayL----GP~GTfS~~AA~~~--fg--~~~~~~~~si~~Vf~aV~~g~ad~gVVPiE 149 (339)
..++|+- -|.|-|++++-.+. .. ...++.-.+..+++..|++|++|+|+|=.-
T Consensus 135 ~~~lai~~p~~~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~s 195 (258)
T COG0725 135 DVRLAIGDPKTVPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYVS 195 (258)
T ss_pred CcEEEecCCCCCCchHHHHHHHHHhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEEE
Confidence 5667664 47899999986642 11 246788899999999999999999998543
No 194
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=53.92 E-value=26 Score=34.07 Aligned_cols=45 Identities=9% Similarity=0.152 Sum_probs=34.3
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEE
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVD 331 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~ 331 (339)
+.-|.+.-+|+||-.+.+=+.++++|+|+..+... .....-.||.
T Consensus 9 ~~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~-~d~~~~~ffm 53 (289)
T PRK13010 9 SYVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQF-DDDESGRFFM 53 (289)
T ss_pred CEEEEEECCCCCCcHHHHHHHHHHCCCCEEecccc-cccccCcEEE
Confidence 33455666999999999999999999999999986 2233334443
No 195
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=53.91 E-value=50 Score=36.17 Aligned_cols=47 Identities=17% Similarity=0.285 Sum_probs=39.6
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEE
Q 019548 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVV 330 (339)
Q Consensus 284 ~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~ 330 (339)
...+.|.+...|++|.|.++++.+++.++|+.++.++...++.....
T Consensus 625 ~f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~~~~~~~ 671 (701)
T COG0317 625 VYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQFATMQ 671 (701)
T ss_pred ceEEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCCceEEEE
Confidence 35677888889999999999999999999999999999855544433
No 196
>PRK03381 PII uridylyl-transferase; Provisional
Probab=53.47 E-value=35 Score=37.62 Aligned_cols=52 Identities=10% Similarity=0.065 Sum_probs=41.4
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCC-CceEEEecCCCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR-PLRVVDDSNNGT 337 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~-~w~~~~~~~~~~ 337 (339)
-|.|.+..+|+||-|+++-+.|+..|+|+..-..--..+. .-.|+|+..+|.
T Consensus 707 ~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d~~g~ 759 (774)
T PRK03381 707 ATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTGAAGG 759 (774)
T ss_pred eEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEECCCCC
Confidence 4777788899999999999999999999988766655433 356777776665
No 197
>cd04923 ACT_AK-LysC-DapG-like_2 ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168 and related domains. This CD includes the C-terminal of the two ACT domains of the lysine-sensitive aspartokinase isoenzyme AKII of Bacillus subtilis (BS) strain 168, and the lysine plus threonine-sensitive aspartokinase of Corynebacterium glutamicum, as well as, the second and fourth, of four, ACT domains present in cyanobacteria AK. Also included are the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase isoenzyme AKI found in Bacilli (B. subtilis strain 168), Clostridia, and Actinobacteria bacterial species. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=53.01 E-value=17 Score=25.44 Aligned_cols=38 Identities=24% Similarity=0.343 Sum_probs=30.0
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
.++.||.+.++++.+++++||+-.|-+. +....|+++.
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~s---~~~is~~v~~ 47 (63)
T cd04923 10 MRSHPGVAAKMFKALAEAGINIEMISTS---EIKISCLVDE 47 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEcc---CCeEEEEEeH
Confidence 5678999999999999999999988643 3445566654
No 198
>PRK05092 PII uridylyl-transferase; Provisional
Probab=52.84 E-value=36 Score=38.28 Aligned_cols=52 Identities=13% Similarity=0.064 Sum_probs=39.6
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCC-CCceEEEecCCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK-RPLRVVDDSNNG 336 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~-~~w~~~~~~~~~ 336 (339)
+.|.|.+..+|+||-|+++.+.|++.|||+..-...-..+ ..--|+|+..+|
T Consensus 842 ~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g 894 (931)
T PRK05092 842 RFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFG 894 (931)
T ss_pred CeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCC
Confidence 3578888999999999999999999999998776664332 234566655444
No 199
>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=52.52 E-value=1.4e+02 Score=24.87 Aligned_cols=121 Identities=12% Similarity=0.020 Sum_probs=60.9
Q ss_pred hCCCCccccCC-CHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCC---
Q 019548 117 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ--- 192 (339)
Q Consensus 117 ~fg~~~~~~~~-si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~--- 192 (339)
.+++.++.... +-+++++.+.+|++|+|++.......+... ..|.+..+.+ ..+-.|.|...+..+++|
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 45665544332 347889999999999999864432222111 1122223322 233445554333233333
Q ss_pred ccEEE-ecHH-HHHHHHHHHHhcCC--e-eEecCCHHHHHHHHHhcCCCCeEEecCHHHH
Q 019548 193 LKRVL-SHPQ-ALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAA 247 (339)
Q Consensus 193 I~~Vy-SHpq-al~QC~~~L~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~AA 247 (339)
..-|. ++.. ......+|+.+++. . ...++|...+.++++.+ ...++.+...+
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~ 154 (196)
T cd08457 98 ERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREG---LGIAIIDPATA 154 (196)
T ss_pred CceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcC---CeEEEEChHHh
Confidence 33343 2222 23446667766543 2 34456666666666654 34666655433
No 200
>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=52.14 E-value=40 Score=31.22 Aligned_cols=73 Identities=27% Similarity=0.191 Sum_probs=43.0
Q ss_pred CCceEEEEECCCCcHHHHHHH---HhCC-CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhH-HHhhcCCeE
Q 019548 95 GTKVRISFKGLPGSFSEDAAL---KAYP-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNY-DLLLRHRLH 169 (339)
Q Consensus 95 ~~~~~VayLGP~GTfS~~AA~---~~fg-~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tl-DlL~~~~l~ 169 (339)
....+|++.= +||=.+.-++ ++.+ ..+++..++..++++++++|++|-+|||-+ +.. .+++ |+|.+.+++
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 3445899887 7887765444 3344 489999999999999999999999999933 322 5566 677778887
Q ss_pred EEE
Q 019548 170 IVG 172 (339)
Q Consensus 170 I~g 172 (339)
+=|
T Consensus 141 ~Pg 143 (201)
T PF12916_consen 141 APG 143 (201)
T ss_dssp ---
T ss_pred CCh
Confidence 754
No 201
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=51.92 E-value=32 Score=30.89 Aligned_cols=45 Identities=24% Similarity=0.310 Sum_probs=36.5
Q ss_pred EEEEecCCcchHHHHHHHHHhCCceeeeeeee-e-CCCCCceEEEec
Q 019548 289 IVFTLDEGPGVLFKALAVFALREINLTKIESR-P-QRKRPLRVVDDS 333 (339)
Q Consensus 289 i~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSR-P-~~~~~w~~~~~~ 333 (339)
+..+..+.||.|..+++.++++||+..-+-|+ | ...++.=|+|+-
T Consensus 98 i~~~~~~~pgi~A~V~~~iak~gi~Irqi~~~dpe~~~e~~l~IVte 144 (167)
T COG2150 98 IYPEDARYPGILAGVASLIAKRGISIRQIISEDPELQEEPKLTIVTE 144 (167)
T ss_pred EEeccCCCccHHHHHHHHHHHcCceEEEEecCCcccCCCceEEEEEe
Confidence 33445689999999999999999999999887 6 567777777653
No 202
>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=51.87 E-value=1.3e+02 Score=24.47 Aligned_cols=122 Identities=20% Similarity=0.105 Sum_probs=60.5
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc--
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (339)
.+++.++.-. .+..++.+.+.+|++|+|+..-.....+... ..|.+.++.++ .+-+|-+...+..+++++
T Consensus 25 ~~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~~----~~~~~pl~~~~~~~~~~l~~ 97 (197)
T cd08440 25 RHPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDLEF---EPLLRDPFVLV----CPKDHPLARRRSVTWAELAG 97 (197)
T ss_pred hCCCcEEEEEeCChHHHHHHHHcCCccEEEEeCCCCCCCeeE---EEeecccEEEE----ecCCCCcccCCccCHHHHcc
Confidence 3566544332 3568899999999999999853321111110 11112222222 233343432222233333
Q ss_pred -cEE-EecHHH-HHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 194 -KRV-LSHPQA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 194 -~~V-ySHpqa-l~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
.-| +.+... .....+|+.+.+.. ...++|...+..+++.+ ...|+.++..+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (197)
T cd08440 98 YPLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAG---LGVAVLPALALP 155 (197)
T ss_pred CCEEecCCCccHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEcchhHHH
Confidence 223 222221 22344566655432 34566776677777764 457888876554
No 203
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=51.75 E-value=2e+02 Score=26.52 Aligned_cols=144 Identities=13% Similarity=0.075 Sum_probs=73.5
Q ss_pred CCceEEEEECCCCc-HHHH---HHHHhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeec--cCccchhhhHHHhhcCC
Q 019548 95 GTKVRISFKGLPGS-FSED---AALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIEN--SSSGSIHRNYDLLLRHR 167 (339)
Q Consensus 95 ~~~~~VayLGP~GT-fS~~---AA~~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiEN--S~~G~V~~tlDlL~~~~ 167 (339)
....+|++...-+. +-.. +..+.|+++++.- ..+-+++++.+.+|++|+|++.-.. ...+... ..|.+.+
T Consensus 96 ~~~l~I~~~~~~~~~~l~~~l~~f~~~~p~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~l~~---~~l~~~~ 172 (294)
T PRK09986 96 AGRIEIGIVGTALWGRLRPAMRHFLKENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNPGFTS---RRLHESA 172 (294)
T ss_pred cceEEEEEehHHhHHHHHHHHHHHHHhCCCeEEEEEeCCHHHHHHHHHcCCCCEEEecCCccCCCCCeEE---EEeeccc
Confidence 45688888544432 1111 2233456654432 3456889999999999999973210 0111110 1111222
Q ss_pred eEEEEEEEEeeeeeeccCCCCCcCCcc---EEEecH--HHHH-HHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCe
Q 019548 168 LHIVGEVQLAANFCLLALPGIKADQLK---RVLSHP--QALA-SSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDA 238 (339)
Q Consensus 168 l~I~gEi~l~I~h~Ll~~~g~~l~~I~---~VySHp--qal~-QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~ 238 (339)
+.+ ..+-.|-|...+..+++|+. -|...+ ..+. +...|+.+.+.. ...++|......+++.+ ..
T Consensus 173 ~~~----v~~~~~~l~~~~~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g 245 (294)
T PRK09986 173 FAV----AVPEEHPLASRSSVPLKALRNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG---IG 245 (294)
T ss_pred EEE----EEcCCCCcccCCccCHHHHcCCCEEecCCCchhHHHHHHHHHHHCCCCCceeeecCCHHHHHHHHHcC---Ce
Confidence 222 23444555443333444443 344322 2233 556666655432 24567776667777664 56
Q ss_pred EEecCHHHHH
Q 019548 239 GAVASARAAE 248 (339)
Q Consensus 239 AAIas~~AA~ 248 (339)
.++.++..++
T Consensus 246 i~~l~~~~~~ 255 (294)
T PRK09986 246 ITLLPDSYAQ 255 (294)
T ss_pred EEEccHHHhh
Confidence 7888876654
No 204
>PRK09224 threonine dehydratase; Reviewed
Probab=51.57 E-value=22 Score=37.10 Aligned_cols=46 Identities=24% Similarity=0.296 Sum_probs=35.7
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEE
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVD 331 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~ 331 (339)
+..-+.|..|.|||+|.+.|+.+. -+-|+|.++=|-.....+..++
T Consensus 422 ~e~~~~~~fPerpGal~~Fl~~l~-~~~~It~f~Yr~~~~~~g~vlv 467 (504)
T PRK09224 422 DERLYRFEFPERPGALLKFLSTLG-THWNISLFHYRNHGADYGRVLA 467 (504)
T ss_pred ceEEEEEeCCCCCCHHHHHHHhcC-CCCeeEEEEEccCCcccccEEE
Confidence 355677889999999999999887 7889999998844444455544
No 205
>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=51.54 E-value=1.4e+02 Score=24.75 Aligned_cols=121 Identities=12% Similarity=0.015 Sum_probs=61.0
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeecc--CccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS--~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (339)
.|++.++.-. .+-+++.+.+.+|++|+|+++-... ..+.. ...|.+.++.++ .+-+|-|......+++|+
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l~---~~~l~~~~~~~~----~~~~hpl~~~~~i~~~dL 97 (198)
T cd08437 25 TGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSALH---SKIIKTQHFMII----VSKDHPLAKAKKVNFADL 97 (198)
T ss_pred hCCceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCcccce---EEEeecceEEEE----ecCCCcccccCcccHHHH
Confidence 4566555433 4678899999999999999853211 01111 112222233322 333444443322334333
Q ss_pred c---EEE-ecHH-HHHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHH
Q 019548 194 K---RVL-SHPQ-ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAA 247 (339)
Q Consensus 194 ~---~Vy-SHpq-al~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA 247 (339)
. .|. .... ...+...|+.+.+.. . ..++|...+.++++.+ ...++.+...+
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 156 (198)
T cd08437 98 KKENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVREN---VGIGFLTDIAV 156 (198)
T ss_pred cCCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CcEEEEEhhhc
Confidence 3 232 1111 124456666665432 2 3456666666666664 35677777544
No 206
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=51.53 E-value=1.7e+02 Score=27.68 Aligned_cols=144 Identities=13% Similarity=0.051 Sum_probs=70.8
Q ss_pred CCCceEEEEECCCCcH-HHHHHH---HhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHH--HhhcC
Q 019548 94 DGTKVRISFKGLPGSF-SEDAAL---KAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYD--LLLRH 166 (339)
Q Consensus 94 l~~~~~VayLGP~GTf-S~~AA~---~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlD--lL~~~ 166 (339)
.....+|+....-+.+ -..+.. +.+++..+.. ..+..++++.+.+|++|+++.+-.+... ..++ -|.+.
T Consensus 91 ~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~~----~~l~~~~l~~~ 166 (313)
T PRK12684 91 DQGNLTIATTHTQARYALPAAIKEFKKRYPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIADY----KELVSLPCYQW 166 (313)
T ss_pred CCCeEEEEechHHHHHHhHHHHHHHHHHCCCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCCC----CCceEEEeccc
Confidence 3456788875443332 112222 2356654433 3467899999999999999986321111 1111 11122
Q ss_pred CeEEEEEEEEeeeeeeccCCCCCcC---CccEEEecH-H-HHHHHHHHHHhcCC--e-eEecCCHHHHHHHHHhcCCCCe
Q 019548 167 RLHIVGEVQLAANFCLLALPGIKAD---QLKRVLSHP-Q-ALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDA 238 (339)
Q Consensus 167 ~l~I~gEi~l~I~h~Ll~~~g~~l~---~I~~VySHp-q-al~QC~~~L~~~~~--~-~i~~~STA~AA~~v~~~~~~~~ 238 (339)
.+.+ ..+..|-+......+++ +..-|.-.+ . -..+...|+...+. . ...++|......+|..+ ..
T Consensus 167 ~~~~----v~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~G 239 (313)
T PRK12684 167 NHCV----VVPPDHPLLERKPLTLEDLAQYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELG---LG 239 (313)
T ss_pred eEEE----EeCCCCccccCCCcCHHHHhcCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhC---Cc
Confidence 2222 23445555433222222 223232111 1 12345666766543 2 34566777677777764 33
Q ss_pred EEecCHHHHH
Q 019548 239 GAVASARAAE 248 (339)
Q Consensus 239 AAIas~~AA~ 248 (339)
.++.+..+++
T Consensus 240 v~~lp~~~~~ 249 (313)
T PRK12684 240 VGIVADMAFD 249 (313)
T ss_pred eEEeehhhcc
Confidence 5666665544
No 207
>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=51.10 E-value=33 Score=28.88 Aligned_cols=121 Identities=19% Similarity=0.119 Sum_probs=62.9
Q ss_pred hCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc--
Q 019548 117 AYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK-- 194 (339)
Q Consensus 117 ~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~-- 194 (339)
.|++.++.......++.+.+.+|++|+|++.......+.. ...|.+..+.+ ..+-.|-|...+ .+++|+.
T Consensus 25 ~~P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~----v~~~~hpl~~~~-~~l~dl~~~ 96 (200)
T cd08460 25 EAPGVRLRFVPESDKDVDALREGRIDLEIGVLGPTGPEIR---VQTLFRDRFVG----VVRAGHPLARGP-ITPERYAAA 96 (200)
T ss_pred HCCCCEEEEecCchhHHHHHHCCCccEEEecCCCCCcchh---eeeeeccceEE----EEeCCCCCCCCC-CCHHHHhcC
Confidence 4666555443322378899999999999984322111111 11222223322 234455554322 3344433
Q ss_pred -EEE-ecHH-HHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 195 -RVL-SHPQ-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 195 -~Vy-SHpq-al~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
.|. +... ...+..+|+.+.+.. ...++|...+..+++.+ ...|+.+...++
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 124567777776543 24567777777777764 456777776654
No 208
>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=51.04 E-value=33 Score=37.30 Aligned_cols=42 Identities=21% Similarity=0.283 Sum_probs=35.1
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRP 326 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~ 326 (339)
..+.|.+...|++|.|.++...+++.++|+..+.++-..+..
T Consensus 609 f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~~~ 650 (683)
T TIGR00691 609 FIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGKRE 650 (683)
T ss_pred eEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCE
Confidence 466777888999999999999999999999999986543333
No 209
>PRK05007 PII uridylyl-transferase; Provisional
Probab=50.56 E-value=18 Score=40.38 Aligned_cols=52 Identities=15% Similarity=0.153 Sum_probs=39.1
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeee--eeeeeCCCCCceEEEecCCCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTK--IESRPQRKRPLRVVDDSNNGT 337 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtk--IeSRP~~~~~w~~~~~~~~~~ 337 (339)
+.|.|=+..+|+||-|+++...|++.||++.. |.. --..-.--|||+.++|.
T Consensus 807 ~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T-~gera~DvFyV~~~~g~ 860 (884)
T PRK05007 807 RRSYMELIALDQPGLLARVGKIFADLGISLHGARITT-IGERVEDLFILATADRR 860 (884)
T ss_pred CeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEec-cCceEEEEEEEEcCCCC
Confidence 47888899999999999999999999999864 333 11123466777776664
No 210
>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=50.34 E-value=1.5e+02 Score=24.81 Aligned_cols=122 Identities=16% Similarity=0.061 Sum_probs=62.0
Q ss_pred hCCCCccccCC-CHHHHHHHHHhCCCCeEEEeeecc-CccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc-
Q 019548 117 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENS-SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 193 (339)
Q Consensus 117 ~fg~~~~~~~~-si~~Vf~aV~~g~ad~gVVPiENS-~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I- 193 (339)
.|++.++.... +-.++.+.+.+|++|+|+.+-... ..+... ..|.+.++. +..+..|-|......+++++
T Consensus 25 ~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~---~~l~~~~~~----~v~~~~hpl~~~~~i~~~~l~ 97 (198)
T cd08413 25 RYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLVT---LPCYRWNHC----VIVPPGHPLADLGPLTLEDLA 97 (198)
T ss_pred hCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCcEE---EEeeeeeEE----EEecCCCcccccCCCCHHHHh
Confidence 45665554433 457889999999999999853211 111110 111112221 22344555543333333333
Q ss_pred --cEEEec-HH-HHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 194 --KRVLSH-PQ-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 194 --~~VySH-pq-al~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
.-|.-. .. -..+-..|+.+.+.. ...++|......+++.+ ...|+.++..+.
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08413 98 QYPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLG---LGVGIIAEMAYD 156 (198)
T ss_pred cCCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhC---CCEEEccccccC
Confidence 233211 11 234456677766532 34466777777777764 346777765443
No 211
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=50.08 E-value=1.4e+02 Score=24.44 Aligned_cols=33 Identities=15% Similarity=-0.028 Sum_probs=23.9
Q ss_pred hCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeee
Q 019548 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIE 149 (339)
Q Consensus 117 ~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiE 149 (339)
.|++.++.- ..+..+..+.+.+|++|+|++...
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (197)
T cd08449 25 QYPNVTVRFHELSPEAQKAALLSKRIDLGFVRFA 58 (197)
T ss_pred HCCCeEEEEEECCHHHHHHHHhCCCccEEEeccc
Confidence 356654433 235788999999999999997543
No 212
>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=49.84 E-value=31 Score=25.55 Aligned_cols=24 Identities=33% Similarity=0.425 Sum_probs=21.5
Q ss_pred CCcchHHHHHHHHHhCCceeeeee
Q 019548 295 EGPGVLFKALAVFALREINLTKIE 318 (339)
Q Consensus 295 ~~pGaL~~iL~~Fa~~gINLtkIe 318 (339)
+.||-+.++.+++++.|||+--|-
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 599999999999999999998877
No 213
>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=49.38 E-value=53 Score=29.86 Aligned_cols=108 Identities=21% Similarity=0.247 Sum_probs=64.4
Q ss_pred HHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeec---cCCCCCc---CC--ccEEEe-c
Q 019548 129 FEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLL---ALPGIKA---DQ--LKRVLS-H 199 (339)
Q Consensus 129 i~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll---~~~g~~l---~~--I~~VyS-H 199 (339)
..|+-..|+.|.+|+||+= .|.|.++.-.+.--..|+..+|=+ +.++.+. ++ -++|.+ .
T Consensus 49 ~~Dip~yV~~G~aDlGI~G------------~D~l~E~~~~v~~~~dL~fg~crl~vA~p~~~~~~~~~~l~~~rIATky 116 (182)
T TIGR00070 49 PQDIPTYVEHGAADLGITG------------YDVLLESGADVYELLDLGFGKCRLVLAVPQESDISSVEDLKGKRIATKY 116 (182)
T ss_pred cchhHHHHhCCCccEEEec------------chhhhhCCCCEEEEeecCcCceEEEEEEECCCCCCChHHhCCCEEEECC
Confidence 3578899999999999852 466666654444444567666633 3333221 22 135666 5
Q ss_pred HHHHHHHHHHHHhcCC--eeEecCCHHHHHHHHHhcCCCCeEEe----cCHHHHHHcCCceee
Q 019548 200 PQALASSDIVLTQLGV--ARENVDDTASAAQYVASNGLRDAGAV----ASARAAEIYGLNILA 256 (339)
Q Consensus 200 pqal~QC~~~L~~~~~--~~i~~~STA~AA~~v~~~~~~~~AAI----as~~AA~~ygL~il~ 256 (339)
|. -.++|++++++ +++..+-+.|+|-. .+-+-|| .+-..-+.+||+++.
T Consensus 117 p~---i~~~~f~~~Gi~v~ii~l~GsvE~aP~-----~GlaD~IvDiv~TG~TL~~NgL~~ie 171 (182)
T TIGR00070 117 PN---LARRYFEKKGIDVEIIKLNGSVELAPL-----LGLADAIVDIVSTGTTLRENGLRIIE 171 (182)
T ss_pred HH---HHHHHHHHcCCeEEEEECcceeecccC-----CCceeEEEEEeCCHHHHHHCCCEEee
Confidence 65 34679999865 45665555544322 1223344 344556779999985
No 214
>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=49.15 E-value=32 Score=24.53 Aligned_cols=37 Identities=16% Similarity=0.257 Sum_probs=29.4
Q ss_pred cCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 294 DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 294 ~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
+++||...++++.|+++|||.-.|.+ ......|+++.
T Consensus 11 ~~~~~~~~~if~~l~~~~i~v~~i~t---~~~~is~~v~~ 47 (62)
T cd04890 11 NGEVGFLRKIFEILEKHGISVDLIPT---SENSVTLYLDD 47 (62)
T ss_pred CcccCHHHHHHHHHHHcCCeEEEEec---CCCEEEEEEeh
Confidence 56899999999999999999999955 33556666654
No 215
>TIGR00656 asp_kin_monofn aspartate kinase, monofunctional class. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. The protein slr0657 from Synechocystis PCC6803 is extended by a duplication of the C-terminal region corresponding to the beta chain. Incorporation of a second copy of the C-terminal domain may be quite common in this subgroup of aspartokinases.
Probab=48.61 E-value=1e+02 Score=30.78 Aligned_cols=110 Identities=18% Similarity=0.155 Sum_probs=65.5
Q ss_pred CCeeEecCCHHHHHHHHHhcCCCCeEEecCHH---HHHHcCCceeeccccCCCCCeeeEEEEeeCCCC-C--CC--CCCc
Q 019548 214 GVARENVDDTASAAQYVASNGLRDAGAVASAR---AAEIYGLNILADRIQDEPDNITRFLVLARDPII-P--RT--DKLF 285 (339)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~---AA~~ygL~il~~~IeD~~~N~TRF~vi~~~~~~-p--~~--~~~~ 285 (339)
+++.+..-|..+|.+++..+ |-+-.+. .|..++.++.-.+..|.. --|.. ...... | ++ ...+
T Consensus 189 ~a~~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~a~~~~i~i~i~~~~~~~-~gT~I---~~~~~~~~~v~~I~~~~~ 259 (401)
T TIGR00656 189 AAKRIDKISYEEALELATFG-----AKVLHPRTVEPAMRSGVPIEVRSSFDPE-EGTLI---TNSMENPPLVKGIALRKN 259 (401)
T ss_pred CcEECCccCHHHHHHHHHcC-----CcccCHHHHHHHHHCCCeEEEEECCCCC-CCeEE---EeCcccCCceEEEEEECC
Confidence 34566667788888876643 2233333 345689999888876543 23332 222111 1 10 1122
Q ss_pred eEEEEEE---ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 286 KTSIVFT---LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 286 Ktsi~~~---~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
-+.+.+. +.++||.+.++++.|+++|||+-.|..=+ ......|+++.
T Consensus 260 va~vsv~g~~~~~~~g~~~~if~~L~~~~I~i~~i~~~~-s~~~Is~~V~~ 309 (401)
T TIGR00656 260 VTRVTVHGLGMLGKRGFLARIFGALAERNINVDLISQTP-SETSISLTVDE 309 (401)
T ss_pred EEEEEEecCCCCCCccHHHHHHHHHHHcCCcEEEEEcCC-CCceEEEEEeH
Confidence 3334343 57899999999999999999998885432 22446666654
No 216
>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=47.93 E-value=40 Score=30.09 Aligned_cols=49 Identities=16% Similarity=0.065 Sum_probs=33.1
Q ss_pred ceEEEEECCCCcHHHHHHHHhCCCCccc---------cCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALKAYPKCETV---------PCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg~~~~~---------~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+|+. +.|+..++...+........ ...|..+++.+|.+|++|.+++.
T Consensus 104 g~~V~v--~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~ 161 (232)
T TIGR03871 104 KLRIGV--FAGTPPAHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVW 161 (232)
T ss_pred CCeEEE--EcCChHHHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEec
Confidence 357877 55887777654432111111 23488999999999999999985
No 217
>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=47.59 E-value=2.8e+02 Score=27.17 Aligned_cols=143 Identities=15% Similarity=0.122 Sum_probs=74.3
Q ss_pred CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhh--cCCeEEEEEEEE-eeeeeeccCCCCCcCCc--c
Q 019548 120 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL--RHRLHIVGEVQL-AANFCLLALPGIKADQL--K 194 (339)
Q Consensus 120 ~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~--~~~l~I~gEi~l-~I~h~Ll~~~g~~l~~I--~ 194 (339)
+++++.+++-.++++++.+|++|+|.+- .. +.+-+.. ..+++|+.-... .-...+++++..+++|. |
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 4688999999999999999999998652 11 1111111 234443321111 11134555544556666 4
Q ss_pred EEEecHHHHHH--HHHHHHhcC-----CeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHH---HcCCceeeccccCCCC
Q 019548 195 RVLSHPQALAS--SDIVLTQLG-----VARENVDDTASAAQYVASNGLRDAGAVASARAAE---IYGLNILADRIQDEPD 264 (339)
Q Consensus 195 ~VySHpqal~Q--C~~~L~~~~-----~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~---~ygL~il~~~IeD~~~ 264 (339)
+|..++-+..+ ....|++.+ ++.+.... +++...+..+ .-+++++-.+..+. ..|.++|... .+.++
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 77665544332 344556553 45566644 4444444443 34555554444432 2466666543 23333
Q ss_pred CeeeEEEEe
Q 019548 265 NITRFLVLA 273 (339)
Q Consensus 265 N~TRF~vi~ 273 (339)
..+-+++..
T Consensus 185 ~~~~~lv~~ 193 (328)
T TIGR03427 185 EILDLMVVN 193 (328)
T ss_pred cceEEEEEC
Confidence 333444443
No 218
>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=47.27 E-value=1.6e+02 Score=24.11 Aligned_cols=32 Identities=19% Similarity=-0.014 Sum_probs=23.5
Q ss_pred hCCCCcccc-CCCHHHHHHHHHhCCCCeEEEee
Q 019548 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPI 148 (339)
Q Consensus 117 ~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPi 148 (339)
.|++.++.- ..+-.++++.+.+|++|+|++.-
T Consensus 25 ~~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~~ 57 (197)
T cd08438 25 RYPNIELELVEYGGKKVEQAVLNGELDVGITVL 57 (197)
T ss_pred HCcCeEEEEEEcCcHHHHHHHHcCCCCEEEEec
Confidence 356654433 24678899999999999999853
No 219
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=46.87 E-value=43 Score=36.92 Aligned_cols=39 Identities=18% Similarity=0.355 Sum_probs=33.9
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
..+.|.+...|++|.|.++...+++.++|+..+.++..+
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 345677788999999999999999999999999987654
No 220
>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=46.67 E-value=2.5e+02 Score=26.24 Aligned_cols=54 Identities=20% Similarity=0.078 Sum_probs=38.6
Q ss_pred CCceEEEEECCCCcHHHHH---HHHh---CCC--CccccCCCHHHHHHHHHhCCCCeEEEee
Q 019548 95 GTKVRISFKGLPGSFSEDA---ALKA---YPK--CETVPCDEFEDTFKAVELWLADKAVLPI 148 (339)
Q Consensus 95 ~~~~~VayLGP~GTfS~~A---A~~~---fg~--~~~~~~~si~~Vf~aV~~g~ad~gVVPi 148 (339)
...++|++..+.|+|.-.+ +..+ +++ +++++..+-.+.+++|.+|++|++++..
T Consensus 29 ~~~l~Ig~~~~~~~~~~~~~~la~~~~~~~~~i~v~~~~~~~~~~~~~~l~~G~~D~~~~~~ 90 (320)
T TIGR02122 29 PTFVTIGTGGTGGVYYPIGGAIAQLINKKSGKLRVRVQSTGGSVENVNLLEAGEADLAIVQS 90 (320)
T ss_pred CceEEEEeCCCCCChHHHHHHHHHHHhccCCCeeEEEEeCcchHHHHHHHhCCCCcEEEEcc
Confidence 4568999998988865432 2222 343 3456666778899999999999999863
No 221
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=46.64 E-value=29 Score=32.90 Aligned_cols=67 Identities=18% Similarity=0.041 Sum_probs=52.7
Q ss_pred cCceeccccCCCCCCCcccchhhHHHH-----------HHHHHHHHHHhhhcCCCCC--CCchhHHHHHhhhhCCCCCCc
Q 019548 19 SGLVFNGVRNSNRTPRKCVCRGGFSGL-----------SGDSVIKSADNQNTGKSSN--VNDVPGKLCKDLISLPKPLTV 85 (339)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~Il~L-----------lneRa~la~eIg~~K~~~~--~~RE~~il~~~~~~n~GPL~~ 85 (339)
.+..|||--..-|-||.-.-..||..| |-|||+||.++|-.-+.-. |...+-.++|++...+++...
T Consensus 111 ~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~e~ 190 (245)
T KOG0850|consen 111 SERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPVEG 190 (245)
T ss_pred ceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCcccc
Confidence 345688888888999999888888776 6689999999998776555 456677889998877776543
No 222
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=45.99 E-value=27 Score=33.73 Aligned_cols=34 Identities=26% Similarity=0.382 Sum_probs=29.2
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeee
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIE 318 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIe 318 (339)
.|-.|-+-+.|+||.|.++=+.|+.+|.|+-.+-
T Consensus 76 krHvinclVqnEpGvlsRisGvlAaRGfNIdSLv 109 (309)
T KOG2663|consen 76 KRHVINCLVQNEPGVLSRISGVLAARGFNIDSLV 109 (309)
T ss_pred cceeEEEEecCCchHHHHHHHHHHhccCCchhee
Confidence 3667777889999999999999999999976653
No 223
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=45.95 E-value=2.6e+02 Score=26.16 Aligned_cols=145 Identities=10% Similarity=0.002 Sum_probs=70.8
Q ss_pred CCCCccccC-CCHHHHHHHHHhCCCCeEEEeeec--cCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc
Q 019548 118 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIEN--SSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK 194 (339)
Q Consensus 118 fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiEN--S~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~ 194 (339)
+++.++.-. .+.+++.+.+.+|++|+|++.... .....+ ....|.+.++.++ .+-.|-+.... .++.+-.
T Consensus 119 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l--~~~~l~~~~~~~~----~~~~~~~~~~~-~~l~~~~ 191 (296)
T PRK11062 119 DESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEGL--FSKKLGECGVSFF----CTNPLPEKPFP-ACLEERR 191 (296)
T ss_pred CCceEEEEEeCCHHHHHHHHHcCCCCEEEecCCCccccccch--hhhhhhccCcceE----ecCCCccccCh-HHHhcCC
Confidence 556555433 577899999999999999974321 111111 1123333343332 12222221111 1233333
Q ss_pred EEEec-HHH-HHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHHHc----CCceeeccccCCCCC
Q 019548 195 RVLSH-PQA-LASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAEIY----GLNILADRIQDEPDN 265 (339)
Q Consensus 195 ~VySH-pqa-l~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~y----gL~il~~~IeD~~~N 265 (339)
-|... ... ..+-..|+..++.. . ..++|......++..+ ...++.+...++.+ +|..+ .+...-
T Consensus 192 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~~~~~~l~~l----~~~~~~ 264 (296)
T PRK11062 192 LLIPGRRTMLGRKLLNWFNSQGLNVEILGEFDDAALMKAFGAYH---DAIFVAPSLYAQDFYADHSVVEI----GRVDNV 264 (296)
T ss_pred eeecCCCchHHHHHHHHHHHcCCCceeeeeeCcHHHHHHHHHcC---CceEECCHHHHHHHHHcCCeEEc----CCcccc
Confidence 33211 111 23345677665543 2 3456666666666653 45888888887654 24433 222223
Q ss_pred eeeEEEEeeCC
Q 019548 266 ITRFLVLARDP 276 (339)
Q Consensus 266 ~TRF~vi~~~~ 276 (339)
...|+++-++.
T Consensus 265 ~~~~~lv~~~~ 275 (296)
T PRK11062 265 KEEYHVIFAER 275 (296)
T ss_pred ceEEEEEEecC
Confidence 44666665543
No 224
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=45.44 E-value=25 Score=39.20 Aligned_cols=52 Identities=19% Similarity=0.189 Sum_probs=37.0
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeee--eeeeeCCCCCceEEEecCCCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTK--IESRPQRKRPLRVVDDSNNGT 337 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtk--IeSRP~~~~~w~~~~~~~~~~ 337 (339)
+.|.|=+..+|+||-|+++-+.|.+.||++.. |..-= -.-.--|||+..+|.
T Consensus 782 ~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~g-erv~D~Fyv~~~~g~ 835 (854)
T PRK01759 782 EQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIG-EKAEDFFILTNQQGQ 835 (854)
T ss_pred CeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccC-ceEEEEEEEECCCCC
Confidence 47888899999999999999999999999864 32211 112345666555553
No 225
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=44.95 E-value=55 Score=30.07 Aligned_cols=49 Identities=16% Similarity=0.161 Sum_probs=36.5
Q ss_pred ceEEEEECCCCcHHHHHHHHhCC--CCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALKAYP--KCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg--~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+|++ +.|+..+.-..+.+. +.+.++.++.++.+++|.+|++|+.+..
T Consensus 133 g~~Igv--~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 133 GKHVGV--LQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred CCEEEE--ecCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeC
Confidence 357887 578766554444333 3567788999999999999999998864
No 226
>PRK09034 aspartate kinase; Reviewed
Probab=44.92 E-value=2.1e+02 Score=29.43 Aligned_cols=111 Identities=14% Similarity=0.040 Sum_probs=66.4
Q ss_pred CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHH---HHHcCCceeeccccCCCCCeeeEEEEeeCCCCC----CC--CCC
Q 019548 214 GVARENVDDTASAAQYVASNGLRDAGAVASARA---AEIYGLNILADRIQDEPDNITRFLVLARDPIIP----RT--DKL 284 (339)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~A---A~~ygL~il~~~IeD~~~N~TRF~vi~~~~~~p----~~--~~~ 284 (339)
+++.+..-|-.||.+++..+ |-+=.+.| |..+++++.-.+..+....-|..- ......+ ++ ...
T Consensus 234 ~A~~l~~lsy~Ea~ela~~G-----akvlhp~ai~~a~~~~Ipi~v~~~~~p~~~GT~I~--~~~~~~~~~~Vk~It~~~ 306 (454)
T PRK09034 234 NPKSIKEITYREMRELSYAG-----FSVFHDEALIPAYRGGIPINIKNTNNPEDPGTLIV--PDRDNKNKNPITGIAGDK 306 (454)
T ss_pred CCeECCccCHHHHHHHHhCC-----cccCCHHHHHHHHHcCCCEEEEcCCCCCCCccEEE--eccccCccccceEEEecC
Confidence 35566777888888876542 33333333 356899999999876544455442 2211110 00 011
Q ss_pred ceEEEEEE---ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 285 FKTSIVFT---LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 285 ~Ktsi~~~---~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
+-+.|-+. .+.+||.+.++++.|+++|||.-.| |.......|+++.+
T Consensus 307 ~i~~Itv~~~~~~~~~g~~a~if~~la~~~I~Vd~i---~ss~~sis~~v~~~ 356 (454)
T PRK09034 307 GFTSIYISKYLMNREVGFGRKVLQILEDHGISYEHM---PSGIDDLSIIIRER 356 (454)
T ss_pred CEEEEEEccCCCCCCccHHHHHHHHHHHcCCeEEEE---cCCCcEEEEEEeHH
Confidence 22333332 3557999999999999999999888 34444566666543
No 227
>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=44.84 E-value=1.8e+02 Score=24.07 Aligned_cols=142 Identities=19% Similarity=0.093 Sum_probs=69.8
Q ss_pred eEEEEECCCCcH--HHH--HHHHhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEE
Q 019548 98 VRISFKGLPGSF--SED--AALKAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVG 172 (339)
Q Consensus 98 ~~VayLGP~GTf--S~~--AA~~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~g 172 (339)
.+|++-.+-+++ ... +..+.|++.++.-. .+-.++.+.+.+|++|+|+.+-.-...+.. ...|.+.++.+
T Consensus 2 l~Ig~~~~~~~~~~~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~-- 76 (198)
T cd08441 2 LRIAVECHSCFDWLMPVLDQFRERWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGIA---YEPLFDYEVVL-- 76 (198)
T ss_pred EEEEeeccchhhhhHHHHHHHHHhCCCeEEEEEeCCchhHHHHHHcCCceEEEecCCcCCCCcE---EEEccCCcEEE--
Confidence 466665554432 111 11234566555433 355788999999999999974221111111 11222223322
Q ss_pred EEEEeeeeeeccCCCCCcCCcc---EEE-ecHHH-HHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCH
Q 019548 173 EVQLAANFCLLALPGIKADQLK---RVL-SHPQA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASA 244 (339)
Q Consensus 173 Ei~l~I~h~Ll~~~g~~l~~I~---~Vy-SHpqa-l~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~ 244 (339)
..+..|-|......+++++. -|. .+... ......|+.+.+.. ...++|...+..+++.+ ...++.+.
T Consensus 77 --~~~~~~~l~~~~~~~~~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~ 151 (198)
T cd08441 77 --VVAPDHPLAAKEFITPEDLADETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASG---RGVAALPN 151 (198)
T ss_pred --EEcCCCChHHcccCCHHHhcCCceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhC---CcEEEeeH
Confidence 23444544433222333333 222 11111 23455677665532 34567777777777764 44677777
Q ss_pred HHHHH
Q 019548 245 RAAEI 249 (339)
Q Consensus 245 ~AA~~ 249 (339)
..++.
T Consensus 152 ~~~~~ 156 (198)
T cd08441 152 WAVRE 156 (198)
T ss_pred HHHHH
Confidence 65543
No 228
>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=44.02 E-value=1.9e+02 Score=24.25 Aligned_cols=108 Identities=19% Similarity=0.102 Sum_probs=54.2
Q ss_pred hCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCccE
Q 019548 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR 195 (339)
Q Consensus 117 ~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~ 195 (339)
.|+++++.. ..+..++.+.+.+|++|+|+...+....+... ..|.+.++. +.++-+| +......+++++..
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----lv~~~~h-~~~~~~i~~~~l~~ 96 (200)
T cd08465 25 EAPGIDLAVSQASREAMLAQVADGEIDLALGVFPELPEELHA---ETLFEERFV----CLADRAT-LPASGGLSLDAWLA 96 (200)
T ss_pred HCCCcEEEEecCChHhHHHHHHCCCccEEEeccccCCcCeeE---EEeeeccEE----EEEeCCC-CccCCCcCHHHHhh
Confidence 356665433 35678999999999999999754322111111 112222222 2334455 33332234444321
Q ss_pred ---EEe--cHHHHHHHHHHHHhcCCee---EecCCHHHHHHHHHh
Q 019548 196 ---VLS--HPQALASSDIVLTQLGVAR---ENVDDTASAAQYVAS 232 (339)
Q Consensus 196 ---VyS--Hpqal~QC~~~L~~~~~~~---i~~~STA~AA~~v~~ 232 (339)
|.- .......-..++++++.+. ..++|......+++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ 141 (200)
T cd08465 97 RPHVLVAMRGDAANEIDRALAARGLRRRVALTLPHWGVAPELIAG 141 (200)
T ss_pred CCcEEEecCCCcCChHHHHHHHcCCceEEEEEcCcHHHHHHHHHc
Confidence 221 1111234556666666442 345666666677765
No 229
>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=43.85 E-value=33 Score=31.48 Aligned_cols=38 Identities=16% Similarity=0.249 Sum_probs=30.9
Q ss_pred EEEEEEecCCcchHHHHHHHHHhCCceeeee-eeeeCCC
Q 019548 287 TSIVFTLDEGPGVLFKALAVFALREINLTKI-ESRPQRK 324 (339)
Q Consensus 287 tsi~~~~~~~pGaL~~iL~~Fa~~gINLtkI-eSRP~~~ 324 (339)
..|++.-.|+||.+.++-..|.++|||+..+ -+|-.++
T Consensus 149 ~~L~~~~~D~PG~Ig~vg~~Lg~~~iNIa~m~v~r~~~g 187 (208)
T TIGR00719 149 PAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIG 187 (208)
T ss_pred cEEEEEeCCCCChHHHHHHHHHhCCccEEEEEEEecCCC
Confidence 5677777899999999999999999999776 4554433
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=43.51 E-value=46 Score=24.86 Aligned_cols=40 Identities=20% Similarity=0.306 Sum_probs=29.1
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
..+.||.+.++++.|++++||+-.+..= .......|+++.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~~~-~~~~~isf~v~~ 50 (80)
T cd04921 11 MVGVPGIAARIFSALARAGINVILISQA-SSEHSISFVVDE 50 (80)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEec-CCcceEEEEEeH
Confidence 4578999999999999999999887532 222344555554
No 231
>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=43.11 E-value=29 Score=24.67 Aligned_cols=41 Identities=20% Similarity=0.220 Sum_probs=30.0
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
+++.||.+.++++.+++.|||+-.|..=. ......|+++..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~i~v~~i~~~~-s~~~isf~v~~~ 51 (66)
T cd04916 11 MKNTVGVSARATAALAKAGINIRMINQGS-SEISIMIGVHNE 51 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEecC-cccEEEEEEeHH
Confidence 45789999999999999999998885322 224455666543
No 232
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=42.63 E-value=34 Score=30.99 Aligned_cols=48 Identities=23% Similarity=0.264 Sum_probs=36.8
Q ss_pred eEEEEECCCCcH--HHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 98 VRISFKGLPGSF--SEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 98 ~~VayLGP~GTf--S~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
.+|+.+ .||. .+..+....+..+.+.+++..+.+.++.+|++|+.+..
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 566663 5666 45544444456889999999999999999999999874
No 233
>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=42.45 E-value=2e+02 Score=24.03 Aligned_cols=121 Identities=15% Similarity=0.035 Sum_probs=60.7
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeecc---CccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCC
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS---SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ 192 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS---~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~ 192 (339)
.++++++... .+-.++.+.+.+|++|+|++.-.+. ..+... ..|.+.++.+ ..+-+|-|.. ..++++
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~~---~~l~~~~~~~----~~~~~hpl~~--~~~~~~ 95 (202)
T cd08468 25 LAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIEE---RDWWEDTYVV----IASRDHPRLS--RLTLDA 95 (202)
T ss_pred hCCCCEEEEEECChHhHHHHHHCCCccEEEecccccccCCCCEEE---EEEecCcEEE----EEeCCCCCcC--CCCHHH
Confidence 4566555443 4678999999999999999854321 111110 0111222221 1222333321 123333
Q ss_pred cc---EEEec--HHHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 193 LK---RVLSH--PQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 193 I~---~VySH--pqal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
+. .|... ...-.+..+++.+.+.. ...++|......+++. ....++.+..+++.
T Consensus 96 L~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~---~~~~~~~p~~~~~~ 157 (202)
T cd08468 96 FLAERHLVVTPWNEDRGVVDQVLEKQGLEREIALQLPNVLNAPFIVAS---SDLLMTLPRQAARA 157 (202)
T ss_pred HhhCCCeEEecCCCCCchHHHHHHHcCCCceEEEEcChhHhHHHHHhc---CCeeeecHHHHHHH
Confidence 22 22111 11224456677665542 3456666666666654 35678888877664
No 234
>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=42.37 E-value=1.7e+02 Score=24.06 Aligned_cols=122 Identities=14% Similarity=0.028 Sum_probs=60.5
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc-
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (339)
.++++++.-. .+-.++.+.+.+|++|+|++.-.....+.. ...|.+.++.++ .+-+|-+.. ...+++++.
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~~~~~-~~~~~~~l~~ 96 (200)
T cd08464 25 EAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWLK---REVLYTEGYACL----FDPQQLSLS-APLTLEDYVA 96 (200)
T ss_pred HCCCcEEEEecCCcccHHHHHhcCcccEEEecCCCCcccce---eeeecccceEEE----EeCCCcccc-CCCCHHHHhc
Confidence 4676555433 345577899999999999975332111111 112222333222 233332221 112333322
Q ss_pred --EE-EecHHH-HHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 195 --RV-LSHPQA-LASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 195 --~V-ySHpqa-l~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
.+ +.+... ......|+.+.+.. . ..++|......++..+ ...||.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 155 (200)
T cd08464 97 RPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGT---PLIATVPARLARA 155 (200)
T ss_pred CCcEEecCCCCCcchHHHHHHHcCCCcceEEEcCchhhHHHHHcCC---CceeecHHHHHHH
Confidence 22 222111 23356677766543 2 3455555555555543 4689999887764
No 235
>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=42.22 E-value=1.9e+02 Score=23.71 Aligned_cols=121 Identities=15% Similarity=0.112 Sum_probs=61.8
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccC--ccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 193 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~--~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I 193 (339)
.+++.++... .+..++.+.+.+|++|+|+....... .+... ..|.+.++.++. +-+|-+.. . .+++++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~---~~l~~~~~~~v~----~~~~~~~~-~-~~~~~l 95 (201)
T cd08418 25 QFPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKELIS---EPLFESDFVVVA----RKDHPLQG-A-RSLEEL 95 (201)
T ss_pred HCCCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCCCCcceeE---EeecCCceEEEe----CCCCcccc-C-CCHHHH
Confidence 3566544333 35678999999999999998532211 11111 112223333322 22232221 1 123333
Q ss_pred c---EEEec--HHHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 194 K---RVLSH--PQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 194 ~---~VySH--pqal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
. .|... ........+|+...+.. ...++|...+..+++.+ ...||.+...++.
T Consensus 96 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 156 (201)
T cd08418 96 LDASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKA---DFLTILSRDMGRG 156 (201)
T ss_pred cCCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhC---CEEEEeEHHHhhh
Confidence 2 23321 12234456677665432 34566777777777764 5678888776653
No 236
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=41.62 E-value=3.2e+02 Score=26.06 Aligned_cols=142 Identities=20% Similarity=0.117 Sum_probs=69.3
Q ss_pred CceEEEEECCCCcH-HHHH---HHHhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEE
Q 019548 96 TKVRISFKGLPGSF-SEDA---ALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHI 170 (339)
Q Consensus 96 ~~~~VayLGP~GTf-S~~A---A~~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I 170 (339)
..++|+...+.+.+ -... -.+.|++..+.. ..+-.++.+.+.+|++|+|+++-.-...+... ..|.+.++.+
T Consensus 89 g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~l~~~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~l 165 (317)
T PRK15421 89 TRLRIAIECHSCIQWLTPALENFHKNWPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGLHY---SPMFDYEVRL 165 (317)
T ss_pred eeEEEEecccchHHHHHHHHHHHHHHCCCceEEEEeCccHHHHHHHHCCCcCEEEecCcccCCCceE---EEeccceEEE
Confidence 45777775433321 1111 122356655433 34567889999999999999863211111111 1122222222
Q ss_pred EEEEEEeeeeeeccCCCCCcCCcc---EEE--ecHHHHHHHHHHHHhcCCe--eEecCCHHHHHHHHHhcCCCCeEEecC
Q 019548 171 VGEVQLAANFCLLALPGIKADQLK---RVL--SHPQALASSDIVLTQLGVA--RENVDDTASAAQYVASNGLRDAGAVAS 243 (339)
Q Consensus 171 ~gEi~l~I~h~Ll~~~g~~l~~I~---~Vy--SHpqal~QC~~~L~~~~~~--~i~~~STA~AA~~v~~~~~~~~AAIas 243 (339)
.++-.|-+......+++++. -|. .+.........|+...+.+ .+.++|.....+++..+ ...++.+
T Consensus 166 ----v~~~~hpl~~~~~i~~~~L~~~p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~i~p 238 (317)
T PRK15421 166 ----VLAPDHPLAAKTRITPEDLASETLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAAR---MGIAALP 238 (317)
T ss_pred ----EEcCCCCccccCcCCHHHhCCCcEEecCCchhhHHHHHHHHHHhCCCCceeecCCHHHHHHHHHhC---CcEEEec
Confidence 23444545433333344433 222 1112234455566665543 33466666666666654 3466777
Q ss_pred HHHH
Q 019548 244 ARAA 247 (339)
Q Consensus 244 ~~AA 247 (339)
+..+
T Consensus 239 ~~~~ 242 (317)
T PRK15421 239 HWVV 242 (317)
T ss_pred chhc
Confidence 6544
No 237
>PRK06635 aspartate kinase; Reviewed
Probab=40.58 E-value=1.2e+02 Score=30.24 Aligned_cols=42 Identities=14% Similarity=0.256 Sum_probs=33.0
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCC--CCceEEEecC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRK--RPLRVVDDSN 334 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~--~~w~~~~~~~ 334 (339)
..++||.|.++++.|+++|||+-.|.+=+..+ ..+.|+++.+
T Consensus 270 ~~~~~g~l~~i~~~L~~~~I~i~~is~s~~~~~~~~is~~v~~~ 313 (404)
T PRK06635 270 VPDKPGIAAQIFGALAEANINVDMIVQNVSEDGKTDITFTVPRD 313 (404)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEecCCCCCceeEEEEEcHH
Confidence 57899999999999999999999886544442 5577777543
No 238
>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=39.91 E-value=2e+02 Score=23.33 Aligned_cols=34 Identities=18% Similarity=0.094 Sum_probs=24.6
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeee
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIE 149 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiE 149 (339)
+.|+++.+.-. .+-.++.+.+.+|++|+|+..-.
T Consensus 24 ~~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (194)
T cd08436 24 RRHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLP 58 (194)
T ss_pred HHCCCcEEEEecCCHHHHHHHHHcCCccEEEEecC
Confidence 34666544332 35778999999999999998643
No 239
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=39.69 E-value=3.1e+02 Score=25.33 Aligned_cols=34 Identities=6% Similarity=-0.090 Sum_probs=25.5
Q ss_pred HhCCCCccc-cCCCHHHHHHHHHhCCCCeEEEeee
Q 019548 116 KAYPKCETV-PCDEFEDTFKAVELWLADKAVLPIE 149 (339)
Q Consensus 116 ~~fg~~~~~-~~~si~~Vf~aV~~g~ad~gVVPiE 149 (339)
+.|++.++. -.....++++.+.+|++|+|+.+..
T Consensus 113 ~~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~~~ 147 (275)
T PRK03601 113 QNQEALQFEARIAQRQSLVKQLHERQLDLLITTEA 147 (275)
T ss_pred HhCCCcEEEEEECChHHHHHHHHcCCCCEEEEcCC
Confidence 346666553 3556778999999999999997543
No 240
>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=39.68 E-value=2.6e+02 Score=24.46 Aligned_cols=105 Identities=16% Similarity=0.055 Sum_probs=65.2
Q ss_pred CccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc-----cE
Q 019548 121 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-----KR 195 (339)
Q Consensus 121 ~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-----~~ 195 (339)
++++...+..++++++.+|++|+|+...... ....-...++++++...-.-...|+++++..+.++ |+
T Consensus 23 ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~-------~~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DLkGK~ 95 (216)
T PF09084_consen 23 VEIVFFGGGGDVLEALASGKADIAVAGPDAV-------LFARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADLKGKK 95 (216)
T ss_dssp EEEEEESSHHHHHHHHHTTSHSEEEEECHHH-------HHHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGGTTSE
T ss_pred EEEEEecChhHHHHHHhcCCceEEeccchHH-------HHHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHhCCCE
Confidence 6889999999999999999999999754311 11111235788888776555567777665433333 36
Q ss_pred EEecH--HHHHHHHHHHHhcCC-----eeEecCCHHHHHHHHHhc
Q 019548 196 VLSHP--QALASSDIVLTQLGV-----ARENVDDTASAAQYVASN 233 (339)
Q Consensus 196 VySHp--qal~QC~~~L~~~~~-----~~i~~~STA~AA~~v~~~ 233 (339)
|...+ .....-+.+|+++++ +.+... ....+..+..+
T Consensus 96 i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~~-~~~~~~al~~g 139 (216)
T PF09084_consen 96 IGVSRGSSSEYFLRALLKKNGIDPDDVKIVNLG-PPELAQALLSG 139 (216)
T ss_dssp EEESTTSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTT
T ss_pred EEEecCcchhHHHHHHHHHhccccccceeeeee-hhhhhhhhhcC
Confidence 66555 334455677877653 344443 44554455554
No 241
>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=39.18 E-value=37 Score=23.33 Aligned_cols=40 Identities=23% Similarity=0.323 Sum_probs=29.1
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
..+.+|.+.++++.|++++|++-.+..=. ......|+++.
T Consensus 10 ~~~~~~~~~~i~~~l~~~~i~v~~i~~~~-~~~~i~~~v~~ 49 (65)
T cd04892 10 MRGTPGVAARIFSALAEAGINIIMISQGS-SEVNISFVVDE 49 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEcCC-CceeEEEEEeH
Confidence 35789999999999999999998885422 22344455554
No 242
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=38.91 E-value=1.7e+02 Score=24.27 Aligned_cols=114 Identities=15% Similarity=0.154 Sum_probs=60.2
Q ss_pred CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCC---cCCcc--
Q 019548 120 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIK---ADQLK-- 194 (339)
Q Consensus 120 ~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~---l~~I~-- 194 (339)
+.++++.+ ..++.+++.+|++|+++.+...+.+ -.+.+. .. .......+.++.+++.. ++|++
T Consensus 39 ~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~-----~~~~~~-----~~-~~~~~~~~~~~~~~~~~~~~~~dl~g~ 106 (218)
T cd00134 39 KVKFVEVD-WDGLITALKSGKVDLIAAGMTITPE-----RAKQVD-----FS-DPYYKSGQVILVKKGSPIKSVKDLKGK 106 (218)
T ss_pred eEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHH-----HHhhcc-----Cc-ccceeccEEEEEECCCCCCChHHhCCC
Confidence 35777777 7899999999999999887521111 011110 00 01112233444443322 23322
Q ss_pred EEEecHHHHHHHHHHHHhc--CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 195 RVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 195 ~VySHpqal~QC~~~L~~~--~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
+|..-+ . .-...++.+. ......+.|..++.+++..+ ...|++.....+..
T Consensus 107 ~i~~~~-~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~~~~~ 159 (218)
T cd00134 107 KVAVQK-G-STAEKYLKKALPEAKVVSYDDNAEALAALENG--RADAVIVDEIALAA 159 (218)
T ss_pred EEEEEc-C-chHHHHHHHhCCcccEEEeCCHHHHHHHHHcC--CccEEEeccHHHHH
Confidence 222111 1 1123455543 35667888888899988876 34566666655543
No 243
>PF03180 Lipoprotein_9: NLPA lipoprotein; InterPro: IPR004872 This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins.; PDB: 4EF2_A 4EF1_B 3GXA_C 3IR1_D 3TQW_A 3K2D_B 3UP9_A 1XS5_A 1P99_A.
Probab=37.87 E-value=2.1e+02 Score=26.91 Aligned_cols=87 Identities=15% Similarity=0.106 Sum_probs=53.6
Q ss_pred eEEEEE-CCCCcHHHHHHHHhC---C-CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhh---cCCeE
Q 019548 98 VRISFK-GLPGSFSEDAALKAY---P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL---RHRLH 169 (339)
Q Consensus 98 ~~VayL-GP~GTfS~~AA~~~f---g-~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~---~~~l~ 169 (339)
.|||+. ||....-+.+ .+.+ | ..+++.++++.+.-.+|.+|++|.-+.=.. .-++.+. ..+|.
T Consensus 1 ikIG~~~~~~~~i~~~v-~~~~~~~Gi~vevv~f~D~~~~N~AL~~G~iDaN~fQh~--------~yl~~~n~~~~~~L~ 71 (237)
T PF03180_consen 1 IKIGVTPGPDAEILEAV-KEKLKKKGIDVEVVEFSDYVQPNEALADGEIDANFFQHI--------PYLEQFNKENGYNLV 71 (237)
T ss_dssp EEEEEETTCHHHHHHHH-HHHHHHTTEEEEEEEESSTTHHHHHHHTTSSSEEEEEEH--------HHHHHHHHHHT--EE
T ss_pred CEEEEeCCCHHHHHHHH-HHHHHhcCCeEEEEEecchhhcChHHHCCCcceeccCCH--------HHHHHHHHHCCCcEE
Confidence 478887 5644444433 3333 2 368899999999999999999997764322 2334333 25688
Q ss_pred EEEEEEEeeeeeeccCCCCCcCCcc
Q 019548 170 IVGEVQLAANFCLLALPGIKADQLK 194 (339)
Q Consensus 170 I~gEi~l~I~h~Ll~~~g~~l~~I~ 194 (339)
.++.+++. ...|.+.+-.++++|.
T Consensus 72 ~v~~~~~~-p~glYS~k~~sl~~lp 95 (237)
T PF03180_consen 72 PVGPTYIE-PMGLYSKKYKSLDDLP 95 (237)
T ss_dssp EEEEEEE----EEEESSSSSGGGS-
T ss_pred EecceeEE-eEEEeecccCchhhcC
Confidence 88876665 3667776655666654
No 244
>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=37.87 E-value=2.3e+02 Score=23.32 Aligned_cols=122 Identities=18% Similarity=0.082 Sum_probs=61.6
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcC---C
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD---Q 192 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~---~ 192 (339)
.+++.++... .+-.++.+.+.+|++|+|+..-.....+... ..|.+..+.+ ..+-.|-+...+..+++ +
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~---~~l~~~~~~~----~~~~~~~~~~~~~~~~~~l~~ 97 (198)
T cd08433 25 RYPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLST---EPLLEEDLFL----VGPADAPLPRGAPVPLAELAR 97 (198)
T ss_pred HCCCcEEEEEecCcHHHHHHHhCCCCcEEEEeCCCCCCCeeE---EEeccccEEE----EecCCCccccCCCCCHHHhCC
Confidence 4566544333 4567889999999999999853322221111 1122222222 23334444322222222 2
Q ss_pred ccEEE-ecHHH-HHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 193 LKRVL-SHPQA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 193 I~~Vy-SHpqa-l~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
..-|. .+... .....+|+..++.. ...++|...+..+++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08433 98 LPLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAG---LGYTILPASAVA 155 (198)
T ss_pred CceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcC---CcEEEcchhhhh
Confidence 33332 22222 23456667665433 34567777777777764 456777766543
No 245
>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=37.49 E-value=3.4e+02 Score=25.13 Aligned_cols=152 Identities=12% Similarity=0.053 Sum_probs=80.7
Q ss_pred EECCCCcHHHHHHHHhC--------CC--CccccC---CCHHHHHHHHHhCCCCeEEEeeeccCc---------------
Q 019548 102 FKGLPGSFSEDAALKAY--------PK--CETVPC---DEFEDTFKAVELWLADKAVLPIENSSS--------------- 153 (339)
Q Consensus 102 yLGP~GTfS~~AA~~~f--------g~--~~~~~~---~si~~Vf~aV~~g~ad~gVVPiENS~~--------------- 153 (339)
..-|+|+...++...+. |. +++.|- -.-.+++++|..|.+|+++++.-+...
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 44588888888776543 22 233333 246899999999999999865322110
Q ss_pred ----------cchhhhH-HHhhcCCeEEEEEEEEeeeeeecc--CCCCCcCCcc--EEEecHHHHHHHHHHHHhcCCeeE
Q 019548 154 ----------GSIHRNY-DLLLRHRLHIVGEVQLAANFCLLA--LPGIKADQLK--RVLSHPQALASSDIVLTQLGVARE 218 (339)
Q Consensus 154 ----------G~V~~tl-DlL~~~~l~I~gEi~l~I~h~Ll~--~~g~~l~~I~--~VySHpqal~QC~~~L~~~~~~~i 218 (339)
+...+.+ +.+.+.++++.+-......+ +.. .+-.+++|++ +|...+-.. -.++++..++..+
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~~g~~~-~~~~~~~i~s~~Dl~G~kir~~~~~~--~~~~~~~~Ga~~v 159 (257)
T TIGR00787 83 DYNHVHKVLDGEVGKALKKSLEKKGLKGLAYWDNGFRQ-FTSSKKPITKPEDLKGLKIRIPNSPM--NEAQFKALGANPE 159 (257)
T ss_pred CHHHHHHHHcCHHHHHHHHHHHHcCcEEEeecCCceeE-eeeCCCccCChHHhCCCEEecCCCHH--HHHHHHHcCCccc
Confidence 0000001 11334466666533322222 222 2323455554 444433221 3567777776655
Q ss_pred ecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCceeeccc
Q 019548 219 NVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRI 259 (339)
Q Consensus 219 ~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~il~~~I 259 (339)
.-+.++.-..+..+ .-.+++.+......++|.=+.+++
T Consensus 160 -~~~~~e~~~aL~~G--~vDg~~~~~~~~~~~~~~ev~~y~ 197 (257)
T TIGR00787 160 -PMAFSEVYTALQTG--VVDGQENPLSNVYSSKFYEVQKYL 197 (257)
T ss_pred -ccCHHHHHHHHHcC--CcccccCCHHHHhhcchhhhcchh
Confidence 44555666655554 245777877766666775444444
No 246
>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=37.48 E-value=2.5e+02 Score=23.84 Aligned_cols=32 Identities=13% Similarity=-0.088 Sum_probs=22.9
Q ss_pred hCCCCcccc-CCCHHHHHHHHHhCCCCeEEEee
Q 019548 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPI 148 (339)
Q Consensus 117 ~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPi 148 (339)
.++++++.- ..+-.++.+.+.+|++|+|+...
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 25 EAPGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred HCCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 356654422 34567889999999999999854
No 247
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=37.19 E-value=1.3e+02 Score=30.88 Aligned_cols=27 Identities=26% Similarity=0.164 Sum_probs=23.0
Q ss_pred CccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 121 CETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 121 ~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
.++++..++++++.++++|++|+++..
T Consensus 82 ~e~v~~~~~~~ll~aL~~G~iDi~~~~ 108 (482)
T PRK10859 82 LEIKVRDNISQLFDALDKGKADLAAAG 108 (482)
T ss_pred EEEEecCCHHHHHHHHhCCCCCEEecc
Confidence 577788999999999999999976543
No 248
>PRK04374 PII uridylyl-transferase; Provisional
Probab=37.10 E-value=95 Score=34.86 Aligned_cols=53 Identities=13% Similarity=0.199 Sum_probs=39.6
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCC-CceEEEecCCCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR-PLRVVDDSNNGT 337 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~-~w~~~~~~~~~~ 337 (339)
+.|.|-+..+|+||-|+++-+.|+..|+|+..=.--...+. .--|+|+..+|.
T Consensus 795 ~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~~g~ 848 (869)
T PRK04374 795 RRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDEHDR 848 (869)
T ss_pred CeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCC
Confidence 46777788899999999999999999999875443333332 456777666654
No 249
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=36.92 E-value=2.3e+02 Score=26.39 Aligned_cols=105 Identities=12% Similarity=-0.033 Sum_probs=53.2
Q ss_pred HHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc---cEEEecHHHHHHHHHH
Q 019548 133 FKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL---KRVLSHPQALASSDIV 209 (339)
Q Consensus 133 f~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHpqal~QC~~~ 209 (339)
.+.+.+|++|+|+++.+....+.... .|.+.++.+ ..+-+|.+......+++|+ .-|...+ ......|
T Consensus 133 ~~~l~~g~~Dl~i~~~~~~~~~l~~~---~l~~~~~~~----~~~~~~~~~~~~~i~~~dL~~~p~i~~~~--~~~~~~~ 203 (297)
T PRK11139 133 LEDFLRDDVDVAIRYGRGNWPGLRVE---KLLDEYLLP----VCSPALLNGGKPLKTPEDLARHTLLHDDS--REDWRAW 203 (297)
T ss_pred hhhhccCCCCEEEEeCCCCCCCceEE---EeccceeEE----EeCHHHhcccCCCCCHHHhhcCceEeecC--cccHHHH
Confidence 46788899999998765433332211 112223322 2333444333322333333 3343322 2345678
Q ss_pred HHhcCC-----e-eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 210 LTQLGV-----A-RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 210 L~~~~~-----~-~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
+...+. . ...+++...+..++..+ ...|+.+...+..
T Consensus 204 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 246 (297)
T PRK11139 204 FRAAGLDDLNVQQGPIFSHSSMALQAAIHG---QGVALGNRVLAQP 246 (297)
T ss_pred HHHhCCCCcCcccceeeCCHHHHHHHHHhC---CCeEecchhhhHH
Confidence 776433 1 23455665555566553 4577777776654
No 250
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=36.63 E-value=3.1e+02 Score=24.77 Aligned_cols=115 Identities=16% Similarity=0.169 Sum_probs=64.8
Q ss_pred CccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHh-hcCCeEEEEEEEE----eeeee-eccCCCC---CcC
Q 019548 121 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLL-LRHRLHIVGEVQL----AANFC-LLALPGI---KAD 191 (339)
Q Consensus 121 ~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL-~~~~l~I~gEi~l----~I~h~-Ll~~~g~---~l~ 191 (339)
+++++..++.+..+++.+|++|+++.+ ..++-.+ .+.++..++...- +..++ ++++.+. +++
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 688999999999999999999999986 1222223 3456666666554 23344 4555543 234
Q ss_pred Cc---cEEEecHHH---HHHHHHHH-HhcCC------eeEecCCHHHHHHHHHhcCCCCeEEecCHH
Q 019548 192 QL---KRVLSHPQA---LASSDIVL-TQLGV------ARENVDDTASAAQYVASNGLRDAGAVASAR 245 (339)
Q Consensus 192 ~I---~~VySHpqa---l~QC~~~L-~~~~~------~~i~~~STA~AA~~v~~~~~~~~AAIas~~ 245 (339)
|+ +..+..|.. .---+.+| ++++. ..+.+.|-..++..+..+ .-++|++.+..
T Consensus 102 dL~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G-~~Da~~~~~~~ 167 (243)
T PF12974_consen 102 DLKGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNG-KADAAAIPSDA 167 (243)
T ss_dssp HHGGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTT-SSSEEEEEHHH
T ss_pred hcCCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcC-CccEEEEechh
Confidence 44 345556653 24456667 56543 345667777778877765 34555554433
No 251
>PRK05007 PII uridylyl-transferase; Provisional
Probab=36.27 E-value=68 Score=35.98 Aligned_cols=52 Identities=12% Similarity=0.100 Sum_probs=39.7
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeee--eeeCCCCCceEEEecCCCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIE--SRPQRKRPLRVVDDSNNGT 337 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIe--SRP~~~~~w~~~~~~~~~~ 337 (339)
-|.|.+..+|+||-|+.+.+.|+.+|+|+..-. +.+-..-.-.|+|...+|.
T Consensus 701 ~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g~ 754 (884)
T PRK05007 701 GTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGS 754 (884)
T ss_pred eEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCC
Confidence 578888889999999999999999999987554 4433233445888777664
No 252
>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=35.76 E-value=2.4e+02 Score=22.95 Aligned_cols=122 Identities=20% Similarity=0.101 Sum_probs=58.9
Q ss_pred hCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc-
Q 019548 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (339)
Q Consensus 117 ~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (339)
.+++.++.- ..+-.++.+.+.+|++|+|+..-.....+... ..|.+.++.+ ..+-.|-|...+..+++++.
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~~---~~l~~~~~~~----~~~~~hpl~~~~~~~~~~L~~ 97 (197)
T cd08448 25 EYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGLSA---RLLHREPFVC----CLPAGHPLAARRRIDLRELAG 97 (197)
T ss_pred HCCCCeEEEEeCCHHHHHHHHHcCCcceEEEeCCCCCcCceE---EEEecCcEEE----EeeCCCCCcCCCCcCHHHhCC
Confidence 466655433 23568899999999999999753322111111 1122233332 23334444333222333322
Q ss_pred --EEE-ecH---HHHHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 195 --RVL-SHP---QALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 195 --~Vy-SHp---qal~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
-|. +.. ....+-..|+.+.+.. . ..++|...+..++..+ ...+|.+...+.
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08448 98 EPFVLFSREVSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAG---MGVALVPRSLAR 157 (197)
T ss_pred CcEEeeCcccChHHHHHHHHHHHHcCCceeeeeccccHHHHHHHHHcC---CceEecchhhhh
Confidence 232 111 1122333455554432 2 3355555566666653 457777776554
No 253
>COG1484 DnaC DNA replication protein [DNA replication, recombination, and repair]
Probab=35.43 E-value=80 Score=29.86 Aligned_cols=72 Identities=14% Similarity=0.114 Sum_probs=50.3
Q ss_pred CCCceEEEEECCCCc-HHHHHHH---HhCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHH-hhcCCe
Q 019548 94 DGTKVRISFKGLPGS-FSEDAAL---KAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDL-LLRHRL 168 (339)
Q Consensus 94 l~~~~~VayLGP~GT-fS~~AA~---~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDl-L~~~~l 168 (339)
+++...+.++||.|+ -||.|+- ......-.+.+-+..|.+..+....-+ |.....+.- +...+|
T Consensus 102 ~~~~~nl~l~G~~G~GKThLa~Ai~~~l~~~g~sv~f~~~~el~~~Lk~~~~~-----------~~~~~~l~~~l~~~dl 170 (254)
T COG1484 102 FERGENLVLLGPPGVGKTHLAIAIGNELLKAGISVLFITAPDLLSKLKAAFDE-----------GRLEEKLLRELKKVDL 170 (254)
T ss_pred hccCCcEEEECCCCCcHHHHHHHHHHHHHHcCCeEEEEEHHHHHHHHHHHHhc-----------CchHHHHHHHhhcCCE
Confidence 557779999999997 7787642 122223557778888999998875433 555555554 778899
Q ss_pred EEEEEEEE
Q 019548 169 HIVGEVQL 176 (339)
Q Consensus 169 ~I~gEi~l 176 (339)
-|.+|+-.
T Consensus 171 LIiDDlG~ 178 (254)
T COG1484 171 LIIDDIGY 178 (254)
T ss_pred EEEecccC
Confidence 99988654
No 254
>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=34.71 E-value=2.6e+02 Score=22.97 Aligned_cols=123 Identities=18% Similarity=0.102 Sum_probs=61.5
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeecc--CccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcC--
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD-- 191 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS--~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~-- 191 (339)
.+++.++.-. .+-.++.+.+.+|++|+|+...... ..+... ..|.+.++.+ ..+-.|-+......+++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~l~~---~~l~~~~~~~----v~~~~hp~~~~~~~~~~~L 97 (199)
T cd08416 25 RRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDFEV---VPLFEDDIFL----AVPATSPLAASSEIDLRDL 97 (199)
T ss_pred hCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCCCCCeEE---EEeecceEEE----EECCCCcccccCccCHHHh
Confidence 3566544333 3556788999999999999864321 111111 1111222222 23444545432222333
Q ss_pred -CccEEE-ecHHH-HHHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 192 -QLKRVL-SHPQA-LASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 192 -~I~~Vy-SHpqa-l~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
+...|. +.... .....+|+...+.. . ..++|...+.++++.+ ...++.+...++.
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 158 (199)
T cd08416 98 KDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGG---VGYALLPGRIADV 158 (199)
T ss_pred cCCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcC---CcEEEechhhhhh
Confidence 333333 22221 23355666665432 2 3456666666777654 4577777765543
No 255
>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=34.40 E-value=2.6e+02 Score=22.85 Aligned_cols=122 Identities=20% Similarity=0.090 Sum_probs=59.7
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeec-----cCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCc
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIEN-----SSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA 190 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiEN-----S~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l 190 (339)
.++++++.-. .+-.++.+.+.+|++|+|+++-.. ...+... ..|.+.++.++ .+-+|-+...+..++
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~~---~~l~~~~~~~~----~~~~~p~~~~~~~~~ 97 (200)
T cd08423 25 RHPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGLTR---VPLLDDPLDLV----LPADHPLAGREEVAL 97 (200)
T ss_pred hCCCCeEEEEeCCHHHHHHHHhcCCccEEEEeccccccCCCCCCcEE---EEeccCcEEEE----ecCCCCccccCCCCH
Confidence 3565544332 356788999999999999986421 0111110 11122222222 233343332222233
Q ss_pred CCc---cEEE-ecHHHH-HHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 191 DQL---KRVL-SHPQAL-ASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 191 ~~I---~~Vy-SHpqal-~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
+++ .-|. +++... ....+|+.+++.. ...++|...+.++++.+ ...+|.++..+.
T Consensus 98 ~~l~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08423 98 ADLADEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAG---LGVALVPRLALG 160 (200)
T ss_pred HHhcCCceEEecCCchHHHHHHHHHHHcCCCCCeeeeeccHHHHHHHHHcC---CCHhhhhhHHHH
Confidence 333 2232 222222 3345666665432 23466666666777664 457777766554
No 256
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=33.92 E-value=1e+02 Score=28.31 Aligned_cols=49 Identities=16% Similarity=0.191 Sum_probs=35.4
Q ss_pred ceEEEEECCCCcHHHHHHHHhCC--CCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALKAYP--KCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg--~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+|++ ..|++.++-...++. +.+++...+.++++++|.+|++|+.+..
T Consensus 133 g~~Igv--~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~ 183 (259)
T PRK15437 133 GKRVGV--LQGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQD 183 (259)
T ss_pred CCEEEE--ecCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEec
Confidence 457887 457765544333332 3567889999999999999999988753
No 257
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=33.81 E-value=73 Score=30.51 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=36.6
Q ss_pred eEEEEECCCCcHHHHHHHHhCC----CCccccCCCHHHHHHHHHhCCCCeEEE
Q 019548 98 VRISFKGLPGSFSEDAALKAYP----KCETVPCDEFEDTFKAVELWLADKAVL 146 (339)
Q Consensus 98 ~~VayLGP~GTfS~~AA~~~fg----~~~~~~~~si~~Vf~aV~~g~ad~gVV 146 (339)
.+||. ..||.+++...++.. +.+++.+++.++.+++|.+|++|+.+.
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 46776 577777766655443 357889999999999999999998875
No 258
>TIGR00656 asp_kin_monofn aspartate kinase, monofunctional class. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. The protein slr0657 from Synechocystis PCC6803 is extended by a duplication of the C-terminal region corresponding to the beta chain. Incorporation of a second copy of the C-terminal domain may be quite common in this subgroup of aspartokinases.
Probab=33.66 E-value=50 Score=32.97 Aligned_cols=41 Identities=17% Similarity=0.320 Sum_probs=32.6
Q ss_pred EecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecCC
Q 019548 292 TLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNN 335 (339)
Q Consensus 292 ~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~~ 335 (339)
.+.+.||.+.++++.|++.|||+..+- +....-.++++..+
T Consensus 346 ~~~~~~g~~a~i~~~L~~~gIni~~i~---~s~~~is~vv~~~d 386 (401)
T TIGR00656 346 GMVGAPGVASEIFSALEEKNINILMIG---SSETNISFLVDEKD 386 (401)
T ss_pred CcccCccHHHHHHHHHHHCCCcEEEEE---cCCCEEEEEEeHHH
Confidence 346899999999999999999998665 45666777776543
No 259
>PRK03059 PII uridylyl-transferase; Provisional
Probab=33.11 E-value=52 Score=36.80 Aligned_cols=34 Identities=15% Similarity=0.313 Sum_probs=29.8
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeee
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIE 318 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIe 318 (339)
+-|.|.+..+|+||-|+++-+.|+..|+|+..=.
T Consensus 785 ~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~Ak 818 (856)
T PRK03059 785 QYYILSVSANDRPGLLYAIARVLAEHRVSVHTAK 818 (856)
T ss_pred CEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEE
Confidence 4678888889999999999999999999997633
No 260
>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=32.87 E-value=3.7e+02 Score=24.17 Aligned_cols=54 Identities=7% Similarity=0.001 Sum_probs=37.1
Q ss_pred CCceEEEEECCCCcHHHH----HHHHhC----C-CCccccCCCHHHHHHHHHhCCCCeEEEee
Q 019548 95 GTKVRISFKGLPGSFSED----AALKAY----P-KCETVPCDEFEDTFKAVELWLADKAVLPI 148 (339)
Q Consensus 95 ~~~~~VayLGP~GTfS~~----AA~~~f----g-~~~~~~~~si~~Vf~aV~~g~ad~gVVPi 148 (339)
..+++|++.+....+... ...+.| | ++++++..++.+.+.++.+|++|+++.+.
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 456899998754433221 111222 2 35777889999999999999999998653
No 261
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=32.68 E-value=4.2e+02 Score=24.77 Aligned_cols=144 Identities=14% Similarity=0.105 Sum_probs=72.7
Q ss_pred CCCceEEEEECCCCc-HHHHH---HHHhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEee--eccC-ccchhhhHHHhhc
Q 019548 94 DGTKVRISFKGLPGS-FSEDA---ALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPI--ENSS-SGSIHRNYDLLLR 165 (339)
Q Consensus 94 l~~~~~VayLGP~GT-fS~~A---A~~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPi--ENS~-~G~V~~tlDlL~~ 165 (339)
....++|+...+-+. +-... ..+.|+++++.- ..+..++.+.+.+|++|+|+.+- .+.. .+.. ...|.+
T Consensus 93 ~~g~l~ig~~~~~~~~~~~~~l~~~~~~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~---~~~l~~ 169 (305)
T CHL00180 93 QRGTLIIGASQTTGTYLMPRLIGLFRQRYPQINVQLQVHSTRRIAWNVANGQIDIAIVGGEVPTELKKILE---ITPYVE 169 (305)
T ss_pred cCceEEEEEcCcchHhHHHHHHHHHHHHCCCceEEEEeCCHHHHHHHHHcCCccEEEEcCccCccccccee---EEEecc
Confidence 456788998877654 32222 123456655543 33578889999999999999842 1110 1111 111122
Q ss_pred CCeEEEEEEEEeeeeeeccCCCCCcCCc---cEEEecH-HHH-HHHHHHHHhcCCe------eEecCCHHHHHHHHHhcC
Q 019548 166 HRLHIVGEVQLAANFCLLALPGIKADQL---KRVLSHP-QAL-ASSDIVLTQLGVA------RENVDDTASAAQYVASNG 234 (339)
Q Consensus 166 ~~l~I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp-qal-~QC~~~L~~~~~~------~i~~~STA~AA~~v~~~~ 234 (339)
.++.++ ++-+|-|..+...+++|+ .-|.... ..+ .+-.+|+...+.+ ...++|...+..+++.+
T Consensus 170 ~~~~~v----~~~~~pl~~~~~i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g- 244 (305)
T CHL00180 170 DELALI----IPKSHPFAKLKKIQKEDLYRLNFITLDSNSTIRKVIDNILIQNGIDSKRFKIEMELNSIEAIKNAVQSG- 244 (305)
T ss_pred CcEEEE----ECCCCccccCCccCHHHHccCCceEecCCCcHHHHHHHHHHHcCCCcccceEEEEeCCHHHHHHHHHcC-
Confidence 233222 344455544333333333 3333322 222 2234556554432 34567777777777664
Q ss_pred CCCeEEecCHHHH
Q 019548 235 LRDAGAVASARAA 247 (339)
Q Consensus 235 ~~~~AAIas~~AA 247 (339)
...++.+...+
T Consensus 245 --~g~~~lp~~~~ 255 (305)
T CHL00180 245 --LGAAFVSVSAI 255 (305)
T ss_pred --CcEEEeEhHHH
Confidence 34566554433
No 262
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=32.67 E-value=3.9e+02 Score=24.43 Aligned_cols=56 Identities=18% Similarity=0.198 Sum_probs=34.7
Q ss_pred CCCceEEEEECCCCcHH--H--HHHHHhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeee
Q 019548 94 DGTKVRISFKGLPGSFS--E--DAALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIE 149 (339)
Q Consensus 94 l~~~~~VayLGP~GTfS--~--~AA~~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiE 149 (339)
.....+|+....-+.+- . ...++.|++.++.- ..+-.++++.+.+|++|+|+++-.
T Consensus 87 ~~g~l~i~~~~~~~~~~~~~~l~~~~~~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~~~ 147 (290)
T PRK10837 87 DNGALRIYASSTIGNYILPAMIARYRRDYPQLPLELSVGNSQDVINAVLDFRVDIGLIEGP 147 (290)
T ss_pred hCCeEEEEecchhHhhhhHHHHHHHHHHCCCceEEEEECCHHHHHHHHHhCCceEEEecCC
Confidence 34567777765444321 1 11233466654432 357778999999999999998643
No 263
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=32.19 E-value=97 Score=34.86 Aligned_cols=53 Identities=13% Similarity=0.127 Sum_probs=38.2
Q ss_pred ceEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCC-CceEEEecCCCC
Q 019548 285 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR-PLRVVDDSNNGT 337 (339)
Q Consensus 285 ~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~-~w~~~~~~~~~~ 337 (339)
+-|-|.+..+|+||-|+++-+.|+..|+|+..=.---..+. .--|+|+..+|.
T Consensus 813 ~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~~g~ 866 (895)
T PRK00275 813 PVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADNQ 866 (895)
T ss_pred CeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCCC
Confidence 36778888899999999999999999999864333222332 345666655553
No 264
>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=31.68 E-value=2.9e+02 Score=22.55 Aligned_cols=123 Identities=15% Similarity=0.048 Sum_probs=62.2
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCc---C
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---D 191 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l---~ 191 (339)
+.+++.++.-. .+..+.++.+.+|++|+|+++-.....+. ....|.+.++.++ .+-.|-+......++ .
T Consensus 24 ~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~~l~~~~~~~~~~l~ 96 (196)
T cd08415 24 ARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPGL---ESEPLASGRAVCV----LPPGHPLARKDVVTPADLA 96 (196)
T ss_pred HHCCCcEEEEEecchHHHHHHHHcCCccEEEEeCCCCCCcc---eeeeecccceEEE----EcCCCChHhcCccCHHHhc
Confidence 44666554333 35678999999999999998643211110 1111222232221 223343332222222 2
Q ss_pred CccEEE-ecH-HHHHHHHHHHHhcCC--e-eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 192 QLKRVL-SHP-QALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 192 ~I~~Vy-SHp-qal~QC~~~L~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
+-.-|. .+. ....+..+|+.+++. . ...++|...+.+++..+ ...++.+...++
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 155 (196)
T cd08415 97 GEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAG---LGVAIVDPLTAA 155 (196)
T ss_pred CCcEEEeCCCccHHHHHHHHHHHcCCCceEEEEEeHHHHHHHHHHcC---CCeEEechhhhh
Confidence 333343 222 223456667766543 2 24566666666666654 457777776544
No 265
>PRK06291 aspartate kinase; Provisional
Probab=31.39 E-value=4.6e+02 Score=26.94 Aligned_cols=112 Identities=12% Similarity=0.011 Sum_probs=63.9
Q ss_pred CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHH---HHcCCceeeccccCCCCCeeeEEEEeeCC-CC-C-CC--CCCc
Q 019548 214 GVARENVDDTASAAQYVASNGLRDAGAVASARAA---EIYGLNILADRIQDEPDNITRFLVLARDP-II-P-RT--DKLF 285 (339)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA---~~ygL~il~~~IeD~~~N~TRF~vi~~~~-~~-p-~~--~~~~ 285 (339)
+++.+..-|..+|.++..-+ +-+-.+.|+ ..+|+++.-.+..+....-|..- .... .. + ++ ...+
T Consensus 248 ~a~~i~~l~~~ea~~l~~~G-----~~v~~~~a~~~~~~~~i~i~i~~~~~~~~~gt~i~--~~~~~~~~~V~~It~~~~ 320 (465)
T PRK06291 248 EARVIPKISYIEAMELSYFG-----AKVLHPRTIEPAMEKGIPVRVKNTFNPEFPGTLIT--SDSESSKRVVKAVTLIKN 320 (465)
T ss_pred CCeEccccCHHHHHHHHhCC-----CcccCHHHHHHHHHcCCcEEEecCCCCCCCceEEE--ecccccCcccceEEeeCC
Confidence 34556666777777765432 344444444 45899999988776544555442 2111 10 0 11 1122
Q ss_pred eEEEEEE---ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEec
Q 019548 286 KTSIVFT---LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDS 333 (339)
Q Consensus 286 Ktsi~~~---~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~ 333 (339)
-+.|.+. ..+.||.+.++++.|+++|||.-.|-.- +....-.++++.
T Consensus 321 valIsI~g~~m~~~~g~~arvf~~L~~~gI~V~mIsq~-sse~sIsf~V~~ 370 (465)
T PRK06291 321 VALINISGAGMVGVPGTAARIFSALAEEGVNVIMISQG-SSESNISLVVDE 370 (465)
T ss_pred EEEEEEeCCCCCCCccHHHHHHHHHHHCCCcEEEEEec-CCCceEEEEEeH
Confidence 2333332 2478999999999999999999887421 233344555544
No 266
>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=31.26 E-value=76 Score=26.11 Aligned_cols=117 Identities=12% Similarity=-0.016 Sum_probs=58.4
Q ss_pred hCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc---
Q 019548 117 AYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL--- 193 (339)
Q Consensus 117 ~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I--- 193 (339)
.|++.++.... .+..+.+.+|++|+|++...-...|.. ...|.+.++.++ .+-+| +......+++|+
T Consensus 25 ~~P~i~l~~~~--~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~-~~~~~~~~~~~L~~~ 94 (190)
T cd08483 25 KHPEIELSLLP--SADLVDLRPDGIDVAIRYGNGDWPGLE---SEPLTAAPFVVV----AAPGL-LGDRKVDSLADLAGL 94 (190)
T ss_pred HCCCceEEEEe--cCCcCCCCCCCcCEEEEecCCCCCCcE---EEeecccceEee----eCHHH-HhhCCCCCHHHHhcC
Confidence 35664433322 234577889999999985321122211 123334444433 23344 333222333333
Q ss_pred cEEEecHHHHHHHHHHHHhcCCe-----eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 194 KRVLSHPQALASSDIVLTQLGVA-----RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 194 ~~VySHpqal~QC~~~L~~~~~~-----~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
+-|. +.. ......|+.+.+.. ...++|......+++.+ ...++.++..++
T Consensus 95 ~~i~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~~ 149 (190)
T cd08483 95 PWLQ-ERG-TNEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAG---LGLSIQARALVE 149 (190)
T ss_pred ceec-cCC-chHHHHHHHHcCCCcccccCceeCcHHHHHHHHHcC---CcEEeecHHhhH
Confidence 3333 221 12346777775532 23456666666667664 457777776554
No 267
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=31.02 E-value=95 Score=34.73 Aligned_cols=52 Identities=12% Similarity=0.189 Sum_probs=38.9
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeee--eeeeeCCCCCceEEEecCCCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTK--IESRPQRKRPLRVVDDSNNGT 337 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtk--IeSRP~~~~~w~~~~~~~~~~ 337 (339)
-|.|.+..+|+||-|+++-+.|+.+|+|+.. |.+.....-.-.|+|...+|.
T Consensus 677 ~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~~g~ 730 (854)
T PRK01759 677 GTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNGK 730 (854)
T ss_pred eEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCCC
Confidence 5788888999999999999999999999954 544444434455666555543
No 268
>PRK09084 aspartate kinase III; Validated
Probab=30.34 E-value=3.1e+02 Score=28.14 Aligned_cols=112 Identities=15% Similarity=0.130 Sum_probs=67.2
Q ss_pred CCeeEecCCHHHHHHHHHhcCCCCeEEecCH--HHHHHcCCceeeccccCCCCCeeeEEEEeeCCCCC--CC--CCCceE
Q 019548 214 GVARENVDDTASAAQYVASNGLRDAGAVASA--RAAEIYGLNILADRIQDEPDNITRFLVLARDPIIP--RT--DKLFKT 287 (339)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~--~AA~~ygL~il~~~IeD~~~N~TRF~vi~~~~~~p--~~--~~~~Kt 287 (339)
+++.+..-|-.+|.+++..+ +-.+-+. ..+..++.++.-.+.-|...--|.+- ......+ ++ ...+-+
T Consensus 234 ~a~~i~~is~~ea~ela~~G----a~vlh~~~~~~~~~~~i~i~i~~~~~~~~~GT~I~--~~~~~~~~v~~it~~~~i~ 307 (448)
T PRK09084 234 AAKRIDEISFEEAAEMATFG----AKVLHPATLLPAVRSNIPVFVGSSKDPEAGGTWIC--NDTENPPLFRAIALRRNQT 307 (448)
T ss_pred CCeEcccCCHHHHHHHHhCC----CcccCHHHHHHHHHcCCcEEEEeCCCCCCCceEEe--cCCCCCCeeEEEEeeCCEE
Confidence 45667777788888876543 2223322 23567899999988776444445442 1111111 00 111222
Q ss_pred EEEEEe---cCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 288 SIVFTL---DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 288 si~~~~---~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
.|-+.- .+.||.+.++++.|+++|||.-.|.| ......|.++.+
T Consensus 308 lItv~~~~~~~~~g~~a~if~~l~~~~I~Vd~I~s---se~sIs~~i~~~ 354 (448)
T PRK09084 308 LLTLHSLNMLHARGFLAEVFGILARHKISVDLITT---SEVSVSLTLDTT 354 (448)
T ss_pred EEEEecCCCCccccHHHHHHHHHHHcCCeEEEEec---cCcEEEEEEech
Confidence 333332 36899999999999999999999975 234566666654
No 269
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=30.21 E-value=70 Score=32.50 Aligned_cols=38 Identities=21% Similarity=0.299 Sum_probs=31.3
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 323 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~ 323 (339)
.-.|++.-+|+||.+.++++.++++|||+-.+..+...
T Consensus 338 ~~rlii~h~d~pG~ia~it~~l~~~~iNI~~m~~~~~~ 375 (409)
T PRK11790 338 GHRLLHIHENRPGVLAAINQIFAEQGINIAAQYLQTDG 375 (409)
T ss_pred CceEEEEeCCCCCHHHHHHHHHHhcCCCHHHheeccCC
Confidence 45677777899999999999999999999887664433
No 270
>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=30.08 E-value=3e+02 Score=22.35 Aligned_cols=123 Identities=15% Similarity=0.136 Sum_probs=61.2
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCC---
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ--- 192 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~--- 192 (339)
.+++.++.-. .+-.++++.+.+|++|+|+........+... ..|.+.++.++ .+-.|-|......++++
T Consensus 24 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~~----~~~~~~l~~~~~~~~~~l~~ 96 (197)
T cd08419 24 RHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDLVA---EPFLDNPLVVI----APPDHPLAGQKRIPLERLAR 96 (197)
T ss_pred HCCCceEEEEECCHHHHHHHHhcCCccEEEecCCCCCCCeEE---EEeccCCEEEE----ecCCCCCcCCCCcCHHHHhC
Confidence 3566544332 4677889999999999999743321111111 11222222222 22233332221122222
Q ss_pred ccEEEecH-H-HHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 193 LKRVLSHP-Q-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 193 I~~VySHp-q-al~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
...|.-.+ . ...+-..|+.+++.. ...++|...+.++++.+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 155 (197)
T cd08419 97 EPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAG---LGLSVLSLHTLAL 155 (197)
T ss_pred CCcEEecCCCcHHHHHHHHHHHCCCCcceEEEECCHHHHHHHHHhC---CceEeecHHHHHH
Confidence 22332111 1 123455666665532 34567777777777764 3477778776643
No 271
>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=30.08 E-value=69 Score=26.35 Aligned_cols=107 Identities=16% Similarity=0.014 Sum_probs=51.0
Q ss_pred HHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc---EEE-ecHH-HHHHH
Q 019548 132 TFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK---RVL-SHPQ-ALASS 206 (339)
Q Consensus 132 Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~---~Vy-SHpq-al~QC 206 (339)
..+.+.+|++|+|+++.+....+... ..|.+.++.++ .+-+|- ..++..+++|+. .|. +... .....
T Consensus 38 ~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~~-~~~~~i~~~~l~~~~~i~~~~~~~~~~~~ 109 (194)
T cd08432 38 RLVDFAREGIDLAIRYGDGDWPGLEA---ERLMDEELVPV----CSPALL-AGLPLLSPADLARHTLLHDATRPEAWQWW 109 (194)
T ss_pred CccccccccccEEEEecCCCCCCcce---EEccCCcEEEe----cCHHHH-HhcCCCCHHHhhcCceEEecCcccccHHH
Confidence 46778899999999865433222211 12223333322 222342 222223444443 232 1111 11222
Q ss_pred HHHHHhcCC--e-eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 207 DIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 207 ~~~L~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
.+++...+. . ...++|......+++.+ ...|+.++..++.
T Consensus 110 ~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 152 (194)
T cd08432 110 LWAAGVADVDARRGPRFDDSSLALQAAVAG---LGVALAPRALVAD 152 (194)
T ss_pred HhcCCeeccccCCeEEECCHHHHHHHHHhC---CCeEEeeHHHhhh
Confidence 222222222 2 34567777777777764 4578888876653
No 272
>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=29.98 E-value=3.1e+02 Score=22.41 Aligned_cols=123 Identities=15% Similarity=0.082 Sum_probs=59.7
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc-
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 193 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I- 193 (339)
+.+++.++.-. .+-.++.+.+.+|++|+|+..-.....+... ..|.+..+.+ ..+-.|-+...+..+++++
T Consensus 24 ~~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~ 96 (196)
T cd08456 24 QRHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIER---ERLLRIDGVC----VLPPGHRLAVKKVLTPSDLE 96 (196)
T ss_pred HHCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCeeE---EEeeccCeEE----EecCCCchhccCccCHHHcC
Confidence 34566544333 2456788999999999999854322222111 1111222222 2233344433222223333
Q ss_pred --cEEE-ecHHH-HHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 194 --KRVL-SHPQA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 194 --~~Vy-SHpqa-l~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
..|. .+... ......|+.+.+.. ...++|...+.+++..+ ...++.+...++
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (196)
T cd08456 97 GEPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAG---VGVSVVNPLTAL 155 (196)
T ss_pred CCcEEEecCCcchHHHHHHHHHHCCCCcceEEEEccHHHHHHHHHcC---CeEEEeChhhhc
Confidence 3333 22222 22345666665432 23456666666677654 456777765544
No 273
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=29.66 E-value=3.3e+02 Score=22.70 Aligned_cols=122 Identities=20% Similarity=0.129 Sum_probs=61.8
Q ss_pred hCCCCccccCC-CHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCcc-
Q 019548 117 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 194 (339)
Q Consensus 117 ~fg~~~~~~~~-si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~- 194 (339)
.+++.++.... +-.++.+.+.+|++|+|+.....-..+ +. ...+.+.++.+ .++-+|-|...+ .+++|+.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~-~~--~~~l~~~~~~~----v~~~~h~l~~~~-~~~~dL~~ 96 (200)
T cd08467 25 RAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVPPDG-LV--VRRLYDDGFAC----LVRHGHPALAQE-WTLDDFAT 96 (200)
T ss_pred hCCCCEEEEecCCcccHHHHhhCCCcCEEEecCCCCCcc-ce--eEEeeeccEEE----EEcCCCccccCC-CCHHHHhC
Confidence 46666654443 445889999999999999753211111 11 01122223322 234445444322 3333332
Q ss_pred --EEEec-HH-HHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 195 --RVLSH-PQ-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 195 --~VySH-pq-al~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
.|.-. .. ....-..|+.+.+.. ...++|.....++++.+ ...|+.+...+..
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08467 97 LRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAAT---DLIATVPRRVATQ 155 (200)
T ss_pred CCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcC---CeEEeeHHHHHHH
Confidence 22211 11 112344566665543 34567777777777764 4577888776654
No 274
>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=29.60 E-value=1.1e+02 Score=34.12 Aligned_cols=52 Identities=13% Similarity=0.213 Sum_probs=38.1
Q ss_pred eEEEEEEecCCcchHHHHHHHHHhCCceeeeeeeeeCCCC--CceEEEecCCCC
Q 019548 286 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR--PLRVVDDSNNGT 337 (339)
Q Consensus 286 Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~--~w~~~~~~~~~~ 337 (339)
-|-|.+..+|+||-|+++.+.|+.+|+|+..=.--.+.++ .--|+|...+|.
T Consensus 668 ~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g~ 721 (850)
T TIGR01693 668 GTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGS 721 (850)
T ss_pred eEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCCC
Confidence 5778888999999999999999999999875443333332 345666655543
No 275
>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=29.52 E-value=2e+02 Score=25.62 Aligned_cols=112 Identities=18% Similarity=0.176 Sum_probs=66.5
Q ss_pred HHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCC---eEEEEEEEEeeeeeec---cCCCC---CcCCcc---EEE
Q 019548 130 EDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHR---LHIVGEVQLAANFCLL---ALPGI---KADQLK---RVL 197 (339)
Q Consensus 130 ~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~---l~I~gEi~l~I~h~Ll---~~~g~---~l~~I~---~Vy 197 (339)
.|+-..|+.|.+|+||+= .|.+.++. -.+.--..|+..+|=+ ...+. ++++++ +|.
T Consensus 4 ~DIp~yV~~G~~DlGI~G------------~D~l~E~~~~~~~v~~~~dL~fg~crl~vAvp~~~~~~~~~~l~~~~rIA 71 (163)
T PF01634_consen 4 QDIPTYVEDGIADLGITG------------KDVLLESGLGRADVEELLDLGFGKCRLVVAVPEDWPYKSVEDLKAGLRIA 71 (163)
T ss_dssp GHHHHHHHTTSSSEEEEE------------HHHHHHHTHH-SSEEEEEEESCSEEEEEEEEETTSCGCCGGGGSSTEEEE
T ss_pred HHHHHHHHCCCCcEEEee------------hheeccCCCCccceEEEeecccccEEEEEEEECCcCCCCHHHhccCCEEE
Confidence 577889999999999963 46666544 2355556777777733 22222 234444 777
Q ss_pred ecHHHHHHHHHHHHhcCC--eeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCceee
Q 019548 198 SHPQALASSDIVLTQLGV--ARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILA 256 (339)
Q Consensus 198 SHpqal~QC~~~L~~~~~--~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~il~ 256 (339)
+...-+. ++||+++++ +.+..+-+.|+|=.+--. +.-.=-+.+-...+.+||+++.
T Consensus 72 Tkyp~l~--~~yf~~~g~~~~ii~l~GsvE~ap~~glA-D~IvDiv~TG~TLr~NgL~~i~ 129 (163)
T PF01634_consen 72 TKYPNLT--RRYFAEKGINVEIIKLSGSVELAPPLGLA-DAIVDIVETGTTLRANGLKEIE 129 (163)
T ss_dssp ES-HHHH--HHHHHHCT-EEEEEE-SS-TTHHHHTTSS-SEEEEEESSSHHHHHTTEEEEE
T ss_pred ECCHHHH--HHHHHHcCCcEEEEEccCCccccCCCCCC-CEEEEeccCcHHHHHCCCEEeE
Confidence 7776664 899999864 566666666665432110 0001112556667889999884
No 276
>PRK06635 aspartate kinase; Reviewed
Probab=29.29 E-value=57 Score=32.60 Aligned_cols=40 Identities=25% Similarity=0.357 Sum_probs=31.5
Q ss_pred EecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 292 TLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 292 ~~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
.+++.||.+.++++.|+++|||+..|.+ ....-.|+++.+
T Consensus 349 ~~~~~~g~~a~i~~~La~~~Ini~~i~s---s~~~is~vv~~~ 388 (404)
T PRK06635 349 GMRSHPGVAAKMFEALAEEGINIQMIST---SEIKISVLIDEK 388 (404)
T ss_pred CCCCCchHHHHHHHHHHHCCCCEEEEEe---cCCeEEEEEcHH
Confidence 3578999999999999999999999864 345566666543
No 277
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=29.16 E-value=4.8e+02 Score=24.39 Aligned_cols=145 Identities=13% Similarity=0.044 Sum_probs=70.7
Q ss_pred CCCceEEEEECCCCcH-HHHH---HHHhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeecc-CccchhhhHHHhhcCC
Q 019548 94 DGTKVRISFKGLPGSF-SEDA---ALKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENS-SSGSIHRNYDLLLRHR 167 (339)
Q Consensus 94 l~~~~~VayLGP~GTf-S~~A---A~~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS-~~G~V~~tlDlL~~~~ 167 (339)
.....+|+.....+++ --.. ..+.|++.++.- ..+.+++.+.+.+|++|+|+.+-... ..+... ..|.+.+
T Consensus 91 ~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~l~~---~~l~~~~ 167 (309)
T PRK12682 91 DSGTLTIATTHTQARYVLPRVVAAFRKRYPKVNLSLHQGSPDEIARMVISGEADIGIATESLADDPDLAT---LPCYDWQ 167 (309)
T ss_pred CCCeEEEeeCchHHHHHHHHHHHHHHHhCCCeEEEEecCCHHHHHHHHHcCCccEEEecCcccCCCcceE---EEeeeee
Confidence 3455788776444332 1111 123356655543 34678999999999999999853211 111000 0000111
Q ss_pred eEEEEEEEEeeeeeeccCCCCCcCCc---cEEEe-cHHH-HHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeE
Q 019548 168 LHIVGEVQLAANFCLLALPGIKADQL---KRVLS-HPQA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAG 239 (339)
Q Consensus 168 l~I~gEi~l~I~h~Ll~~~g~~l~~I---~~VyS-Hpqa-l~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~A 239 (339)
+ -+.++..|-|......+++++ ..|.- .... ..+-..|+..++.. ...++|.....+++..+ ...
T Consensus 168 ~----~~~~~~~~pl~~~~~~~~~~L~~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~Gi 240 (309)
T PRK12682 168 H----AVIVPPDHPLAQEERITLEDLAEYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLG---LGV 240 (309)
T ss_pred E----EEEecCCCccccCCCcCHHHHhcCCceeeCCCccHHHHHHHHHHHcCCCCcEEEEeCCHHHHHHHHHhC---Cce
Confidence 1 123344454443222233333 22321 1111 12345566665543 24567788788888765 346
Q ss_pred EecCHHHHH
Q 019548 240 AVASARAAE 248 (339)
Q Consensus 240 AIas~~AA~ 248 (339)
++.+...++
T Consensus 241 ~~lp~~~~~ 249 (309)
T PRK12682 241 GIVAEMAYR 249 (309)
T ss_pred EEehhhhhh
Confidence 666665543
No 278
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=29.07 E-value=4.5e+02 Score=29.41 Aligned_cols=111 Identities=14% Similarity=0.095 Sum_probs=66.5
Q ss_pred CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHH---HcCCceeeccccCCCCCeeeEEEEeeCCCCC--CC--CCCce
Q 019548 214 GVARENVDDTASAAQYVASNGLRDAGAVASARAAE---IYGLNILADRIQDEPDNITRFLVLARDPIIP--RT--DKLFK 286 (339)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~---~ygL~il~~~IeD~~~N~TRF~vi~~~~~~p--~~--~~~~K 286 (339)
+++.+..-|..+|.+++..+ |.+-.+.|++ .+|.++.-.+..+....-|..- ......+ ++ ...+-
T Consensus 250 ~a~~i~~ls~~e~~el~~~g-----~~v~~~~a~~~a~~~~i~i~v~~~~~~~~~gT~I~--~~~~~~~~v~~It~~~~v 322 (861)
T PRK08961 250 DARLLTRLDYDEAQEIATTG-----AKVLHPRSIKPCRDAGIPMAILDTERPDLSGTSID--GDAEPVPGVKAISRKNGI 322 (861)
T ss_pred CceEecccCHHHHHHHHHCC-----CeEECHHHHHHHHHCCCCEEEEeCCCCCCCccEEe--CCCCCCCcceeEEEECCE
Confidence 34566667777877766542 4555555544 4799999988765443444432 1111111 11 11223
Q ss_pred EEEEEE---ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 287 TSIVFT---LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 287 tsi~~~---~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
+.|.+. ..+.||.+.++++.|+++|||.-.|.|- .....+.++..
T Consensus 323 ~lItv~~~~~~~~~g~~a~if~~la~~~I~Vd~I~ss---e~sis~~i~~~ 370 (861)
T PRK08961 323 VLVSMETIGMWQQVGFLADVFTLFKKHGLSVDLISSS---ETNVTVSLDPS 370 (861)
T ss_pred EEEEEecCCccccccHHHHHHHHHHHcCCeEEEEEcC---CCEEEEEEccc
Confidence 333342 3478999999999999999999999542 34455555543
No 279
>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=28.92 E-value=4.8e+02 Score=24.35 Aligned_cols=136 Identities=14% Similarity=-0.019 Sum_probs=69.4
Q ss_pred EEEEECCCCcHHHHHHHH-hC----C-CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHh-hcCCeEEE
Q 019548 99 RISFKGLPGSFSEDAALK-AY----P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLL-LRHRLHIV 171 (339)
Q Consensus 99 ~VayLGP~GTfS~~AA~~-~f----g-~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL-~~~~l~I~ 171 (339)
+|+|+=.. +-...|-.+ +| | +++++++.+-.++++++.+|++|++++... .++... ...+++++
T Consensus 2 ~~~~~~~~-~p~~va~~~G~~~k~~Gl~Ve~~~~~~~~~~~~al~~G~iD~~~~~~~--------~~~~a~~~g~~~~~v 72 (300)
T TIGR01729 2 TVGYQTIV-EPFKVAQADGAAAKEAGATIDWRKFDSGADISTALASGNVPIGVIGSS--------PLAAAASRGVPIELF 72 (300)
T ss_pred EEEecCCC-CHHHHHHHcCchHHhcCCeeEEEecCcHHHHHHHHHcCCCCEeccCCC--------HHHHHHHCCCCeEEE
Confidence 67885322 323333322 22 3 368899999999999999999999875321 111111 12345544
Q ss_pred EEEE-EeeeeeeccCCCC---CcCCcc--EEEecHHH--HHHHHHHHHhcCC-----eeEecCCHHHHHHHHHhcCCCCe
Q 019548 172 GEVQ-LAANFCLLALPGI---KADQLK--RVLSHPQA--LASSDIVLTQLGV-----ARENVDDTASAAQYVASNGLRDA 238 (339)
Q Consensus 172 gEi~-l~I~h~Ll~~~g~---~l~~I~--~VySHpqa--l~QC~~~L~~~~~-----~~i~~~STA~AA~~v~~~~~~~~ 238 (339)
.-.. ..-.+.|+++++. +++|++ +|..++-. ...-..||++.+. +.+.. +..+++..+..+ .-++
T Consensus 73 ~~~~~~~~~~~lv~~~~s~I~s~~DLkGK~Igv~~~s~~~~~l~~~L~~~Gl~~~dv~~v~~-~~~~~~~al~~G-~vDa 150 (300)
T TIGR01729 73 WILDNIGKSEALVAREGSGIEKPEDLKGKNVAVPFVSTTHYSLLAALKHWKTDPREVNILNL-KPPQIVAAWQRG-DIDA 150 (300)
T ss_pred EEeccCCccceEEecCCCCCCChhHcCCCEEEeCCCCcHHHHHHHHHHHcCCChhheEEEec-CcHHHHHHHHcC-CcCE
Confidence 3221 1123467776552 233433 55544321 1223457876553 34444 344555555554 2344
Q ss_pred EEecCHH
Q 019548 239 GAVASAR 245 (339)
Q Consensus 239 AAIas~~ 245 (339)
+++..+.
T Consensus 151 ~~~~~p~ 157 (300)
T TIGR01729 151 AYVWPPA 157 (300)
T ss_pred EEEecHH
Confidence 4444443
No 280
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=28.70 E-value=3.6e+02 Score=24.57 Aligned_cols=37 Identities=8% Similarity=0.175 Sum_probs=26.0
Q ss_pred HHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEEee
Q 019548 111 EDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPI 148 (339)
Q Consensus 111 ~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPi 148 (339)
++++...--+.++++. +...++.++++|++|..+-|+
T Consensus 57 ~~ia~~lg~~i~~~~~-pw~~~~~~l~~g~~D~~~~~~ 93 (259)
T PRK15437 57 KELCKRINTQCTFVEN-PLDALIPSLKAKKIDAIMSSL 93 (259)
T ss_pred HHHHHHcCCceEEEeC-CHHHHHHHHHCCCCCEEEecC
Confidence 3444433224677775 499999999999999776555
No 281
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.43 E-value=71 Score=23.29 Aligned_cols=40 Identities=23% Similarity=0.218 Sum_probs=29.2
Q ss_pred ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecCC
Q 019548 293 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNN 335 (339)
Q Consensus 293 ~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~~ 335 (339)
+.+.||.+.++++.|++.+|++-..-. ....-.++++.++
T Consensus 10 ~~~~~gv~~~~~~~L~~~~i~~i~~~~---s~~~is~vv~~~d 49 (63)
T cd04920 10 IRSLLHKLGPALEVFGKKPVHLVSQAA---NDLNLTFVVDEDQ 49 (63)
T ss_pred cccCccHHHHHHHHHhcCCceEEEEeC---CCCeEEEEEeHHH
Confidence 457899999999999999998844433 3455667776543
No 282
>PRK02228 V-type ATP synthase subunit F; Provisional
Probab=28.13 E-value=2.8e+02 Score=22.39 Aligned_cols=64 Identities=13% Similarity=0.167 Sum_probs=41.4
Q ss_pred eEEEEECCCCcHHHHHHHHhCCCCccccCCC---HHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhc
Q 019548 98 VRISFKGLPGSFSEDAALKAYPKCETVPCDE---FEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLR 165 (339)
Q Consensus 98 ~~VayLGP~GTfS~~AA~~~fg~~~~~~~~s---i~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~ 165 (339)
||||..|.+-|- -..+..|=....++.+ +.++|+.+.. +-|||||=|.......+.++++-+.+
T Consensus 1 mkIaVIGD~dtv---~GFrLaGi~~~~~~~~~ee~~~~l~~l~~-~~d~gII~Ite~~~~~i~e~i~~~~~ 67 (100)
T PRK02228 1 MEIAVIGSPEFT---TGFRLAGIRKVYEVPDDEKLDEAVEEVLE-DDDVGILVMHDDDLEKLPRRLRRTLE 67 (100)
T ss_pred CEEEEEeCHHHH---HHHHHcCCceEEeeCCHHHHHHHHHHHhh-CCCEEEEEEehhHhHhhHHHHHHHHh
Confidence 688998883322 1223444323444555 5566666643 34999999999999889988886443
No 283
>PRK11074 putative DNA-binding transcriptional regulator; Provisional
Probab=27.86 E-value=2.8e+02 Score=25.87 Aligned_cols=146 Identities=13% Similarity=0.097 Sum_probs=72.1
Q ss_pred CCCceEEEEECCCCcHH-HHHH---HHhCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCc-cchhhhHHHhhcCC
Q 019548 94 DGTKVRISFKGLPGSFS-EDAA---LKAYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSS-GSIHRNYDLLLRHR 167 (339)
Q Consensus 94 l~~~~~VayLGP~GTfS-~~AA---~~~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~-G~V~~tlDlL~~~~ 167 (339)
.....+|++..+-+.+- -.+. .+.|++.++.- ..+-.++.+.+.+|++|+||++..+... +.+ ....|.+.+
T Consensus 90 ~~g~l~Ig~~~~~~~~~l~~~l~~~~~~~p~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l--~~~~l~~~~ 167 (300)
T PRK11074 90 WRGQLSIAVDNIVRPDRTRQLIVDFYRHFDDVELIIRQEVFNGVWDALADGRVDIAIGATRAIPVGGRF--AFRDMGMLS 167 (300)
T ss_pred CCceEEEEEcCccchhHHHHHHHHHHHhCCCceEEEEehhhhHHHHHHHCCCCCEEEecCccCCccccc--ceeecccce
Confidence 45678899765554322 2221 22356654432 2456778999999999999986542111 111 011223334
Q ss_pred eEEEEEEEEeeeeeeccCCC-CCcCC---ccEEEe-cHH-HHHHHHHHHHhcCCeeEecCCHHHHHHHHHhcCCCCeEEe
Q 019548 168 LHIVGEVQLAANFCLLALPG-IKADQ---LKRVLS-HPQ-ALASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAV 241 (339)
Q Consensus 168 l~I~gEi~l~I~h~Ll~~~g-~~l~~---I~~VyS-Hpq-al~QC~~~L~~~~~~~i~~~STA~AA~~v~~~~~~~~AAI 241 (339)
+.++ ++-.|-|...++ .+++| -..|.. +.. ...+...|+..... ...++|.....++++.+ ...++
T Consensus 168 ~~~v----~~~~hpl~~~~~~~~~~dl~~~p~i~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~v~~g---~gi~~ 239 (300)
T PRK11074 168 WACV----VSSDHPLASMDGPLSDDELRPYPSLCLEDTSRTLPKRITWLLDNQR-RLVVPDWESAINCLSAG---LCVGM 239 (300)
T ss_pred EEEE----EcCCCcccccCCCCCHHHHhhCCEEEecCCCcccccCccceecCCc-eEEECCHHHHHHHHHcC---CeEEe
Confidence 4332 344554443322 23333 233322 221 12223334433222 34466666666777654 45777
Q ss_pred cCHHHHHH
Q 019548 242 ASARAAEI 249 (339)
Q Consensus 242 as~~AA~~ 249 (339)
.+....+.
T Consensus 240 lp~~~~~~ 247 (300)
T PRK11074 240 VPTHFAKP 247 (300)
T ss_pred CCHHHhHH
Confidence 77776654
No 284
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=27.62 E-value=97 Score=29.05 Aligned_cols=50 Identities=22% Similarity=0.198 Sum_probs=36.4
Q ss_pred ceEEEEECCCCcHHHHHHHHhCCC-------CccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALKAYPK-------CETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~~fg~-------~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
..+|.+ |+.|+.++....+++.. ...+++.+..+++.++.+|++|.++..
T Consensus 141 gk~v~~-~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 141 GKRVAV-GAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred CCEEec-CCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEEe
Confidence 346765 56677777665554421 224678899999999999999999975
No 285
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=27.35 E-value=1.1e+02 Score=28.54 Aligned_cols=110 Identities=21% Similarity=0.213 Sum_probs=62.0
Q ss_pred CHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeee---eccCCCCCc------CCccEEEe
Q 019548 128 EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFC---LLALPGIKA------DQLKRVLS 198 (339)
Q Consensus 128 si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~---Ll~~~g~~l------~~I~~VyS 198 (339)
-..|+-..|+.|.+|+||+= .|.|.++.-.+.--..|...+| +++.++... ..-++|.+
T Consensus 53 r~~DIp~yV~~G~~DlGItG------------~D~l~E~~~~v~~l~dLgfG~crl~vAvp~~~~~~~~~~~~~~~rIAT 120 (215)
T PRK01686 53 RATDVPTYVEHGAADLGIVG------------KDVLLEHGKDLYEPLDLGIGKCRMSVAVPPGFDYAPAVKQGPRLRVAT 120 (215)
T ss_pred CHHHHHHHHhCCCccEEEee------------eeEeeecCCCeEEEecCCccCEEEEEEEECcccccchhhccCCCEEEe
Confidence 34689999999999999974 3445444322333334566666 333332211 11246666
Q ss_pred cHHHHHHHHHHHHhcCC--eeEecCCHHHHHHHHHhcCCCCeEEe----cCHHHHHHcCCceee
Q 019548 199 HPQALASSDIVLTQLGV--ARENVDDTASAAQYVASNGLRDAGAV----ASARAAEIYGLNILA 256 (339)
Q Consensus 199 Hpqal~QC~~~L~~~~~--~~i~~~STA~AA~~v~~~~~~~~AAI----as~~AA~~ygL~il~ 256 (339)
..--+. ++|++++++ +++..+-..|+|=.+ +-+-|| .+-...+.+||+++.
T Consensus 121 kYp~it--~~yf~~~gv~~~iv~l~GsvE~aP~~-----GlAD~IvDivsTG~TLr~NgL~~ie 177 (215)
T PRK01686 121 KYPNIA--RRYFAEKGEQVEIIKLYGSVELAPLV-----GLADAIVDIVETGNTLRANGLVEVE 177 (215)
T ss_pred CCHHHH--HHHHHHcCCeEEEEECcCceeecccc-----CCccEEEEeecChHHHHHCcCEEee
Confidence 555554 569998865 445544444433211 112133 355667889999986
No 286
>PRK06526 transposase; Provisional
Probab=26.72 E-value=2.6e+02 Score=26.42 Aligned_cols=71 Identities=23% Similarity=0.177 Sum_probs=44.6
Q ss_pred CCCceEEEEECCCCc-HHHHHH---HHhCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeE
Q 019548 94 DGTKVRISFKGLPGS-FSEDAA---LKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (339)
Q Consensus 94 l~~~~~VayLGP~GT-fS~~AA---~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~ 169 (339)
.+....+.+.||.|| =||.|. .........+.+.+..+.++.+.... ..|.....+.-+.+.++-
T Consensus 95 i~~~~nlll~Gp~GtGKThLa~al~~~a~~~g~~v~f~t~~~l~~~l~~~~-----------~~~~~~~~l~~l~~~dlL 163 (254)
T PRK06526 95 VTGKENVVFLGPPGTGKTHLAIGLGIRACQAGHRVLFATAAQWVARLAAAH-----------HAGRLQAELVKLGRYPLL 163 (254)
T ss_pred hhcCceEEEEeCCCCchHHHHHHHHHHHHHCCCchhhhhHHHHHHHHHHHH-----------hcCcHHHHHHHhccCCEE
Confidence 556778999999998 556554 21111223345667778887776432 235555566666677888
Q ss_pred EEEEEE
Q 019548 170 IVGEVQ 175 (339)
Q Consensus 170 I~gEi~ 175 (339)
|++|+-
T Consensus 164 IIDD~g 169 (254)
T PRK06526 164 IVDEVG 169 (254)
T ss_pred EEcccc
Confidence 887763
No 287
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=26.70 E-value=80 Score=35.21 Aligned_cols=35 Identities=26% Similarity=0.226 Sum_probs=30.7
Q ss_pred CceEEEEEEecCCcchHHHHHHHHHhCCceeeeee
Q 019548 284 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIE 318 (339)
Q Consensus 284 ~~Ktsi~~~~~~~pGaL~~iL~~Fa~~gINLtkIe 318 (339)
+++|.|=+...|+||.|+.+.+.|++.++++-...
T Consensus 789 ~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~Ak 823 (867)
T COG2844 789 NDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAK 823 (867)
T ss_pred CCceEEEEEeCCcccHHHHHHHHHHhcccceeeee
Confidence 35888889999999999999999999999987543
No 288
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=26.35 E-value=3.5e+02 Score=21.91 Aligned_cols=122 Identities=12% Similarity=-0.001 Sum_probs=61.9
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCccE
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR 195 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I~~ 195 (339)
.|++.++.-. .+-+++.+.+.+|++|+|++.-..-..+... ..|.+.++.++ .+-+|-+... -.++.+...
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~~~~~~-~~~l~~~~~ 96 (193)
T cd08442 25 RYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLEQ---EPVFQEELVLV----SPKGHPPVSR-AEDLAGSTL 96 (193)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEEeCCCCCCCcEE---EEeecCcEEEE----ecCCCccccc-HHHhCCCce
Confidence 4666554333 3567899999999999999753221111111 11112222221 1222322211 012333333
Q ss_pred EEec-H-HHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHHH
Q 019548 196 VLSH-P-QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 249 (339)
Q Consensus 196 VySH-p-qal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ 249 (339)
|.-. . ....+...|+.+.+.. ...++|...+..++.++ ...++.+...++.
T Consensus 97 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 152 (193)
T cd08442 97 LAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAG---MGIALLPRSVLDS 152 (193)
T ss_pred EEecCCCcHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHhC---CcEEEcCHHHHhh
Confidence 3211 1 1234567788776433 24567776677777664 4578888877653
No 289
>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=26.29 E-value=3.6e+02 Score=21.92 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=23.3
Q ss_pred CCCCccccC-CCHHHHHHHHHhCCCCeEEEeee
Q 019548 118 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIE 149 (339)
Q Consensus 118 fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiE 149 (339)
+++.++.-. .+..++.+.+.+|++|+|++.-+
T Consensus 26 ~p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (197)
T cd08414 26 YPDVELELREMTTAEQLEALRAGRLDVGFVRPP 58 (197)
T ss_pred CCCcEEEEecCChHHHHHHHHcCCccEEEEcCC
Confidence 555544332 35688999999999999998643
No 290
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=26.11 E-value=3.8e+02 Score=22.19 Aligned_cols=121 Identities=15% Similarity=0.079 Sum_probs=60.7
Q ss_pred hCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCCc--
Q 019548 117 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 193 (339)
Q Consensus 117 ~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I-- 193 (339)
.|++.++... .+..++.+.+.+|++|+|+..-.....|... ..|.+..+.+ .++-+|-+...+..+++|+
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~----v~~~~hpl~~~~~i~~~dL~~ 97 (196)
T cd08458 25 DRPDVSVYLDTVPSQTVLELVSLQHYDLGISILAGDYPGLTT---EPVPSFRAVC----LLPPGHRLEDKETVHATDLEG 97 (196)
T ss_pred HCCCcEEEEeccChHHHHHHHHcCCCCEEEEeccCCCCCceE---EEeccCceEE----EecCCCccccCCccCHHHhCC
Confidence 4666555433 4677899999999999999843211111111 1122223222 2344454443322333333
Q ss_pred -cEEE-ecH-HHHHHHHHHHHhcCC--e-eEecCCHHHHHHHHHhcCCCCeEEecCHHHH
Q 019548 194 -KRVL-SHP-QALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAA 247 (339)
Q Consensus 194 -~~Vy-SHp-qal~QC~~~L~~~~~--~-~i~~~STA~AA~~v~~~~~~~~AAIas~~AA 247 (339)
.-|. +.. ....+...|+++.+. . ...++|...+..++..+ ...|+.+...+
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~l~~~~~ 154 (196)
T cd08458 98 ESLICLSPVSLLRMQTDAALDSCGVHCNRRIESSLALNLCDLVSRG---MGVGIVDPFTA 154 (196)
T ss_pred CccEEecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcEEEECchhh
Confidence 2332 211 123455677777653 2 23456666566666654 45667766544
No 291
>PLN02551 aspartokinase
Probab=25.78 E-value=5.2e+02 Score=27.31 Aligned_cols=112 Identities=13% Similarity=0.051 Sum_probs=66.4
Q ss_pred CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHH---HHHcCCceeeccccCCCCCeeeEEEEeeC-CC-CCCC--CCCce
Q 019548 214 GVARENVDDTASAAQYVASNGLRDAGAVASARA---AEIYGLNILADRIQDEPDNITRFLVLARD-PI-IPRT--DKLFK 286 (339)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~A---A~~ygL~il~~~IeD~~~N~TRF~vi~~~-~~-~p~~--~~~~K 286 (339)
++..+..-|-.||.+++.-+ |-+=.+.+ |..++.+|.-+|--+...--|..-- ... .. ..++ ...+-
T Consensus 293 ~A~~l~~lsy~Ea~elA~~G-----akVlhp~ai~pa~~~~Ipi~vknt~~p~~~GT~I~~-~~~~~~~~v~~It~~~~v 366 (521)
T PLN02551 293 NAVPVPYLTFDEAAELAYFG-----AQVLHPQSMRPAREGDIPVRVKNSYNPTAPGTLITK-TRDMSKAVLTSIVLKRNV 366 (521)
T ss_pred CceEecccCHHHHHHHHhCC-----CcccCHHHHHHHHHCCceEEEEecCCCCCCCcEEec-ccccCCCcccceecCCCe
Confidence 35667778899999987653 33333333 4668999999887653333444311 110 00 0111 11223
Q ss_pred EEEEEE---ecCCcchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecC
Q 019548 287 TSIVFT---LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSN 334 (339)
Q Consensus 287 tsi~~~---~~~~pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~ 334 (339)
+.|-+. ..+.||.+.++++.|+++|||.-.|-+ ....-.+.++.+
T Consensus 367 ~li~i~~~~m~~~~g~~arvf~~l~~~~I~Vd~Iss---Se~sIs~~v~~~ 414 (521)
T PLN02551 367 TMLDIVSTRMLGQYGFLAKVFSTFEDLGISVDVVAT---SEVSISLTLDPS 414 (521)
T ss_pred EEEEEecCCCCCcccHHHHHHHHHHHcCCcEEEEec---cCCEEEEEEehh
Confidence 344343 236899999999999999999998843 234455555544
No 292
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=25.72 E-value=5.6e+02 Score=24.00 Aligned_cols=122 Identities=15% Similarity=0.046 Sum_probs=60.0
Q ss_pred hCCCCccc-cCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCc---CC
Q 019548 117 AYPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---DQ 192 (339)
Q Consensus 117 ~fg~~~~~-~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l---~~ 192 (339)
.+++.++. -..+..++.+.+.+|++|+|+..-.=...|... ..+.+.++ -+.+|..|-+...+..++ .+
T Consensus 119 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~----~~~~~~~~pl~~~~~i~~~dL~~ 191 (309)
T PRK11013 119 RYPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAGTER---TELLTLDE----VCVLPAGHPLAAKKVLTPDDFAG 191 (309)
T ss_pred HCCCCeEEEEeCCHHHHHHHHHcCCCCEEEEcCCCCCCCcee---eeecceeE----EEEEcCCCccccCCccCHHHHCC
Confidence 35665443 234567889999999999999742100111111 11111111 133566666654332233 33
Q ss_pred ccEEEecH-HHH-HHHHHHHHhcCCe--e-EecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 193 LKRVLSHP-QAL-ASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 193 I~~VySHp-qal-~QC~~~L~~~~~~--~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
.+.|.-.+ ... ..+..|+..++.. . ..++|...+.+++..+ ...++.+...+.
T Consensus 192 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gv~~~p~~~~~ 249 (309)
T PRK11013 192 ENFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAG---VGVSIVNPLTAL 249 (309)
T ss_pred CcEEeecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEeChhhhc
Confidence 34454332 222 3356677776543 2 3344444455555543 345666655443
No 293
>TIGR00657 asp_kinases aspartate kinase. The Lys-sensitive enzyme of Bacillus subtilis resembles the E. coli form but is an alpha 2/beta 2 heterotetramer, where the beta subunit is translated from an in-phase alternative initiator at Met-246. This may be a feature of a number of closely related forms, including a paralog from B. subtilis.
Probab=25.36 E-value=4.7e+02 Score=26.53 Aligned_cols=119 Identities=13% Similarity=0.088 Sum_probs=0.0
Q ss_pred CCeeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCceeeccccCCCCCeeeEEEEe--eCCCCCCCCCCceEEEEE
Q 019548 214 GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLA--RDPIIPRTDKLFKTSIVF 291 (339)
Q Consensus 214 ~~~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~il~~~IeD~~~N~TRF~vi~--~~~~~p~~~~~~Ktsi~~ 291 (339)
+++.+..-|..+|.+++..+ ...-=..+-.-+..++.++.-.+-.+....-|..---. ......+.-...+--.++
T Consensus 228 ~a~~i~~is~~ea~el~~~G--~~v~~~~a~~~~~~~~i~i~i~~~~~~~~~GT~I~~~~~~~~~~~i~~It~~~~v~~I 305 (441)
T TIGR00657 228 DARRIDEISYEEMLELASFG--AKVLHPRTLEPAMRAKIPIVVKSTFNPEAPGTLIVASTKEMEEPIVKGLSLDRNQARV 305 (441)
T ss_pred CCeECCccCHHHHHHHHhcC--CcccCHHHHHHHHHcCCeEEEecCCCCCCCceEEEeCCCccccCccceEEEeCCEEEE
Q ss_pred Ee---cCC-cchHHHHHHHHHhCCceeeeeeeeeCCCCCceEEEecCC
Q 019548 292 TL---DEG-PGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNN 335 (339)
Q Consensus 292 ~~---~~~-pGaL~~iL~~Fa~~gINLtkIeSRP~~~~~w~~~~~~~~ 335 (339)
++ ... ||.+.++++.|+++|||.-.| +-++....-.++++.++
T Consensus 306 sv~g~~~~~~g~la~if~~L~~~~I~I~~i-~q~~se~sIs~~I~~~~ 352 (441)
T TIGR00657 306 TVSGLGMKGPGFLARVFGALAEAGINVDLI-TQSSSETSISFTVDKED 352 (441)
T ss_pred EEECCCCCCccHHHHHHHHHHHcCCeEEEE-EecCCCceEEEEEEHHH
No 294
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=25.20 E-value=1.3e+02 Score=31.69 Aligned_cols=78 Identities=17% Similarity=0.176 Sum_probs=50.0
Q ss_pred CHHHHHHcCCceeeccc--cCCCCCeeeEEEEeeCCCC-----CCC---------------CCCceEEEEEEecCCcchH
Q 019548 243 SARAAEIYGLNILADRI--QDEPDNITRFLVLARDPII-----PRT---------------DKLFKTSIVFTLDEGPGVL 300 (339)
Q Consensus 243 s~~AA~~ygL~il~~~I--eD~~~N~TRF~vi~~~~~~-----p~~---------------~~~~Ktsi~~~~~~~pGaL 300 (339)
+...|+..|+++-.... .+...|+-++.+-+..... ..+ -..+...|++.-.|+||.+
T Consensus 387 A~~iA~e~GI~~~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~ggg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I 466 (526)
T PRK13581 387 APLLAKERGIEVEESKSEESPDYSNLITVTVTTDDGERSVAGTVFGDGEPRIVEIDGYRVDAKPEGHMLIIRNRDRPGVI 466 (526)
T ss_pred HHHHHHHcCCEEEEEEecCCCCCCCEEEEEEEeCCeEEEEEEEEecCCceEEEEECCEEEEeeCCceEEEEEeCCcCChh
Confidence 34567778887655333 3345677677654432110 000 0112456677778999999
Q ss_pred HHHHHHHHhCCceeeeee-ee
Q 019548 301 FKALAVFALREINLTKIE-SR 320 (339)
Q Consensus 301 ~~iL~~Fa~~gINLtkIe-SR 320 (339)
..+...|++++||..... +|
T Consensus 467 ~~v~~~L~~~~iNIa~m~~~r 487 (526)
T PRK13581 467 GKVGTLLGEAGINIAGMQLGR 487 (526)
T ss_pred HHHHHHHhhcCCCchhcEecc
Confidence 999999999999997775 45
No 295
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=24.92 E-value=5.9e+02 Score=23.97 Aligned_cols=145 Identities=14% Similarity=0.017 Sum_probs=70.1
Q ss_pred ceEEEEECCCCc-HHHHHH---HHhCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccC----ccchh----hhHHHhh
Q 019548 97 KVRISFKGLPGS-FSEDAA---LKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSS----SGSIH----RNYDLLL 164 (339)
Q Consensus 97 ~~~VayLGP~GT-fS~~AA---~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~----~G~V~----~tlDlL~ 164 (339)
..+|+..-+.+. |--... .+.|+++++.....-.++.+.+.+|++|+|++.- +.. .|... .....|.
T Consensus 98 ~l~I~~~~~~~~~~~~~~l~~f~~~~P~v~v~i~~~~~~~~~~l~~g~~D~~i~~~-~~~~~~~~~~~~~~~~~~~~~l~ 176 (319)
T PRK10216 98 KFELAAESPLMMIMLNALSKRIYQRYPQATIKLRNWDYDSLDAITRGEVDIGFTGR-ESHPRSRELLSLLPLAIDFEVLF 176 (319)
T ss_pred EEEEEecchhHHHHHHHHHHHHHHHCCCCEEEEEeCCcchHHHHhcCCccEEEecC-CCCccccccccccccccceeeee
Confidence 467766533322 222211 3346664433222222478999999999999842 111 11110 0011111
Q ss_pred cCCeEEEEEEEEeeeeeeccCCCCCcCCc---cEEEecH--HHHHHHHHHHHhcCCe---eEecCCHHHHHHHHHhcCCC
Q 019548 165 RHRLHIVGEVQLAANFCLLALPGIKADQL---KRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLR 236 (339)
Q Consensus 165 ~~~l~I~gEi~l~I~h~Ll~~~g~~l~~I---~~VySHp--qal~QC~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~ 236 (339)
+.++. +.++-+|-+... ...++|+ ..|.--+ ....+...|+...+.. ...++|...+.++++..+ .
T Consensus 177 ~~~~~----~v~~~~hp~~~~-~~~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~-~ 250 (319)
T PRK10216 177 SDLPC----VWLRKDHPALHE-EWNLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPEFEQSLFMAAQPD-H 250 (319)
T ss_pred ecceE----EEEeCCCCccCC-CCCHHHHhhCCCeEecCCCCCcchHHHHHHHhCCccceEEECCcHHHHHHHHHcCC-c
Confidence 22222 234555654322 2233333 2333211 1234567777776543 356777777788887631 2
Q ss_pred CeEEecCHHHHH
Q 019548 237 DAGAVASARAAE 248 (339)
Q Consensus 237 ~~AAIas~~AA~ 248 (339)
...+|.++.+++
T Consensus 251 ~gi~ilp~~~~~ 262 (319)
T PRK10216 251 LLLATAPRYCQY 262 (319)
T ss_pred ceEeccHHHHHH
Confidence 358888886553
No 296
>COG3482 Uncharacterized conserved protein [Function unknown]
Probab=24.92 E-value=99 Score=29.29 Aligned_cols=45 Identities=22% Similarity=0.229 Sum_probs=35.2
Q ss_pred EEEEECCCCcHHHHHHHHhCCCCccccCCCHHHHHHHHHhCCCCeEEE
Q 019548 99 RISFKGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVL 146 (339)
Q Consensus 99 ~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVV 146 (339)
+|.|.|| |-||..+++.. +.++.|-.-..+++.+|..|-...|+|
T Consensus 3 ~vvf~Gp--ti~~~~~~~v~-~~~~~~Pa~~g~~~~av~~~~~~i~ii 47 (237)
T COG3482 3 PVVFAGP--TISHADAEKVL-DAIYLPPAAQGDVLSAVQRGPAAIGII 47 (237)
T ss_pred ceeecCC--CccHHHHHhhh-cccccCchhhhhHHHHHHhcCceEEEe
Confidence 4899999 67788877654 567788888899999999996655554
No 297
>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=24.76 E-value=2.4e+02 Score=24.67 Aligned_cols=51 Identities=24% Similarity=0.079 Sum_probs=34.4
Q ss_pred ceEEEEECCCCcHHHHH---HHHhCC----CCccccCCCHHHHHHHHHhCCCCeEEEeeec
Q 019548 97 KVRISFKGLPGSFSEDA---ALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLPIEN 150 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~A---A~~~fg----~~~~~~~~si~~Vf~aV~~g~ad~gVVPiEN 150 (339)
..+|++.. |+.++.. +.+.+| +++++... ..+...++.+|++|.+++..++
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 46999765 7666643 344444 24566665 5667779999999999977775
No 298
>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=24.32 E-value=95 Score=30.53 Aligned_cols=48 Identities=13% Similarity=-0.039 Sum_probs=35.9
Q ss_pred ceEEEEECCCCcHHHHHHHH---hCC----CCccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 97 KVRISFKGLPGSFSEDAALK---AYP----KCETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 97 ~~~VayLGP~GTfS~~AA~~---~fg----~~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
-.|||+ +.||.+|....+ ..| ++++++++ ..+...++.+|++|.++++
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 778988855433 333 36778875 4788999999999999874
No 299
>PRK08181 transposase; Validated
Probab=23.32 E-value=1.9e+02 Score=27.65 Aligned_cols=71 Identities=17% Similarity=0.105 Sum_probs=45.2
Q ss_pred CCCceEEEEECCCCc-HHHHHH---HHhCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeE
Q 019548 94 DGTKVRISFKGLPGS-FSEDAA---LKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (339)
Q Consensus 94 l~~~~~VayLGP~GT-fS~~AA---~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~ 169 (339)
.+....+.+.||.|| =||.|. .........+.+-+..+.++.+..... ++.....+..|.+.+|-
T Consensus 103 ~~~~~nlll~Gp~GtGKTHLa~Aia~~a~~~g~~v~f~~~~~L~~~l~~a~~-----------~~~~~~~l~~l~~~dLL 171 (269)
T PRK08181 103 LAKGANLLLFGPPGGGKSHLAAAIGLALIENGWRVLFTRTTDLVQKLQVARR-----------ELQLESAIAKLDKFDLL 171 (269)
T ss_pred HhcCceEEEEecCCCcHHHHHHHHHHHHHHcCCceeeeeHHHHHHHHHHHHh-----------CCcHHHHHHHHhcCCEE
Confidence 445667999999998 455442 222222233455567888888865421 34455667777888999
Q ss_pred EEEEEE
Q 019548 170 IVGEVQ 175 (339)
Q Consensus 170 I~gEi~ 175 (339)
|++|+-
T Consensus 172 IIDDlg 177 (269)
T PRK08181 172 ILDDLA 177 (269)
T ss_pred EEeccc
Confidence 988864
No 300
>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=23.07 E-value=4.2e+02 Score=21.60 Aligned_cols=126 Identities=14% Similarity=0.074 Sum_probs=63.5
Q ss_pred HhCCCCccccC-CCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCC-CC---Cc
Q 019548 116 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALP-GI---KA 190 (339)
Q Consensus 116 ~~fg~~~~~~~-~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~-g~---~l 190 (339)
+.|+++++.-. .+..++++.+.+|++|+|++.-.......+ ....|.+.++.+ ..+-+|-+...+ .. ++
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 44677655433 467889999999999999985321111101 011222233322 234455543321 11 23
Q ss_pred CCccEEEecHH-HHHHHHHHHHhcCC--ee-EecCCHHHHHHHHHhcCCCCeEEecCHHHHHHc
Q 019548 191 DQLKRVLSHPQ-ALASSDIVLTQLGV--AR-ENVDDTASAAQYVASNGLRDAGAVASARAAEIY 250 (339)
Q Consensus 191 ~~I~~VySHpq-al~QC~~~L~~~~~--~~-i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~y 250 (339)
.+..-|...+. ....-.+|+.+++. .. ..++|.....++++.+ ...|+.++..++.+
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~lp~~~~~~~ 158 (199)
T cd08430 98 SRLPFILPERGLARERLDQWFRRRGIKPNIYAQVAGHEAIVSMVALG---CGVGIVPELVLDNS 158 (199)
T ss_pred ccCCeEEccCChHHHHHHHHHHHcCCCCCeeEEEccHHHHHHHHHhC---CeEEEccHHHhhhh
Confidence 33333432111 12334567766543 22 3355555555566653 46788888766543
No 301
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=22.95 E-value=4.2e+02 Score=21.61 Aligned_cols=122 Identities=17% Similarity=0.129 Sum_probs=59.4
Q ss_pred hCCCCcccc-CCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeeeeccCCCCCcCC---
Q 019548 117 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ--- 192 (339)
Q Consensus 117 ~fg~~~~~~-~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~Ll~~~g~~l~~--- 192 (339)
.+++.++.. ..+.+++.+.+.+|++|+|+..-.....+... ..|.+.++.+ ..+-.|-|...+..++++
T Consensus 25 ~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~----v~~~~~pl~~~~~~~~~~l~~ 97 (198)
T cd08447 25 ALPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLET---RPLVREPLVA----AVPAGHPLAGAERLTLEDLDG 97 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHcCCceEEEecCCCCCCCeeE---EEeecCceEE----EecCCCchhhcCcccHHHhCC
Confidence 356554433 23678999999999999999753322111111 1111222221 122233333221122222
Q ss_pred ccEEE-ecH--HHHHH-HHHHHHhcCCe---eEecCCHHHHHHHHHhcCCCCeEEecCHHHHH
Q 019548 193 LKRVL-SHP--QALAS-SDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 248 (339)
Q Consensus 193 I~~Vy-SHp--qal~Q-C~~~L~~~~~~---~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~ 248 (339)
-..|. .+. ....+ -..|+.+.+.. ...++|...+.++++.+ ...++.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (198)
T cd08447 98 QPFIMYSPTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAG---LGVALVPASASR 157 (198)
T ss_pred CeEEEeCCCCCchHHHHHHHHHHHcCCCCCceeecCCHHHHHHHHHcC---CCeEEhhHHHhh
Confidence 23332 211 11222 24566665432 24567777777777764 346777776654
No 302
>PF00072 Response_reg: Response regulator receiver domain; InterPro: IPR001789 Two-component signal transduction systems enable bacteria to sense, respond, and adapt to a wide range of environments, stressors, and growth conditions []. Some bacteria can contain up to as many as 200 two-component systems that need tight regulation to prevent unwanted cross-talk []. These pathways have been adapted to response to a wide variety of stimuli, including nutrients, cellular redox state, changes in osmolarity, quorum signals, antibiotics, and more []. Two-component systems are comprised of a sensor histidine kinase (HK) and its cognate response regulator (RR) []. The HK catalyses its own auto-phosphorylation followed by the transfer of the phosphoryl group to the receiver domain on RR; phosphorylation of the RR usually activates an attached output domain, which can then effect changes in cellular physiology, often by regulating gene expression. Some HK are bifunctional, catalysing both the phosphorylation and dephosphorylation of their cognate RR. The input stimuli can regulate either the kinase or phosphatase activity of the bifunctional HK. A variant of the two-component system is the phospho-relay system. Here a hybrid HK auto-phosphorylates and then transfers the phosphoryl group to an internal receiver domain, rather than to a separate RR protein. The phosphoryl group is then shuttled to histidine phosphotransferase (HPT) and subsequently to a terminal RR, which can evoke the desired response [, ]. Bipartite response regulator proteins are involved in a two-component signal transduction system in bacteria, and certain eukaryotes like protozoa, that functions to detect and respond to environmental changes []. These systems have been detected during host invasion, drug resistance, motility, phosphate uptake, osmoregulation, and nitrogen fixation, amongst others []. The two-component system consists of a histidine protein kinase environmental sensor that phosphorylates the receiver domain of a response regulator protein; phosphorylation induces a conformational change in the response regulator, which activates the effector domain, triggering the cellular response []. The domains of the two-component proteins are highly modular, but the core structures and activities are maintained. The response regulators act as phosphorylation-activated switches to affect a cellular response, usually by transcriptional regulation. Most of these proteins consist of two domains, an N-terminal response regulator receiver domain, and a variable C-terminal effector domain with DNA-binding activity. This entry represents the response regulator receiver domain, which belongs to the CheY family, and receives the signal from the sensor partner in the two-component system.; GO: 0000156 two-component response regulator activity, 0000160 two-component signal transduction system (phosphorelay), 0006355 regulation of transcription, DNA-dependent; PDB: 2QR3_A 2QXY_A 1I3C_A 1JLK_A 2PKX_A 2PL1_A 3H1F_A 3H1E_A 3GWG_A 3H1G_A ....
Probab=22.44 E-value=72 Score=24.52 Aligned_cols=77 Identities=14% Similarity=0.178 Sum_probs=48.1
Q ss_pred EEecHHHHHHHHHHHHhcCC-eeEecCCHHHHHHHHHhcCCCCeEEecCHHHHHHcCCceeeccccCCCCCeeeEEEEee
Q 019548 196 VLSHPQALASSDIVLTQLGV-ARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLAR 274 (339)
Q Consensus 196 VySHpqal~QC~~~L~~~~~-~~i~~~STA~AA~~v~~~~~~~~AAIas~~AA~~ygL~il~~~IeD~~~N~TRF~vi~~ 274 (339)
|-.||.-..-.+.+|...+. ....+.|..+|...+.... ++..-|- -......|+.++. .|.... ..+++++++.
T Consensus 4 vd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~~-~d~iiid-~~~~~~~~~~~~~-~i~~~~-~~~~ii~~t~ 79 (112)
T PF00072_consen 4 VDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLKKHP-PDLIIID-LELPDGDGLELLE-QIRQIN-PSIPIIVVTD 79 (112)
T ss_dssp EESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHST-ESEEEEE-SSSSSSBHHHHHH-HHHHHT-TTSEEEEEES
T ss_pred EECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhcccC-ceEEEEE-eeecccccccccc-cccccc-ccccEEEecC
Confidence 34577777888899997788 6677888888888887653 4433333 2222234444333 233323 7888888885
Q ss_pred CC
Q 019548 275 DP 276 (339)
Q Consensus 275 ~~ 276 (339)
..
T Consensus 80 ~~ 81 (112)
T PF00072_consen 80 ED 81 (112)
T ss_dssp ST
T ss_pred CC
Confidence 54
No 303
>PRK13584 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=22.24 E-value=1.9e+02 Score=26.90 Aligned_cols=108 Identities=15% Similarity=0.173 Sum_probs=64.7
Q ss_pred HHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeEEEEEEEEeeeee---eccCCCCCcCCccEEEecHHHHHH
Q 019548 129 FEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFC---LLALPGIKADQLKRVLSHPQALAS 205 (339)
Q Consensus 129 i~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~I~gEi~l~I~h~---Ll~~~g~~l~~I~~VySHpqal~Q 205 (339)
..|+-..|+.|.+|.||+= .|.|.++.-.+..-..|.+.+| +++.++. .+.++|.+..--+.
T Consensus 52 ~~DIp~yV~~G~aDlGI~G------------~D~l~E~~~~v~el~dLgfG~crl~vA~p~~~--~~~~rVATkyp~it- 116 (204)
T PRK13584 52 GSDVPIYVEQGMADIGIVG------------SDILDERQYNVNNLLNMPFGACHFAVAAKPET--TNYRKIATSYVHTA- 116 (204)
T ss_pred HHHHHHHHhCCCccEEEee------------eeEeeccCCCeEEEecCCCCcEEEEEEEEcCC--CCceEEEeCcHHHH-
Confidence 4678899999999999974 3555554433333456666666 3343432 45678887766554
Q ss_pred HHHHHHhcCC--eeEecCCHHHHHHHHHhcCCCCeEEe----cCHHHHHHcCCceeec
Q 019548 206 SDIVLTQLGV--ARENVDDTASAAQYVASNGLRDAGAV----ASARAAEIYGLNILAD 257 (339)
Q Consensus 206 C~~~L~~~~~--~~i~~~STA~AA~~v~~~~~~~~AAI----as~~AA~~ygL~il~~ 257 (339)
++|+.++|+ +.+..+-.-|.|=.+ +-+-+| .+-...+.+||.++.+
T Consensus 117 -~~yf~~~Gi~~~ii~l~GsvElaP~~-----GlAD~IvDiv~TG~TLr~NgL~~~e~ 168 (204)
T PRK13584 117 -ETYFKSKGIDVELIKLNGSVELACVV-----DMVDGIVDIVQTGTTLKANGLVEKQH 168 (204)
T ss_pred -HHHHHHcCCeEEEEECCCceeecccc-----CCccEEEEEECccHHHHHCCCEEEEE
Confidence 679999865 445444333332211 111122 3556678899988743
No 304
>PRK03957 V-type ATP synthase subunit F; Provisional
Probab=22.11 E-value=2.7e+02 Score=22.52 Aligned_cols=60 Identities=12% Similarity=0.112 Sum_probs=35.3
Q ss_pred eEEEEECCCCcHHHHHHHHhCCCCccccCCCHHHH---HHHHHhCCCCeEEEeeeccCccchhhhHH
Q 019548 98 VRISFKGLPGSFSEDAALKAYPKCETVPCDEFEDT---FKAVELWLADKAVLPIENSSSGSIHRNYD 161 (339)
Q Consensus 98 ~~VayLGP~GTfS~~AA~~~fg~~~~~~~~si~~V---f~aV~~g~ad~gVVPiENS~~G~V~~tlD 161 (339)
||||..|.+-| ....+..|-....++.+.+++ |+.+.+ +-|||||-|.+.+...+.++.+
T Consensus 1 mkIaVIgD~dt---v~GFrLaGi~~~~~v~~~ee~~~~l~~l~~-~~d~gII~ite~~~~~i~~~i~ 63 (100)
T PRK03957 1 MKIAVVGDRDT---VTGFRLAGLTEVYEVKNPEEAKNAIKELVE-NDEIGIIIITERIAEEIRDLIS 63 (100)
T ss_pred CEEEEEeCHHH---HHHHHHcCCCceEEeCCHHHHHHHHHHHhh-CCCeEEEEEcHHHHHHHHHHHh
Confidence 58888886322 122233443233456555555 554443 3489999999877777765555
No 305
>PRK09861 cytoplasmic membrane lipoprotein-28; Provisional
Probab=20.69 E-value=7.4e+02 Score=23.60 Aligned_cols=109 Identities=16% Similarity=0.065 Sum_probs=62.6
Q ss_pred CceEEEEE-CCCCcHHHHHHHHhC---C-CCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhh-cCCeE
Q 019548 96 TKVRISFK-GLPGSFSEDAALKAY---P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL-RHRLH 169 (339)
Q Consensus 96 ~~~~VayL-GP~GTfS~~AA~~~f---g-~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~-~~~l~ 169 (339)
++++|++. ||...+.+.+..... | +++++.++......+++.+|++|..+. .-...++... +.+..
T Consensus 32 ~tLkVG~~~~~~~~~~e~a~~~~k~~~G~~Velv~fsd~~~~n~AL~~G~ID~n~~--------qh~~yl~~~~~~~g~~ 103 (272)
T PRK09861 32 KHIKVGVINGAEQDVAEVAKKVAKEKYGLDVELVGFSGSLLPNDATNHGELDANVF--------QHRPFLEQDNQAHGYK 103 (272)
T ss_pred CcEEEEEcCCchHHHHHHHHHHHHHcCCCeEEEEecCchhhHHHHHHcCCcceehh--------hhHHHHHHHHHhcCCC
Confidence 36899996 777777776654322 3 267788888888889999999998771 1122233333 34445
Q ss_pred EEEEEEEee-eeeeccCCCCCcCCcc---EE-Ee-cHHHHHHHHHHHHh
Q 019548 170 IVGEVQLAA-NFCLLALPGIKADQLK---RV-LS-HPQALASSDIVLTQ 212 (339)
Q Consensus 170 I~gEi~l~I-~h~Ll~~~g~~l~~I~---~V-yS-Hpqal~QC~~~L~~ 212 (339)
+++-....+ ...+.+.+-.+++|++ +| +. -|--.++.-..|..
T Consensus 104 lv~~~~~~~~P~~~Ys~~iksl~DL~~Ga~IAipnd~~n~~ral~lL~~ 152 (272)
T PRK09861 104 LVAVGNTFVFPMAGYSKKIKTVAQIKEGATVAIPNDPTNLGRALLLLQK 152 (272)
T ss_pred eEEEeEEEEEeeeccccCCCCHHHcCCCCEEEEeCCCccHHHHHHHHHH
Confidence 544333111 1334454444667766 22 22 33445555566655
No 306
>PF01695 IstB_IS21: IstB-like ATP binding protein; InterPro: IPR002611 Proteins in this entry contain an ATP/GTP binding P-loop motif. They are found associated with IS21 family insertion sequences []. Functionally they have not been characterised, but they may be involved in transposition [].; GO: 0005524 ATP binding; PDB: 3EC2_A 3ECC_A 2W58_A 2QGZ_A.
Probab=20.39 E-value=1.3e+02 Score=26.75 Aligned_cols=70 Identities=21% Similarity=0.145 Sum_probs=45.5
Q ss_pred CCCceEEEEECCCCc-HHHHHH---HHhCCCCccccCCCHHHHHHHHHhCCCCeEEEeeeccCccchhhhHHHhhcCCeE
Q 019548 94 DGTKVRISFKGLPGS-FSEDAA---LKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLH 169 (339)
Q Consensus 94 l~~~~~VayLGP~GT-fS~~AA---~~~fg~~~~~~~~si~~Vf~aV~~g~ad~gVVPiENS~~G~V~~tlDlL~~~~l~ 169 (339)
++....+.+.||.|| =||.|+ .........+.+-+..+.++.+.... ..+.....++.|.+.+|-
T Consensus 44 ~~~~~~l~l~G~~G~GKThLa~ai~~~~~~~g~~v~f~~~~~L~~~l~~~~-----------~~~~~~~~~~~l~~~dlL 112 (178)
T PF01695_consen 44 IENGENLILYGPPGTGKTHLAVAIANEAIRKGYSVLFITASDLLDELKQSR-----------SDGSYEELLKRLKRVDLL 112 (178)
T ss_dssp -SC--EEEEEESTTSSHHHHHHHHHHHHHHTT--EEEEEHHHHHHHHHCCH-----------CCTTHCHHHHHHHTSSCE
T ss_pred cccCeEEEEEhhHhHHHHHHHHHHHHHhccCCcceeEeecCceeccccccc-----------cccchhhhcCccccccEe
Confidence 456678999999998 566553 22222334456677899999998542 134556678888899998
Q ss_pred EEEEE
Q 019548 170 IVGEV 174 (339)
Q Consensus 170 I~gEi 174 (339)
|.+++
T Consensus 113 ilDDl 117 (178)
T PF01695_consen 113 ILDDL 117 (178)
T ss_dssp EEETC
T ss_pred ccccc
Confidence 98775
No 307
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=20.03 E-value=1.6e+02 Score=27.89 Aligned_cols=47 Identities=21% Similarity=0.128 Sum_probs=32.8
Q ss_pred eEEEEECCCCcHHHHHHHHhCCC-------CccccCCCHHHHHHHHHhCCCCeEEEe
Q 019548 98 VRISFKGLPGSFSEDAALKAYPK-------CETVPCDEFEDTFKAVELWLADKAVLP 147 (339)
Q Consensus 98 ~~VayLGP~GTfS~~AA~~~fg~-------~~~~~~~si~~Vf~aV~~g~ad~gVVP 147 (339)
.+|++ |.||.+|....+++.. ++++ ..++.+.+.++.+|++|.+++.
T Consensus 130 k~I~~--~~gs~~~~~l~~~l~~~g~~~~dv~~v-~~~~~~~~~al~~G~vDa~~~~ 183 (314)
T PRK11553 130 HKVAF--QKGSSSHNLLLRALRKAGLKFTDIQPT-YLTPADARAAFQQGNVDAWAIW 183 (314)
T ss_pred CEEee--cCCCcHHHHHHHHHHHcCCCHHHeEEE-ecChHHHHHHHHcCCCCEEEEc
Confidence 56887 5688777665554421 2333 3477788999999999998873
Done!