Query 048784
Match_columns 282
No_of_seqs 201 out of 1142
Neff 6.7
Searched_HMMs 46136
Date Fri Mar 29 13:11:26 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/048784.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/048784hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG0077 PheA Prephenate dehydr 100.0 1.2E-91 2.5E-96 637.6 30.3 265 1-279 9-277 (279)
2 PRK11899 prephenate dehydratas 100.0 3.5E-89 7.5E-94 627.1 31.4 266 1-279 11-277 (279)
3 PLN02317 arogenate dehydratase 100.0 7.4E-89 1.6E-93 643.8 31.3 280 1-280 101-381 (382)
4 PRK10622 pheA bifunctional cho 100.0 3.9E-83 8.5E-88 611.0 30.2 265 1-278 110-379 (386)
5 PRK11898 prephenate dehydratas 100.0 8.5E-82 1.8E-86 580.5 31.2 264 1-278 8-279 (283)
6 KOG2797 Prephenate dehydratase 100.0 4.5E-76 9.8E-81 531.5 20.5 275 1-279 97-373 (377)
7 PF00800 PDT: Prephenate dehyd 100.0 4.9E-56 1.1E-60 384.9 16.6 173 1-173 5-181 (181)
8 cd04904 ACT_AAAH ACT domain of 99.9 1.4E-22 3E-27 151.2 9.4 73 184-271 1-73 (74)
9 cd04931 ACT_PAH ACT domain of 99.9 1E-21 2.2E-26 152.0 9.9 71 180-264 11-81 (90)
10 cd04930 ACT_TH ACT domain of t 99.8 3.2E-21 7E-26 155.6 9.1 76 181-271 39-114 (115)
11 cd04929 ACT_TPH ACT domain of 99.8 3.3E-21 7.1E-26 144.0 8.0 70 184-268 1-70 (74)
12 cd04905 ACT_CM-PDT C-terminal 99.8 1.7E-20 3.7E-25 141.4 10.9 80 183-275 1-80 (80)
13 cd04880 ACT_AAAH-PDT-like ACT 99.8 6.9E-20 1.5E-24 136.2 9.9 75 185-272 1-75 (75)
14 TIGR01268 Phe4hydrox_tetr phen 99.8 4E-18 8.7E-23 164.0 11.0 80 182-275 15-95 (436)
15 TIGR01270 Trp_5_monoox tryptop 99.6 9.2E-16 2E-20 148.3 9.8 76 180-270 28-104 (464)
16 PRK06034 hypothetical protein; 99.0 4.9E-10 1.1E-14 102.9 4.9 66 1-70 102-169 (279)
17 PRK08818 prephenate dehydrogen 98.9 3E-09 6.6E-14 101.8 8.0 66 182-262 294-360 (370)
18 TIGR01269 Tyr_3_monoox tyrosin 98.9 9.7E-09 2.1E-13 99.0 9.3 72 183-266 37-109 (457)
19 KOG3820 Aromatic amino acid hy 98.6 1.8E-07 3.8E-12 88.7 7.9 78 182-274 35-112 (461)
20 cd04886 ACT_ThrD-II-like C-ter 98.3 6E-06 1.3E-10 59.0 9.1 69 187-267 2-70 (73)
21 PF01842 ACT: ACT domain; Int 98.3 4.2E-06 9E-11 59.3 7.9 38 184-221 1-38 (66)
22 cd04882 ACT_Bt0572_2 C-termina 97.7 0.0003 6.5E-09 49.6 7.9 60 186-265 2-61 (65)
23 cd04884 ACT_CBS C-terminal ACT 97.6 0.00056 1.2E-08 49.9 8.2 65 186-264 2-66 (72)
24 PRK06737 acetolactate synthase 97.5 0.0012 2.6E-08 49.6 9.1 69 184-268 3-71 (76)
25 cd04874 ACT_Af1403 N-terminal 97.5 0.0012 2.6E-08 46.9 8.8 64 185-266 2-65 (72)
26 cd04883 ACT_AcuB C-terminal AC 97.4 0.0012 2.6E-08 47.6 8.4 65 184-266 2-66 (72)
27 cd04878 ACT_AHAS N-terminal AC 97.4 0.0022 4.8E-08 45.3 9.3 66 185-266 2-67 (72)
28 PF13710 ACT_5: ACT domain; PD 97.2 0.0022 4.7E-08 46.2 7.5 59 192-266 1-59 (63)
29 cd04888 ACT_PheB-BS C-terminal 97.2 0.0045 9.8E-08 45.0 9.4 73 185-272 2-76 (76)
30 cd04908 ACT_Bt0572_1 N-termina 97.2 0.0026 5.6E-08 45.6 7.9 35 185-219 3-37 (66)
31 cd04902 ACT_3PGDH-xct C-termin 97.2 0.0025 5.4E-08 45.8 7.6 61 186-264 2-62 (73)
32 cd02116 ACT ACT domains are co 97.1 0.0032 6.9E-08 40.9 7.1 58 187-261 2-59 (60)
33 PF13291 ACT_4: ACT domain; PD 97.1 0.0054 1.2E-07 45.5 8.9 71 181-266 4-74 (80)
34 cd04909 ACT_PDH-BS C-terminal 97.0 0.0052 1.1E-07 44.1 8.3 64 185-265 3-66 (69)
35 cd04896 ACT_ACR-like_3 ACT dom 97.0 0.0035 7.6E-08 46.9 7.3 65 185-263 2-70 (75)
36 cd04903 ACT_LSD C-terminal ACT 97.0 0.0055 1.2E-07 43.2 7.7 62 186-265 2-63 (71)
37 TIGR00119 acolac_sm acetolacta 96.9 0.0089 1.9E-07 50.9 9.7 69 185-269 3-71 (157)
38 PRK11152 ilvM acetolactate syn 96.9 0.0091 2E-07 44.8 8.5 67 183-266 3-69 (76)
39 PRK11895 ilvH acetolactate syn 96.9 0.01 2.2E-07 50.7 10.0 70 184-269 3-72 (161)
40 cd04885 ACT_ThrD-I Tandem C-te 96.9 0.0035 7.6E-08 45.4 6.1 62 187-265 2-63 (68)
41 cd04887 ACT_MalLac-Enz ACT_Mal 96.8 0.0088 1.9E-07 43.3 7.9 63 186-264 2-64 (74)
42 PRK13562 acetolactate synthase 96.7 0.014 3.1E-07 44.5 8.7 71 184-269 3-73 (84)
43 CHL00100 ilvH acetohydroxyacid 96.7 0.01 2.2E-07 51.4 8.9 71 184-270 3-73 (174)
44 cd04901 ACT_3PGDH C-terminal A 96.7 0.0045 9.8E-08 44.1 5.7 60 186-265 2-61 (69)
45 cd04879 ACT_3PGDH-like ACT_3PG 96.7 0.0084 1.8E-07 42.0 7.0 62 186-265 2-63 (71)
46 cd04926 ACT_ACR_4 C-terminal 96.7 0.015 3.2E-07 42.6 8.1 36 184-219 2-37 (72)
47 PRK04435 hypothetical protein; 96.6 0.025 5.5E-07 47.5 10.5 77 182-273 68-146 (147)
48 PRK08198 threonine dehydratase 96.6 0.053 1.1E-06 52.5 14.2 76 183-271 327-403 (404)
49 PRK08178 acetolactate synthase 96.5 0.028 6E-07 44.0 9.3 71 183-270 8-78 (96)
50 cd04906 ACT_ThrD-I_1 First of 96.5 0.023 5E-07 43.0 8.6 71 185-272 3-73 (85)
51 cd04881 ACT_HSDH-Hom ACT_HSDH_ 96.4 0.026 5.6E-07 40.5 7.9 64 186-264 3-66 (79)
52 PRK00194 hypothetical protein; 96.3 0.028 6E-07 42.6 7.9 36 183-218 3-38 (90)
53 cd04895 ACT_ACR_1 ACT domain-c 96.2 0.031 6.8E-07 41.4 7.5 29 184-212 2-30 (72)
54 cd04872 ACT_1ZPV ACT domain pr 96.1 0.033 7.2E-07 42.2 7.6 67 184-264 2-69 (88)
55 cd04870 ACT_PSP_1 CT domains f 96.0 0.049 1.1E-06 40.0 7.9 63 188-264 4-66 (75)
56 cd04875 ACT_F4HF-DF N-terminal 96.0 0.072 1.6E-06 38.8 8.8 33 186-218 2-34 (74)
57 PF13740 ACT_6: ACT domain; PD 96.0 0.042 9.2E-07 40.6 7.4 36 186-221 3-40 (76)
58 cd04899 ACT_ACR-UUR-like_2 C-t 96.0 0.077 1.7E-06 37.8 8.6 37 185-221 2-38 (70)
59 cd04877 ACT_TyrR N-terminal AC 95.9 0.053 1.1E-06 39.7 7.6 60 186-265 3-62 (74)
60 cd04873 ACT_UUR-ACR-like ACT d 95.9 0.09 2E-06 37.0 8.6 36 185-220 2-37 (70)
61 TIGR01127 ilvA_1Cterm threonin 95.9 0.049 1.1E-06 52.3 9.2 73 183-268 305-378 (380)
62 PRK08577 hypothetical protein; 95.8 0.13 2.9E-06 42.3 10.6 69 183-265 56-124 (136)
63 cd04876 ACT_RelA-SpoT ACT dom 95.7 0.13 2.8E-06 34.8 8.7 63 187-265 2-64 (71)
64 PRK06382 threonine dehydratase 95.6 0.039 8.5E-07 53.6 7.5 74 182-268 329-403 (406)
65 cd04889 ACT_PDH-BS-like C-term 95.5 0.045 9.8E-07 37.5 5.7 34 187-220 2-35 (56)
66 COG2061 ACT-domain-containing 95.3 0.11 2.4E-06 43.9 8.1 74 183-271 5-79 (170)
67 PRK08526 threonine dehydratase 95.3 0.37 8E-06 47.0 13.0 214 28-268 161-399 (403)
68 cd04869 ACT_GcvR_2 ACT domains 95.0 0.22 4.9E-06 36.5 8.4 35 186-220 2-36 (81)
69 COG4747 ACT domain-containing 94.8 0.2 4.3E-06 40.7 8.1 67 184-273 70-136 (142)
70 PRK07334 threonine dehydratase 94.8 0.23 5E-06 48.2 10.2 76 182-270 325-401 (403)
71 cd04900 ACT_UUR-like_1 ACT dom 94.5 0.42 9.2E-06 34.7 8.6 34 184-217 2-37 (73)
72 COG4492 PheB ACT domain-contai 94.3 0.29 6.3E-06 40.5 8.1 77 181-273 70-149 (150)
73 cd04897 ACT_ACR_3 ACT domain-c 94.3 0.32 7E-06 36.3 7.6 29 184-212 2-30 (75)
74 cd04893 ACT_GcvR_1 ACT domains 94.1 0.56 1.2E-05 34.6 8.7 64 186-264 4-67 (77)
75 cd04935 ACT_AKiii-DAPDC_1 ACT 94.0 0.48 1E-05 35.0 8.1 63 190-271 11-74 (75)
76 TIGR01124 ilvA_2Cterm threonin 93.8 1.3 2.8E-05 44.4 13.3 72 182-271 324-395 (499)
77 PRK08639 threonine dehydratase 93.3 0.52 1.1E-05 46.1 9.4 73 183-271 336-409 (420)
78 cd04932 ACT_AKiii-LysC-EC_1 AC 93.2 0.92 2E-05 33.5 8.5 58 190-265 11-69 (75)
79 PRK11589 gcvR glycine cleavage 92.9 0.62 1.3E-05 40.9 8.3 36 185-220 97-132 (190)
80 TIGR02079 THD1 threonine dehyd 92.9 0.77 1.7E-05 44.8 9.8 74 183-271 325-398 (409)
81 PRK09224 threonine dehydratase 92.4 0.7 1.5E-05 46.3 9.0 72 183-271 328-399 (504)
82 PLN02550 threonine dehydratase 92.4 1.6 3.4E-05 44.8 11.6 72 183-272 417-488 (591)
83 cd04927 ACT_ACR-like_2 Second 92.2 1.7 3.6E-05 32.1 8.8 27 187-213 4-30 (76)
84 cd04912 ACT_AKiii-LysC-EC-like 91.9 1.7 3.7E-05 31.7 8.5 56 190-263 11-67 (75)
85 COG3830 ACT domain-containing 91.5 0.52 1.1E-05 36.4 5.4 71 186-270 6-78 (90)
86 cd04934 ACT_AK-Hom3_1 CT domai 91.3 1.1 2.5E-05 32.9 7.0 55 192-265 13-67 (73)
87 cd04907 ACT_ThrD-I_2 Second of 91.2 2 4.3E-05 32.3 8.3 66 185-268 3-68 (81)
88 PRK12483 threonine dehydratase 90.9 1.6 3.5E-05 44.0 9.8 72 182-271 344-416 (521)
89 COG0440 IlvH Acetolactate synt 90.6 1.2 2.5E-05 38.2 7.2 73 183-271 4-76 (163)
90 PRK13011 formyltetrahydrofolat 90.4 2.8 6.1E-05 39.0 10.3 68 183-264 7-76 (286)
91 COG1707 ACT domain-containing 89.8 1.1 2.5E-05 38.6 6.5 62 186-264 5-66 (218)
92 cd04891 ACT_AK-LysC-DapG-like_ 89.6 2.9 6.2E-05 27.9 7.4 31 188-218 6-36 (61)
93 cd04925 ACT_ACR_2 ACT domain-c 89.5 3.6 7.8E-05 30.0 8.3 32 186-217 3-34 (74)
94 COG2716 GcvR Glycine cleavage 89.1 2 4.3E-05 37.1 7.5 76 186-273 95-171 (176)
95 PRK06545 prephenate dehydrogen 88.7 1.7 3.7E-05 41.4 7.7 40 183-222 290-329 (359)
96 PRK13010 purU formyltetrahydro 88.2 2.6 5.6E-05 39.4 8.3 66 185-264 11-80 (289)
97 PRK11092 bifunctional (p)ppGpp 87.1 6.7 0.00014 41.1 11.3 70 181-266 624-693 (702)
98 PRK06349 homoserine dehydrogen 87.0 2.6 5.7E-05 41.3 8.0 66 183-264 348-413 (426)
99 cd04933 ACT_AK1-AT_1 ACT domai 86.2 4.2 9.2E-05 30.4 7.0 58 190-265 11-72 (78)
100 PF00497 SBP_bac_3: Bacterial 86.0 7.1 0.00015 32.7 9.3 42 3-44 117-159 (225)
101 cd04913 ACT_AKii-LysC-BS-like_ 85.9 6.2 0.00013 27.5 7.6 29 188-216 7-35 (75)
102 PRK11790 D-3-phosphoglycerate 85.6 3.1 6.7E-05 40.6 7.6 63 183-266 338-401 (409)
103 COG0317 SpoT Guanosine polypho 85.2 11 0.00023 39.6 11.5 70 181-266 625-694 (701)
104 cd04928 ACT_TyrKc Uncharacteri 85.2 6.9 0.00015 28.6 7.5 36 186-221 4-39 (68)
105 cd04890 ACT_AK-like_1 ACT doma 85.0 3.7 8E-05 28.4 5.9 51 191-261 11-61 (62)
106 PRK11151 DNA-binding transcrip 84.9 25 0.00055 31.8 13.0 122 14-145 116-246 (305)
107 PF00585 Thr_dehydrat_C: C-ter 83.5 2.4 5.3E-05 32.5 4.7 69 182-267 9-77 (91)
108 TIGR01693 UTase_glnD [Protein- 83.4 6.3 0.00014 42.0 9.4 50 182-245 778-827 (850)
109 TIGR00719 sda_beta L-serine de 83.1 5.6 0.00012 35.2 7.5 55 184-253 149-204 (208)
110 KOG2663 Acetolactate synthase, 82.8 4.4 9.6E-05 37.2 6.7 74 181-272 75-150 (309)
111 TIGR00691 spoT_relA (p)ppGpp s 82.6 7.9 0.00017 40.4 9.5 68 182-265 609-676 (683)
112 PRK05007 PII uridylyl-transfer 82.5 4 8.6E-05 43.9 7.4 53 181-249 806-861 (884)
113 PRK05092 PII uridylyl-transfer 81.6 7.6 0.00016 41.9 9.2 52 183-248 843-895 (931)
114 PRK10872 relA (p)ppGpp synthet 81.3 9.4 0.0002 40.3 9.4 69 182-265 665-733 (743)
115 PRK06027 purU formyltetrahydro 80.9 17 0.00037 33.7 10.2 64 185-264 8-76 (286)
116 cd08417 PBP2_Nitroaromatics_li 79.4 31 0.00067 27.8 12.5 120 15-145 26-154 (200)
117 PF12727 PBP_like: PBP superfa 79.3 11 0.00025 32.7 8.1 129 19-153 14-165 (193)
118 TIGR00655 PurU formyltetrahydr 79.3 14 0.00031 34.3 9.1 65 186-264 3-71 (280)
119 cd08452 PBP2_AlsR The C-termin 78.0 36 0.00078 27.7 13.7 31 14-44 25-56 (197)
120 PRK09959 hybrid sensory histid 77.9 2.5 5.5E-05 46.2 4.3 43 2-44 170-212 (1197)
121 PRK15007 putative ABC transpor 77.9 4.8 0.0001 35.2 5.3 42 3-44 133-174 (243)
122 TIGR01096 3A0103s03R lysine-ar 77.3 4.9 0.00011 35.1 5.2 42 3-44 138-180 (250)
123 cd04922 ACT_AKi-HSDH-ThrA_2 AC 76.9 15 0.00033 25.1 6.8 27 190-216 11-37 (66)
124 cd08445 PBP2_BenM_CatM_CatR Th 76.8 39 0.00085 27.5 13.0 120 15-144 27-158 (203)
125 PRK13581 D-3-phosphoglycerate 76.8 6.4 0.00014 39.7 6.5 105 141-264 388-515 (526)
126 cd04868 ACT_AK-like ACT domain 76.7 10 0.00022 24.7 5.6 27 192-218 12-38 (60)
127 COG4747 ACT domain-containing 76.7 3.1 6.7E-05 34.0 3.3 27 187-213 7-33 (142)
128 cd04924 ACT_AK-Arch_2 ACT doma 76.3 16 0.00034 25.0 6.7 52 190-263 11-62 (66)
129 PRK01759 glnD PII uridylyl-tra 75.8 8 0.00017 41.4 7.2 53 182-248 782-835 (854)
130 PF13840 ACT_7: ACT domain ; P 75.3 19 0.00042 25.5 7.0 33 183-215 8-42 (65)
131 PRK11260 cystine transporter s 74.8 5.8 0.00013 35.5 5.1 42 3-44 156-197 (266)
132 PRK12679 cbl transcriptional r 74.3 71 0.0015 29.3 12.4 120 15-143 119-247 (316)
133 cd04919 ACT_AK-Hom3_2 ACT doma 73.9 21 0.00045 24.6 6.8 52 191-264 12-63 (66)
134 cd04914 ACT_AKi-DapG-BS_1 ACT 73.6 13 0.00028 26.5 5.7 28 190-218 9-36 (67)
135 PF09084 NMT1: NMT1/THI5 like; 73.2 57 0.0012 27.7 13.7 112 17-138 22-145 (216)
136 PRK12683 transcriptional regul 72.5 78 0.0017 28.9 13.1 119 15-143 119-247 (309)
137 cd08411 PBP2_OxyR The C-termin 72.4 49 0.0011 26.6 13.2 122 15-146 27-157 (200)
138 cd04923 ACT_AK-LysC-DapG-like_ 71.7 25 0.00053 23.6 6.7 27 190-216 10-36 (63)
139 PRK12684 transcriptional regul 71.6 82 0.0018 28.8 12.4 30 15-44 119-149 (313)
140 TIGR01728 SsuA_fam ABC transpo 71.1 18 0.00038 32.0 7.3 117 17-142 30-157 (288)
141 cd04892 ACT_AK-like_2 ACT doma 70.9 25 0.00054 23.3 6.6 53 190-264 10-62 (65)
142 PF00497 SBP_bac_3: Bacterial 70.9 36 0.00078 28.3 8.9 115 17-146 39-165 (225)
143 PRK09508 leuO leucine transcri 70.8 36 0.00077 31.1 9.5 121 15-146 138-266 (314)
144 cd04936 ACT_AKii-LysC-BS-like_ 70.8 25 0.00053 23.6 6.5 27 190-216 10-36 (63)
145 PRK09959 hybrid sensory histid 70.5 5.5 0.00012 43.6 4.6 43 2-44 413-455 (1197)
146 PRK09495 glnH glutamine ABC tr 70.4 8.1 0.00018 34.0 4.9 42 3-44 138-179 (247)
147 TIGR01327 PGDH D-3-phosphoglyc 70.4 9 0.0002 38.6 5.8 104 141-263 387-513 (525)
148 cd04937 ACT_AKi-DapG-BS_2 ACT 70.3 24 0.00053 24.6 6.5 51 190-264 11-61 (64)
149 smart00062 PBPb Bacterial peri 69.7 57 0.0012 26.2 9.8 112 17-144 40-158 (219)
150 PRK04374 PII uridylyl-transfer 69.3 25 0.00054 37.8 9.0 52 182-249 795-849 (869)
151 cd08462 PBP2_NodD The C-termin 68.5 63 0.0014 26.3 10.2 32 14-45 25-56 (200)
152 cd08453 PBP2_IlvR The C-termin 68.0 63 0.0014 26.1 13.0 122 15-145 26-160 (200)
153 smart00062 PBPb Bacterial peri 68.0 10 0.00022 30.7 4.8 43 4-46 114-156 (219)
154 cd08446 PBP2_Chlorocatechol Th 67.8 62 0.0013 25.9 13.2 122 14-145 26-158 (198)
155 cd00134 PBPb Bacterial peripla 67.4 12 0.00026 30.5 5.0 42 3-44 112-153 (218)
156 cd08443 PBP2_CysB The C-termin 67.1 68 0.0015 26.1 13.3 122 14-144 25-155 (198)
157 PRK11589 gcvR glycine cleavage 66.4 22 0.00049 31.1 6.7 37 183-221 6-44 (190)
158 cd08486 PBP2_CbnR The C-termin 66.1 72 0.0016 26.0 12.1 120 14-143 26-156 (198)
159 PRK03059 PII uridylyl-transfer 65.3 30 0.00066 37.1 8.7 36 182-217 785-822 (856)
160 PF01193 RNA_pol_L: RNA polyme 65.1 29 0.00063 24.6 6.1 63 187-265 2-65 (66)
161 cd04916 ACT_AKiii-YclM-BS_2 AC 65.1 39 0.00085 23.0 6.7 27 190-216 11-37 (66)
162 cd08435 PBP2_GbpR The C-termin 64.4 72 0.0016 25.4 13.0 31 14-44 25-56 (201)
163 smart00079 PBPe Eukaryotic hom 64.2 13 0.00028 29.2 4.5 73 3-84 20-104 (134)
164 cd04918 ACT_AK1-AT_2 ACT domai 64.1 47 0.001 23.2 7.7 59 184-264 4-62 (65)
165 cd04871 ACT_PSP_2 ACT domains 64.0 24 0.00052 26.5 5.7 67 191-264 7-75 (84)
166 TIGR02995 ectoine_ehuB ectoine 63.6 13 0.00028 33.5 4.9 43 2-44 150-193 (275)
167 PF12974 Phosphonate-bd: ABC t 62.8 5 0.00011 35.4 2.0 58 19-85 139-202 (243)
168 PRK11917 bifunctional adhesin/ 61.5 20 0.00043 32.2 5.7 88 3-110 155-246 (259)
169 cd08450 PBP2_HcaR The C-termin 61.4 82 0.0018 25.1 12.7 32 14-45 25-57 (196)
170 PRK03381 PII uridylyl-transfer 60.8 38 0.00083 35.9 8.4 36 183-218 707-742 (774)
171 PRK00275 glnD PII uridylyl-tra 60.6 43 0.00092 36.2 8.8 35 183-217 814-850 (895)
172 PRK10820 DNA-binding transcrip 60.3 25 0.00054 35.4 6.7 59 186-264 3-61 (520)
173 PRK03601 transcriptional regul 59.8 1.3E+02 0.0028 26.9 12.0 32 14-45 114-146 (275)
174 PRK10859 membrane-bound lytic 59.7 34 0.00074 33.9 7.5 42 3-44 156-202 (482)
175 cd08485 PBP2_ClcR The C-termin 59.6 95 0.0021 25.2 12.5 31 14-44 26-57 (198)
176 PRK05007 PII uridylyl-transfer 59.1 47 0.001 35.8 8.9 32 183-214 701-732 (884)
177 cd04915 ACT_AK-Ectoine_2 ACT d 59.0 49 0.0011 23.4 6.3 50 193-264 14-63 (66)
178 cd04911 ACT_AKiii-YclM-BS_1 AC 58.9 41 0.00089 25.1 6.0 57 191-266 12-68 (76)
179 cd08412 PBP2_PAO1_like The C-t 58.9 91 0.002 24.8 13.3 122 14-145 25-154 (198)
180 PF07485 DUF1529: Domain of Un 58.6 37 0.0008 27.7 6.2 52 194-260 67-118 (123)
181 cd08425 PBP2_CynR The C-termin 58.0 95 0.0021 24.8 8.9 31 15-45 27-58 (197)
182 COG0725 ModA ABC-type molybdat 57.2 20 0.00043 32.9 4.9 44 2-45 147-194 (258)
183 cd04921 ACT_AKi-HSDH-ThrA-like 57.1 69 0.0015 22.9 7.9 27 190-216 11-37 (80)
184 KOG3217 Protein tyrosine phosp 57.0 7.2 0.00016 33.0 1.8 63 198-277 58-124 (159)
185 cd08459 PBP2_DntR_NahR_LinR_li 56.5 1E+02 0.0022 24.7 10.7 121 15-146 26-155 (201)
186 cd08461 PBP2_DntR_like_3 The C 55.9 1E+02 0.0023 24.6 9.3 123 14-147 25-157 (198)
187 TIGR01693 UTase_glnD [Protein- 55.3 56 0.0012 35.0 8.6 32 183-214 668-699 (850)
188 PRK09906 DNA-binding transcrip 55.0 1.6E+02 0.0034 26.3 13.0 121 14-144 115-246 (296)
189 PRK11242 DNA-binding transcrip 54.6 1.6E+02 0.0034 26.2 12.2 121 15-145 117-247 (296)
190 PRK09224 threonine dehydratase 54.2 33 0.00071 34.5 6.4 35 182-217 422-456 (504)
191 TIGR02424 TF_pcaQ pca operon t 53.8 1.6E+02 0.0036 26.2 13.0 121 15-145 119-251 (300)
192 PF11966 SSURE: Fibronectin-bi 53.2 32 0.00069 25.7 4.5 38 236-273 18-60 (81)
193 PRK09034 aspartate kinase; Rev 53.0 2.1E+02 0.0046 28.2 11.8 124 114-263 237-372 (454)
194 COG0834 HisJ ABC-type amino ac 52.8 24 0.00053 30.8 4.7 42 3-44 153-196 (275)
195 cd08413 PBP2_CysB_like The C-t 52.1 1.3E+02 0.0027 24.4 12.3 120 15-144 26-155 (198)
196 TIGR03427 ABC_peri_uca ABC tra 52.0 1.3E+02 0.0029 28.3 9.8 130 17-154 36-178 (328)
197 PRK10341 DNA-binding transcrip 51.7 1.9E+02 0.0041 26.3 12.3 33 15-47 123-156 (312)
198 COG2844 GlnD UTP:GlnB (protein 51.3 60 0.0013 34.7 7.7 32 181-212 789-820 (867)
199 cd08440 PBP2_LTTR_like_4 TThe 50.9 1.2E+02 0.0026 23.8 13.3 30 15-44 26-56 (197)
200 TIGR01096 3A0103s03R lysine-ar 49.8 1.4E+02 0.003 25.8 9.1 114 17-146 64-186 (250)
201 cd08437 PBP2_MleR The substrat 48.9 1.4E+02 0.003 23.9 12.2 122 14-144 25-156 (198)
202 TIGR00656 asp_kin_monofn aspar 48.7 94 0.002 29.8 8.4 95 114-217 192-297 (401)
203 PF03466 LysR_substrate: LysR 47.7 1.5E+02 0.0032 23.9 13.5 114 14-145 31-161 (209)
204 cd08444 PBP2_Cbl The C-termina 47.5 1.5E+02 0.0033 23.9 13.2 122 14-145 25-156 (198)
205 cd08465 PBP2_ToxR The C-termin 47.4 1.5E+02 0.0033 24.0 10.3 31 15-45 26-57 (200)
206 PRK12680 transcriptional regul 47.4 2.3E+02 0.0051 26.1 13.1 122 15-145 119-250 (327)
207 cd08466 PBP2_LeuO The C-termin 46.4 1.5E+02 0.0033 23.7 11.1 122 14-146 25-155 (200)
208 PRK12682 transcriptional regul 46.2 2.3E+02 0.0049 25.6 13.8 30 15-44 119-149 (309)
209 cd08436 PBP2_LTTR_like_3 The C 46.2 1.5E+02 0.0031 23.4 12.7 32 14-45 25-57 (194)
210 PRK01759 glnD PII uridylyl-tra 46.1 1E+02 0.0022 33.2 8.8 35 183-217 677-713 (854)
211 PF12974 Phosphonate-bd: ABC t 46.0 1.1E+02 0.0023 26.8 7.7 115 17-142 30-166 (243)
212 PRK11553 alkanesulfonate trans 45.6 62 0.0013 29.6 6.4 26 18-43 58-83 (314)
213 PRK06635 aspartate kinase; Rev 45.5 77 0.0017 30.5 7.2 52 189-264 349-400 (404)
214 cd08468 PBP2_Pa0477 The C-term 44.4 1.7E+02 0.0037 23.6 10.1 32 14-45 25-57 (202)
215 cd08451 PBP2_BudR The C-termin 44.4 1.6E+02 0.0035 23.3 14.6 32 14-45 26-58 (199)
216 PF06153 DUF970: Protein of un 44.3 1E+02 0.0022 24.7 6.5 53 199-268 15-67 (109)
217 PRK11139 DNA-binding transcrip 44.2 2.4E+02 0.0051 25.3 10.2 117 15-145 120-245 (297)
218 cd08457 PBP2_OccR The C-termin 43.7 1.7E+02 0.0036 23.4 13.6 119 14-142 25-152 (196)
219 PRK10859 membrane-bound lytic 43.0 1.1E+02 0.0024 30.3 8.1 27 17-43 81-107 (482)
220 TIGR03871 ABC_peri_MoxJ_2 quin 43.0 38 0.00083 29.1 4.3 43 2-44 110-161 (232)
221 TIGR00363 lipoprotein, YaeC fa 42.7 2.6E+02 0.0057 25.4 11.6 123 17-151 47-200 (258)
222 COG2107 Predicted periplasmic 42.5 45 0.00098 30.8 4.7 43 3-46 101-145 (272)
223 cd08421 PBP2_LTTR_like_1 The C 42.0 1.8E+02 0.0038 23.1 13.5 31 14-44 25-56 (198)
224 PF13379 NMT1_2: NMT1-like fam 41.6 1.6E+02 0.0035 26.0 8.2 120 17-142 36-180 (252)
225 PRK08210 aspartate kinase I; R 41.4 1.2E+02 0.0025 29.3 7.8 89 118-214 200-303 (403)
226 COG0788 PurU Formyltetrahydrof 41.3 1.8E+02 0.0038 27.2 8.3 35 183-217 7-41 (287)
227 PRK10216 DNA-binding transcrip 41.2 2.8E+02 0.006 25.2 10.4 125 14-145 122-262 (319)
228 PRK06635 aspartate kinase; Rev 41.0 1.1E+02 0.0023 29.5 7.5 29 190-218 270-298 (404)
229 cd04920 ACT_AKiii-DAPDC_2 ACT 41.0 1.2E+02 0.0026 21.0 6.1 51 190-264 10-60 (63)
230 PRK15010 ABC transporter lysin 40.7 60 0.0013 28.7 5.3 43 2-44 139-183 (260)
231 PRK10797 glutamate and asparta 40.6 34 0.00074 31.6 3.8 42 2-43 159-204 (302)
232 cd08432 PBP2_GcdR_TrpI_HvrB_Am 39.8 1.7E+02 0.0037 23.1 7.5 30 15-46 26-55 (194)
233 PF12916 DUF3834: Protein of u 39.5 31 0.00067 30.5 3.1 50 17-70 94-144 (201)
234 TIGR00656 asp_kin_monofn aspar 39.3 91 0.002 29.9 6.7 51 190-264 347-397 (401)
235 PRK11482 putative DNA-binding 39.2 3.1E+02 0.0066 25.1 12.6 122 13-146 141-270 (317)
236 PRK05092 PII uridylyl-transfer 38.9 1.6E+02 0.0035 31.9 9.1 33 183-215 732-764 (931)
237 cd08441 PBP2_MetR The C-termin 37.5 2.1E+02 0.0046 22.8 12.9 122 14-145 25-155 (198)
238 PRK06291 aspartate kinase; Pro 37.0 4E+02 0.0086 26.4 10.9 94 115-215 252-356 (465)
239 PF03401 TctC: Tripartite tric 36.9 52 0.0011 30.1 4.4 126 3-130 114-261 (274)
240 cd08420 PBP2_CysL_like C-termi 36.4 2.1E+02 0.0046 22.4 13.1 121 15-145 26-158 (201)
241 PF00072 Response_reg: Respons 35.8 33 0.00072 25.5 2.5 77 93-173 4-81 (112)
242 COG2150 Predicted regulator of 35.8 62 0.0013 27.8 4.2 35 184-218 96-130 (167)
243 PRK09986 DNA-binding transcrip 34.7 3.2E+02 0.007 24.1 13.5 122 14-145 122-255 (294)
244 TIGR03339 phn_lysR aminoethylp 34.2 3.2E+02 0.0068 23.8 14.0 118 15-142 110-236 (279)
245 PRK15437 histidine ABC transpo 34.0 3E+02 0.0066 24.1 8.8 35 10-45 59-93 (259)
246 PRK11716 DNA-binding transcrip 34.0 3.1E+02 0.0067 23.7 13.2 122 15-145 93-223 (269)
247 PRK00275 glnD PII uridylyl-tra 33.2 2.1E+02 0.0046 31.0 8.8 32 183-214 704-735 (895)
248 PRK15437 histidine ABC transpo 31.5 1E+02 0.0022 27.3 5.2 42 3-44 140-183 (259)
249 TIGR01098 3A0109s03R phosphate 31.0 3.5E+02 0.0076 23.4 10.3 120 17-147 65-208 (254)
250 cd08438 PBP2_CidR The C-termin 30.6 2.7E+02 0.0058 21.9 13.3 30 15-44 26-56 (197)
251 cd08426 PBP2_LTTR_like_5 The C 30.2 2.8E+02 0.006 21.9 14.9 121 15-145 26-155 (199)
252 cd08415 PBP2_LysR_opines_like 29.5 2.8E+02 0.0061 21.8 12.9 33 13-45 24-57 (196)
253 PRK02047 hypothetical protein; 29.3 2.6E+02 0.0056 21.3 8.2 59 191-265 24-85 (91)
254 cd08483 PBP2_HvrB The C-termin 29.2 1.4E+02 0.0031 23.6 5.4 116 15-145 26-149 (190)
255 PRK07431 aspartate kinase; Pro 29.1 1.9E+02 0.0041 29.4 7.4 58 189-262 277-334 (587)
256 cd00460 RNAP_RPB11_RPB3 RPB11 28.5 1.3E+02 0.0028 22.5 4.6 30 237-266 54-84 (86)
257 COG3283 TyrR Transcriptional r 28.4 1.5E+02 0.0032 29.2 5.9 72 187-278 4-77 (511)
258 PRK15385 magnesium transport p 28.3 4.2E+02 0.009 23.9 8.5 66 185-264 144-212 (225)
259 cd05466 PBP2_LTTR_substrate Th 27.7 2.8E+02 0.0061 21.2 12.2 32 15-46 26-58 (197)
260 PRK04998 hypothetical protein; 27.6 2.7E+02 0.0059 21.0 7.9 60 190-265 22-82 (88)
261 cd08416 PBP2_MdcR The C-termin 27.5 3.1E+02 0.0067 21.6 13.4 122 14-145 25-157 (199)
262 cd08469 PBP2_PnbR The C-termin 26.9 3.5E+02 0.0076 22.1 10.3 31 15-45 26-57 (221)
263 TIGR00657 asp_kinases aspartat 26.8 3E+02 0.0065 26.9 8.0 51 190-264 388-438 (441)
264 PF09383 NIL: NIL domain; Int 26.8 1.2E+02 0.0027 21.7 4.1 30 240-271 47-76 (76)
265 PRK00341 hypothetical protein; 26.6 2.9E+02 0.0064 21.1 7.2 59 191-265 25-85 (91)
266 TIGR02122 TRAP_TAXI TRAP trans 26.5 72 0.0016 28.9 3.5 44 1-44 147-197 (320)
267 PF03480 SBP_bac_7: Bacterial 26.5 4.8E+02 0.01 23.5 11.5 146 2-154 6-195 (286)
268 PF13379 NMT1_2: NMT1-like fam 26.2 94 0.002 27.5 4.1 42 2-44 128-177 (252)
269 cd08448 PBP2_LTTR_aromatics_li 26.1 3.2E+02 0.007 21.4 14.2 31 14-44 25-56 (197)
270 cd00134 PBPb Bacterial peripla 25.8 3.4E+02 0.0074 21.6 9.6 113 17-145 39-158 (218)
271 PRK08961 bifunctional aspartat 25.6 8.7E+02 0.019 26.2 14.3 126 113-263 252-388 (861)
272 cd08423 PBP2_LTTR_like_6 The C 25.4 3.4E+02 0.0073 21.3 12.8 31 15-45 26-57 (200)
273 PF09967 DUF2201: VWA-like dom 25.4 70 0.0015 25.8 2.8 27 240-266 2-28 (126)
274 PRK00907 hypothetical protein; 25.2 3.2E+02 0.007 21.0 6.6 59 191-264 25-85 (92)
275 KOG4028 Uncharacterized conser 24.9 66 0.0014 26.8 2.5 26 2-27 115-141 (175)
276 TIGR00787 dctP tripartite ATP- 24.8 4.9E+02 0.011 23.0 9.6 145 2-154 6-195 (257)
277 cd08467 PBP2_SyrM The C-termin 24.7 3.7E+02 0.008 21.6 10.7 121 14-145 25-154 (200)
278 cd00404 Aconitase_swivel Aconi 24.3 58 0.0013 25.0 2.0 41 3-46 27-68 (88)
279 PRK09181 aspartate kinase; Val 24.1 7.3E+02 0.016 24.8 10.9 121 115-264 260-391 (475)
280 TIGR00149 TIGR00149_YbjQ secon 24.1 50 0.0011 27.2 1.7 14 236-249 108-121 (132)
281 PLN02550 threonine dehydratase 23.9 5.8E+02 0.013 26.4 9.7 70 183-270 510-579 (591)
282 cd08427 PBP2_LTTR_like_2 The C 23.9 3.6E+02 0.0077 21.1 14.9 30 15-44 26-56 (195)
283 cd08481 PBP2_GcdR_like The C-t 23.8 3.6E+02 0.0078 21.1 7.1 30 15-46 26-55 (194)
284 COG1910 Periplasmic molybdate- 23.2 70 0.0015 28.8 2.5 127 18-153 20-170 (223)
285 TIGR01124 ilvA_2Cterm threonin 23.0 1.8E+02 0.0039 29.2 5.8 34 185-219 421-454 (499)
286 PF01894 UPF0047: Uncharacteri 22.8 46 0.001 26.9 1.3 13 236-248 96-108 (118)
287 cd08433 PBP2_Nac The C-teminal 22.5 3.9E+02 0.0085 21.1 13.7 120 15-144 26-154 (198)
288 PRK09495 glnH glutamine ABC tr 22.5 2.8E+02 0.006 24.1 6.3 113 17-145 64-184 (247)
289 cd01579 AcnA_Bact_Swivel Bacte 22.5 64 0.0014 26.2 2.0 41 3-46 60-101 (121)
290 PRK09436 thrA bifunctional asp 22.4 7.6E+02 0.017 26.5 10.6 96 113-215 244-350 (819)
291 PF08212 Lipocalin_2: Lipocali 22.3 1.3E+02 0.0029 24.4 4.0 25 194-218 118-142 (143)
292 cd08460 PBP2_DntR_like_1 The C 22.0 1.5E+02 0.0033 23.8 4.3 121 14-145 25-153 (200)
293 COG3870 Uncharacterized protei 21.8 4.1E+02 0.009 21.1 6.5 57 191-267 10-66 (109)
294 PLN02551 aspartokinase 21.8 7.6E+02 0.017 25.0 10.0 103 144-264 324-432 (521)
295 PRK11062 nhaR transcriptional 21.6 5.9E+02 0.013 22.8 11.4 30 15-44 119-149 (296)
296 TIGR03124 ctirate_citX holo-AC 21.4 2.8E+02 0.006 23.7 5.8 50 197-264 53-102 (165)
297 cd08456 PBP2_LysR The C-termin 21.3 4.1E+02 0.0089 20.8 13.5 31 14-44 25-56 (196)
298 CHL00180 rbcR LysR transcripti 21.3 6E+02 0.013 22.8 13.9 31 14-44 120-151 (305)
299 PRK07431 aspartate kinase; Pro 21.2 2.3E+02 0.0051 28.8 6.3 51 190-264 529-579 (587)
300 cd08434 PBP2_GltC_like The sub 21.0 4E+02 0.0088 20.7 10.9 30 15-44 26-56 (195)
301 PRK09084 aspartate kinase III; 20.9 8.1E+02 0.018 24.1 11.5 126 114-263 237-374 (448)
302 PRK12483 threonine dehydratase 20.2 5.8E+02 0.013 25.9 8.7 66 183-266 440-505 (521)
303 TIGR03870 ABC_MoxJ methanol ox 20.1 1.9E+02 0.0041 25.4 4.8 20 25-44 151-170 (246)
304 TIGR01093 aroD 3-dehydroquinat 20.0 1.4E+02 0.0031 26.3 4.0 34 241-276 94-127 (228)
No 1
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=1.2e-91 Score=637.57 Aligned_cols=265 Identities=47% Similarity=0.751 Sum_probs=251.6
Q ss_pred CCCCcHHHHHHHhhCCC-CceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeee
Q 048784 1 GVRGAYSESAAEKAYPN-CEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCL 79 (282)
Q Consensus 1 GP~GTfS~~Aa~~~~~~-~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L 79 (282)
||+|||||+||+++|++ .+..||+||+|||++|++|++||||||||||++|+|++|+|+|...+++|+||+++||+|||
T Consensus 9 GP~Gtfs~~Aa~~~f~~~~~~~p~~ti~evf~ave~g~aD~gVVPIENS~eG~V~~tlDlL~~~~l~IvgE~~lpI~h~L 88 (279)
T COG0077 9 GPEGTFSEQAARKLFGSGAELLPCSTIEDVFKAVENGEADYGVVPIENSIEGSVNETLDLLAETDLQIVGEIVLPIHHCL 88 (279)
T ss_pred CCCccHHHHHHHHhccccceeccCCCHHHHHHHHHcCCCceEEEEeeecCCcchHHHHHhhccCCcEEEEEEEEEEEEEE
Confidence 99999999999999998 79999999999999999999999999999999999999999999999999999999999999
Q ss_pred eecCCCCCCCccEEEechHHHHHHHHHHHhc--CCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeecccc
Q 048784 80 LANPGVKVEDLKRVLSHPQALAQCENTLTKL--GLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAEDIQ 157 (282)
Q Consensus 80 ~a~~~~~l~~I~~V~SHpqal~QC~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~~I~ 157 (282)
+++.+.++++|++|||||||++||++||+++ +++++++.|||+||+++++..+...|||||+.||++|||.+|++|||
T Consensus 89 ~~~~~~~l~~Ik~vySHpqalaQc~~~L~~~~p~~~~~~~~STa~Aak~v~~~~~~~~AAIas~~aA~~YgL~il~~~I~ 168 (279)
T COG0077 89 LVKGGVDLEEIKTVYSHPQALAQCRKFLRAHLPGVEIEYTSSTAEAAKLVAEGPDETVAAIASELAAELYGLDILAENIE 168 (279)
T ss_pred EecCCCChhhCeEEEeCcHHHHHHHHHHHHcCCCceEEEcCCHHHHHHHHHhCCCcCeeEEcCHHHHHHcCcHhHhhccc
Confidence 9998889999999999999999999999998 68899999999999999998778999999999999999999999999
Q ss_pred cCCCCceEEEEEeeC-CCCCCCCCCcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcc
Q 048784 158 DDCDNVTRFLMLARE-PIIPGTDRPFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKY 236 (282)
Q Consensus 158 d~~~N~TRF~vl~~~-~~~~~~~~~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~ 236 (282)
|.++|+|||+||+|. +.... +...||||+|+++|+||+|+++|++|+.||||||||||||+++. .
T Consensus 169 D~~~N~TRF~vl~r~~~~~~~-~~~~kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~~-------------~ 234 (279)
T COG0077 169 DEPNNRTRFLVLSRRKPPSVS-DGPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTG-------------L 234 (279)
T ss_pred CCCCCeEEEEEEeccCCCCcC-CCCceEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCCC-------------C
Confidence 999999999999985 32222 24579999999999999999999999999999999999999985 5
Q ss_pred eeEEEEEEeecCCCcHHHHHHHHHHHhhcCceEEEccccCCCC
Q 048784 237 FDYLFYVDFEASMADQKAQNALRHLKEFATFLRVLGSYPIDTT 279 (282)
Q Consensus 237 ~~y~F~vd~~g~~~~~~~~~al~~l~~~~~~v~~LGsY~~~~~ 279 (282)
|+|+||||++||.+|+.+++||++|++.+.++|+|||||....
T Consensus 235 ~~Y~F~iD~eg~~~~~~v~~AL~el~~~t~~~kilGsYp~~~~ 277 (279)
T COG0077 235 GEYLFFIDIEGHIDDPLVKEALEELKEITEFVKILGSYPSARV 277 (279)
T ss_pred eeEEEEEEEecCcCcHhHHHHHHHHHhheeEEEEEeecccccc
Confidence 9999999999999999999999999999999999999998653
No 2
>PRK11899 prephenate dehydratase; Provisional
Probab=100.00 E-value=3.5e-89 Score=627.09 Aligned_cols=266 Identities=42% Similarity=0.631 Sum_probs=251.8
Q ss_pred CCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeee
Q 048784 1 GVRGAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLL 80 (282)
Q Consensus 1 GP~GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~ 80 (282)
||+|||||+||+++|++.+++||.||++||++|++|++||||||||||++|+|.+|+|+|.+++++|+||+.+||+|||+
T Consensus 11 Gp~GsfS~~Aa~~~~~~~~~v~~~s~~~vf~av~~g~~d~gVvPiENS~~G~V~~~~Dll~~~~l~Iv~E~~l~I~h~Ll 90 (279)
T PRK11899 11 GEPGANSHLACRDAFPDMEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVADIHHLLPESGLHIVGEYFLPIRHQLM 90 (279)
T ss_pred CCCCCHHHHHHHHhcCcCceeecCCHHHHHHHHHCCCCCEEEEEeeccCCccHHHHHHHHhcCCCEEEEEEEEEeeEEEe
Confidence 99999999999999998899999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCCCCccEEEechHHHHHHHHHHHhcCCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeecccccCC
Q 048784 81 ANPGVKVEDLKRVLSHPQALAQCENTLTKLGLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAEDIQDDC 160 (282)
Q Consensus 81 a~~~~~l~~I~~V~SHpqal~QC~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~~I~d~~ 160 (282)
+.++.++++|++||||||||+||++||++++++.+++.|||+||++|++.++++.|||||+.||++|||+||+++|||.+
T Consensus 91 ~~~~~~l~~I~~V~SHpqal~QC~~fL~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAIas~~aa~~YgL~il~~~IqD~~ 170 (279)
T PRK11899 91 ALPGATLEEIKTVHSHPHALGQCRKIIRALGLKPVVAADTAGAARLVAERGDPSMAALASRLAAELYGLDILAENIEDAD 170 (279)
T ss_pred cCCCCCHHHCeEEEEeHHHHHHHHHHHHHcCCeEEEcCChHHHHHHHHhcCCCCeeEeCCHHHHHHcCCcchhhcccCCc
Confidence 99999999999999999999999999999988899999999999999987777899999999999999999999999999
Q ss_pred CCceEEEEEeeCCCC-CCCCCCcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeE
Q 048784 161 DNVTRFLMLAREPII-PGTDRPFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDY 239 (282)
Q Consensus 161 ~N~TRF~vl~~~~~~-~~~~~~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y 239 (282)
+|+|||+||+|++.. +.....+||||+|+++|+||+|+++|++|+.+|||||||||||.++. .|+|
T Consensus 171 ~N~TRF~vi~~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~-------------~~~Y 237 (279)
T PRK11899 171 HNTTRFVVLSREADWAARGDGPIVTTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGS-------------FTAT 237 (279)
T ss_pred ccceeEEEEecCCCCCCCCCCCceEEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCC-------------CceE
Confidence 999999999997642 22223469999999999999999999999999999999999999985 4999
Q ss_pred EEEEEeecCCCcHHHHHHHHHHHhhcCceEEEccccCCCC
Q 048784 240 LFYVDFEASMADQKAQNALRHLKEFATFLRVLGSYPIDTT 279 (282)
Q Consensus 240 ~F~vd~~g~~~~~~~~~al~~l~~~~~~v~~LGsY~~~~~ 279 (282)
+||||++||.+|++++++|++|++.+.++|+|||||..+.
T Consensus 238 ~F~id~eg~~~d~~v~~aL~~l~~~~~~~kvLGsYp~~~~ 277 (279)
T PRK11899 238 QFYADIEGHPEDRNVALALEELRFFSEEVRILGVYPAHPF 277 (279)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHHhcCcEEEeeeecCccc
Confidence 9999999999999999999999999999999999997653
No 3
>PLN02317 arogenate dehydratase
Probab=100.00 E-value=7.4e-89 Score=643.81 Aligned_cols=280 Identities=82% Similarity=1.248 Sum_probs=266.4
Q ss_pred CCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeee
Q 048784 1 GVRGAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLL 80 (282)
Q Consensus 1 GP~GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~ 80 (282)
||+|||||+||+++|++.+++||+||++||+||++|++||||||||||++|.|.+|||+|.+++++|+||+++||+|||+
T Consensus 101 Gp~GtfSe~AA~~~f~~~e~vp~~sf~~vf~AVe~g~ad~gVvPIENS~~GsV~~t~DlL~~~~l~IvgEv~l~I~h~Ll 180 (382)
T PLN02317 101 GVPGAYSEAAARKAYPNCEAVPCEQFEAAFQAVELWLADRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHHCLL 180 (382)
T ss_pred CCCcCHHHHHHHHhhCcCceeecCCHHHHHHHHHCCCCCEEEEEEeccCccchHHHHHHHhcCCCEEEEEEEEEeeeEEe
Confidence 99999999999999998899999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCCCCccEEEechHHHHHHHHHHHhcCCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeecccccCC
Q 048784 81 ANPGVKVEDLKRVLSHPQALAQCENTLTKLGLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAEDIQDDC 160 (282)
Q Consensus 81 a~~~~~l~~I~~V~SHpqal~QC~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~~I~d~~ 160 (282)
+++|.++++|++||||||||+||++||++++++++++.|||+||++|++.+.++.|||||+.||++|||+||+++|||++
T Consensus 181 ~~~g~~l~~Ik~VySHPQALaQC~~~L~~~~~~~~~~~sTA~AA~~Va~~~~~~~AAIaS~~aA~~YgL~iLa~~IqD~~ 260 (382)
T PLN02317 181 ALPGVRKEELKRVISHPQALAQCENTLTKLGVVREAVDDTAGAAKMVAANGLRDTAAIASARAAELYGLDILAEGIQDDS 260 (382)
T ss_pred cCCCCCHHHCeEEEEehHHHHHHHHHHHHcCCeEEEcCCHHHHHHHHHhcCCCCceeecCHHHHHHcCCcchhhhhcCCC
Confidence 99999999999999999999999999999999999999999999999987777899999999999999999999999999
Q ss_pred CCceEEEEEeeCCCCCCCCCCcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCC-CCCCCcceeE
Q 048784 161 DNVTRFLMLAREPIIPGTDRPFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDD-NSGFGKYFDY 239 (282)
Q Consensus 161 ~N~TRF~vl~~~~~~~~~~~~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~-~~g~~~~~~y 239 (282)
+|+|||+||+|++..+..+..+||||+|+++++||+|+++|++|+.+|||||||||||.++.|+.+.|+ +.|..+.|+|
T Consensus 261 ~N~TRFlvl~r~~~~~~~~~~~KTSivfsl~~~pG~L~k~L~~Fa~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~~eY 340 (382)
T PLN02317 261 DNVTRFLMLAREPIIPRTDRPFKTSIVFSLEEGPGVLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNSGTAKYFDY 340 (382)
T ss_pred CCeeeEEEEecCCcCCCCCCCccEEEEEEcCCCCchHHHHHHHHHHCCCCEEEEEeeecCCCCccccccccccccccccE
Confidence 999999999998754433455699999999999999999999999999999999999999999888887 8888889999
Q ss_pred EEEEEeecCCCcHHHHHHHHHHHhhcCceEEEccccCCCCC
Q 048784 240 LFYVDFEASMADQKAQNALRHLKEFATFLRVLGSYPIDTTI 280 (282)
Q Consensus 240 ~F~vd~~g~~~~~~~~~al~~l~~~~~~v~~LGsY~~~~~~ 280 (282)
.|||||+|+..|++++++|++|++.+.++|+|||||...+.
T Consensus 341 ~FyVD~eg~~~d~~~~~aL~~L~~~~~~lrvLGsYp~~~~~ 381 (382)
T PLN02317 341 LFYVDFEASMADPRAQNALAHLQEFATFLRVLGSYPMDMTP 381 (382)
T ss_pred EEEEEEEcCcCCHHHHHHHHHHHHhcCeEEEEeeeecCCCC
Confidence 99999999999999999999999999999999999987653
No 4
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=100.00 E-value=3.9e-83 Score=611.00 Aligned_cols=265 Identities=34% Similarity=0.580 Sum_probs=247.8
Q ss_pred CCCCcHHHHHHHhhCCC----CceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeee
Q 048784 1 GVRGAYSESAAEKAYPN----CEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVR 76 (282)
Q Consensus 1 GP~GTfS~~Aa~~~~~~----~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~ 76 (282)
||+|||||+||+++|+. ...+||+||++||++|++|++||||||||||++|.|.+|||+|.+++++|+||+.+||+
T Consensus 110 Gp~GtfSh~Aa~~~~~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~DlL~~~~l~I~~E~~l~I~ 189 (386)
T PRK10622 110 GPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVLPIENTSSGAINDVYDLLQHTSLSIVGEMTLPID 189 (386)
T ss_pred CCCCcHHHHHHHHhhccccccccccCCCCHHHHHHHHHCCCCCEEEEEEecCCceehHHHHHHHhcCCCEEEEEEEEEEE
Confidence 99999999999998753 23458999999999999999999999999999999999999999999999999999999
Q ss_pred eeeeecCCCCCCCccEEEechHHHHHHHHHHHhc-CCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeecc
Q 048784 77 HCLLANPGVKVEDLKRVLSHPQALAQCENTLTKL-GLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAED 155 (282)
Q Consensus 77 ~~L~a~~~~~l~~I~~V~SHpqal~QC~~fl~~~-~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~~ 155 (282)
|||++.++.++++|++||||||||+||++||+++ +++.+++.|||+||++|++.++++.|||||+.||++|||+||+++
T Consensus 190 h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~aa~~ygL~vl~~~ 269 (386)
T PRK10622 190 HCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRYPHWKIEYTESTAAAMEKVAQANSPHVAALGSEAGGALYGLQVLERN 269 (386)
T ss_pred EEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHCCCceEEEcCChHHHHHHHHhcCCCCEEEECCHHHHHHcCCcChhhc
Confidence 9999999999999999999999999999999998 678899999999999999877778899999999999999999999
Q ss_pred cccCCCCceEEEEEeeCCCCCCCCCCcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCc
Q 048784 156 IQDDCDNVTRFLMLAREPIIPGTDRPFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGK 235 (282)
Q Consensus 156 I~d~~~N~TRF~vl~~~~~~~~~~~~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~ 235 (282)
|||.++|+|||+||++++..+..+..+||||+|.++|+||+|+++|++|+.+|||||||||||.++.
T Consensus 270 I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~~L~~Fa~~giNLtkIeSRP~~~~------------- 336 (386)
T PRK10622 270 LANQQQNITRFIVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTKLESRPIHGN------------- 336 (386)
T ss_pred CcCCccccceEEEEecCCCCCCCCCCCcEEEEEEcCCCCcHHHHHHHHHHHcCCCeeEEEeeecCCC-------------
Confidence 9999999999999999864232233469999999999999999999999999999999999999985
Q ss_pred ceeEEEEEEeecCCCcHHHHHHHHHHHhhcCceEEEccccCCC
Q 048784 236 YFDYLFYVDFEASMADQKAQNALRHLKEFATFLRVLGSYPIDT 278 (282)
Q Consensus 236 ~~~y~F~vd~~g~~~~~~~~~al~~l~~~~~~v~~LGsY~~~~ 278 (282)
.|+|+||||++||.+|++++++|++|++.+.++|+|||||..+
T Consensus 337 ~~~Y~Ffid~eg~~~d~~~~~aL~~l~~~~~~~kvLGsYp~~~ 379 (386)
T PRK10622 337 PWEEMFYLDVQANLRSAEMQKALKELGEITRSLKVLGCYPSEN 379 (386)
T ss_pred CceEEEEEEEeCCCCCHHHHHHHHHHHHhcCcEEEeeeecCCc
Confidence 4999999999999999999999999999999999999999764
No 5
>PRK11898 prephenate dehydratase; Provisional
Probab=100.00 E-value=8.5e-82 Score=580.52 Aligned_cols=264 Identities=43% Similarity=0.631 Sum_probs=245.8
Q ss_pred CCCCcHHHHHHHhhCCC---CceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccC-CeEEEEEEEEeee
Q 048784 1 GVRGAYSESAAEKAYPN---CEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRH-RLHIVGEVKFAVR 76 (282)
Q Consensus 1 GP~GTfS~~Aa~~~~~~---~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~-~l~I~~E~~l~I~ 76 (282)
||+|||||+||+++|++ .++++|+||++||++|++|++||||||||||++|.|.+|+|+|.++ +++|+||+.+||+
T Consensus 8 Gp~Gs~s~~Aa~~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~v~~~~d~L~~~~~~~iv~E~~l~I~ 87 (283)
T PRK11898 8 GPEGTFTEAAALKFFPADGEAELVPYDSIPDVLDAVEAGEVDYAVVPIENSIEGSVNPTLDYLAHGSPLQIVAEIVLPIA 87 (283)
T ss_pred CCCCCHHHHHHHHhhccccccceEecCCHHHHHHHHHcCCCCEEEEEecccCceecHHHHHHhccCCCcEEEEEEEeeee
Confidence 99999999999999976 7899999999999999999999999999999999999999988764 8999999999999
Q ss_pred eeeeecCCCCCCCccEEEechHHHHHHHHHHHhc--CCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeec
Q 048784 77 HCLLANPGVKVEDLKRVLSHPQALAQCENTLTKL--GLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAE 154 (282)
Q Consensus 77 ~~L~a~~~~~l~~I~~V~SHpqal~QC~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~ 154 (282)
|||+++++.. ++|++||||||||+||++||+++ +++.+++.|||+||+++++++..+.|||||+.||++|||++|++
T Consensus 88 ~~L~~~~~~~-~~i~~V~SHpqal~QC~~~l~~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~ 166 (283)
T PRK11898 88 QHLLVHPGHA-AKIRTVYSHPQALAQCRKWLAEHLPGAELEPANSTAAAAQYVAEHPDEPIAAIASELAAELYGLEILAE 166 (283)
T ss_pred EEEeCCCCCh-hcCeEEEEeHHHHHHHHHHHHhcCCCCEEEEcCchHHHHHHHhcCCCCCeEEECCHHHHHHcCCcEehh
Confidence 9999998865 99999999999999999999997 78899999999999999987666789999999999999999999
Q ss_pred ccccCCCCceEEEEEeeCCC-CCCCCCCcEEEEEEEcCC-CccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCC
Q 048784 155 DIQDDCDNVTRFLMLAREPI-IPGTDRPFKTSIVFSLEE-GPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSG 232 (282)
Q Consensus 155 ~I~d~~~N~TRF~vl~~~~~-~~~~~~~~ktsi~~~~~~-~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g 232 (282)
||||.++|+|||+||+|++. .+.....+||||+|++++ +||+|+++|++|+++|||||||||||.++.
T Consensus 167 ~I~d~~~N~TRF~vi~~~~~~~~~~~~~~ktslif~l~~~~pGsL~~~L~~F~~~~INLt~IeSRP~~~~---------- 236 (283)
T PRK11898 167 DIQDYPNNRTRFWLLGRKKPPPPLRTGGDKTSLVLTLPNNLPGALYKALSEFAWRGINLTRIESRPTKTG---------- 236 (283)
T ss_pred cCCCCCccceEEEEEEcCcccCCCCCCCCeEEEEEEeCCCCccHHHHHHHHHHHCCCCeeeEecccCCCC----------
Confidence 99999999999999999864 222234569999999987 499999999999999999999999999884
Q ss_pred CCcceeEEEEEEeecCCCcHHHHHHHHHHHhhcCceEEEccccCCC
Q 048784 233 FGKYFDYLFYVDFEASMADQKAQNALRHLKEFATFLRVLGSYPIDT 278 (282)
Q Consensus 233 ~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~~~v~~LGsY~~~~ 278 (282)
.|+|.|||||+|+.++++++++|++|++.+.++|+|||||...
T Consensus 237 ---~~~y~F~vd~eg~~~~~~~~~al~~L~~~~~~~k~LGsY~~~~ 279 (283)
T PRK11898 237 ---LGTYFFFIDVEGHIDDVLVAEALKELEALGEDVKVLGSYPVYW 279 (283)
T ss_pred ---CccEEEEEEEEccCCCHHHHHHHHHHHHhcCcEEEEEeecccc
Confidence 5999999999999999999999999999999999999999754
No 6
>KOG2797 consensus Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=4.5e-76 Score=531.51 Aligned_cols=275 Identities=72% Similarity=1.129 Sum_probs=264.8
Q ss_pred CCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeee
Q 048784 1 GVRGAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLL 80 (282)
Q Consensus 1 GP~GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~ 80 (282)
||+|+|||+||.+.|++.+-+||..|+.+|+||+...+||+|||||||+.|+|...||||..+.+.|+||+.+||+|||+
T Consensus 97 g~pgaysesaa~ka~pn~~avpc~~f~~afqave~w~vD~AVLPiENS~gGsIhrnYDLLlrh~lhiVgEv~vPvhHCLi 176 (377)
T KOG2797|consen 97 GVPGAYSESAALKAYPNCEAVPCDQFEAAFQAVELWIVDYAVLPIENSTGGSIHRNYDLLLRHRLHIVGEVQVPVHHCLI 176 (377)
T ss_pred cCCchhhhhhhhhhcCCcccccHhHHHHHHHHHHHhhccceeeeeeccCCceeeechHHHhhcchheeeEEecceeeeEe
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ecCCCCCCCccEEEechHHHHHHHHHHHhcC--CeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeeccccc
Q 048784 81 ANPGVKVEDLKRVLSHPQALAQCENTLTKLG--LVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAEDIQD 158 (282)
Q Consensus 81 a~~~~~l~~I~~V~SHpqal~QC~~fl~~~~--~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~~I~d 158 (282)
+.+|...+++++|.||||||+||..||.+++ +.++.+.|||+||+.++.+...+.+||+|+.||++|||.||+++|||
T Consensus 177 ~~~gv~~e~~~~VlSHPQal~Qce~~L~~l~~~~~r~a~~dTa~Aa~~~s~~~~~d~~AIASe~aA~ly~l~Il~~~IqD 256 (377)
T KOG2797|consen 177 ALPGVRKEEVVRVLSHPQALGQCECSLTKLGPNAAREAVSDTAGAAEQISASNTADTAAIASERAAELYGLNILEKNIQD 256 (377)
T ss_pred cCCCCChhheeeeecCcHHHHHHHHHHHhcccceeeeeccchHHHHHHHHhcccccHHHHHHHHHHHHhcchhhhhhccc
Confidence 9999999999999999999999999999984 77889999999999999888788999999999999999999999999
Q ss_pred CCCCceEEEEEeeCCCCCCCCCCcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCccee
Q 048784 159 DCDNVTRFLMLAREPIIPGTDRPFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFD 238 (282)
Q Consensus 159 ~~~N~TRF~vl~~~~~~~~~~~~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~ 238 (282)
+.+|+|||++|.|++..|..++..||||+|...+.||.|.++|++|+-|+||||+|||||.+..|++..|+. +.|+
T Consensus 257 d~~NvTRFLmLar~p~ip~t~rl~ktsivf~~~~gp~vLfkvl~vfa~r~inltkIesRP~h~~p~r~v~~~----k~f~ 332 (377)
T KOG2797|consen 257 DLGNVTRFLMLAREPIIPDTDRLFKTSIVFFREKGPGVLFKVLSVFAFRSINLTKIESRPFHNRPLRVVDDS----KNFE 332 (377)
T ss_pred ccCCeeEEEEEeccCCCCCCCccceeeEEEEeecCCchHHHHHHHHHhhhceeeeeecccccCCCccccccc----cccc
Confidence 999999999999999988878889999999998999999999999999999999999999999998888774 7899
Q ss_pred EEEEEEeecCCCcHHHHHHHHHHHhhcCceEEEccccCCCC
Q 048784 239 YLFYVDFEASMADQKAQNALRHLKEFATFLRVLGSYPIDTT 279 (282)
Q Consensus 239 y~F~vd~~g~~~~~~~~~al~~l~~~~~~v~~LGsY~~~~~ 279 (282)
|.||||+|....+++.++++.++++.+.++++|||||.+.+
T Consensus 333 ylFyidfeasmae~~aq~al~~~~e~~sflrvlGsyp~d~t 373 (377)
T KOG2797|consen 333 YLFYIDFEASMAEPRAQNALGEVQEFTSFLRVLGSYPMDMT 373 (377)
T ss_pred EEEEEEEEeccCcHHHHHHHHHHHHHHHHHHHhcCCccccc
Confidence 99999999999999999999999999999999999998754
No 7
>PF00800 PDT: Prephenate dehydratase Caution this is only a partial structure.; InterPro: IPR001086 Prephenate dehydratase (4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate to phenylpyruvate. In microorganisms it is part of the terminal pathway of phenylalanine biosynthesis. In some bacteria such as Escherichia coli PDT is part of a bifunctional enzyme (P-protein) that also catalyses the transformation of chorismate into prephenate (chorismate mutase, IPR002701 from INTERPRO, 5.4.99.5 from EC) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional PDT aligns well with the C-terminal part of P-proteins [].; GO: 0004664 prephenate dehydratase activity, 0009094 L-phenylalanine biosynthetic process; PDB: 3MWB_B 2QMX_A 2QMW_A 3LUY_A.
Probab=100.00 E-value=4.9e-56 Score=384.91 Aligned_cols=173 Identities=47% Similarity=0.760 Sum_probs=160.4
Q ss_pred CCCCcHHHHHHHhhC--CCCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeee
Q 048784 1 GVRGAYSESAAEKAY--PNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHC 78 (282)
Q Consensus 1 GP~GTfS~~Aa~~~~--~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~ 78 (282)
||+|||||+||++|| ++.++++|+||++||++|.+|++||||||||||++|.|.+|+|+|.+.++.|+||+.+||+||
T Consensus 5 GP~GT~S~~Aa~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~~vvPiENs~~G~V~~t~d~L~~~~l~i~~e~~l~i~~~ 84 (181)
T PF00800_consen 5 GPEGTFSHEAAQQYFGGPDAEIVPCDSFEEVFDAVEEGEADYGVVPIENSLEGSVSETLDLLIDSDLYIVGEIVLPIHHC 84 (181)
T ss_dssp SSTTSHHHHHHCCCCTTTCSEEEEESSHHHHHHHHHCTSSSEEEEEEECTTTCECHHHHHHHHTSSCEEEEEEEEE--EE
T ss_pred CCCCCHHHHHHHHHHHhhccceEecCCHHHHHHHHHcCCCceEEEeEeeecCCEeHHHHHHHhcCCceEEEEEEeccccE
Confidence 999999999999999 578999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeecCCCCCCCccEEEechHHHHHHHHHHHhc--CCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeeccc
Q 048784 79 LLANPGVKVEDLKRVLSHPQALAQCENTLTKL--GLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAEDI 156 (282)
Q Consensus 79 L~a~~~~~l~~I~~V~SHpqal~QC~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~~I 156 (282)
|+++++.++++|++||||||+++||++||+++ +++++.+.||++||++++..+.+.+|||||+.||++|||++|+++|
T Consensus 85 L~~~~~~~l~~i~~V~SHp~al~Qc~~~l~~~~p~~~~~~~~Sta~Aa~~v~~~~~~~~aAI~s~~aa~~y~L~il~~~I 164 (181)
T PF00800_consen 85 LLAKPGTSLSDIKTVYSHPQALAQCREFLEKHLPGAEIVEASSTAEAAEKVAASEGPGDAAIASEEAAELYGLEILARNI 164 (181)
T ss_dssp EEECTT--GGG-SEEEEEHHHHHHTHHHHHHT-TTSEEEEESSHHHHHHHCCCCTBTTEEEEEECCHHHHTTEEEEECS-
T ss_pred EeccCCCchhcceEEEEchHHHHHHHHHHHhcCCceEEEeCCCHHHHHHHHHhccCCCeEEECCHHHHHHcCccChhhcC
Confidence 99999988999999999999999999999998 7889999999999999877777889999999999999999999999
Q ss_pred ccCCCCceEEEEEeeCC
Q 048784 157 QDDCDNVTRFLMLAREP 173 (282)
Q Consensus 157 ~d~~~N~TRF~vl~~~~ 173 (282)
||.++|+|||+||+|++
T Consensus 165 ~d~~~N~TRF~vi~~~~ 181 (181)
T PF00800_consen 165 QDNPNNYTRFLVIGKEP 181 (181)
T ss_dssp SSSTT-EEEEEEEECCT
T ss_pred CCCCCCeEeEEEEecCC
Confidence 99999999999999864
No 8
>cd04904 ACT_AAAH ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH). ACT domain of the nonheme iron-dependent, aromatic amino acid hydroxylases (AAAH): Phenylalanine hydroxylases (PAH), tyrosine hydroxylases (TH) and tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. This family of enzymes shares a common catalytic mechanism, in which dioxygen is used by an active site containing a single, reduced iron atom to hydroxylate an unactivated aromatic substrate, concomitant with a two-electron oxidation of tetrahydropterin (BH4) cofactor to its quinonoid dihydropterin form. PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe; TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines; and TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxy
Probab=99.88 E-value=1.4e-22 Score=151.20 Aligned_cols=73 Identities=37% Similarity=0.556 Sum_probs=68.1
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
|||+|+++|+||+|+++|+.|+.+|||||||||||.++. .|+|.|||||+| +++++++++++|++
T Consensus 1 tsl~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~-------------~~~y~Ffvd~~~--~~~~~~~~l~~L~~ 65 (74)
T cd04904 1 TSLIFSLKEEVGALARALKLFEEFGVNLTHIESRPSRRN-------------GSEYEFFVDCEV--DRGDLDQLISSLRR 65 (74)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCCC-------------CceEEEEEEEEc--ChHHHHHHHHHHHH
Confidence 689999999999999999999999999999999999984 599999999999 56789999999999
Q ss_pred hcCceEEE
Q 048784 264 FATFLRVL 271 (282)
Q Consensus 264 ~~~~v~~L 271 (282)
.+..+|++
T Consensus 66 ~~~~~~~~ 73 (74)
T cd04904 66 VVADVNIL 73 (74)
T ss_pred hcCeEEEc
Confidence 99999875
No 9
>cd04931 ACT_PAH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, phenylalanine hydroxylases (PAH). PAH catalyzes the hydroxylation of L-Phe to L-Tyr, the first step in the catabolic degradation of L-Phe. In PAH, an autoregulatory sequence, N-terminal of the ACT domain, extends across the catalytic domain active site and regulates the enzyme by intrasteric regulation. It appears that the activation by L-Phe induces a conformational change that converts the enzyme to a high-affinity and high-activity state. Modulation of activity is achieved through inhibition by BH4 and activation by phosphorylation of serine residues of the autoregulatory region. The molecular basis for the cooperative activation process is not fully understood yet. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.86 E-value=1e-21 Score=151.98 Aligned_cols=71 Identities=32% Similarity=0.514 Sum_probs=65.5
Q ss_pred CCcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHH
Q 048784 180 RPFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALR 259 (282)
Q Consensus 180 ~~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~ 259 (282)
...||||+|+++|+||+|+++|++|+.+||||+||||||+++. .|+|.|||||+|+ .+++++++|+
T Consensus 11 ~~~ktslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~-------------~~~Y~FfVDieg~-~~~~~~~~l~ 76 (90)
T cd04931 11 KNGVISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLN-------------KDEYEFFINLDKK-SAPALDPIIK 76 (90)
T ss_pred CCCcEEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCC-------------CceEEEEEEEEcC-CCHHHHHHHH
Confidence 3458999999999999999999999999999999999999884 5999999999998 6899999999
Q ss_pred HHHhh
Q 048784 260 HLKEF 264 (282)
Q Consensus 260 ~l~~~ 264 (282)
+|++.
T Consensus 77 ~L~~~ 81 (90)
T cd04931 77 SLRND 81 (90)
T ss_pred HHHHH
Confidence 99873
No 10
>cd04930 ACT_TH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tyrosine hydroxylases (TH). TH catalyses the hydroxylation of L-Tyr to 3,4-dihydroxyphenylalanine, the rate limiting step in the biosynthesis of catecholamines (dopamine, noradrenaline and adrenaline), functioning as hormones and neurotransmitters. The enzyme is not regulated by its amino acid substrate, but instead by phosphorylation at several serine residues located N-terminal of the ACT domain, and by feedback inhibition by catecholamines at the active site. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.85 E-value=3.2e-21 Score=155.58 Aligned_cols=76 Identities=29% Similarity=0.393 Sum_probs=69.5
Q ss_pred CcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHH
Q 048784 181 PFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRH 260 (282)
Q Consensus 181 ~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~ 260 (282)
++||||+|+++|+||+|+++|++|+.+|||||||||||++.. .|+|.|||||+|+.+ .++++|++
T Consensus 39 ~~ktSlifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~~~-------------~~eY~FfIdieg~~~--~~~~aL~~ 103 (115)
T cd04930 39 PQKATLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSRKE-------------GGDLEVLVRCEVHRS--DLLQLISS 103 (115)
T ss_pred cccEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCCCC-------------CceEEEEEEEEeCHH--HHHHHHHH
Confidence 358999999999999999999999999999999999999884 599999999999864 69999999
Q ss_pred HHhhcCceEEE
Q 048784 261 LKEFATFLRVL 271 (282)
Q Consensus 261 l~~~~~~v~~L 271 (282)
|++.+.++++-
T Consensus 104 L~~~~~~~kv~ 114 (115)
T cd04930 104 LRQVAEDVRLT 114 (115)
T ss_pred HHHhcCeeEec
Confidence 99999988763
No 11
>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=99.85 E-value=3.3e-21 Score=143.97 Aligned_cols=70 Identities=31% Similarity=0.442 Sum_probs=64.2
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
||++|+++|+||+|+++|+.|+.+||||+||||||.+.. .|+|.|||||+||. .++++++++|++
T Consensus 1 tsl~~~l~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~-------------~~~y~F~id~e~~~--~~i~~~l~~l~~ 65 (74)
T cd04929 1 TSVIFSLKNEVGGLAKALKLFQELGINVVHIESRKSKRR-------------SSEFEIFVDCECDQ--RRLDELVQLLKR 65 (74)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCC-------------CceEEEEEEEEcCH--HHHHHHHHHHHH
Confidence 589999999999999999999999999999999999884 59999999999987 489999999998
Q ss_pred hcCce
Q 048784 264 FATFL 268 (282)
Q Consensus 264 ~~~~v 268 (282)
.+...
T Consensus 66 ~~~~~ 70 (74)
T cd04929 66 EVASV 70 (74)
T ss_pred hcccc
Confidence 87654
No 12
>cd04905 ACT_CM-PDT C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme. The C-terminal ACT domain of the bifunctional chorismate mutase-prephenate dehydratase (CM-PDT) enzyme and the prephenate dehydratase (PDT) enzyme, found in plants, fungi, bacteria, and archaea. The P-protein of E. coli (CM-PDT, PheA) catalyzes the conversion of chorismate to prephenate and then the decarboxylation and dehydration to form phenylpyruvate. These are the first two steps in the biosynthesis of L-Phe and L-Tyr via the shikimate pathway in microorganisms and plants. The E. coli P-protein (CM-PDT) has three domains with an N-terminal domain with chorismate mutase activity, a middle domain with prephenate dehydratase activity, and an ACT regulatory C-terminal domain. The prephenate dehydratase enzyme has a PDT and ACT domain. The ACT domain is essential to bring about the negative allosteric regulation by L-Phe bindi
Probab=99.84 E-value=1.7e-20 Score=141.38 Aligned_cols=80 Identities=53% Similarity=0.935 Sum_probs=75.2
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
|+|++|.++|+||+|.++|+.|+++||||++|+|||.+. ..|+|.||||++++.++++++++++.|+
T Consensus 1 ~~sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~-------------~~~~~~f~vd~~~~~~~~~~~~~l~~l~ 67 (80)
T cd04905 1 KTSIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKG-------------GLWEYVFFIDFEGHIEDPNVAEALEELK 67 (80)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCC-------------CCceEEEEEEEECCCCCHHHHHHHHHHH
Confidence 589999999999999999999999999999999999976 3589999999999877889999999999
Q ss_pred hhcCceEEEcccc
Q 048784 263 EFATFLRVLGSYP 275 (282)
Q Consensus 263 ~~~~~v~~LGsY~ 275 (282)
+.+.++|+||+||
T Consensus 68 ~~~~~~~~lG~y~ 80 (80)
T cd04905 68 RLTEFVKVLGSYP 80 (80)
T ss_pred HhCCeEEEeeeeC
Confidence 9999999999997
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=99.82 E-value=6.9e-20 Score=136.24 Aligned_cols=75 Identities=53% Similarity=0.822 Sum_probs=70.8
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
|++|+++|+||+|.++|+.|+.+|+||++|||||.++. .|+|.||||++|+.++.+++++++.|++.
T Consensus 1 sl~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~-------------~~~~~f~id~~~~~~~~~~~~~l~~l~~~ 67 (75)
T cd04880 1 SLVFSLKNKPGALAKALKVFAERGINLTKIESRPSRKG-------------LWEYEFFVDFEGHIDDPDVKEALEELKRV 67 (75)
T ss_pred CEEEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCC-------------CceEEEEEEEECCCCCHHHHHHHHHHHHh
Confidence 57899999999999999999999999999999999874 48999999999987889999999999999
Q ss_pred cCceEEEc
Q 048784 265 ATFLRVLG 272 (282)
Q Consensus 265 ~~~v~~LG 272 (282)
+.++++||
T Consensus 68 ~~~~~~lG 75 (75)
T cd04880 68 TEDVKVLG 75 (75)
T ss_pred CCeeEECC
Confidence 99999998
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=99.75 E-value=4e-18 Score=163.99 Aligned_cols=80 Identities=36% Similarity=0.616 Sum_probs=74.6
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
+||||+|+++|+||+|+++|++|+.+||||+||||||+++. .|+|.|||||+|+. ++++.++|++|
T Consensus 15 ~KTSLiFsL~d~pGaL~~vL~vFa~~gINLthIESRPsk~~-------------~~eY~FFVD~eg~~-~~~v~~aL~~L 80 (436)
T TIGR01268 15 AKTSLIFSLKEEAGALAETLKLFQAHDVNLTHIESRPSKTH-------------PGEYEFFVEFDEAS-DRKLEGVIEHL 80 (436)
T ss_pred CeEEEEEEcCCCCcHHHHHHHHHHHCCCCeeEEecccCCCC-------------CccEEEEEEEecCc-cHHHHHHHHHH
Confidence 48999999999999999999999999999999999999884 59999999999987 58999999999
Q ss_pred Hhhc-CceEEEcccc
Q 048784 262 KEFA-TFLRVLGSYP 275 (282)
Q Consensus 262 ~~~~-~~v~~LGsY~ 275 (282)
++.+ ..+++||+-.
T Consensus 81 k~~~~~~vkiLGs~~ 95 (436)
T TIGR01268 81 RQKAEVTVNILSRDN 95 (436)
T ss_pred HHhccceEEEeCCCC
Confidence 9999 8999999854
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=99.63 E-value=9.2e-16 Score=148.25 Aligned_cols=76 Identities=33% Similarity=0.309 Sum_probs=68.9
Q ss_pred CCcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCccee-EEEEEEeecCCCcHHHHHHH
Q 048784 180 RPFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFD-YLFYVDFEASMADQKAQNAL 258 (282)
Q Consensus 180 ~~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~-y~F~vd~~g~~~~~~~~~al 258 (282)
+..||||+|+++|+||+|+++|+.|+.+||||+||||||+++. .|+ |.|||||+|+. .+++++|
T Consensus 28 ~~~ktSLIFsL~d~pGaL~~vL~vFa~~gINLThIESRPsk~~-------------~~e~Y~FfVD~Eg~~--~~l~~aL 92 (464)
T TIGR01270 28 GVQRLSIIFSLSNVVGDLSKAIAIFQDRHINILHLESRDSKDG-------------TSKTMDVLVDVELFH--YGLQEAM 92 (464)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHCCCCEEEEECCcCCCC-------------CCccEEEEEEEEcCH--HHHHHHH
Confidence 4569999999999999999999999999999999999999874 489 99999999976 6899999
Q ss_pred HHHHhhcCceEE
Q 048784 259 RHLKEFATFLRV 270 (282)
Q Consensus 259 ~~l~~~~~~v~~ 270 (282)
++|++.+..+++
T Consensus 93 ~~Lk~~~~~~~~ 104 (464)
T TIGR01270 93 DLLKSGLDVHEV 104 (464)
T ss_pred HHHHHhccccee
Confidence 999998887555
No 16
>PRK06034 hypothetical protein; Provisional
Probab=98.97 E-value=4.9e-10 Score=102.89 Aligned_cols=66 Identities=18% Similarity=0.111 Sum_probs=53.3
Q ss_pred CCCCcHHHHHHHhhCCC-CceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccc-cCCeEEEEE
Q 048784 1 GVRGAYSESAAEKAYPN-CEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLL-RHRLHIVGE 70 (282)
Q Consensus 1 GP~GTfS~~Aa~~~~~~-~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~-~~~l~I~~E 70 (282)
||+|||||+||++||+. .++++|.||++||++|++|++|||||||+++ .+.. +-.|. ....+|++-
T Consensus 102 G~~gs~s~~AA~~~FG~s~~~~~~~s~~dVf~AV~~g~adyGVVPI~~~-~~~W---W~~L~~~~~~~iiar 169 (279)
T PRK06034 102 SGGEAAMRDSARFHFGFTVPYVPHFSAQAVVEAVARSKGDLGLVSLTSS-DTPW---WGRLEAEGAPKIIAR 169 (279)
T ss_pred CCccHHHHHHHHHHhccccCCccCCCHHHHHHHHHcCCCCEEEEECCCC-CCcH---HHHhccCCCCeEEEe
Confidence 89999999999999984 6889999999999999999999999999544 3433 34333 444677665
No 17
>PRK08818 prephenate dehydrogenase; Provisional
Probab=98.91 E-value=3e-09 Score=101.84 Aligned_cols=66 Identities=24% Similarity=0.308 Sum_probs=55.1
Q ss_pred cEEEEEEEcC-CCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHH
Q 048784 182 FKTSIVFSLE-EGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRH 260 (282)
Q Consensus 182 ~ktsi~~~~~-~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~ 260 (282)
.-++|.|.++ |+||+|+++|++|+.+|||||+||| .+. +.|+|.|||||++..+-..+.++-.+
T Consensus 294 ~~~~l~~~v~~d~pG~L~~vl~~la~~~INit~Ies--~~~-------------r~~~y~f~i~~~~~~~~~~~~~~~~~ 358 (370)
T PRK08818 294 EPLTLSVYLPEDRPGSLRTLLHVFEQHGVNLSSIHS--SRT-------------PAGELHFRIGFEPGSDRAALARAAAE 358 (370)
T ss_pred cceEEEEECCCCCCChHHHHHHHHHHcCcccceEEE--ecc-------------cCceEEEEEEEeccccHHHHHHHHhh
Confidence 4689999997 9999999999999999999999999 555 45999999999996655556666655
Q ss_pred HH
Q 048784 261 LK 262 (282)
Q Consensus 261 l~ 262 (282)
+.
T Consensus 359 ~~ 360 (370)
T PRK08818 359 ID 360 (370)
T ss_pred hc
Confidence 54
No 18
>TIGR01269 Tyr_3_monoox tyrosine 3-monooxygenase, tetrameric. This model describes tyrosine 3-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tryptophan 5-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=98.86 E-value=9.7e-09 Score=99.00 Aligned_cols=72 Identities=19% Similarity=0.252 Sum_probs=59.7
Q ss_pred EEEEEEEcCCC-ccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 183 KTSIVFSLEEG-PGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 183 ktsi~~~~~~~-pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
.++++|+++++ +|+|.++|+.|+.++|||+||||||++... . ...+|.|||||+++. .++.++++.|
T Consensus 37 ~~~~~~~~~~~~~g~L~~~l~~f~~~~inl~hiEsr~~~~~~-------~---~~~~~~~~v~~~~~~--~~~~~~~~~l 104 (457)
T TIGR01269 37 MQNNQFYIRTKEISSLHRILKYIETFKLNLVHFETRPTRTLS-------N---ADVDYSCLITLEANE--INMSLLIESL 104 (457)
T ss_pred ceeEEEEeccCcchhHHHHHHHHHHcCCcEEEeecCCccccC-------C---CCCceEEEEEEeccH--hhHHHHHHHH
Confidence 47778888754 999999999999999999999999987632 0 124799999999864 7789999999
Q ss_pred HhhcC
Q 048784 262 KEFAT 266 (282)
Q Consensus 262 ~~~~~ 266 (282)
++.+.
T Consensus 105 ~~~~~ 109 (457)
T TIGR01269 105 RGNSF 109 (457)
T ss_pred Hhhhc
Confidence 98764
No 19
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=98.56 E-value=1.8e-07 Score=88.73 Aligned_cols=78 Identities=29% Similarity=0.433 Sum_probs=65.6
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
..++++|++++++|+|.++|+.|..+++|++||||||++.. ..+|.|||+++... .++.++++.|
T Consensus 35 ~~~~~if~~r~~~~~l~~~Lk~f~~~~vnl~HiEsR~s~~~-------------~~~~evlv~~~~~~--~~l~~~i~~l 99 (461)
T KOG3820|consen 35 ARISLIFSLRNKVGALARALKAFEEFHVNLLHIESRPSERR-------------SSGYEVLVELDATR--GQLIQAIELL 99 (461)
T ss_pred ceEEEEEEecccchHHHHHHHHhhhcCceEEEeeccccccc-------------CCCceEEEeeccch--hhHHHHHHHH
Confidence 36889999999999999999999999999999999999763 24699999999865 4788999999
Q ss_pred HhhcCceEEEccc
Q 048784 262 KEFATFLRVLGSY 274 (282)
Q Consensus 262 ~~~~~~v~~LGsY 274 (282)
++.+..+....++
T Consensus 100 rq~~~~~~~~s~~ 112 (461)
T KOG3820|consen 100 RQNHVALSYFSSF 112 (461)
T ss_pred HHhcccceecccc
Confidence 9887655444443
No 20
>cd04886 ACT_ThrD-II-like C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. This CD includes the C-terminal ACT domain of biodegradative (catabolic) threonine dehydratase II (ThrD-II) and other related ACT domains. The Escherichia coli tdcB gene product, ThrD-II, anaerobically catalyzes the pyridoxal phosphate-dependent dehydration of L-threonine and L-serine to ammonia and to alpha-ketobutyrate and pyruvate, respectively. Tetrameric ThrD-II is subject to allosteric activation by AMP, inhibition by alpha-keto acids, and catabolite inactivation by several metabolites of glycolysis and the citric acid cycle. Also included in this CD are N-terminal ACT domains present in smaller (~170 a.a.) archaeal proteins of unknown function. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=98.31 E-value=6e-06 Score=59.04 Aligned_cols=69 Identities=19% Similarity=0.177 Sum_probs=54.8
Q ss_pred EEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhcC
Q 048784 187 VFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFAT 266 (282)
Q Consensus 187 ~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~~ 266 (282)
.+.++|+||.|.++++.++..|+|++.|.+++.+..- ..+.+.+++.++.. +...++.+++.|++.+.
T Consensus 2 ~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~-----------~~~~~~~~i~v~~~-~~~~l~~l~~~l~~~g~ 69 (73)
T cd04886 2 RVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTL-----------PLGEVEVELTLETR-GAEHIEEIIAALREAGY 69 (73)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCC-----------CCceEEEEEEEEeC-CHHHHHHHHHHHHHcCC
Confidence 4677999999999999999999999999999865310 12467888888884 45678899999988754
Q ss_pred c
Q 048784 267 F 267 (282)
Q Consensus 267 ~ 267 (282)
.
T Consensus 70 ~ 70 (73)
T cd04886 70 D 70 (73)
T ss_pred E
Confidence 3
No 21
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=98.30 E-value=4.2e-06 Score=59.28 Aligned_cols=38 Identities=18% Similarity=0.334 Sum_probs=35.0
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCC
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRN 221 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~ 221 (282)
+.+.+.++|+||.|.++++.|+++|||+..+.+++.+.
T Consensus 1 ~~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~ 38 (66)
T PF01842_consen 1 YRVRVIVPDRPGILADVTEILADHGINIDSISQSSDKD 38 (66)
T ss_dssp EEEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred CEEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence 45778889999999999999999999999999999876
No 22
>cd04882 ACT_Bt0572_2 C-terminal ACT domain of a novel protein composed of just two ACT domains. Included in this CD is the C-terminal ACT domain of a novel protein composed of just two ACT domains, as seen in the yet uncharacterized structure (pdb 2F06) of the Bt0572 protein from Bacteroides thetaiotaomicron and related proteins. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.67 E-value=0.0003 Score=49.56 Aligned_cols=60 Identities=18% Similarity=0.240 Sum_probs=44.2
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
+.+.++|+||.|.++++.|+++|+|+.++...+.... ....+++.+++ ..++++.|++..
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~--------------~~~~v~~~ve~------~~~~~~~L~~~G 61 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKG--------------GKALLIFRTED------IEKAIEVLQERG 61 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCC--------------CeEEEEEEeCC------HHHHHHHHHHCC
Confidence 4567899999999999999999999999987665421 13455666654 346677776653
No 23
>cd04884 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.57 E-value=0.00056 Score=49.89 Aligned_cols=65 Identities=15% Similarity=0.133 Sum_probs=44.3
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+.+.++|+||+|.++++.++++|+|+..+...+..... +....+|.+++.. +..++++++.|++.
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~-------------~~~~~~v~v~~e~-~~~~~~i~~~L~~~ 66 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPD-------------GMRRVFIRVTPMD-RSKENELIEELKAK 66 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCC-------------CccEEEEEEEEec-chHHHHHHHHHhCc
Confidence 45678999999999999999999999998766643211 1223444444422 22366777778655
No 24
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=97.48 E-value=0.0012 Score=49.55 Aligned_cols=69 Identities=14% Similarity=0.220 Sum_probs=53.6
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
-+|.+-+.|+||.|.++...|+.||.|+..|...|+... .-..+-|-+.| ++..+..+.+.|++
T Consensus 3 ~tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te~~--------------~~sriti~~~~--~~~~i~qi~kQL~K 66 (76)
T PRK06737 3 HTFSLVIHNDPSVLLRISGIFARRGYYISSLNLNERDTS--------------GVSEMKLTAVC--TENEATLLVSQLKK 66 (76)
T ss_pred EEEEEEEecCCCHHHHHHHHHhccCcceEEEEecccCCC--------------CeeEEEEEEEC--CHHHHHHHHHHHhC
Confidence 456777789999999999999999999999999987652 23455566555 45678888898887
Q ss_pred hcCce
Q 048784 264 FATFL 268 (282)
Q Consensus 264 ~~~~v 268 (282)
.-.=+
T Consensus 67 LidV~ 71 (76)
T PRK06737 67 LINVL 71 (76)
T ss_pred CcCEE
Confidence 75433
No 25
>cd04874 ACT_Af1403 N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, and related domains. This CD includes the N-terminal ACT domain of the yet uncharacterized, small (~133 a.a.), putative amino acid binding protein, Af1403, from Archaeoglobus fulgidus and other related archeal ACT domains. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.48 E-value=0.0012 Score=46.94 Aligned_cols=64 Identities=20% Similarity=0.251 Sum_probs=48.2
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
.+.+..+|+||.|.++++.|+++++|+.++...+... +.+.+++++++. ..+..+++.|++.
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~---------------~~~~~~i~~~~~---~~~~~~~~~L~~~ 63 (72)
T cd04874 2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIERE---------------GKARIYMELEGV---GDIEELVEELRSL 63 (72)
T ss_pred eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccCC---------------CeEEEEEEEecc---ccHHHHHHHHhCC
Confidence 4667788999999999999999999999998766432 235567888874 2445677777765
Q ss_pred cC
Q 048784 265 AT 266 (282)
Q Consensus 265 ~~ 266 (282)
..
T Consensus 64 ~~ 65 (72)
T cd04874 64 PI 65 (72)
T ss_pred CC
Confidence 43
No 26
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.42 E-value=0.0012 Score=47.60 Aligned_cols=65 Identities=15% Similarity=0.301 Sum_probs=46.1
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
+.+.+.++|+||.|.++++.|+++|+|+.++...+.... ....++|.+++. +. .++++.|++
T Consensus 2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~--------------~~~~v~i~v~~~--~~--~~~~~~L~~ 63 (72)
T cd04883 2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEE--------------DNKILVFRVQTM--NP--RPIIEDLRR 63 (72)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCC--------------CeEEEEEEEecC--CH--HHHHHHHHH
Confidence 357778899999999999999999999999976554321 134455666652 22 256777776
Q ss_pred hcC
Q 048784 264 FAT 266 (282)
Q Consensus 264 ~~~ 266 (282)
...
T Consensus 64 ~G~ 66 (72)
T cd04883 64 AGY 66 (72)
T ss_pred CCC
Confidence 643
No 27
>cd04878 ACT_AHAS N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the Escherichia coli IlvH-like regulatory subunit of acetohydroxyacid synthase (AHAS). AHAS catalyses the first common step in the biosynthesis of the three branched-chain amino acids. The first step involves the condensation of either pyruvate or 2-ketobutyrate with the two-carbon hydroxyethyl fragment derived from another pyruvate molecule, covalently bound to the coenzyme thiamine diphosphate. Bacterial AHASs generally consist of regulatory and catalytic subunits. The effector (valine) binding sites are proposed to be located in two symmetrically related positions in the interface between a pair of N-terminal ACT domains with the C-terminal domain of IlvH contacting the catalytic dimer. Plants Arabidopsis and Oryza have tandem IlvH subunits; both the first and second ACT domain sequences are present in this CD. Members of
Probab=97.39 E-value=0.0022 Score=45.31 Aligned_cols=66 Identities=18% Similarity=0.306 Sum_probs=49.7
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+|.+...|+||.|.++++.|+.+++|+.++...+.+.. . ...+++.++. .+ +.+.++++.|++.
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~------------~--~~~~~~~~~~-~~-~~~~~l~~~l~~~ 65 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDP------------G--ISRITIVVEG-DD-DVIEQIVKQLNKL 65 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCC------------C--eEEEEEEEEC-CH-HHHHHHHHHHhCC
Confidence 46778889999999999999999999999998765221 1 2344555544 34 7788999999876
Q ss_pred cC
Q 048784 265 AT 266 (282)
Q Consensus 265 ~~ 266 (282)
..
T Consensus 66 ~~ 67 (72)
T cd04878 66 VD 67 (72)
T ss_pred cc
Confidence 54
No 28
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=97.20 E-value=0.0022 Score=46.19 Aligned_cols=59 Identities=19% Similarity=0.322 Sum_probs=46.4
Q ss_pred CCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhcC
Q 048784 192 EGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFAT 266 (282)
Q Consensus 192 ~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~~ 266 (282)
|+||+|.++++.|..+|+|+..|..-|+... .-+.+-+.++|. +..+..+.+.|++...
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~--------------~~~riti~v~~~--~~~i~~l~~Ql~Klid 59 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDP--------------GISRITIVVSGD--DREIEQLVKQLEKLID 59 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-SST--------------TEEEEEEEEES---CCHHHHHHHHHHCSTT
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecCCC--------------CEEEEEEEEeeC--chhHHHHHHHHhccCC
Confidence 6899999999999999999999999995542 357888888874 4567788888887654
No 29
>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=97.20 E-value=0.0045 Score=44.97 Aligned_cols=73 Identities=22% Similarity=0.286 Sum_probs=50.9
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+|.+..+|+||.|.++++.+++.|+|+..+.+..... +.+...|-++... .+..+.++++.|++.
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~-------------~~~~i~~~v~v~~--~~~~l~~l~~~L~~i 66 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIH-------------GRANVTISIDTST--MNGDIDELLEELREI 66 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCC-------------CeEEEEEEEEcCc--hHHHHHHHHHHHhcC
Confidence 5677889999999999999999999999998743221 1234555555533 333677888888765
Q ss_pred c--CceEEEc
Q 048784 265 A--TFLRVLG 272 (282)
Q Consensus 265 ~--~~v~~LG 272 (282)
- ..|+++|
T Consensus 67 ~~V~~v~~~~ 76 (76)
T cd04888 67 DGVEKVELVG 76 (76)
T ss_pred CCeEEEEEeC
Confidence 3 3455554
No 30
>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=97.20 E-value=0.0026 Score=45.62 Aligned_cols=35 Identities=20% Similarity=0.282 Sum_probs=31.0
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeC
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPL 219 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~ 219 (282)
-+.+.++|+||.|.++++.|+++|||+..+..-+.
T Consensus 3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~ 37 (66)
T cd04908 3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADT 37 (66)
T ss_pred EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEec
Confidence 35668899999999999999999999999987664
No 31
>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=97.17 E-value=0.0025 Score=45.83 Aligned_cols=61 Identities=16% Similarity=0.264 Sum_probs=43.6
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+++..+|+||.|.++++.|+++|+|+..+.+.+.... ......+++++.. .. +++++|++.
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~--------------~~~~~~i~v~~~~-~~---~~~~~l~~~ 62 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPG--------------GEALMVLSVDEPV-PD---EVLEELRAL 62 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCC--------------CEEEEEEEeCCCC-CH---HHHHHHHcC
Confidence 4567899999999999999999999999987665321 2445666777733 33 445555543
No 32
>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=97.11 E-value=0.0032 Score=40.91 Aligned_cols=58 Identities=28% Similarity=0.338 Sum_probs=42.9
Q ss_pred EEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 187 VFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 187 ~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
.+..+++||.|.++++.|+.+++|+.++.+++.... +...+++.++... ....++++|
T Consensus 2 ~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~--------------~~~~~~~~~~~~~---~~~~~~~~l 59 (60)
T cd02116 2 TVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSGDG--------------GEADIFIVVDGDG---DLEKLLEAL 59 (60)
T ss_pred EEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcCCC--------------CeEEEEEEEechH---HHHHHHHHh
Confidence 456778999999999999999999999998876431 3566777776532 445555554
No 33
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=97.09 E-value=0.0054 Score=45.49 Aligned_cols=71 Identities=17% Similarity=0.304 Sum_probs=52.1
Q ss_pred CcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHH
Q 048784 181 PFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRH 260 (282)
Q Consensus 181 ~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~ 260 (282)
.+.+.|.+...|+||.|.++.+.+++.|+|+..+..+..+.. ..+.+.++++-. +-..+..+++.
T Consensus 4 ~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~--------------~~~~~~l~v~V~-d~~~L~~ii~~ 68 (80)
T PF13291_consen 4 SFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDD--------------GTARITLTVEVK-DLEHLNQIIRK 68 (80)
T ss_dssp -EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ET--------------TEEEEEEEEEES-SHHHHHHHHHH
T ss_pred EEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccC--------------CEEEEEEEEEEC-CHHHHHHHHHH
Confidence 457889999999999999999999999999999999997521 134555555543 34678899999
Q ss_pred HHhhcC
Q 048784 261 LKEFAT 266 (282)
Q Consensus 261 l~~~~~ 266 (282)
|++.-.
T Consensus 69 L~~i~~ 74 (80)
T PF13291_consen 69 LRQIPG 74 (80)
T ss_dssp HCTSTT
T ss_pred HHCCCC
Confidence 987643
No 34
>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=97.05 E-value=0.0052 Score=44.05 Aligned_cols=64 Identities=17% Similarity=0.178 Sum_probs=44.9
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
.+.+.++|+||.|.++++.|+.+|+|+..+...+.+... .....|.++... ...++++.|++.
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~------------~~~~~i~v~~~~-----~~~~~~~~L~~~ 65 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIREGI------------GGILRISFKTQE-----DRERAKEILKEA 65 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEeecCC------------cEEEEEEECCHH-----HHHHHHHHHHHc
Confidence 466788999999999999999999999999876654210 123455555332 345677777765
Q ss_pred c
Q 048784 265 A 265 (282)
Q Consensus 265 ~ 265 (282)
.
T Consensus 66 G 66 (69)
T cd04909 66 G 66 (69)
T ss_pred C
Confidence 3
No 35
>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=97.03 E-value=0.0035 Score=46.87 Aligned_cols=65 Identities=18% Similarity=0.193 Sum_probs=44.3
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceee--eeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCC-CcH-HHHHHHHH
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLT--KIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASM-ADQ-KAQNALRH 260 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt--~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~-~~~-~~~~al~~ 260 (282)
.|-+..+|+||-|+++...|++.|+++. ||.|.-... .-.=.||||.+|.. .|+ +.+.+-+.
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Ge--------------rv~D~Fyv~~~g~kl~d~~~~~~L~~~ 67 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGY--------------REVDLFIVQSDGKKIMDPKKQAALCAR 67 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccC--------------EEEEEEEEeCCCCccCCHHHHHHHHHH
Confidence 3556778999999999999999999976 666433222 23458999988754 444 33444444
Q ss_pred HHh
Q 048784 261 LKE 263 (282)
Q Consensus 261 l~~ 263 (282)
|.+
T Consensus 68 L~~ 70 (75)
T cd04896 68 LRE 70 (75)
T ss_pred HHH
Confidence 443
No 36
>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=96.95 E-value=0.0055 Score=43.18 Aligned_cols=62 Identities=15% Similarity=0.306 Sum_probs=44.2
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
|.+..+|+||.|.++++.|+++|+|+..+..++.... ..-...++++.. .+.++++.|++..
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~--------------~~~~i~i~v~~~----~~~~~i~~l~~~~ 63 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKG--------------DQALMVIEVDQP----IDEEVIEEIKKIP 63 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCC--------------CeEEEEEEeCCC----CCHHHHHHHHcCC
Confidence 5667789999999999999999999999988764321 122334666553 3446777777543
No 37
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=96.90 E-value=0.0089 Score=50.90 Aligned_cols=69 Identities=16% Similarity=0.288 Sum_probs=53.5
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
.|.+.+.|+||.|.++.+.|+++|+|+..+-.-|.... ..+.+.+-+++ ++..+..+.+.|++.
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~--------------~~sriti~V~~--d~~~i~qi~kQl~Kl 66 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTEDP--------------DLSRMTIVVVG--DDKVLEQITKQLNKL 66 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecCCC--------------CEEEEEEEEEC--CHHHHHHHHHHHhcC
Confidence 56677899999999999999999999999988887531 24556666666 467788888888877
Q ss_pred cCceE
Q 048784 265 ATFLR 269 (282)
Q Consensus 265 ~~~v~ 269 (282)
-.=++
T Consensus 67 i~V~~ 71 (157)
T TIGR00119 67 VDVIK 71 (157)
T ss_pred ccEEE
Confidence 54333
No 38
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=96.88 E-value=0.0091 Score=44.77 Aligned_cols=67 Identities=12% Similarity=0.177 Sum_probs=49.7
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
|.+|.+.+.|+||.|.++++.|+.||.|+..|.--|+... ..+.-.+-+ + ++..+..+.+.|.
T Consensus 3 ~~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~------------~~sriti~v--~---~~~~i~ql~kQL~ 65 (76)
T PRK11152 3 QHQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDA------------QNINIELTV--A---SERPIDLLSSQLN 65 (76)
T ss_pred eEEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCC------------CEEEEEEEE--C---CCchHHHHHHHHh
Confidence 4567777889999999999999999999999999997642 122333333 2 3567778888887
Q ss_pred hhcC
Q 048784 263 EFAT 266 (282)
Q Consensus 263 ~~~~ 266 (282)
+.-.
T Consensus 66 KL~d 69 (76)
T PRK11152 66 KLVD 69 (76)
T ss_pred cCcC
Confidence 7643
No 39
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=96.88 E-value=0.01 Score=50.71 Aligned_cols=70 Identities=17% Similarity=0.287 Sum_probs=54.3
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
-+|.+.++|+||.|.++.+.|+++|+|+..+-.-|.... ..+.+.+-++| ++..+.++.+.|++
T Consensus 3 ~~IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~--------------~~sriti~V~~--~~~~i~qi~kQl~K 66 (161)
T PRK11895 3 HTLSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTEDP--------------GLSRMTIVTSG--DEQVIEQITKQLNK 66 (161)
T ss_pred EEEEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecCCC--------------CEEEEEEEEEC--CHHHHHHHHHHHhc
Confidence 456777899999999999999999999999988887531 24556666666 46778889999988
Q ss_pred hcCceE
Q 048784 264 FATFLR 269 (282)
Q Consensus 264 ~~~~v~ 269 (282)
...=++
T Consensus 67 LidV~~ 72 (161)
T PRK11895 67 LIDVLK 72 (161)
T ss_pred cccEEE
Confidence 754333
No 40
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.88 E-value=0.0035 Score=45.36 Aligned_cols=62 Identities=18% Similarity=0.221 Sum_probs=45.2
Q ss_pred EEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 187 VFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 187 ~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
.+.+|++||+|.++++.++. +.|++.+.=|-... +.....+=+++.+ ...++++++.|++..
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~-------------~~~~v~v~ie~~~---~~~~~~i~~~L~~~G 63 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGG-------------DEARVLVGIQVPD---REDLAELKERLEALG 63 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCC-------------CceEEEEEEEeCC---HHHHHHHHHHHHHcC
Confidence 46789999999999999999 99999998665432 1234554555543 356677888887754
No 41
>cd04887 ACT_MalLac-Enz ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI and related domains. The ACT_MalLac-Enz CD includes the N-terminal ACT domain of putative NAD-dependent malic enzyme 1, Bacillus subtilis YqkI, a malolactic enzyme (MalLac-Enz) which converts malate to lactate, and other related ACT domains. The yqkJ product is predicted to convert malate directly to lactate, as opposed to related malic enzymes that convert malate to pyruvate. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.81 E-value=0.0088 Score=43.32 Aligned_cols=63 Identities=14% Similarity=0.203 Sum_probs=46.6
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
|.+..+|+||.|.++.+.+++.|+|+..++++..+.. .....|-+++.. .+.+.+++..|++.
T Consensus 2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~-------------~~~~~~~vev~~---~~~l~~i~~~L~~i 64 (74)
T cd04887 2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRD-------------YTVRDITVDAPS---EEHAETIVAAVRAL 64 (74)
T ss_pred EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCC-------------EEEEEEEEEcCC---HHHHHHHHHHHhcC
Confidence 5677889999999999999999999999998864421 123444444433 35677888888765
No 42
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=96.74 E-value=0.014 Score=44.55 Aligned_cols=71 Identities=15% Similarity=0.209 Sum_probs=51.4
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
-.|.+-+.|+||.|.++-+.|++||+|+..|.--|+... | -....+-++. | ++..+.++.+.|++
T Consensus 3 ~~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~---------~---iSRmtivv~~-~--d~~~ieqI~kQL~K 67 (84)
T PRK13562 3 RILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQP---------G---ISNMEIQVDI-Q--DDTSLHILIKKLKQ 67 (84)
T ss_pred EEEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCCC---------C---ceEEEEEEeC-C--CHHHHHHHHHHHhC
Confidence 456666789999999999999999999999999998652 1 1233333332 4 45667888999987
Q ss_pred hcCceE
Q 048784 264 FATFLR 269 (282)
Q Consensus 264 ~~~~v~ 269 (282)
.-.=++
T Consensus 68 lidVik 73 (84)
T PRK13562 68 QINVLT 73 (84)
T ss_pred CccEEE
Confidence 754333
No 43
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=96.73 E-value=0.01 Score=51.42 Aligned_cols=71 Identities=18% Similarity=0.298 Sum_probs=53.0
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
-.+.+...|+||.|.++-+.|+.||+|+..+.+.|+... .-..+-+.+.+. +..+.++.+.|++
T Consensus 3 ~~isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~--------------~~sr~TIvv~~~--~~~ieqL~kQL~K 66 (174)
T CHL00100 3 HTLSVLVEDESGVLTRIAGLFARRGFNIESLAVGPAEQK--------------GISRITMVVPGD--DRTIEQLTKQLYK 66 (174)
T ss_pred EEEEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCC--------------CccEEEEEEECC--HHHHHHHHHHHHH
Confidence 456667789999999999999999999999999887652 123666667763 2336777777777
Q ss_pred hcCceEE
Q 048784 264 FATFLRV 270 (282)
Q Consensus 264 ~~~~v~~ 270 (282)
.+.-+++
T Consensus 67 LidVl~V 73 (174)
T CHL00100 67 LVNILKV 73 (174)
T ss_pred HhHhhEE
Confidence 7665444
No 44
>cd04901 ACT_3PGDH C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. The C-terminal ACT (regulatory) domain of D-3-Phosphoglycerate Dehydrogenase (3PGDH) found in fungi and bacteria. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In Escherichia coli, the SerA 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. In the homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-
Probab=96.72 E-value=0.0045 Score=44.11 Aligned_cols=60 Identities=18% Similarity=0.231 Sum_probs=43.6
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
+++...|+||.|.++++.++++|+|+..+.+++..+ .-...++++.. .+.++++.|++.-
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~----------------~a~~~~~~~~~----~l~~li~~l~~~~ 61 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGE----------------IGYVVIDIDSE----VSEELLEALRAIP 61 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCC----------------EEEEEEEcCCC----CCHHHHHHHHcCC
Confidence 456778999999999999999999999987765322 22334566654 3346777777653
No 45
>cd04879 ACT_3PGDH-like ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active
Probab=96.72 E-value=0.0084 Score=42.04 Aligned_cols=62 Identities=16% Similarity=0.260 Sum_probs=44.7
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
+.+..+|+||.|.++++.|+++|+|+.++.+.+.... ..+...++++.. . ..+++++|++..
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~--------------~~~~~~~~v~~~-~---~~~l~~~l~~~~ 63 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKG--------------GIAYMVLDVDSP-V---PEEVLEELKALP 63 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCC--------------CEEEEEEEcCCC-C---CHHHHHHHHcCC
Confidence 5667889999999999999999999999999875421 134455566442 2 346677776654
No 46
>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=96.66 E-value=0.015 Score=42.62 Aligned_cols=36 Identities=19% Similarity=0.269 Sum_probs=31.0
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeC
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPL 219 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~ 219 (282)
|-+.+..+|+||.|+++.+.|+.+|+|+......+.
T Consensus 2 tri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~ 37 (72)
T cd04926 2 VRLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQ 37 (72)
T ss_pred eEEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecC
Confidence 457778899999999999999999999987766554
No 47
>PRK04435 hypothetical protein; Provisional
Probab=96.64 E-value=0.025 Score=47.46 Aligned_cols=77 Identities=18% Similarity=0.213 Sum_probs=56.6
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
.+++|.+.+.|+||.|.++++.++..|+|+..|....... ......|=||... .+..+.++++.|
T Consensus 68 r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~-------------g~a~vs~tVevs~--~~~~L~~Li~~L 132 (147)
T PRK04435 68 KIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQ-------------GRANVTISIDTSS--MEGDIDELLEKL 132 (147)
T ss_pred cEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCC-------------CEEEEEEEEEeCC--hHHHHHHHHHHH
Confidence 3688999999999999999999999999999998642211 1235566666643 234678888888
Q ss_pred Hhh--cCceEEEcc
Q 048784 262 KEF--ATFLRVLGS 273 (282)
Q Consensus 262 ~~~--~~~v~~LGs 273 (282)
++. ...++++|.
T Consensus 133 ~~i~gV~~V~i~~~ 146 (147)
T PRK04435 133 RNLDGVEKVELIGM 146 (147)
T ss_pred HcCCCcEEEEEEec
Confidence 865 346777774
No 48
>PRK08198 threonine dehydratase; Provisional
Probab=96.63 E-value=0.053 Score=52.50 Aligned_cols=76 Identities=16% Similarity=0.207 Sum_probs=55.9
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeee-CCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRP-LRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP-~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
..++.+.++|+||.|.++|+.++..|.|+..|.-+. .++.+ .....+.|.+|.. +...++++++.|
T Consensus 327 ~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~~~~~~~------------~~~~~v~v~ie~~-~~~~~~~l~~~L 393 (404)
T PRK08198 327 YLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDRFSPDLR------------LGEVEVELTLETR-GPEHIEEILDAL 393 (404)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEEccCCCC------------CceEEEEEEEEeC-CHHHHHHHHHHH
Confidence 568889999999999999999999999999987654 33322 1245566666653 334677899999
Q ss_pred HhhcCceEEE
Q 048784 262 KEFATFLRVL 271 (282)
Q Consensus 262 ~~~~~~v~~L 271 (282)
++..-.++++
T Consensus 394 ~~~G~~v~~~ 403 (404)
T PRK08198 394 RDAGYEVKVV 403 (404)
T ss_pred HHCCCeEEEc
Confidence 8876655543
No 49
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=96.54 E-value=0.028 Score=44.00 Aligned_cols=71 Identities=18% Similarity=0.381 Sum_probs=53.1
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
+..|.+-+.|+||.|.++-+.|++||.|+..|-.-|+... .-..+.|-+. ++..+.++++.|+
T Consensus 8 ~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~~--------------~iSRmtivv~---~~~~i~Qi~kQL~ 70 (96)
T PRK08178 8 NVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQDG--------------DKSRIWLLVN---DDQRLEQMISQIE 70 (96)
T ss_pred CEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCCC--------------CceEEEEEEc---CchHHHHHHHHHh
Confidence 4567777789999999999999999999999988887652 1233444443 2568889999998
Q ss_pred hhcCceEE
Q 048784 263 EFATFLRV 270 (282)
Q Consensus 263 ~~~~~v~~ 270 (282)
+.-.=+++
T Consensus 71 KLidVikV 78 (96)
T PRK08178 71 KLEDVLKV 78 (96)
T ss_pred CCcCEEEE
Confidence 87554433
No 50
>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=96.50 E-value=0.023 Score=42.99 Aligned_cols=71 Identities=18% Similarity=0.193 Sum_probs=45.6
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
.+.+.+||+||+|.++|+.++.. |++.+.=+-.... .....+-+++.+. .+.++++++.|++.
T Consensus 3 vl~v~ipD~PG~L~~ll~~l~~a--nI~~~~y~~~~~~-------------~~~v~i~ie~~~~--~~~~~~i~~~L~~~ 65 (85)
T cd04906 3 LLAVTIPERPGSFKKFCELIGPR--NITEFNYRYADEK-------------DAHIFVGVSVANG--AEELAELLEDLKSA 65 (85)
T ss_pred EEEEecCCCCcHHHHHHHHhCCC--ceeEEEEEccCCC-------------eeEEEEEEEeCCc--HHHHHHHHHHHHHC
Confidence 36778899999999999999944 5544443332211 1245555676541 25567788888877
Q ss_pred cCceEEEc
Q 048784 265 ATFLRVLG 272 (282)
Q Consensus 265 ~~~v~~LG 272 (282)
...+..+.
T Consensus 66 G~~~~~~~ 73 (85)
T cd04906 66 GYEVVDLS 73 (85)
T ss_pred CCCeEECC
Confidence 66555543
No 51
>cd04881 ACT_HSDH-Hom ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) and related domains. The ACT_HSDH_Hom CD includes the C-terminal ACT domain of the NAD(P)H-dependent, homoserine dehydrogenase (HSDH) encoded by the hom gene of Bacillus subtilis and other related sequences. HSDH reduces aspartate semi-aldehyde to the amino acid homoserine, one that is required for the biosynthesis of Met, Thr, and Ile from Asp. Neither the enzyme nor the aspartate pathway is found in the animal kingdom. This mostly bacterial HSDH group has a C-terminal ACT domain and is believed to be involved in enzyme regulation. A C-terminal deletion in the Corynebacterium glutamicum HSDH abolished allosteric inhibition by L-threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.38 E-value=0.026 Score=40.45 Aligned_cols=64 Identities=14% Similarity=0.262 Sum_probs=46.4
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
|.+...|+||.|.++++.|+++|+|+.++.+++.... ......|-++. .+...++++++.|++.
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~------------~~~~~~i~~~~---~~~~~l~~~i~~L~~~ 66 (79)
T cd04881 3 LRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGG------------ETAPVVIVTHE---TSEAALNAALAEIEAL 66 (79)
T ss_pred EEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCC------------CceeEEEEEcc---CCHHHHHHHHHHHHcC
Confidence 4567789999999999999999999999988765321 11233333332 2457788899999865
No 52
>PRK00194 hypothetical protein; Validated
Probab=96.29 E-value=0.028 Score=42.64 Aligned_cols=36 Identities=19% Similarity=0.211 Sum_probs=31.7
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeee
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRP 218 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP 218 (282)
+-.+.+.-+|+||.+.++.+.|+.+|+|+..+++.=
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~ 38 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTI 38 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHh
Confidence 456677779999999999999999999999998774
No 53
>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=96.21 E-value=0.031 Score=41.40 Aligned_cols=29 Identities=24% Similarity=0.405 Sum_probs=25.7
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceee
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLT 212 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt 212 (282)
|-|-+..+|+||-|+++.++|++.|+++.
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~ 30 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCIT 30 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEE
Confidence 45667779999999999999999999987
No 54
>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=96.13 E-value=0.033 Score=42.16 Aligned_cols=67 Identities=18% Similarity=0.264 Sum_probs=46.9
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeec-CCCcHHHHHHHHHHH
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEA-SMADQKAQNALRHLK 262 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g-~~~~~~~~~al~~l~ 262 (282)
-.+.+.-+|+||-+.++.+.|+.+|+|+..++..-..+ .+...+-+++.+ ..+-..+++.++.|.
T Consensus 2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~--------------~f~~~~~v~~~~~~~~~~~L~~~l~~l~ 67 (88)
T cd04872 2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDG--------------YFTMIMIVDISESNLDFAELQEELEELG 67 (88)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCC--------------ccEEEEEEEeCCCCCCHHHHHHHHHHHH
Confidence 45677779999999999999999999999998764221 133344555554 233456677777776
Q ss_pred hh
Q 048784 263 EF 264 (282)
Q Consensus 263 ~~ 264 (282)
+.
T Consensus 68 ~~ 69 (88)
T cd04872 68 KE 69 (88)
T ss_pred HH
Confidence 44
No 55
>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=96.03 E-value=0.049 Score=39.97 Aligned_cols=63 Identities=11% Similarity=0.114 Sum_probs=44.8
Q ss_pred EEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 188 FSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 188 ~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+.=+|+||-+.++-+.|+.+|+|+..++++=..+ .+...|.+++....+-..+++.++.+.+.
T Consensus 4 v~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~--------------~f~~~~~v~~p~~~~~~~l~~~l~~l~~~ 66 (75)
T cd04870 4 VTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHG--------------RLSLGILVQIPDSADSEALLKDLLFKAHE 66 (75)
T ss_pred EEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcC--------------eeEEEEEEEcCCCCCHHHHHHHHHHHHHH
Confidence 4447999999999999999999999998766543 23455666654333345677777776643
No 56
>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=96.02 E-value=0.072 Score=38.83 Aligned_cols=33 Identities=15% Similarity=0.227 Sum_probs=29.5
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeee
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRP 218 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP 218 (282)
|.+.-+|+||-+.++-+.|+++|+|+..+++.-
T Consensus 2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~ 34 (74)
T cd04875 2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFV 34 (74)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeee
Confidence 445668999999999999999999999998884
No 57
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=95.99 E-value=0.042 Score=40.58 Aligned_cols=36 Identities=19% Similarity=0.350 Sum_probs=26.3
Q ss_pred EEEEc--CCCccHHHHHHHHHHHCCceeeeeeeeeCCC
Q 048784 186 IVFSL--EEGPGVLFKALAVFALRQINLTKIESRPLRN 221 (282)
Q Consensus 186 i~~~~--~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~ 221 (282)
+++++ +|+||-+..+.+.++++|.|+..++-.-..+
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 34444 8999999999999999999998777665543
No 58
>cd04899 ACT_ACR-UUR-like_2 C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD and related domains. This ACT domain family, ACT_ACR-UUR-like_2, includes the second of two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the second and fourth ACT domains of a novel protein composed almost entirely of ACT domain repeats, the ACR protein. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.97 E-value=0.077 Score=37.75 Aligned_cols=37 Identities=19% Similarity=0.276 Sum_probs=32.2
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCC
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRN 221 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~ 221 (282)
-+.+..+|+||.|.++.+.|+.+|+|+.++...+..+
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~ 38 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGE 38 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCC
Confidence 4566778999999999999999999999999887543
No 59
>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=95.90 E-value=0.053 Score=39.66 Aligned_cols=60 Identities=20% Similarity=0.361 Sum_probs=47.7
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
|.+...|++|.|.++++.+++.|+|+..+++++. + + .+++++.. +-..+..+++.|++.-
T Consensus 3 l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~-----------------~-i~l~i~v~-~~~~L~~li~~L~~i~ 62 (74)
T cd04877 3 LEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-G-----------------R-IYLNFPTI-EFEKLQTLMPEIRRID 62 (74)
T ss_pred EEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-C-----------------e-EEEEeEec-CHHHHHHHHHHHhCCC
Confidence 5666789999999999999999999999999763 2 2 56677654 3456888899888653
No 60
>cd04873 ACT_UUR-ACR-like ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD. This ACT domain family, ACT_UUR_ACR-like, includes the two C-terminal ACT domains of the bacterial signal-transducing uridylyltransferase /uridylyl-removing (UUR) enzyme, GlnD; including those enzymes similar to the GlnD found in enteric Escherichia coli and those found in photosynthetic, nitrogen-fixing bacterium Rhodospirillum rubrum. Also included in this CD are the four ACT domains of a novel protein composed almost entirely of ACT domain repeats (the ACR protein) and like proteins. These ACR proteins, found in Arabidopsis and Oryza, are proposed to function as novel regulatory or sensor proteins in plants. This CD also includes the first of the two ACT domains that comprise the Glycine Cleavage System Transcriptional Repressor (GcvR) protein and related domains, as well as, the N-terminal ACT domain of a yet characterized Arabidopsis/Oryza predicted t
Probab=95.89 E-value=0.09 Score=37.05 Aligned_cols=36 Identities=17% Similarity=0.182 Sum_probs=31.6
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCC
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLR 220 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~ 220 (282)
-+.+..+|+||.|.++.+.|+.+|+|+..+......
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~ 37 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTG 37 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecC
Confidence 356778899999999999999999999999887654
No 61
>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=95.86 E-value=0.049 Score=52.28 Aligned_cols=73 Identities=21% Similarity=0.298 Sum_probs=49.8
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeee-eCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESR-PLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSR-P~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
...|.+.++|+||.|.++++.+++.+.|++.|.-+ ..+..+ .......|.+|.. +....+++++.|
T Consensus 305 ~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~r~~~~~~------------~~~~~v~v~vet~-~~~~~~~i~~~L 371 (380)
T TIGR01127 305 KVRIETVLPDRPGALYHLLESIAEARANIVKIDHDRLSKEIP------------PGFAMVEITLETR-GKEHLDEILKIL 371 (380)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeccccCCC------------CceEEEEEEEEeC-CHHHHHHHHHHH
Confidence 34788899999999999999999999999999754 222211 0123344444443 234556788888
Q ss_pred HhhcCce
Q 048784 262 KEFATFL 268 (282)
Q Consensus 262 ~~~~~~v 268 (282)
++....+
T Consensus 372 ~~~G~~v 378 (380)
T TIGR01127 372 RDMGYNF 378 (380)
T ss_pred HHcCCcc
Confidence 8765444
No 62
>PRK08577 hypothetical protein; Provisional
Probab=95.84 E-value=0.13 Score=42.29 Aligned_cols=69 Identities=23% Similarity=0.363 Sum_probs=50.1
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
...|.+...|+||.|.++++.|+.+++|+..+.++..... ..+.-.|-+|+... +..+.+++++|+
T Consensus 56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~------------~~~~i~l~vev~~~--~~~l~~l~~~L~ 121 (136)
T PRK08577 56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRG------------ELAECVIIVDLSKS--DIDLEELEEELK 121 (136)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCC------------CEEEEEEEEEeCCc--hhhHHHHHHHHH
Confidence 5678888899999999999999999999999998876531 11222344565442 245678888887
Q ss_pred hhc
Q 048784 263 EFA 265 (282)
Q Consensus 263 ~~~ 265 (282)
+..
T Consensus 122 ~l~ 124 (136)
T PRK08577 122 KLE 124 (136)
T ss_pred cCC
Confidence 654
No 63
>cd04876 ACT_RelA-SpoT ACT domain found C-terminal of the RelA/SpoT domains. ACT_RelA-SpoT: the ACT domain found C-terminal of the RelA/SpoT domains. Enzymes of the Rel/Spo family enable bacteria to survive prolonged periods of nutrient limitation by controlling guanosine-3'-diphosphate-5'-(tri)diphosphate ((p)ppGpp) production and subsequent rRNA repression (stringent response). Both the synthesis of (p)ppGpp from ATP and GDP(GTP), and its hydrolysis to GDP(GTP) and pyrophosphate, are catalyzed by Rel/Spo proteins. In Escherichia coli and its close relatives, the metabolism of (p)ppGpp is governed by two homologous proteins, RelA and SpoT. The RelA protein catalyzes (p)ppGpp synthesis in a reaction requiring its binding to ribosomes bearing codon-specified uncharged tRNA. The major role of the SpoT protein is the breakdown of (p)ppGpp by a manganese-dependent (p)ppGpp pyrophosphohydrolase activity. Although the stringent response appears to be tightly regulated by these two enzymes i
Probab=95.72 E-value=0.13 Score=34.82 Aligned_cols=63 Identities=17% Similarity=0.257 Sum_probs=44.3
Q ss_pred EEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 187 VFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 187 ~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
.+..+|+||.|.++++.|+++++|+.+++....... ...+.+.++.. ....+..+++.|+...
T Consensus 2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~---------------~~~~~~~~~~~-~~~~~~~~~~~l~~~~ 64 (71)
T cd04876 2 RVEAIDRPGLLADITTVIAEEKINILSVNTRTDDDG---------------LATIRLTLEVR-DLEHLARIMRKLRQIP 64 (71)
T ss_pred EEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCCC---------------EEEEEEEEEEC-CHHHHHHHHHHHhCCC
Confidence 356789999999999999999999999988764310 12234444432 2356778888887653
No 64
>PRK06382 threonine dehydratase; Provisional
Probab=95.58 E-value=0.039 Score=53.62 Aligned_cols=74 Identities=18% Similarity=0.243 Sum_probs=49.5
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeee-eCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESR-PLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRH 260 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSR-P~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~ 260 (282)
.++.|.+.++|+||.|.++++.|+.+|+|+++|+-. ...... . ......|-||..+. ...+++++.
T Consensus 329 ~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~~~~~~~~~---------~-~~~~v~i~vet~~~---~~~~~v~~~ 395 (406)
T PRK06382 329 QLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEVDNLRKETP---------P-GFQSVTFTVNVRGQ---DHLDRILNA 395 (406)
T ss_pred CEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEEeeccccCC---------C-CcEEEEEEEEeCCH---HHHHHHHHH
Confidence 367888899999999999999999999999999863 221110 0 12344555555421 233467777
Q ss_pred HHhhcCce
Q 048784 261 LKEFATFL 268 (282)
Q Consensus 261 l~~~~~~v 268 (282)
|++....+
T Consensus 396 L~~~Gy~~ 403 (406)
T PRK06382 396 LREMGYKF 403 (406)
T ss_pred HHHCCCCe
Confidence 87765443
No 65
>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=95.53 E-value=0.045 Score=37.54 Aligned_cols=34 Identities=26% Similarity=0.330 Sum_probs=30.2
Q ss_pred EEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCC
Q 048784 187 VFSLEEGPGVLFKALAVFALRQINLTKIESRPLR 220 (282)
Q Consensus 187 ~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~ 220 (282)
.+.++|+||.|.++++.|.++|+|+..+...+..
T Consensus 2 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~ 35 (56)
T cd04889 2 SVFVENKPGRLAEVTEILAEAGINIKAISIAETR 35 (56)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEcc
Confidence 3567899999999999999999999999877765
No 66
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=95.30 E-value=0.11 Score=43.91 Aligned_cols=74 Identities=23% Similarity=0.351 Sum_probs=51.7
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceee-eeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLT-KIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt-~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
+.++-+.++|+||.|.++|++++..|.|+. =|.||--+..| .--.-|-|++.. .++.++.++.+
T Consensus 5 ritldIEL~D~PGQLl~vLqPls~~g~NiItIiH~r~kk~g~--------------r~pV~i~~~~d~-~~~~~~i~~~~ 69 (170)
T COG2061 5 RITLDIELKDKPGQLLKVLQPLSKTGANIITIIHSRDKKYGP--------------RVPVQIVFEGDR-EDKDAKIIRLL 69 (170)
T ss_pred EEEEEEEecCCCcchhhhhcchhhcCccEEEEEeecCcccCC--------------ceeEEEEEEecc-cHHHHHHHHHH
Confidence 568888999999999999999999999954 56788755432 222233344432 35667888888
Q ss_pred HhhcCceEEE
Q 048784 262 KEFATFLRVL 271 (282)
Q Consensus 262 ~~~~~~v~~L 271 (282)
++....++-.
T Consensus 70 e~~Gi~I~~~ 79 (170)
T COG2061 70 EEEGIIIIRF 79 (170)
T ss_pred HhCCcEEEEe
Confidence 7766555444
No 67
>PRK08526 threonine dehydratase; Provisional
Probab=95.27 E-value=0.37 Score=46.96 Aligned_cols=214 Identities=18% Similarity=0.182 Sum_probs=110.5
Q ss_pred HHHHHHHcCCCCeEEEeeeeccccceeccccccc--cCCeEEEEEEEEe---eeeeeeecCCCCCCCccEEE----e---
Q 048784 28 TAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLL--RHRLHIVGEVKFA---VRHCLLANPGVKVEDLKRVL----S--- 95 (282)
Q Consensus 28 ~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~--~~~l~I~~E~~l~---I~~~L~a~~~~~l~~I~~V~----S--- 95 (282)
|+++.+ +..|+-|+|+- ..|.+.-+...+. ..+.+|+|--.-. ....+-.........+.++. .
T Consensus 161 EI~eq~--~~~D~vvvpvG--gGGl~aGia~~~k~~~p~~kvigVep~~~~~~~~s~~~g~~~~~~~~~tiadgiav~~~ 236 (403)
T PRK08526 161 EMLDEI--SDLDMVVVPVG--GGGLISGIASAAKQINPNIKIIGVGAKGAPAMYESFHAKKIINSKSVRTIADGIAVRDA 236 (403)
T ss_pred HHHHhc--CCCCEEEEecC--hHHHHHHHHHHHHHhCCCCEEEEEEECCCChHHHHHHcCCcccCCCCCceeccccCCCC
Confidence 444444 25899999985 3455544444442 2456666543311 10111111101112222221 1
Q ss_pred chHHHHHHHHHHHhcCCeEEEec--CHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeecccccCCCCceEEEEEeeCC
Q 048784 96 HPQALAQCENTLTKLGLVREAVD--DTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAEDIQDDCDNVTRFLMLAREP 173 (282)
Q Consensus 96 Hpqal~QC~~fl~~~~~~~~~~~--sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~~I~d~~~N~TRF~vl~~~~ 173 (282)
-|..+..|++++++ .+.++ ....|.+.+++.. +. .+.+..|+-+-+|.--...+ ..+.+=-++++-..
T Consensus 237 ~~~~~~~~~~~vd~----~v~V~d~ei~~A~~~l~~~~--gi-~ve~aga~~lAall~~~~~~---~~~~~Vv~ilsGGn 306 (403)
T PRK08526 237 SPINLAIILECVDD----FVQVDDEEIANAILFLLEKQ--KI-VVEGAGAASVAALLHQKIDL---KKGKKIGVVLSGGN 306 (403)
T ss_pred CHHHHHHHHHhCCE----EEEECHHHHHHHHHHHHHhc--Cc-EeeHHHHHHHHHHHhCcccc---ccCCeEEEEECCCC
Confidence 16777777776653 23333 3345556666541 22 23444444444442111111 12223333333221
Q ss_pred CCCC----------CCCCcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeee-eeCCCCCCCCCCCCCCCCcceeEEEE
Q 048784 174 IIPG----------TDRPFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIES-RPLRNQPLRSSDDNSGFGKYFDYLFY 242 (282)
Q Consensus 174 ~~~~----------~~~~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeS-RP~~~~~~~~~~~~~g~~~~~~y~F~ 242 (282)
.... .....+..+.+.++|+||+|.++++.+...+.|++.|+= |.....+ ..+-...
T Consensus 307 id~~~~~~i~~~~l~~~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~~~~~------------~~~~~~~ 374 (403)
T PRK08526 307 IDVQMLNIIIEKGLIKSYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFSTKLD------------YGDAMIS 374 (403)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEeccCCCC------------CccEEEE
Confidence 1100 011236788889999999999999999999999999986 5544321 1233455
Q ss_pred EEeecCCCcHHHHHHHHHHHhhcCce
Q 048784 243 VDFEASMADQKAQNALRHLKEFATFL 268 (282)
Q Consensus 243 vd~~g~~~~~~~~~al~~l~~~~~~v 268 (282)
|.+|.. +.+.++++++.|++....+
T Consensus 375 ~~~e~~-~~~~~~~~~~~l~~~g~~~ 399 (403)
T PRK08526 375 ITLETK-GKEHQEEIRKILTEKGFNF 399 (403)
T ss_pred EEEEeC-CHHHHHHHHHHHHHCCCCe
Confidence 556553 3456788888888765444
No 68
>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=94.99 E-value=0.22 Score=36.50 Aligned_cols=35 Identities=17% Similarity=0.395 Sum_probs=30.0
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCC
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLR 220 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~ 220 (282)
+.+..+|+||-+.++-+.|+.+|+|+..+++.-..
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~ 36 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYS 36 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence 45667899999999999999999999999876543
No 69
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=94.85 E-value=0.2 Score=40.75 Aligned_cols=67 Identities=24% Similarity=0.362 Sum_probs=48.9
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
.-+.+..+|+||+|.+++++|.+++||+--|.---.+.+ .-..++-++ .+.++++.|++
T Consensus 70 dVlaVEmeD~PG~l~~I~~vl~d~diNldYiYAFv~ek~---------------KAlli~r~e------d~d~~~~aLed 128 (142)
T COG4747 70 DVLAVEMEDVPGGLSRIAEVLGDADINLDYIYAFVTEKQ---------------KALLIVRVE------DIDRAIKALED 128 (142)
T ss_pred eEEEEEecCCCCcHHHHHHHHhhcCcCceeeeeeeecCc---------------eEEEEEEhh------HHHHHHHHHHH
Confidence 457778899999999999999999999998887766542 334555443 34566777766
Q ss_pred hcCceEEEcc
Q 048784 264 FATFLRVLGS 273 (282)
Q Consensus 264 ~~~~v~~LGs 273 (282)
.. ++++|+
T Consensus 129 ~g--i~~~~~ 136 (142)
T COG4747 129 AG--IKLIGM 136 (142)
T ss_pred cC--CeecCh
Confidence 53 666665
No 70
>PRK07334 threonine dehydratase; Provisional
Probab=94.82 E-value=0.23 Score=48.20 Aligned_cols=76 Identities=14% Similarity=0.218 Sum_probs=56.0
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCC-CCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLR-NQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRH 260 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~-~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~ 260 (282)
..+.|.+...|+||.|.++++.+++.++|+.++.++... ..+ ...+...|-|++. +.+.+.++++.
T Consensus 325 y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~----------~~~~~i~l~i~V~---d~~~L~~vi~~ 391 (403)
T PRK07334 325 RLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLP----------AKGAELELVIETR---DAAHLQEVIAA 391 (403)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCC----------CCeEEEEEEEEeC---CHHHHHHHHHH
Confidence 468999999999999999999999999999999988641 100 0123444555553 34678899999
Q ss_pred HHhhcCceEE
Q 048784 261 LKEFATFLRV 270 (282)
Q Consensus 261 l~~~~~~v~~ 270 (282)
|++....+.+
T Consensus 392 Lr~~g~~~~~ 401 (403)
T PRK07334 392 LRAAGFEARL 401 (403)
T ss_pred HHHcCCeeEe
Confidence 9987655543
No 71
>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=94.46 E-value=0.42 Score=34.72 Aligned_cols=34 Identities=15% Similarity=0.284 Sum_probs=28.2
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeee--eeee
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTK--IESR 217 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~--IeSR 217 (282)
+.+.+..+|+||-|+++-++|+.+|+|+.. |.+.
T Consensus 2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~ 37 (73)
T cd04900 2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTT 37 (73)
T ss_pred EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEe
Confidence 346677789999999999999999999884 4444
No 72
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=94.34 E-value=0.29 Score=40.50 Aligned_cols=77 Identities=22% Similarity=0.396 Sum_probs=58.7
Q ss_pred CcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeee-eeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHH
Q 048784 181 PFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIE-SRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALR 259 (282)
Q Consensus 181 ~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~Ie-SRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~ 259 (282)
....+|.+.+.|+.|.|.++|.+.++.++|+..|. +-|..+. ..--.-+|..+ -...+.+.++
T Consensus 70 ~ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~--------------Anvtlsi~~ss--m~~~V~~ii~ 133 (150)
T COG4492 70 ERIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGR--------------ANVTLSIDTSS--MEKDVDKIIE 133 (150)
T ss_pred ceEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCce--------------eeEEEEEEchh--hhhhHHHHHH
Confidence 34679999999999999999999999999976664 6676553 24556667654 3467888999
Q ss_pred HHHhh--cCceEEEcc
Q 048784 260 HLKEF--ATFLRVLGS 273 (282)
Q Consensus 260 ~l~~~--~~~v~~LGs 273 (282)
+|++. ...|.++|+
T Consensus 134 kl~k~e~V~kVeivgs 149 (150)
T COG4492 134 KLRKVEGVEKVEIVGS 149 (150)
T ss_pred HHhcccceeEEEEeec
Confidence 98854 446777775
No 73
>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=94.28 E-value=0.32 Score=36.31 Aligned_cols=29 Identities=10% Similarity=0.245 Sum_probs=25.5
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceee
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLT 212 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt 212 (282)
|-|-+..+|+||-|+++...|.+.|+++.
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~ 30 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVF 30 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEE
Confidence 44556779999999999999999999987
No 74
>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=94.10 E-value=0.56 Score=34.61 Aligned_cols=64 Identities=20% Similarity=0.091 Sum_probs=42.9
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
|.+.-+|+||-.+++-+.++++|.|+..+...=..+ .+-+..-++++. ..-+.+++.++.+.+.
T Consensus 4 ltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~--------------~F~m~~~~~~~~-~~~~~l~~~l~~~~~~ 67 (77)
T cd04893 4 ISALGTDRPGILNELTRAVSESGCNILDSRMAILGT--------------EFALTMLVEGSW-DAIAKLEAALPGLARR 67 (77)
T ss_pred EEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcC--------------EEEEEEEEEecc-ccHHHHHHHHHHHHHH
Confidence 445669999999999999999999999776554222 123333445442 2235677777777644
No 75
>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=93.95 E-value=0.48 Score=35.03 Aligned_cols=63 Identities=11% Similarity=0.234 Sum_probs=47.0
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecC-CCcHHHHHHHHHHHhhcCce
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEAS-MADQKAQNALRHLKEFATFL 268 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~-~~~~~~~~al~~l~~~~~~v 268 (282)
.++.||.+.++++.|+++|||+-.|-+ + . ..+.|-|+-... ..++.+++++++|++.+ .|
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~vDmI~~-s--~---------------~~isftv~~~~~~~~~~~~~~l~~el~~~~-~v 71 (75)
T cd04935 11 MWQQVGFLADVFAPFKKHGVSVDLVST-S--E---------------TNVTVSLDPDPNGLDPDVLDALLDDLNQIC-RV 71 (75)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe-C--C---------------CEEEEEEeCcccccchHHHHHHHHHHHhce-EE
Confidence 357799999999999999999999965 1 1 257888876542 23348899999999854 45
Q ss_pred EEE
Q 048784 269 RVL 271 (282)
Q Consensus 269 ~~L 271 (282)
.++
T Consensus 72 ~~~ 74 (75)
T cd04935 72 KII 74 (75)
T ss_pred EEe
Confidence 543
No 76
>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=93.81 E-value=1.3 Score=44.42 Aligned_cols=72 Identities=21% Similarity=0.255 Sum_probs=52.3
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
....+.+++|++||+|.++++.+.. -|+|.++=|-.... .=..||-++.. +.+.++++++.|
T Consensus 324 re~~l~V~iPerPGal~~f~~~i~~--~nItef~yr~~~~~---------------~a~v~vgie~~-~~~~~~~l~~~L 385 (499)
T TIGR01124 324 REALLAVTIPEQPGSFLKFCELLGN--RNITEFNYRYADRK---------------DAHIFVGVQLS-NPQERQEILARL 385 (499)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhhh--cceEEEEEEecCCC---------------eEEEEEEEEeC-CHHHHHHHHHHH
Confidence 3678889999999999999999997 48898888853321 22344555554 346778888899
Q ss_pred HhhcCceEEE
Q 048784 262 KEFATFLRVL 271 (282)
Q Consensus 262 ~~~~~~v~~L 271 (282)
++..-.+..+
T Consensus 386 ~~~Gy~~~dl 395 (499)
T TIGR01124 386 NDGGYSVVDL 395 (499)
T ss_pred HHcCCCeEEC
Confidence 8876666555
No 77
>PRK08639 threonine dehydratase; Validated
Probab=93.34 E-value=0.52 Score=46.06 Aligned_cols=73 Identities=16% Similarity=0.251 Sum_probs=50.2
Q ss_pred EEEEEEEcCCCccHHHHHHH-HHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALA-VFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~-~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
+..+.|.+||+||+|.++|+ .++... |++.|+-|..... ..+. ..|.+|.. +.+.+++.++.|
T Consensus 336 ~~~~~v~ipdrPGaL~~~l~~i~~~~~-NI~~~~~~~~~~~------------~~~~--v~v~iE~~-~~~h~~~i~~~L 399 (420)
T PRK08639 336 KHYFIVNFPQRPGALREFLDDVLGPND-DITRFEYLKKNNR------------ETGP--VLVGIELK-DAEDYDGLIERM 399 (420)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCC-cEEEEEEeecCCC------------CceE--EEEEEEeC-CHHHHHHHHHHH
Confidence 67899999999999999999 555544 9999977764332 1233 44445543 234667788888
Q ss_pred HhhcCceEEE
Q 048784 262 KEFATFLRVL 271 (282)
Q Consensus 262 ~~~~~~v~~L 271 (282)
++....++.+
T Consensus 400 ~~~Gy~~~~~ 409 (420)
T PRK08639 400 EAFGPSYIDI 409 (420)
T ss_pred HHCCCceEEC
Confidence 8776655544
No 78
>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=93.22 E-value=0.92 Score=33.53 Aligned_cols=58 Identities=21% Similarity=0.300 Sum_probs=42.7
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHH-HHHHHHHhhc
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQ-NALRHLKEFA 265 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~-~al~~l~~~~ 265 (282)
.++.||.+.++++.|+++|||+-.|-+ +. ..+.|-|+-.-...++.++ +++++|++.+
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~VDmI~~-s~-----------------~~iSftv~~~d~~~~~~~~~~l~~~l~~~~ 69 (75)
T cd04932 11 MLHAQGFLAKVFGILAKHNISVDLITT-SE-----------------ISVALTLDNTGSTSDQLLTQALLKELSQIC 69 (75)
T ss_pred CCCCcCHHHHHHHHHHHcCCcEEEEee-cC-----------------CEEEEEEeccccchhHHHHHHHHHHHHhcc
Confidence 467899999999999999999999965 11 2578888753322234565 7888888743
No 79
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=92.90 E-value=0.62 Score=40.88 Aligned_cols=36 Identities=17% Similarity=0.338 Sum_probs=30.5
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCC
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLR 220 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~ 220 (282)
.+.+.-+|+||-++++=+.|+.+|||+..+.++-..
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 344455899999999999999999999999988544
No 80
>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=92.89 E-value=0.77 Score=44.75 Aligned_cols=74 Identities=14% Similarity=0.136 Sum_probs=48.9
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
...+.|.+|++||+|.++|+.....+-|++++.-|..... +..+. .|.+|.. +.+.+++.++.|+
T Consensus 325 ~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~y~~~~~~------------~~~~v--~v~iE~~-~~~h~~~i~~~L~ 389 (409)
T TIGR02079 325 KHYFIVRFPQRPGALREFLNDVLGPNDDITRFEYTKKSNR------------ETGPA--LIGIELN-DKEDFAGLLERMA 389 (409)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeecCCC------------CeEEE--EEEEEeC-CHHHHHHHHHHHH
Confidence 6788899999999999999944444559999888862221 12334 4444443 2355677788888
Q ss_pred hhcCceEEE
Q 048784 263 EFATFLRVL 271 (282)
Q Consensus 263 ~~~~~v~~L 271 (282)
+....++.+
T Consensus 390 ~~Gy~~~~~ 398 (409)
T TIGR02079 390 AADIHYEDI 398 (409)
T ss_pred HCCCCeEEC
Confidence 776555443
No 81
>PRK09224 threonine dehydratase; Reviewed
Probab=92.40 E-value=0.7 Score=46.34 Aligned_cols=72 Identities=15% Similarity=0.261 Sum_probs=50.6
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
...+.+++|++||+|.++++.+. +-|+|.++=|-.... +=..+|-++....+..++++++.|+
T Consensus 328 e~~l~v~iPerPGaL~~f~~~l~--~~nItef~yr~~~~~---------------~a~V~vgie~~~~~~~~~~i~~~L~ 390 (504)
T PRK09224 328 EALLAVTIPEEPGSFLKFCELLG--GRNVTEFNYRYADAK---------------EAHIFVGVQLSRGQEERAEIIAQLR 390 (504)
T ss_pred EEEEEEEeCCCCCHHHHHHHHhc--cCcEEEEEEEecCCC---------------eEEEEEEEEeCChhhHHHHHHHHHH
Confidence 67888999999999999999998 688898887763321 2234455554322234677888887
Q ss_pred hhcCceEEE
Q 048784 263 EFATFLRVL 271 (282)
Q Consensus 263 ~~~~~v~~L 271 (282)
+..-.++.+
T Consensus 391 ~~gy~~~~l 399 (504)
T PRK09224 391 AHGYPVVDL 399 (504)
T ss_pred HcCCCeEEC
Confidence 766555544
No 82
>PLN02550 threonine dehydratase
Probab=92.38 E-value=1.6 Score=44.78 Aligned_cols=72 Identities=14% Similarity=0.126 Sum_probs=53.0
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
+..+.+.++++||+|.++++.+... |++.|+=|-... .+=..+|.+|.. +.+.++++++.|+
T Consensus 417 ~~~~~v~ipd~pG~l~~~~~~l~~~--ni~~~~~~~~~~---------------~~~~v~v~ie~~-~~~~~~~i~~~l~ 478 (591)
T PLN02550 417 EAVLATFMPEEPGSFKRFCELVGPM--NITEFKYRYSSE---------------KEALVLYSVGVH-TEQELQALKKRME 478 (591)
T ss_pred EEEEEEEcCCCCCHHHHHHHHhhhh--cceEEEEEecCC---------------CceEEEEEEEeC-CHHHHHHHHHHHH
Confidence 5678889999999999999999986 999998776322 123455556554 3467888999998
Q ss_pred hhcCceEEEc
Q 048784 263 EFATFLRVLG 272 (282)
Q Consensus 263 ~~~~~v~~LG 272 (282)
+....++.|-
T Consensus 479 ~~g~~~~~l~ 488 (591)
T PLN02550 479 SAQLRTVNLT 488 (591)
T ss_pred HCCCCeEeCC
Confidence 8766555543
No 83
>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=92.25 E-value=1.7 Score=32.10 Aligned_cols=27 Identities=11% Similarity=0.218 Sum_probs=23.7
Q ss_pred EEEcCCCccHHHHHHHHHHHCCceeee
Q 048784 187 VFSLEEGPGVLFKALAVFALRQINLTK 213 (282)
Q Consensus 187 ~~~~~~~pG~L~~~L~~F~~~~INlt~ 213 (282)
-+..+|+||-|+++.+.|+.+|+|+..
T Consensus 4 ei~~~Dr~gLfa~i~~~l~~~~l~I~~ 30 (76)
T cd04927 4 KLFCSDRKGLLHDVTEVLYELELTIER 30 (76)
T ss_pred EEEECCCCCHHHHHHHHHHHCCCeEEE
Confidence 345589999999999999999999884
No 84
>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=91.94 E-value=1.7 Score=31.72 Aligned_cols=56 Identities=14% Similarity=0.248 Sum_probs=43.6
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCC-cHHHHHHHHHHHh
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMA-DQKAQNALRHLKE 263 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~-~~~~~~al~~l~~ 263 (282)
+.+.||.+.++++.|+++|||+-.+-+.+ ....|.|+-+.... +..+++++++|++
T Consensus 11 l~~~~g~~~~if~~L~~~~I~v~~i~~s~------------------~~is~~v~~~~~~~~~~~~~~~~~~l~~ 67 (75)
T cd04912 11 MLGAHGFLAKVFEIFAKHGLSVDLISTSE------------------VSVSLTLDPTKNLSDQLLLDALVKDLSQ 67 (75)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEcCC------------------cEEEEEEEchhhccchHHHHHHHHHHHh
Confidence 46779999999999999999998886421 26889998754322 3578889999987
No 85
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=91.53 E-value=0.52 Score=36.42 Aligned_cols=71 Identities=17% Similarity=0.252 Sum_probs=48.9
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecC-CCcHHHHH-HHHHHHh
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEAS-MADQKAQN-ALRHLKE 263 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~-~~~~~~~~-al~~l~~ 263 (282)
|.+.=.|+||-...+-++|+++|+|+..|+---..+ .+...++||+.-. .+-..+++ +-++.++
T Consensus 6 ITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~--------------~ftm~~lV~~~~~~~d~~~lr~~l~~~~~~ 71 (90)
T COG3830 6 ITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDG--------------FFTMIMLVDISKEVVDFAALRDELAAEGKK 71 (90)
T ss_pred EEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhh--------------hceeeeEEcCChHhccHHHHHHHHHHHHHh
Confidence 334447999999999999999999999998655443 3577899999532 22234443 4445566
Q ss_pred hcCceEE
Q 048784 264 FATFLRV 270 (282)
Q Consensus 264 ~~~~v~~ 270 (282)
....+++
T Consensus 72 lgv~V~v 78 (90)
T COG3830 72 LGVDVRV 78 (90)
T ss_pred cCcEEEE
Confidence 6666654
No 86
>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=91.33 E-value=1.1 Score=32.88 Aligned_cols=55 Identities=15% Similarity=0.283 Sum_probs=43.3
Q ss_pred CCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 192 EGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 192 ~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
..||.+.++++.|+++|||+-.|-+.. ..+.|-|+-.. ..++.+++++++|++.+
T Consensus 13 ~~~g~~~~If~~la~~~I~vd~I~~s~------------------~~isftv~~~~-~~~~~l~~l~~el~~~~ 67 (73)
T cd04934 13 LSHGFLARIFAILDKYRLSVDLISTSE------------------VHVSMALHMEN-AEDTNLDAAVKDLQKLG 67 (73)
T ss_pred cccCHHHHHHHHHHHcCCcEEEEEeCC------------------CEEEEEEehhh-cChHHHHHHHHHHHHhe
Confidence 469999999999999999999996611 26888888743 33358889999998843
No 87
>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=91.17 E-value=2 Score=32.30 Aligned_cols=66 Identities=21% Similarity=0.231 Sum_probs=45.4
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
.+.++.|.+||+|.+.|+.+.. +-|+|.++=|-.... .+ .-||-++-. ++.+.++++.|++.
T Consensus 3 ~~~v~iPErpGal~~Fl~~l~p-~~~ITeF~YR~~~~~-------------~a--~vlvGi~~~--~~~~~~l~~~l~~~ 64 (81)
T cd04907 3 LFRFEFPERPGALKKFLNELLP-KWNITLFHYRNQGSD-------------YG--RVLVGIQVP--DADLDELKERLDAL 64 (81)
T ss_pred EEEEEcCCCCCHHHHHHHHhCC-CCeEeEEEEecCCCC-------------ce--eEEEEEEeC--hHHHHHHHHHHHHc
Confidence 4678899999999999999843 789999998875431 12 234444432 12667788888776
Q ss_pred cCce
Q 048784 265 ATFL 268 (282)
Q Consensus 265 ~~~v 268 (282)
.-.+
T Consensus 65 g~~~ 68 (81)
T cd04907 65 GYPY 68 (81)
T ss_pred CCCe
Confidence 4433
No 88
>PRK12483 threonine dehydratase; Reviewed
Probab=90.91 E-value=1.6 Score=44.05 Aligned_cols=72 Identities=17% Similarity=0.210 Sum_probs=51.8
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHH-HHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKA-QNALRH 260 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~-~~al~~ 260 (282)
.+..+.+.++++||+|.++++.+... |++.++=|-... + +=..+|.+|... .+.. +++++.
T Consensus 344 r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~~~~~-------------~--~~~v~v~ie~~~-~~~~~~~i~~~ 405 (521)
T PRK12483 344 REAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYRYADA-------------R--EAHLFVGVQTHP-RHDPRAQLLAS 405 (521)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEEecCC-------------C--eeEEEEEEEeCC-hhhhHHHHHHH
Confidence 36788999999999999999999988 999998775222 1 234555665542 2344 788888
Q ss_pred HHhhcCceEEE
Q 048784 261 LKEFATFLRVL 271 (282)
Q Consensus 261 l~~~~~~v~~L 271 (282)
|++..-.++.+
T Consensus 406 l~~~g~~~~dl 416 (521)
T PRK12483 406 LRAQGFPVLDL 416 (521)
T ss_pred HHHCCCCeEEC
Confidence 88776666655
No 89
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=90.64 E-value=1.2 Score=38.22 Aligned_cols=73 Identities=19% Similarity=0.348 Sum_probs=53.0
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
+-.+.+-+.|+||.|.++.+.|+.+|.|+-.|---|+.... .-.--+-..| ++..++++.+.|.
T Consensus 4 ~rilsvlv~ne~GvLsRv~glfsrRG~NIeSltv~~tE~~~--------------~SRiTivv~g--~~~~~EQi~kQL~ 67 (163)
T COG0440 4 RRILSLLVENEPGVLSRVTGLFSRRGYNIESLTVGPTETPG--------------LSRITIVVSG--DEQVLEQIIKQLN 67 (163)
T ss_pred eEEEEEEEECCCCeeehhhHHHHhcCcccceEEEEecCCCC--------------ceEEEEEEcC--CcchHHHHHHHHH
Confidence 44566667899999999999999999999999988876631 1122233334 4567788888888
Q ss_pred hhcCceEEE
Q 048784 263 EFATFLRVL 271 (282)
Q Consensus 263 ~~~~~v~~L 271 (282)
+.-.-+|++
T Consensus 68 kLidV~kV~ 76 (163)
T COG0440 68 KLIDVLKVL 76 (163)
T ss_pred hhccceeEE
Confidence 876656555
No 90
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=90.39 E-value=2.8 Score=39.01 Aligned_cols=68 Identities=12% Similarity=0.182 Sum_probs=47.3
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEee--cCCCcHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFE--ASMADQKAQNALRH 260 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~--g~~~~~~~~~al~~ 260 (282)
+..+.+.-+|+||-..++=+.|+++|+|+..+.+.-.... ..|...++++ ...+-..++++|+.
T Consensus 7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~--------------~~F~m~~~~~~p~~~~~~~L~~~L~~ 72 (286)
T PRK13011 7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLS--------------GRFFMRVEFHSEEGLDEDALRAGFAP 72 (286)
T ss_pred eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCC--------------CeEEEEEEEecCCCCCHHHHHHHHHH
Confidence 3445556689999999999999999999999999833332 1233344554 22334677888888
Q ss_pred HHhh
Q 048784 261 LKEF 264 (282)
Q Consensus 261 l~~~ 264 (282)
+.+.
T Consensus 73 l~~~ 76 (286)
T PRK13011 73 IAAR 76 (286)
T ss_pred HHHH
Confidence 7654
No 91
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=89.84 E-value=1.1 Score=38.61 Aligned_cols=62 Identities=24% Similarity=0.281 Sum_probs=46.3
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
|.+...|+||.|.++-...+++|.|+|....--.+.. ..-..|+++||-.+ . ++++++|+..
T Consensus 5 lsi~~enk~GvL~~ltgiiae~ggNIt~~q~~~~~~g--------------~~~~iYmEiEgi~d-~--e~l~~~lks~ 66 (218)
T COG1707 5 LSIIAENKPGVLRDLTGIIAEEGGNITYAQQFLEKDG--------------EKALIYMEIEGIDD-F--EKLLERLKSF 66 (218)
T ss_pred eEEEeecCccHHHHHHHHHHhcCCceEeeehhhhccC--------------ceEEEEEEeeCCCC-H--HHHHHHhhcc
Confidence 4455679999999999999999999999887655441 13478899999543 3 4567777654
No 92
>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=89.61 E-value=2.9 Score=27.91 Aligned_cols=31 Identities=26% Similarity=0.305 Sum_probs=26.3
Q ss_pred EEcCCCccHHHHHHHHHHHCCceeeeeeeee
Q 048784 188 FSLEEGPGVLFKALAVFALRQINLTKIESRP 218 (282)
Q Consensus 188 ~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP 218 (282)
...++.||.+.++++.|+++|||+..|..-+
T Consensus 6 ~~~~~~~~~~~~i~~~L~~~~i~i~~i~~~~ 36 (61)
T cd04891 6 KGVPDKPGVAAKIFSALAEAGINVDMIVQSV 36 (61)
T ss_pred ecCCCCCcHHHHHHHHHHHcCCcEEEEEEcC
Confidence 3457889999999999999999998876544
No 93
>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=89.54 E-value=3.6 Score=29.99 Aligned_cols=32 Identities=25% Similarity=0.348 Sum_probs=26.2
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeee
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESR 217 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSR 217 (282)
|-+..+|+||-|+++-+.|+.+|+|+..-...
T Consensus 3 ~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~ 34 (74)
T cd04925 3 IELTGTDRPGLLSEVFAVLADLHCNVVEARAW 34 (74)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCCcEEEEEEE
Confidence 44556899999999999999999998854433
No 94
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=89.12 E-value=2 Score=37.10 Aligned_cols=76 Identities=21% Similarity=0.271 Sum_probs=51.0
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCc-HHHHHHHHHHHhh
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMAD-QKAQNALRHLKEF 264 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~-~~~~~al~~l~~~ 264 (282)
+-+...|+||-+.++=..|..+||||-.++||-...- |. ..=.|.+++..+..- ..+..+..+++..
T Consensus 95 v~v~a~DrpgIv~~~T~lf~~~~inie~L~~~~~~a~---------~s---~~~lfha~it~~lPa~~~i~~l~~~f~al 162 (176)
T COG2716 95 VYVDANDRPGIVEEFTALFDGHGINIENLVSRTYPAP---------GS---SAPLFHAQITARLPANLSISALRDAFEAL 162 (176)
T ss_pred EEEEecCCccHHHHHHHHHHhcCCchhhceeeeeecC---------CC---CccceehhhhccCCCcCcHHHHHHHHHHH
Confidence 3345579999999999999999999999998854431 11 245899998654321 1334455556666
Q ss_pred cCceEEEcc
Q 048784 265 ATFLRVLGS 273 (282)
Q Consensus 265 ~~~v~~LGs 273 (282)
|..+.+=|+
T Consensus 163 ~~~L~v~~~ 171 (176)
T COG2716 163 CDELNVDGS 171 (176)
T ss_pred HHhhcceee
Confidence 665655444
No 95
>PRK06545 prephenate dehydrogenase; Validated
Probab=88.70 E-value=1.7 Score=41.41 Aligned_cols=40 Identities=15% Similarity=0.313 Sum_probs=35.4
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCC
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQ 222 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~ 222 (282)
-..+.+.++|+||.|.+++..+...|||+..|+-.-.+..
T Consensus 290 ~~~~~v~v~d~pg~~~~~~~~~~~~~i~i~~~~i~~~~~~ 329 (359)
T PRK06545 290 FYDLYVDVPDEPGVIARVTAILGEEGISIENLRILEARED 329 (359)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHcCCCeecceeeeccCC
Confidence 4678889999999999999999999999999988776653
No 96
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=88.18 E-value=2.6 Score=39.37 Aligned_cols=66 Identities=11% Similarity=0.201 Sum_probs=47.3
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeec----CCCcHHHHHHHHH
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEA----SMADQKAQNALRH 260 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g----~~~~~~~~~al~~ 260 (282)
-|.+.-+|+||-.+++=+.++++|+|+..+... .... ...|+..++++. ..+-..+++++++
T Consensus 11 iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~-~d~~-------------~~~ffm~i~~~~~~~~~~~~~~l~~~l~~ 76 (289)
T PRK13010 11 VLTLACPSAPGIVAAVSGFLAEKGCYIVELTQF-DDDE-------------SGRFFMRVSFHAQSAEAASVDTFRQEFQP 76 (289)
T ss_pred EEEEECCCCCCcHHHHHHHHHHCCCCEEecccc-cccc-------------cCcEEEEEEEEcCCCCCCCHHHHHHHHHH
Confidence 455566999999999999999999999999886 2111 135666666662 2334677888888
Q ss_pred HHhh
Q 048784 261 LKEF 264 (282)
Q Consensus 261 l~~~ 264 (282)
+.+.
T Consensus 77 l~~~ 80 (289)
T PRK13010 77 VAEK 80 (289)
T ss_pred HHHH
Confidence 7654
No 97
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=87.07 E-value=6.7 Score=41.12 Aligned_cols=70 Identities=11% Similarity=0.198 Sum_probs=51.4
Q ss_pred CcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHH
Q 048784 181 PFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRH 260 (282)
Q Consensus 181 ~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~ 260 (282)
...+.|.+...|++|.|.++...++..++|+.++.++..+. +...-.|-|++.. -..+..++..
T Consensus 624 ~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~-------------~~~~~~~~ieV~~---~~~L~~i~~~ 687 (702)
T PRK11092 624 EFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDG-------------RVYSAFIRLTARD---RVHLANIMRK 687 (702)
T ss_pred eeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCC-------------CEEEEEEEEEECC---HHHHHHHHHH
Confidence 35678888899999999999999999999999999875432 1122234444432 3578889999
Q ss_pred HHhhcC
Q 048784 261 LKEFAT 266 (282)
Q Consensus 261 l~~~~~ 266 (282)
|++.-.
T Consensus 688 Lr~i~~ 693 (702)
T PRK11092 688 IRVMPD 693 (702)
T ss_pred HhCCCC
Confidence 986643
No 98
>PRK06349 homoserine dehydrogenase; Provisional
Probab=86.98 E-value=2.6 Score=41.28 Aligned_cols=66 Identities=20% Similarity=0.272 Sum_probs=48.3
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
+-.|.+.+.|+||.|.++-+.|++++||+..+...+.... ..+..+.++-. .+..+++++++|+
T Consensus 348 ~yylRl~v~d~pGvLa~I~~~f~~~~vsI~si~q~~~~~~-------------~~~ivivT~~~---~e~~l~~~i~~L~ 411 (426)
T PRK06349 348 KYYLRLLVADKPGVLAKIAAIFAENGISIESILQKGAGGE-------------GAEIVIVTHET---SEAALRAALAAIE 411 (426)
T ss_pred eEEEEEEecCCcchHHHHHHHHhhcCccEEEEEeccCCCC-------------ceeEEEEEEeC---CHHHHHHHHHHHh
Confidence 3456667789999999999999999999999887764321 12445444432 3477888999988
Q ss_pred hh
Q 048784 263 EF 264 (282)
Q Consensus 263 ~~ 264 (282)
+.
T Consensus 412 ~l 413 (426)
T PRK06349 412 AL 413 (426)
T ss_pred cC
Confidence 64
No 99
>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=86.18 E-value=4.2 Score=30.38 Aligned_cols=58 Identities=16% Similarity=0.196 Sum_probs=40.6
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCC-C---cHHHHHHHHHHHhhc
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASM-A---DQKAQNALRHLKEFA 265 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~-~---~~~~~~al~~l~~~~ 265 (282)
.++.||.+.++++.|+++|||+-.|-+.. ..+.|-|+-+.-. . +..++++.++|++.+
T Consensus 11 ~~~~~g~~a~IF~~La~~~InVDmI~qs~------------------~sISftV~~sd~~~~~~~~~~l~~~~~~~~~~~ 72 (78)
T cd04933 11 MLGQYGFLAKVFSIFETLGISVDVVATSE------------------VSISLTLDPSKLWSRELIQQELDHVVEELEKDA 72 (78)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEecC------------------CEEEEEEEhhhhhhhhhHHHHHHHHHHHHHHcC
Confidence 35789999999999999999999996511 2578888753211 0 135566667776554
No 100
>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=86.03 E-value=7.1 Score=32.75 Aligned_cols=42 Identities=24% Similarity=0.343 Sum_probs=35.2
Q ss_pred CCcHHHHHHHhhCC-CCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 3 RGAYSESAAEKAYP-NCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 3 ~GTfS~~Aa~~~~~-~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
.|++......+.++ +.+++.+.+..+++++|.+|++|+.+++
T Consensus 117 ~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~ 159 (225)
T PF00497_consen 117 RGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVD 159 (225)
T ss_dssp TTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEE
T ss_pred cchhHHHHhhhhccchhhhcccccHHHHHHHHhcCCeeeeecc
Confidence 57777766666665 7888999999999999999999999875
No 101
>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=85.88 E-value=6.2 Score=27.49 Aligned_cols=29 Identities=28% Similarity=0.362 Sum_probs=24.6
Q ss_pred EEcCCCccHHHHHHHHHHHCCceeeeeee
Q 048784 188 FSLEEGPGVLFKALAVFALRQINLTKIES 216 (282)
Q Consensus 188 ~~~~~~pG~L~~~L~~F~~~~INlt~IeS 216 (282)
+.+++.||.+.++++.+++.|||+.-|..
T Consensus 7 ~~~~~~~g~~~~i~~~L~~~~I~i~~i~~ 35 (75)
T cd04913 7 RGVPDKPGVAAKIFGALAEANINVDMIVQ 35 (75)
T ss_pred CCCCCCCcHHHHHHHHHHHcCCeEEEEEe
Confidence 34578899999999999999999986643
No 102
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=85.58 E-value=3.1 Score=40.64 Aligned_cols=63 Identities=25% Similarity=0.322 Sum_probs=45.2
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeE-EEEEEeecCCCcHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDY-LFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y-~F~vd~~g~~~~~~~~~al~~l 261 (282)
.-.|++.-+|+||.+.++++.++++|||+-.+..+... ++ +..||+++... + +++++|
T Consensus 338 ~~rlii~h~d~pG~ia~it~~l~~~~iNI~~m~~~~~~-----------------~~A~~iie~D~~~~-~---~~~~~i 396 (409)
T PRK11790 338 GHRLLHIHENRPGVLAAINQIFAEQGINIAAQYLQTDG-----------------EIGYVVIDVDADYA-E---EALDAL 396 (409)
T ss_pred CceEEEEeCCCCCHHHHHHHHHHhcCCCHHHheeccCC-----------------CEEEEEEEeCCCCc-H---HHHHHH
Confidence 45677777899999999999999999999877664322 23 34459988553 3 456666
Q ss_pred HhhcC
Q 048784 262 KEFAT 266 (282)
Q Consensus 262 ~~~~~ 266 (282)
++...
T Consensus 397 ~~i~~ 401 (409)
T PRK11790 397 KAIPG 401 (409)
T ss_pred HcCCC
Confidence 65443
No 103
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=85.20 E-value=11 Score=39.58 Aligned_cols=70 Identities=19% Similarity=0.226 Sum_probs=54.3
Q ss_pred CcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHH
Q 048784 181 PFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRH 260 (282)
Q Consensus 181 ~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~ 260 (282)
...+.|.+...|++|.|.++++++++.++|+.++.++...+. .+.+.++++-+ +-..+..++..
T Consensus 625 ~f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~~---------------~~~~~~~i~v~-n~~~L~~i~~~ 688 (701)
T COG0317 625 VYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQ---------------FATMQFTIEVK-NLNHLGRVLAR 688 (701)
T ss_pred ceEEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCCc---------------eEEEEEEEEEC-cHHHHHHHHHH
Confidence 457889999999999999999999999999999999987331 34555555543 23567888888
Q ss_pred HHhhcC
Q 048784 261 LKEFAT 266 (282)
Q Consensus 261 l~~~~~ 266 (282)
|++...
T Consensus 689 l~~~~~ 694 (701)
T COG0317 689 LKQLPD 694 (701)
T ss_pred HhcCCC
Confidence 887643
No 104
>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=85.15 E-value=6.9 Score=28.57 Aligned_cols=36 Identities=14% Similarity=0.254 Sum_probs=28.6
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCC
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRN 221 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~ 221 (282)
|++..+|+||-+.++-++|+.+|+|+..=....++.
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 566678999999999999999999988544444433
No 105
>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=84.98 E-value=3.7 Score=28.36 Aligned_cols=51 Identities=20% Similarity=0.257 Sum_probs=37.6
Q ss_pred CCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 191 EEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 191 ~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
.++||...++++.|+++|||+-.|.+ .. ....|+|+-.-. +..+++++++|
T Consensus 11 ~~~~~~~~~if~~l~~~~i~v~~i~t----~~--------------~~is~~v~~~~~--~~~~~~l~~~l 61 (62)
T cd04890 11 NGEVGFLRKIFEILEKHGISVDLIPT----SE--------------NSVTLYLDDSLL--PKKLKRLLAEL 61 (62)
T ss_pred CcccCHHHHHHHHHHHcCCeEEEEec----CC--------------CEEEEEEehhhh--hHHHHHHHHhh
Confidence 46799999999999999999999954 11 268899887322 24566666665
No 106
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=84.87 E-value=25 Score=31.84 Aligned_cols=122 Identities=15% Similarity=0.104 Sum_probs=65.0
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCcc-
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLK- 91 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~- 91 (282)
.+|+.++.... +.+++++++.+|++|+||++......+... ..|...++.++ .+-+|-+...+..+++++.
T Consensus 116 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~~----~~~~hpl~~~~~i~~~~L~~ 188 (305)
T PRK11151 116 TFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFIE---VPLFDEPMLLA----VYEDHPWANRDRVPMSDLAG 188 (305)
T ss_pred HCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCeEE---EEeccCcEEEE----ecCCCCcccCCccCHHHhcC
Confidence 35676665444 589999999999999999876544333221 23333333322 2334444332222333322
Q ss_pred -EEEechHH---HHHHHHHHHhcCC--e-EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 -RVLSHPQA---LAQCENTLTKLGL--V-REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 -~V~SHpqa---l~QC~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
..++++.. ..+...|+..++. . ...+.|...+.++++.+ ...+|.+...+.
T Consensus 189 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~ilp~~~~~ 246 (305)
T PRK11151 189 EKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAG---SGITLLPALAVP 246 (305)
T ss_pred CCeEeecCCccHHHHHHHHHHHCCCCCCceEEeccHHHHHHHHHcC---CCEEEeeHHhhh
Confidence 22222221 2344455555432 2 34567777777777754 346777776553
No 107
>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=83.53 E-value=2.4 Score=32.52 Aligned_cols=69 Identities=19% Similarity=0.264 Sum_probs=43.6
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
.+..+.+..|.+||+|.+.|+.+..++ |+|.+.=|-.... .. .-+|-++-.. .+..+++++.|
T Consensus 9 ~E~~~~v~~PE~pGal~~F~~~l~~~~-nITeF~YR~~~~~-------------~a--~vlvgi~v~~-~~~~~~l~~~L 71 (91)
T PF00585_consen 9 REALFAVEFPERPGALKRFLDALGPRN-NITEFHYRYSGDD-------------FA--RVLVGIEVPD-AEDLEELIERL 71 (91)
T ss_dssp -EEEEEEE--BSTTHCHHHHHCCSSSE--EEEEEEE-TTTS-------------CS--EEEEEEE-SS-THHHHHHHHHH
T ss_pred CEEEEEEECCCCccHHHHHHHHhCCCc-eEEEEEEcCCCCC-------------ee--eEEEEEEeCC-HHHHHHHHHHH
Confidence 367888999999999999999886655 5998888876542 12 3344444332 34467888888
Q ss_pred HhhcCc
Q 048784 262 KEFATF 267 (282)
Q Consensus 262 ~~~~~~ 267 (282)
++..-.
T Consensus 72 ~~~gy~ 77 (91)
T PF00585_consen 72 KALGYP 77 (91)
T ss_dssp TSSS-E
T ss_pred HHcCCC
Confidence 776543
No 108
>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=83.43 E-value=6.3 Score=42.04 Aligned_cols=50 Identities=14% Similarity=0.190 Sum_probs=40.4
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEe
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDF 245 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~ 245 (282)
..|.+-+...|+||-|+++.++|+++|||+......-.... ..-.|||..
T Consensus 778 ~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~--------------~~d~F~v~~ 827 (850)
T TIGR01693 778 KATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEK--------------AEDVFYVTD 827 (850)
T ss_pred CeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCcc--------------ceeEEEEEC
Confidence 46888899999999999999999999999996666544331 356899964
No 109
>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=83.06 E-value=5.6 Score=35.18 Aligned_cols=55 Identities=15% Similarity=0.224 Sum_probs=43.0
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeee-eeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHH
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIE-SRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQK 253 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~Ie-SRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~ 253 (282)
..|++.-.|+||.+.++-+.|.+++||+..+. +|-.++ .+=+-.+.++....++.
T Consensus 149 ~~L~~~~~D~PG~Ig~vg~~Lg~~~iNIa~m~v~r~~~g---------------~~Ai~vl~vD~~v~~~v 204 (208)
T TIGR00719 149 PAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIG---------------NIALLTIEIDKNIDDHI 204 (208)
T ss_pred cEEEEEeCCCCChHHHHHHHHHhCCccEEEEEEEecCCC---------------CEEEEEEEeCCCCCHHH
Confidence 56777778999999999999999999997775 554333 25678889988776544
No 110
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=82.85 E-value=4.4 Score=37.20 Aligned_cols=74 Identities=20% Similarity=0.262 Sum_probs=53.7
Q ss_pred CcEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEE--EEEeecCCCcHHHHHHH
Q 048784 181 PFKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLF--YVDFEASMADQKAQNAL 258 (282)
Q Consensus 181 ~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F--~vd~~g~~~~~~~~~al 258 (282)
..+-.|-+-+.|+||.|.++=++|+.||.|+-.+----... +-.| =|=+.| .|..++++.
T Consensus 75 ~krHvinclVqnEpGvlsRisGvlAaRGfNIdSLvVc~tev----------------k~LsrmTIVl~G--td~VveQa~ 136 (309)
T KOG2663|consen 75 VKRHVINCLVQNEPGVLSRISGVLAARGFNIDSLVVCLTEV----------------KALSRMTIVLQG--TDGVVEQAR 136 (309)
T ss_pred ccceeEEEEecCCchHHHHHHHHHHhccCCchheeeechhh----------------hhhhhceEEEec--cHHHHHHHH
Confidence 34566767778999999999999999999976554433322 2234 455666 578899999
Q ss_pred HHHHhhcCceEEEc
Q 048784 259 RHLKEFATFLRVLG 272 (282)
Q Consensus 259 ~~l~~~~~~v~~LG 272 (282)
+.|++...-++++.
T Consensus 137 rQiedlVnV~aVlD 150 (309)
T KOG2663|consen 137 RQIEDLVNVYAVLD 150 (309)
T ss_pred HHHHHhhhhheeee
Confidence 99998876666653
No 111
>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=82.57 E-value=7.9 Score=40.45 Aligned_cols=68 Identities=13% Similarity=0.210 Sum_probs=49.6
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
..+.|.+...|++|.|.++.+.++..++|+..+.++-... . .+.+-++++-. +-..+..++..|
T Consensus 609 f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~-------------~--~~~~~~~ieV~-~~~~L~~ii~~L 672 (683)
T TIGR00691 609 FIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGK-------------R--EAILNITVEIK-NYKHLLKIMLKI 672 (683)
T ss_pred eEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCC-------------C--EEEEEEEEEEC-CHHHHHHHHHHH
Confidence 4667888889999999999999999999999999864322 1 23333344332 236788889888
Q ss_pred Hhhc
Q 048784 262 KEFA 265 (282)
Q Consensus 262 ~~~~ 265 (282)
+...
T Consensus 673 ~~i~ 676 (683)
T TIGR00691 673 KTKN 676 (683)
T ss_pred hCCC
Confidence 8664
No 112
>PRK05007 PII uridylyl-transferase; Provisional
Probab=82.54 E-value=4 Score=43.87 Aligned_cols=53 Identities=19% Similarity=0.259 Sum_probs=40.0
Q ss_pred CcEEEEEEEcCCCccHHHHHHHHHHHCCceee--eeeeeeCCCCCCCCCCCCCCCCcceeEEEEE-EeecCC
Q 048784 181 PFKTSIVFSLEEGPGVLFKALAVFALRQINLT--KIESRPLRNQPLRSSDDNSGFGKYFDYLFYV-DFEASM 249 (282)
Q Consensus 181 ~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt--~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~v-d~~g~~ 249 (282)
...|.|=+..+|+||-|+++..+|.+.||++. ||.+.= ..-.=.||| |-+|..
T Consensus 806 ~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~g----------------era~DvFyV~~~~g~~ 861 (884)
T PRK05007 806 DRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIG----------------ERVEDLFILATADRRA 861 (884)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccC----------------ceEEEEEEEEcCCCCc
Confidence 34688888999999999999999999999987 454421 123458898 666664
No 113
>PRK05092 PII uridylyl-transferase; Provisional
Probab=81.62 E-value=7.6 Score=41.95 Aligned_cols=52 Identities=19% Similarity=0.245 Sum_probs=39.5
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEE-EeecC
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYV-DFEAS 248 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~v-d~~g~ 248 (282)
.|.|.+..+|+||-|+++.++|+.+|||+..-...-... ...-.||| |-+|.
T Consensus 843 ~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~--------------~~~D~F~v~d~~g~ 895 (931)
T PRK05092 843 FTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGE--------------RAVDVFYVTDLFGL 895 (931)
T ss_pred eEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCC--------------EEEEEEEEeCCCCC
Confidence 577888889999999999999999999998555542222 23568888 55554
No 114
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=81.30 E-value=9.4 Score=40.29 Aligned_cols=69 Identities=14% Similarity=0.203 Sum_probs=50.6
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
..+.|.+...|++|.|.++.+.+++.++|+..+.++..+.. ....-.|-|++.. -..+..++..|
T Consensus 665 ~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~------------~~~~~~~~ieV~~---~~~L~~l~~~L 729 (743)
T PRK10872 665 YSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQ------------QLATIDMTIEIYN---LQVLGRVLGKL 729 (743)
T ss_pred eEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCC------------CEEEEEEEEEECC---HHHHHHHHHHH
Confidence 45678888899999999999999999999999998765421 1123345555543 35788888888
Q ss_pred Hhhc
Q 048784 262 KEFA 265 (282)
Q Consensus 262 ~~~~ 265 (282)
++.-
T Consensus 730 ~~i~ 733 (743)
T PRK10872 730 NQVP 733 (743)
T ss_pred hcCC
Confidence 8653
No 115
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=80.86 E-value=17 Score=33.75 Aligned_cols=64 Identities=13% Similarity=0.109 Sum_probs=43.6
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCC-----CcHHHHHHHH
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASM-----ADQKAQNALR 259 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~-----~~~~~~~al~ 259 (282)
.+.+.-+|+||-..++-+.|+++|+|+..+.+.=... +. .|++-++.+. +-..++++|+
T Consensus 8 vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~---------------~g-~F~m~i~v~~~~~~~~~~~L~~~L~ 71 (286)
T PRK06027 8 VLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPE---------------TG-RFFMRVEFEGDGLIFNLETLRADFA 71 (286)
T ss_pred EEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCC---------------CC-eEEEEEEEEeCCCCCCHHHHHHHHH
Confidence 3445558999999999999999999999888665222 11 2555433332 2356777777
Q ss_pred HHHhh
Q 048784 260 HLKEF 264 (282)
Q Consensus 260 ~l~~~ 264 (282)
.|.+.
T Consensus 72 ~l~~~ 76 (286)
T PRK06027 72 ALAEE 76 (286)
T ss_pred HHHHH
Confidence 77654
No 116
>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=79.39 E-value=31 Score=27.76 Aligned_cols=120 Identities=22% Similarity=0.138 Sum_probs=62.8
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCcc--
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLK-- 91 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~-- 91 (282)
+|+.++... .+-.++.+.+.+|++|+|++.-.+...+. ....|.+.++.++ .+-.|-+.. ...+++++.
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~~~~~-~~~~~~~L~~~ 97 (200)
T cd08417 26 APGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGL---RSQPLFEDRFVCV----ARKDHPLAG-GPLTLEDYLAA 97 (200)
T ss_pred CCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccCCCcc---chhhhhcCceEEE----ecCCCcccc-cccCHHHHhCC
Confidence 466655433 35678999999999999998644321111 1123333444433 233444433 222334432
Q ss_pred -E-EEechH-HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 -R-VLSHPQ-ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 -~-V~SHpq-al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
- ++.+.. .......|+.+++.. ...++|...+.+++..+ ...|+.+...++
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 154 (200)
T cd08417 98 PHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGT---DLIATVPRRLAE 154 (200)
T ss_pred CeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcC---CeeeeccHHHHH
Confidence 2 233322 223456677665432 23455666666777654 345677766554
No 117
>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=79.35 E-value=11 Score=32.71 Aligned_cols=129 Identities=19% Similarity=0.231 Sum_probs=73.6
Q ss_pred ceeecCCHHHHHHHHHcCCCCeEEEeeeecccc--ceeccccccccCCeEEEEEEEEeeeeeeeecCC-----CCCCCc-
Q 048784 19 EAVPCEQFDTAFEAVERWLVDRAVLPIENSLGG--SIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPG-----VKVEDL- 90 (282)
Q Consensus 19 ~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G--~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~-----~~l~~I- 90 (282)
...+..|. +.+.++.+|.+|.|.+=+-..-.| .+...-++|...++.++.=.. -...|+.+++ ..++|+
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 667889999999998733222111 122222344444444432222 2356777777 334444
Q ss_pred --c-EEEechHHHHHHHHHHHh----cCCe-------EEEecCHHHHHHHhhhcCCCCeEEecChhhHHH-cCCceee
Q 048784 91 --K-RVLSHPQALAQCENTLTK----LGLV-------REAVDDTAGAAKYVSFEQLKDAGAVASSSAAAI-YGLNILA 153 (282)
Q Consensus 91 --~-~V~SHpqal~QC~~fl~~----~~~~-------~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~-ygL~vl~ 153 (282)
. ++..-+..- =.|.+|++ .++. ...+.|..+.|..|+.+ ..+++++...+|+. |||.++.
T Consensus 91 ~~~~r~vnR~~GS-GtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G--~AD~G~g~~~~A~~~~gL~Fvp 165 (193)
T PF12727_consen 91 DPGLRFVNRQPGS-GTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASG--KADAGIGIRAAAEEFYGLDFVP 165 (193)
T ss_pred cCCcEEEECCCCC-HHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcC--CCCEEeehHHHHHhhcCCCcEE
Confidence 2 334444332 24555544 2221 13455667788888877 67899999999975 7999885
No 118
>TIGR00655 PurU formyltetrahydrofolate deformylase. This model describes formyltetrahydrofolate deformylases. The enzyme is a homohexamer. Sequences from a related enzyme formyl tetrahydrofolate-specific enzyme, phosphoribosylglycinamide formyltransferase, serve as an outgroup for phylogenetic analysis. Putative members of this family, scoring below the trusted cutoff, include a sequence from Rhodobacter capsulatus that lacks an otherwise conserved C-terminal region.
Probab=79.35 E-value=14 Score=34.28 Aligned_cols=65 Identities=14% Similarity=0.222 Sum_probs=44.6
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecC---CCcHHHHHHHHH-H
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEAS---MADQKAQNALRH-L 261 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~---~~~~~~~~al~~-l 261 (282)
|.+.-+|+||-.+++=+.++++|+|++.+...=.... ..|.--++++.. .+-+.+++++++ +
T Consensus 3 itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~--------------~~F~mr~~v~~~~~~~~~~~l~~~l~~~~ 68 (280)
T TIGR00655 3 LLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPET--------------GRFFMRVEFQLEGFRLEESSLLAAFKSAL 68 (280)
T ss_pred EEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCC--------------CeEEEEEEEEeCCCCCCHHHHHHHHHHHH
Confidence 5566799999999999999999999998876643221 123333344432 334677778887 6
Q ss_pred Hhh
Q 048784 262 KEF 264 (282)
Q Consensus 262 ~~~ 264 (282)
.+.
T Consensus 69 ~~~ 71 (280)
T TIGR00655 69 AEK 71 (280)
T ss_pred HHH
Confidence 544
No 119
>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=77.96 E-value=36 Score=27.67 Aligned_cols=31 Identities=13% Similarity=0.109 Sum_probs=23.9
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
.+|+.++... .+..++.+.+.+|++|+|++.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (197)
T cd08452 25 KFPSVKVELRELSSPDQVEELLKGRIDIGFLH 56 (197)
T ss_pred HCCCcEEEEEecChHHHHHHHHCCCccEEEee
Confidence 3576665433 367889999999999999974
No 120
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=77.91 E-value=2.5 Score=46.17 Aligned_cols=43 Identities=12% Similarity=0.153 Sum_probs=39.3
Q ss_pred CCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 2 VRGAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 2 P~GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
+.|++.+..+++.+|+.+++.++|..++++||.+|++|..|..
T Consensus 170 ~~g~~~~~~~~~~~p~~~i~~~~s~~~al~av~~G~~Da~i~~ 212 (1197)
T PRK09959 170 VANYPPDEVIHQSFPKATIISFTNLYQALASVSAGQNDYFIGS 212 (1197)
T ss_pred eCCCCCHHHHHHhCCCCEEEeCCCHHHHHHHHHcCCCCEEEcc
Confidence 5688888888999999999999999999999999999988864
No 121
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=77.86 E-value=4.8 Score=35.15 Aligned_cols=42 Identities=14% Similarity=0.190 Sum_probs=35.3
Q ss_pred CCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 3 RGAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 3 ~GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
.|++..+...+.+++.+.+++.+..+++.+|.+|++|..+.+
T Consensus 133 ~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~grvDa~i~~ 174 (243)
T PRK15007 133 NGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGD 174 (243)
T ss_pred cCcHHHHHHHHhCCCCeEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 577776666666778889999999999999999999999875
No 122
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=77.30 E-value=4.9 Score=35.09 Aligned_cols=42 Identities=14% Similarity=0.207 Sum_probs=35.6
Q ss_pred CCcHHHHHHHhhCC-CCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 3 RGAYSESAAEKAYP-NCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 3 ~GTfS~~Aa~~~~~-~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
.|+..++...++++ +.+++.+.+.++++++|.+|++|+.+..
T Consensus 138 ~g~~~~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~ 180 (250)
T TIGR01096 138 SGTTHEQYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTD 180 (250)
T ss_pred cCchHHHHHHHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 56777776777777 7788999999999999999999999974
No 123
>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=76.91 E-value=15 Score=25.11 Aligned_cols=27 Identities=22% Similarity=0.392 Sum_probs=23.7
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeee
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIES 216 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeS 216 (282)
+++.||.+.++++.|++.|||+-.|..
T Consensus 11 ~~~~~~~~~~i~~~l~~~~I~v~~i~~ 37 (66)
T cd04922 11 MAGTPGVAATFFSALAKANVNIRAIAQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 457899999999999999999988854
No 124
>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=76.82 E-value=39 Score=27.52 Aligned_cols=120 Identities=17% Similarity=0.112 Sum_probs=58.8
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecC-CCCCCCc--
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANP-GVKVEDL-- 90 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~-~~~l~~I-- 90 (282)
+|+.++.... +-.++.+.+.+|++|+|+........+... ..|.+.++. +..+-+|-|.... ..+++++
T Consensus 27 ~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----~v~~~~hpl~~~~~~i~~~dL~~ 99 (203)
T cd08445 27 APDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRR---IVLREEPLV----VALPAGHPLAQEKAPLTLAQLAD 99 (203)
T ss_pred CCCeEEEEEeCChHHHHHHHHcCCCcEEEecCCCCCCCcee---EEEEeccEE----EEeeCCCCCccCCCCcCHHHhcC
Confidence 5666655443 468999999999999999642211111111 112222222 2223344444332 2223332
Q ss_pred -cEEEechH---H-HHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhH
Q 048784 91 -KRVLSHPQ---A-LAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAA 144 (282)
Q Consensus 91 -~~V~SHpq---a-l~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa 144 (282)
.-|.-... . ..+..+|+.+.+.. ...++|...+.++++.+ ...++.+...+
T Consensus 100 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 158 (203)
T cd08445 100 EPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAG---EGVTLVPASVQ 158 (203)
T ss_pred CCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcC---CCeEEehHHhh
Confidence 33331111 1 23455566665432 23355666667777764 34566666544
No 125
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=76.80 E-value=6.4 Score=39.69 Aligned_cols=105 Identities=16% Similarity=0.251 Sum_probs=67.7
Q ss_pred hhhHHHcCCceeeccc--ccCCCCceEEEEEeeCCCC------CCC--------C------CCcEEEEEEEcCCCccHHH
Q 048784 141 SSAAAIYGLNILAEDI--QDDCDNVTRFLMLAREPII------PGT--------D------RPFKTSIVFSLEEGPGVLF 198 (282)
Q Consensus 141 ~~Aa~~ygL~vl~~~I--~d~~~N~TRF~vl~~~~~~------~~~--------~------~~~ktsi~~~~~~~pG~L~ 198 (282)
..-|+..|+++-.... .+.-.|+-++.+-+..... .++ + .....++++.-.|+||.+.
T Consensus 388 ~~iA~e~GI~~~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~ggg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I~ 467 (526)
T PRK13581 388 PLLAKERGIEVEESKSEESPDYSNLITVTVTTDDGERSVAGTVFGDGEPRIVEIDGYRVDAKPEGHMLIIRNRDRPGVIG 467 (526)
T ss_pred HHHHHHcCCEEEEEEecCCCCCCCEEEEEEEeCCeEEEEEEEEecCCceEEEEECCEEEEeeCCceEEEEEeCCcCChhH
Confidence 4567888888755433 3334677777765433110 000 0 1124567777789999999
Q ss_pred HHHHHHHHCCceeeeee-eeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 199 KALAVFALRQINLTKIE-SRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 199 ~~L~~F~~~~INlt~Ie-SRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
++.+.|.+++||+.... +|-.++ .+.+..++++.... + +++++|++.
T Consensus 468 ~v~~~L~~~~iNIa~m~~~r~~~g---------------~~al~~i~~D~~v~-~---~~l~~i~~~ 515 (526)
T PRK13581 468 KVGTLLGEAGINIAGMQLGRREAG---------------GEALMVLSVDDPVP-E---EVLEELRAL 515 (526)
T ss_pred HHHHHHhhcCCCchhcEeccCCCC---------------CeEEEEEECCCCCC-H---HHHHHHhcC
Confidence 99999999999998775 553322 36788899988764 3 455666543
No 126
>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=76.68 E-value=10 Score=24.72 Aligned_cols=27 Identities=30% Similarity=0.368 Sum_probs=23.5
Q ss_pred CCccHHHHHHHHHHHCCceeeeeeeee
Q 048784 192 EGPGVLFKALAVFALRQINLTKIESRP 218 (282)
Q Consensus 192 ~~pG~L~~~L~~F~~~~INlt~IeSRP 218 (282)
+.||.+.++++.+++++||+..+....
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~~~~ 38 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMISQSE 38 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEEcCC
Confidence 578999999999999999998886544
No 127
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=76.65 E-value=3.1 Score=33.98 Aligned_cols=27 Identities=26% Similarity=0.271 Sum_probs=23.0
Q ss_pred EEEcCCCccHHHHHHHHHHHCCceeee
Q 048784 187 VFSLEEGPGVLFKALAVFALRQINLTK 213 (282)
Q Consensus 187 ~~~~~~~pG~L~~~L~~F~~~~INlt~ 213 (282)
.+-+.|+||-|.++++.++++|||+.-
T Consensus 7 SvFlENk~GRL~~~~~~L~eagINiRA 33 (142)
T COG4747 7 SVFLENKPGRLASVANKLKEAGINIRA 33 (142)
T ss_pred EEEecCCcchHHHHHHHHHHcCCceEE
Confidence 334579999999999999999999753
No 128
>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=76.33 E-value=16 Score=24.98 Aligned_cols=52 Identities=17% Similarity=0.297 Sum_probs=36.3
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
+++.||.+.++++.++++|||+--|..-+.. -.+.|.|+- ....++++.|.+
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~q~~s~----------------~~isf~i~~------~~~~~~~~~Lh~ 62 (66)
T cd04924 11 MRGTPGVAGRVFGALGKAGINVIMISQGSSE----------------YNISFVVAE------DDGWAAVKAVHD 62 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEecCcc----------------ceEEEEEeH------HHHHHHHHHHHH
Confidence 4577999999999999999999877543321 157788876 233455555544
No 129
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=75.84 E-value=8 Score=41.42 Aligned_cols=53 Identities=17% Similarity=0.255 Sum_probs=38.8
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEE-EeecC
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYV-DFEAS 248 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~v-d~~g~ 248 (282)
..|.|=+..+|+||-|+++-++|.+.||++. +-.+.+. |..-.=.||| |-+|.
T Consensus 782 ~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~---~AkI~T~-----------gerv~D~Fyv~~~~g~ 835 (854)
T PRK01759 782 EQTEMELFALDRAGLLAQVSQVFSELNLNLL---NAKITTI-----------GEKAEDFFILTNQQGQ 835 (854)
T ss_pred CeEEEEEEeCCchHHHHHHHHHHHHCCCEEE---EEEEccc-----------CceEEEEEEEECCCCC
Confidence 4688888899999999999999999999976 3332221 1223457888 66665
No 130
>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=75.28 E-value=19 Score=25.47 Aligned_cols=33 Identities=36% Similarity=0.417 Sum_probs=25.6
Q ss_pred EEEEEEE-cC-CCccHHHHHHHHHHHCCceeeeee
Q 048784 183 KTSIVFS-LE-EGPGVLFKALAVFALRQINLTKIE 215 (282)
Q Consensus 183 ktsi~~~-~~-~~pG~L~~~L~~F~~~~INlt~Ie 215 (282)
+.++.-. ++ +.||.+.++.+.+++.|||+.-|-
T Consensus 8 ~i~v~g~g~~~~~~Gv~a~i~~~La~~~I~i~~is 42 (65)
T PF13840_consen 8 KISVVGPGLRFDVPGVAAKIFSALAEAGINIFMIS 42 (65)
T ss_dssp EEEEEEECGTTTSHHHHHHHHHHHHHTTS-ECEEE
T ss_pred EEEEEccccCCCcccHHHHHHHHHHHCCCCEEEEE
Confidence 3444444 44 489999999999999999998887
No 131
>PRK11260 cystine transporter subunit; Provisional
Probab=74.78 E-value=5.8 Score=35.47 Aligned_cols=42 Identities=10% Similarity=0.098 Sum_probs=35.8
Q ss_pred CCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 3 RGAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 3 ~GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
.|+..+....+.++..++..+++..+++++|.+|++|+.+.+
T Consensus 156 ~G~~~~~~l~~~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d 197 (266)
T PRK11260 156 LGTNYEQWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVD 197 (266)
T ss_pred cCCcHHHHHHHhCCCCceEecCCHHHHHHHHHcCCCCEEEec
Confidence 577666666677778889999999999999999999998874
No 132
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=74.31 E-value=71 Score=29.27 Aligned_cols=120 Identities=10% Similarity=0.074 Sum_probs=57.9
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc---
Q 048784 15 YPNCEAVP-CEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL--- 90 (282)
Q Consensus 15 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I--- 90 (282)
+|+.++.. ..+-.++++++.+|++|+|+.+-.......+ ....|.+.++. +.++.+|-|......+++++
T Consensus 119 ~P~i~l~l~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~l--~~~~l~~~~~~----~v~~~~hpl~~~~~i~~~~L~~~ 192 (316)
T PRK12679 119 FPEVRLELIQGTPQEIATLLQNGEADIGIASERLSNDPQL--VAFPWFRWHHS----LLVPHDHPLTQITPLTLESIAKW 192 (316)
T ss_pred CCCeEEEEecCCHHHHHHHHHcCCCCEEEecccCCCCCCc--eEEEccCCcEE----EEecCCCccccCCCCCHHHHhCC
Confidence 46655543 3456789999999999999974221000001 01122222222 33455565543322233332
Q ss_pred cEEEechH--HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhh
Q 048784 91 KRVLSHPQ--ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSA 143 (282)
Q Consensus 91 ~~V~SHpq--al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~A 143 (282)
+-|.-++. .-.....|+...+.. ...+.|+..+..++..+ .+ .|+.+..+
T Consensus 193 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g--~G-i~~lp~~~ 247 (316)
T PRK12679 193 PLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALG--LG-IGLVAEQS 247 (316)
T ss_pred CeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcC--Cc-EEEecccc
Confidence 22322221 222355666665442 23455666566666654 33 45555543
No 133
>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=73.94 E-value=21 Score=24.57 Aligned_cols=52 Identities=17% Similarity=0.183 Sum_probs=36.3
Q ss_pred CCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 191 EEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 191 ~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
.++||.+.++++.|+++|||+-.|..-++. -...|.|+= ....++++.|.+.
T Consensus 12 ~~~~~~~~~if~~L~~~~I~v~~i~q~~s~----------------~~isf~v~~------~~~~~a~~~lh~~ 63 (66)
T cd04919 12 KNMIGIAGRMFTTLADHRINIEMISQGASE----------------INISCVIDE------KDAVKALNIIHTN 63 (66)
T ss_pred CCCcCHHHHHHHHHHHCCCCEEEEEecCcc----------------ceEEEEEeH------HHHHHHHHHHHHH
Confidence 467999999999999999999888542221 156777764 2344566666543
No 134
>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=73.59 E-value=13 Score=26.53 Aligned_cols=28 Identities=11% Similarity=0.118 Sum_probs=24.2
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeee
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRP 218 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP 218 (282)
.++.||.+.++++.++++|||+-.| ++-
T Consensus 9 ~~~~~~~~a~if~~La~~~InvDmI-~~~ 36 (67)
T cd04914 9 KDNENDLQQRVFKALANAGISVDLI-NVS 36 (67)
T ss_pred CCCCccHHHHHHHHHHHcCCcEEEE-Eec
Confidence 3567999999999999999999999 443
No 135
>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=73.23 E-value=57 Score=27.70 Aligned_cols=112 Identities=14% Similarity=0.066 Sum_probs=69.2
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc-----c
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL-----K 91 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I-----~ 91 (282)
+.+++.+.+-.++++++.+|++|+|+......+ ...-...++++++...-.-...|+++++..+.++ |
T Consensus 22 ~ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~-------~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DLkGK 94 (216)
T PF09084_consen 22 DVEIVFFGGGGDVLEALASGKADIAVAGPDAVL-------FARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADLKGK 94 (216)
T ss_dssp EEEEEEESSHHHHHHHHHTTSHSEEEEECHHHH-------HHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGGTTS
T ss_pred EEEEEEecChhHHHHHHhcCCceEEeccchHHH-------HHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHhCCC
Confidence 468899999999999999999999987644222 1111234678887766555577888776544444 3
Q ss_pred EEEech--HHHHHHHHHHHhcCC-----eEEEecCHHHHHHHhhhcCCCCeEEe
Q 048784 92 RVLSHP--QALAQCENTLTKLGL-----VREAVDDTAGAAKYVSFEQLKDAGAV 138 (282)
Q Consensus 92 ~V~SHp--qal~QC~~fl~~~~~-----~~~~~~sTa~Aa~~v~~~~~~~~AAI 138 (282)
+|...+ .....-+.+|+++++ +.+.. +....+..+.++ .-.|++
T Consensus 95 ~i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~-~~~~~~~al~~g--~vDa~~ 145 (216)
T PF09084_consen 95 KIGVSRGSSSEYFLRALLKKNGIDPDDVKIVNL-GPPELAQALLSG--QVDAAI 145 (216)
T ss_dssp EEEESTTSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTT--SSSEEE
T ss_pred EEEEecCcchhHHHHHHHHHhccccccceeeee-ehhhhhhhhhcC--CCCEEE
Confidence 776666 344455677877754 22322 344455555554 234444
No 136
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=72.52 E-value=78 Score=28.94 Aligned_cols=119 Identities=12% Similarity=0.055 Sum_probs=59.5
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCCCeEEEeeeec-cccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc--
Q 048784 15 YPNCEAVP-CEQFDTAFEAVERWLVDRAVLPIENS-LGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL-- 90 (282)
Q Consensus 15 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS-~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I-- 90 (282)
+|+.++.. ..+..++.+.|.+|++|+|+.+-... ..+. ....|.+.++. +..+..|-|...+..+++++
T Consensus 119 ~P~i~l~~~~~~~~~~~~~L~~~~~D~~i~~~~~~~~~~l---~~~~l~~~~~~----~v~~~~hpl~~~~~~~~~~L~~ 191 (309)
T PRK12683 119 FPKVHLALRQGSPQEIAEMLLNGEADIGIATEALDREPDL---VSFPYYSWHHV----VVVPKGHPLTGRENLTLEAIAE 191 (309)
T ss_pred CCCceEEEEeCCHHHHHHHHHcCCccEEEecCCCCCCCCc---eEEEcccCeEE----EEecCCCCcccCCccCHHHHhc
Confidence 56665543 34678999999999999999742111 1111 11122222332 33455555543333333332
Q ss_pred -cEEEech--HHHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhh
Q 048784 91 -KRVLSHP--QALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSA 143 (282)
Q Consensus 91 -~~V~SHp--qal~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~A 143 (282)
.-|.-.+ .--.+...|+.+.+.. ...+.|......++..+ .+. ++.+..+
T Consensus 192 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~Gi-~~lp~~~ 247 (309)
T PRK12683 192 YPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELG--MGV-GIVAAMA 247 (309)
T ss_pred CCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhC--CCe-EEeehhh
Confidence 3332111 1234566777776543 23345555555666654 344 4444443
No 137
>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=72.37 E-value=49 Score=26.61 Aligned_cols=122 Identities=16% Similarity=0.108 Sum_probs=60.2
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc---
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL--- 90 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I--- 90 (282)
+|+.++... .+..++++.+.+|++|+|+..-.....+. ....|.+..+.++ .+-.|-|......+++++
T Consensus 27 ~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~~ 99 (200)
T cd08411 27 YPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGL---EEEPLFDEPFLLA----VPKDHPLAKRKSVTPEDLAGE 99 (200)
T ss_pred CCCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCCCCCc---eEEEeeccceEEE----ecCCCCccccCccCHHHHcCC
Confidence 566655444 36789999999999999997533211111 1112222232222 122333322111222222
Q ss_pred cEEE-ech-HHHHHHHHHHHhcCC--e-EEEecCHHHHHHHhhhcCCCCeEEecChhhHHH
Q 048784 91 KRVL-SHP-QALAQCENTLTKLGL--V-REAVDDTAGAAKYVSFEQLKDAGAVASSSAAAI 146 (282)
Q Consensus 91 ~~V~-SHp-qal~QC~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ 146 (282)
.-|. +.. ....+...|+.+++. . ...++|...+..++..+ ...|+.+...++.
T Consensus 100 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 157 (200)
T cd08411 100 RLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAG---LGITLLPELAVPS 157 (200)
T ss_pred ceEecCCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CCEEEeCHHHhcc
Confidence 2222 111 122344455655543 2 34556777777777764 3467777776653
No 138
>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=71.70 E-value=25 Score=23.61 Aligned_cols=27 Identities=30% Similarity=0.434 Sum_probs=23.8
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeee
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIES 216 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeS 216 (282)
+.+.||.+.++++.+++++||+-.|.+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04923 10 MRSHPGVAAKMFKALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEc
Confidence 457799999999999999999988864
No 139
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=71.63 E-value=82 Score=28.81 Aligned_cols=30 Identities=20% Similarity=0.094 Sum_probs=23.3
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
+|+.++... .+..++++.+.+|++|+++.+
T Consensus 119 ~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~ 149 (313)
T PRK12684 119 YPKVRLSILQGSPTQIAEMVLHGQADLAIAT 149 (313)
T ss_pred CCCceEEEEeCChHHHHHHHHCCCcCEEEee
Confidence 466655443 467899999999999999976
No 140
>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=71.11 E-value=18 Score=32.00 Aligned_cols=117 Identities=18% Similarity=0.042 Sum_probs=61.7
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCC---CCCc--c
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVK---VEDL--K 91 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~---l~~I--~ 91 (282)
+.+++++.+..+++++|.+|++|+|++.....+. ......++.+++-..-.-..+++++++.. ++|+ +
T Consensus 30 ~v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~-------~~~~g~~~~~i~~~~~~~~~~~v~~~~~~i~s~~dL~Gk 102 (288)
T TIGR01728 30 KVEWVEFPAGPPALEALGAGSLDFGYIGPGPALF-------AYAAGADIKAVGLVSDNKATAIVVIKGSPIRTVADLKGK 102 (288)
T ss_pred eEEEEecCCCcHHHHHHhcCCccccccCCcHHHH-------HHhcCCCEEEEEEecCCCceEEEECCCCCCCCHHHcCCC
Confidence 3567788888899999999999999864331110 00111245555433321245566654432 2333 2
Q ss_pred EEEechH--HHHHHHHHHHhcCCe---E-EEecCHHHHHHHhhhcCCCCeEEecChh
Q 048784 92 RVLSHPQ--ALAQCENTLTKLGLV---R-EAVDDTAGAAKYVSFEQLKDAGAVASSS 142 (282)
Q Consensus 92 ~V~SHpq--al~QC~~fl~~~~~~---~-~~~~sTa~Aa~~v~~~~~~~~AAI~s~~ 142 (282)
+|...+- .......+|.++++. . ....+.+.+...+..+ ...|++....
T Consensus 103 ~i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g--~vda~~~~~p 157 (288)
T TIGR01728 103 RIAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAG--QVDAWAIWEP 157 (288)
T ss_pred EEEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCC--CCCEEEeccc
Confidence 5553221 123344567665442 2 2223556666666655 3455655543
No 141
>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=70.95 E-value=25 Score=23.31 Aligned_cols=53 Identities=26% Similarity=0.361 Sum_probs=36.7
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
..+.+|.+.++++.|++++|++-.+..-.. . ..+.|.|+- ..+.++++.|++.
T Consensus 10 ~~~~~~~~~~i~~~l~~~~i~v~~i~~~~~-~---------------~~i~~~v~~------~~~~~~~~~l~~~ 62 (65)
T cd04892 10 MRGTPGVAARIFSALAEAGINIIMISQGSS-E---------------VNISFVVDE------DDADKAVKALHEE 62 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEcCCC-c---------------eeEEEEEeH------HHHHHHHHHHHHH
Confidence 346799999999999999999987754221 1 257788876 2344566666543
No 142
>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=70.94 E-value=36 Score=28.33 Aligned_cols=115 Identities=15% Similarity=0.133 Sum_probs=66.2
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCC-----C---CC
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGV-----K---VE 88 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~-----~---l~ 88 (282)
+.++++. ++..+++++.+|++|.++-++..+.+- - ..+.... -+....+.++.+++. . ++
T Consensus 39 ~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~r--------~--~~~~~s~-p~~~~~~~~~~~~~~~~~~~~~~~~~ 106 (225)
T PF00497_consen 39 KIEFVPM-PWSRLLEMLENGKADIIIGGLSITPER--------A--KKFDFSD-PYYSSPYVLVVRKGDAPPIKTIKSLD 106 (225)
T ss_dssp EEEEEEE-EGGGHHHHHHTTSSSEEESSEB-BHHH--------H--TTEEEES-ESEEEEEEEEEETTSTCSTSSHSSGG
T ss_pred ccceeec-ccccccccccccccccccccccccccc--------c--ccccccc-cccchhheeeeccccccccccccchh
Confidence 4678888 999999999999999887454432221 0 1111111 122334555555431 1 22
Q ss_pred Cc--cEEEechHHH--HHHHHHHHhcCCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHH
Q 048784 89 DL--KRVLSHPQAL--AQCENTLTKLGLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAI 146 (282)
Q Consensus 89 ~I--~~V~SHpqal--~QC~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ 146 (282)
++ ++|..-.-.. ...++...+ +.+.+.+.|..++.+++..+ +..|+|+....+..
T Consensus 107 dl~~~~i~~~~g~~~~~~l~~~~~~-~~~~~~~~~~~~~~~~l~~g--~~d~~i~~~~~~~~ 165 (225)
T PF00497_consen 107 DLKGKRIGVVRGSSYADYLKQQYPS-NINIVEVDSPEEALEALLSG--RIDAFIVDESTAEY 165 (225)
T ss_dssp GGTTSEEEEETTSHHHHHHHHHTHH-TSEEEEESSHHHHHHHHHTT--SSSEEEEEHHHHHH
T ss_pred hhcCcccccccchhHHHHhhhhccc-hhhhcccccHHHHHHHHhcC--Ceeeeeccchhhhh
Confidence 44 2344333322 123333322 56777889999999998876 56788887766543
No 143
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=70.79 E-value=36 Score=31.13 Aligned_cols=121 Identities=13% Similarity=-0.041 Sum_probs=65.0
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCcc--
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLK-- 91 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~-- 91 (282)
+|+.++.... +-.++++.+.+|++|+|+++-.-...+... ..|.+.++.+ +.+-+|-|. ....+++++.
T Consensus 138 ~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~l~~---~~l~~~~~~l----v~~~~hpl~-~~~~~~~~L~~~ 209 (314)
T PRK09508 138 APNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFTS---VPLFKDELVL----VASKNHPRI-KGPITEEQLYNE 209 (314)
T ss_pred CCCcEEEEEeCcchhHHHHHhcCCccEEEecCCCCccccce---eeeecCceEE----EEcCCCCcc-CCCCCHHHHhhC
Confidence 5666655443 467899999999999999875422111111 1223333332 234445443 2223344442
Q ss_pred --EEEechHHHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHHH
Q 048784 92 --RVLSHPQALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAAI 146 (282)
Q Consensus 92 --~V~SHpqal~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ 146 (282)
.+.+++....+...|+.+.+.. ...++|......+++.+ ...++.+...++.
T Consensus 210 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 266 (314)
T PRK09508 210 QHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQT---HLVAIAPRWLAEE 266 (314)
T ss_pred CCEEecCCCCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhC---ChHHHHHHHHHHH
Confidence 1233333334456677765432 24556666677777765 2356777766653
No 144
>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=70.78 E-value=25 Score=23.60 Aligned_cols=27 Identities=30% Similarity=0.439 Sum_probs=23.8
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeee
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIES 216 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeS 216 (282)
+++.||.+.++++.++++|||+-.|.+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04936 10 MRSHPGVAAKMFEALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 567799999999999999999988864
No 145
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=70.50 E-value=5.5 Score=43.59 Aligned_cols=43 Identities=21% Similarity=0.187 Sum_probs=38.2
Q ss_pred CCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 2 VRGAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 2 P~GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
+.|++.+...++.+|+.+++.+++..+++.+|.+|++|.+|.+
T Consensus 413 ~~g~~~~~~~~~~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~ 455 (1197)
T PRK09959 413 PYYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDALVAT 455 (1197)
T ss_pred eCCcchHHHHHHHCCCcEEEEcCCHHHHHHHHHcCCCCEEehh
Confidence 4678778888888899999999999999999999999998864
No 146
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=70.45 E-value=8.1 Score=33.99 Aligned_cols=42 Identities=14% Similarity=0.071 Sum_probs=34.5
Q ss_pred CCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 3 RGAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 3 ~GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
.|+..+.-..+.+++.+++.+++.++++.+|.+|++|+.+..
T Consensus 138 ~g~~~~~~l~~~~~~~~i~~~~~~~~~~~~L~~grvDa~i~~ 179 (247)
T PRK09495 138 SGTGSVDYAKANIKTKDLRQFPNIDNAYLELGTGRADAVLHD 179 (247)
T ss_pred cCchHHHHHHhcCCCCceEEcCCHHHHHHHHHcCceeEEEeC
Confidence 577666666666677788899999999999999999988853
No 147
>TIGR01327 PGDH D-3-phosphoglycerate dehydrogenase. This model represents a long form of D-3-phosphoglycerate dehydrogenase, the serA gene of one pathway of serine biosynthesis. Shorter forms, scoring between trusted and noise cutoff, include SerA from E. coli.
Probab=70.39 E-value=9 Score=38.63 Aligned_cols=104 Identities=16% Similarity=0.252 Sum_probs=66.3
Q ss_pred hhhHHHcCCceeeccccc--CCCCceEEEEEeeCCCC------CCCC--------C------CcEEEEEEEcCCCccHHH
Q 048784 141 SSAAAIYGLNILAEDIQD--DCDNVTRFLMLAREPII------PGTD--------R------PFKTSIVFSLEEGPGVLF 198 (282)
Q Consensus 141 ~~Aa~~ygL~vl~~~I~d--~~~N~TRF~vl~~~~~~------~~~~--------~------~~ktsi~~~~~~~pG~L~ 198 (282)
..-|+..|+++....... .-.|+-++-+-+..... -++. + ..-..+++.-.|+||.+.
T Consensus 387 ~~iA~e~GI~v~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~gGg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I~ 466 (525)
T TIGR01327 387 PAVAKERGITVEESKSESSPDYKNYLSVTVTGDSGTVSVAGTVFGGFSPRIVEIDGFHVDLEPEGIMLIILHLDKPGVIG 466 (525)
T ss_pred HHHHHHcCCEEEEEEccCCCCCCCEEEEEEEeCCcEEEEEEEEecCCcEEEEEECCEEEEEecCccEEEEEecCcCCcch
Confidence 466888999986654432 23566666554332110 0000 0 112456667789999999
Q ss_pred HHHHHHHHCCceeeeee-eeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 199 KALAVFALRQINLTKIE-SRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 199 ~~L~~F~~~~INlt~Ie-SRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
++.+.+.+++||+..+. +|-.++ .+.+..++++....+ +++++|++
T Consensus 467 ~v~~~L~~~~iNIa~m~~~R~~~g---------------~~al~~i~~D~~v~~----~~l~~i~~ 513 (525)
T TIGR01327 467 KVGTLLGTAGINIASMQLGRKEKG---------------GEALMLLSLDQPVPD----EVLEEIKA 513 (525)
T ss_pred HHHhHHhhcCCChHHcEeecCCCC---------------CeEEEEEEcCCCCCH----HHHHHHhc
Confidence 99999999999998764 665443 367888999887642 34555554
No 148
>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=70.28 E-value=24 Score=24.55 Aligned_cols=51 Identities=18% Similarity=0.252 Sum_probs=35.9
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+.+.||.+.++++.+++.|||+..+-.. . -.-.|+||- ....++++.|.+.
T Consensus 11 ~~~~~gi~~~if~aL~~~~I~v~~~~~S--e----------------~~is~~v~~------~~~~~av~~Lh~~ 61 (64)
T cd04937 11 IRGVPGVMAKIVGALSKEGIEILQTADS--H----------------TTISCLVSE------DDVKEAVNALHEA 61 (64)
T ss_pred ccCCcCHHHHHHHHHHHCCCCEEEEEcC--c----------------cEEEEEEcH------HHHHHHHHHHHHH
Confidence 3578999999999999999999755431 1 145677764 3445677776654
No 149
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=69.71 E-value=57 Score=26.24 Aligned_cols=112 Identities=21% Similarity=0.195 Sum_probs=60.8
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCC---CCCCc--c
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGV---KVEDL--K 91 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~---~l~~I--~ 91 (282)
+.++++. +..++++++.+|++|+++.+..+..+... .+. ...........++.+++. +++|+ +
T Consensus 40 ~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~~~-----~~~------~~~~~~~~~~~~~~~~~~~~~~~~dL~g~ 107 (219)
T smart00062 40 KVEFVEV-SFDNLLTALKSGKIDVVAAGMTITPERAK-----QVD------FSDPYYKSGQVILVRKDSPIKSLEDLKGK 107 (219)
T ss_pred eEEEEec-cHHHHHHHHHCCcccEEeccccCCHHHHh-----hee------eccceeeceeEEEEecCCCCCChHHhCCC
Confidence 3577788 88999999999999999875432211110 010 011111222455555443 22333 2
Q ss_pred EEEechHHHHHHHHHHHhc--CCeEEEecCHHHHHHHhhhcCCCCeEEecChhhH
Q 048784 92 RVLSHPQALAQCENTLTKL--GLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAA 144 (282)
Q Consensus 92 ~V~SHpqal~QC~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa 144 (282)
+|..-+ . .-...++... +.......+..++.+++..+ +..|++.....+
T Consensus 108 ~i~~~~-g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~~~ 158 (219)
T smart00062 108 KVAVVA-G-TTGEELLKKLYPEAKIVSYDSQAEALAALKAG--RADAAVADAPAL 158 (219)
T ss_pred EEEEec-C-ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcC--cccEEEeccHHH
Confidence 333322 1 1233555554 45566677778888888765 445666555533
No 150
>PRK04374 PII uridylyl-transferase; Provisional
Probab=69.35 E-value=25 Score=37.85 Aligned_cols=52 Identities=17% Similarity=0.276 Sum_probs=39.3
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceee--eeeeeeCCCCCCCCCCCCCCCCcceeEEEEE-EeecCC
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLT--KIESRPLRNQPLRSSDDNSGFGKYFDYLFYV-DFEASM 249 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt--~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~v-d~~g~~ 249 (282)
..|.|.+...|+||-|+++-.+|+.+|+|+. ||.+. .+ ...=.||| |-+|..
T Consensus 795 ~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~--g~--------------~a~D~F~V~d~~g~~ 849 (869)
T PRK04374 795 RRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATF--GE--------------RAEDQFQITDEHDRP 849 (869)
T ss_pred CeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEec--CC--------------EEEEEEEEECCCCCc
Confidence 4677888889999999999999999999987 55544 22 23457787 666653
No 151
>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=68.52 E-value=63 Score=26.26 Aligned_cols=32 Identities=25% Similarity=0.159 Sum_probs=23.3
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCCCeEEEee
Q 048784 14 AYPNCEAVPCEQFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 14 ~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPi 45 (282)
.+|+.++.....-.++++.+.+|++|+|+++-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~l~~g~~D~~i~~~ 56 (200)
T cd08462 25 EAPGVRFELLPPDDQPHELLERGEVDLLIAPE 56 (200)
T ss_pred HCCCCEEEEecCChhHHHHHhcCCeeEEEecC
Confidence 35666554443223999999999999999853
No 152
>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=68.00 E-value=63 Score=26.05 Aligned_cols=122 Identities=15% Similarity=0.104 Sum_probs=60.5
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeec--cccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc-
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENS--LGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL- 90 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS--~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I- 90 (282)
+|+.++.... +-.++.+++.+|++|+|+..-... ....+ ....|.+.++.+ .++-.|-+...+..+++++
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~--~~~~l~~~~~~~----v~~~~hp~~~~~~i~~~~L~ 99 (200)
T cd08453 26 YPDVELQLREATSDVQLEALLAGEIDAGIVIPPPGASAPPAL--AYRPLLSEPLVL----AVPAAWAAEGGAPLALAAVA 99 (200)
T ss_pred CCCceEEEEeCCHHHHHHHHHcCCCCEEEEecCcccCCCcce--eEEEeeeCceEE----EEECCCccccCCCCCHHHhc
Confidence 5666655443 466899999999999999743211 01100 112233333332 2333444433322233333
Q ss_pred --cEEE-ech---HHHHHHHHHHHhcCCe--E-EEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 91 --KRVL-SHP---QALAQCENTLTKLGLV--R-EAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 91 --~~V~-SHp---qal~QC~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
.-|. +.. .....+..|+.+.+.. . ..++|...+.++++.+ ...++.+...++
T Consensus 100 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08453 100 AEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAG---MGVALVPASLRN 160 (200)
T ss_pred cCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcC---CcEEEeEhHHhh
Confidence 3332 221 1234567778776543 2 2344555556666654 345666665543
No 153
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=67.99 E-value=10 Score=30.75 Aligned_cols=43 Identities=26% Similarity=0.315 Sum_probs=33.3
Q ss_pred CcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEeee
Q 048784 4 GAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLPIE 46 (282)
Q Consensus 4 GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 46 (282)
|+..........++.+.+.+.+..+++.+|.+|++|+++++-.
T Consensus 114 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~ 156 (219)
T smart00062 114 GTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADAP 156 (219)
T ss_pred CccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEeccH
Confidence 5545545454455678889999999999999999999998643
No 154
>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=67.81 E-value=62 Score=25.95 Aligned_cols=122 Identities=17% Similarity=0.140 Sum_probs=58.8
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCC---C
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVE---D 89 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~---~ 89 (282)
.+|+.++.-.. +..++.+.+.+|++|+|+.+......+... ..|.+..+. +..+-+|-+......+++ +
T Consensus 26 ~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----~v~~~~~pl~~~~~~~~~~l~~ 98 (198)
T cd08446 26 ARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIAV---ENVAQERLY----LAVPKSHPLAARPAVSLADLRN 98 (198)
T ss_pred HCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecCCCCCCcee---EEeeeccEE----EEEeCCCCcccCCccCHHHHcC
Confidence 35766554333 567888999999999999753211111111 112222222 223334444322212222 2
Q ss_pred ccEEE-ech---HHHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 90 LKRVL-SHP---QALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 90 I~~V~-SHp---qal~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
..-|. ..+ ....+...|+.+.+.. ...++|...+.++++.+ ...++.+...+.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (198)
T cd08446 99 EPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAG---FGVCIVPESVAA 158 (198)
T ss_pred CCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcC---CcEEEchhhhhc
Confidence 33332 111 1123345566665432 23456666666777654 345666665443
No 155
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=67.35 E-value=12 Score=30.54 Aligned_cols=42 Identities=24% Similarity=0.360 Sum_probs=33.7
Q ss_pred CCcHHHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 3 RGAYSESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 3 ~GTfS~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
.|+..+....+.++..+++++.+.++++++|.+|++|.++++
T Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 153 (218)
T cd00134 112 KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVD 153 (218)
T ss_pred cCchHHHHHHHhCCcccEEEeCCHHHHHHHHHcCCccEEEec
Confidence 355555566666666788999999999999999999988875
No 156
>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=67.12 E-value=68 Score=26.13 Aligned_cols=122 Identities=16% Similarity=0.118 Sum_probs=58.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCcc-
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLK- 91 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~- 91 (282)
.+|+.++... .+..++.+.+.+|++|+|+..-.-.....+ ....|.+.++.+ ..+-+|.+......+++++.
T Consensus 25 ~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~--~~~~l~~~~~~~----v~~~~hpl~~~~~i~~~~l~~ 98 (198)
T cd08443 25 RYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDL--ITLPCYHWNRCV----VVKRDHPLADKQSISIEELAT 98 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccccccCCc--eEeeeeeceEEE----EEcCCCccccCCCCCHHHHhc
Confidence 3566655444 467889999999999999974210000111 011222223322 23334444432222333332
Q ss_pred -EEEechH--H-HHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhH
Q 048784 92 -RVLSHPQ--A-LAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAA 144 (282)
Q Consensus 92 -~V~SHpq--a-l~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa 144 (282)
...+++. . ......|+.+++.. ...+.+......+++.+ .+ .|+.+...+
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~G-ia~~p~~~~ 155 (198)
T cd08443 99 YPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLG--LG-VGVIASMAY 155 (198)
T ss_pred CCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC--Cc-EEEeecccc
Confidence 2223332 1 22334555555442 23456667677777765 34 455555544
No 157
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=66.44 E-value=22 Score=31.07 Aligned_cols=37 Identities=16% Similarity=0.205 Sum_probs=30.1
Q ss_pred EEEEEEEc--CCCccHHHHHHHHHHHCCceeeeeeeeeCCC
Q 048784 183 KTSIVFSL--EEGPGVLFKALAVFALRQINLTKIESRPLRN 221 (282)
Q Consensus 183 ktsi~~~~--~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~ 221 (282)
++.+++++ +|+||-..++-+.++++|.|+. +||-+..
T Consensus 6 ~~~lviTviG~DrpGIVa~vs~~l~~~g~NI~--ds~~t~l 44 (190)
T PRK11589 6 QHYLVITALGADRPGIVNTITRHVSSCGCNIE--DSRLAML 44 (190)
T ss_pred ccEEEEEEEcCCCChHHHHHHHHHHHcCCCee--ehhhHhh
Confidence 35566666 8999999999999999999987 6776554
No 158
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=66.10 E-value=72 Score=26.04 Aligned_cols=120 Identities=13% Similarity=0.052 Sum_probs=60.5
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc--
Q 048784 14 AYPNCEAVP-CEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL-- 90 (282)
Q Consensus 14 ~~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I-- 90 (282)
.+|+.++.- ..+-.++.+.+.+|++|+|++.-..-..|. ....+.+.++. +.++-+|-+......+++++
T Consensus 26 ~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~~~~~---~~~~l~~~~~~----lv~~~~h~l~~~~~i~~~dL~~ 98 (198)
T cd08486 26 STPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGI---EIVNIAQEDLY----LAVHRSQSGKFGKTCKLADLRA 98 (198)
T ss_pred hCCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCCCCce---EEEEEeeccEE----EEecCCCccccCCcccHHHHcC
Confidence 357665542 356789999999999999997422111111 01112222332 22344454443333334433
Q ss_pred -cEEEech----HHHHHHHHHHHhcCCe--E-EEecCHHHHHHHhhhcCCCCeEEecChhh
Q 048784 91 -KRVLSHP----QALAQCENTLTKLGLV--R-EAVDDTAGAAKYVSFEQLKDAGAVASSSA 143 (282)
Q Consensus 91 -~~V~SHp----qal~QC~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~AAI~s~~A 143 (282)
.-|.-.+ ....+..+++.+.+.. . ..+++......+++.+ ...+|.+..+
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~ 156 (198)
T cd08486 99 VELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG---AASSIVPASV 156 (198)
T ss_pred CCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---ceEEEcchhh
Confidence 3332111 2345667777776533 2 3345555555566653 3456666554
No 159
>PRK03059 PII uridylyl-transferase; Provisional
Probab=65.29 E-value=30 Score=37.11 Aligned_cols=36 Identities=22% Similarity=0.364 Sum_probs=30.5
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceee--eeeee
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLT--KIESR 217 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt--~IeSR 217 (282)
..|.|.+..+|+||-|+++-++|+.+|+|+. +|.+.
T Consensus 785 ~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~ 822 (856)
T PRK03059 785 QYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTL 822 (856)
T ss_pred CEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeec
Confidence 3577888889999999999999999999987 45544
No 160
>PF01193 RNA_pol_L: RNA polymerase Rpb3/Rpb11 dimerisation domain; InterPro: IPR011261 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. RNA polymerase (RNAP) II, which is responsible for all mRNA synthesis in eukaryotes, consists of 12 subunits. Subunits Rpb3 and Rpb11 form a heterodimer that is functionally analogous to the archaeal RNAP D/L heterodimer, and to the prokaryotic RNAP alpha subunit (RpoA) homodimer. In each case, they play a key role in RNAP assembly by forming a platform on which the catalytic subunits (eukaryotic Rpb1/Rpb2, and prokaryotic beta/beta') can interact []. These different subunits share regions of homology required for dimerisation. In eukaryotic Rpb11 and archaeal L subunits, the dimerisation domain consists of a contiguous Rpb11-like domain, whereas in eukaryotic Rpb3, archaeal D and bacterial RpoA subunits (IPR011263 from INTERPRO), the dimerisation domain consists of the Rpb11-like domain interrupted by an insert domain. In the prokaryotic alpha subunit, this dimerisation domain is the N-terminal domain [].; GO: 0003899 DNA-directed RNA polymerase activity, 0046983 protein dimerization activity, 0006351 transcription, DNA-dependent; PDB: 1HQM_B 1YNJ_A 1YNN_A 1I6V_A 2GHO_A 3HKZ_V 2PMZ_X 2PA8_L 3GTK_C 1TWH_C ....
Probab=65.11 E-value=29 Score=24.62 Aligned_cols=63 Identities=22% Similarity=0.280 Sum_probs=44.8
Q ss_pred EEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHH-HHHHHHHHHhhc
Q 048784 187 VFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQK-AQNALRHLKEFA 265 (282)
Q Consensus 187 ~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~-~~~al~~l~~~~ 265 (282)
-|.+.+..-+|..+|...-...+.-..|...|. ..+|.|.|+-.|...... +.+|++.|++.+
T Consensus 2 ~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~~~~----------------~~~~~~~IeT~g~~~p~~~l~~A~~~l~~~~ 65 (66)
T PF01193_consen 2 EFLLKGEDHTLGNALRRILLSEVPGVAIDGHPN----------------EDKFVFRIETDGSLTPKEALLKAIKILKEKL 65 (66)
T ss_dssp EEEEESHHHHHHHHHHHHHHSSSEEEEEEESSE----------------EEEEEEEEEEBSSS-HHHHHHHHHHHHHHHH
T ss_pred EeEEcCCchHHHHHHHHHHHhcCCCceEEecCC----------------CCEEEEEEEECCCCCHHHHHHHHHHHHHHhc
Confidence 345555566788888877778888777877442 347999999999875443 688888887653
No 161
>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=65.09 E-value=39 Score=22.97 Aligned_cols=27 Identities=30% Similarity=0.356 Sum_probs=23.3
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeee
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIES 216 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeS 216 (282)
+++.||.+.++++.+++.|||+-.|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 37 (66)
T cd04916 11 MKNTVGVSARATAALAKAGINIRMINQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 456799999999999999999987743
No 162
>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=64.37 E-value=72 Score=25.43 Aligned_cols=31 Identities=16% Similarity=0.056 Sum_probs=23.9
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
.+|+.++... .+..++.+.+.+|++|+|++.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (201)
T cd08435 25 RHPRLTVRVVEGTSDELLEGLRAGELDLAIGR 56 (201)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHcCCccEEEEe
Confidence 3566655443 467899999999999999975
No 163
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=64.24 E-value=13 Score=29.23 Aligned_cols=73 Identities=12% Similarity=0.047 Sum_probs=45.7
Q ss_pred CCcHHHHHHHhhCCC-----------CceeecCCHHHHHHHHHcCCCCeEEEeeeecccc-ceeccccccccCCeEEEEE
Q 048784 3 RGAYSESAAEKAYPN-----------CEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGG-SIHRNYDLLLRHRLHIVGE 70 (282)
Q Consensus 3 ~GTfS~~Aa~~~~~~-----------~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G-~V~~t~d~L~~~~l~I~~E 70 (282)
.||+.+..+++..+. .+++.+++..+++.+|.+|+ |..+.. ++... .+.. ..++.++++
T Consensus 20 ~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d--~~~~~~~~~~------~~~~~~~~~ 90 (134)
T smart00079 20 RGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLME--STYLDYELSQ------NCDLMTVGE 90 (134)
T ss_pred cCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEee--hHhHHHHHhC------CCCeEEcCc
Confidence 689999888876543 25678999999999999999 865554 22221 1111 224556665
Q ss_pred EEEeeeeeeeecCC
Q 048784 71 VKFAVRHCLLANPG 84 (282)
Q Consensus 71 ~~l~I~~~L~a~~~ 84 (282)
..-+-..+++.+++
T Consensus 91 ~~~~~~~~ia~~k~ 104 (134)
T smart00079 91 NFGRKGYGIAFPKG 104 (134)
T ss_pred ccCCCceEEEecCC
Confidence 44344455555544
No 164
>cd04918 ACT_AK1-AT_2 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the second of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine (SAM). This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. In its inactive state, Arabidopsis AK1 binds the effectors lysine and SAM (two molecules each) at the interface of two ACT1 domain subunits. The second ACT domain (ACT2), this CD, does not interact with an effector. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=64.12 E-value=47 Score=23.22 Aligned_cols=59 Identities=15% Similarity=0.226 Sum_probs=39.7
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
.+++=.+...||.+.++++.|++.|||+..|-.-++.. .-.|.||- +...++++.|.+
T Consensus 4 VsvVG~~~~~~~~~~~i~~aL~~~~I~v~~i~~g~s~~----------------sis~~v~~------~~~~~av~~Lh~ 61 (65)
T cd04918 4 ISLIGNVQRSSLILERAFHVLYTKGVNVQMISQGASKV----------------NISLIVND------SEAEGCVQALHK 61 (65)
T ss_pred EEEECCCCCCccHHHHHHHHHHHCCCCEEEEEecCccc----------------eEEEEEeH------HHHHHHHHHHHH
Confidence 34443445578999999999999999998776444322 35677764 344567776654
Q ss_pred h
Q 048784 264 F 264 (282)
Q Consensus 264 ~ 264 (282)
.
T Consensus 62 ~ 62 (65)
T cd04918 62 S 62 (65)
T ss_pred H
Confidence 4
No 165
>cd04871 ACT_PSP_2 ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). The ACT_PSP_2 CD includes the second of the two ACT domains found N-terminal of phosphoserine phosphatase (PSP, SerB). PSPs belong to the L-2-haloacid dehalogenase-like protein superfamily. PSP is involved in serine metabolism; serine is synthesized from phosphoglycerate through sequential reactions catalyzed by 3-phosphoglycerate dehydrogenase (SerA), 3-phosphoserine aminotransferase (SerC), and SerB. Members of this CD belong to the superfamily of ACT regulatory domains
Probab=63.98 E-value=24 Score=26.45 Aligned_cols=67 Identities=18% Similarity=0.100 Sum_probs=40.5
Q ss_pred CC-CccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCC-CcHHHHHHHHHHHhh
Q 048784 191 EE-GPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASM-ADQKAQNALRHLKEF 264 (282)
Q Consensus 191 ~~-~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~-~~~~~~~al~~l~~~ 264 (282)
++ .+|.++++=+.++.+|+|+.+|...-.. .++. .+. ....|..-+++++.. +...++++|.++.+.
T Consensus 7 ~~~~a~~ia~Vs~~lA~~~~NI~~I~~l~~~-~~~~-~~~-----~~~~~~~e~~v~~~~~~~~~lr~~L~~la~e 75 (84)
T cd04871 7 RPLTAEQLAAVTRVVADQGLNIDRIRRLSGR-VPLE-EQD-----DSPKACVEFSVRGQPADLEALRAALLELASE 75 (84)
T ss_pred CcCCHHHHHHHHHHHHHcCCCHHHHHHhhcc-cccc-ccC-----CCCcEEEEEEEeCCCCCHHHHHHHHHHHhcc
Confidence 45 7899999999999999998888763111 0000 000 112465555666543 334677777776544
No 166
>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=63.58 E-value=13 Score=33.47 Aligned_cols=43 Identities=16% Similarity=0.108 Sum_probs=34.7
Q ss_pred CCCcHHHHHHHhh-CCCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 2 VRGAYSESAAEKA-YPNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 2 P~GTfS~~Aa~~~-~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
+.|++.+...+.. ++..+++.+++..+++++|.+|++|+.+..
T Consensus 150 ~~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d 193 (275)
T TIGR02995 150 PGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGRADAYSLT 193 (275)
T ss_pred eCCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCCCCEEecC
Confidence 4677777776653 455678899999999999999999988864
No 167
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=62.85 E-value=5 Score=35.43 Aligned_cols=58 Identities=21% Similarity=0.228 Sum_probs=42.1
Q ss_pred ceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccc------cCCeEEEEEEEEeeeeeeeecCCC
Q 048784 19 EAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLL------RHRLHIVGEVKFAVRHCLLANPGV 85 (282)
Q Consensus 19 ~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~------~~~l~I~~E~~l~I~~~L~a~~~~ 85 (282)
..++..+...++.+|.+|++|.|+++- .+++.+. ..+++|.++...-..+.++++++.
T Consensus 139 ~~~~~~~~~~~~~~l~~G~~Da~~~~~---------~~~~~~~~~~~~~~~~~rvl~~s~~~p~~~~~~~~~~ 202 (243)
T PF12974_consen 139 KQVFVGSHDAVLEALLNGKADAAAIPS---------DAFERLEAEGPDIPSQLRVLWTSPPYPNWPLVASPDL 202 (243)
T ss_dssp SEEEEE-HHHHHHHHHTTSSSEEEEEH---------HHHHHHHHH-HHHHTTEEEEEEEEEEE--EEEEETTS
T ss_pred eEEEeCCHHHHHHHHHcCCccEEEEec---------hhHHHHHHccCcccccEEEEEEeCCCCCcEEEEeCCC
Confidence 456788999999999999999999873 3444332 246999998877777788887753
No 168
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=61.54 E-value=20 Score=32.17 Aligned_cols=88 Identities=11% Similarity=0.081 Sum_probs=49.1
Q ss_pred CCcHHHHHHHhhC----CCCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeee
Q 048784 3 RGAYSESAAEKAY----PNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHC 78 (282)
Q Consensus 3 ~GTfS~~Aa~~~~----~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~ 78 (282)
.||..+.....+. ...+++.+++..+++++|.+|++|..+..- ..+.+. ......++.+..-+..++
T Consensus 155 ~gs~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~l~~GrvDa~~~d~-~~~~~~--------~~~~~~~~~~~~~~~~~~ 225 (259)
T PRK11917 155 QAATTKKAIGEAAKKIGIDVKFSEFPDYPSIKAALDAKRVDAFSVDK-SILLGY--------VDDKSEILPDSFEPQSYG 225 (259)
T ss_pred cCCcHHHHHHHhhHhcCCceeEEecCCHHHHHHHHHcCCCcEEEecH-HHHHHh--------hhcCCeecCCcCCCCceE
Confidence 4565554333322 234677899999999999999999776521 111111 111222333332233345
Q ss_pred eeecCCCCCCCccEEEechHHHHHHHHHHHhc
Q 048784 79 LLANPGVKVEDLKRVLSHPQALAQCENTLTKL 110 (282)
Q Consensus 79 L~a~~~~~l~~I~~V~SHpqal~QC~~fl~~~ 110 (282)
++.+++ +++-..+..++|.++
T Consensus 226 ~a~~k~-----------~~~l~~~ln~~l~~~ 246 (259)
T PRK11917 226 IVTKKD-----------DPAFAKYVDDFVKEH 246 (259)
T ss_pred EEEeCC-----------CHHHHHHHHHHHHHH
Confidence 555544 466677777777654
No 169
>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=61.42 E-value=82 Score=25.10 Aligned_cols=32 Identities=19% Similarity=0.066 Sum_probs=24.2
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEee
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPi 45 (282)
.+|+.++.... +-.++++.+.+|++|+|++..
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08450 25 EHPDLDVELSSLFSPQLAEALMRGKLDVAFMRP 57 (196)
T ss_pred hCCCcEEEEEecChHHHHHHHhcCCccEEEEeC
Confidence 35776665444 467899999999999999753
No 170
>PRK03381 PII uridylyl-transferase; Provisional
Probab=60.78 E-value=38 Score=35.90 Aligned_cols=36 Identities=11% Similarity=0.183 Sum_probs=30.2
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeee
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRP 218 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP 218 (282)
-|.|.+..+|+||-|+++-++|+.+|+|+..-..--
T Consensus 707 ~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T 742 (774)
T PRK03381 707 ATVLEVRAADRPGLLARLARALERAGVDVRWARVAT 742 (774)
T ss_pred eEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEee
Confidence 467777889999999999999999999998554443
No 171
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=60.64 E-value=43 Score=36.21 Aligned_cols=35 Identities=23% Similarity=0.311 Sum_probs=30.3
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceee--eeeee
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLT--KIESR 217 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt--~IeSR 217 (282)
-|.|.+..+|+||-|+++-++|+..|+|+. +|.+.
T Consensus 814 ~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~ 850 (895)
T PRK00275 814 VTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATL 850 (895)
T ss_pred eEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEec
Confidence 577788889999999999999999999987 55555
No 172
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=60.26 E-value=25 Score=35.37 Aligned_cols=59 Identities=20% Similarity=0.390 Sum_probs=44.4
Q ss_pred EEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 186 IVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 186 i~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
|-+...|+.|--.++|..|..++|||..||=-|.. ..|++|. ..+....+.+++++++.
T Consensus 3 l~~~~~dr~g~~~~~l~~~~~~~~~~~~~e~~~~~-------------------~~~~~~~-~~~~~~~~~~~~~~~~~ 61 (520)
T PRK10820 3 LEVFCEDRLGLTRELLDLLVLRSIDLRGIEIDPIG-------------------RIYLNFA-ELEFESFSSLMAEIRRI 61 (520)
T ss_pred EEEEeeccccHHHHHHHHHHhcCCCccEEEEcCCC-------------------eEEEeCC-CcChhhHHHHHHHHhcC
Confidence 44566799999999999999999999999975531 3677776 34444567778887654
No 173
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=59.84 E-value=1.3e+02 Score=26.86 Aligned_cols=32 Identities=6% Similarity=-0.052 Sum_probs=24.6
Q ss_pred hCCCCcee-ecCCHHHHHHHHHcCCCCeEEEee
Q 048784 14 AYPNCEAV-PCEQFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 14 ~~~~~~~~-~~~s~~~v~~av~~g~~d~gVvPi 45 (282)
.+|+.++. -.....++++.+.+|++|+|+...
T Consensus 114 ~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~~ 146 (275)
T PRK03601 114 NQEALQFEARIAQRQSLVKQLHERQLDLLITTE 146 (275)
T ss_pred hCCCcEEEEEECChHHHHHHHHcCCCCEEEEcC
Confidence 45666654 355677999999999999999753
No 174
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=59.68 E-value=34 Score=33.92 Aligned_cols=42 Identities=14% Similarity=0.215 Sum_probs=31.3
Q ss_pred CCcHHHHHHHh---hCCCCc--eeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 3 RGAYSESAAEK---AYPNCE--AVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 3 ~GTfS~~Aa~~---~~~~~~--~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
.||..++...+ .+++.. .+.+.+.++++++|.+|++|+.|+.
T Consensus 156 ~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d 202 (482)
T PRK10859 156 AGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIAD 202 (482)
T ss_pred CCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEEC
Confidence 57776665543 245543 3567899999999999999999874
No 175
>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=59.59 E-value=95 Score=25.24 Aligned_cols=31 Identities=13% Similarity=0.108 Sum_probs=24.5
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEe
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvP 44 (282)
.+|+.++.... +-+++++++.+|++|.|+++
T Consensus 26 ~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~ 57 (198)
T cd08485 26 VAPSATVSLTQMSKNRQIEALDAGTIDIGFGR 57 (198)
T ss_pred hCCCcEEEEEECCHHHHHHHHHcCCccEEEec
Confidence 35777665543 67789999999999999985
No 176
>PRK05007 PII uridylyl-transferase; Provisional
Probab=59.12 E-value=47 Score=35.81 Aligned_cols=32 Identities=16% Similarity=0.170 Sum_probs=28.3
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeee
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKI 214 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~I 214 (282)
-|.|.+..+|+||-|+++.++|+.+|+|+..-
T Consensus 701 ~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A 732 (884)
T PRK05007 701 GTEIFIWSPDRPYLFAAVCAELDRRNLSVHDA 732 (884)
T ss_pred eEEEEEEecCCcCHHHHHHHHHHHCCCEEEEE
Confidence 47777888999999999999999999998743
No 177
>cd04915 ACT_AK-Ectoine_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase of the ectoine (1,4,5,6-tetrahydro-2-methyl pyrimidine-4-carboxylate) biosynthetic pathway found in Methylomicrobium alcaliphilum, Vibrio cholerae, and various other halotolerant or halophilic bacteria. Bacteria exposed to hyperosmotic stress accumulate organic solutes called 'compatible solutes' of which ectoine, a heterocyclic amino acid, is one. Apart from its osmotic function, ectoine also exhibits a protective effect on proteins, nucleic acids and membranes against a variety of stress factors. de novo synthesis of ectoine starts with the phosphorylation of L-aspartate and shares its first two enzymatic steps with the biosynthesis of amino acids of the aspartate family: aspartokinas
Probab=59.02 E-value=49 Score=23.37 Aligned_cols=50 Identities=30% Similarity=0.326 Sum_probs=37.2
Q ss_pred CccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 193 GPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 193 ~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+||.+.++++.+++.|||+..|-.-++.. .-.|.|+- ....++++.|.+.
T Consensus 14 ~~gv~~ki~~~L~~~~I~v~~i~~~~s~~----------------~is~~V~~------~~~~~av~~Lh~~ 63 (66)
T cd04915 14 TPGVLARGLAALAEAGIEPIAAHQSMRNV----------------DVQFVVDR------DDYDNAIKALHAA 63 (66)
T ss_pred cchHHHHHHHHHHHCCCCEEEEEecCCee----------------EEEEEEEH------HHHHHHHHHHHHH
Confidence 78999999999999999998877766432 35577764 4556777777654
No 178
>cd04911 ACT_AKiii-YclM-BS_1 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the first of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. Bacillus subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from Bacillus subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=58.93 E-value=41 Score=25.10 Aligned_cols=57 Identities=21% Similarity=0.208 Sum_probs=40.4
Q ss_pred CCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhcC
Q 048784 191 EEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFAT 266 (282)
Q Consensus 191 ~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~~ 266 (282)
....|-+.++|++|.++||+.-++ |+.- ......|+=.- ..+++.++.+++|++.+.
T Consensus 12 n~evGF~rk~L~I~E~~~is~Eh~---PSGI---------------D~~Siii~~~~-~~~~~~~~i~~~i~~~~~ 68 (76)
T cd04911 12 NREVGFGRKLLSILEDNGISYEHM---PSGI---------------DDISIIIRDNQ-LTDEKEQKILAEIKEELH 68 (76)
T ss_pred cchhcHHHHHHHHHHHcCCCEeee---cCCC---------------ccEEEEEEccc-cchhhHHHHHHHHHHhcC
Confidence 457899999999999999987665 5432 23555555332 333488899999998654
No 179
>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=58.86 E-value=91 Score=24.80 Aligned_cols=122 Identities=15% Similarity=0.070 Sum_probs=59.6
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCC---C
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVE---D 89 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~---~ 89 (282)
.+|+.++... .+-.++++.+.+|++|+|++.-.....|.. ...|.+..+. +..+-.|-|...+..+++ +
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~----~~~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08412 25 AYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIA---FEPLARLPPY----VWLPADHPLAGKDEVSLADLAA 97 (198)
T ss_pred HCCCcEEEEEECCHHHHHHHHHcCCCcEEEEcCCCCCcccc---eeeeeccceE----EEecCCCCCCCCCcCCHHHHcC
Confidence 3566655433 357889999999999999984332111111 1112222221 222334444332222222 2
Q ss_pred ccEEE-echHHHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 90 LKRVL-SHPQALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 90 I~~V~-SHpqal~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
..-|. .......+-.+|+.+.+.. ...+.+...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (198)
T cd08412 98 EPLILLDLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANG---LGYSLLNDRPYR 154 (198)
T ss_pred CcEEecCchhHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CCEEEeeccccc
Confidence 23332 2222223344566655432 23456666666677654 345677666554
No 180
>PF07485 DUF1529: Domain of Unknown Function (DUF1259); InterPro: IPR011094 This family is the lppY/lpqO homologue family. They are related to 'probable conserved lipoproteins' LppY and LpqO from Mycobacterium bovis.
Probab=58.64 E-value=37 Score=27.73 Aligned_cols=52 Identities=19% Similarity=0.238 Sum_probs=40.6
Q ss_pred ccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHH
Q 048784 194 PGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRH 260 (282)
Q Consensus 194 pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~ 260 (282)
+..+..+++.+.++||.+|-|.+--...+| =+||+.++++-+..++.+.++.
T Consensus 67 ~~EV~pvi~aL~~~GI~vtAlHNH~l~e~P---------------rl~ymH~~~~gdp~~lA~~vr~ 118 (123)
T PF07485_consen 67 EDEVNPVISALRKNGIEVTALHNHWLFEQP---------------RLFYMHIWGVGDPAKLARKVRA 118 (123)
T ss_pred HHHHHHHHHHHHHCCceEEEEecccccCCC---------------CEEEEEEEecCCHHHHHHHHHH
Confidence 345667888889999999999998888766 3899999998766566555544
No 181
>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=58.05 E-value=95 Score=24.79 Aligned_cols=31 Identities=13% Similarity=-0.002 Sum_probs=23.2
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEee
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPi 45 (282)
+|+.++... .+..++++.+.+|++|+|+..-
T Consensus 27 ~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~ 58 (197)
T cd08425 27 YPGIALSLREMPQERIEAALADDRLDLGIAFA 58 (197)
T ss_pred CCCcEEEEEECcHHHHHHHHHcCCccEEEEec
Confidence 466655443 3567899999999999999753
No 182
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=57.21 E-value=20 Score=32.85 Aligned_cols=44 Identities=20% Similarity=0.130 Sum_probs=36.7
Q ss_pred CCCcHHHHHHHhhC--C--CCceeecCCHHHHHHHHHcCCCCeEEEee
Q 048784 2 VRGAYSESAAEKAY--P--NCEAVPCEQFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 2 P~GTfS~~Aa~~~~--~--~~~~~~~~s~~~v~~av~~g~~d~gVvPi 45 (282)
|.|-|++++....- . ...++.-.+..+++.-|++|++|+|+|=.
T Consensus 147 P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~ 194 (258)
T COG0725 147 PAGKYAKEALELLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYV 194 (258)
T ss_pred CchHHHHHHHHHhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEE
Confidence 88999999987641 1 34788999999999999999999999854
No 183
>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=57.05 E-value=69 Score=22.85 Aligned_cols=27 Identities=22% Similarity=0.342 Sum_probs=23.6
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeee
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIES 216 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeS 216 (282)
+.+.+|.+.++++.|++++||+-.|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~~ 37 (80)
T cd04921 11 MVGVPGIAARIFSALARAGINVILISQ 37 (80)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEe
Confidence 456899999999999999999987754
No 184
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=56.97 E-value=7.2 Score=32.96 Aligned_cols=63 Identities=19% Similarity=0.393 Sum_probs=39.9
Q ss_pred HHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHH--HHh--hcCceEEEcc
Q 048784 198 FKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRH--LKE--FATFLRVLGS 273 (282)
Q Consensus 198 ~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~--l~~--~~~~v~~LGs 273 (282)
.+.|+++++|||.++|. +|+.+... + +.++|+|=+ ++.+++++++. ... .-..|.+||+
T Consensus 58 ~R~~s~lK~hGI~~~H~-aRqit~~D------F----~~FDYI~~M------DesN~~dL~~~a~~~~~~~kakV~Llgs 120 (159)
T KOG3217|consen 58 PRTLSILKKHGIKIDHL-ARQITTSD------F----REFDYILAM------DESNLRDLLRKASNQPKGSKAKVLLLGS 120 (159)
T ss_pred hHHHHHHHHcCCcchhh-cccccHhH------h----hhcceeEEe------cHHHHHHHHHHhccCCCCcceEEEEeec
Confidence 48899999999997775 78877632 2 234555433 45565555553 221 1235999999
Q ss_pred ccCC
Q 048784 274 YPID 277 (282)
Q Consensus 274 Y~~~ 277 (282)
|-..
T Consensus 121 y~~~ 124 (159)
T KOG3217|consen 121 YDKN 124 (159)
T ss_pred cCCC
Confidence 9754
No 185
>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=56.54 E-value=1e+02 Score=24.74 Aligned_cols=121 Identities=18% Similarity=0.154 Sum_probs=59.7
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc---
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL--- 90 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I--- 90 (282)
+|+.++.... +..++.+.+.+|++|+|+.+......+ + ....|.+.++.+ +.+-+|-+...+ .+++++
T Consensus 26 ~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~-l--~~~~l~~~~~~~----v~~~~~~l~~~~-i~~~~L~~~ 97 (201)
T cd08459 26 APGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAG-F--FQQRLFRERYVC----LVRKDHPRIGST-LTLEQFLAA 97 (201)
T ss_pred CCCCeEEEEecCccCHHHHhhCCCceEEEEcCCCCccc-c--eEEEeecCceEE----EEcCCCccccCC-cCHHHHhhC
Confidence 5666554443 445889999999999999764321111 1 111222223322 233444443221 233322
Q ss_pred cEEEechH--HHHHHHHHHHhcCCe--E-EEecCHHHHHHHhhhcCCCCeEEecChhhHHH
Q 048784 91 KRVLSHPQ--ALAQCENTLTKLGLV--R-EAVDDTAGAAKYVSFEQLKDAGAVASSSAAAI 146 (282)
Q Consensus 91 ~~V~SHpq--al~QC~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ 146 (282)
.-|...+. ...+.++|+.+++.. . ..++|.....++++.+ ...++.+...++.
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (201)
T cd08459 98 RHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQT---DLVATVPERLARL 155 (201)
T ss_pred CcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcC---CEEEecHHHHHHH
Confidence 22332221 123456677666442 2 2344444455666653 4577878776653
No 186
>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=55.93 E-value=1e+02 Score=24.58 Aligned_cols=123 Identities=20% Similarity=0.183 Sum_probs=60.6
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc--
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL-- 90 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I-- 90 (282)
.+|+.++.... +-+++.+.+.+|++|+|++.......+.. ...|.+.++.++. +-.|-+.. ...+++++
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~---~~~l~~~~~~lv~----~~~~p~~~-~~~~~~~L~~ 96 (198)
T cd08461 25 EAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLR---SRPLFEERYVCVT----RRGHPLLQ-GPLSLDQFCA 96 (198)
T ss_pred HCCCcEEEEeeCCcccHHHHHhcCCCcEEEecCccCCccce---eeeeecCcEEEEE----cCCChhhc-CCCCHHHHhh
Confidence 35776655443 35678999999999999975332111111 1122233333222 22332222 11222222
Q ss_pred -cEEEechHH---HHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHHHc
Q 048784 91 -KRVLSHPQA---LAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIY 147 (282)
Q Consensus 91 -~~V~SHpqa---l~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~y 147 (282)
.-|.-.+.. -.+-.+|+.+.+.. ...+.|...+..+++.+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~ 157 (198)
T cd08461 97 LDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAAT---DMVAFVPSRLVPNL 157 (198)
T ss_pred CCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcC---CeEEEchHHHHHhh
Confidence 223222111 12345667665432 23455656666667654 45678887766544
No 187
>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=55.26 E-value=56 Score=34.96 Aligned_cols=32 Identities=16% Similarity=0.339 Sum_probs=28.4
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeee
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKI 214 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~I 214 (282)
-|-|.+..+|+||-|+++.++|+.+|+|+..=
T Consensus 668 ~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A 699 (850)
T TIGR01693 668 GTEVFIYAPDQPGLFAKVAGALAMLSLSVHDA 699 (850)
T ss_pred eEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEE
Confidence 57788888999999999999999999998743
No 188
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=55.00 E-value=1.6e+02 Score=26.33 Aligned_cols=121 Identities=12% Similarity=0.066 Sum_probs=60.7
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCC---CC
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKV---ED 89 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l---~~ 89 (282)
.+|+.++.... +.+++++.+.+|++|+|++.-.....+ -....|.+.++.++ .+-.|-|......++ .+
T Consensus 115 ~~p~v~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~---l~~~~l~~~~~~~v----~~~~~pl~~~~~i~~~~L~~ 187 (296)
T PRK09906 115 RHPDTLIELVSLITTQQEEKLRRGELDVGFMRHPVYSDE---IDYLELLDEPLVVV----LPVDHPLAHEKEITAAQLDG 187 (296)
T ss_pred HCCCeEEEEEeCCcHHHHHHHHcCCeeEEEecCCCCCCC---ceEEEEecccEEEE----ecCCCccccCCCcCHHHHcC
Confidence 35666655443 468899999999999999854321111 11123333333322 233343432222222 23
Q ss_pred ccEEEech---H-HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhH
Q 048784 90 LKRVLSHP---Q-ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAA 144 (282)
Q Consensus 90 I~~V~SHp---q-al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa 144 (282)
..-|.--+ . ...+...|+...++. ...++|......+++.+ .+ .++.+...+
T Consensus 188 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~g-~~~~p~~~~ 246 (296)
T PRK09906 188 VNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG--LG-CTIIPGYMN 246 (296)
T ss_pred CCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC--Cc-EEEeeHHHh
Confidence 33332211 1 134456677765442 23456666666777754 33 455555544
No 189
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=54.61 E-value=1.6e+02 Score=26.22 Aligned_cols=121 Identities=12% Similarity=0.073 Sum_probs=59.4
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCC-CCCC---C
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPG-VKVE---D 89 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~-~~l~---~ 89 (282)
+|+..+... .+..++.+.+.+|++|+|+++......+... ..|.+.++.+ +.+-+|-|...+. .+++ +
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 466666554 4568899999999999999864433222211 1222223322 2223333322211 1222 2
Q ss_pred ccEEEechHHH--HHHHHHHHhcCCe--E-EEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 90 LKRVLSHPQAL--AQCENTLTKLGLV--R-EAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 90 I~~V~SHpqal--~QC~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
-.-|.-.+... ..-..|+.+.+.. . ..+.|-..+.++++.+ . ..++.++..++
T Consensus 190 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~-gi~~~p~~~~~ 247 (296)
T PRK11242 190 EPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG--R-LATLLPAAIAR 247 (296)
T ss_pred CCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhC--C-eEEEeehhhcc
Confidence 23333333321 2234556655433 2 3345555666777765 2 35666665544
No 190
>PRK09224 threonine dehydratase; Reviewed
Probab=54.21 E-value=33 Score=34.46 Aligned_cols=35 Identities=26% Similarity=0.393 Sum_probs=30.9
Q ss_pred cEEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeee
Q 048784 182 FKTSIVFSLEEGPGVLFKALAVFALRQINLTKIESR 217 (282)
Q Consensus 182 ~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSR 217 (282)
+...+.|..|.+||+|.+.|+.+. -+-|+|.++=|
T Consensus 422 ~e~~~~~~fPerpGal~~Fl~~l~-~~~~It~f~Yr 456 (504)
T PRK09224 422 DERLYRFEFPERPGALLKFLSTLG-THWNISLFHYR 456 (504)
T ss_pred ceEEEEEeCCCCCCHHHHHHHhcC-CCCeeEEEEEc
Confidence 356788899999999999999887 68899999998
No 191
>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=53.77 E-value=1.6e+02 Score=26.24 Aligned_cols=121 Identities=21% Similarity=0.190 Sum_probs=59.2
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeecc--ccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCcc
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSL--GGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLK 91 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~--~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~ 91 (282)
+|+.++.... +-.++++++.+|++|+|++...+.. .+.. +..|.+.++.++ ++-.|-|...+..+++|+.
T Consensus 119 ~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~~---~~~l~~~~~~~~----~~~~hpl~~~~~i~~~dL~ 191 (300)
T TIGR02424 119 APRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGLS---FEHLYNEPVVFV----VRAGHPLLAAPSLPVASLA 191 (300)
T ss_pred CCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCccccccee---eeeecCCceEEE----EcCCCccccCCCCCHHHHh
Confidence 5666554443 6678999999999999997443221 1111 112222232222 2223434332222233322
Q ss_pred --EEEechHH---HHHHHHHHHhcCCe----EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 --RVLSHPQA---LAQCENTLTKLGLV----REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 --~V~SHpqa---l~QC~~fl~~~~~~----~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
..+..+.. ......|+.+++.. ...+.+......++..+ ...++.+...++
T Consensus 192 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 251 (300)
T TIGR02424 192 DYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQES---DAIWIISRGVVA 251 (300)
T ss_pred CCCEEecCCCCchHHHHHHHHHHCCCCCCCceEEeccHHHHHHHHHhC---CceEeCcHHHHh
Confidence 12222222 13345677665432 24456666666666654 335666666654
No 192
>PF11966 SSURE: Fibronectin-binding repeat; InterPro: IPR021021 Streptococcal surface repeat domain - SSURE - is a protein fragment found to bind to extracellular matrix protein fibronectin but not to collagen or submaxillary mucin in Streptococci. Anti-SSURE antibodies recognised the corresponding protein on the surface of streptococcal cells. The full-length proteins are thus fibronectin-binding surface adhesins []. The proteins are further characterised by having an N-terminal motif resembling [YF]SIRKxxxGxxS[VIA] IPR005877 from INTERPRO and a C-terminal LPXTG motif-containing region which is a characteristic of many surface proteins of Streptococcus and Streptomyces species. Cleavage between the Thr and Gly by sortase or a related enzyme leads to covalent anchoring at the new C-terminal Thr to the cell wall (see IPR019931 from INTERPRO).
Probab=53.16 E-value=32 Score=25.75 Aligned_cols=38 Identities=26% Similarity=0.442 Sum_probs=30.1
Q ss_pred ceeEEEEEEeecCCCcHHHHHHHHHHHhhcC-----ceEEEcc
Q 048784 236 YFDYLFYVDFEASMADQKAQNALRHLKEFAT-----FLRVLGS 273 (282)
Q Consensus 236 ~~~y~F~vd~~g~~~~~~~~~al~~l~~~~~-----~v~~LGs 273 (282)
.+.|+|=||+.|+.....=+++|..|+.... .|++-|.
T Consensus 18 kGkYFYqV~L~Gnt~Gk~~q~LLDqlraNGt~tY~ATv~VYga 60 (81)
T PF11966_consen 18 KGKYFYQVDLNGNTAGKQGQALLDQLRANGTHTYQATVKVYGA 60 (81)
T ss_pred CccEEEEEecCCcccCcchHHHHHHHHhCCceeeEEEEEEEec
Confidence 4589999999998777777889999987644 3777776
No 193
>PRK09034 aspartate kinase; Reviewed
Probab=53.02 E-value=2.1e+02 Score=28.22 Aligned_cols=124 Identities=16% Similarity=0.070 Sum_probs=69.6
Q ss_pred EEEecCHHHHHHHhhhcCCCCeEEecChhh---HHHcCCceeecccccCCCCceEEEEEeeCCCCC-C-----CCCCcEE
Q 048784 114 REAVDDTAGAAKYVSFEQLKDAGAVASSSA---AAIYGLNILAEDIQDDCDNVTRFLMLAREPIIP-G-----TDRPFKT 184 (282)
Q Consensus 114 ~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~A---a~~ygL~vl~~~I~d~~~N~TRF~vl~~~~~~~-~-----~~~~~kt 184 (282)
....-|-.+|.++...+ |-+=.+.| |..+++++...+..+....-|..- ....... . ....+-+
T Consensus 237 ~l~~lsy~Ea~ela~~G-----akvlhp~ai~~a~~~~Ipi~v~~~~~p~~~GT~I~--~~~~~~~~~~Vk~It~~~~i~ 309 (454)
T PRK09034 237 SIKEITYREMRELSYAG-----FSVFHDEALIPAYRGGIPINIKNTNNPEDPGTLIV--PDRDNKNKNPITGIAGDKGFT 309 (454)
T ss_pred ECCccCHHHHHHHHhCC-----cccCCHHHHHHHHHcCCCEEEEcCCCCCCCccEEE--eccccCccccceEEEecCCEE
Confidence 34455677787775432 12222222 356899999998876554555542 2211110 0 0011223
Q ss_pred EEEEE---cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHH
Q 048784 185 SIVFS---LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHL 261 (282)
Q Consensus 185 si~~~---~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l 261 (282)
.|.+. ..+.||.+.++++.|+++|||.-.| |. + .....|+|+=+ ..+...+.+++++|
T Consensus 310 ~Itv~~~~~~~~~g~~a~if~~la~~~I~Vd~i---~s-s--------------~~sis~~v~~~-~~~~a~~~~l~~el 370 (454)
T PRK09034 310 SIYISKYLMNREVGFGRKVLQILEDHGISYEHM---PS-G--------------IDDLSIIIRER-QLTPKKEDEILAEI 370 (454)
T ss_pred EEEEccCCCCCCccHHHHHHHHHHHcCCeEEEE---cC-C--------------CcEEEEEEeHH-HhhHHHHHHHHHHH
Confidence 33332 3457999999999999999999888 22 1 13678888842 22111225666776
Q ss_pred Hh
Q 048784 262 KE 263 (282)
Q Consensus 262 ~~ 263 (282)
++
T Consensus 371 ~~ 372 (454)
T PRK09034 371 KQ 372 (454)
T ss_pred HH
Confidence 53
No 194
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=52.80 E-value=24 Score=30.84 Aligned_cols=42 Identities=26% Similarity=0.253 Sum_probs=33.6
Q ss_pred CCcH--HHHHHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 3 RGAY--SESAAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 3 ~GTf--S~~Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
.||. .+..+....+..+++.+++..+++.++.+|++|..+..
T Consensus 153 ~gt~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d 196 (275)
T COG0834 153 LGTTDEAEEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSD 196 (275)
T ss_pred cCcchhHHHHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcc
Confidence 4666 45555555567899999999999999999999999864
No 195
>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=52.06 E-value=1.3e+02 Score=24.40 Aligned_cols=120 Identities=16% Similarity=0.062 Sum_probs=59.0
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeec-cccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc--
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENS-LGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL-- 90 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS-~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I-- 90 (282)
+|+.++.... +-.++.+++.+|++|+|+.+-... ..+.. ...|.+.++. ++.+-.|-|......+++++
T Consensus 26 ~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~~l~~~~~~----~v~~~~hpl~~~~~i~~~~l~~ 98 (198)
T cd08413 26 YPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDLV---TLPCYRWNHC----VIVPPGHPLADLGPLTLEDLAQ 98 (198)
T ss_pred CCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCcE---EEEeeeeeEE----EEecCCCcccccCCCCHHHHhc
Confidence 5666655444 456899999999999999752110 01111 0112222221 22344554543322333332
Q ss_pred -cEEEec-hH-HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhH
Q 048784 91 -KRVLSH-PQ-ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAA 144 (282)
Q Consensus 91 -~~V~SH-pq-al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa 144 (282)
.-|.-. .. -..+-+.|+.+.+.. ...++|......+++.+ .+ .|+.+..++
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~G-i~~lp~~~~ 155 (198)
T cd08413 99 YPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLG--LG-VGIIAEMAY 155 (198)
T ss_pred CCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhC--CC-EEEcccccc
Confidence 223211 11 223445666665432 23456666677777765 33 466665544
No 196
>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=52.03 E-value=1.3e+02 Score=28.32 Aligned_cols=130 Identities=12% Similarity=0.028 Sum_probs=66.1
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEE-EeeeeeeeecCCCCCCCc--cEE
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVK-FAVRHCLLANPGVKVEDL--KRV 93 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~-l~I~~~L~a~~~~~l~~I--~~V 93 (282)
+++++.+.+-.++++++.+|++|+|.+--.-++.... -...++.|+.-.. -.-...+++++..+++|. |+|
T Consensus 36 ~Ve~~~f~~~~~~l~Al~aG~iD~~~~g~~~~~~~~~------a~g~~~~iv~v~~~~~g~~~ivv~~i~svaDLKGKkI 109 (328)
T TIGR03427 36 TIEVVQINDYVESINQYTAGKFDGCTMTNMDALTIPA------AGGVDTTALIVGDFSNGNDGIVLKGGKSLADLKGQKV 109 (328)
T ss_pred eEEEEECCChHHHHHHHHcCCCCEEeecCHHHHHHHH------hCCCCeEEEEEEccCCCceEEEECCCCCHHHcCCCEE
Confidence 4688999999999999999999998652110000000 0112222221111 111134555555566777 488
Q ss_pred EechHHHHH--HHHHHHhcCC-----eEEEecCHHHHHHHhhhcCCCCeEEecChhhHH---HcCCceeec
Q 048784 94 LSHPQALAQ--CENTLTKLGL-----VREAVDDTAGAAKYVSFEQLKDAGAVASSSAAA---IYGLNILAE 154 (282)
Q Consensus 94 ~SHpqal~Q--C~~fl~~~~~-----~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~---~ygL~vl~~ 154 (282)
..++-...+ ..+.|++.+. +.+... .+.+...+..++ -+++++-.+..+. ..|..+|..
T Consensus 110 av~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~-~~d~~aAl~~G~-VDAa~~~eP~~s~~~~~~g~~~l~~ 178 (328)
T TIGR03427 110 NLVELSVSHYLLARALESVGLSEKDVKVVNTS-DADIVAAFITKD-VTAVVTWNPQLSEIKAQPGANEVFD 178 (328)
T ss_pred eccCCChHHHHHHHHHHHcCCCHHHeEEEeCC-hHHHHHHHhcCC-CcEEEEcCchHHHHHhCCCcEEecc
Confidence 665544433 3445665543 334443 344555555442 3444444444332 246666654
No 197
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=51.66 E-value=1.9e+02 Score=26.27 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=24.3
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCCCeEEEeeee
Q 048784 15 YPNCEAVP-CEQFDTAFEAVERWLVDRAVLPIEN 47 (282)
Q Consensus 15 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiEN 47 (282)
+|+.++.. ..+-.+++++|.+|++|+|+++..+
T Consensus 123 ~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~ 156 (312)
T PRK10341 123 FPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSN 156 (312)
T ss_pred CCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCc
Confidence 46665543 3346899999999999999986543
No 198
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=51.29 E-value=60 Score=34.74 Aligned_cols=32 Identities=28% Similarity=0.274 Sum_probs=29.0
Q ss_pred CcEEEEEEEcCCCccHHHHHHHHHHHCCceee
Q 048784 181 PFKTSIVFSLEEGPGVLFKALAVFALRQINLT 212 (282)
Q Consensus 181 ~~ktsi~~~~~~~pG~L~~~L~~F~~~~INlt 212 (282)
..+|.|=+...|+||.|+.+.++|++.++++.
T Consensus 789 ~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~ 820 (867)
T COG2844 789 NDKTVLEVRALDRPGLLAALAGVFADLGLSLH 820 (867)
T ss_pred CCceEEEEEeCCcccHHHHHHHHHHhccccee
Confidence 34788888889999999999999999999987
No 199
>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=50.94 E-value=1.2e+02 Score=23.83 Aligned_cols=30 Identities=20% Similarity=0.067 Sum_probs=23.0
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
+|+.++.-. .+..++.+.+.+|++|.|+..
T Consensus 26 ~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~ 56 (197)
T cd08440 26 HPGIRVRLRDVSAEQVIEAVRSGEVDFGIGS 56 (197)
T ss_pred CCCcEEEEEeCChHHHHHHHHcCCccEEEEe
Confidence 566655433 356889999999999999975
No 200
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=49.84 E-value=1.4e+02 Score=25.75 Aligned_cols=114 Identities=18% Similarity=0.179 Sum_probs=59.0
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCC----CCCCc--
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGV----KVEDL-- 90 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~----~l~~I-- 90 (282)
+.++++. +..++++++.+|++|.++.++..+.+-. ..+. ...++. .....++.+.+. .++++
T Consensus 64 ~~~~~~~-~~~~~~~~l~~G~~D~~~~~~~~~~~r~--~~~~--~s~p~~-------~~~~~~~~~~~~~~~~~~~dl~g 131 (250)
T TIGR01096 64 KCKFVEQ-NFDGLIPSLKAKKVDAIMATMSITPKRQ--KQID--FSDPYY-------ATGQGFVVKKGSDLAKTLEDLDG 131 (250)
T ss_pred eEEEEeC-CHHHHHHHHhCCCcCEEEecCccCHHHh--hccc--cccchh-------cCCeEEEEECCCCcCCChHHcCC
Confidence 4577774 6899999999999998875432221110 0011 001111 111223333221 12222
Q ss_pred cEEEechHHHHHHHHHHHhc---CCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHH
Q 048784 91 KRVLSHPQALAQCENTLTKL---GLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAI 146 (282)
Q Consensus 91 ~~V~SHpqal~QC~~fl~~~---~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ 146 (282)
++|-. .....+. .++.+. +...+.+.|..++.+++..+ +.+++|.....+..
T Consensus 132 ~~i~~-~~g~~~~-~~l~~~~~~~~~~~~~~s~~~~~~~L~~g--~vD~~v~~~~~~~~ 186 (250)
T TIGR01096 132 KTVGV-QSGTTHE-QYLKDYFKPGVDIVEYDSYDNANMDLKAG--RIDAVFTDASVLAE 186 (250)
T ss_pred CEEEE-ecCchHH-HHHHHhccCCcEEEEcCCHHHHHHHHHcC--CCCEEEeCHHHHHH
Confidence 12322 2222222 334432 45566778888888888876 56778877766543
No 201
>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=48.94 E-value=1.4e+02 Score=23.91 Aligned_cols=122 Identities=13% Similarity=0.034 Sum_probs=59.1
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeecc-ccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCcc
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENSL-GGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLK 91 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~-~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~ 91 (282)
.+|+.++... .+-.++.+.+.+|++|+|++.-.... .+.+ ....|.+.++.+ ..+-+|-|......+++++.
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l--~~~~l~~~~~~~----~~~~~hpl~~~~~i~~~dL~ 98 (198)
T cd08437 25 TGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSAL--HSKIIKTQHFMI----IVSKDHPLAKAKKVNFADLK 98 (198)
T ss_pred hCCceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCcccc--eEEEeecceEEE----EecCCCcccccCcccHHHHc
Confidence 3576665544 35789999999999999997532110 0100 111223333322 22334444332222333332
Q ss_pred ---EEE-echH-HHHHHHHHHHhcCCe--E-EEecCHHHHHHHhhhcCCCCeEEecChhhH
Q 048784 92 ---RVL-SHPQ-ALAQCENTLTKLGLV--R-EAVDDTAGAAKYVSFEQLKDAGAVASSSAA 144 (282)
Q Consensus 92 ---~V~-SHpq-al~QC~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa 144 (282)
-|. .... .-.+...++.+.+.. . ..+.|.....++++.+ . ..++.+...+
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~-gi~~~p~~~~ 156 (198)
T cd08437 99 KENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVREN--V-GIGFLTDIAV 156 (198)
T ss_pred CCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC--C-cEEEEEhhhc
Confidence 222 1111 123455666665432 2 3455665666677764 2 3466665544
No 202
>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=48.67 E-value=94 Score=29.84 Aligned_cols=95 Identities=20% Similarity=0.128 Sum_probs=54.6
Q ss_pred EEEecCHHHHHHHhhhcCCCCeEEecChh---hHHHcCCceeecccccCCCCceEEEEEeeCCC-CCC----CCCCcEEE
Q 048784 114 REAVDDTAGAAKYVSFEQLKDAGAVASSS---AAAIYGLNILAEDIQDDCDNVTRFLMLAREPI-IPG----TDRPFKTS 185 (282)
Q Consensus 114 ~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~---Aa~~ygL~vl~~~I~d~~~N~TRF~vl~~~~~-~~~----~~~~~kts 185 (282)
.+..-|..+|.++...+ |-+-.+. -|..++.++.-.+..+.. --|.. .+... .+. ....+.+.
T Consensus 192 ~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~a~~~~i~i~i~~~~~~~-~gT~I---~~~~~~~~~v~~I~~~~~va~ 262 (401)
T TIGR00656 192 RIDKISYEEALELATFG-----AKVLHPRTVEPAMRSGVPIEVRSSFDPE-EGTLI---TNSMENPPLVKGIALRKNVTR 262 (401)
T ss_pred ECCccCHHHHHHHHHcC-----CcccCHHHHHHHHHCCCeEEEEECCCCC-CCeEE---EeCcccCCceEEEEEECCEEE
Confidence 34445666777766532 1222223 245689999888766533 23433 22211 110 00112333
Q ss_pred EEEE---cCCCccHHHHHHHHHHHCCceeeeeeee
Q 048784 186 IVFS---LEEGPGVLFKALAVFALRQINLTKIESR 217 (282)
Q Consensus 186 i~~~---~~~~pG~L~~~L~~F~~~~INlt~IeSR 217 (282)
+.+. +.++||.+.++++.|++++||+-.|..-
T Consensus 263 vsv~g~~~~~~~g~~~~if~~L~~~~I~i~~i~~~ 297 (401)
T TIGR00656 263 VTVHGLGMLGKRGFLARIFGALAERNINVDLISQT 297 (401)
T ss_pred EEEecCCCCCCccHHHHHHHHHHHcCCcEEEEEcC
Confidence 4343 5688999999999999999999887543
No 203
>PF03466 LysR_substrate: LysR substrate binding domain; InterPro: IPR005119 The structure of this domain is known and is similar to the periplasmic binding proteins []. This domain is found in members of the LysR family of prokaryotic transcriptional regulatory proteins IPR000847 from INTERPRO which share sequence similarities over approximately 280 residues including a putative helix-turn-helix DNA-binding motif at their N terminus.; PDB: 3ONM_B 3FZJ_J 3FXR_B 3N6T_A 3FXQ_A 3FXU_A 3N6U_A 2QSX_B 3HO7_B 1IZ1_B ....
Probab=47.73 E-value=1.5e+02 Score=23.91 Aligned_cols=114 Identities=22% Similarity=0.143 Sum_probs=63.7
Q ss_pred hCCCCcee-ecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCC--------
Q 048784 14 AYPNCEAV-PCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPG-------- 84 (282)
Q Consensus 14 ~~~~~~~~-~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~-------- 84 (282)
.+|+.++. -..+..++.+++.+|++|+|+........| +..+.....+.+++++++
T Consensus 31 ~~P~i~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~---------------~~~~~l~~~~~~~~~~~~~pl~~~~~ 95 (209)
T PF03466_consen 31 RHPNIRIEIREGDSDELIEALRSGELDLAITFGPPPPPG---------------LESEPLGEEPLVLVVSPDHPLAQKKP 95 (209)
T ss_dssp HSTTEEEEEEEESHHHHHHHHHTTSSSEEEESSSSSSTT---------------EEEEEEEEEEEEEEEETTSGGGTTSS
T ss_pred HCCCcEEEEEeccchhhhHHHhcccccEEEEEeeccccc---------------cccccccceeeeeeeecccccccccc
Confidence 35665543 335558999999999999999875531111 122222233334443332
Q ss_pred CCCCCc---cEEEec--hHHHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 85 VKVEDL---KRVLSH--PQALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 85 ~~l~~I---~~V~SH--pqal~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
.+++++ .-|.-. ..-..+..+++.+++.. ...+.|...+..++..+ ...++.+...+.
T Consensus 96 i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 161 (209)
T PF03466_consen 96 ITLEDLADYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASG---DGIAILPDSLAQ 161 (209)
T ss_dssp SSGGGGTTSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTT---SEBEEEEHHHHH
T ss_pred chhhhhhhccccccccccccccccccccccccccccccccccchhhhccccccc---cceeecCccccc
Confidence 233333 333321 22456666677766553 24466777777777764 456777777664
No 204
>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=47.48 E-value=1.5e+02 Score=23.94 Aligned_cols=122 Identities=11% Similarity=0.052 Sum_probs=60.9
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEeee-eccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCC---C
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIE-NSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKV---E 88 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiE-NS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l---~ 88 (282)
.+|+.++... .+-.++.+.+.+|++|+|+..-. +...+.. ...|...++ .+..+..|-|......++ .
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 3566655443 35678999999999999997411 0001110 111122222 233444555543222222 3
Q ss_pred CccEEEechH-H-HHHHHHHHHhcCC--e-EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 89 DLKRVLSHPQ-A-LAQCENTLTKLGL--V-REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 89 ~I~~V~SHpq-a-l~QC~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
+..-|.-.+. . -.++..|+.+++. . ...+++...+.+++..+ ...++.+..+++
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08444 98 KWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLG---MGIGIVAEMAFE 156 (198)
T ss_pred CCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcC---CcEEeccHHHHh
Confidence 3334433322 1 2345677776543 2 23456666666677764 235666665543
No 205
>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=47.44 E-value=1.5e+02 Score=24.01 Aligned_cols=31 Identities=13% Similarity=0.076 Sum_probs=24.1
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEee
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPi 45 (282)
+|+.++... .+..++++.+.+|++|+|+...
T Consensus 26 ~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~ 57 (200)
T cd08465 26 APGIDLAVSQASREAMLAQVADGEIDLALGVF 57 (200)
T ss_pred CCCcEEEEecCChHhHHHHHHCCCccEEEecc
Confidence 567665433 4678999999999999999743
No 206
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=47.38 E-value=2.3e+02 Score=26.13 Aligned_cols=122 Identities=16% Similarity=0.088 Sum_probs=62.7
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeec-CCCCCCCc--
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLAN-PGVKVEDL-- 90 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~-~~~~l~~I-- 90 (282)
+|+.++.... +.+++++++.+|++|+|+++--+...+... ...|.+.++. +.++..|-|... ...+++|+
T Consensus 119 ~P~v~i~l~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~~----l~~~~~hpl~~~~~~~~~~dl~~ 192 (327)
T PRK12680 119 YPQVSVHLQQAAESAALDLLGQGDADIAIVSTAGGEPSAGI--AVPLYRWRRL----VVVPRGHALDTPRRAPDMAALAE 192 (327)
T ss_pred CCCcEEEEEeCChHHHHHHHHCCCCcEEEEecCCCCCCcce--EEEeeccceE----EEEeCCChhhccCCCCCHHHHhc
Confidence 5666665444 568999999999999999863211111110 1122233332 234556666532 12233332
Q ss_pred -cEEEech-HHH-HHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 91 -KRVLSHP-QAL-AQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 91 -~~V~SHp-qal-~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
.-|..-+ ... ....+|+..++.. ...+.+......+|+.+ .+ .|+.+..++.
T Consensus 193 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G--~G-ia~lp~~~~~ 250 (327)
T PRK12680 193 HPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAG--LG-VGLLAEMAVN 250 (327)
T ss_pred CCEEEecCCCchHHHHHHHHHHCCCCCcEEEEECCHHHHHHHHHcC--CC-EEEeechhcc
Confidence 3332222 122 4456677766432 23456666667777765 34 4555555443
No 207
>cd08466 PBP2_LeuO The C-terminal substrate binding domain of LysR-type transcriptional regulator LeuO, an activator of leucine synthesis operon, contains the type 2 periplasmic binding fold. LeuO, a LysR-type transcriptional regulator, was originally identified as an activator of the leucine synthesis operon (leuABCD). Subsequently, LeuO was found to be not a specific regulator of the leu gene but a global regulator of unrelated various genes. LeuO activates bglGFB (utilization of beta-D-glucoside) and represses cadCBA (lysine decarboxylation) and dsrA (encoding a regulatory small RNA for translational control of rpoS and hns). LeuO also regulates the yjjQ-bglJ operon which coding for a LuxR-type transcription factor. In Salmonella enterica serovar Typhi, LeuO is a positive regulator of ompS1 (encoding an outer membrane), ompS2 (encoding a pathogenicity determinant), and assT, while LeuO represses the expression of OmpX and Tpx. Both osmS1 and osmS2 influence virulence in the mouse mo
Probab=46.45 E-value=1.5e+02 Score=23.65 Aligned_cols=122 Identities=20% Similarity=0.086 Sum_probs=59.5
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc--
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL-- 90 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I-- 90 (282)
.+|+.++.... +..++.+.+.+|++|+|++--.....+. ....|.+.++.++. +-.|-+... ..+++++
T Consensus 25 ~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~lv~----~~~~~~~~~-~~~~~~L~~ 96 (200)
T cd08466 25 LAPNISLRESPSSEEDLFEDLRLQEVDLVIDYVPFRDPSF---KSELLFEDELVCVA----RKDHPRIQG-SLSLEQYLA 96 (200)
T ss_pred HCCCCEEEEecCchHhHHHHHHcCCccEEEecccCCCCCc---eeeeecccceEEEE----eCCCCCCCC-CcCHHHHhh
Confidence 35776665444 5678999999999999997321111111 11123333333322 233433321 2234444
Q ss_pred -cEEEechHH-HHHHHHHHHhcCC---e-EEEecCHHHHHHHhhhcCCCCeEEecChhhHHH
Q 048784 91 -KRVLSHPQA-LAQCENTLTKLGL---V-REAVDDTAGAAKYVSFEQLKDAGAVASSSAAAI 146 (282)
Q Consensus 91 -~~V~SHpqa-l~QC~~fl~~~~~---~-~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ 146 (282)
..+.-.+.. ..+-..|+.+.+. . ...+.|.....++++.+ ...|+.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08466 97 EKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQT---DLIAIAPRWLADQ 155 (200)
T ss_pred CCcEEecCCCCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCC---CeehhhHHHHHHH
Confidence 222222221 1233455555443 2 23445555556666654 3457777666543
No 208
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=46.24 E-value=2.3e+02 Score=25.64 Aligned_cols=30 Identities=17% Similarity=0.077 Sum_probs=23.2
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
+|+.++... .+.+++++.+.+|++|+|+.+
T Consensus 119 ~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~ 149 (309)
T PRK12682 119 YPKVNLSLHQGSPDEIARMVISGEADIGIAT 149 (309)
T ss_pred CCCeEEEEecCCHHHHHHHHHcCCccEEEec
Confidence 466665543 357899999999999999975
No 209
>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=46.19 E-value=1.5e+02 Score=23.40 Aligned_cols=32 Identities=19% Similarity=0.150 Sum_probs=24.1
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEee
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPi 45 (282)
.+|+.++.-.. +-.++.+.+.+|++|+|+..-
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (194)
T cd08436 25 RHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGL 57 (194)
T ss_pred HCCCcEEEEecCCHHHHHHHHHcCCccEEEEec
Confidence 45766554433 567899999999999999864
No 210
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=46.08 E-value=1e+02 Score=33.18 Aligned_cols=35 Identities=11% Similarity=0.327 Sum_probs=29.8
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceee--eeeee
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLT--KIESR 217 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt--~IeSR 217 (282)
-|.|.+..+|+||-|+++-++|+.+|+|+. +|-+.
T Consensus 677 ~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~ 713 (854)
T PRK01759 677 GTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITS 713 (854)
T ss_pred eEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEc
Confidence 477888889999999999999999999987 44443
No 211
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=46.01 E-value=1.1e+02 Score=26.84 Aligned_cols=115 Identities=17% Similarity=0.175 Sum_probs=63.5
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccc-cCCeEEEEEEEE-----eeeeeeeecCCCC---C
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLL-RHRLHIVGEVKF-----AVRHCLLANPGVK---V 87 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~-~~~l~I~~E~~l-----~I~~~L~a~~~~~---l 87 (282)
..++++..++.+..+++.+|++|+++.+-. ++-.+. +.++..++...- ...-.++++++.. +
T Consensus 30 ~v~~~~~~~~~~~~~~l~~g~~D~~~~~~~---------~~~~~~~~~~~~~la~~~~~~g~~~~~~~ivv~~ds~i~~l 100 (243)
T PF12974_consen 30 PVELVPADDYAEFIEALRSGEIDLAFMGPL---------PYVQARQRAGVEPLATPVGPDGSPSYRSVIVVRADSPITSL 100 (243)
T ss_dssp EEEEE--SSHHHHHHHHHTTS-SEEE--HH---------HHHHHHHHSSEEEEEEEEETTT-SCEEEEEEEETTSS--SH
T ss_pred CEEEEEcCCHHHHHHHHHcCCccEEEECcH---------HHHHHhhcCcEEEEEEecccCCCcceeEEEEEECCCCCCCh
Confidence 367899999999999999999999997511 222222 245555555554 3344555666643 3
Q ss_pred CCc---cEEEechHH---HHHHHHHH-HhcCC------eEEEecCHHHHHHHhhhcCCCCeEEecChh
Q 048784 88 EDL---KRVLSHPQA---LAQCENTL-TKLGL------VREAVDDTAGAAKYVSFEQLKDAGAVASSS 142 (282)
Q Consensus 88 ~~I---~~V~SHpqa---l~QC~~fl-~~~~~------~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~ 142 (282)
+|+ +..+..|.. .--.+.+| +++++ ..+.+.+-.++++.+..+ ...||+.+..
T Consensus 101 ~dL~Gk~v~~~~~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G--~~Da~~~~~~ 166 (243)
T PF12974_consen 101 ADLKGKRVAFPDPSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNG--KADAAAIPSD 166 (243)
T ss_dssp HHHGGSEEEEE-TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTT--SSSEEEEEHH
T ss_pred hhcCCCEEEEecCCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcC--CccEEEEech
Confidence 444 344445553 34456667 56543 345666777788888876 3344444433
No 212
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=45.61 E-value=62 Score=29.58 Aligned_cols=26 Identities=15% Similarity=-0.040 Sum_probs=22.0
Q ss_pred CceeecCCHHHHHHHHHcCCCCeEEE
Q 048784 18 CEAVPCEQFDTAFEAVERWLVDRAVL 43 (282)
Q Consensus 18 ~~~~~~~s~~~v~~av~~g~~d~gVv 43 (282)
.+++.+.+-.++++++.+|++|+|+.
T Consensus 58 ie~~~~~~~~~~~~aL~~G~iDia~~ 83 (314)
T PRK11553 58 ISWVEFPAGPQMLEALNVGSIDLGST 83 (314)
T ss_pred eEEEECCCcHHHHHHHHcCCCCEEcc
Confidence 45677767789999999999999985
No 213
>PRK06635 aspartate kinase; Reviewed
Probab=45.46 E-value=77 Score=30.49 Aligned_cols=52 Identities=25% Similarity=0.328 Sum_probs=37.8
Q ss_pred EcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 189 SLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 189 ~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
.+++.||.+.++++.|+++|||+..|.+. . -...|.|+-+ ...++++.|.+.
T Consensus 349 ~~~~~~g~~a~i~~~La~~~Ini~~i~ss---~---------------~~is~vv~~~------d~~~a~~~Lh~~ 400 (404)
T PRK06635 349 GMRSHPGVAAKMFEALAEEGINIQMISTS---E---------------IKISVLIDEK------YLELAVRALHEA 400 (404)
T ss_pred CCCCCchHHHHHHHHHHHCCCCEEEEEec---C---------------CeEEEEEcHH------HHHHHHHHHHHH
Confidence 34789999999999999999999988641 1 1467777652 345566666544
No 214
>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=44.37 E-value=1.7e+02 Score=23.65 Aligned_cols=32 Identities=13% Similarity=-0.033 Sum_probs=24.5
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEee
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPi 45 (282)
.+|+.++... .+-.++.+.+.+|++|+|++.-
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~ 57 (202)
T cd08468 25 LAPSVRLNLVHAEQKLPLDALLAGEIDFALGYS 57 (202)
T ss_pred hCCCCEEEEEECChHhHHHHHHCCCccEEEecc
Confidence 3566665544 3578999999999999999753
No 215
>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=44.35 E-value=1.6e+02 Score=23.34 Aligned_cols=32 Identities=28% Similarity=0.300 Sum_probs=24.0
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEee
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPi 45 (282)
.+|+.++.... +-.++++.+.+|++|+|+++.
T Consensus 26 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~ 58 (199)
T cd08451 26 AYPDVELTLEEANTAELLEALREGRLDAAFVRP 58 (199)
T ss_pred HCCCcEEEEecCChHHHHHHHHCCCccEEEEec
Confidence 45766554443 467899999999999999753
No 216
>PF06153 DUF970: Protein of unknown function (DUF970); InterPro: IPR010375 This is a family of uncharacterised bacterial proteins.; PDB: 3M05_A.
Probab=44.31 E-value=1e+02 Score=24.69 Aligned_cols=53 Identities=21% Similarity=0.220 Sum_probs=37.6
Q ss_pred HHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhcCce
Q 048784 199 KALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFATFL 268 (282)
Q Consensus 199 ~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~~~v 268 (282)
++.+.|.++|+..|||-|.= |.-+.+.--|+|-+| |++++++|+-|++.|..-
T Consensus 15 ~l~~~L~~~g~~~TkLsstG-------------GFLr~GNtTlliGve----de~v~~vl~iIk~~c~~R 67 (109)
T PF06153_consen 15 DLSDALNENGFRVTKLSSTG-------------GFLREGNTTLLIGVE----DEKVDEVLEIIKENCKKR 67 (109)
T ss_dssp HHHHHHHHTT--EEEEEEEE-------------TTTTEEEEEEEEEEE----GGGHHHHHHHHHHHH--E
T ss_pred HHHHHHHHCCceEEEEeccc-------------ceeccCCEEEEEEec----HHHHHHHHHHHHHhhcCc
Confidence 55666789999999999874 222456778899886 578899999999988753
No 217
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=44.19 E-value=2.4e+02 Score=25.26 Aligned_cols=117 Identities=16% Similarity=0.019 Sum_probs=55.5
Q ss_pred CCCCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc---c
Q 048784 15 YPNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL---K 91 (282)
Q Consensus 15 ~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I---~ 91 (282)
+|+.++....+ +..+.+.+|++|+|++..+....+... ..|.+.++.+ ..+-.|.+......+++++ .
T Consensus 120 ~p~i~i~l~~~--~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~----~~~~~~~~~~~~~i~~~dL~~~p 190 (297)
T PRK11139 120 HPDIDVRLKAV--DRLEDFLRDDVDVAIRYGRGNWPGLRV---EKLLDEYLLP----VCSPALLNGGKPLKTPEDLARHT 190 (297)
T ss_pred CCCceEEEEeC--CChhhhccCCCCEEEEeCCCCCCCceE---EEeccceeEE----EeCHHHhcccCCCCCHHHhhcCc
Confidence 46654433322 335778899999999876533332221 1222223322 2333444333322233332 2
Q ss_pred EEEechHHHHHHHHHHHhcCC---e---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 RVLSHPQALAQCENTLTKLGL---V---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 ~V~SHpqal~QC~~fl~~~~~---~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
-|...+ ......|+...+. . ...+++...+..+++.+ ...|+.+...++
T Consensus 191 ~i~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 245 (297)
T PRK11139 191 LLHDDS--REDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG---QGVALGNRVLAQ 245 (297)
T ss_pred eEeecC--cccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhC---CCeEecchhhhH
Confidence 333222 2345667766433 1 12345555555566654 345666666554
No 218
>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=43.70 E-value=1.7e+02 Score=23.41 Aligned_cols=119 Identities=16% Similarity=-0.010 Sum_probs=58.1
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCC---
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVED--- 89 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~--- 89 (282)
.+|+.++.... +-.++++.+.+|++|+|++.......+... ..|.+..+. +..+-.|.|......++++
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----~~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08457 25 LRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGFL---IETRSLPAV----VAVPMGHPLAQLDVVSPQDLAG 97 (196)
T ss_pred HCCCeEEEEEecCcHHHHHHHHcCCccEEEeccCCCCCCcEE---EEeccCCeE----EEeeCCCccccCCccCHHHhCC
Confidence 35666554433 347889999999999999864322111111 122222322 2223345554332223333
Q ss_pred ccEEE-echH-HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChh
Q 048784 90 LKRVL-SHPQ-ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSS 142 (282)
Q Consensus 90 I~~V~-SHpq-al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~ 142 (282)
..-|. ++.. ......+++.+++.. ...+.|...+.++++.+ ...++.+..
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~ 152 (196)
T cd08457 98 ERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREG---LGIAIIDPA 152 (196)
T ss_pred CceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcC---CeEEEEChH
Confidence 23333 2222 224456667665432 23455555556666654 234555544
No 219
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=43.02 E-value=1.1e+02 Score=30.27 Aligned_cols=27 Identities=19% Similarity=0.214 Sum_probs=22.9
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEE
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVL 43 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVv 43 (282)
+.+++...+++++++++.+|++|+++-
T Consensus 81 ~~e~v~~~~~~~ll~aL~~G~iDi~~~ 107 (482)
T PRK10859 81 KLEIKVRDNISQLFDALDKGKADLAAA 107 (482)
T ss_pred cEEEEecCCHHHHHHHHhCCCCCEEec
Confidence 456777899999999999999997653
No 220
>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=42.98 E-value=38 Score=29.09 Aligned_cols=43 Identities=14% Similarity=0.000 Sum_probs=28.9
Q ss_pred CCCcHHHHHHHhhCCCCcee---------ecCCHHHHHHHHHcCCCCeEEEe
Q 048784 2 VRGAYSESAAEKAYPNCEAV---------PCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 2 P~GTfS~~Aa~~~~~~~~~~---------~~~s~~~v~~av~~g~~d~gVvP 44 (282)
+.|+..++...+.....++. ...|..+++.+|.+|++|.+++.
T Consensus 110 ~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~ 161 (232)
T TIGR03871 110 FAGTPPAHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVW 161 (232)
T ss_pred EcCChHHHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEec
Confidence 35777766655432111222 13478999999999999999985
No 221
>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=42.75 E-value=2.6e+02 Score=25.41 Aligned_cols=123 Identities=21% Similarity=0.161 Sum_probs=65.1
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceecccccccc--CCeEEEEEEE-EeeeeeeeecCCCCCCCcc--
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLR--HRLHIVGEVK-FAVRHCLLANPGVKVEDLK-- 91 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~--~~l~I~~E~~-l~I~~~L~a~~~~~l~~I~-- 91 (282)
+.+++.+.+..+..+|+.+|++|.+.. +........... .++.+++-.. .| ..+.+.+=.+++|++
T Consensus 47 ~Ve~~~f~d~~~~~~Al~~G~ID~~~~-------q~~~~l~~~~~~~g~~lv~v~~~~~~p--~~~ys~~~~sl~dlk~G 117 (258)
T TIGR00363 47 DVELVEFNDYALPNEAVSKGDLDANAF-------QHKPYLDQDAKAKGYKLVAVGNTFVYP--LAGYSKKIKNVNELQDG 117 (258)
T ss_pred EEEEEEeCCcHHHHHHHHcCCCCeEec-------CCHHHHHHHHHhCCCcEEEEeeeEEec--ccccCcCCCCHHHcCCC
Confidence 468899999999999999999998763 111111111112 3455555332 22 244444444667773
Q ss_pred -EEEec--hHHHHHHHHHHHhcCC-----------------------eEEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 -RVLSH--PQALAQCENTLTKLGL-----------------------VREAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 -~V~SH--pqal~QC~~fl~~~~~-----------------------~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
+|.-. |.-.++.-..|.+.++ +.+.. +.+..+..+..+ .-+||+....-+.
T Consensus 118 ~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel-~~~~~~~al~~g--~vDaa~v~~~~~~ 194 (258)
T TIGR00363 118 AKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITEL-ETSQLPRALDDP--KVDLAVINTTYAG 194 (258)
T ss_pred CEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEc-CHHHHHHHhhcc--cccEEEEChHHHH
Confidence 55433 3333443345665332 23333 333444444432 2456666655566
Q ss_pred HcCCce
Q 048784 146 IYGLNI 151 (282)
Q Consensus 146 ~ygL~v 151 (282)
..||..
T Consensus 195 ~agl~~ 200 (258)
T TIGR00363 195 QVGLNP 200 (258)
T ss_pred HcCCCc
Confidence 777763
No 222
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=42.55 E-value=45 Score=30.84 Aligned_cols=43 Identities=37% Similarity=0.389 Sum_probs=32.1
Q ss_pred CCcHHHHH--HHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEeee
Q 048784 3 RGAYSESA--AEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLPIE 46 (282)
Q Consensus 3 ~GTfS~~A--a~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 46 (282)
+|-+|-.+ .+-+.|+.++++.+ |+++..||.+|++|-|++=.|
T Consensus 101 pG~~TTA~lL~rl~~p~~~~V~m~-fdeI~~Avl~G~VDaGvlIHE 145 (272)
T COG2107 101 PGEMTTAALLFRLAYPKAEIVYMP-FDEIIPAVLEGKVDAGVLIHE 145 (272)
T ss_pred CCcccHHHHHHHHhCCCceEEEee-HHHHHHHHHcCCCccceEEee
Confidence 34444333 34456888887764 899999999999999999776
No 223
>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=41.97 E-value=1.8e+02 Score=23.14 Aligned_cols=31 Identities=16% Similarity=0.057 Sum_probs=23.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
.+|+.++... .+-.++.+.+.+|++|+|++.
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~ 56 (198)
T cd08421 25 AHPDVRIDLEERLSADIVRAVAEGRADLGIVA 56 (198)
T ss_pred HCCCceEEEEecCcHHHHHHHhcCCceEEEEe
Confidence 3566665443 356889999999999999985
No 224
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=41.60 E-value=1.6e+02 Score=25.95 Aligned_cols=120 Identities=16% Similarity=0.080 Sum_probs=62.9
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecC-------CCCCCC
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANP-------GVKVED 89 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~-------~~~l~~ 89 (282)
+.+++.+.+-.++.+++.+|++|++.+ ....+.+.-.-. .-...++.+.+-...- ..+++++. -.+++|
T Consensus 36 ~ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~--~~~~~~~~~~~~~~~~-g~~lvv~~~~~~~~~~~~~~d 111 (252)
T PF13379_consen 36 DVEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGA--GGPDVDIVVLAGLSQN-GNALVVRNDLKDASDIKSLAD 111 (252)
T ss_dssp CEEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTT--TT----EEEEEECSBS-SEEEEECGGGTTCSTTCCGHH
T ss_pred EEEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCC--CCcccceEEeeccCCC-ceEEEEcCccccCCCccCHHH
Confidence 467899999999999999999999998 443332221110 0001133333222111 12455542 234455
Q ss_pred c---------cEEEe-chHH--HHHHHHHHHhcCC------eEEEecCHHHHHHHhhhcCCCCeEEecChh
Q 048784 90 L---------KRVLS-HPQA--LAQCENTLTKLGL------VREAVDDTAGAAKYVSFEQLKDAGAVASSS 142 (282)
Q Consensus 90 I---------~~V~S-Hpqa--l~QC~~fl~~~~~------~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~ 142 (282)
+ ++|.. ++-. ....+.+|+++++ ..+.... .++...+..++ -+.+++.-+.
T Consensus 112 l~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~-iDa~~~~eP~ 180 (252)
T PF13379_consen 112 LIKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGE-IDAAVLWEPF 180 (252)
T ss_dssp HHHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS--SEEEEETTH
T ss_pred HHhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCC-cCEEEecCCH
Confidence 5 36665 5533 3346788987633 3444444 66777776653 3444444444
No 225
>PRK08210 aspartate kinase I; Reviewed
Probab=41.40 E-value=1.2e+02 Score=29.31 Aligned_cols=89 Identities=12% Similarity=-0.037 Sum_probs=49.0
Q ss_pred cCHHHHHHHhhhcCCCCeEEecChhh---HHHcCCceeecccccCCCCceEEEEEeeCCC-------CCC----CCCCcE
Q 048784 118 DDTAGAAKYVSFEQLKDAGAVASSSA---AAIYGLNILAEDIQDDCDNVTRFLMLAREPI-------IPG----TDRPFK 183 (282)
Q Consensus 118 ~sTa~Aa~~v~~~~~~~~AAI~s~~A---a~~ygL~vl~~~I~d~~~N~TRF~vl~~~~~-------~~~----~~~~~k 183 (282)
-|..+|.++...+ +-+-.+.| |..++.++.-.+..+.+. -|..- .+.+. .+. ....+-
T Consensus 200 ls~~ea~~l~~~G-----~~v~~~~a~~~~~~~~i~i~i~~~~~~~~-gT~I~--~~~~~~~~~~~~~~~v~~It~~~~i 271 (403)
T PRK08210 200 VSYNEVFQMAYQG-----AKVIHPRAVEIAMQANIPLRIRSTYSDSP-GTLIT--SLGDAKGGIDVEERLITGIAHVSNV 271 (403)
T ss_pred cCHHHHHHHHHCC-----ccccCHHHHHHHHHCCCeEEEEecCCCcC-CcEEE--ecCccccccccccCceEEEEEcCCc
Confidence 3445555554432 22333333 356799998888775322 44431 11110 000 001122
Q ss_pred EEEEEE-cCCCccHHHHHHHHHHHCCceeeee
Q 048784 184 TSIVFS-LEEGPGVLFKALAVFALRQINLTKI 214 (282)
Q Consensus 184 tsi~~~-~~~~pG~L~~~L~~F~~~~INlt~I 214 (282)
+.+.+. .++.||.+.++++.|+++|||+-.|
T Consensus 272 ~~isv~~~~~~~g~la~If~~L~~~~I~i~~i 303 (403)
T PRK08210 272 TQIKVKAKENAYDLQQEVFKALAEAGISVDFI 303 (403)
T ss_pred EEEEEecCCCcchHHHHHHHHHHHcCCeEEEE
Confidence 333333 3445999999999999999999888
No 226
>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]
Probab=41.27 E-value=1.8e+02 Score=27.20 Aligned_cols=35 Identities=14% Similarity=0.193 Sum_probs=30.4
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeee
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESR 217 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSR 217 (282)
+..|.++.+|+||-...+=+.+.++|.|+.+-..-
T Consensus 7 ~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf 41 (287)
T COG0788 7 TFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQF 41 (287)
T ss_pred ceEEEEecCCCCCcHHHHHHHHHHcCCceeecccc
Confidence 46788899999999999999999999999866554
No 227
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=41.19 E-value=2.8e+02 Score=25.23 Aligned_cols=125 Identities=13% Similarity=0.031 Sum_probs=60.6
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCCCeEEEeeeecc----cccee----ccccccccCCeEEEEEEEEeeeeeeeecCCC
Q 048784 14 AYPNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSL----GGSIH----RNYDLLLRHRLHIVGEVKFAVRHCLLANPGV 85 (282)
Q Consensus 14 ~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~----~G~V~----~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~ 85 (282)
.+|+.++.....-.++.+.+.+|++|+|++.- +.. .|... .....|...++. +.++-+|-+.. ...
T Consensus 122 ~~P~v~v~i~~~~~~~~~~l~~g~~D~~i~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~----~v~~~~hp~~~-~~~ 195 (319)
T PRK10216 122 RYPQATIKLRNWDYDSLDAITRGEVDIGFTGR-ESHPRSRELLSLLPLAIDFEVLFSDLPC----VWLRKDHPALH-EEW 195 (319)
T ss_pred HCCCCEEEEEeCCcchHHHHhcCCccEEEecC-CCCccccccccccccccceeeeeecceE----EEEeCCCCccC-CCC
Confidence 35665544333223578999999999999842 111 11100 011112222222 23444554322 222
Q ss_pred CCCCc---cEEEec-h-HHHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 86 KVEDL---KRVLSH-P-QALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 86 ~l~~I---~~V~SH-p-qal~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
.++|+ .-|..- + ....+...++.+.+.. ...+.|.....++++.+. ....+|.+..+++
T Consensus 196 ~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~-~~gi~ilp~~~~~ 262 (319)
T PRK10216 196 NLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPEFEQSLFMAAQPD-HLLLATAPRYCQY 262 (319)
T ss_pred CHHHHhhCCCeEecCCCCCcchHHHHHHHhCCccceEEECCcHHHHHHHHHcCC-cceEeccHHHHHH
Confidence 22322 233211 1 1233566777766432 345667777777777531 2357888876543
No 228
>PRK06635 aspartate kinase; Reviewed
Probab=41.04 E-value=1.1e+02 Score=29.49 Aligned_cols=29 Identities=21% Similarity=0.354 Sum_probs=25.4
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeee
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRP 218 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP 218 (282)
..++||.|.++++.|+++|||+-.|.+-.
T Consensus 270 ~~~~~g~l~~i~~~L~~~~I~i~~is~s~ 298 (404)
T PRK06635 270 VPDKPGIAAQIFGALAEANINVDMIVQNV 298 (404)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEecC
Confidence 56899999999999999999999885543
No 229
>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=41.00 E-value=1.2e+02 Score=21.01 Aligned_cols=51 Identities=22% Similarity=0.206 Sum_probs=34.4
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+.+.||.+.++++.|++.+|++-..-... -.-.|+||- .+..++++.|.+.
T Consensus 10 ~~~~~gv~~~~~~~L~~~~i~~i~~~~s~------------------~~is~vv~~------~d~~~av~~LH~~ 60 (63)
T cd04920 10 IRSLLHKLGPALEVFGKKPVHLVSQAAND------------------LNLTFVVDE------DQADGLCARLHFQ 60 (63)
T ss_pred cccCccHHHHHHHHHhcCCceEEEEeCCC------------------CeEEEEEeH------HHHHHHHHHHHHH
Confidence 34679999999999999888884433321 135688875 3445677766543
No 230
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=40.71 E-value=60 Score=28.73 Aligned_cols=43 Identities=16% Similarity=0.280 Sum_probs=31.8
Q ss_pred CCCcHHHHHHHhhCC--CCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 2 VRGAYSESAAEKAYP--NCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 2 P~GTfS~~Aa~~~~~--~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
+.||..+.-....+. +.+++.+.+.++++++|.+|++|+.+..
T Consensus 139 ~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 139 LQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred ecCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeC
Confidence 356665554444332 3578889999999999999999998764
No 231
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=40.62 E-value=34 Score=31.57 Aligned_cols=42 Identities=17% Similarity=0.192 Sum_probs=34.0
Q ss_pred CCCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHcCCCCeEEE
Q 048784 2 VRGAYSESAAEKAYP----NCEAVPCEQFDTAFEAVERWLVDRAVL 43 (282)
Q Consensus 2 P~GTfS~~Aa~~~~~----~~~~~~~~s~~~v~~av~~g~~d~gVv 43 (282)
..||.+++.++.+.+ +.+++.+.+.++++.+|.+|++|..+.
T Consensus 159 ~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~ 204 (302)
T PRK10797 159 TSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMM 204 (302)
T ss_pred eCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEc
Confidence 467777776665542 467899999999999999999998875
No 232
>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=39.76 E-value=1.7e+02 Score=23.08 Aligned_cols=30 Identities=13% Similarity=-0.012 Sum_probs=19.9
Q ss_pred CCCCceeecCCHHHHHHHHHcCCCCeEEEeee
Q 048784 15 YPNCEAVPCEQFDTAFEAVERWLVDRAVLPIE 46 (282)
Q Consensus 15 ~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 46 (282)
+|+.++....+- ..+.+.+|++|+|++..+
T Consensus 26 ~P~v~i~~~~~~--~~~~l~~g~~D~~i~~~~ 55 (194)
T cd08432 26 HPDIDLRLSTSD--RLVDFAREGIDLAIRYGD 55 (194)
T ss_pred CCCeEEEEEecC--CccccccccccEEEEecC
Confidence 465554443322 567789999999998644
No 233
>PF12916 DUF3834: Protein of unknown function (DUF3834); InterPro: IPR024533 This family is likely to be related to solute-binding lipo-proteins.; PDB: 3MST_A.
Probab=39.55 E-value=31 Score=30.53 Aligned_cols=50 Identities=24% Similarity=0.264 Sum_probs=27.6
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccc-cccccCCeEEEEE
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNY-DLLLRHRLHIVGE 70 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~-d~L~~~~l~I~~E 70 (282)
..+++..++..++++++.+|++|-|||+.+ +.. .+++ |+|.+.++++=|-
T Consensus 94 ~~EvVytdD~~~i~~Ml~~g~vdsAVv~~~--~~~--G~~fEdl~~~~g~~~Pgs 144 (201)
T PF12916_consen 94 KAEVVYTDDMSEIVKMLNEGEVDSAVVGSE--FSK--GETFEDLLGSLGLYAPGS 144 (201)
T ss_dssp T-EEEE---HHHHHHHHHTT-E--EEEETT--T-----EEHHHHHHHTT------
T ss_pred cceeEEecCHHHHHHHHhcCceeeeeecch--hcc--chhHHHHHhhcCCCCChh
Confidence 579999999999999999999999999933 322 4555 4666677765554
No 234
>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=39.29 E-value=91 Score=29.93 Aligned_cols=51 Identities=29% Similarity=0.442 Sum_probs=37.1
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+.+.||.+.++++.+++.|||+..|-+ .. -.-.|.|+- ....++++.|.+.
T Consensus 347 ~~~~~g~~a~i~~~L~~~gIni~~i~~---s~---------------~~is~vv~~------~d~~~av~~Lh~~ 397 (401)
T TIGR00656 347 MVGAPGVASEIFSALEEKNINILMIGS---SE---------------TNISFLVDE------KDAEKAVRKLHEV 397 (401)
T ss_pred cccCccHHHHHHHHHHHCCCcEEEEEc---CC---------------CEEEEEEeH------HHHHHHHHHHHHH
Confidence 468899999999999999999986642 11 145677765 3446677777655
No 235
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=39.24 E-value=3.1e+02 Score=25.14 Aligned_cols=122 Identities=15% Similarity=0.100 Sum_probs=62.9
Q ss_pred hhCCCCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCccE
Q 048784 13 KAYPNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLKR 92 (282)
Q Consensus 13 ~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~~ 92 (282)
+.+|+.++... +..++++.|.+|++|+|+.+-.....|... ..|.+.++.+ .++-.|-|... ..+++++..
T Consensus 141 ~~~P~i~i~~~-~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~l----v~~~~hpl~~~-~~~~~dL~~ 211 (317)
T PRK11482 141 THYPQLLLRNI-PISDAENQLSQFQTDLIIDTHSCSNRTIQH---HVLFTDNVVL----VCRQGHPLLSL-EDDEETLDN 211 (317)
T ss_pred HHCCCCEEEEe-cchhHHHHHHCCCcCEEEeccCCCCCceEE---EEEecCcEEE----EEeCCCCccCC-CCCHHHHhh
Confidence 34567665433 446899999999999999865432233222 2333334432 34555666432 345555542
Q ss_pred ----EE-echHHHHHHHHHHHhc--CCeE-EEecCHHHHHHHhhhcCCCCeEEecChhhHHH
Q 048784 93 ----VL-SHPQALAQCENTLTKL--GLVR-EAVDDTAGAAKYVSFEQLKDAGAVASSSAAAI 146 (282)
Q Consensus 93 ----V~-SHpqal~QC~~fl~~~--~~~~-~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ 146 (282)
++ ..+......++++.+. .... ..+.+......+++.+ ...+|.+...+..
T Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~ilp~~~~~~ 270 (317)
T PRK11482 212 AEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASS---DMLGIMPSRFYNL 270 (317)
T ss_pred CCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcC---CeeEEeHHHHHHH
Confidence 22 2222212334555543 2222 3345555556667654 3456766666543
No 236
>PRK05092 PII uridylyl-transferase; Provisional
Probab=38.91 E-value=1.6e+02 Score=31.90 Aligned_cols=33 Identities=15% Similarity=0.238 Sum_probs=28.7
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeee
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIE 215 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~Ie 215 (282)
-|.|.+..+|+||-|.++.++|+.+|+|+..-.
T Consensus 732 ~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~ 764 (931)
T PRK05092 732 VTEVTVLAADHPGLFSRIAGACAAAGANIVDAR 764 (931)
T ss_pred eEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEE
Confidence 577888889999999999999999999987433
No 237
>cd08441 PBP2_MetR The C-terminal substrate binding domain of LysR-type transcriptional regulator metR, which regulates the expression of methionine biosynthetic genes, contains type 2 periplasmic binding fold. MetR, a member of the LysR family, is a positive regulator for the metA, metE, metF, and metH genes. The sulfur-containing amino acid methionine is the universal initiator of protein synthesis in all known organisms and its derivative S-adenosylmethionine (SAM) and autoinducer-2 (AI-2) are involved in various cellular processes. SAM plays a central role as methyl donor in methylation reactions, which are essential for the biosynthesis of phospholipids, proteins, DNA and RNA. The interspecies signaling molecule AI-2 is involved in cell-cell communication process (quorum sensing) and gene regulation in bacteria. Although methionine biosynthetic enzymes and metabolic pathways are well conserved in bacteria, the regulation of methionine biosynthesis involves various regulatory mecha
Probab=37.50 E-value=2.1e+02 Score=22.78 Aligned_cols=122 Identities=21% Similarity=0.189 Sum_probs=59.5
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCcc-
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLK- 91 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~- 91 (282)
.+|+.++... .+-.++.+.+.+|++|+|+..-.....+. ....|.+.++. +..+-.|-|......+++++.
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~----~~~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08441 25 RWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGI---AYEPLFDYEVV----LVVAPDHPLAAKEFITPEDLAD 97 (198)
T ss_pred hCCCeEEEEEeCCchhHHHHHHcCCceEEEecCCcCCCCc---EEEEccCCcEE----EEEcCCCChHHcccCCHHHhcC
Confidence 3566665544 34578999999999999996421100110 01122222332 223344444332222333322
Q ss_pred -EEEech--H-HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 -RVLSHP--Q-ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 -~V~SHp--q-al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
....++ . .......|+.+.+.. ...++|...+.++++.+ .+ .++.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~g-i~~lp~~~~~ 155 (198)
T cd08441 98 ETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASG--RG-VAALPNWAVR 155 (198)
T ss_pred CceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhC--Cc-EEEeeHHHHH
Confidence 222222 1 123345666665432 23566666677777765 33 4566655443
No 238
>PRK06291 aspartate kinase; Provisional
Probab=37.02 E-value=4e+02 Score=26.35 Aligned_cols=94 Identities=14% Similarity=0.025 Sum_probs=53.7
Q ss_pred EEecCHHHHHHHhhhcCCCCeEEecChhhH---HHcCCceeecccccCCCCceEEEEEeeCC-CCC---C-CCCCcEEEE
Q 048784 115 EAVDDTAGAAKYVSFEQLKDAGAVASSSAA---AIYGLNILAEDIQDDCDNVTRFLMLAREP-IIP---G-TDRPFKTSI 186 (282)
Q Consensus 115 ~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa---~~ygL~vl~~~I~d~~~N~TRF~vl~~~~-~~~---~-~~~~~ktsi 186 (282)
+..-|..+|.++...+ +-+-.+.|+ ..+|+++.-.+..+..+.-|..- .... ..+ . ...++.+.+
T Consensus 252 i~~l~~~ea~~l~~~G-----~~v~~~~a~~~~~~~~i~i~i~~~~~~~~~gt~i~--~~~~~~~~~V~~It~~~~valI 324 (465)
T PRK06291 252 IPKISYIEAMELSYFG-----AKVLHPRTIEPAMEKGIPVRVKNTFNPEFPGTLIT--SDSESSKRVVKAVTLIKNVALI 324 (465)
T ss_pred ccccCHHHHHHHHhCC-----CcccCHHHHHHHHHcCCcEEEecCCCCCCCceEEE--ecccccCcccceEEeeCCEEEE
Confidence 3344555666554322 233334443 45899999988776554555542 2111 100 0 001222333
Q ss_pred EEE---cCCCccHHHHHHHHHHHCCceeeeee
Q 048784 187 VFS---LEEGPGVLFKALAVFALRQINLTKIE 215 (282)
Q Consensus 187 ~~~---~~~~pG~L~~~L~~F~~~~INlt~Ie 215 (282)
.+. ..+.||.+.++++.|+++|||+-.|-
T Consensus 325 sI~g~~m~~~~g~~arvf~~L~~~gI~V~mIs 356 (465)
T PRK06291 325 NISGAGMVGVPGTAARIFSALAEEGVNVIMIS 356 (465)
T ss_pred EEeCCCCCCCccHHHHHHHHHHHCCCcEEEEE
Confidence 332 24679999999999999999998884
No 239
>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=36.90 E-value=52 Score=30.06 Aligned_cols=126 Identities=18% Similarity=0.127 Sum_probs=67.4
Q ss_pred CCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHcCCCCeEEEeeeec----cccceeccc-------ccccc----C
Q 048784 3 RGAYSESAAEKAYP----NCEAVPCEQFDTAFEAVERWLVDRAVLPIENS----LGGSIHRNY-------DLLLR----H 63 (282)
Q Consensus 3 ~GTfS~~Aa~~~~~----~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS----~~G~V~~t~-------d~L~~----~ 63 (282)
.|+.+|.++..+.. +.+.+|+++-.+.+.++..|++|.++...-+. -.|.+..-. +.|-+ .
T Consensus 114 ~g~~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~~~~~~~~~~G~~k~Lav~~~~r~~~~pdvPT~~ 193 (274)
T PF03401_consen 114 PGSSDHLAAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSPGEALPYVEAGDLKPLAVFSDERSPALPDVPTFK 193 (274)
T ss_dssp TTSHHHHHHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHTTSEEEEEECSSS-BTTCTTS-BTT
T ss_pred CCchHHHHHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecHHHHHHHHhCCCceEEEEecCccccccCCCCCHH
Confidence 48889988776542 46789999999999999999999998765433 234443211 11111 0
Q ss_pred CeEEEEEEEEeeeeeeeecCCCCCCCccEEEechH---HHHHHHHHHHhcCCeEEEecCHHHHHHHhhhc
Q 048784 64 RLHIVGEVKFAVRHCLLANPGVKVEDLKRVLSHPQ---ALAQCENTLTKLGLVREAVDDTAGAAKYVSFE 130 (282)
Q Consensus 64 ~l~I~~E~~l~I~~~L~a~~~~~l~~I~~V~SHpq---al~QC~~fl~~~~~~~~~~~sTa~Aa~~v~~~ 130 (282)
+.-+ .++.+..-+.+++++|++.+-+.++..--+ .....++|+++.+.... ..+..+..+.+.++
T Consensus 194 E~G~-~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~~g~~~~-~~~~~~~~~~l~~~ 261 (274)
T PF03401_consen 194 EQGY-PDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEKMGLEPV-YMDGEEFDAFLAEE 261 (274)
T ss_dssp TTT--TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHHHTEEEE-CESHHHHHHHHHHH
T ss_pred HhCc-cceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHHCCCcCC-CCCHHHHHHHHHHH
Confidence 0100 022344557788888875333222221111 11233455665555433 45566666666553
No 240
>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=36.36 E-value=2.1e+02 Score=22.45 Aligned_cols=121 Identities=18% Similarity=0.134 Sum_probs=59.3
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCC---c
Q 048784 15 YPNCEAVP-CEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVED---L 90 (282)
Q Consensus 15 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~---I 90 (282)
+|+.++.. ..+..++.+++.+|++|+|++.......+... ..|.+..+.++ ++-.|-+......++++ .
T Consensus 26 ~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~~~~~~~~~i~~~~l~~~ 98 (201)
T cd08420 26 YPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLIV---EPFAEDELVLV----VPPDHPLAGRKEVTAEELAAE 98 (201)
T ss_pred CCCceEEEEeCCcHHHHHHHHCCCccEEEecCCCCCcceEE---EeecCccEEEE----ecCCCCccccCccCHHHHhcC
Confidence 56665433 34667899999999999999854332122111 12223333322 22333333222222222 3
Q ss_pred cEEEechH--HHHHHHHHHHhcC-----Ce-EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 91 KRVLSHPQ--ALAQCENTLTKLG-----LV-REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 91 ~~V~SHpq--al~QC~~fl~~~~-----~~-~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
.-|.-.+. -..+..+|+.+.+ .. ...+.+...+.++++.+ ...|+.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08420 99 PWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAG---LGISILSRLAVR 158 (201)
T ss_pred CEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcC---CCEEEeeHHHHH
Confidence 33332211 1234556666432 12 23456666677777754 345666665553
No 241
>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=35.78 E-value=33 Score=25.47 Aligned_cols=77 Identities=16% Similarity=0.152 Sum_probs=48.8
Q ss_pred EEechHHHHHHHHHHHhcCC-eEEEecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeecccccCCCCceEEEEEee
Q 048784 93 VLSHPQALAQCENTLTKLGL-VREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAEDIQDDCDNVTRFLMLAR 171 (282)
Q Consensus 93 V~SHpqal~QC~~fl~~~~~-~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~~I~d~~~N~TRF~vl~~ 171 (282)
|-.||.-..-.+.+|...+. ....+.|..+|.+.+.... ++ .+|..-.-....|+.++.. |.... ..+++++++.
T Consensus 4 vd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~~-~d-~iiid~~~~~~~~~~~~~~-i~~~~-~~~~ii~~t~ 79 (112)
T PF00072_consen 4 VDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLKKHP-PD-LIIIDLELPDGDGLELLEQ-IRQIN-PSIPIIVVTD 79 (112)
T ss_dssp EESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHST-ES-EEEEESSSSSSBHHHHHHH-HHHHT-TTSEEEEEES
T ss_pred EECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhcccC-ce-EEEEEeeeccccccccccc-ccccc-ccccEEEecC
Confidence 44578888888899997787 6677788888888876652 33 3443322223445554443 43333 7788888886
Q ss_pred CC
Q 048784 172 EP 173 (282)
Q Consensus 172 ~~ 173 (282)
..
T Consensus 80 ~~ 81 (112)
T PF00072_consen 80 ED 81 (112)
T ss_dssp ST
T ss_pred CC
Confidence 53
No 242
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=35.75 E-value=62 Score=27.80 Aligned_cols=35 Identities=26% Similarity=0.270 Sum_probs=29.5
Q ss_pred EEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeee
Q 048784 184 TSIVFSLEEGPGVLFKALAVFALRQINLTKIESRP 218 (282)
Q Consensus 184 tsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP 218 (282)
..+.-+..+.||.|..+.+..++|||++-.+-|+=
T Consensus 96 iei~~~~~~~pgi~A~V~~~iak~gi~Irqi~~~d 130 (167)
T COG2150 96 IEIYPEDARYPGILAGVASLIAKRGISIRQIISED 130 (167)
T ss_pred EEEEeccCCCccHHHHHHHHHHHcCceEEEEecCC
Confidence 34555567899999999999999999999888873
No 243
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=34.73 E-value=3.2e+02 Score=24.11 Aligned_cols=122 Identities=16% Similarity=0.124 Sum_probs=60.5
Q ss_pred hCCCCceee-cCCHHHHHHHHHcCCCCeEEEeeeeccccceeccc--cccccCCeEEEEEEEEeeeeeeeecCCCCCCCc
Q 048784 14 AYPNCEAVP-CEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNY--DLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL 90 (282)
Q Consensus 14 ~~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~--d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I 90 (282)
.+|+.++.- ..+-.++++++.+|++|+|++.-.... ....+ ..|.+.++. +..+-+|-|...+..+++++
T Consensus 122 ~~p~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~---~~~~l~~~~l~~~~~~----~v~~~~~~l~~~~~~~~~dL 194 (294)
T PRK09986 122 ENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLE---PNPGFTSRRLHESAFA----VAVPEEHPLASRSSVPLKAL 194 (294)
T ss_pred hCCCeEEEEEeCCHHHHHHHHHcCCCCEEEecCCccC---CCCCeEEEEeecccEE----EEEcCCCCcccCCccCHHHH
Confidence 356655433 345688999999999999997311000 01111 122222222 22334444443333334443
Q ss_pred c---EEEech--HHHH-HHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 91 K---RVLSHP--QALA-QCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 91 ~---~V~SHp--qal~-QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
. -|...+ ..+. +...++.+.+.. ...++|......+|+.+ ...++.++..++
T Consensus 195 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~l~~~~~~ 255 (294)
T PRK09986 195 RNEYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG---IGITLLPDSYAQ 255 (294)
T ss_pred cCCCEEecCCCchhHHHHHHHHHHHCCCCCceeeecCCHHHHHHHHHcC---CeEEEccHHHhh
Confidence 3 343222 1233 555566555432 23456666666667654 356777776654
No 244
>TIGR03339 phn_lysR aminoethylphosphonate catabolism associated LysR family transcriptional regulator. This group of sequences represents a number of related clades with numerous examples of members adjacent to operons for the degradation of 2-aminoethylphosphonate (AEP) in Pseudomonas, Ralstonia, Bordetella and Burkholderia species. These are transcriptional regulators of the LysR family which contain a helix-turn-helix (HTH) domain (pfam00126) and a periplasmic substrate-binding protein-like domain (pfam03466).
Probab=34.18 E-value=3.2e+02 Score=23.81 Aligned_cols=118 Identities=19% Similarity=0.153 Sum_probs=59.6
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCC---c
Q 048784 15 YPNCEAVP-CEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVED---L 90 (282)
Q Consensus 15 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~---I 90 (282)
+|+.++.. ..+..++++.+.+|++|.|++.......+.. ...|...++.++ .+-+|-|......++++ .
T Consensus 110 ~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~lv----~s~~~pl~~~~~i~~~~L~~~ 182 (279)
T TIGR03339 110 YPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRLD---RVVLGNDPLVAV----VHRQHPLAERESVTLEELAGQ 182 (279)
T ss_pred CCCcEEEEEECCHHHHHHHHHcCCCcEEEEecccCCCceE---EEEcCCceEEEE----ECCCCccccCCCcCHHHHhCC
Confidence 46665543 3578899999999999999975332221111 112222222221 12233333222223223 2
Q ss_pred cEEEech--HHHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChh
Q 048784 91 KRVLSHP--QALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSS 142 (282)
Q Consensus 91 ~~V~SHp--qal~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~ 142 (282)
.-|...+ ........|+.+++.. ...+.|...+.+++..+ .+ .++.+..
T Consensus 183 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~g-i~~lp~~ 236 (279)
T TIGR03339 183 PLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAG--LG-VSVVSAA 236 (279)
T ss_pred CeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcC--CC-EEEcchh
Confidence 3333222 1234567777776432 23466777667777654 33 4555554
No 245
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=34.04 E-value=3e+02 Score=24.10 Aligned_cols=35 Identities=11% Similarity=0.244 Sum_probs=25.1
Q ss_pred HHHhhCCCCceeecCCHHHHHHHHHcCCCCeEEEee
Q 048784 10 AAEKAYPNCEAVPCEQFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 10 Aa~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPi 45 (282)
++++.--+.++++. ++..+++++++|++|.++-++
T Consensus 59 ia~~lg~~i~~~~~-pw~~~~~~l~~g~~D~~~~~~ 93 (259)
T PRK15437 59 LCKRINTQCTFVEN-PLDALIPSLKAKKIDAIMSSL 93 (259)
T ss_pred HHHHcCCceEEEeC-CHHHHHHHHHCCCCCEEEecC
Confidence 34443235677775 599999999999999776444
No 246
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=33.98 E-value=3.1e+02 Score=23.66 Aligned_cols=122 Identities=13% Similarity=0.096 Sum_probs=59.4
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecC----CCCCCC
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANP----GVKVED 89 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~----~~~l~~ 89 (282)
+|+.++... .+.+++.+.+.+|++|+|++...+...+.+. ...|...++.++ .+-+|.+.... -.++.+
T Consensus 93 ~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~--~~~l~~~~~~~v----~~~~~~~~~~~~~~~~~~l~~ 166 (269)
T PRK11716 93 HPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVA--FSPIDEIPLVLI----APALPCPVRQQLSQEKPDWSR 166 (269)
T ss_pred CCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcceE--EEEcccceEEEE----EcCCcchhhhccccchhhHhh
Confidence 566655443 5678999999999999999854332222111 122333333332 23333332211 112223
Q ss_pred ccEEE-echHHHHHHHHHHHhcCCe--E-EEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 90 LKRVL-SHPQALAQCENTLTKLGLV--R-EAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 90 I~~V~-SHpqal~QC~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
..-|. +.......-..|+..++.. . ..++|......++..+ ...++.+...++
T Consensus 167 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 223 (269)
T PRK11716 167 IPFILPEHGPARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALG---CGVGLLPEVVLE 223 (269)
T ss_pred CCeeecCCCchHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcC---CCeEeccHHHhh
Confidence 33332 1111112234566655432 2 3455665566666654 345777776654
No 247
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=33.21 E-value=2.1e+02 Score=30.98 Aligned_cols=32 Identities=13% Similarity=0.159 Sum_probs=28.3
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeee
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKI 214 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~I 214 (282)
-|-+++..+|+||-+.++-++|+.+|+|+..=
T Consensus 704 ~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A 735 (895)
T PRK00275 704 GTQIFIYAPDQHDFFAATVAAMDQLNLNIHDA 735 (895)
T ss_pred eEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEE
Confidence 46788888999999999999999999999853
No 248
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=31.55 E-value=1e+02 Score=27.27 Aligned_cols=42 Identities=17% Similarity=0.242 Sum_probs=30.5
Q ss_pred CCcHHHHHHHhhC--CCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 3 RGAYSESAAEKAY--PNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 3 ~GTfS~~Aa~~~~--~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
.|++.++-...++ .+.+++...+.++++++|.+|++|+.+..
T Consensus 140 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~ 183 (259)
T PRK15437 140 QGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQD 183 (259)
T ss_pred cCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEec
Confidence 4665544433332 24678899999999999999999998753
No 249
>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=30.95 E-value=3.5e+02 Score=23.37 Aligned_cols=120 Identities=17% Similarity=0.102 Sum_probs=0.0
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceecccccc-ccCCeEEEEEEEEee------eeeeeecCCCCCCC
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLL-LRHRLHIVGEVKFAV------RHCLLANPGVKVED 89 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L-~~~~l~I~~E~~l~I------~~~L~a~~~~~l~~ 89 (282)
+.++++..++.+.+.++.+|++|+++.+ ..++... .+.+.......+... ...|+++++..+.+
T Consensus 65 ~v~~~~~~~~~~~~~~l~~g~~Di~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~lvv~~d~~i~~ 135 (254)
T TIGR01098 65 KVQLFVATDYSAVIEAMRFGRVDIAWFG---------PSSYVLAHYRANAEVFALTAVSTDGSPGYYSVIIVKADSPIKS 135 (254)
T ss_pred cEEEEeCCCHHHHHHHHHcCCccEEEEC---------cHHHHHHHHhcCCceEEeeccccCCCCceEEEEEEECCCCCCC
Q ss_pred cc-----EEEech----HHHHHHHHHHHhc-C-------CeEEEecCHHHHHHHhhhcCCCCeEEecChhhHHHc
Q 048784 90 LK-----RVLSHP----QALAQCENTLTKL-G-------LVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIY 147 (282)
Q Consensus 90 I~-----~V~SHp----qal~QC~~fl~~~-~-------~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~y 147 (282)
+. +|.... ....--..+|.+. + ..++...+..++.+.+..+ +..|++.....+..+
T Consensus 136 ~~dL~gk~I~~~~~~s~~~~~~~~~~l~~~~~~~~~~~~~~i~~~~~~~~~~~al~~G--~~Da~~~~~~~~~~~ 208 (254)
T TIGR01098 136 LKDLKGKTFAFGDPASTSGYLVPRYQLKKEGGLDADGFFSEVVFSGSHDASALAVANG--KVDAATNNSSAIGRL 208 (254)
T ss_pred hHHhcCCEEEeeCCCCccchHhHHHHHHHhcCCChHHhhhheeecCchHHHHHHHHcC--CCCeEEecHHHHHHH
No 250
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=30.57 E-value=2.7e+02 Score=21.87 Aligned_cols=30 Identities=23% Similarity=0.084 Sum_probs=23.1
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
+|+.++... .+-.++++.+.+|++|+|++.
T Consensus 26 ~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~ 56 (197)
T cd08438 26 YPNIELELVEYGGKKVEQAVLNGELDVGITV 56 (197)
T ss_pred CcCeEEEEEEcCcHHHHHHHHcCCCCEEEEe
Confidence 566655433 466889999999999999975
No 251
>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=30.18 E-value=2.8e+02 Score=21.95 Aligned_cols=121 Identities=14% Similarity=0.054 Sum_probs=59.3
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc---
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL--- 90 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I--- 90 (282)
+|+.++.... +..++.+.+.+|++|+|+..-.....+.. ...|.+.++.+ ..+-+|-+...+..+++++
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~----v~~~~hpl~~~~~~~~~~l~~~ 98 (199)
T cd08426 26 YPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGIR---VHSRQPAPIGA----VVPPGHPLARQPSVTLAQLAGY 98 (199)
T ss_pred CCCeEEEEEeCCcHHHHHHHHCCCccEEEecCCCCCCCeE---EEeeccCcEEE----EecCCCCcccCCccCHHHHhCC
Confidence 4665554433 56789999999999999975332212111 11222223322 2233343332222222222
Q ss_pred cEEEechH--HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 91 KRVLSHPQ--ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 91 ~~V~SHpq--al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
.-|.-.+. .......|+.+++.. ...+.|...+..++..+ ...|+.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (199)
T cd08426 99 PLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAG---GGISLLTELAVR 155 (199)
T ss_pred CeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcC---CCEEEEchHhhh
Confidence 23322211 123345666665432 23456666677777765 345676765443
No 252
>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=29.53 E-value=2.8e+02 Score=21.79 Aligned_cols=33 Identities=18% Similarity=0.074 Sum_probs=24.4
Q ss_pred hhCCCCceeec-CCHHHHHHHHHcCCCCeEEEee
Q 048784 13 KAYPNCEAVPC-EQFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 13 ~~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPi 45 (282)
+.+|+.++... .+..+..+++.+|++|+|++.-
T Consensus 24 ~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08415 24 ARHPDVRISLHTLSSSTVVEAVLSGQADLGLASL 57 (196)
T ss_pred HHCCCcEEEEEecchHHHHHHHHcCCccEEEEeC
Confidence 34577665433 3567899999999999999863
No 253
>PRK02047 hypothetical protein; Provisional
Probab=29.27 E-value=2.6e+02 Score=21.33 Aligned_cols=59 Identities=22% Similarity=0.357 Sum_probs=39.6
Q ss_pred CCCccHHHHHHHHHHHC--CceeeeeeeeeCCCCCCCCCCCCCCCCcceeE-EEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 191 EEGPGVLFKALAVFALR--QINLTKIESRPLRNQPLRSSDDNSGFGKYFDY-LFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 191 ~~~pG~L~~~L~~F~~~--~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y-~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
++.++....+.+++..+ ++....|.+||+++. .| .+=|.+.... .+.+..+.++|.+.-
T Consensus 24 ~~~~~~~~~v~~iv~~~~~~~~~~~i~~k~Ss~G---------------kY~Svtv~v~v~s-~eq~~~iY~~L~~~~ 85 (91)
T PRK02047 24 KAHPEFADTIFKVVSVHDPEFDLEKIEERPSSGG---------------NYTGLTITVRATS-REQLDNIYRALTGHP 85 (91)
T ss_pred eCcHhHHHHHHHHHHHhCCCCccCceEEccCCCC---------------eEEEEEEEEEECC-HHHHHHHHHHHhhCC
Confidence 45566666777777766 566788999999872 45 3555555543 456677888887653
No 254
>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=29.23 E-value=1.4e+02 Score=23.56 Aligned_cols=116 Identities=12% Similarity=-0.019 Sum_probs=55.6
Q ss_pred CCCCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCc---c
Q 048784 15 YPNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDL---K 91 (282)
Q Consensus 15 ~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I---~ 91 (282)
+|+.++.... .+..+.+.+|++|+|+..-.-...|. ....|.+.++.++ .+-+| +......+++++ .
T Consensus 26 ~P~i~l~~~~--~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~-~~~~~~~~~~~L~~~~ 95 (190)
T cd08483 26 HPEIELSLLP--SADLVDLRPDGIDVAIRYGNGDWPGL---ESEPLTAAPFVVV----AAPGL-LGDRKVDSLADLAGLP 95 (190)
T ss_pred CCCceEEEEe--cCCcCCCCCCCcCEEEEecCCCCCCc---EEEeecccceEee----eCHHH-HhhCCCCCHHHHhcCc
Confidence 5665544332 23467789999999998532111221 1123344444433 23334 332222233333 3
Q ss_pred EEEechHHHHHHHHHHHhcCCe-----EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 RVLSHPQALAQCENTLTKLGLV-----REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 ~V~SHpqal~QC~~fl~~~~~~-----~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
-|. +.. ......|+.+++.. ...+.|.....++++.+ ...++.+...++
T Consensus 96 ~i~-~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~~ 149 (190)
T cd08483 96 WLQ-ERG-TNEQRVWLASMGVVPDLERGVTFLPGQLVLEAARAG---LGLSIQARALVE 149 (190)
T ss_pred eec-cCC-chHHHHHHHHcCCCcccccCceeCcHHHHHHHHHcC---CcEEeecHHhhH
Confidence 332 221 12345677765432 13345666666667654 345666655443
No 255
>PRK07431 aspartate kinase; Provisional
Probab=29.07 E-value=1.9e+02 Score=29.44 Aligned_cols=58 Identities=17% Similarity=0.197 Sum_probs=39.0
Q ss_pred EcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 189 SLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 189 ~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
.+.+.||.+.++++.|+++|||.-.|-.-+.... ..++.|.|+-+- -.+..+++++++
T Consensus 277 ~~~~~~g~~a~if~~l~~~~I~v~~i~qs~~~~~-------------~~~isf~i~~~d---~~~~~~~l~~l~ 334 (587)
T PRK07431 277 RVPDRPGIAAQLFEELAAQGVNVDLIIQSIHEGN-------------SNDIAFTVAENE---LKKAEAVAEAIA 334 (587)
T ss_pred cCCCcccHHHHHHHHHHHcCCcEEEEEeccCCCC-------------CccEEEEEeHHH---HHHHHHHHHHHH
Confidence 3467899999999999999999999964443221 136788885421 123445555554
No 256
>cd00460 RNAP_RPB11_RPB3 RPB11 and RPB3 subunits of RNA polymerase. The eukaryotic RPB11 and RPB3 subunits of RNA polymerase (RNAP), as well as their archaeal (L and D subunits) and bacterial (alpha subunit) counterparts, are involved in the assembly of RNAP, a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is a final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei: RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. The assembly of the two largest eukaryotic RNAP subunits that provide most of the enzyme's catalytic functions depends on the presence of RPB3/RPB11 heterodimer subunits. This is also true for the
Probab=28.47 E-value=1.3e+02 Score=22.54 Aligned_cols=30 Identities=10% Similarity=0.204 Sum_probs=22.5
Q ss_pred eeEEEEEEeecCCCcH-HHHHHHHHHHhhcC
Q 048784 237 FDYLFYVDFEASMADQ-KAQNALRHLKEFAT 266 (282)
Q Consensus 237 ~~y~F~vd~~g~~~~~-~~~~al~~l~~~~~ 266 (282)
..+.|.|+-.|..... .+.+|++.|.+.+.
T Consensus 54 d~~~~~VeT~Gs~~P~~al~~Ai~~L~~~~~ 84 (86)
T cd00460 54 DKFILRIETVGSIPPEEALRRAVEILRKKLE 84 (86)
T ss_pred CeEEEEEEECCCCCHHHHHHHHHHHHHHHHh
Confidence 3688899999876544 46788888887754
No 257
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=28.38 E-value=1.5e+02 Score=29.24 Aligned_cols=72 Identities=21% Similarity=0.343 Sum_probs=53.5
Q ss_pred EEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh--
Q 048784 187 VFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF-- 264 (282)
Q Consensus 187 ~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~-- 264 (282)
-+...|+-|-.-++|..+..++|||..||--|.. ..|++|-. .+-+.+++++.+|+..
T Consensus 4 eV~cedRlGltrelLdlLv~r~idl~~iEid~~~-------------------~IYln~p~-l~~~~fs~L~aei~~I~G 63 (511)
T COG3283 4 EVFCEDRLGLTRELLDLLVLRGIDLRGIEIDPIG-------------------RIYLNFPE-LEFESFSSLMAEIRRIPG 63 (511)
T ss_pred EEEehhhhchHHHHHHHHHhcccCccceeecCCC-------------------eEEEeccc-cCHHHHHHHHHHHhcCCC
Confidence 3455789999999999999999999999986643 34566633 3446778888888865
Q ss_pred cCceEEEccccCCC
Q 048784 265 ATFLRVLGSYPIDT 278 (282)
Q Consensus 265 ~~~v~~LGsY~~~~ 278 (282)
...|+..+-.|..+
T Consensus 64 V~~vr~V~~mPseR 77 (511)
T COG3283 64 VTDVRTVPWMPSER 77 (511)
T ss_pred ccceeeecCCcchh
Confidence 34677777777543
No 258
>PRK15385 magnesium transport protein MgtC; Provisional
Probab=28.27 E-value=4.2e+02 Score=23.94 Aligned_cols=66 Identities=11% Similarity=0.032 Sum_probs=43.0
Q ss_pred EEEEEcCCCc--cHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCC-CcHHHHHHHHHH
Q 048784 185 SIVFSLEEGP--GVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASM-ADQKAQNALRHL 261 (282)
Q Consensus 185 si~~~~~~~p--G~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~-~~~~~~~al~~l 261 (282)
.+.+...+++ ..+..+++.+...++.+..+++++.++. .+..-..++..+. ++..+.+++..|
T Consensus 144 ~~~v~~~~~~~~~vr~~L~~~l~~~~~~~~~l~~~~~~~~--------------~~~ei~a~l~~~~~~~~~le~iv~~L 209 (225)
T PRK15385 144 ILKVTCNKEDESAVRQWLLNIVKEAAICLQGLGSVPAQEQ--------------GYKEIRAELVGHADYRKTRELIISRI 209 (225)
T ss_pred EEEEEEcCcchhHHHHHHHHHHHhCCCceEEeEeeecCCC--------------CeEEEEEEEEecCCchhhHHHHHHHH
Confidence 3344444444 4577888999999999999999987542 1334444444332 456778888888
Q ss_pred Hhh
Q 048784 262 KEF 264 (282)
Q Consensus 262 ~~~ 264 (282)
...
T Consensus 210 ~~~ 212 (225)
T PRK15385 210 GDN 212 (225)
T ss_pred hCC
Confidence 754
No 259
>cd05466 PBP2_LTTR_substrate The substrate binding domain of LysR-type transcriptional regulators (LTTRs), a member of the type 2 periplasmic binding fold protein superfamily. This model and hierarchy represent the the substrate-binding domain of the LysR-type transcriptional regulators that form 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 bin
Probab=27.68 E-value=2.8e+02 Score=21.24 Aligned_cols=32 Identities=22% Similarity=0.255 Sum_probs=22.3
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEeee
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIE 46 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiE 46 (282)
+|+.++... .+-.++.+.+.+|++|+|+....
T Consensus 26 ~p~i~i~~~~~~~~~~~~~l~~g~~D~~i~~~~ 58 (197)
T cd05466 26 YPGVELSLVEGGSSELLEALLEGELDLAIVALP 58 (197)
T ss_pred CCCCEEEEEECChHHHHHHHHcCCceEEEEcCC
Confidence 465544322 23458999999999999997643
No 260
>PRK04998 hypothetical protein; Provisional
Probab=27.59 E-value=2.7e+02 Score=20.98 Aligned_cols=60 Identities=10% Similarity=0.081 Sum_probs=40.9
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeE-EEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDY-LFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y-~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
-+..++.+..+..+|.++--.-..+.+||+++ +.| .+=|.+..+. .+.+....++|++.-
T Consensus 22 g~~~~~~~~~v~~v~~~~~~~~~~~~~r~S~~---------------GkY~Svtv~v~v~s-~eq~~~iY~~L~~~~ 82 (88)
T PRK04998 22 GLARPELVDQVVEVVQRHAPGDYTPTVKPSSK---------------GNYHSVSITITATS-IEQVETLYEELAKIE 82 (88)
T ss_pred EeCcHhHHHHHHHHHHHhCCCCCCceEccCCC---------------CEEEEEEEEEEECC-HHHHHHHHHHHhcCC
Confidence 34567788888888877643444588999876 256 4666666654 456677888887653
No 261
>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=27.48 E-value=3.1e+02 Score=21.65 Aligned_cols=122 Identities=13% Similarity=0.047 Sum_probs=59.6
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeec--cccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCC--
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENS--LGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVE-- 88 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS--~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~-- 88 (282)
.+|+.++... .+-.++.+.+.+|++|+|+...... -.+.. ...|.+.++. +.++-.|-+......+++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~l~---~~~l~~~~~~----~v~~~~hp~~~~~~~~~~~L 97 (199)
T cd08416 25 RRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDFE---VVPLFEDDIF----LAVPATSPLAASSEIDLRDL 97 (199)
T ss_pred hCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCCCCCeE---EEEeecceEE----EEECCCCcccccCccCHHHh
Confidence 3576655444 3456789999999999999864321 01111 1112222222 233444544432222222
Q ss_pred -CccEEE-echH-HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 89 -DLKRVL-SHPQ-ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 89 -~I~~V~-SHpq-al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
+..-|. +... ......+++.+.+.. ...++|...+.++++.+ ...++++...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (199)
T cd08416 98 KDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGG---VGYALLPGRIAD 157 (199)
T ss_pred cCCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcC---CcEEEechhhhh
Confidence 333332 2222 122355566655432 23455666666777754 235666665444
No 262
>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=26.91 E-value=3.5e+02 Score=22.07 Aligned_cols=31 Identities=10% Similarity=-0.124 Sum_probs=22.6
Q ss_pred CCCCceee-cCCHHHHHHHHHcCCCCeEEEee
Q 048784 15 YPNCEAVP-CEQFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 15 ~~~~~~~~-~~s~~~v~~av~~g~~d~gVvPi 45 (282)
+|+.++.- ..+-.++.+.+.+|++|+|+...
T Consensus 26 ~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 26 APGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred CCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 56655433 23566889999999999999853
No 263
>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=26.77 E-value=3e+02 Score=26.87 Aligned_cols=51 Identities=31% Similarity=0.434 Sum_probs=37.7
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+.+.||.+.++++.++++|||+..|.+ +. -...|.|+- ....++++.|.+.
T Consensus 388 ~~~~~g~~a~if~~La~~~Inv~~i~~--se----------------~~Is~vV~~------~d~~~a~~~Lh~~ 438 (441)
T TIGR00657 388 MKSAPGVASKIFEALAQNGINIEMISS--SE----------------INISFVVDE------KDAEKAVRLLHNA 438 (441)
T ss_pred CCCCCchHHHHHHHHHHCCCCEEEEEe--cC----------------CcEEEEEeH------HHHHHHHHHHHHH
Confidence 467899999999999999999999974 11 146777764 3345667776654
No 264
>PF09383 NIL: NIL domain; InterPro: IPR018449 This domain is found at the C terminus of ABC transporter proteins involved in D-methionine transport as well as a number of ferredoxin-like proteins. This domain is likely to act as a substrate binding domain. The domain has been named after a conserved sequence in some members of the family. ; PDB: 2QRR_A 3CED_A 2QSW_A 3TUZ_D 3TUJ_D 3DHX_B 3TUI_H 3DHW_D.
Probab=26.76 E-value=1.2e+02 Score=21.70 Aligned_cols=30 Identities=20% Similarity=0.409 Sum_probs=23.4
Q ss_pred EEEEEeecCCCcHHHHHHHHHHHhhcCceEEE
Q 048784 240 LFYVDFEASMADQKAQNALRHLKEFATFLRVL 271 (282)
Q Consensus 240 ~F~vd~~g~~~~~~~~~al~~l~~~~~~v~~L 271 (282)
.+++++.|+ +++++++++.|++....+.+|
T Consensus 47 ~l~l~l~g~--~~~~~~a~~~L~~~~v~vEvl 76 (76)
T PF09383_consen 47 ILILELPGD--DEEIEKAIAYLREQGVEVEVL 76 (76)
T ss_dssp EEEEEEES---HHHHHHHHHHHHHTTEEEEEE
T ss_pred EEEEEEECC--HHHHHHHHHHHHHCCCeEEEC
Confidence 678899884 467899999999887666654
No 265
>PRK00341 hypothetical protein; Provisional
Probab=26.65 E-value=2.9e+02 Score=21.08 Aligned_cols=59 Identities=15% Similarity=0.250 Sum_probs=40.1
Q ss_pred CCCccHHHHHHHHHHHC-CceeeeeeeeeCCCCCCCCCCCCCCCCcceeE-EEEEEeecCCCcHHHHHHHHHHHhhc
Q 048784 191 EEGPGVLFKALAVFALR-QINLTKIESRPLRNQPLRSSDDNSGFGKYFDY-LFYVDFEASMADQKAQNALRHLKEFA 265 (282)
Q Consensus 191 ~~~pG~L~~~L~~F~~~-~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y-~F~vd~~g~~~~~~~~~al~~l~~~~ 265 (282)
.+.++....+++++.++ .++...|.+||+++ +.| .+=|.+.... .+.+..+.++|+...
T Consensus 25 ~~~~~~~~~V~~iv~~~~~~~~~~~~~k~Ss~---------------GkY~S~tv~i~~~s-~~q~~~iy~~L~~~~ 85 (91)
T PRK00341 25 DTGVGFKDLVIEILQKHADVDLSTLAERQSSN---------------GKYTTVQLHIVATD-EDQLQDINSALRATG 85 (91)
T ss_pred cCchhHHHHHHHHHHHhCCCcccceeeccCCC---------------CEEEEEEEEEEECC-HHHHHHHHHHHhhCC
Confidence 35677777777777655 44567889999987 245 3555555543 466778888887664
No 266
>TIGR02122 TRAP_TAXI TRAP transporter solute receptor, TAXI family. This family is one of at least three major families of extracytoplasmic solute receptor (ESR) for TRAP (Tripartite ATP-independent Periplasmic Transporter) transporters. The others are the DctP (TIGR00787) and SmoM (pfam03480) families. These transporters are secondary (driven by an ion gradient) but composed of three polypeptides, although in some species the 4-TM and 12-TM integral membrane proteins are fused. Substrates for this transporter family are not fully characterized but, besides C4 dicarboxylates, may include mannitol and other compounds.
Probab=26.52 E-value=72 Score=28.87 Aligned_cols=44 Identities=20% Similarity=0.231 Sum_probs=32.8
Q ss_pred CCCCcHHHHHHHhhCC--C-----CceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 1 GVRGAYSESAAEKAYP--N-----CEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 1 GP~GTfS~~Aa~~~~~--~-----~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
|+.|+.++....+++. + ...+++.+..+++.+|.+|++|.++..
T Consensus 147 ~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 147 GAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred CCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEEe
Confidence 4567777776665543 1 224688899999999999999999875
No 267
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=26.47 E-value=4.8e+02 Score=23.47 Aligned_cols=146 Identities=21% Similarity=0.180 Sum_probs=90.0
Q ss_pred CCCcHHHHHHHhhCC--------C--CceeecC---CHHHHHHHHHcCCCCeEEEeeeeccccceecccc----------
Q 048784 2 VRGAYSESAAEKAYP--------N--CEAVPCE---QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYD---------- 58 (282)
Q Consensus 2 P~GTfS~~Aa~~~~~--------~--~~~~~~~---s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d---------- 58 (282)
|+|+...+++.++.. . .++.|-. +-.+++++|.+|.+|.++++.-+. .+.+ +.+.
T Consensus 6 p~~~~~~~~~~~fa~~v~e~t~G~v~i~v~~~g~lg~~~e~~~~v~~G~vdm~~~~~~~~-~~~~-p~~~~~~lP~~~~~ 83 (286)
T PF03480_consen 6 PEGHPITQAVEKFAEEVEERTGGRVKIEVFPAGQLGKEAEVLEAVQDGAVDMAVVSPSYL-AGFV-PEFGVFDLPFLFRD 83 (286)
T ss_dssp TTTSHHHHHHHHHHHHHHHHTTTSEEEEEEETTSSSSHHHHHHHHHTTSSSEEEEEGGGG-TTTS-GGGGGGGSTTTSSS
T ss_pred CCCCHHHHHHHHHHHHHHHHcCCeEEEEEecCcccCCHHHHHHHHhCCCccEEeecchhh-hhhc-hhheeeeCCCCCCC
Confidence 788888888866532 2 2444544 477999999999999999887443 2221 1111
Q ss_pred ------------------ccccCCeEEEEEEEEeeeeeeee-cCCCCCCCcc--EEEechHHHHHHHHHHHhcCCeEEEe
Q 048784 59 ------------------LLLRHRLHIVGEVKFAVRHCLLA-NPGVKVEDLK--RVLSHPQALAQCENTLTKLGLVREAV 117 (282)
Q Consensus 59 ------------------~L~~~~l~I~~E~~l~I~~~L~a-~~~~~l~~I~--~V~SHpqal~QC~~fl~~~~~~~~~~ 117 (282)
.+.+.++++.+-...+-.+.... .|-.+++|++ ++.+-+.+ ....+++..++..+..
T Consensus 84 ~~~~~~~~~~~~~~~l~~~~~~~g~~~L~~~~~g~~~~~~~~~pi~s~~DlkG~kiR~~~~~--~~~~~~~~lGa~pv~i 161 (286)
T PF03480_consen 84 YEELDRVMDSGYGPELREELEEKGIKLLGWFPGGPRQFFSTKKPIRSPEDLKGLKIRVPGSP--VMSDFFEALGASPVPI 161 (286)
T ss_dssp HHHHHHHHHSHHHHHHHHHHHHTTEEEEEEEEEEEEEEEESSS--SSGGGGTTEEEEETSSH--HHHHHHHHCTSEEEE-
T ss_pred HHHHHHHHhCcHHHHHHHHHHhhceEEEEEecCCceEEEecccCCccHhhHhhCeEEecCCH--HHHHHHHHcCCeeecC
Confidence 11123677777777777665553 4555677776 77776433 4467888888876544
Q ss_pred cCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeec
Q 048784 118 DDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAE 154 (282)
Q Consensus 118 ~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~ 154 (282)
.-+ +....+..+ .-.|++.+......+++.=+.+
T Consensus 162 p~~-evy~aLq~G--~vDg~~~~~~~~~~~~~~ev~~ 195 (286)
T PF03480_consen 162 PWS-EVYQALQQG--VVDGAENSASSIYSLGLYEVAK 195 (286)
T ss_dssp TGG-GHHHHHHTT--SSSEEEEEHHHHHHTTGGGTSS
T ss_pred cHH-HHHHHHhcC--CcCeEecCHHHHHhcChhhhCC
Confidence 322 333334433 4578888888887777754433
No 268
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=26.16 E-value=94 Score=27.46 Aligned_cols=42 Identities=17% Similarity=0.086 Sum_probs=30.7
Q ss_pred CCCcHHHHHHHhhC--------CCCceeecCCHHHHHHHHHcCCCCeEEEe
Q 048784 2 VRGAYSESAAEKAY--------PNCEAVPCEQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 2 P~GTfS~~Aa~~~~--------~~~~~~~~~s~~~v~~av~~g~~d~gVvP 44 (282)
+.||-+|...+.++ .+.+++.++. .+...++.+|++|.++++
T Consensus 128 ~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~iDa~~~~ 177 (252)
T PF13379_consen 128 FPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGEIDAAVLW 177 (252)
T ss_dssp STTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-SEEEEE
T ss_pred CCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCCcCEEEec
Confidence 56777777766543 2467888888 999999999999999985
No 269
>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=26.14 E-value=3.2e+02 Score=21.38 Aligned_cols=31 Identities=23% Similarity=0.208 Sum_probs=23.4
Q ss_pred hCCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 14 AYPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 14 ~~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
.+|+.++... .+-.++.+.+.+|++|+|+..
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~ 56 (197)
T cd08448 25 EYPGIEVALHEMSSAEQIEALLRGELDLGFVH 56 (197)
T ss_pred HCCCCeEEEEeCCHHHHHHHHHcCCcceEEEe
Confidence 4576655433 356889999999999999974
No 270
>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=25.84 E-value=3.4e+02 Score=21.58 Aligned_cols=113 Identities=19% Similarity=0.216 Sum_probs=60.3
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCC---CCCcc--
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVK---VEDLK-- 91 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~---l~~I~-- 91 (282)
+.++++.. ..++.+++.+|++|+++.+...+-+.. ..+. . ..-.......++++++.. ++|++
T Consensus 39 ~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~~~--~~~~--------~-~~~~~~~~~~~~~~~~~~~~~~~dl~g~ 106 (218)
T cd00134 39 KVKFVEVD-WDGLITALKSGKVDLIAAGMTITPERA--KQVD--------F-SDPYYKSGQVILVKKGSPIKSVKDLKGK 106 (218)
T ss_pred eEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHHHH--hhcc--------C-cccceeccEEEEEECCCCCCChHHhCCC
Confidence 45777877 789999999999999987752111110 0000 0 011122234455544432 22321
Q ss_pred EEEechHHHHHHHHHHHhc--CCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 RVLSHPQALAQCENTLTKL--GLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 ~V~SHpqal~QC~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
+|..-+ .. -...++.+. ......+.+...+.+++..+ ...|++.....+.
T Consensus 107 ~i~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~~~~~~~~~ 158 (218)
T cd00134 107 KVAVQK-GS-TAEKYLKKALPEAKVVSYDDNAEALAALENG--RADAVIVDEIALA 158 (218)
T ss_pred EEEEEc-Cc-hHHHHHHHhCCcccEEEeCCHHHHHHHHHcC--CccEEEeccHHHH
Confidence 222211 11 122344443 24456778888888888876 4567776665554
No 271
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=25.57 E-value=8.7e+02 Score=26.15 Aligned_cols=126 Identities=12% Similarity=0.069 Sum_probs=71.8
Q ss_pred eEEEecCHHHHHHHhhhcCCCCeEEecChhhH---HHcCCceeecccccCCCCceEEEEEeeCCCCCC----CCCCcEEE
Q 048784 113 VREAVDDTAGAAKYVSFEQLKDAGAVASSSAA---AIYGLNILAEDIQDDCDNVTRFLMLAREPIIPG----TDRPFKTS 185 (282)
Q Consensus 113 ~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa---~~ygL~vl~~~I~d~~~N~TRF~vl~~~~~~~~----~~~~~kts 185 (282)
+.+..-|..+|.++...+ |.+-...|+ ..+|.++...+..+....-|..- ......+. ....+-+.
T Consensus 252 ~~i~~ls~~e~~el~~~g-----~~v~~~~a~~~a~~~~i~i~v~~~~~~~~~gT~I~--~~~~~~~~v~~It~~~~v~l 324 (861)
T PRK08961 252 RLLTRLDYDEAQEIATTG-----AKVLHPRSIKPCRDAGIPMAILDTERPDLSGTSID--GDAEPVPGVKAISRKNGIVL 324 (861)
T ss_pred eEecccCHHHHHHHHHCC-----CeEECHHHHHHHHHCCCCEEEEeCCCCCCCccEEe--CCCCCCCcceeEEEECCEEE
Confidence 344455666666665532 345455554 45799999888765544445442 21111110 01122334
Q ss_pred EEEE---cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCC-CcHHHHHHHHHH
Q 048784 186 IVFS---LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASM-ADQKAQNALRHL 261 (282)
Q Consensus 186 i~~~---~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~-~~~~~~~al~~l 261 (282)
|.+. ..+.||.+.++++.|+++|||+-.|.|-. ....|.+|-.... .+..++.++++|
T Consensus 325 Itv~~~~~~~~~g~~a~if~~la~~~I~Vd~I~sse------------------~sis~~i~~~~~~~~~~~~~~l~~~l 386 (861)
T PRK08961 325 VSMETIGMWQQVGFLADVFTLFKKHGLSVDLISSSE------------------TNVTVSLDPSENLVNTDVLAALSADL 386 (861)
T ss_pred EEEecCCccccccHHHHHHHHHHHcCCeEEEEEcCC------------------CEEEEEEccccccchHHHHHHHHHHH
Confidence 4442 24689999999999999999999994321 2567777654321 123455566666
Q ss_pred Hh
Q 048784 262 KE 263 (282)
Q Consensus 262 ~~ 263 (282)
++
T Consensus 387 ~~ 388 (861)
T PRK08961 387 SQ 388 (861)
T ss_pred hh
Confidence 53
No 272
>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=25.39 E-value=3.4e+02 Score=21.33 Aligned_cols=31 Identities=23% Similarity=0.104 Sum_probs=23.1
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEee
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLPI 45 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPi 45 (282)
+|+.++.... +-.++.+.+.+|++|+|+++-
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (200)
T cd08423 26 HPGLEVRLREAEPPESLDALRAGELDLAVVFD 57 (200)
T ss_pred CCCCeEEEEeCCHHHHHHHHhcCCccEEEEec
Confidence 4666554433 467899999999999999853
No 273
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=25.38 E-value=70 Score=25.80 Aligned_cols=27 Identities=15% Similarity=0.274 Sum_probs=22.4
Q ss_pred EEEEEeecCCCcHHHHHHHHHHHhhcC
Q 048784 240 LFYVDFEASMADQKAQNALRHLKEFAT 266 (282)
Q Consensus 240 ~F~vd~~g~~~~~~~~~al~~l~~~~~ 266 (282)
.+.||..|++.++.+.+.+.++.....
T Consensus 2 ~vaiDtSGSis~~~l~~fl~ev~~i~~ 28 (126)
T PF09967_consen 2 VVAIDTSGSISDEELRRFLSEVAGILR 28 (126)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHHHH
Confidence 478999999999999999998775543
No 274
>PRK00907 hypothetical protein; Provisional
Probab=25.16 E-value=3.2e+02 Score=21.04 Aligned_cols=59 Identities=14% Similarity=0.132 Sum_probs=40.9
Q ss_pred CCCccHHHHHHHHHHHCCc--eeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 191 EEGPGVLFKALAVFALRQI--NLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 191 ~~~pG~L~~~L~~F~~~~I--Nlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
.++++-...++.++..+.- +..+++.||+++. +.-.+-+-|.+++ .+.+..+.++|...
T Consensus 25 ~a~~~l~~~V~~vv~~h~p~~~~~~i~~r~Ss~G------------kY~Svtv~i~ats---~eQld~iY~~L~~~ 85 (92)
T PRK00907 25 TAERGLETELPRLLAATGVELLQERISWKHSSSG------------KYVSVRIGFRAES---REQYDAAHQALRDH 85 (92)
T ss_pred cCchhHHHHHHHHHHHhCCCCCcCcEEeccCCCC------------EEEEEEEEEEECC---HHHHHHHHHHHhhC
Confidence 4678888888999988754 6789999999872 2222334444443 46778888888765
No 275
>KOG4028 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.88 E-value=66 Score=26.81 Aligned_cols=26 Identities=12% Similarity=0.217 Sum_probs=20.0
Q ss_pred CCCcHHHHHHHhhCCC-CceeecCCHH
Q 048784 2 VRGAYSESAAEKAYPN-CEAVPCEQFD 27 (282)
Q Consensus 2 P~GTfS~~Aa~~~~~~-~~~~~~~s~~ 27 (282)
|+||+-|+-|+++.+. .++..-++++
T Consensus 115 p~gswreel~~~~vggg~ql~~~~ai~ 141 (175)
T KOG4028|consen 115 PKGSWREELAHAFVGGGLQLLHGDAIE 141 (175)
T ss_pred CCCcHHHHHHHHHhcCCceeecccccc
Confidence 8999999999998764 5666655543
No 276
>TIGR00787 dctP tripartite ATP-independent periplasmic transporter solute receptor, DctP family. TRAP-T (Tripartite ATP-independent Periplasmic Transporter) family proteins generally consist of three components, and these systems have so far been found in Gram-negative bacteria, Gram-postive bacteria and archaea. The best characterized example is the DctPQM system of Rhodobacter capsulatus, a C4 dicarboxylate (malate, fumarate, succinate) transporter. This model represents the DctP family, one of at least three major families of extracytoplasmic solute receptor for TRAP family transporters. Other are the SnoM family (see pfam03480) and TAXI (TRAP-associated extracytoplasmic immunogenic) family.
Probab=24.84 E-value=4.9e+02 Score=23.05 Aligned_cols=145 Identities=17% Similarity=0.096 Sum_probs=76.1
Q ss_pred CCCcHHHHHHHhhCC--------CC--ceeec---CCHHHHHHHHHcCCCCeEEEeeeecccccee-----------ccc
Q 048784 2 VRGAYSESAAEKAYP--------NC--EAVPC---EQFDTAFEAVERWLVDRAVLPIENSLGGSIH-----------RNY 57 (282)
Q Consensus 2 P~GTfS~~Aa~~~~~--------~~--~~~~~---~s~~~v~~av~~g~~d~gVvPiENS~~G~V~-----------~t~ 57 (282)
|+|+...++...+.. .. ++.|- -.-.+++++|..|.+|.++++.-+.. +.+. .+.
T Consensus 6 p~~~~~~~~~~~f~~~v~e~t~G~v~v~~~~~g~Lg~~~e~~~~v~~G~~d~~~~~~~~~~-~~~p~~~~~~lP~~~~~~ 84 (257)
T TIGR00787 6 ARSSPKHKAAEKFAKLVNEKTNGEIKISVFPSSQLGSDRAMLEALQGGALDMTAPSSSKFG-PLVPELAVFDLPFLFRDY 84 (257)
T ss_pred CCCCHHHHHHHHHHHHHHHHcCCeEEEEEcCCCCCCChHHHHHHHhCCCccEEeccccccc-ccCcchhhccCCeecCCH
Confidence 788888887776532 12 23332 24679999999999999986532211 1000 000
Q ss_pred c----------------ccccCCeEEEEEEEEeeeeeeee---cCCCCCCCcc--EEEechHHHHHHHHHHHhcCCeEEE
Q 048784 58 D----------------LLLRHRLHIVGEVKFAVRHCLLA---NPGVKVEDLK--RVLSHPQALAQCENTLTKLGLVREA 116 (282)
Q Consensus 58 d----------------~L~~~~l~I~~E~~l~I~~~L~a---~~~~~l~~I~--~V~SHpqal~QC~~fl~~~~~~~~~ 116 (282)
+ .+.+.++.+.+-. +....++. ++-.+++|++ +|...+-.. -.++++..+...+
T Consensus 85 ~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~--~~g~~~~~~~~~~i~s~~Dl~G~kir~~~~~~--~~~~~~~~Ga~~v- 159 (257)
T TIGR00787 85 NHVHKVLDGEVGKALKKSLEKKGLKGLAYW--DNGFRQFTSSKKPITKPEDLKGLKIRIPNSPM--NEAQFKALGANPE- 159 (257)
T ss_pred HHHHHHHcCHHHHHHHHHHHHcCcEEEeec--CCceeEeeeCCCccCChHHhCCCEEecCCCHH--HHHHHHHcCCccc-
Confidence 0 1122345555432 22233332 2223556664 555543222 3566777776554
Q ss_pred ecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceeec
Q 048784 117 VDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILAE 154 (282)
Q Consensus 117 ~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~~ 154 (282)
..+.++.-..+..+ .-.+++.+......++|.-..+
T Consensus 160 ~~~~~e~~~aL~~G--~vDg~~~~~~~~~~~~~~ev~~ 195 (257)
T TIGR00787 160 PMAFSEVYTALQTG--VVDGQENPLSNVYSSKFYEVQK 195 (257)
T ss_pred ccCHHHHHHHHHcC--CcccccCCHHHHhhcchhhhcc
Confidence 34555555555554 4567787766655556654433
No 277
>cd08467 PBP2_SyrM The C-terminal substrate binding of LysR-type symbiotic regulator SyrM, which activates expression of nodulation gene NodD3, contains the type 2 periplasmic binding fold. Rhizobium is a nitrogen fixing bacteria present in the roots of leguminous plants, which fixes atmospheric nitrogen to the soil. Most Rhizobium species possess multiple nodulation (nod) genes for the development of nodules. For example, Rhizobium meliloti possesses three copies of nodD genes. NodD1 and NodD2 activate nod operons when Rhizobium is exposed to inducers synthesized by the host plant, while NodD3 acts independent of plant inducers and requires the symbiotic regulator SyrM for nod gene expression. SyrM activates the expression of the regulatory nodulation gene nodD3. In turn, NodD3 activates expression of syrM. In addition, SyrM is involved in exopolysaccharide synthesis. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are
Probab=24.71 E-value=3.7e+02 Score=21.58 Aligned_cols=121 Identities=22% Similarity=0.163 Sum_probs=58.6
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCcc-
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLK- 91 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~- 91 (282)
.+|+.++.... +-.++.+.+.+|++|+|+.....- .+.+. ...+.+.++.+ .++-+|-|... ..+++++.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~-~~~~~--~~~l~~~~~~~----v~~~~h~l~~~-~~~~~dL~~ 96 (200)
T cd08467 25 RAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVP-PDGLV--VRRLYDDGFAC----LVRHGHPALAQ-EWTLDDFAT 96 (200)
T ss_pred hCCCCEEEEecCCcccHHHHhhCCCcCEEEecCCCC-Cccce--eEEeeeccEEE----EEcCCCccccC-CCCHHHHhC
Confidence 35777665554 345889999999999999742111 11111 11222333322 22334444322 22333322
Q ss_pred --EEE-echH-HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 --RVL-SHPQ-ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 --~V~-SHpq-al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
-|. .-.. ...+..+++.+.+.. ...+.|.....++++.+ ...|+.+...++
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 154 (200)
T cd08467 97 LRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAAT---DLIATVPRRVAT 154 (200)
T ss_pred CCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcC---CeEEeeHHHHHH
Confidence 221 1111 112334555555432 23456666667777664 345666666554
No 278
>cd00404 Aconitase_swivel Aconitase swivel domain. Aconitase (aconitate hydratase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. This is the aconitase swivel domain, which undergoes swivelling conformational change in the enzyme mechanism. The aconitase family contains the following proteins: - Iron-responsive element binding protein (IRE-BP). IRE-BP is a cytosolic protein that binds to iron-responsive elements (IREs). IREs are stem-loop structures found in the 5'UTR of ferritin, and delta aminolevulinic acid synthase mRNAs, and in the 3'UTR of transferrin receptor mRNA. IRE-BP also express aconitase activity. - 3-isopropylmalate dehydratase (isopropylmalate isomerase), the enzyme that catalyzes the second step in the biosynthesis of leucine. - Homoaconitase (homoaconitate hydratase), an enzyme that participates in the alpha-aminoadipate pathway of lysine biosynthesis and that converts cis-homoaconitate into homoisocitric acid.
Probab=24.32 E-value=58 Score=25.04 Aligned_cols=41 Identities=37% Similarity=0.443 Sum_probs=32.3
Q ss_pred CCcHHHHHHHhhC-CCCceeecCCHHHHHHHHHcCCCCeEEEeee
Q 048784 3 RGAYSESAAEKAY-PNCEAVPCEQFDTAFEAVERWLVDRAVLPIE 46 (282)
Q Consensus 3 ~GTfS~~Aa~~~~-~~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 46 (282)
.||..|.|+.... -....+-..||..+|. ++....|++|++
T Consensus 27 ~GSSRE~A~~al~~~Gi~aVia~sfa~If~---rN~~n~Gll~l~ 68 (88)
T cd00404 27 TGSSREHAALELRLLGGRAVIAKSFARIFF---RNLVDQGLLPLE 68 (88)
T ss_pred cCCCHHHHHHHHHHhCCCEEEEeCHHHHHH---hhHHhcCCceEE
Confidence 4889999998643 3568899999999996 455677899986
No 279
>PRK09181 aspartate kinase; Validated
Probab=24.13 E-value=7.3e+02 Score=24.80 Aligned_cols=121 Identities=7% Similarity=-0.022 Sum_probs=68.6
Q ss_pred EEecCHHHHHHHhhhcCCCCeEEecChh---hHHHcCCceeecccccCCCCceEEEEEeeCC-CCC---C-CCCCcEEEE
Q 048784 115 EAVDDTAGAAKYVSFEQLKDAGAVASSS---AAAIYGLNILAEDIQDDCDNVTRFLMLAREP-IIP---G-TDRPFKTSI 186 (282)
Q Consensus 115 ~~~~sTa~Aa~~v~~~~~~~~AAI~s~~---Aa~~ygL~vl~~~I~d~~~N~TRF~vl~~~~-~~~---~-~~~~~ktsi 186 (282)
+..-|-.+|.++...+ |-+=.+. -|..++.++..+|-.+...--|..- .... ..+ . ...++-+.|
T Consensus 260 i~~lsy~Ea~ELA~~G-----AkVLHp~ti~pa~~~~Ipi~V~nt~~p~~~GT~I~--~~~~~~~~~ik~It~~~~~~~i 332 (475)
T PRK09181 260 IGRTNYDVADQLANLG-----MEAIHPKAAKGLRQAGIPLRIKNTFEPEHPGTLIT--KDYVSEQPRVEIIAGSDKVFAL 332 (475)
T ss_pred cCccCHHHHHHHHHcC-----chhcCHHHHHHHHHcCCeEEEecCCCCCCCCeEEe--cCcccccccceeEeccCCEEEE
Confidence 3345666677665543 1121222 2456788988888775433445442 1111 000 0 011223333
Q ss_pred EEE---cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHh
Q 048784 187 VFS---LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKE 263 (282)
Q Consensus 187 ~~~---~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~ 263 (282)
.+. ..+.||.+.++++.|++++||+-.|-|- . ....|.|+-+ ...+++++++|++
T Consensus 333 ~i~~~~~~~~~g~~~~if~~l~~~~i~v~~i~ss---~---------------~sis~~v~~~----~~~~~~~~~~L~~ 390 (475)
T PRK09181 333 EVFDQDMVGEDGYDLEILEILTRHKVSYISKATN---A---------------NTITHYLWGS----LKTLKRVIAELEK 390 (475)
T ss_pred EEcCCCCCCcchHHHHHHHHHHHcCCeEEEEEec---C---------------cEEEEEEcCC----hHHHHHHHHHHHH
Confidence 432 2367999999999999999999866332 1 2578888764 1345677888875
Q ss_pred h
Q 048784 264 F 264 (282)
Q Consensus 264 ~ 264 (282)
.
T Consensus 391 ~ 391 (475)
T PRK09181 391 R 391 (475)
T ss_pred h
Confidence 3
No 280
>TIGR00149 TIGR00149_YbjQ secondary thiamine-phosphate synthase enzyme. Members of this protein family have been studied extensively by crystallography. Members from several different species have been shown to have sufficient thiamin phosphate synthase activity (EC 2.5.1.3) to complement thiE mutants. However, it is presumed that this is a secondary activity, and the primary function of this enzyme remains unknown.
Probab=24.12 E-value=50 Score=27.22 Aligned_cols=14 Identities=14% Similarity=0.600 Sum_probs=12.3
Q ss_pred ceeEEEEEEeecCC
Q 048784 236 YFDYLFYVDFEASM 249 (282)
Q Consensus 236 ~~~y~F~vd~~g~~ 249 (282)
.|+.+||+|++|..
T Consensus 108 twQ~I~l~E~Dg~r 121 (132)
T TIGR00149 108 TWQGIFFAEFDGPR 121 (132)
T ss_pred CccEEEEEECCCCC
Confidence 59999999999864
No 281
>PLN02550 threonine dehydratase
Probab=23.92 E-value=5.8e+02 Score=26.40 Aligned_cols=70 Identities=17% Similarity=0.192 Sum_probs=47.0
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
-..+.|+.|.+||+|.+.|+.|.. .-|+|.++=|-.... .=.-||-++-. +..+..+++.|+
T Consensus 510 E~l~~v~fPErpGAl~~Fl~~lg~-~~nITeF~YR~~~~~---------------~a~vlvGi~v~--~~e~~~l~~~l~ 571 (591)
T PLN02550 510 ELLYRFVFPERPGALMKFLDAFSP-RWNISLFHYRGQGET---------------GANVLVGIQVP--PEEMQEFKSRAN 571 (591)
T ss_pred eEEEEEEecCcCCHHHHHHHhhCC-CCceeeEEeecCCCC---------------CccEEEEEeeC--HHHHHHHHHHHH
Confidence 467888999999999999998864 357888888843321 11245555543 356677888888
Q ss_pred hhcCceEE
Q 048784 263 EFATFLRV 270 (282)
Q Consensus 263 ~~~~~v~~ 270 (282)
+....+..
T Consensus 572 ~~gy~~~d 579 (591)
T PLN02550 572 ALGYEYQD 579 (591)
T ss_pred HcCCCeEE
Confidence 76554443
No 282
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=23.90 E-value=3.6e+02 Score=21.12 Aligned_cols=30 Identities=17% Similarity=0.115 Sum_probs=23.4
Q ss_pred CCCCceeecC-CHHHHHHHHHcCCCCeEEEe
Q 048784 15 YPNCEAVPCE-QFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 15 ~~~~~~~~~~-s~~~v~~av~~g~~d~gVvP 44 (282)
+|+.++.... +.+++.+.+.+|++|+|+.+
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~ 56 (195)
T cd08427 26 HPDLEVHIVPGLSAELLARVDAGELDAAIVV 56 (195)
T ss_pred CCCceEEEEeCCcHHHHHHHHCCCCCEEEEc
Confidence 5666655433 56889999999999999985
No 283
>cd08481 PBP2_GcdR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators GcdR-like, contains the type 2 periplasmic binding fold. GcdR is involved in the glutaconate/glutarate-specific activation of the Pg promoter driving expression of a glutaryl-CoA dehydrogenase-encoding gene (gcdH). The GcdH protein is essential for the anaerobic catabolism of many aromatic compounds and some alicyclic and dicarboxylic acids. The structural topology of this substrate-binding domain is most similar to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate membrane transport complex comprised of two integral membrane domains and two cytoplas
Probab=23.78 E-value=3.6e+02 Score=21.09 Aligned_cols=30 Identities=10% Similarity=-0.122 Sum_probs=18.2
Q ss_pred CCCCceeecCCHHHHHHHHHcCCCCeEEEeee
Q 048784 15 YPNCEAVPCEQFDTAFEAVERWLVDRAVLPIE 46 (282)
Q Consensus 15 ~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 46 (282)
+|+.++.....- -.+.+.+|++|+|++...
T Consensus 26 ~P~i~i~i~~~~--~~~~l~~~~~Dl~l~~~~ 55 (194)
T cd08481 26 HPDITVNLVTRD--EPFDFSQGSFDAAIHFGD 55 (194)
T ss_pred CCCceEEEEecc--cccCcccCCCCEEEEcCC
Confidence 566554433221 123688999999997643
No 284
>COG1910 Periplasmic molybdate-binding protein/domain [Inorganic ion transport and metabolism]
Probab=23.21 E-value=70 Score=28.83 Aligned_cols=127 Identities=17% Similarity=0.205 Sum_probs=67.1
Q ss_pred CceeecCCHHHHHHHHHcCCCCeE---EEeeeeccccc-eeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCccEE
Q 048784 18 CEAVPCEQFDTAFEAVERWLVDRA---VLPIENSLGGS-IHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLKRV 93 (282)
Q Consensus 18 ~~~~~~~s~~~v~~av~~g~~d~g---VvPiENS~~G~-V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~~V 93 (282)
...+.+-|...+. ++..|++|.+ ++|.+ +|. ..++++-+......+++=+ + =++.|+.++|. ...|+-+
T Consensus 20 ~~~~~vGS~gG~~-~i~~G~adiag~hlld~~---~g~ynip~v~~~~~~~~~LI~g~-~-Re~Gl~v~~gn-pk~i~~~ 92 (223)
T COG1910 20 AKTVYVGSMGGLL-AIKRGEADIAGIHLLDNE---SGTYNIPYVKKYLPGEAVLIRGY-L-REQGLMVQKGN-PKNISSL 92 (223)
T ss_pred cceEEeccccchH-hhhhcccceeeeeeccCC---CCceehhhhhhcCCCceEEEeee-e-eeeeeEEecCC-CCccccH
Confidence 4566777776655 6788999988 55655 454 3344443222233333222 2 23677777664 2222211
Q ss_pred ---------EechHH----HHHHHHHHHhcCC-----e-E-EEecCHHHHHHHhhhcCCCCeEEecChhhHHHcCCceee
Q 048784 94 ---------LSHPQA----LAQCENTLTKLGL-----V-R-EAVDDTAGAAKYVSFEQLKDAGAVASSSAAAIYGLNILA 153 (282)
Q Consensus 94 ---------~SHpqa----l~QC~~fl~~~~~-----~-~-~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~~ygL~vl~ 153 (282)
+---+- =.--.++|.+.+. . . ..+.|-...|+.|+.+ +.+|.|+=+.+|+.|||.++.
T Consensus 93 edl~~~d~~fVNR~rGSGTR~LlD~~L~~~~~~~~~I~GY~~e~~th~avA~aVa~G--~AD~GvGlr~~A~~~gL~Fip 170 (223)
T COG1910 93 EDLLRKDLRFVNRNRGSGTRILLDELLGELNILPDSIKGYSDEATTHDAVASAVASG--RADAGVGLRHAAEKYGLDFIP 170 (223)
T ss_pred HHHhhcCcEEEecCCCccHHHHHHHHHHHcCcCchhcCCccccccccHHHHHHHHcC--CCCccccHHHHHHHcCCceEE
Confidence 111110 0011122332211 1 0 1233444567788876 678999999999999998775
No 285
>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=23.00 E-value=1.8e+02 Score=29.22 Aligned_cols=34 Identities=24% Similarity=0.327 Sum_probs=27.3
Q ss_pred EEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeC
Q 048784 185 SIVFSLEEGPGVLFKALAVFALRQINLTKIESRPL 219 (282)
Q Consensus 185 si~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~ 219 (282)
..-|..|.+||+|.+.|+.+.. +-|+|.++=|-.
T Consensus 421 ~~~~~fperpgaL~~Fl~~l~~-~~~It~f~Yr~~ 454 (499)
T TIGR01124 421 LYSFEFPERPGALLRFLNTLQG-YWNISLFHYRNH 454 (499)
T ss_pred EEEEeCCCCccHHHHHHHhcCC-CCceeeEEEecC
Confidence 4667789999999999997754 558888888764
No 286
>PF01894 UPF0047: Uncharacterised protein family UPF0047; InterPro: IPR001602 This family contains small uncharacterised proteins of 14 to 16 kDa mainly from bacteria although the signatures also occur in a hypothetical protein from archaea and from yeast.; PDB: 1VPH_E 2P6C_A 2CU5_A 1VMJ_A 1XBF_B 1VMH_A 1VE0_A 2P6H_B 1VMF_C.
Probab=22.79 E-value=46 Score=26.87 Aligned_cols=13 Identities=15% Similarity=0.595 Sum_probs=10.8
Q ss_pred ceeEEEEEEeecC
Q 048784 236 YFDYLFYVDFEAS 248 (282)
Q Consensus 236 ~~~y~F~vd~~g~ 248 (282)
.|+.+||+|++|.
T Consensus 96 twQ~I~l~E~dgp 108 (118)
T PF01894_consen 96 TWQGIYLVEFDGP 108 (118)
T ss_dssp TTEEEEEEESS-S
T ss_pred CcCEEEEEECCCC
Confidence 6999999999983
No 287
>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=22.52 E-value=3.9e+02 Score=21.08 Aligned_cols=120 Identities=18% Similarity=0.116 Sum_probs=57.7
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCC---Cc
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVE---DL 90 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~---~I 90 (282)
+|+.++... .+-.++.+.+.+|++|+|+..-.+...+.. ...|.+..+. +..+-.|-+...+..+++ +.
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~----~~~~~~~~~~~~~~~~~~~l~~~ 98 (198)
T cd08433 26 YPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGLS---TEPLLEEDLF----LVGPADAPLPRGAPVPLAELARL 98 (198)
T ss_pred CCCcEEEEEecCcHHHHHHHhCCCCcEEEEeCCCCCCCee---EEEeccccEE----EEecCCCccccCCCCCHHHhCCC
Confidence 466655443 356789999999999999974322211111 1122222222 222333433322222222 22
Q ss_pred cEEE-echHH-HHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhH
Q 048784 91 KRVL-SHPQA-LAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAA 144 (282)
Q Consensus 91 ~~V~-SHpqa-l~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa 144 (282)
.-|. .+... ...+.+|+.+++.. ...+++...+.++++.+ ...|+.+...+
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~ 154 (198)
T cd08433 99 PLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAG---LGYTILPASAV 154 (198)
T ss_pred ceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcC---CcEEEcchhhh
Confidence 2232 22222 23455666665433 23456666666777764 23456555544
No 288
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=22.48 E-value=2.8e+02 Score=24.09 Aligned_cols=113 Identities=12% Similarity=0.092 Sum_probs=57.1
Q ss_pred CCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCC----CCCCCcc-
Q 048784 17 NCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPG----VKVEDLK- 91 (282)
Q Consensus 17 ~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~----~~l~~I~- 91 (282)
..++++. ++.++++++.+|++|.++..+. .+... ...++. ..++ ......++.+++ .++++++
T Consensus 64 ~~~~~~~-~~~~~~~~l~~G~vDi~~~~~~-~t~~R-~~~~~f--s~p~-------~~~~~~~~~~~~~~~~~~~~dL~g 131 (247)
T PRK09495 64 DYTLKPM-DFSGIIPALQTKNVDLALAGIT-ITDER-KKAIDF--SDGY-------YKSGLLVMVKANNNDIKSVKDLDG 131 (247)
T ss_pred ceEEEeC-CHHHHHHHHhCCCcCEEEecCc-cCHHH-Hhhccc--cchh-------eecceEEEEECCCCCCCChHHhCC
Confidence 4567766 6999999999999999864431 01111 001110 0111 112223333322 1233442
Q ss_pred -EEEechHHHHHHHHHHHhc--CCeEEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 -RVLSHPQALAQCENTLTKL--GLVREAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 -~V~SHpqal~QC~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
+|..-... .. ..|+.+. ....+...|...+..++..+ +-.|+|+....+.
T Consensus 132 ~~I~v~~g~-~~-~~~l~~~~~~~~i~~~~~~~~~~~~L~~g--rvDa~i~~~~~~~ 184 (247)
T PRK09495 132 KVVAVKSGT-GS-VDYAKANIKTKDLRQFPNIDNAYLELGTG--RADAVLHDTPNIL 184 (247)
T ss_pred CEEEEecCc-hH-HHHHHhcCCCCceEEcCCHHHHHHHHHcC--ceeEEEeChHHHH
Confidence 44332221 11 2456553 34455566777777777765 5677777665443
No 289
>cd01579 AcnA_Bact_Swivel Bacterial Aconitase-like swivel domain. Aconitase (aconitate hydratase or citrate hydrolyase) catalyzes the reversible isomerization of citrate and isocitrate as part of the TCA cycle. Cis-aconitate is formed as an intermediate product during the course of the reaction. This is the aconitase-like swivel domain, which is believed to undergo swivelling conformational change in the enzyme mechanism. This distinct subfamily is found only in bacteria and archea. Its exact characteristics are not known.
Probab=22.48 E-value=64 Score=26.20 Aligned_cols=41 Identities=24% Similarity=0.335 Sum_probs=32.3
Q ss_pred CCcHHHHHHHhhCC-CCceeecCCHHHHHHHHHcCCCCeEEEeee
Q 048784 3 RGAYSESAAEKAYP-NCEAVPCEQFDTAFEAVERWLVDRAVLPIE 46 (282)
Q Consensus 3 ~GTfS~~Aa~~~~~-~~~~~~~~s~~~v~~av~~g~~d~gVvPiE 46 (282)
-||..|+|+..... +...+-.+||..+|. ++.+..|++|++
T Consensus 60 ~GSSRE~A~~al~~~Gi~aVIA~SFa~If~---rN~in~Gll~i~ 101 (121)
T cd01579 60 QGSSREHAALAPMYLGVRAVLAKSFARIHR---ANLINFGILPLT 101 (121)
T ss_pred CCccHHHHHHHHHHHCCCEEEEccHHHHHH---hHHhhcCcceEE
Confidence 48999999986533 578899999999996 445677899986
No 290
>PRK09436 thrA bifunctional aspartokinase I/homoserine dehydrogenase I; Provisional
Probab=22.38 E-value=7.6e+02 Score=26.50 Aligned_cols=96 Identities=14% Similarity=0.054 Sum_probs=52.3
Q ss_pred eEEEecCHHHHHHHhhhcCCCCeEEecChhh---HHHcCCceeecccccCCCCceEEEEEeeCC-C-C--CC-CCCCcEE
Q 048784 113 VREAVDDTAGAAKYVSFEQLKDAGAVASSSA---AAIYGLNILAEDIQDDCDNVTRFLMLAREP-I-I--PG-TDRPFKT 184 (282)
Q Consensus 113 ~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~A---a~~ygL~vl~~~I~d~~~N~TRF~vl~~~~-~-~--~~-~~~~~kt 184 (282)
+.+..-|-.+|.++...+ . -+-.+.| |..+|.++.-.|..+...--|+.- +... . . .. ...++-+
T Consensus 244 ~~i~~isy~ea~el~~~G----~-kvlhp~a~~~a~~~~Ipi~i~n~~~p~~~GT~I~--~~~~~~~~~Vk~It~~~dva 316 (819)
T PRK09436 244 RLLKSLSYQEAMELSYFG----A-KVLHPRTIAPIAQFQIPCLIKNTFNPQAPGTLIG--AESDEDSLPVKGISNLNNMA 316 (819)
T ss_pred eEeeEecHHHHHHHHhcC----C-ccchHHHHHHHHHCCceEEEccCCCCCCCceEEE--ecCcccccccceEEEeCCEE
Confidence 344444555666654322 1 2223333 345788888887654333344431 1110 0 0 00 0112233
Q ss_pred EEEE---EcCCCccHHHHHHHHHHHCCceeeeee
Q 048784 185 SIVF---SLEEGPGVLFKALAVFALRQINLTKIE 215 (282)
Q Consensus 185 si~~---~~~~~pG~L~~~L~~F~~~~INlt~Ie 215 (282)
.|.+ .+...||.+.++++.|+++|||+-.|.
T Consensus 317 lIsV~G~gm~~~~G~~arIf~~La~~gI~V~mIs 350 (819)
T PRK09436 317 MFNVSGPGMKGMVGMASRVFAALSRAGISVVLIT 350 (819)
T ss_pred EEEEEcCCCCCCcCHHHHHHHHHHHCCCcEEEEE
Confidence 3434 235789999999999999999998775
No 291
>PF08212 Lipocalin_2: Lipocalin-like domain; InterPro: IPR000566 Proteins which transport small hydrophobic molecules such as steroids, bilins, retinoids, and lipids share limited regions of sequence homology and a common tertiary structure architecture [, , , , ]. This is an eight stranded antiparallel beta-barrel with a repeated + 1 topology enclosing a internal ligand binding site [, ]. The name 'lipocalin' has been proposed [] for this protein family, but cytosolic fatty-acid binding proteins are also included. The sequences of most members of the family, the core or kernal lipocalins, are characterised by three short conserved stretches of residues, while others, the outlier lipocalin group, share only one or two of these [, ]. Proteins known to belong to this family include alpha-1-microglobulin (protein HC); alpha-1-acid glycoprotein (orosomucoid) []; aphrodisin; apolipoprotein D; beta-lactoglobulin; complement component C8 gamma chain []; crustacyanin []; epididymal-retinoic acid binding protein (E-RABP) []; insectacyanin; odorant-binding protein (OBP); human pregnancy-associated endometrial alpha-2 globulin; probasin (PB), a rat prostatic protein; prostaglandin D synthase (5.3.99.2 from EC) []; purpurin; Von Ebner's gland protein (VEGP) []; and lizard epididymal secretory protein IV (LESP IV) [].; GO: 0005488 binding; PDB: 3EBW_B 1QWD_A 2ACO_A 3MBT_A.
Probab=22.34 E-value=1.3e+02 Score=24.35 Aligned_cols=25 Identities=12% Similarity=0.094 Sum_probs=18.4
Q ss_pred ccHHHHHHHHHHHCCceeeeeeeee
Q 048784 194 PGVLFKALAVFALRQINLTKIESRP 218 (282)
Q Consensus 194 pG~L~~~L~~F~~~~INlt~IeSRP 218 (282)
+..+.++|+.++..|+++++++.-|
T Consensus 118 ~~~~~~~~~~~~~~G~d~~~l~~~~ 142 (143)
T PF08212_consen 118 EETYAEILDRAKQQGYDVSKLIWTP 142 (143)
T ss_dssp HHHHHHHHHHHHHTT--GGGEEE--
T ss_pred HHHHHHHHHHHHHcCCCHHHeEECC
Confidence 4578899999999999999998654
No 292
>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=21.96 E-value=1.5e+02 Score=23.83 Aligned_cols=121 Identities=18% Similarity=0.115 Sum_probs=60.1
Q ss_pred hCCCCceeecCCHHHHHHHHHcCCCCeEEEeeeeccccceeccccccccCCeEEEEEEEEeeeeeeeecCCCCCCCcc--
Q 048784 14 AYPNCEAVPCEQFDTAFEAVERWLVDRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVKFAVRHCLLANPGVKVEDLK-- 91 (282)
Q Consensus 14 ~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~a~~~~~l~~I~-- 91 (282)
.+|+.++.......++.+.+.+|++|+|+........+. ....|.+..+. +..+-+|-|... ..+++|+.
T Consensus 25 ~~P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~----~v~~~~hpl~~~-~~~l~dl~~~ 96 (200)
T cd08460 25 EAPGVRLRFVPESDKDVDALREGRIDLEIGVLGPTGPEI---RVQTLFRDRFV----GVVRAGHPLARG-PITPERYAAA 96 (200)
T ss_pred HCCCCEEEEecCchhHHHHHHCCCccEEEecCCCCCcch---heeeeeccceE----EEEeCCCCCCCC-CCCHHHHhcC
Confidence 357666655443338899999999999997432110110 11122222332 223444544322 12333332
Q ss_pred -EEE-echH-HHHHHHHHHHhcCCe---EEEecCHHHHHHHhhhcCCCCeEEecChhhHH
Q 048784 92 -RVL-SHPQ-ALAQCENTLTKLGLV---REAVDDTAGAAKYVSFEQLKDAGAVASSSAAA 145 (282)
Q Consensus 92 -~V~-SHpq-al~QC~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~Aa~ 145 (282)
-|. +... .-.+..+|+.+.+.. ...++|...+..+++.+ ...|+.+...++
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 153 (200)
T cd08460 97 PHVSVSRRGRLHGPIDDALAALGLTRRVVAVVPTFAAALFLARGS---DLIALVPERVTA 153 (200)
T ss_pred CCEEEecCCCCcchHHHHHHhcCCceeEEEEcCcHHHHHHHHhcC---CHHHHHHHHHHH
Confidence 222 1111 123467777766543 23456666677777764 235666665543
No 293
>COG3870 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.83 E-value=4.1e+02 Score=21.09 Aligned_cols=57 Identities=25% Similarity=0.265 Sum_probs=39.3
Q ss_pred CCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhhcCc
Q 048784 191 EEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEFATF 267 (282)
Q Consensus 191 ~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~~~~ 267 (282)
....+.|.+.| .++|..+||+-|-= |.-+.+.--|.|-+| |+++..++..|++.|..
T Consensus 10 d~da~~l~~~L---~d~~fraTkLAsTG-------------GFlkaGNTTfliGve----d~~vd~~~s~Ike~C~~ 66 (109)
T COG3870 10 DQDANELEDAL---TDKNFRATKLASTG-------------GFLKAGNTTFLIGVE----DDRVDALRSLIKENCKS 66 (109)
T ss_pred cccHHHHHHHH---HhCCceeEEeeccC-------------ceeecCCeEEEEecc----cchhHHHHHHHHHHhhh
Confidence 34566777666 78999999998753 122345667888775 56777788888877654
No 294
>PLN02551 aspartokinase
Probab=21.83 E-value=7.6e+02 Score=25.01 Aligned_cols=103 Identities=13% Similarity=0.070 Sum_probs=0.0
Q ss_pred HHHcCCceeecccccCCCCceEEEEEe--eCCCCCCCCCCcEEEEE----EEcCCCccHHHHHHHHHHHCCceeeeeeee
Q 048784 144 AAIYGLNILAEDIQDDCDNVTRFLMLA--REPIIPGTDRPFKTSIV----FSLEEGPGVLFKALAVFALRQINLTKIESR 217 (282)
Q Consensus 144 a~~ygL~vl~~~I~d~~~N~TRF~vl~--~~~~~~~~~~~~ktsi~----~~~~~~pG~L~~~L~~F~~~~INlt~IeSR 217 (282)
|..++.+|..+|--+...--|..---. .......-.......++ ....+.||.+.++++.|+++|||+-.|-+
T Consensus 324 a~~~~Ipi~vknt~~p~~~GT~I~~~~~~~~~~v~~It~~~~v~li~i~~~~m~~~~g~~arvf~~l~~~~I~Vd~Iss- 402 (521)
T PLN02551 324 AREGDIPVRVKNSYNPTAPGTLITKTRDMSKAVLTSIVLKRNVTMLDIVSTRMLGQYGFLAKVFSTFEDLGISVDVVAT- 402 (521)
T ss_pred HHHCCceEEEEecCCCCCCCcEEecccccCCCcccceecCCCeEEEEEecCCCCCcccHHHHHHHHHHHcCCcEEEEec-
Q ss_pred eCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 218 PLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 218 P~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+.. ...|.||-+--...+.+++.+..|...
T Consensus 403 -Se~----------------sIs~~v~~~~~~~~~~i~~~l~~l~~e 432 (521)
T PLN02551 403 -SEV----------------SISLTLDPSKLWSRELIQQELDHLVEE 432 (521)
T ss_pred -cCC----------------EEEEEEehhHhhhhhhHHHHHHHHHHH
No 295
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=21.63 E-value=5.9e+02 Score=22.76 Aligned_cols=30 Identities=7% Similarity=0.000 Sum_probs=23.2
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
+|+.++... .+-+++.+.+.+|++|+|+..
T Consensus 119 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~ 149 (296)
T PRK11062 119 DESIHLRCFESTHEMLLEQLSQHKLDMILSD 149 (296)
T ss_pred CCceEEEEEeCCHHHHHHHHHcCCCCEEEec
Confidence 456555443 467899999999999999974
No 296
>TIGR03124 ctirate_citX holo-ACP synthase CitX. Members of this protein family are the CitX protein, or CitX domain of the CitXG bifunctional protein, of the citrate lyase system. CitX transfers the prosthetic group 2'-(5''-triphosphoribosyl)-3'-dephospho-CoA to the citrate lyase gamma chain, an acyl carrier protein. This enzyme may be designated holo-ACP synthase, holo-citrate lyase synthase, or apo-citrate lyase phosphoribosyl-dephospho-CoA transferase. In a few genera, including Haemophilus, this protein occurs as a fusion protein with CitG (2.7.8.25), an enzyme involved in prosthetic group biosynthesis. This CitX family is easily separated from the holo-ACP synthases of other enzyme systems.
Probab=21.45 E-value=2.8e+02 Score=23.72 Aligned_cols=50 Identities=14% Similarity=0.049 Sum_probs=36.2
Q ss_pred HHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 197 LFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 197 L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+..+.+.|...++.+...+++..++. .+|+|-||.+. ..+++..-.|++.
T Consensus 53 ~~~l~~~~~~~~~~~~~~~~~~~~tG--------------~E~~~~v~~~a----~~vK~~~i~iEe~ 102 (165)
T TIGR03124 53 IKAIEALLAKNGWTILVQQALNEATG--------------PEAFLVVDAPA----LELKRLMIKLEES 102 (165)
T ss_pred HHHHHHHHHhcCCeeeeeeeccCCCC--------------cEEEEEeCCCH----HHHHHHHHHHHhC
Confidence 34456667778888888888776653 47888888765 5688888888765
No 297
>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=21.29 E-value=4.1e+02 Score=20.85 Aligned_cols=31 Identities=10% Similarity=-0.004 Sum_probs=22.5
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEe
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvP 44 (282)
.+|+.++.... +-.++.+.+.+|++|+|+..
T Consensus 25 ~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~ 56 (196)
T cd08456 25 RHPDVTISIHTRDSPTVEQWLSAQQCDLGLVS 56 (196)
T ss_pred HCCCcEEEEEeCCHHHHHHHHHcCCccEEEEe
Confidence 35666554333 45678899999999999975
No 298
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=21.25 E-value=6e+02 Score=22.76 Aligned_cols=31 Identities=16% Similarity=0.070 Sum_probs=23.6
Q ss_pred hCCCCceeecC-CHHHHHHHHHcCCCCeEEEe
Q 048784 14 AYPNCEAVPCE-QFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 14 ~~~~~~~~~~~-s~~~v~~av~~g~~d~gVvP 44 (282)
.+|+.++.... +..++.+.+.+|++|+|+.+
T Consensus 120 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 120 RYPQINVQLQVHSTRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred HCCCceEEEEeCCHHHHHHHHHcCCccEEEEc
Confidence 35666655433 57889999999999999974
No 299
>PRK07431 aspartate kinase; Provisional
Probab=21.18 E-value=2.3e+02 Score=28.81 Aligned_cols=51 Identities=20% Similarity=0.241 Sum_probs=38.6
Q ss_pred cCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHHhh
Q 048784 190 LEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLKEF 264 (282)
Q Consensus 190 ~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~~~ 264 (282)
+++.||.+.++++.+++.|||+..|-+++. .-.|+||- ...+++++.|.+.
T Consensus 529 m~~~~gv~~ri~~aL~~~~I~v~~i~~S~~------------------~Is~vV~~------~~~~~av~~Lh~~ 579 (587)
T PRK07431 529 MPGTPGVAARMFRALADAGINIEMIATSEI------------------RTSCVVAE------DDGVKALQAVHQA 579 (587)
T ss_pred ccCCcCHHHHHHHHHHHCCCcEEEeeccce------------------EEEEEEeH------HHHHHHHHHHHHH
Confidence 468899999999999999999988774321 45677775 4456677777655
No 300
>cd08434 PBP2_GltC_like The substrate binding domain of LysR-type transcriptional regulator GltC, which activates gltA expression of glutamate synthase operon, contains type 2 periplasmic binding fold. GltC, a member of the LysR family of bacterial transcriptional factors, activates the expression of gltA gene of glutamate synthase operon and is essential for cell growth in the absence of glutamate. Glutamate synthase is a heterodimeric protein that encoded by gltA and gltB, whose expression is subject to nutritional regulation. GltC also negatively auto-regulates its own expression. This substrate-binding domain has strong 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,
Probab=20.99 E-value=4e+02 Score=20.67 Aligned_cols=30 Identities=20% Similarity=0.226 Sum_probs=22.3
Q ss_pred CCCCceeec-CCHHHHHHHHHcCCCCeEEEe
Q 048784 15 YPNCEAVPC-EQFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 15 ~~~~~~~~~-~s~~~v~~av~~g~~d~gVvP 44 (282)
+|+.++.-. .+..++.+.+.+|++|+|++.
T Consensus 26 ~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~ 56 (195)
T cd08434 26 YPNVTFELHQGSTDELLDDLKNGELDLALCS 56 (195)
T ss_pred CCCeEEEEecCcHHHHHHHHHcCCccEEEEc
Confidence 566554433 346788999999999999975
No 301
>PRK09084 aspartate kinase III; Validated
Probab=20.89 E-value=8.1e+02 Score=24.12 Aligned_cols=126 Identities=17% Similarity=0.138 Sum_probs=69.9
Q ss_pred EEEecCHHHHHHHhhhcCCCCeEEecCh--hhHHHcCCceeecccccCCCCceEEEEEeeCCCCCC----CCCCcEEEEE
Q 048784 114 REAVDDTAGAAKYVSFEQLKDAGAVASS--SAAAIYGLNILAEDIQDDCDNVTRFLMLAREPIIPG----TDRPFKTSIV 187 (282)
Q Consensus 114 ~~~~~sTa~Aa~~v~~~~~~~~AAI~s~--~Aa~~ygL~vl~~~I~d~~~N~TRF~vl~~~~~~~~----~~~~~ktsi~ 187 (282)
....-|-.+|.++...+ .-.+-+. .-+..+|.++.-.+..|...--|.+- ......+. ....+-+.+.
T Consensus 237 ~i~~is~~ea~ela~~G----a~vlh~~~~~~~~~~~i~i~i~~~~~~~~~GT~I~--~~~~~~~~v~~it~~~~i~lIt 310 (448)
T PRK09084 237 RIDEISFEEAAEMATFG----AKVLHPATLLPAVRSNIPVFVGSSKDPEAGGTWIC--NDTENPPLFRAIALRRNQTLLT 310 (448)
T ss_pred EcccCCHHHHHHHHhCC----CcccCHHHHHHHHHcCCcEEEEeCCCCCCCceEEe--cCCCCCCeeEEEEeeCCEEEEE
Confidence 34445666677765533 1223222 22567899999888766444455542 11111110 0112223344
Q ss_pred EEc---CCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCC---cHHHHHHHHHH
Q 048784 188 FSL---EEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMA---DQKAQNALRHL 261 (282)
Q Consensus 188 ~~~---~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~---~~~~~~al~~l 261 (282)
+.- .+.||.+.++++.|+++|||+-.|.|- . ....|.||=..... ....++++++|
T Consensus 311 v~~~~~~~~~g~~a~if~~l~~~~I~Vd~I~ss---e---------------~sIs~~i~~~~~~~~~~~~~~~~l~~el 372 (448)
T PRK09084 311 LHSLNMLHARGFLAEVFGILARHKISVDLITTS---E---------------VSVSLTLDTTGSTSTGDTLLTQALLTEL 372 (448)
T ss_pred EecCCCCccccHHHHHHHHHHHcCCeEEEEecc---C---------------cEEEEEEechhhhhhhhHHHHHHHHHHH
Confidence 432 367999999999999999999999641 1 25788888532110 01235666677
Q ss_pred Hh
Q 048784 262 KE 263 (282)
Q Consensus 262 ~~ 263 (282)
++
T Consensus 373 ~~ 374 (448)
T PRK09084 373 SQ 374 (448)
T ss_pred hc
Confidence 53
No 302
>PRK12483 threonine dehydratase; Reviewed
Probab=20.19 E-value=5.8e+02 Score=25.87 Aligned_cols=66 Identities=17% Similarity=0.220 Sum_probs=42.5
Q ss_pred EEEEEEEcCCCccHHHHHHHHHHHCCceeeeeeeeeCCCCCCCCCCCCCCCCcceeEEEEEEeecCCCcHHHHHHHHHHH
Q 048784 183 KTSIVFSLEEGPGVLFKALAVFALRQINLTKIESRPLRNQPLRSSDDNSGFGKYFDYLFYVDFEASMADQKAQNALRHLK 262 (282)
Q Consensus 183 ktsi~~~~~~~pG~L~~~L~~F~~~~INlt~IeSRP~~~~~~~~~~~~~g~~~~~~y~F~vd~~g~~~~~~~~~al~~l~ 262 (282)
-..+.|+.|.+||+|.+.|+.+.. .-|+|-..=|-.... .=..||-++-. +...+.+++.|+
T Consensus 440 E~~~~v~iPE~pGa~~~f~~~l~~-~~niTeF~YR~~~~~---------------~a~v~vgi~~~--~~~~~~~~~~l~ 501 (521)
T PRK12483 440 ERLFRFEFPERPGALMKFLSRLGP-RWNISLFHYRNHGAA---------------DGRVLAGLQVP--EDERAALDAALA 501 (521)
T ss_pred eEEEEEEcCCCCcHHHHHHHHhCC-CcceeeeeecCCCCC---------------ceEEEEEEeeC--hhHHHHHHHHHH
Confidence 357888999999999999999875 245665566654321 11345555542 244567777777
Q ss_pred hhcC
Q 048784 263 EFAT 266 (282)
Q Consensus 263 ~~~~ 266 (282)
+..-
T Consensus 502 ~~gy 505 (521)
T PRK12483 502 ALGY 505 (521)
T ss_pred HCCC
Confidence 6643
No 303
>TIGR03870 ABC_MoxJ methanol oxidation system protein MoxJ. This predicted periplasmic protein, called MoxJ or MxaJ, is required for methanol oxidation in Methylobacterium extorquens. Two differing lines of evidence suggest two different roles. Forming one view, homology suggests it is the substrate-binding protein of an ABC transporter associated with methanol oxidation. The gene, furthermore, is found regular in genomes with, and only two or three genes away from, a corresponding permease and ATP-binding cassette gene pair. The other view is that this protein is an accessory factor or additional subunit of methanol dehydrogenase itself. Mutational studies show a dependence on this protein for expression of the PQQ-dependent, two-subunit methanol dehydrogenase (MxaF and MxaI) in Methylobacterium extorquens, as if it is a chaperone for enzyme assembly or a third subunit. A homologous N-terminal sequence was found in Paracoccus denitrificans as a 32Kd third subunit. This protein may, in
Probab=20.14 E-value=1.9e+02 Score=25.44 Aligned_cols=20 Identities=20% Similarity=-0.056 Sum_probs=17.6
Q ss_pred CHHHHHHHHHcCCCCeEEEe
Q 048784 25 QFDTAFEAVERWLVDRAVLP 44 (282)
Q Consensus 25 s~~~v~~av~~g~~d~gVvP 44 (282)
+..+++.+|.+|++|..+..
T Consensus 151 ~~~~~~~aL~~GrvDa~i~~ 170 (246)
T TIGR03870 151 DPRKLVSEVATGKADLAVAF 170 (246)
T ss_pred CHHHHHHHHHcCCCCEEEee
Confidence 46789999999999999875
No 304
>TIGR01093 aroD 3-dehydroquinate dehydratase, type I. Type II 3-dehydroquinate dehydratase, designated AroQ, is described by TIGR01088.
Probab=20.04 E-value=1.4e+02 Score=26.34 Aligned_cols=34 Identities=21% Similarity=0.253 Sum_probs=20.6
Q ss_pred EEEEeecCCCcHHHHHHHHHHHhhcCceEEEccccC
Q 048784 241 FYVDFEASMADQKAQNALRHLKEFATFLRVLGSYPI 276 (282)
Q Consensus 241 F~vd~~g~~~~~~~~~al~~l~~~~~~v~~LGsY~~ 276 (282)
-|||+|-...+..++++++..++ ...++++||=.
T Consensus 94 d~vDiEl~~~~~~~~~l~~~~~~--~~~kvI~S~H~ 127 (228)
T TIGR01093 94 DFVDIELFLPDDAVKELINIAKK--GGTKIIMSYHD 127 (228)
T ss_pred CEEEEEccCCHHHHHHHHHHHHH--CCCEEEEeccC
Confidence 46788766555555555554443 34678888743
Done!