Query 023305
Match_columns 284
No_of_seqs 208 out of 1126
Neff 6.8
Searched_HMMs 46136
Date Fri Mar 29 03:01:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023305.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023305hhsearch_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 2.3E-93 4.9E-98 648.4 29.9 268 1-282 6-276 (279)
2 PRK11899 prephenate dehydratas 100.0 2E-91 4.4E-96 641.7 31.2 268 1-282 8-276 (279)
3 PLN02317 arogenate dehydratase 100.0 2.3E-91 4.9E-96 660.6 31.3 283 1-283 98-380 (382)
4 PRK10622 pheA bifunctional cho 100.0 2.9E-85 6.2E-90 625.7 30.3 268 1-282 107-379 (386)
5 PRK11898 prephenate dehydratas 100.0 3.2E-84 7E-89 596.6 31.7 267 1-282 5-279 (283)
6 KOG2797 Prephenate dehydratase 100.0 3.6E-78 7.8E-83 544.6 20.6 278 1-283 94-373 (377)
7 PF00800 PDT: Prephenate dehyd 100.0 1.2E-57 2.5E-62 395.1 16.4 176 1-176 2-181 (181)
8 cd04904 ACT_AAAH ACT domain of 99.9 7.6E-23 1.7E-27 152.5 9.6 73 187-275 1-73 (74)
9 cd04931 ACT_PAH ACT domain of 99.9 1.1E-21 2.4E-26 151.6 10.0 70 183-267 11-80 (90)
10 cd04930 ACT_TH ACT domain of t 99.9 2.2E-21 4.8E-26 156.4 9.0 76 184-275 39-114 (115)
11 cd04905 ACT_CM-PDT C-terminal 99.8 8.5E-21 1.8E-25 143.1 11.3 80 186-279 1-80 (80)
12 cd04929 ACT_TPH ACT domain of 99.8 2.5E-21 5.5E-26 144.5 8.2 71 187-273 1-71 (74)
13 cd04880 ACT_AAAH-PDT-like ACT 99.8 4E-20 8.6E-25 137.5 9.9 75 188-276 1-75 (75)
14 TIGR01268 Phe4hydrox_tetr phen 99.8 3.4E-18 7.3E-23 164.4 10.2 79 185-278 15-94 (436)
15 TIGR01270 Trp_5_monoox tryptop 99.6 6.5E-16 1.4E-20 149.2 9.7 76 183-274 28-104 (464)
16 PRK06034 hypothetical protein; 99.2 1.6E-11 3.4E-16 112.6 4.7 69 1-73 99-169 (279)
17 PRK08818 prephenate dehydrogen 98.9 5.8E-09 1.3E-13 99.9 8.1 65 185-265 294-359 (370)
18 TIGR01269 Tyr_3_monoox tyrosin 98.8 8.9E-09 1.9E-13 99.2 8.6 72 186-270 37-109 (457)
19 KOG3820 Aromatic amino acid hy 98.6 1.2E-07 2.6E-12 89.8 8.4 74 185-274 35-108 (461)
20 cd04886 ACT_ThrD-II-like C-ter 98.3 6.6E-06 1.4E-10 58.8 9.2 68 190-270 2-69 (73)
21 PF01842 ACT: ACT domain; Int 98.3 5.5E-06 1.2E-10 58.7 8.0 38 187-224 1-38 (66)
22 cd04882 ACT_Bt0572_2 C-termina 97.7 0.00025 5.3E-09 50.0 8.0 59 189-268 2-60 (65)
23 PRK06737 acetolactate synthase 97.7 0.00047 1E-08 51.7 9.5 70 187-273 3-72 (76)
24 cd04884 ACT_CBS C-terminal ACT 97.6 0.00046 9.9E-09 50.3 8.6 65 189-268 2-66 (72)
25 PF13710 ACT_5: ACT domain; PD 97.6 0.00058 1.3E-08 49.2 8.0 62 195-273 1-62 (63)
26 cd04878 ACT_AHAS N-terminal AC 97.6 0.0012 2.6E-08 46.8 9.7 67 188-271 2-68 (72)
27 cd04883 ACT_AcuB C-terminal AC 97.5 0.00084 1.8E-08 48.4 8.7 65 187-270 2-66 (72)
28 cd04874 ACT_Af1403 N-terminal 97.5 0.0014 3E-08 46.6 9.1 64 188-270 2-65 (72)
29 PF13291 ACT_4: ACT domain; PD 97.3 0.0025 5.5E-08 47.3 9.0 71 184-270 4-74 (80)
30 cd02116 ACT ACT domains are co 97.3 0.0019 4.1E-08 42.1 7.3 58 190-265 2-59 (60)
31 cd04888 ACT_PheB-BS C-terminal 97.3 0.0035 7.5E-08 45.6 9.3 73 188-276 2-76 (76)
32 PRK11152 ilvM acetolactate syn 97.2 0.0037 8E-08 46.8 8.6 67 186-270 3-69 (76)
33 PRK11895 ilvH acetolactate syn 97.1 0.0048 1E-07 52.7 10.3 71 187-274 3-73 (161)
34 cd04902 ACT_3PGDH-xct C-termin 97.1 0.0025 5.4E-08 45.8 7.5 61 189-265 2-62 (73)
35 cd04903 ACT_LSD C-terminal ACT 97.1 0.0032 6.9E-08 44.5 7.8 63 189-270 2-64 (71)
36 TIGR00119 acolac_sm acetolacta 97.1 0.0052 1.1E-07 52.3 10.2 70 188-274 3-72 (157)
37 cd04908 ACT_Bt0572_1 N-termina 97.1 0.0046 1E-07 44.3 8.2 35 188-222 3-37 (66)
38 cd04909 ACT_PDH-BS C-terminal 97.1 0.0049 1.1E-07 44.2 8.3 63 188-268 3-65 (69)
39 cd04885 ACT_ThrD-I Tandem C-te 97.1 0.0033 7.2E-08 45.4 7.3 62 190-269 2-63 (68)
40 PRK13562 acetolactate synthase 97.0 0.0072 1.6E-07 46.1 9.2 72 187-274 3-74 (84)
41 CHL00100 ilvH acetohydroxyacid 97.0 0.0046 1E-07 53.5 9.2 71 187-274 3-73 (174)
42 cd04887 ACT_MalLac-Enz ACT_Mal 97.0 0.0053 1.1E-07 44.5 7.7 63 189-268 2-64 (74)
43 cd04879 ACT_3PGDH-like ACT_3PG 96.9 0.0052 1.1E-07 43.1 7.4 62 189-269 2-63 (71)
44 cd04896 ACT_ACR-like_3 ACT dom 96.9 0.007 1.5E-07 45.2 7.9 64 188-266 2-69 (75)
45 PRK08178 acetolactate synthase 96.8 0.014 2.9E-07 45.7 9.2 71 186-274 8-78 (96)
46 PRK04435 hypothetical protein; 96.7 0.019 4.1E-07 48.2 10.0 77 185-277 68-146 (147)
47 cd04906 ACT_ThrD-I_1 First of 96.6 0.016 3.4E-07 43.9 8.4 69 189-275 4-72 (85)
48 cd04901 ACT_3PGDH C-terminal A 96.6 0.006 1.3E-07 43.4 5.4 61 189-270 2-62 (69)
49 cd04881 ACT_HSDH-Hom ACT_HSDH_ 96.6 0.018 4E-07 41.3 8.1 64 189-268 3-66 (79)
50 PRK08198 threonine dehydratase 96.5 0.023 5E-07 55.0 10.8 76 186-275 327-403 (404)
51 cd04926 ACT_ACR_4 C-terminal 96.3 0.031 6.7E-07 40.9 7.9 36 187-222 2-37 (72)
52 cd04872 ACT_1ZPV ACT domain pr 96.2 0.029 6.2E-07 42.5 7.8 66 187-267 2-68 (88)
53 PRK00194 hypothetical protein; 96.2 0.033 7.2E-07 42.2 7.8 36 186-221 3-38 (90)
54 PF13740 ACT_6: ACT domain; PD 96.2 0.031 6.6E-07 41.3 7.4 35 189-223 3-39 (76)
55 cd04870 ACT_PSP_1 CT domains f 96.2 0.055 1.2E-06 39.7 8.7 61 191-266 4-64 (75)
56 cd04873 ACT_UUR-ACR-like ACT d 96.1 0.072 1.6E-06 37.6 8.8 48 188-250 2-49 (70)
57 cd04899 ACT_ACR-UUR-like_2 C-t 96.0 0.07 1.5E-06 38.0 8.7 37 187-223 1-37 (70)
58 TIGR01127 ilvA_1Cterm threonin 96.0 0.038 8.3E-07 53.0 9.4 73 186-272 305-378 (380)
59 PRK08577 hypothetical protein; 96.0 0.11 2.5E-06 42.7 11.0 69 186-269 56-124 (136)
60 cd04877 ACT_TyrR N-terminal AC 96.0 0.048 1E-06 39.9 7.8 60 188-268 2-61 (74)
61 cd04876 ACT_RelA-SpoT ACT dom 96.0 0.1 2.3E-06 35.3 9.0 63 190-269 2-64 (71)
62 cd04889 ACT_PDH-BS-like C-term 95.9 0.027 5.9E-07 38.7 5.7 34 190-223 2-35 (56)
63 cd04895 ACT_ACR_1 ACT domain-c 95.9 0.071 1.5E-06 39.5 8.0 29 187-215 2-30 (72)
64 PRK06382 threonine dehydratase 95.8 0.054 1.2E-06 52.7 9.5 74 185-272 329-403 (406)
65 cd04875 ACT_F4HF-DF N-terminal 95.5 0.18 3.9E-06 36.7 9.0 33 189-221 2-34 (74)
66 cd04869 ACT_GcvR_2 ACT domains 95.3 0.16 3.4E-06 37.3 8.4 34 189-222 2-35 (81)
67 COG4492 PheB ACT domain-contai 95.2 0.12 2.7E-06 42.6 7.9 77 184-277 70-149 (150)
68 COG2061 ACT-domain-containing 95.0 0.19 4.2E-06 42.4 8.8 74 186-275 5-79 (170)
69 PRK07334 threonine dehydratase 95.0 0.19 4E-06 48.9 10.1 76 185-274 325-401 (403)
70 PRK08526 threonine dehydratase 94.8 0.24 5.1E-06 48.3 10.1 209 40-273 168-400 (403)
71 PRK08639 threonine dehydratase 94.2 0.27 5.9E-06 48.0 9.3 74 185-275 335-409 (420)
72 cd04893 ACT_GcvR_1 ACT domains 94.0 0.55 1.2E-05 34.6 8.6 69 189-273 4-73 (77)
73 cd04900 ACT_UUR-like_1 ACT dom 94.0 0.45 9.7E-06 34.6 8.0 31 187-217 2-32 (73)
74 TIGR02079 THD1 threonine dehyd 93.9 0.49 1.1E-05 46.1 10.2 74 185-274 324-397 (409)
75 COG2716 GcvR Glycine cleavage 93.8 0.33 7.1E-06 41.8 7.7 93 170-277 76-171 (176)
76 TIGR01124 ilvA_2Cterm threonin 93.5 1.3 2.8E-05 44.4 12.7 214 31-275 158-395 (499)
77 cd04897 ACT_ACR_3 ACT domain-c 93.4 0.71 1.5E-05 34.4 8.2 29 187-215 2-30 (75)
78 PRK11589 gcvR glycine cleavage 93.4 0.44 9.5E-06 41.8 8.1 35 189-223 98-132 (190)
79 COG0440 IlvH Acetolactate synt 93.2 0.52 1.1E-05 40.3 8.0 73 186-275 4-76 (163)
80 COG4747 ACT domain-containing 93.0 0.72 1.6E-05 37.5 8.0 40 186-225 69-108 (142)
81 COG3830 ACT domain-containing 92.6 0.38 8.2E-06 37.1 5.7 71 189-274 4-78 (90)
82 cd04927 ACT_ACR-like_2 Second 92.3 1.5 3.4E-05 32.2 8.6 26 191-216 5-30 (76)
83 cd04935 ACT_AKiii-DAPDC_1 ACT 92.2 1.3 2.7E-05 32.7 8.0 63 193-275 11-74 (75)
84 cd04907 ACT_ThrD-I_2 Second of 92.1 1.5 3.2E-05 33.0 8.4 65 188-271 3-67 (81)
85 cd04912 ACT_AKiii-LysC-EC-like 91.6 1.6 3.5E-05 31.9 8.0 56 193-267 11-67 (75)
86 cd04932 ACT_AKiii-LysC-EC_1 AC 91.4 1.9 4.2E-05 31.8 8.3 58 193-269 11-69 (75)
87 PRK09224 threonine dehydratase 91.2 1.5 3.2E-05 44.0 9.8 73 185-275 327-399 (504)
88 COG1707 ACT domain-containing 91.2 0.74 1.6E-05 39.7 6.5 61 189-267 5-65 (218)
89 PRK12483 threonine dehydratase 91.0 1.6 3.4E-05 44.1 9.8 72 185-275 344-416 (521)
90 PRK13010 purU formyltetrahydro 90.5 1.5 3.3E-05 40.9 8.6 64 189-267 12-79 (289)
91 PRK13011 formyltetrahydrofolat 90.5 2.1 4.5E-05 39.9 9.5 65 188-267 9-75 (286)
92 PLN02550 threonine dehydratase 89.7 2.1 4.6E-05 43.9 9.5 208 40-275 258-487 (591)
93 cd04925 ACT_ACR_2 ACT domain-c 89.3 4.2 9.1E-05 29.6 8.5 32 189-220 3-34 (74)
94 cd04934 ACT_AK-Hom3_1 CT domai 89.0 2.1 4.6E-05 31.4 6.7 55 195-269 13-67 (73)
95 PRK06349 homoserine dehydrogen 89.0 1.8 3.9E-05 42.4 8.2 63 189-268 351-413 (426)
96 cd04891 ACT_AK-LysC-DapG-like_ 88.6 3.4 7.3E-05 27.5 7.2 30 192-221 7-36 (61)
97 PRK11092 bifunctional (p)ppGpp 88.1 4.9 0.00011 42.1 11.1 70 184-270 624-693 (702)
98 PRK11151 DNA-binding transcrip 87.9 16 0.00035 33.1 13.4 122 17-148 116-246 (305)
99 PRK06545 prephenate dehydrogen 86.8 1.7 3.6E-05 41.5 6.4 40 186-225 290-329 (359)
100 COG0317 SpoT Guanosine polypho 86.8 7.9 0.00017 40.5 11.5 70 184-270 625-694 (701)
101 PRK11790 D-3-phosphoglycerate 86.8 2.1 4.6E-05 41.8 7.2 63 186-270 338-401 (409)
102 PF00497 SBP_bac_3: Bacterial 86.4 7 0.00015 32.8 9.4 43 5-47 116-159 (225)
103 PF00585 Thr_dehydrat_C: C-ter 86.3 2.2 4.8E-05 32.7 5.6 67 185-269 9-75 (91)
104 cd08445 PBP2_BenM_CatM_CatR Th 85.5 19 0.0004 29.5 12.8 121 17-147 26-158 (203)
105 PRK06027 purU formyltetrahydro 85.3 5.5 0.00012 37.0 8.8 35 187-221 5-41 (286)
106 cd08452 PBP2_AlsR The C-termin 84.5 20 0.00044 29.2 13.5 122 17-148 25-157 (197)
107 PRK10872 relA (p)ppGpp synthet 84.0 6.4 0.00014 41.5 9.4 69 185-269 665-733 (743)
108 TIGR00691 spoT_relA (p)ppGpp s 83.6 8.5 0.00018 40.2 10.2 68 185-269 609-676 (683)
109 TIGR01693 UTase_glnD [Protein- 83.3 7.3 0.00016 41.6 9.8 50 185-249 778-827 (850)
110 cd04913 ACT_AKii-LysC-BS-like_ 82.8 6.4 0.00014 27.4 6.5 27 192-218 8-34 (75)
111 cd08453 PBP2_IlvR The C-termin 82.8 24 0.00052 28.6 12.4 122 18-148 26-160 (200)
112 TIGR00719 sda_beta L-serine de 82.2 6.4 0.00014 34.8 7.6 55 186-256 148-203 (208)
113 cd08411 PBP2_OxyR The C-termin 81.2 27 0.00059 28.2 13.3 123 17-149 26-157 (200)
114 PRK05092 PII uridylyl-transfer 81.0 8.9 0.00019 41.5 9.5 52 186-252 843-895 (931)
115 cd04890 ACT_AK-like_1 ACT doma 79.7 7.4 0.00016 26.8 5.8 51 194-265 11-61 (62)
116 TIGR00655 PurU formyltetrahydr 79.6 12 0.00026 34.7 8.8 64 189-267 3-70 (280)
117 cd08417 PBP2_Nitroaromatics_li 79.3 31 0.00068 27.8 12.2 121 18-149 26-155 (200)
118 PRK13581 D-3-phosphoglycerate 78.8 7.9 0.00017 39.0 7.8 104 144-267 388-514 (526)
119 cd04928 ACT_TyrKc Uncharacteri 78.6 17 0.00036 26.5 7.4 34 189-222 4-37 (68)
120 KOG2663 Acetolactate synthase, 78.2 8.1 0.00017 35.5 6.8 72 186-276 77-150 (309)
121 cd04933 ACT_AK1-AT_1 ACT domai 78.0 10 0.00022 28.3 6.3 58 193-269 11-72 (78)
122 PRK05007 PII uridylyl-transfer 77.9 6.2 0.00013 42.4 7.1 31 185-215 807-837 (884)
123 PRK15007 putative ABC transpor 77.8 4.7 0.0001 35.2 5.3 43 5-47 132-174 (243)
124 PRK11589 gcvR glycine cleavage 77.6 11 0.00025 32.9 7.5 37 186-224 6-44 (190)
125 PRK09959 hybrid sensory histid 77.3 2.7 5.8E-05 46.0 4.3 43 5-47 170-212 (1197)
126 cd08462 PBP2_NodD The C-termin 77.0 38 0.00083 27.6 10.4 122 17-149 25-155 (200)
127 PF12727 PBP_like: PBP superfa 76.1 20 0.00043 31.2 8.6 140 23-175 15-177 (193)
128 cd08486 PBP2_CbnR The C-termin 75.9 42 0.00092 27.5 12.1 120 17-146 26-156 (198)
129 PRK09508 leuO leucine transcri 75.8 18 0.0004 33.1 8.9 121 18-149 138-266 (314)
130 TIGR01096 3A0103s03R lysine-ar 75.7 5.8 0.00012 34.7 5.2 43 5-47 137-180 (250)
131 PRK11260 cystine transporter s 74.7 5.8 0.00012 35.5 5.1 43 5-47 155-197 (266)
132 cd08435 PBP2_GbpR The C-termin 74.4 43 0.00093 26.8 12.8 122 17-148 25-158 (201)
133 cd04871 ACT_PSP_2 ACT domains 74.4 7.5 0.00016 29.2 4.9 66 194-267 7-74 (84)
134 COG4747 ACT domain-containing 73.7 5.3 0.00011 32.6 3.9 28 189-216 6-33 (142)
135 PRK10341 DNA-binding transcrip 72.4 77 0.0017 28.9 12.8 119 18-148 123-252 (312)
136 PF12974 Phosphonate-bd: ABC t 71.9 3.4 7.3E-05 36.5 2.8 74 6-88 113-202 (243)
137 cd08450 PBP2_HcaR The C-termin 71.9 50 0.0011 26.4 12.2 32 17-48 25-57 (196)
138 PF03466 LysR_substrate: LysR 71.7 53 0.0011 26.7 13.7 115 17-149 31-162 (209)
139 PRK11242 DNA-binding transcrip 71.3 76 0.0016 28.3 12.6 121 18-148 117-247 (296)
140 PRK09495 glnH glutamine ABC tr 71.0 7.7 0.00017 34.2 4.9 43 5-47 137-179 (247)
141 PF00497 SBP_bac_3: Bacterial 70.6 36 0.00078 28.4 8.9 122 12-149 31-165 (225)
142 PRK12683 transcriptional regul 70.5 86 0.0019 28.6 13.4 120 18-147 119-248 (309)
143 PRK04374 PII uridylyl-transfer 70.4 23 0.00049 38.2 9.0 51 185-252 795-848 (869)
144 PRK12684 transcriptional regul 70.0 89 0.0019 28.6 12.5 120 18-148 119-249 (313)
145 PRK12679 cbl transcriptional r 69.8 90 0.002 28.6 12.3 120 18-146 119-247 (316)
146 TIGR02424 TF_pcaQ pca operon t 69.8 84 0.0018 28.2 12.7 121 18-148 119-251 (300)
147 PRK09959 hybrid sensory histid 69.3 6 0.00013 43.3 4.6 44 5-48 413-456 (1197)
148 TIGR01728 SsuA_fam ABC transpo 68.9 24 0.00053 31.1 7.8 115 21-144 31-156 (288)
149 KOG3217 Protein tyrosine phosp 68.8 6.7 0.00014 33.1 3.7 62 201-280 58-123 (159)
150 PRK03381 PII uridylyl-transfer 68.7 23 0.00049 37.6 8.5 37 186-222 707-743 (774)
151 cd04923 ACT_AK-LysC-DapG-like_ 68.4 28 0.0006 23.3 6.4 27 193-219 10-36 (63)
152 TIGR01327 PGDH D-3-phosphoglyc 68.2 11 0.00024 38.0 5.9 105 143-267 386-513 (525)
153 PRK01759 glnD PII uridylyl-tra 68.0 18 0.00039 38.8 7.6 31 185-215 782-812 (854)
154 cd08459 PBP2_DntR_NahR_LinR_li 67.6 64 0.0014 26.0 10.8 122 17-149 25-155 (201)
155 cd08412 PBP2_PAO1_like The C-t 67.6 62 0.0013 25.8 13.0 122 17-148 25-154 (198)
156 cd00134 PBPb Bacterial peripla 67.0 12 0.00026 30.6 5.0 42 6-47 112-153 (218)
157 cd08461 PBP2_DntR_like_3 The C 67.0 64 0.0014 25.9 9.4 123 17-150 25-157 (198)
158 smart00062 PBPb Bacterial peri 66.2 12 0.00025 30.5 4.8 43 7-49 114-156 (219)
159 cd04936 ACT_AKii-LysC-BS-like_ 65.5 34 0.00075 22.8 6.4 27 193-219 10-36 (63)
160 PF07485 DUF1529: Domain of Un 64.9 51 0.0011 26.9 8.1 52 197-264 67-118 (123)
161 cd08440 PBP2_LTTR_like_4 TThe 64.7 69 0.0015 25.3 13.4 121 18-148 26-155 (197)
162 PRK09906 DNA-binding transcrip 64.4 1.1E+02 0.0023 27.4 13.6 121 17-147 115-246 (296)
163 cd08413 PBP2_CysB_like The C-t 63.7 79 0.0017 25.7 12.3 122 17-147 25-155 (198)
164 PRK00275 glnD PII uridylyl-tra 63.6 36 0.00077 36.8 8.9 36 185-220 813-850 (895)
165 cd08446 PBP2_Chlorocatechol Th 63.6 76 0.0016 25.4 13.4 122 17-148 26-158 (198)
166 TIGR03427 ABC_peri_uca ABC tra 63.3 1.4E+02 0.0029 28.3 12.5 130 20-157 36-178 (328)
167 cd08437 PBP2_MleR The substrat 63.2 78 0.0017 25.4 13.0 122 17-147 25-156 (198)
168 PRK03059 PII uridylyl-transfer 62.9 41 0.0009 36.1 9.2 36 185-220 785-822 (856)
169 PF09084 NMT1: NMT1/THI5 like; 62.8 95 0.0021 26.3 14.3 105 21-133 23-139 (216)
170 TIGR02995 ectoine_ehuB ectoine 62.7 14 0.0003 33.3 4.9 43 5-47 150-193 (275)
171 smart00079 PBPe Eukaryotic hom 62.5 15 0.00033 28.9 4.6 74 5-87 19-104 (134)
172 cd08460 PBP2_DntR_like_1 The C 62.3 59 0.0013 26.4 8.4 121 17-148 25-153 (200)
173 PRK11917 bifunctional adhesin/ 61.8 23 0.00049 31.8 6.1 88 6-113 155-246 (259)
174 TIGR03339 phn_lysR aminoethylp 61.5 1.1E+02 0.0024 26.7 12.3 118 18-145 110-236 (279)
175 PRK10820 DNA-binding transcrip 61.5 23 0.0005 35.6 6.7 59 189-268 3-61 (520)
176 cd04868 ACT_AK-like ACT domain 61.3 20 0.00043 23.2 4.4 27 195-221 12-38 (60)
177 cd04924 ACT_AK-Arch_2 ACT doma 61.0 46 0.00099 22.6 6.4 27 193-219 11-37 (66)
178 cd08468 PBP2_Pa0477 The C-term 59.9 93 0.002 25.3 10.5 122 17-149 25-157 (202)
179 cd08443 PBP2_CysB The C-termin 59.5 95 0.0021 25.2 13.7 122 17-147 25-155 (198)
180 PRK11716 DNA-binding transcrip 59.4 1.2E+02 0.0026 26.4 12.9 122 18-148 93-223 (269)
181 PRK12680 transcriptional regul 59.2 1.5E+02 0.0033 27.4 13.3 122 18-148 119-250 (327)
182 PRK09224 threonine dehydratase 58.9 25 0.00054 35.3 6.4 35 185-220 422-456 (504)
183 TIGR00070 hisG ATP phosphoribo 58.8 66 0.0014 28.0 8.2 107 30-156 50-171 (182)
184 cd04937 ACT_AKi-DapG-BS_2 ACT 58.3 43 0.00093 23.2 5.9 33 187-219 4-37 (64)
185 cd04892 ACT_AK-like_2 ACT doma 57.9 52 0.0011 21.7 6.3 27 193-219 10-36 (65)
186 cd04914 ACT_AKi-DapG-BS_1 ACT 57.9 16 0.00035 26.0 3.6 28 193-221 9-36 (67)
187 cd08444 PBP2_Cbl The C-termina 57.7 1E+02 0.0022 25.0 14.0 122 17-148 25-156 (198)
188 cd04911 ACT_AKiii-YclM-BS_1 AC 57.7 52 0.0011 24.5 6.3 57 194-270 12-68 (76)
189 PRK12682 transcriptional regul 57.5 1.5E+02 0.0032 26.9 13.6 120 18-148 119-249 (309)
190 cd08451 PBP2_BudR The C-termin 56.4 1E+02 0.0022 24.6 14.2 122 17-148 26-159 (199)
191 cd08485 PBP2_ClcR The C-termin 56.0 1.1E+02 0.0024 24.9 12.9 122 17-148 26-158 (198)
192 PRK10859 membrane-bound lytic 55.7 50 0.0011 32.7 7.9 43 5-47 155-202 (482)
193 cd04922 ACT_AKi-HSDH-ThrA_2 AC 54.8 32 0.0007 23.4 4.7 27 193-219 11-37 (66)
194 cd04918 ACT_AK1-AT_2 ACT domai 54.3 72 0.0016 22.2 7.2 34 186-219 3-36 (65)
195 cd08436 PBP2_LTTR_like_3 The C 53.2 1.1E+02 0.0024 24.1 12.9 33 17-49 25-58 (194)
196 cd04919 ACT_AK-Hom3_2 ACT doma 53.0 38 0.00082 23.2 4.9 27 193-219 11-37 (66)
197 PRK09034 aspartate kinase; Rev 52.8 2.1E+02 0.0045 28.3 11.7 126 115-267 235-372 (454)
198 PRK11482 putative DNA-binding 52.8 1.9E+02 0.0041 26.6 13.0 122 16-149 141-270 (317)
199 TIGR00656 asp_kin_monofn aspar 52.7 2.2E+02 0.0047 27.4 11.6 96 115-219 190-296 (401)
200 cd08421 PBP2_LTTR_like_1 The C 52.6 1.2E+02 0.0026 24.2 12.9 122 17-148 25-155 (198)
201 COG0725 ModA ABC-type molybdat 52.5 27 0.00059 31.9 5.0 46 4-49 146-195 (258)
202 cd08457 PBP2_OccR The C-termin 52.0 1.2E+02 0.0027 24.2 12.9 119 17-145 25-152 (196)
203 COG0834 HisJ ABC-type amino ac 51.4 26 0.00057 30.7 4.7 42 6-47 153-196 (275)
204 PF13379 NMT1_2: NMT1-like fam 51.3 1.5E+02 0.0032 26.2 9.6 119 21-145 37-180 (252)
205 TIGR01096 3A0103s03R lysine-ar 51.1 1.6E+02 0.0035 25.3 9.9 114 20-149 64-186 (250)
206 PRK10216 DNA-binding transcrip 51.1 1.9E+02 0.0042 26.3 11.3 125 17-148 122-262 (319)
207 cd08466 PBP2_LeuO The C-termin 50.7 1.3E+02 0.0028 24.1 11.1 122 17-149 25-155 (200)
208 cd08420 PBP2_CysL_like C-termi 50.4 1.2E+02 0.0027 23.9 13.6 122 17-148 25-158 (201)
209 smart00062 PBPb Bacterial peri 49.9 1.3E+02 0.0029 24.0 11.5 109 21-145 41-156 (219)
210 cd08426 PBP2_LTTR_like_5 The C 49.4 1.3E+02 0.0029 23.9 15.3 121 18-148 26-155 (199)
211 PRK05007 PII uridylyl-transfer 49.3 66 0.0014 34.7 8.0 32 186-217 701-732 (884)
212 PF01193 RNA_pol_L: RNA polyme 49.2 61 0.0013 22.9 5.5 62 190-268 2-64 (66)
213 PF13840 ACT_7: ACT domain ; P 48.6 37 0.00081 24.0 4.3 33 186-218 8-42 (65)
214 COG3978 Acetolactate synthase 48.6 1E+02 0.0022 23.4 6.6 60 191-265 8-67 (86)
215 PRK09986 DNA-binding transcrip 48.1 2E+02 0.0043 25.5 13.3 124 17-148 122-255 (294)
216 PF11966 SSURE: Fibronectin-bi 46.7 50 0.0011 24.7 4.6 38 240-277 18-60 (81)
217 COG2844 GlnD UTP:GlnB (protein 46.2 82 0.0018 33.7 7.8 32 184-215 789-820 (867)
218 PF03401 TctC: Tripartite tric 45.7 30 0.00064 31.7 4.2 125 6-133 114-261 (274)
219 cd08464 PBP2_DntR_like_2 The C 45.7 1.5E+02 0.0033 23.5 9.2 122 17-149 25-155 (200)
220 TIGR01693 UTase_glnD [Protein- 45.3 83 0.0018 33.7 8.0 31 186-216 668-698 (850)
221 cd00134 PBPb Bacterial peripla 45.2 1.1E+02 0.0023 24.7 7.3 113 20-148 39-158 (218)
222 PRK11139 DNA-binding transcrip 45.1 2.3E+02 0.005 25.4 10.2 118 18-149 120-246 (297)
223 cd08418 PBP2_TdcA The C-termin 45.0 1.6E+02 0.0034 23.5 12.1 120 18-149 26-156 (201)
224 cd08438 PBP2_CidR The C-termin 44.6 1.6E+02 0.0034 23.3 13.4 30 18-47 26-56 (197)
225 PHA03169 hypothetical protein; 43.5 1.2E+02 0.0027 29.4 7.9 70 183-265 320-389 (413)
226 cd08423 PBP2_LTTR_like_6 The C 43.5 1.6E+02 0.0036 23.2 12.5 124 18-148 26-160 (200)
227 PRK02047 hypothetical protein; 43.0 1.5E+02 0.0033 22.6 7.7 59 193-268 23-84 (91)
228 PRK01759 glnD PII uridylyl-tra 42.6 96 0.0021 33.4 8.0 35 186-220 677-713 (854)
229 PRK13584 hisG ATP phosphoribos 42.2 1.6E+02 0.0034 26.2 8.0 119 29-170 52-177 (204)
230 PRK08961 bifunctional aspartat 42.1 4.7E+02 0.01 28.1 13.2 127 115-267 251-388 (861)
231 COG2107 Predicted periplasmic 42.0 45 0.00099 30.8 4.7 45 4-49 99-145 (272)
232 PRK11553 alkanesulfonate trans 41.9 1.2E+02 0.0026 27.7 7.7 106 21-133 58-175 (314)
233 PRK04998 hypothetical protein; 41.3 1.5E+02 0.0033 22.3 7.3 59 193-268 22-81 (88)
234 cd08414 PBP2_LTTR_aromatics_li 40.9 1.8E+02 0.0039 22.9 15.3 32 18-49 26-58 (197)
235 cd08416 PBP2_MdcR The C-termin 40.7 1.9E+02 0.004 23.0 13.6 122 17-148 25-157 (199)
236 TIGR03871 ABC_peri_MoxJ_2 quin 40.6 45 0.00097 28.7 4.4 43 5-47 110-161 (232)
237 PRK10797 glutamate and asparta 40.5 34 0.00075 31.5 3.8 43 5-47 159-205 (302)
238 cd08425 PBP2_CynR The C-termin 39.9 1.9E+02 0.0041 23.0 11.6 121 18-148 27-157 (197)
239 PRK10859 membrane-bound lytic 39.8 1.5E+02 0.0032 29.4 8.4 27 20-46 81-107 (482)
240 PRK05092 PII uridylyl-transfer 39.8 1.7E+02 0.0037 31.8 9.4 32 186-217 732-763 (931)
241 PRK08210 aspartate kinase I; R 39.4 1.3E+02 0.0028 29.0 7.8 94 116-217 195-303 (403)
242 PRK15010 ABC transporter lysin 38.9 65 0.0014 28.5 5.3 43 5-47 139-183 (260)
243 cd08465 PBP2_ToxR The C-termin 38.2 2.2E+02 0.0047 23.1 9.6 107 18-132 26-141 (200)
244 cd08483 PBP2_HvrB The C-termin 38.1 81 0.0018 25.1 5.4 116 18-148 26-149 (190)
245 cd08449 PBP2_XapR The C-termin 38.0 2E+02 0.0044 22.7 14.1 32 17-48 25-57 (197)
246 PRK06635 aspartate kinase; Rev 37.9 1.2E+02 0.0026 29.1 7.3 29 193-221 270-298 (404)
247 cd08469 PBP2_PnbR The C-termin 37.7 2.3E+02 0.005 23.3 9.8 31 18-48 26-57 (221)
248 cd08427 PBP2_LTTR_like_2 The C 37.6 2E+02 0.0044 22.6 15.1 121 17-148 25-153 (195)
249 cd08448 PBP2_LTTR_aromatics_li 37.3 2.1E+02 0.0045 22.6 14.3 122 17-148 25-157 (197)
250 cd04916 ACT_AKiii-YclM-BS_2 AC 36.5 45 0.00097 22.7 3.1 26 193-218 11-36 (66)
251 PRK03601 transcriptional regul 36.0 3.1E+02 0.0068 24.3 14.5 114 17-148 114-231 (275)
252 cd08430 PBP2_IlvY The C-termin 35.5 2.2E+02 0.0048 22.5 14.8 125 16-149 24-157 (199)
253 TIGR00363 lipoprotein, YaeC fa 34.1 3.6E+02 0.0079 24.5 11.4 130 12-153 35-199 (258)
254 PF06153 DUF970: Protein of un 33.8 1.2E+02 0.0027 24.2 5.4 53 201-271 14-66 (109)
255 cd08441 PBP2_MetR The C-termin 33.7 2.5E+02 0.0053 22.4 12.9 122 17-148 25-155 (198)
256 PRK10837 putative DNA-binding 33.7 3.4E+02 0.0073 24.0 12.8 32 17-48 114-146 (290)
257 cd00460 RNAP_RPB11_RPB3 RPB11 33.5 2E+02 0.0044 21.4 6.8 74 186-270 8-84 (86)
258 COG0788 PurU Formyltetrahydrof 33.2 3E+02 0.0065 25.7 8.5 35 186-220 7-41 (287)
259 TIGR01098 3A0109s03R phosphate 33.1 3.2E+02 0.007 23.6 11.0 29 21-49 66-94 (254)
260 cd04921 ACT_AKi-HSDH-ThrA-like 33.0 1.8E+02 0.0039 20.6 7.5 27 193-219 11-37 (80)
261 PF12916 DUF3834: Protein of u 33.0 47 0.001 29.4 3.2 63 6-72 76-143 (201)
262 cd08433 PBP2_Nac The C-teminal 32.7 2.5E+02 0.0055 22.3 13.2 121 18-148 26-155 (198)
263 PRK01686 hisG ATP phosphoribos 32.7 2.8E+02 0.006 24.8 8.2 112 28-156 53-177 (215)
264 PLN02550 threonine dehydratase 32.7 3.4E+02 0.0074 28.1 9.8 97 150-273 480-578 (591)
265 PRK11063 metQ DL-methionine tr 32.4 3.1E+02 0.0067 25.1 8.7 85 20-114 60-153 (271)
266 PRK00341 hypothetical protein; 32.4 2.3E+02 0.005 21.7 7.2 59 194-269 25-85 (91)
267 COG3181 Uncharacterized protei 32.4 35 0.00077 32.4 2.5 91 6-96 158-265 (319)
268 PRK06635 aspartate kinase; Rev 32.0 1.4E+02 0.0031 28.7 6.7 28 192-219 349-376 (404)
269 PF01250 Ribosomal_S6: Ribosom 31.9 2.2E+02 0.0047 21.2 8.0 60 199-274 21-87 (92)
270 TIGR01124 ilvA_2Cterm threonin 31.8 1.1E+02 0.0024 30.7 6.1 34 188-222 421-454 (499)
271 PRK15437 histidine ABC transpo 31.7 2.9E+02 0.0064 24.2 8.3 37 11-48 57-93 (259)
272 PRK15385 magnesium transport p 31.2 3.8E+02 0.0082 24.2 8.8 66 188-268 144-212 (225)
273 TIGR00149 TIGR00149_YbjQ secon 30.8 33 0.00072 28.3 1.8 18 233-253 104-121 (132)
274 cd08481 PBP2_GcdR_like The C-t 30.8 1.8E+02 0.0039 22.9 6.3 105 34-150 40-153 (194)
275 cd08467 PBP2_SyrM The C-termin 30.5 2.9E+02 0.0063 22.2 10.4 122 17-149 25-155 (200)
276 cd08415 PBP2_LysR_opines_like 30.1 2.7E+02 0.0059 21.9 12.8 123 16-148 24-155 (196)
277 PRK09791 putative DNA-binding 29.6 4.1E+02 0.0089 23.7 13.9 31 18-48 121-152 (302)
278 PRK15437 histidine ABC transpo 29.6 1.1E+02 0.0024 26.9 5.2 42 6-47 140-183 (259)
279 cd04920 ACT_AKiii-DAPDC_2 ACT 29.0 2E+02 0.0043 19.9 5.9 33 187-219 3-36 (63)
280 COG2150 Predicted regulator of 28.9 3.1E+02 0.0066 23.6 7.3 36 186-221 95-130 (167)
281 COG3283 TyrR Transcriptional r 28.2 2E+02 0.0043 28.4 6.7 70 190-280 4-75 (511)
282 TIGR02122 TRAP_TAXI TRAP trans 28.0 66 0.0014 29.1 3.5 45 3-47 146-197 (320)
283 PRK15010 ABC transporter lysin 27.8 4.2E+02 0.009 23.2 10.8 113 20-148 66-188 (260)
284 PRK07431 aspartate kinase; Pro 27.3 2.1E+02 0.0046 29.1 7.3 58 192-266 277-334 (587)
285 PRK15421 DNA-binding transcrip 27.2 4.9E+02 0.011 23.8 12.3 120 18-147 115-242 (317)
286 cd08442 PBP2_YofA_SoxR_like Th 26.7 3.1E+02 0.0068 21.4 13.2 122 17-149 25-152 (193)
287 PRK12483 threonine dehydratase 26.5 3.2E+02 0.0069 27.7 8.3 63 188-269 442-504 (521)
288 PRK11013 DNA-binding transcrip 26.3 4.8E+02 0.011 23.5 12.3 120 18-147 120-248 (309)
289 PF09967 DUF2201: VWA-like dom 26.3 64 0.0014 26.0 2.7 25 244-268 2-26 (126)
290 PF09383 NIL: NIL domain; Int 26.0 1.3E+02 0.0029 21.5 4.2 30 244-275 47-76 (76)
291 TIGR00656 asp_kin_monofn aspar 25.7 1.7E+02 0.0036 28.1 6.0 27 192-218 346-372 (401)
292 CHL00180 rbcR LysR transcripti 25.7 4.9E+02 0.011 23.3 14.1 31 17-47 120-151 (305)
293 TIGR01098 3A0109s03R phosphate 25.6 94 0.002 27.1 3.9 64 21-87 175-238 (254)
294 PF13379 NMT1_2: NMT1-like fam 25.6 1.3E+02 0.0028 26.6 4.8 43 4-47 127-177 (252)
295 cd08456 PBP2_LysR The C-termin 25.2 3.4E+02 0.0074 21.3 13.5 122 17-148 25-155 (196)
296 KOG4028 Uncharacterized conser 25.1 65 0.0014 26.8 2.5 29 3-31 113-142 (175)
297 PF03480 SBP_bac_7: Bacterial 25.0 5.1E+02 0.011 23.3 11.1 148 4-160 5-198 (286)
298 cd08447 PBP2_LTTR_aromatics_li 24.9 3.5E+02 0.0075 21.3 13.6 121 18-148 26-157 (198)
299 PF00072 Response_reg: Respons 24.9 81 0.0018 23.3 3.0 77 96-176 4-81 (112)
300 cd08458 PBP2_NocR The C-termin 24.6 3.6E+02 0.0079 21.5 14.9 121 17-147 25-154 (196)
301 TIGR00787 dctP tripartite ATP- 24.5 5E+02 0.011 23.0 10.4 147 3-157 4-195 (257)
302 PF01894 UPF0047: Uncharacteri 24.5 39 0.00085 27.3 1.1 17 233-252 92-108 (118)
303 cd08419 PBP2_CbbR_RubisCO_like 24.4 3.5E+02 0.0076 21.2 12.3 122 17-148 24-154 (197)
304 PRK11062 nhaR transcriptional 22.3 5.7E+02 0.012 22.9 12.3 145 18-176 119-275 (296)
305 PRK07377 hypothetical protein; 21.1 1.4E+02 0.0031 26.1 3.9 34 15-48 104-137 (184)
306 PRK00907 hypothetical protein; 21.0 3.9E+02 0.0085 20.5 6.7 62 194-273 25-89 (92)
307 cd08439 PBP2_LrhA_like The C-t 21.0 1.4E+02 0.003 23.8 3.8 31 17-47 25-56 (185)
308 PRK00275 glnD PII uridylyl-tra 20.9 4.9E+02 0.011 28.3 8.8 31 186-216 704-734 (895)
309 PF01522 Polysacc_deac_1: Poly 20.6 1.1E+02 0.0023 23.5 2.9 30 186-215 5-35 (123)
310 TIGR03870 ABC_MoxJ methanol ox 20.4 1.9E+02 0.004 25.5 4.8 20 28-47 151-170 (246)
No 1
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=2.3e-93 Score=648.40 Aligned_cols=268 Identities=47% Similarity=0.701 Sum_probs=254.3
Q ss_pred CccCCCCcHHHHHHHhhCCC-CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeee
Q 023305 1 MMQGLPGSFSEDAALKAYPK-CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAAN 79 (284)
Q Consensus 1 aylGp~GtfS~~Aa~~~f~~-~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~ 79 (284)
|||||+|||||+||+++|++ .+..||+||+|||++|++|++||||||||||++|+|++|+|+|...+|.|+||+.+||+
T Consensus 6 ayLGP~Gtfs~~Aa~~~f~~~~~~~p~~ti~evf~ave~g~aD~gVVPIENS~eG~V~~tlDlL~~~~l~IvgE~~lpI~ 85 (279)
T COG0077 6 AYLGPEGTFSEQAARKLFGSGAELLPCSTIEDVFKAVENGEADYGVVPIENSIEGSVNETLDLLAETDLQIVGEIVLPIH 85 (279)
T ss_pred EEeCCCccHHHHHHHHhccccceeccCCCHHHHHHHHHcCCCceEEEEeeecCCcchHHHHHhhccCCcEEEEEEEEEEE
Confidence 69999999999999999998 79999999999999999999999999999999999999999999999999999999999
Q ss_pred eEeeecCCCCcCCccEEEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeec
Q 023305 80 FCLLALPGIKADQLKRVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILAD 157 (284)
Q Consensus 80 ~~L~~~~~~~l~~i~~V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~ 157 (284)
|||+++++.++++|++|||||||++||++||+++ +++.++++|||+||+++++.++...|||||+.||++|||++|++
T Consensus 86 h~L~~~~~~~l~~Ik~vySHpqalaQc~~~L~~~~p~~~~~~~~STa~Aak~v~~~~~~~~AAIas~~aA~~YgL~il~~ 165 (279)
T COG0077 86 HCLLVKGGVDLEEIKTVYSHPQALAQCRKFLRAHLPGVEIEYTSSTAEAAKLVAEGPDETVAAIASELAAELYGLDILAE 165 (279)
T ss_pred EEEEecCCCChhhCeEEEeCcHHHHHHHHHHHHcCCCceEEEcCCHHHHHHHHHhCCCcCeeEEcCHHHHHHcCcHhHhh
Confidence 9999998889999999999999999999999997 69999999999999999998888999999999999999999999
Q ss_pred cccCCCCCeeEEEEEeeCCCCCCCCCCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCC
Q 023305 158 RIQDEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGT 237 (284)
Q Consensus 158 ~I~d~~~N~TRF~vl~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~ 237 (284)
||||.++|+|||+||+|........+..||||+|+++|+||+|+++|++|+.||||||||||||+++.+
T Consensus 166 ~I~D~~~N~TRF~vl~r~~~~~~~~~~~kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~~~----------- 234 (279)
T COG0077 166 NIEDEPNNRTRFLVLSRRKPPSVSDGPEKTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTGL----------- 234 (279)
T ss_pred cccCCCCCeEEEEEEeccCCCCcCCCCceEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCCCC-----------
Confidence 999999999999999985211112245799999999999999999999999999999999999999874
Q ss_pred CccceeEEEEEeecCCCcHHHHHHHHHHHhcCCceEEEceeeCCC
Q 023305 238 AKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDA 282 (284)
Q Consensus 238 ~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~~~vkvLGsYp~~~ 282 (284)
|+|+||||++||.+|+.+++||++|++.+.++|+|||||...
T Consensus 235 ---~~Y~F~iD~eg~~~~~~v~~AL~el~~~t~~~kilGsYp~~~ 276 (279)
T COG0077 235 ---GEYLFFIDIEGHIDDPLVKEALEELKEITEFVKILGSYPSAR 276 (279)
T ss_pred ---eeEEEEEEEecCcCcHhHHHHHHHHHhheeEEEEEeeccccc
Confidence 999999999999999999999999999999999999999864
No 2
>PRK11899 prephenate dehydratase; Provisional
Probab=100.00 E-value=2e-91 Score=641.73 Aligned_cols=268 Identities=41% Similarity=0.574 Sum_probs=255.0
Q ss_pred CccCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeee
Q 023305 1 MMQGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANF 80 (284)
Q Consensus 1 aylGp~GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~ 80 (284)
|||||+|||||+||+++|++.+++||+||++||++|++|++||||||||||++|+|.+|+|+|.+++++|+||+.+||+|
T Consensus 8 aylGp~GsfS~~Aa~~~~~~~~~v~~~s~~~vf~av~~g~~d~gVvPiENS~~G~V~~~~Dll~~~~l~Iv~E~~l~I~h 87 (279)
T PRK11899 8 AFQGEPGANSHLACRDAFPDMEPLPCATFEDAFEAVESGEADLAMIPIENSLAGRVADIHHLLPESGLHIVGEYFLPIRH 87 (279)
T ss_pred EEECCCCCHHHHHHHHhcCcCceeecCCHHHHHHHHHCCCCCEEEEEeeccCCccHHHHHHHHhcCCCEEEEEEEEEeeE
Confidence 69999999999999999998899999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeecCCCCcCCccEEEecHHHHHHHHHHHHhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeecccc
Q 023305 81 CLLALPGIKADQLKRVLSHPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQ 160 (284)
Q Consensus 81 ~L~~~~~~~l~~i~~V~SHpqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~ 160 (284)
||++++|.++++|++||||||||+||++||++++++.+++.|||+||++|++.++++.|||||+.||++|||+||+++||
T Consensus 88 ~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~~~~~~~~~sTa~Aa~~v~~~~~~~~AAIas~~aa~~YgL~il~~~Iq 167 (279)
T PRK11899 88 QLMALPGATLEEIKTVHSHPHALGQCRKIIRALGLKPVVAADTAGAARLVAERGDPSMAALASRLAAELYGLDILAENIE 167 (279)
T ss_pred EEecCCCCCHHHCeEEEEeHHHHHHHHHHHHHcCCeEEEcCChHHHHHHHHhcCCCCeeEeCCHHHHHHcCCcchhhccc
Confidence 99999999999999999999999999999999999999999999999999987777899999999999999999999999
Q ss_pred CCCCCeeEEEEEeeCCCC-CCCCCCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCc
Q 023305 161 DEPDNITRFLVLARDPII-PRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAK 239 (284)
Q Consensus 161 d~~~N~TRF~vl~~~~~~-~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~ 239 (284)
|.++|+|||+||+|++.. +...+.+||||+|+++|+||+|+++|++|+.+|||||||||||.++++
T Consensus 168 D~~~N~TRF~vi~~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~------------- 234 (279)
T PRK11899 168 DADHNTTRFVVLSREADWAARGDGPIVTTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSF------------- 234 (279)
T ss_pred CCcccceeEEEEecCCCCCCCCCCCceEEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCC-------------
Confidence 999999999999998642 222345699999999999999999999999999999999999999875
Q ss_pred cceeEEEEEeecCCCcHHHHHHHHHHHhcCCceEEEceeeCCC
Q 023305 240 YFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDA 282 (284)
Q Consensus 240 ~~~y~F~id~eg~~~d~~~~~al~~L~~~~~~vkvLGsYp~~~ 282 (284)
|+|.||||++||.+|++++++|++|++.+.++|+|||||+..
T Consensus 235 -~~Y~F~id~eg~~~d~~v~~aL~~l~~~~~~~kvLGsYp~~~ 276 (279)
T PRK11899 235 -TATQFYADIEGHPEDRNVALALEELRFFSEEVRILGVYPAHP 276 (279)
T ss_pred -ceEEEEEEEECCCCCHHHHHHHHHHHHhcCcEEEeeeecCcc
Confidence 999999999999999999999999999999999999999764
No 3
>PLN02317 arogenate dehydratase
Probab=100.00 E-value=2.3e-91 Score=660.65 Aligned_cols=283 Identities=78% Similarity=1.237 Sum_probs=272.1
Q ss_pred CccCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeee
Q 023305 1 MMQGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANF 80 (284)
Q Consensus 1 aylGp~GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~ 80 (284)
|||||+|||||+||+++|++.+++||+||++||++|++|++||||||||||++|+|.+|||+|.+++++|+||+++||+|
T Consensus 98 aylGp~GtfSe~AA~~~f~~~e~vp~~sf~~vf~AVe~g~ad~gVvPIENS~~GsV~~t~DlL~~~~l~IvgEv~l~I~h 177 (382)
T PLN02317 98 AYQGVPGAYSEAAARKAYPNCEAVPCEQFEAAFQAVELWLADRAVLPIENSLGGSIHRNYDLLLRHRLHIVGEVQLPVHH 177 (382)
T ss_pred EEECCCcCHHHHHHHHhhCcCceeecCCHHHHHHHHHCCCCCEEEEEEeccCccchHHHHHHHhcCCCEEEEEEEEEeee
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeecCCCCcCCccEEEecHHHHHHHHHHHHhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeecccc
Q 023305 81 CLLALPGIKADQLKRVLSHPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQ 160 (284)
Q Consensus 81 ~L~~~~~~~l~~i~~V~SHpqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~ 160 (284)
||++++|.++++|++||||||||+||++||++++++++++.|||+||++|++.+..+.|||||+.||++|||+||+++||
T Consensus 178 ~Ll~~~g~~l~~Ik~VySHPQALaQC~~~L~~~~~~~~~~~sTA~AA~~Va~~~~~~~AAIaS~~aA~~YgL~iLa~~Iq 257 (382)
T PLN02317 178 CLLALPGVRKEELKRVISHPQALAQCENTLTKLGVVREAVDDTAGAAKMVAANGLRDTAAIASARAAELYGLDILAEGIQ 257 (382)
T ss_pred EEecCCCCCHHHCeEEEEehHHHHHHHHHHHHcCCeEEEcCCHHHHHHHHHhcCCCCceeecCHHHHHHcCCcchhhhhc
Confidence 99999999999999999999999999999999999999999999999999987777899999999999999999999999
Q ss_pred CCCCCeeEEEEEeeCCCCCCCCCCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcc
Q 023305 161 DEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKY 240 (284)
Q Consensus 161 d~~~N~TRF~vl~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~ 240 (284)
|.++|+|||+||+|++..+..+..+||||+|+++++||+|+++|++|+.+|||||||||||.++.+.++.|+...|..+.
T Consensus 258 D~~~N~TRFlvl~r~~~~~~~~~~~KTSivfsl~~~pG~L~k~L~~Fa~~~INLtkIESRP~~~~~~~~~~~~~~~~~~~ 337 (382)
T PLN02317 258 DDSDNVTRFLMLAREPIIPRTDRPFKTSIVFSLEEGPGVLFKALAVFALRDINLTKIESRPQRKRPLRVVDDSNSGTAKY 337 (382)
T ss_pred CCCCCeeeEEEEecCCcCCCCCCCccEEEEEEcCCCCchHHHHHHHHHHCCCCEEEEEeeecCCCCcccccccccccccc
Confidence 99999999999999875444445679999999999999999999999999999999999999999999999999999999
Q ss_pred ceeEEEEEeecCCCcHHHHHHHHHHHhcCCceEEEceeeCCCC
Q 023305 241 FDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDAT 283 (284)
Q Consensus 241 ~~y~F~id~eg~~~d~~~~~al~~L~~~~~~vkvLGsYp~~~~ 283 (284)
|+|.|||||||+..|++++++|++|++.+.++|+|||||+..+
T Consensus 338 ~eY~FyVD~eg~~~d~~~~~aL~~L~~~~~~lrvLGsYp~~~~ 380 (382)
T PLN02317 338 FDYLFYVDFEASMADPRAQNALAHLQEFATFLRVLGSYPMDMT 380 (382)
T ss_pred ccEEEEEEEEcCcCCHHHHHHHHHHHHhcCeEEEEeeeecCCC
Confidence 9999999999999999999999999999999999999998764
No 4
>PRK10622 pheA bifunctional chorismate mutase/prephenate dehydratase; Provisional
Probab=100.00 E-value=2.9e-85 Score=625.66 Aligned_cols=268 Identities=35% Similarity=0.550 Sum_probs=251.4
Q ss_pred CccCCCCcHHHHHHHhhCCC----CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEE
Q 023305 1 MMQGLPGSFSEDAALKAYPK----CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQL 76 (284)
Q Consensus 1 aylGp~GtfS~~Aa~~~f~~----~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l 76 (284)
|||||+|||||+||+++|+. ...+||+||++||++|++|++||||||||||++|+|.+|||+|.+++++|+||+++
T Consensus 107 a~lGp~GtfSh~Aa~~~~~~~~~~~~~~~~~s~~~v~~av~~g~~d~gVvPiENS~~G~V~~t~DlL~~~~l~I~~E~~l 186 (386)
T PRK10622 107 AFLGPKGSYSHLAARQYAARHFEQFIESGCAKFADIFNQVETGQADYAVLPIENTSSGAINDVYDLLQHTSLSIVGEMTL 186 (386)
T ss_pred EEECCCCcHHHHHHHHhhccccccccccCCCCHHHHHHHHHCCCCCEEEEEEecCCceehHHHHHHHhcCCCEEEEEEEE
Confidence 69999999999999998753 23458999999999999999999999999999999999999999999999999999
Q ss_pred eeeeEeeecCCCCcCCccEEEecHHHHHHHHHHHHhc-CCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCcee
Q 023305 77 AANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL-GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNIL 155 (284)
Q Consensus 77 ~I~~~L~~~~~~~l~~i~~V~SHpqal~Qc~~fl~~~-~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il 155 (284)
||+|||++.++.++++|++||||||||+||++||+++ +++.++++|||+||++|++.++++.|||||+.||++|||+||
T Consensus 187 ~I~h~Ll~~~~~~l~~I~~V~SHpqal~QC~~fL~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~AAI~s~~aa~~ygL~vl 266 (386)
T PRK10622 187 PIDHCVLVSGTTDLSTIETVYSHPQPFQQCSQFLNRYPHWKIEYTESTAAAMEKVAQANSPHVAALGSEAGGALYGLQVL 266 (386)
T ss_pred EEEEEEecCCCCCHHHCeEEEEehHHHHHHHHHHHHCCCceEEEcCChHHHHHHHHhcCCCCEEEECCHHHHHHcCCcCh
Confidence 9999999999999999999999999999999999997 789999999999999999887778899999999999999999
Q ss_pred eccccCCCCCeeEEEEEeeCCCCCCCCCCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCC
Q 023305 156 ADRIQDEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNN 235 (284)
Q Consensus 156 ~~~I~d~~~N~TRF~vl~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~ 235 (284)
+++|||.++|+|||+||++++..+.....+||||+|+++|+||+|+++|++|+.+|||||||||||.++.+
T Consensus 267 ~~~I~D~~~N~TRF~vi~~~~~~~~~~~~~ktsl~~~~~~~pGaL~~~L~~Fa~~giNLtkIeSRP~~~~~--------- 337 (386)
T PRK10622 267 ERNLANQQQNITRFIVLARKAINVSDQVPAKTTLLMATGQQAGALVEALLVLRNHNLIMTKLESRPIHGNP--------- 337 (386)
T ss_pred hhcCcCCccccceEEEEecCCCCCCCCCCCcEEEEEEcCCCCcHHHHHHHHHHHcCCCeeEEEeeecCCCC---------
Confidence 99999999999999999998643322334699999999999999999999999999999999999999875
Q ss_pred CCCccceeEEEEEeecCCCcHHHHHHHHHHHhcCCceEEEceeeCCC
Q 023305 236 GTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDA 282 (284)
Q Consensus 236 g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~~~vkvLGsYp~~~ 282 (284)
|+|+||||++||.+|++++++|++|++.+.++|+|||||+.+
T Consensus 338 -----~~Y~Ffid~eg~~~d~~~~~aL~~l~~~~~~~kvLGsYp~~~ 379 (386)
T PRK10622 338 -----WEEMFYLDVQANLRSAEMQKALKELGEITRSLKVLGCYPSEN 379 (386)
T ss_pred -----ceEEEEEEEeCCCCCHHHHHHHHHHHHhcCcEEEeeeecCCc
Confidence 999999999999999999999999999999999999999764
No 5
>PRK11898 prephenate dehydratase; Provisional
Probab=100.00 E-value=3.2e-84 Score=596.59 Aligned_cols=267 Identities=44% Similarity=0.603 Sum_probs=249.9
Q ss_pred CccCCCCcHHHHHHHhhCCC---CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccC-CeEEEEEEEE
Q 023305 1 MMQGLPGSFSEDAALKAYPK---CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRH-RLHIVGEVQL 76 (284)
Q Consensus 1 aylGp~GtfS~~Aa~~~f~~---~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~-~l~I~~E~~l 76 (284)
|||||+|||||+||+++|++ .+++||+||++||++|++|++||||||||||++|+|.+|+|+|.++ +++|+||+.+
T Consensus 5 a~lGp~Gs~s~~Aa~~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~v~~~~d~L~~~~~~~iv~E~~l 84 (283)
T PRK11898 5 AYLGPEGTFTEAAALKFFPADGEAELVPYDSIPDVLDAVEAGEVDYAVVPIENSIEGSVNPTLDYLAHGSPLQIVAEIVL 84 (283)
T ss_pred EEECCCCCHHHHHHHHhhccccccceEecCCHHHHHHHHHcCCCCEEEEEecccCceecHHHHHHhccCCCcEEEEEEEe
Confidence 69999999999999999976 7899999999999999999999999999999999999999998765 8999999999
Q ss_pred eeeeEeeecCCCCcCCccEEEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCce
Q 023305 77 AANFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNI 154 (284)
Q Consensus 77 ~I~~~L~~~~~~~l~~i~~V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~i 154 (284)
||+|||+++++.. ++|++||||||||+||++||+++ +++.+++.|||+||+++++++..+.|||+|+.||++|||+|
T Consensus 85 ~I~~~L~~~~~~~-~~i~~V~SHpqal~QC~~~l~~~~p~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~i 163 (283)
T PRK11898 85 PIAQHLLVHPGHA-AKIRTVYSHPQALAQCRKWLAEHLPGAELEPANSTAAAAQYVAEHPDEPIAAIASELAAELYGLEI 163 (283)
T ss_pred eeeEEEeCCCCCh-hcCeEEEEeHHHHHHHHHHHHhcCCCCEEEEcCchHHHHHHHhcCCCCCeEEECCHHHHHHcCCcE
Confidence 9999999998865 99999999999999999999996 89999999999999999988767789999999999999999
Q ss_pred eeccccCCCCCeeEEEEEeeCCC-CCCCCCCceEEEEEEecC-CCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccC
Q 023305 155 LADRIQDEPDNITRFLVLARDPI-IPRTDKLFKTSIVFTLDE-GPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDD 232 (284)
Q Consensus 155 l~~~I~d~~~N~TRF~vl~~~~~-~~~~~~~~ktsi~f~~~~-~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~ 232 (284)
|++||||.++|+|||++|+|++. .+...+.+||||+|++++ +||+|+++|++|+.+|||||||||||+++++
T Consensus 164 l~~~I~d~~~N~TRF~vi~~~~~~~~~~~~~~ktslif~l~~~~pGsL~~~L~~F~~~~INLt~IeSRP~~~~~------ 237 (283)
T PRK11898 164 LAEDIQDYPNNRTRFWLLGRKKPPPPLRTGGDKTSLVLTLPNNLPGALYKALSEFAWRGINLTRIESRPTKTGL------ 237 (283)
T ss_pred ehhcCCCCCccceEEEEEEcCcccCCCCCCCCeEEEEEEeCCCCccHHHHHHHHHHHCCCCeeeEecccCCCCC------
Confidence 99999999999999999999864 222345679999999987 5999999999999999999999999999875
Q ss_pred CCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcCCceEEEceeeCCC
Q 023305 233 SNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDA 282 (284)
Q Consensus 233 ~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~~~vkvLGsYp~~~ 282 (284)
|+|.|||||+|+.+|++++++|++|++.+.++|+|||||...
T Consensus 238 --------~~y~F~vd~eg~~~~~~~~~al~~L~~~~~~~k~LGsY~~~~ 279 (283)
T PRK11898 238 --------GTYFFFIDVEGHIDDVLVAEALKELEALGEDVKVLGSYPVYW 279 (283)
T ss_pred --------ccEEEEEEEEccCCCHHHHHHHHHHHHhcCcEEEEEeecccc
Confidence 999999999999999999999999999999999999999764
No 6
>KOG2797 consensus Prephenate dehydratase [Amino acid transport and metabolism]
Probab=100.00 E-value=3.6e-78 Score=544.55 Aligned_cols=278 Identities=69% Similarity=1.127 Sum_probs=267.4
Q ss_pred CccCCCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeee
Q 023305 1 MMQGLPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANF 80 (284)
Q Consensus 1 aylGp~GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~ 80 (284)
|||||+|+|||.||.+.|+.++-+||+.|+.+|++|+...+||+|+|||||+.|+|..+||||.++++.|+||+.+||+|
T Consensus 94 a~qg~pgaysesaa~ka~pn~~avpc~~f~~afqave~w~vD~AVLPiENS~gGsIhrnYDLLlrh~lhiVgEv~vPvhH 173 (377)
T KOG2797|consen 94 AYQGVPGAYSESAALKAYPNCEAVPCDQFEAAFQAVELWIVDYAVLPIENSTGGSIHRNYDLLLRHRLHIVGEVQVPVHH 173 (377)
T ss_pred EeecCCchhhhhhhhhhcCCcccccHhHHHHHHHHHHHhhccceeeeeeccCCceeeechHHHhhcchheeeEEecceee
Confidence 69999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EeeecCCCCcCCccEEEecHHHHHHHHHHHHhcC--CeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeecc
Q 023305 81 CLLALPGIKADQLKRVLSHPQALASSDIVLTQLG--VARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADR 158 (284)
Q Consensus 81 ~L~~~~~~~l~~i~~V~SHpqal~Qc~~fl~~~~--~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~ 158 (284)
||++.+|...+++++|.||||||+||+.||++++ +.++.++|||+||+.++.+...+.+||+|+.||++|||.||+++
T Consensus 174 CLi~~~gv~~e~~~~VlSHPQal~Qce~~L~~l~~~~~r~a~~dTa~Aa~~~s~~~~~d~~AIASe~aA~ly~l~Il~~~ 253 (377)
T KOG2797|consen 174 CLIALPGVRKEEVVRVLSHPQALGQCECSLTKLGPNAAREAVSDTAGAAEQISASNTADTAAIASERAAELYGLNILEKN 253 (377)
T ss_pred eEecCCCCChhheeeeecCcHHHHHHHHHHHhcccceeeeeccchHHHHHHHHhcccccHHHHHHHHHHHHhcchhhhhh
Confidence 9999999999999999999999999999999974 88999999999999999988889999999999999999999999
Q ss_pred ccCCCCCeeEEEEEeeCCCCCCCCCCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCC
Q 023305 159 IQDEPDNITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTA 238 (284)
Q Consensus 159 I~d~~~N~TRF~vl~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~ 238 (284)
|||+.+|+|||++|.|++..|..+...||||+|...+.||.|.++|++|+.|+||||+|||||.+..|.++.|+ .
T Consensus 254 IqDd~~NvTRFLmLar~p~ip~t~rl~ktsivf~~~~gp~vLfkvl~vfa~r~inltkIesRP~h~~p~r~v~~-----~ 328 (377)
T KOG2797|consen 254 IQDDLGNVTRFLMLAREPIIPDTDRLFKTSIVFFREKGPGVLFKVLSVFAFRSINLTKIESRPFHNRPLRVVDD-----S 328 (377)
T ss_pred cccccCCeeEEEEEeccCCCCCCCccceeeEEEEeecCCchHHHHHHHHHhhhceeeeeecccccCCCcccccc-----c
Confidence 99999999999999999998887788999999998899999999999999999999999999999999887665 5
Q ss_pred ccceeEEEEEeecCCCcHHHHHHHHHHHhcCCceEEEceeeCCCC
Q 023305 239 KYFDYLFYIDFEASMADPRAQNALGHLQEFATFLRVLGCYPMDAT 283 (284)
Q Consensus 239 ~~~~y~F~id~eg~~~d~~~~~al~~L~~~~~~vkvLGsYp~~~~ 283 (284)
+.|+|.||||+|..+.+++.++++.++++.+.++|+|||||.+.+
T Consensus 329 k~f~ylFyidfeasmae~~aq~al~~~~e~~sflrvlGsyp~d~t 373 (377)
T KOG2797|consen 329 KNFEYLFYIDFEASMAEPRAQNALGEVQEFTSFLRVLGSYPMDMT 373 (377)
T ss_pred ccccEEEEEEEEeccCcHHHHHHHHHHHHHHHHHHHhcCCccccc
Confidence 679999999999999999999999999999999999999998753
No 7
>PF00800 PDT: Prephenate dehydratase Caution this is only a partial structure.; InterPro: IPR001086 Prephenate dehydratase (4.2.1.51 from EC, PDT) catalyses the decarboxylation of prephenate to phenylpyruvate. In microorganisms it is part of the terminal pathway of phenylalanine biosynthesis. In some bacteria such as Escherichia coli PDT is part of a bifunctional enzyme (P-protein) that also catalyses the transformation of chorismate into prephenate (chorismate mutase, IPR002701 from INTERPRO, 5.4.99.5 from EC) while in other bacteria it is a monofunctional enzyme. The sequence of monofunctional PDT aligns well with the C-terminal part of P-proteins [].; GO: 0004664 prephenate dehydratase activity, 0009094 L-phenylalanine biosynthetic process; PDB: 3MWB_B 2QMX_A 2QMW_A 3LUY_A.
Probab=100.00 E-value=1.2e-57 Score=395.09 Aligned_cols=176 Identities=47% Similarity=0.707 Sum_probs=163.2
Q ss_pred CccCCCCcHHHHHHHhhC--CCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEee
Q 023305 1 MMQGLPGSFSEDAALKAY--PKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAA 78 (284)
Q Consensus 1 aylGp~GtfS~~Aa~~~f--~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I 78 (284)
|||||+|||||+||+++| ++.+++||+||++||++|.+|++||||||+|||++|.|.+|+|+|.+.++.|+||+.+||
T Consensus 2 a~LGP~GT~S~~Aa~~~~~~~~~~~~~~~s~~~v~~av~~~~~d~~vvPiENs~~G~V~~t~d~L~~~~l~i~~e~~l~i 81 (181)
T PF00800_consen 2 AYLGPEGTFSHEAAQQYFGGPDAEIVPCDSFEEVFDAVEEGEADYGVVPIENSLEGSVSETLDLLIDSDLYIVGEIVLPI 81 (181)
T ss_dssp EEESSTTSHHHHHHCCCCTTTCSEEEEESSHHHHHHHHHCTSSSEEEEEEECTTTCECHHHHHHHHTSSCEEEEEEEEE-
T ss_pred EEeCCCCCHHHHHHHHHHHhhccceEecCCHHHHHHHHHcCCCceEEEeEeeecCCEeHHHHHHHhcCCceEEEEEEecc
Confidence 699999999999999999 668999999999999999999999999999999999999999999998999999999999
Q ss_pred eeEeeecCCCCcCCccEEEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceee
Q 023305 79 NFCLLALPGIKADQLKRVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILA 156 (284)
Q Consensus 79 ~~~L~~~~~~~l~~i~~V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~ 156 (284)
+|||+++++.++++|++|||||||++||++||+++ +++.+.+.||++||++|+..+.++.|||+|+.||++|||+||+
T Consensus 82 ~~~L~~~~~~~l~~i~~V~SHp~al~Qc~~~l~~~~p~~~~~~~~Sta~Aa~~v~~~~~~~~aAI~s~~aa~~y~L~il~ 161 (181)
T PF00800_consen 82 HHCLLAKPGTSLSDIKTVYSHPQALAQCREFLEKHLPGAEIVEASSTAEAAEKVAASEGPGDAAIASEEAAELYGLEILA 161 (181)
T ss_dssp -EEEEECTT--GGG-SEEEEEHHHHHHTHHHHHHT-TTSEEEEESSHHHHHHHCCCCTBTTEEEEEECCHHHHTTEEEEE
T ss_pred ccEEeccCCCchhcceEEEEchHHHHHHHHHHHhcCCceEEEeCCCHHHHHHHHHhccCCCeEEECCHHHHHHcCccChh
Confidence 99999999988999999999999999999999997 7999999999999999887777889999999999999999999
Q ss_pred ccccCCCCCeeEEEEEeeCC
Q 023305 157 DRIQDEPDNITRFLVLARDP 176 (284)
Q Consensus 157 ~~I~d~~~N~TRF~vl~~~~ 176 (284)
++|||.++|+|||+||+|++
T Consensus 162 ~~I~d~~~N~TRF~vi~~~~ 181 (181)
T PF00800_consen 162 RNIQDNPNNYTRFLVIGKEP 181 (181)
T ss_dssp CS-SSSTT-EEEEEEEECCT
T ss_pred hcCCCCCCCeEeEEEEecCC
Confidence 99999999999999999874
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=99.89 E-value=7.6e-23 Score=152.51 Aligned_cols=73 Identities=34% Similarity=0.571 Sum_probs=68.6
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHH
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 266 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~ 266 (284)
|||+|+++|+||+|+++|+.|+.+|||||||||||.+..+ |+|.|||||+| .+++++++|++|+
T Consensus 1 tsl~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~--------------~~y~Ffvd~~~--~~~~~~~~l~~L~ 64 (74)
T cd04904 1 TSLIFSLKEEVGALARALKLFEEFGVNLTHIESRPSRRNG--------------SEYEFFVDCEV--DRGDLDQLISSLR 64 (74)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCC--------------ceEEEEEEEEc--ChHHHHHHHHHHH
Confidence 6899999999999999999999999999999999999874 99999999999 5678999999999
Q ss_pred hcCCceEEE
Q 023305 267 EFATFLRVL 275 (284)
Q Consensus 267 ~~~~~vkvL 275 (284)
+.+..+|++
T Consensus 65 ~~~~~~~~~ 73 (74)
T cd04904 65 RVVADVNIL 73 (74)
T ss_pred HhcCeEEEc
Confidence 999999875
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=1.1e-21 Score=151.62 Aligned_cols=70 Identities=36% Similarity=0.574 Sum_probs=65.4
Q ss_pred CCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHH
Q 023305 183 KLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNAL 262 (284)
Q Consensus 183 ~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al 262 (284)
...||||+|+++|+||+|+++|++|+.+||||+||||||++..+ |+|.|||||+|+ .+++++++|
T Consensus 11 ~~~ktslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~--------------~~Y~FfVDieg~-~~~~~~~~l 75 (90)
T cd04931 11 KNGVISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNK--------------DEYEFFINLDKK-SAPALDPII 75 (90)
T ss_pred CCCcEEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCC--------------ceEEEEEEEEcC-CCHHHHHHH
Confidence 44689999999999999999999999999999999999998764 999999999998 689999999
Q ss_pred HHHHh
Q 023305 263 GHLQE 267 (284)
Q Consensus 263 ~~L~~ 267 (284)
++|++
T Consensus 76 ~~L~~ 80 (90)
T cd04931 76 KSLRN 80 (90)
T ss_pred HHHHH
Confidence 99986
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=2.2e-21 Score=156.44 Aligned_cols=76 Identities=28% Similarity=0.370 Sum_probs=69.7
Q ss_pred CceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHH
Q 023305 184 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 263 (284)
Q Consensus 184 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~ 263 (284)
.+||||+|+++|+||+|+++|++|+.+|||||||||||++..+ |+|.|||||+|+.+ +++++|+
T Consensus 39 ~~ktSlifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~~~~--------------~eY~FfIdieg~~~--~~~~aL~ 102 (115)
T cd04930 39 PQKATLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSRKEG--------------GDLEVLVRCEVHRS--DLLQLIS 102 (115)
T ss_pred cccEEEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCCCCC--------------ceEEEEEEEEeCHH--HHHHHHH
Confidence 3489999999999999999999999999999999999998774 99999999999863 6999999
Q ss_pred HHHhcCCceEEE
Q 023305 264 HLQEFATFLRVL 275 (284)
Q Consensus 264 ~L~~~~~~vkvL 275 (284)
+|++.+.++++-
T Consensus 103 ~L~~~~~~~kv~ 114 (115)
T cd04930 103 SLRQVAEDVRLT 114 (115)
T ss_pred HHHHhcCeeEec
Confidence 999999988763
No 11
>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=99.85 E-value=8.5e-21 Score=143.06 Aligned_cols=80 Identities=54% Similarity=0.956 Sum_probs=75.4
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 265 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L 265 (284)
|+|++|.++|+||+|.++|+.|+++||||++|+|||.+.. .|+|.||||++++.++++++++++.|
T Consensus 1 ~~sl~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~--------------~~~~~f~vd~~~~~~~~~~~~~l~~l 66 (80)
T cd04905 1 KTSIVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGG--------------LWEYVFFIDFEGHIEDPNVAEALEEL 66 (80)
T ss_pred CEEEEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCC--------------CceEEEEEEEECCCCCHHHHHHHHHH
Confidence 5899999999999999999999999999999999999765 38999999999987789999999999
Q ss_pred HhcCCceEEEceee
Q 023305 266 QEFATFLRVLGCYP 279 (284)
Q Consensus 266 ~~~~~~vkvLGsYp 279 (284)
++.+.++|+||+||
T Consensus 67 ~~~~~~~~~lG~y~ 80 (80)
T cd04905 67 KRLTEFVKVLGSYP 80 (80)
T ss_pred HHhCCeEEEeeeeC
Confidence 99999999999997
No 12
>cd04929 ACT_TPH ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. ACT domain of the nonheme iron-dependent aromatic amino acid hydroxylase, tryptophan hydroxylases (TPH), both peripheral (TPH1) and neuronal (TPH2) enzymes. TPH catalyses the hydroxylation of L-Trp to 5-hydroxytryptophan, the rate limiting step in the biosynthesis of 5-hydroxytryptamine (serotonin) and the first reaction in the synthesis of melatonin. Very little is known about the role of the ACT domain in TPH, which appears to be regulated by phosphorylation but not by its substrate or cofactor. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=99.85 E-value=2.5e-21 Score=144.45 Aligned_cols=71 Identities=30% Similarity=0.456 Sum_probs=65.0
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHH
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 266 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~ 266 (284)
||++|+++|+||+|+++|+.|+.+||||+||||||++..+ |+|.|||||+|+. .++++++++|+
T Consensus 1 tsl~~~l~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~--------------~~y~F~id~e~~~--~~i~~~l~~l~ 64 (74)
T cd04929 1 TSVIFSLKNEVGGLAKALKLFQELGINVVHIESRKSKRRS--------------SEFEIFVDCECDQ--RRLDELVQLLK 64 (74)
T ss_pred CEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCC--------------ceEEEEEEEEcCH--HHHHHHHHHHH
Confidence 6899999999999999999999999999999999998774 9999999999986 48999999999
Q ss_pred hcCCceE
Q 023305 267 EFATFLR 273 (284)
Q Consensus 267 ~~~~~vk 273 (284)
+.+...+
T Consensus 65 ~~~~~~~ 71 (74)
T cd04929 65 REVASVN 71 (74)
T ss_pred Hhccccc
Confidence 8776543
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=99.83 E-value=4e-20 Score=137.54 Aligned_cols=75 Identities=52% Similarity=0.844 Sum_probs=71.0
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
|++|+++|+||+|.++|+.|+.+|+||++|||||.++.+ |+|.||||++|+.++.++++++++|++
T Consensus 1 sl~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~--------------~~~~f~id~~~~~~~~~~~~~l~~l~~ 66 (75)
T cd04880 1 SLVFSLKNKPGALAKALKVFAERGINLTKIESRPSRKGL--------------WEYEFFVDFEGHIDDPDVKEALEELKR 66 (75)
T ss_pred CEEEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCC--------------ceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 588999999999999999999999999999999998764 999999999998778999999999999
Q ss_pred cCCceEEEc
Q 023305 268 FATFLRVLG 276 (284)
Q Consensus 268 ~~~~vkvLG 276 (284)
.+.++|+||
T Consensus 67 ~~~~~~~lG 75 (75)
T cd04880 67 VTEDVKVLG 75 (75)
T ss_pred hCCeeEECC
Confidence 999999998
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=3.4e-18 Score=164.42 Aligned_cols=79 Identities=34% Similarity=0.648 Sum_probs=74.2
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
+||||+|+++|+||+|+++|++|+.+||||+||||||++..+ |+|.|||||+|+. +++++++|++
T Consensus 15 ~KTSLiFsL~d~pGaL~~vL~vFa~~gINLthIESRPsk~~~--------------~eY~FFVD~eg~~-~~~v~~aL~~ 79 (436)
T TIGR01268 15 AKTSLIFSLKEEAGALAETLKLFQAHDVNLTHIESRPSKTHP--------------GEYEFFVEFDEAS-DRKLEGVIEH 79 (436)
T ss_pred CeEEEEEEcCCCCcHHHHHHHHHHHCCCCeeEEecccCCCCC--------------ccEEEEEEEecCc-cHHHHHHHHH
Confidence 489999999999999999999999999999999999998874 9999999999986 5899999999
Q ss_pred HHhcC-CceEEEcee
Q 023305 265 LQEFA-TFLRVLGCY 278 (284)
Q Consensus 265 L~~~~-~~vkvLGsY 278 (284)
|++.+ ..+++||+-
T Consensus 80 Lk~~~~~~vkiLGs~ 94 (436)
T TIGR01268 80 LRQKAEVTVNILSRD 94 (436)
T ss_pred HHHhccceEEEeCCC
Confidence 99999 899999983
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=99.64 E-value=6.5e-16 Score=149.21 Aligned_cols=76 Identities=29% Similarity=0.318 Sum_probs=69.3
Q ss_pred CCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccce-eEEEEEeecCCCcHHHHHH
Q 023305 183 KLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFD-YLFYIDFEASMADPRAQNA 261 (284)
Q Consensus 183 ~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~-y~F~id~eg~~~d~~~~~a 261 (284)
+..||||+|+++|+||+|+++|++|+.+||||+||||||++..+ |+ |.|||||+|+. .+++++
T Consensus 28 ~~~ktSLIFsL~d~pGaL~~vL~vFa~~gINLThIESRPsk~~~--------------~e~Y~FfVD~Eg~~--~~l~~a 91 (464)
T TIGR01270 28 GVQRLSIIFSLSNVVGDLSKAIAIFQDRHINILHLESRDSKDGT--------------SKTMDVLVDVELFH--YGLQEA 91 (464)
T ss_pred CCceEEEEEECCCCchHHHHHHHHHHHCCCCEEEEECCcCCCCC--------------CccEEEEEEEEcCH--HHHHHH
Confidence 45699999999999999999999999999999999999998764 89 99999999975 689999
Q ss_pred HHHHHhcCCceEE
Q 023305 262 LGHLQEFATFLRV 274 (284)
Q Consensus 262 l~~L~~~~~~vkv 274 (284)
|++|++.+..+++
T Consensus 92 L~~Lk~~~~~~~~ 104 (464)
T TIGR01270 92 MDLLKSGLDVHEV 104 (464)
T ss_pred HHHHHHhccccee
Confidence 9999998887555
No 16
>PRK06034 hypothetical protein; Provisional
Probab=99.19 E-value=1.6e-11 Score=112.63 Aligned_cols=69 Identities=14% Similarity=0.041 Sum_probs=55.5
Q ss_pred CccCCCCcHHHHHHHhhCCC-CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccc-cCCeEEEEE
Q 023305 1 MMQGLPGSFSEDAALKAYPK-CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL-RHRLHIVGE 73 (284)
Q Consensus 1 aylGp~GtfS~~Aa~~~f~~-~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~-~~~l~I~~E 73 (284)
+||||+|||||+||++||+. .++++|.||++||++|++|++|||||||+++ .+. -+-.|. ....+|++-
T Consensus 99 a~lG~~gs~s~~AA~~~FG~s~~~~~~~s~~dVf~AV~~g~adyGVVPI~~~-~~~---WW~~L~~~~~~~iiar 169 (279)
T PRK06034 99 ADGSGGEAAMRDSARFHFGFTVPYVPHFSAQAVVEAVARSKGDLGLVSLTSS-DTP---WWGRLEAEGAPKIIAR 169 (279)
T ss_pred EEeCCccHHHHHHHHHHhccccCCccCCCHHHHHHHHHcCCCCEEEEECCCC-CCc---HHHHhccCCCCeEEEe
Confidence 59999999999999999985 5888999999999999999999999999544 233 344343 344666554
No 17
>PRK08818 prephenate dehydrogenase; Provisional
Probab=98.86 E-value=5.8e-09 Score=99.92 Aligned_cols=65 Identities=26% Similarity=0.343 Sum_probs=53.6
Q ss_pred ceEEEEEEec-CCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHH
Q 023305 185 FKTSIVFTLD-EGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 263 (284)
Q Consensus 185 ~ktsi~f~~~-~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~ 263 (284)
.-++|+|.++ |+||+|+++|++|+.+||||++||| .+.++ |+|.|||||++..+-..+..+-.
T Consensus 294 ~~~~l~~~v~~d~pG~L~~vl~~la~~~INit~Ies--~~~r~--------------~~y~f~i~~~~~~~~~~~~~~~~ 357 (370)
T PRK08818 294 EPLTLSVYLPEDRPGSLRTLLHVFEQHGVNLSSIHS--SRTPA--------------GELHFRIGFEPGSDRAALARAAA 357 (370)
T ss_pred cceEEEEECCCCCCChHHHHHHHHHHcCcccceEEE--ecccC--------------ceEEEEEEEeccccHHHHHHHHh
Confidence 4689999997 9999999999999999999999999 55543 99999999998654455555554
Q ss_pred HH
Q 023305 264 HL 265 (284)
Q Consensus 264 ~L 265 (284)
++
T Consensus 358 ~~ 359 (370)
T PRK08818 358 EI 359 (370)
T ss_pred hh
Confidence 44
No 18
>TIGR01269 Tyr_3_monoox tyrosine 3-monooxygenase, tetrameric. This model describes tyrosine 3-monooxygenase, a member of the family of tetrameric, biopterin-dependent aromatic amino acid hydroxylases found in metazoans. It is closely related to tetrameric phenylalanine-4-hydroxylase and tryptophan 5-monooxygenase, and more distantly related to the monomeric phenylalanine-4-hydroxylase found in some Gram-negative bacteria.
Probab=98.85 E-value=8.9e-09 Score=99.20 Aligned_cols=72 Identities=22% Similarity=0.275 Sum_probs=60.0
Q ss_pred eEEEEEEecCC-CchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 186 KTSIVFTLDEG-PGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 186 ktsi~f~~~~~-pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
.++++|+++++ +|+|.++|++|+.++|||+||||||++... .+ ..+|.|||||++. +.++.++++.
T Consensus 37 ~~~~~~~~~~~~~g~L~~~l~~f~~~~inl~hiEsr~~~~~~--------~~---~~~~~~~v~~~~~--~~~~~~~~~~ 103 (457)
T TIGR01269 37 MQNNQFYIRTKEISSLHRILKYIETFKLNLVHFETRPTRTLS--------NA---DVDYSCLITLEAN--EINMSLLIES 103 (457)
T ss_pred ceeEEEEeccCcchhHHHHHHHHHHcCCcEEEeecCCccccC--------CC---CCceEEEEEEecc--HhhHHHHHHH
Confidence 57888888754 999999999999999999999999987542 00 2469999999986 4789999999
Q ss_pred HHhcCC
Q 023305 265 LQEFAT 270 (284)
Q Consensus 265 L~~~~~ 270 (284)
|++.+.
T Consensus 104 l~~~~~ 109 (457)
T TIGR01269 104 LRGNSF 109 (457)
T ss_pred HHhhhc
Confidence 998664
No 19
>KOG3820 consensus Aromatic amino acid hydroxylase [Amino acid transport and metabolism]
Probab=98.62 E-value=1.2e-07 Score=89.76 Aligned_cols=74 Identities=28% Similarity=0.434 Sum_probs=63.7
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
..++++|++++++|+|.++|+.|..+++|+.||||||++... .+|.|||+++... .++.++++.
T Consensus 35 ~~~~~if~~r~~~~~l~~~Lk~f~~~~vnl~HiEsR~s~~~~--------------~~~evlv~~~~~~--~~l~~~i~~ 98 (461)
T KOG3820|consen 35 ARISLIFSLRNKVGALARALKAFEEFHVNLLHIESRPSERRS--------------SGYEVLVELDATR--GQLIQAIEL 98 (461)
T ss_pred ceEEEEEEecccchHHHHHHHHhhhcCceEEEeecccccccC--------------CCceEEEeeccch--hhHHHHHHH
Confidence 478899999999999999999999999999999999997653 4699999999865 588899999
Q ss_pred HHhcCCceEE
Q 023305 265 LQEFATFLRV 274 (284)
Q Consensus 265 L~~~~~~vkv 274 (284)
|+..+..+..
T Consensus 99 lrq~~~~~~~ 108 (461)
T KOG3820|consen 99 LRQNHVALSY 108 (461)
T ss_pred HHHhccccee
Confidence 9987654433
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=6.6e-06 Score=58.82 Aligned_cols=68 Identities=21% Similarity=0.210 Sum_probs=54.3
Q ss_pred EEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcC
Q 023305 190 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFA 269 (284)
Q Consensus 190 ~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~ 269 (284)
.+.++|+||.|.++++.++..|+|++.|.++|.+... ..+.+.+++.++.. +...++.+++.|++.+
T Consensus 2 ~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~------------~~~~~~~~i~v~~~-~~~~l~~l~~~l~~~g 68 (73)
T cd04886 2 RVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTL------------PLGEVEVELTLETR-GAEHIEEIIAALREAG 68 (73)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCC------------CCceEEEEEEEEeC-CHHHHHHHHHHHHHcC
Confidence 4678999999999999999999999999999865310 01567888888874 4577889999998765
Q ss_pred C
Q 023305 270 T 270 (284)
Q Consensus 270 ~ 270 (284)
.
T Consensus 69 ~ 69 (73)
T cd04886 69 Y 69 (73)
T ss_pred C
Confidence 4
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=98.27 E-value=5.5e-06 Score=58.67 Aligned_cols=38 Identities=18% Similarity=0.372 Sum_probs=34.9
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCC
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRK 224 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~ 224 (284)
+.+.+.++|+||.|.++++.|+++|+|+..+.+++.+.
T Consensus 1 ~~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~ 38 (66)
T PF01842_consen 1 YRVRVIVPDRPGILADVTEILADHGINIDSISQSSDKD 38 (66)
T ss_dssp EEEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred CEEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence 45778889999999999999999999999999999865
No 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=97.72 E-value=0.00025 Score=50.02 Aligned_cols=59 Identities=22% Similarity=0.283 Sum_probs=43.4
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
+.+.++|+||.|.++++.|+++|+|+..+...|.... ....+++.++. ...+++.|++.
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~---------------~~~~v~~~ve~------~~~~~~~L~~~ 60 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKG---------------GKALLIFRTED------IEKAIEVLQER 60 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCC---------------CeEEEEEEeCC------HHHHHHHHHHC
Confidence 4567899999999999999999999999987665421 23455666654 33566666654
No 23
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=97.70 E-value=0.00047 Score=51.67 Aligned_cols=70 Identities=13% Similarity=0.232 Sum_probs=54.3
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHH
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 266 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~ 266 (284)
-+|.+-+.|+||.|.+++..|++||.|+..|..-|+... .-..+-|-+.| ++..+..+.++|+
T Consensus 3 ~tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te~~---------------~~sriti~~~~--~~~~i~qi~kQL~ 65 (76)
T PRK06737 3 HTFSLVIHNDPSVLLRISGIFARRGYYISSLNLNERDTS---------------GVSEMKLTAVC--TENEATLLVSQLK 65 (76)
T ss_pred EEEEEEEecCCCHHHHHHHHHhccCcceEEEEecccCCC---------------CeeEEEEEEEC--CHHHHHHHHHHHh
Confidence 356677789999999999999999999999998887543 23556666666 4578888999998
Q ss_pred hcCCceE
Q 023305 267 EFATFLR 273 (284)
Q Consensus 267 ~~~~~vk 273 (284)
+.-.=++
T Consensus 66 KLidV~~ 72 (76)
T PRK06737 66 KLINVLQ 72 (76)
T ss_pred CCcCEEE
Confidence 7755443
No 24
>cd04884 ACT_CBS C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This CD includes the C-terminal ACT domain of the cystathionine beta-synthase (CBS) domain protein found in Thermotoga maritima, Tm0935, and delta proteobacteria. This protein has two N-terminal tandem CBS domains and a single C-terminal ACT domain. The CBS domain is found in a wide range of proteins, often in tandem arrangements and together with a variety of other functional domains. It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.63 E-value=0.00046 Score=50.34 Aligned_cols=65 Identities=12% Similarity=0.155 Sum_probs=44.3
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
+.+.++|+||+|.++++.++.+|+|+..+...+..... +....+|.+++. .+..++.+++.|++.
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~--------------~~~~~~v~v~~e-~~~~~~~i~~~L~~~ 66 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPD--------------GMRRVFIRVTPM-DRSKENELIEELKAK 66 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCC--------------CccEEEEEEEEe-cchHHHHHHHHHhCc
Confidence 55688999999999999999999999998766643221 122344444432 223466777777654
No 25
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=97.56 E-value=0.00058 Score=49.16 Aligned_cols=62 Identities=19% Similarity=0.296 Sum_probs=48.4
Q ss_pred CCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcCCceE
Q 023305 195 EGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLR 273 (284)
Q Consensus 195 ~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~~~vk 273 (284)
|+||.|.++++.|.+||+|+..|..-|+... .-+.+-|.++|. +..+..+.++|++...-++
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~---------------~~~riti~v~~~--~~~i~~l~~Ql~KlidV~~ 62 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDP---------------GISRITIVVSGD--DREIEQLVKQLEKLIDVVK 62 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-SST---------------TEEEEEEEEES---CCHHHHHHHHHHCSTTEEE
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecCCC---------------CEEEEEEEEeeC--chhHHHHHHHHhccCCeEe
Confidence 6899999999999999999999999995443 457888888884 4678888999988765433
No 26
>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=97.55 E-value=0.0012 Score=46.75 Aligned_cols=67 Identities=18% Similarity=0.252 Sum_probs=50.8
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
+|.+..+|+||.|.++++.|+.+|+|+.++..++.+.. ....+++.++. .+ ..+.+++++|++
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~---------------~~~~~~~~~~~-~~-~~~~~l~~~l~~ 64 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDP---------------GISRITIVVEG-DD-DVIEQIVKQLNK 64 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCC---------------CeEEEEEEEEC-CH-HHHHHHHHHHhC
Confidence 46778899999999999999999999999998765322 12345555554 34 789999999987
Q ss_pred cCCc
Q 023305 268 FATF 271 (284)
Q Consensus 268 ~~~~ 271 (284)
...-
T Consensus 65 ~~~v 68 (72)
T cd04878 65 LVDV 68 (72)
T ss_pred CccE
Confidence 6543
No 27
>cd04883 ACT_AcuB C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. This CD includes the C-terminal ACT domain of the Bacillus subtilis acetoin utilization protein, AcuB. AcuB is putatively involved in the anaerobic catabolism of acetoin, and related proteins. Studies report the induction of AcuB by nitrate respiration and also by fermentation. Since acetoin can be secreted and later serve as a source of carbon, it has been proposed that, during anaerobic growth when other carbon sources are exhausted, the induction of the AcuB protein results in acetoin catabolism. AcuB-like proteins have two N-terminal tandem CBS domains and a single C-terminal ACT domain. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.53 E-value=0.00084 Score=48.45 Aligned_cols=65 Identities=15% Similarity=0.272 Sum_probs=45.9
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHH
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 266 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~ 266 (284)
+.+.+.++|+||.|.++++.|+.+|+|+.++...+.... ....++|.+++. +.. .+++.|+
T Consensus 2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~---------------~~~~v~i~v~~~-~~~---~~~~~L~ 62 (72)
T cd04883 2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEE---------------DNKILVFRVQTM-NPR---PIIEDLR 62 (72)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCC---------------CeEEEEEEEecC-CHH---HHHHHHH
Confidence 457788899999999999999999999999976554322 234455666652 222 5666666
Q ss_pred hcCC
Q 023305 267 EFAT 270 (284)
Q Consensus 267 ~~~~ 270 (284)
+..-
T Consensus 63 ~~G~ 66 (72)
T cd04883 63 RAGY 66 (72)
T ss_pred HCCC
Confidence 6543
No 28
>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=97.47 E-value=0.0014 Score=46.59 Aligned_cols=64 Identities=19% Similarity=0.263 Sum_probs=48.4
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
.|.+..+|+||.|.++++.|+++++|+.++...+... +.+.+.+++++. ..+..+++.|++
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~----------------~~~~~~i~~~~~---~~~~~~~~~L~~ 62 (72)
T cd04874 2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIERE----------------GKARIYMELEGV---GDIEELVEELRS 62 (72)
T ss_pred eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccCC----------------CeEEEEEEEecc---ccHHHHHHHHhC
Confidence 4667789999999999999999999999998766432 235567888764 345567777776
Q ss_pred cCC
Q 023305 268 FAT 270 (284)
Q Consensus 268 ~~~ 270 (284)
...
T Consensus 63 ~~~ 65 (72)
T cd04874 63 LPI 65 (72)
T ss_pred CCC
Confidence 543
No 29
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=97.29 E-value=0.0025 Score=47.28 Aligned_cols=71 Identities=14% Similarity=0.253 Sum_probs=52.5
Q ss_pred CceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHH
Q 023305 184 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 263 (284)
Q Consensus 184 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~ 263 (284)
.+.+.|.+...|+||.|.++++.++..|+|+..++.+..+.. ..+.+.++++-. +-..+..+++
T Consensus 4 ~f~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~---------------~~~~~~l~v~V~-d~~~L~~ii~ 67 (80)
T PF13291_consen 4 SFPVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDD---------------GTARITLTVEVK-DLEHLNQIIR 67 (80)
T ss_dssp -EEEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ET---------------TEEEEEEEEEES-SHHHHHHHHH
T ss_pred EEEEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccC---------------CEEEEEEEEEEC-CHHHHHHHHH
Confidence 467889999999999999999999999999999999997522 235555555543 4578899999
Q ss_pred HHHhcCC
Q 023305 264 HLQEFAT 270 (284)
Q Consensus 264 ~L~~~~~ 270 (284)
.|++.-.
T Consensus 68 ~L~~i~~ 74 (80)
T PF13291_consen 68 KLRQIPG 74 (80)
T ss_dssp HHCTSTT
T ss_pred HHHCCCC
Confidence 9986543
No 30
>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=97.27 E-value=0.0019 Score=42.10 Aligned_cols=58 Identities=28% Similarity=0.331 Sum_probs=43.7
Q ss_pred EEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHH
Q 023305 190 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 265 (284)
Q Consensus 190 ~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L 265 (284)
.+..+++||.|.++++.|+.+++++.++.+++.... +...+++.++... .+..++++|
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 466788999999999999999999999998876431 4566777776531 455555554
No 31
>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=97.26 E-value=0.0035 Score=45.60 Aligned_cols=73 Identities=22% Similarity=0.276 Sum_probs=50.8
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
+|.+..+|+||.|.++++.+++.|+|+..+.+...... .+...|-|+... .+..+.++++.|++
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~--------------~~~i~~~v~v~~--~~~~l~~l~~~L~~ 65 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHG--------------RANVTISIDTST--MNGDIDELLEELRE 65 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCC--------------eEEEEEEEEcCc--hHHHHHHHHHHHhc
Confidence 57788899999999999999999999999987532111 134555555532 33377888888875
Q ss_pred c--CCceEEEc
Q 023305 268 F--ATFLRVLG 276 (284)
Q Consensus 268 ~--~~~vkvLG 276 (284)
. ...|+++|
T Consensus 66 i~~V~~v~~~~ 76 (76)
T cd04888 66 IDGVEKVELVG 76 (76)
T ss_pred CCCeEEEEEeC
Confidence 4 33466655
No 32
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=97.16 E-value=0.0037 Score=46.82 Aligned_cols=67 Identities=10% Similarity=0.147 Sum_probs=49.3
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 265 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L 265 (284)
|-+|.+.+.|+||.|.++++.|+.||.|+..|.--|..... .+.-.+- ++ ++..+..+.++|
T Consensus 3 ~~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~~-------------~sriti~--v~---~~~~i~ql~kQL 64 (76)
T PRK11152 3 QHQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDAQ-------------NINIELT--VA---SERPIDLLSSQL 64 (76)
T ss_pred eEEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCCC-------------EEEEEEE--EC---CCchHHHHHHHH
Confidence 44677778899999999999999999999999998865321 1223233 32 456778888888
Q ss_pred HhcCC
Q 023305 266 QEFAT 270 (284)
Q Consensus 266 ~~~~~ 270 (284)
.+.-.
T Consensus 65 ~KL~d 69 (76)
T PRK11152 65 NKLVD 69 (76)
T ss_pred hcCcC
Confidence 77644
No 33
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=97.15 E-value=0.0048 Score=52.74 Aligned_cols=71 Identities=17% Similarity=0.265 Sum_probs=54.7
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHH
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 266 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~ 266 (284)
-.|.+.++|+||.|.++.+.|++||+|+..+-.-|.... ..+.+.+-+++ ++..+.++.++|+
T Consensus 3 ~~IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~---------------~~sriti~V~~--~~~~i~qi~kQl~ 65 (161)
T PRK11895 3 HTLSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTEDP---------------GLSRMTIVTSG--DEQVIEQITKQLN 65 (161)
T ss_pred EEEEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecCCC---------------CEEEEEEEEEC--CHHHHHHHHHHHh
Confidence 456777899999999999999999999999988887422 24556666666 5678889999998
Q ss_pred hcCCceEE
Q 023305 267 EFATFLRV 274 (284)
Q Consensus 267 ~~~~~vkv 274 (284)
+.-.=+++
T Consensus 66 KLidV~~V 73 (161)
T PRK11895 66 KLIDVLKV 73 (161)
T ss_pred ccccEEEE
Confidence 77554443
No 34
>cd04902 ACT_3PGDH-xct C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH). The C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with an extended C-terminal (xct) region from bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback-controlled by the end product L-serine in an allosteric manner. Some 3PGDH enzymes have an additional domain formed by an extended C-terminal region. This additional domain introduces significant asymmetry to the homotetramer. Adjacent ACT (regulatory) domains interact, creating two serine-binding sites, however, this asymmetric arrangement results in the formation of two different and distinct domain interfaces between iden
Probab=97.14 E-value=0.0025 Score=45.83 Aligned_cols=61 Identities=16% Similarity=0.237 Sum_probs=43.0
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHH
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 265 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L 265 (284)
+++..+|+||.|.++++.|+++|+|+..+.+.+.... ......+++++. .++.+.+.|+++
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~---------------~~~~~~i~v~~~-~~~~~~~~l~~~ 62 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPG---------------GEALMVLSVDEP-VPDEVLEELRAL 62 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCC---------------CEEEEEEEeCCC-CCHHHHHHHHcC
Confidence 4567899999999999999999999999987765322 234566677773 333444444433
No 35
>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=97.13 E-value=0.0032 Score=44.46 Aligned_cols=63 Identities=17% Similarity=0.335 Sum_probs=44.6
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
|.+..+|+||.|.++++.|+++|+|+..+..++.... ..-...++++.. .+.+++++|++.
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~---------------~~~~i~i~v~~~----~~~~~i~~l~~~ 62 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKG---------------DQALMVIEVDQP----IDEEVIEEIKKI 62 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCC---------------CeEEEEEEeCCC----CCHHHHHHHHcC
Confidence 5667889999999999999999999999988764221 122334666553 344677777754
Q ss_pred CC
Q 023305 269 AT 270 (284)
Q Consensus 269 ~~ 270 (284)
..
T Consensus 63 ~~ 64 (71)
T cd04903 63 PN 64 (71)
T ss_pred CC
Confidence 33
No 36
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=97.12 E-value=0.0052 Score=52.30 Aligned_cols=70 Identities=17% Similarity=0.269 Sum_probs=54.0
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
.|.+.+.|+||.|.++.+.|++||+|+..+-.-|.... ..+.+.+-+++ ++..+.++.++|++
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~---------------~~sriti~V~~--d~~~i~qi~kQl~K 65 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTEDP---------------DLSRMTIVVVG--DDKVLEQITKQLNK 65 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecCCC---------------CEEEEEEEEEC--CHHHHHHHHHHHhc
Confidence 46677899999999999999999999999988887422 24556666666 46788888899887
Q ss_pred cCCceEE
Q 023305 268 FATFLRV 274 (284)
Q Consensus 268 ~~~~vkv 274 (284)
.-.=+++
T Consensus 66 li~V~~V 72 (157)
T TIGR00119 66 LVDVIKV 72 (157)
T ss_pred CccEEEE
Confidence 6554333
No 37
>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=97.07 E-value=0.0046 Score=44.26 Aligned_cols=35 Identities=17% Similarity=0.293 Sum_probs=31.1
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeC
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 222 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~ 222 (284)
.|.+.++|+||.|.++++.|+++|+|+..+..-+.
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 36678899999999999999999999999987664
No 38
>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=97.06 E-value=0.0049 Score=44.16 Aligned_cols=63 Identities=16% Similarity=0.135 Sum_probs=44.1
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
.+.+.++|+||.|.++++.|+.+|+|+..+...+.+... .....|.++.. ....++++.|++
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~-------------~~~~~i~v~~~-----~~~~~~~~~L~~ 64 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIREGI-------------GGILRISFKTQ-----EDRERAKEILKE 64 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEeecCC-------------cEEEEEEECCH-----HHHHHHHHHHHH
Confidence 466778999999999999999999999999876653211 12345555532 244566677765
Q ss_pred c
Q 023305 268 F 268 (284)
Q Consensus 268 ~ 268 (284)
.
T Consensus 65 ~ 65 (69)
T cd04909 65 A 65 (69)
T ss_pred c
Confidence 4
No 39
>cd04885 ACT_ThrD-I Tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase). This CD includes each of two tandem C-terminal ACT domains of threonine dehydratase I (ThrD-I; L-threonine hydrolyase) which catalyzes the committed step in branched chain amino acid biosynthesis in plants and microorganisms, the pyridoxal 5'-phosphate (PLP)-dependent dehydration/deamination of L-threonine (or L-serine) to 2-ketobutyrate (or pyruvate). ThrD-I is a cooperative, feedback-regulated (isoleucine and valine) allosteric enzyme that forms a tetramer and contains four pyridoxal phosphate moieties. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.05 E-value=0.0033 Score=45.45 Aligned_cols=62 Identities=23% Similarity=0.220 Sum_probs=44.7
Q ss_pred EEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcC
Q 023305 190 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFA 269 (284)
Q Consensus 190 ~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~ 269 (284)
.+.+|++||+|.++++.++. +.|++.+.=|-.... .....+=+++.+ ...++++++.|++..
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~~--------------~~~v~v~ie~~~---~~~~~~i~~~L~~~G 63 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGGD--------------EARVLVGIQVPD---REDLAELKERLEALG 63 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCCC--------------ceEEEEEEEeCC---HHHHHHHHHHHHHcC
Confidence 57789999999999999999 999999977754311 134444455543 356777777777654
No 40
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=97.03 E-value=0.0072 Score=46.07 Aligned_cols=72 Identities=11% Similarity=0.161 Sum_probs=52.1
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHH
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 266 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~ 266 (284)
-.|.+-+.|+||.|.++-+.|++||.|+..|.--|+.... ..+..+-++. | ++..+.++.++|+
T Consensus 3 ~~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~~-------------iSRmtivv~~-~--d~~~ieqI~kQL~ 66 (84)
T PRK13562 3 RILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQPG-------------ISNMEIQVDI-Q--DDTSLHILIKKLK 66 (84)
T ss_pred EEEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCCCC-------------ceEEEEEEeC-C--CHHHHHHHHHHHh
Confidence 3566667899999999999999999999999888875431 1234333332 4 4567788999998
Q ss_pred hcCCceEE
Q 023305 267 EFATFLRV 274 (284)
Q Consensus 267 ~~~~~vkv 274 (284)
+.-.=+++
T Consensus 67 KlidVikV 74 (84)
T PRK13562 67 QQINVLTV 74 (84)
T ss_pred CCccEEEE
Confidence 77554443
No 41
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=97.03 E-value=0.0046 Score=53.45 Aligned_cols=71 Identities=17% Similarity=0.288 Sum_probs=52.9
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHH
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 266 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~ 266 (284)
-.|.+...|+||.|.++.+.|++||+|+..+.+.|.... ....+-|.+.+. +..+.++.++|+
T Consensus 3 ~~isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~---------------~~sr~TIvv~~~--~~~ieqL~kQL~ 65 (174)
T CHL00100 3 HTLSVLVEDESGVLTRIAGLFARRGFNIESLAVGPAEQK---------------GISRITMVVPGD--DRTIEQLTKQLY 65 (174)
T ss_pred EEEEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCC---------------CccEEEEEEECC--HHHHHHHHHHHH
Confidence 356667789999999999999999999999999886543 224566667663 233677777777
Q ss_pred hcCCceEE
Q 023305 267 EFATFLRV 274 (284)
Q Consensus 267 ~~~~~vkv 274 (284)
+.+.-+++
T Consensus 66 KLidVl~V 73 (174)
T CHL00100 66 KLVNILKV 73 (174)
T ss_pred HHhHhhEE
Confidence 76665444
No 42
>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=96.96 E-value=0.0053 Score=44.50 Aligned_cols=63 Identities=14% Similarity=0.217 Sum_probs=46.6
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
|.+..+|+||.|.++.+.++..|+|+.+++++..+.. .....|-|++. +...+.++++.|+..
T Consensus 2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~--------------~~~~~~~vev~---~~~~l~~i~~~L~~i 64 (74)
T cd04887 2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRD--------------YTVRDITVDAP---SEEHAETIVAAVRAL 64 (74)
T ss_pred EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCC--------------EEEEEEEEEcC---CHHHHHHHHHHHhcC
Confidence 6678899999999999999999999999999864321 12334444443 336777888888754
No 43
>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=96.93 E-value=0.0052 Score=43.15 Aligned_cols=62 Identities=16% Similarity=0.285 Sum_probs=44.5
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
+.+..+|+||.|.++++.|+.+|+|+.++.+.+.... ..+...++++.. . ..+++++|++.
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~---------------~~~~~~~~v~~~-~---~~~l~~~l~~~ 62 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKG---------------GIAYMVLDVDSP-V---PEEVLEELKAL 62 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCC---------------CEEEEEEEcCCC-C---CHHHHHHHHcC
Confidence 5677899999999999999999999999999875321 134455566442 2 34666677654
Q ss_pred C
Q 023305 269 A 269 (284)
Q Consensus 269 ~ 269 (284)
-
T Consensus 63 ~ 63 (71)
T cd04879 63 P 63 (71)
T ss_pred C
Confidence 3
No 44
>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.89 E-value=0.007 Score=45.21 Aligned_cols=64 Identities=16% Similarity=0.224 Sum_probs=43.3
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceee--eeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCC-CcHH-HHHHHH
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLT--KIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASM-ADPR-AQNALG 263 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt--~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~-~d~~-~~~al~ 263 (284)
-|-+..+|+||-|+++.++|++.|+++. ||.|--... .-.=.||||.+|.. .|+. .+.+-+
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Ge---------------rv~D~Fyv~~~g~kl~d~~~~~~L~~ 66 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGY---------------REVDLFIVQSDGKKIMDPKKQAALCA 66 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccC---------------EEEEEEEEeCCCCccCCHHHHHHHHH
Confidence 3456778999999999999999999997 565432221 23457999987754 4543 333333
Q ss_pred HHH
Q 023305 264 HLQ 266 (284)
Q Consensus 264 ~L~ 266 (284)
.|.
T Consensus 67 ~L~ 69 (75)
T cd04896 67 RLR 69 (75)
T ss_pred HHH
Confidence 444
No 45
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=96.81 E-value=0.014 Score=45.69 Aligned_cols=71 Identities=20% Similarity=0.376 Sum_probs=52.8
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 265 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L 265 (284)
+-.|.+-+.|+||.|.++-..|++||.|+..|-.-|+.... -..+.|-+. +|..+.+++++|
T Consensus 8 ~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~~~---------------iSRmtivv~---~~~~i~Qi~kQL 69 (96)
T PRK08178 8 NVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQDGD---------------KSRIWLLVN---DDQRLEQMISQI 69 (96)
T ss_pred CEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCCCC---------------ceEEEEEEc---CchHHHHHHHHH
Confidence 45566677899999999999999999999999887875431 233444443 357889999999
Q ss_pred HhcCCceEE
Q 023305 266 QEFATFLRV 274 (284)
Q Consensus 266 ~~~~~~vkv 274 (284)
++.-.=+++
T Consensus 70 ~KLidVikV 78 (96)
T PRK08178 70 EKLEDVLKV 78 (96)
T ss_pred hCCcCEEEE
Confidence 887654444
No 46
>PRK04435 hypothetical protein; Provisional
Probab=96.69 E-value=0.019 Score=48.22 Aligned_cols=77 Identities=18% Similarity=0.216 Sum_probs=56.7
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
.+++|.+.++|+||.|.++++.++..|+|+..|........ .....|=||+.. .+..+.++++.
T Consensus 68 r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g--------------~a~vs~tVevs~--~~~~L~~Li~~ 131 (147)
T PRK04435 68 KIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQG--------------RANVTISIDTSS--MEGDIDELLEK 131 (147)
T ss_pred cEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCC--------------EEEEEEEEEeCC--hHHHHHHHHHH
Confidence 47889999999999999999999999999999986522111 134566666633 23478888888
Q ss_pred HHhc--CCceEEEce
Q 023305 265 LQEF--ATFLRVLGC 277 (284)
Q Consensus 265 L~~~--~~~vkvLGs 277 (284)
|+.. ...++++|.
T Consensus 132 L~~i~gV~~V~i~~~ 146 (147)
T PRK04435 132 LRNLDGVEKVELIGM 146 (147)
T ss_pred HHcCCCcEEEEEEec
Confidence 8854 446777774
No 47
>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=96.63 E-value=0.016 Score=43.91 Aligned_cols=69 Identities=16% Similarity=0.175 Sum_probs=44.3
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
+.+.+||+||+|.++|+.++..||| .+.=+-.... ..+..+-+++.+. ...++++++.|++.
T Consensus 4 l~v~ipD~PG~L~~ll~~l~~anI~--~~~y~~~~~~--------------~~~v~i~ie~~~~--~~~~~~i~~~L~~~ 65 (85)
T cd04906 4 LAVTIPERPGSFKKFCELIGPRNIT--EFNYRYADEK--------------DAHIFVGVSVANG--AEELAELLEDLKSA 65 (85)
T ss_pred EEEecCCCCcHHHHHHHHhCCCcee--EEEEEccCCC--------------eeEEEEEEEeCCc--HHHHHHHHHHHHHC
Confidence 6678899999999999999955444 4443332211 1345555676541 25677778888776
Q ss_pred CCceEEE
Q 023305 269 ATFLRVL 275 (284)
Q Consensus 269 ~~~vkvL 275 (284)
.-.+..+
T Consensus 66 G~~~~~~ 72 (85)
T cd04906 66 GYEVVDL 72 (85)
T ss_pred CCCeEEC
Confidence 6555543
No 48
>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=96.56 E-value=0.006 Score=43.43 Aligned_cols=61 Identities=20% Similarity=0.233 Sum_probs=43.7
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
+++...|+||.|.++++.++++|+|+..+.+++.. . .-...++++.. .+++++++|++.
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~-~----------------~a~~~~~~~~~----~l~~li~~l~~~ 60 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRG-E----------------IGYVVIDIDSE----VSEELLEALRAI 60 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCC-C----------------EEEEEEEcCCC----CCHHHHHHHHcC
Confidence 45677899999999999999999999998776543 1 12334466554 345677777764
Q ss_pred CC
Q 023305 269 AT 270 (284)
Q Consensus 269 ~~ 270 (284)
-.
T Consensus 61 ~~ 62 (69)
T cd04901 61 PG 62 (69)
T ss_pred CC
Confidence 43
No 49
>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=96.56 E-value=0.018 Score=41.25 Aligned_cols=64 Identities=16% Similarity=0.259 Sum_probs=46.3
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
|.+...|+||.|.++++.|+.+|+|+.++.+++..... .....|-++. .+...++++++.|++.
T Consensus 3 l~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~-------------~~~~~i~~~~---~~~~~l~~~i~~L~~~ 66 (79)
T cd04881 3 LRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGGE-------------TAPVVIVTHE---TSEAALNAALAEIEAL 66 (79)
T ss_pred EEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCC-------------ceeEEEEEcc---CCHHHHHHHHHHHHcC
Confidence 45667899999999999999999999999887653211 1223333332 3567888999999864
No 50
>PRK08198 threonine dehydratase; Provisional
Probab=96.51 E-value=0.023 Score=54.99 Aligned_cols=76 Identities=16% Similarity=0.198 Sum_probs=56.3
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeee-CCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP-QRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP-~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
..++.+.++|+||.|.++|+.++..|.|+..|.-+. .++.+ .....+.|.+|.. +...++++++.
T Consensus 327 ~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~~~~~~~-------------~~~~~v~v~ie~~-~~~~~~~l~~~ 392 (404)
T PRK08198 327 YLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDRFSPDLR-------------LGEVEVELTLETR-GPEHIEEILDA 392 (404)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEEccCCCC-------------CceEEEEEEEEeC-CHHHHHHHHHH
Confidence 568889999999999999999999999999987654 33222 1345566666653 33467788999
Q ss_pred HHhcCCceEEE
Q 023305 265 LQEFATFLRVL 275 (284)
Q Consensus 265 L~~~~~~vkvL 275 (284)
|++..-.++++
T Consensus 393 L~~~G~~v~~~ 403 (404)
T PRK08198 393 LRDAGYEVKVV 403 (404)
T ss_pred HHHCCCeEEEc
Confidence 98876666543
No 51
>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=96.29 E-value=0.031 Score=40.86 Aligned_cols=36 Identities=19% Similarity=0.302 Sum_probs=31.3
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeC
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 222 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~ 222 (284)
|.+.+..+|+||.|+++.+.|+.+|+|+......+.
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 457778899999999999999999999987776654
No 52
>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=96.25 E-value=0.029 Score=42.52 Aligned_cols=66 Identities=17% Similarity=0.255 Sum_probs=45.9
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeec-CCCcHHHHHHHHHH
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEA-SMADPRAQNALGHL 265 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg-~~~d~~~~~al~~L 265 (284)
-.+.+.-+|+||-+.++.+.|+.+|+|+..++..-..+ .+...+-+++.+ ..+-..+++.++.|
T Consensus 2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~---------------~f~~~~~v~~~~~~~~~~~L~~~l~~l 66 (88)
T cd04872 2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDG---------------YFTMIMIVDISESNLDFAELQEELEEL 66 (88)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCC---------------ccEEEEEEEeCCCCCCHHHHHHHHHHH
Confidence 45667779999999999999999999999998775211 133445555544 23345666666666
Q ss_pred Hh
Q 023305 266 QE 267 (284)
Q Consensus 266 ~~ 267 (284)
.+
T Consensus 67 ~~ 68 (88)
T cd04872 67 GK 68 (88)
T ss_pred HH
Confidence 53
No 53
>PRK00194 hypothetical protein; Validated
Probab=96.17 E-value=0.033 Score=42.18 Aligned_cols=36 Identities=19% Similarity=0.218 Sum_probs=31.2
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeee
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP 221 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP 221 (284)
+-.+.+.-+|+||.+.++.+.|+.+|+|+..+++.-
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~ 38 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTI 38 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHh
Confidence 345666678999999999999999999999998874
No 54
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=96.17 E-value=0.031 Score=41.33 Aligned_cols=35 Identities=20% Similarity=0.313 Sum_probs=25.6
Q ss_pred EEEEe--cCCCchHHHHHHHHHhCCceeeeeeeeeCC
Q 023305 189 IVFTL--DEGPGVLFKALAVFALREINLTKIESRPQR 223 (284)
Q Consensus 189 i~f~~--~~~pGaL~~~L~~F~~~~INLt~IeSRP~~ 223 (284)
+++++ +|+||-++++.++++++|.|+..++-.-..
T Consensus 3 ~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~ 39 (76)
T PF13740_consen 3 LVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLG 39 (76)
T ss_dssp EEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEET
T ss_pred EEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEc
Confidence 44444 899999999999999999999866666543
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=96.16 E-value=0.055 Score=39.70 Aligned_cols=61 Identities=11% Similarity=0.083 Sum_probs=43.6
Q ss_pred EEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHH
Q 023305 191 FTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 266 (284)
Q Consensus 191 f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~ 266 (284)
+.=+|+||-++++-+.|+.+|+|+..++++=..+ .+...|.+++....+-..+++.|+.+.
T Consensus 4 v~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~---------------~f~~~~~v~~p~~~~~~~l~~~l~~l~ 64 (75)
T cd04870 4 VTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHG---------------RLSLGILVQIPDSADSEALLKDLLFKA 64 (75)
T ss_pred EEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcC---------------eeEEEEEEEcCCCCCHHHHHHHHHHHH
Confidence 3447999999999999999999999998765432 144556666533223466777777665
No 56
>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=96.07 E-value=0.072 Score=37.57 Aligned_cols=48 Identities=19% Similarity=0.231 Sum_probs=38.7
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEee
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFE 250 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~e 250 (284)
.+.+..+|+||.|.++.+.|+.+|+|+..+........ ....|+|+-.
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~---------------~~~~~~v~~~ 49 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGER---------------ALDVFYVTDS 49 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCE---------------EEEEEEEECC
Confidence 35677899999999999999999999999988775431 4567777653
No 57
>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=96.05 E-value=0.07 Score=37.99 Aligned_cols=37 Identities=22% Similarity=0.240 Sum_probs=32.4
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCC
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 223 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~ 223 (284)
|-+.+..+|+||.|.++.+.|+.+|+|+.++..++..
T Consensus 1 ~~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~ 37 (70)
T cd04899 1 TVLELTALDRPGLLADVTRVLAELGLNIHSAKIATLG 37 (70)
T ss_pred CEEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecC
Confidence 3456677899999999999999999999999988764
No 58
>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=96.04 E-value=0.038 Score=53.02 Aligned_cols=73 Identities=22% Similarity=0.277 Sum_probs=49.9
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeee-eCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESR-PQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSR-P~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
+..|.+.++|+||.|.++++.++..+.|++.|.-+ ..+..+ .......|.+|.. +....+++++.
T Consensus 305 ~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~r~~~~~~-------------~~~~~v~v~vet~-~~~~~~~i~~~ 370 (380)
T TIGR01127 305 KVRIETVLPDRPGALYHLLESIAEARANIVKIDHDRLSKEIP-------------PGFAMVEITLETR-GKEHLDEILKI 370 (380)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeccccCCC-------------CceEEEEEEEEeC-CHHHHHHHHHH
Confidence 44888899999999999999999999999999654 222211 1223344444442 23556678888
Q ss_pred HHhcCCce
Q 023305 265 LQEFATFL 272 (284)
Q Consensus 265 L~~~~~~v 272 (284)
|++..-.+
T Consensus 371 L~~~G~~v 378 (380)
T TIGR01127 371 LRDMGYNF 378 (380)
T ss_pred HHHcCCcc
Confidence 88765444
No 59
>PRK08577 hypothetical protein; Provisional
Probab=96.04 E-value=0.11 Score=42.66 Aligned_cols=69 Identities=17% Similarity=0.318 Sum_probs=49.7
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 265 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L 265 (284)
...|.+...|+||.|.++++.|+.+|+|+..+.++...... .+.-.|-+|+... +..+.+++++|
T Consensus 56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~-------------~~~i~l~vev~~~--~~~l~~l~~~L 120 (136)
T PRK08577 56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGE-------------LAECVIIVDLSKS--DIDLEELEEEL 120 (136)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCC-------------EEEEEEEEEeCCc--hhhHHHHHHHH
Confidence 56777888999999999999999999999999988764221 1222344555442 24577888888
Q ss_pred HhcC
Q 023305 266 QEFA 269 (284)
Q Consensus 266 ~~~~ 269 (284)
++..
T Consensus 121 ~~l~ 124 (136)
T PRK08577 121 KKLE 124 (136)
T ss_pred HcCC
Confidence 7654
No 60
>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=96.01 E-value=0.048 Score=39.89 Aligned_cols=60 Identities=18% Similarity=0.356 Sum_probs=47.9
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
.|.+...|++|.|.++++.++..|+|+..+++++. . + .+++++.. +-..+..+++.|++
T Consensus 2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~--~-----------------~-i~l~i~v~-~~~~L~~li~~L~~ 60 (74)
T cd04877 2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK--G-----------------R-IYLNFPTI-EFEKLQTLMPEIRR 60 (74)
T ss_pred EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC--C-----------------e-EEEEeEec-CHHHHHHHHHHHhC
Confidence 35667789999999999999999999999999763 2 2 66677653 45678888888876
Q ss_pred c
Q 023305 268 F 268 (284)
Q Consensus 268 ~ 268 (284)
.
T Consensus 61 i 61 (74)
T cd04877 61 I 61 (74)
T ss_pred C
Confidence 4
No 61
>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=95.96 E-value=0.1 Score=35.31 Aligned_cols=63 Identities=16% Similarity=0.222 Sum_probs=44.7
Q ss_pred EEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcC
Q 023305 190 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFA 269 (284)
Q Consensus 190 ~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~ 269 (284)
.+..+++||.|.++++.|+.+++|+.+++....... ...+.+.++.. +...+..+++.|+...
T Consensus 2 ~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~----------------~~~~~~~~~~~-~~~~~~~~~~~l~~~~ 64 (71)
T cd04876 2 RVEAIDRPGLLADITTVIAEEKINILSVNTRTDDDG----------------LATIRLTLEVR-DLEHLARIMRKLRQIP 64 (71)
T ss_pred EEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCCC----------------EEEEEEEEEEC-CHHHHHHHHHHHhCCC
Confidence 456789999999999999999999999988764311 12233444432 3456778888887543
No 62
>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=95.90 E-value=0.027 Score=38.68 Aligned_cols=34 Identities=24% Similarity=0.342 Sum_probs=30.4
Q ss_pred EEEecCCCchHHHHHHHHHhCCceeeeeeeeeCC
Q 023305 190 VFTLDEGPGVLFKALAVFALREINLTKIESRPQR 223 (284)
Q Consensus 190 ~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~ 223 (284)
.+.++|+||.|.++++.|.++|+|+..+...+..
T Consensus 2 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~ 35 (56)
T cd04889 2 SVFVENKPGRLAEVTEILAEAGINIKAISIAETR 35 (56)
T ss_pred EEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEcc
Confidence 4577899999999999999999999999877765
No 63
>cd04895 ACT_ACR_1 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the N-terminal ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.86 E-value=0.071 Score=39.49 Aligned_cols=29 Identities=24% Similarity=0.416 Sum_probs=25.7
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceee
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLT 215 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt 215 (284)
|-|-+..+|+||-|+++.++|++.|+++.
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~ 30 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCIT 30 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEE
Confidence 44556779999999999999999999997
No 64
>PRK06382 threonine dehydratase; Provisional
Probab=95.82 E-value=0.054 Score=52.68 Aligned_cols=74 Identities=18% Similarity=0.295 Sum_probs=49.2
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeee-eeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIES-RPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 263 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeS-RP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~ 263 (284)
.++.|.+.++|+||.|.++++.|..+|+|+++|+- |...... .+ .....|-||..+. ...+.+++
T Consensus 329 ~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~~~~~~~~~--------~~---~~~v~i~vet~~~---~~~~~v~~ 394 (406)
T PRK06382 329 QLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEVDNLRKETP--------PG---FQSVTFTVNVRGQ---DHLDRILN 394 (406)
T ss_pred CEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEEeeccccCC--------CC---cEEEEEEEEeCCH---HHHHHHHH
Confidence 47788889999999999999999999999999987 3221111 00 1334444554321 23346777
Q ss_pred HHHhcCCce
Q 023305 264 HLQEFATFL 272 (284)
Q Consensus 264 ~L~~~~~~v 272 (284)
.|++..-.+
T Consensus 395 ~L~~~Gy~~ 403 (406)
T PRK06382 395 ALREMGYKF 403 (406)
T ss_pred HHHHCCCCe
Confidence 777665443
No 65
>cd04875 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase). This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.47 E-value=0.18 Score=36.69 Aligned_cols=33 Identities=12% Similarity=0.220 Sum_probs=29.4
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeee
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRP 221 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP 221 (284)
|.+.-+|+||-+.++.+.|+.+|+|+..++++-
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 345568999999999999999999999998884
No 66
>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=95.30 E-value=0.16 Score=37.32 Aligned_cols=34 Identities=18% Similarity=0.417 Sum_probs=29.6
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeC
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 222 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~ 222 (284)
+.+..+|+||-+.++-+.|+.+|+|+..+++.-.
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~ 35 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETY 35 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeee
Confidence 3456689999999999999999999999988654
No 67
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=95.19 E-value=0.12 Score=42.62 Aligned_cols=77 Identities=21% Similarity=0.320 Sum_probs=60.0
Q ss_pred CceEEEEEEecCCCchHHHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHH
Q 023305 184 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIE-SRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNAL 262 (284)
Q Consensus 184 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~Ie-SRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al 262 (284)
..+.+|.+.+.|+.|.|.++|.+.+++++|+..|. +-|..+. ..-..-||..+ -...+.+++
T Consensus 70 ~ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~---------------Anvtlsi~~ss--m~~~V~~ii 132 (150)
T COG4492 70 ERIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGR---------------ANVTLSIDTSS--MEKDVDKII 132 (150)
T ss_pred ceEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCce---------------eeEEEEEEchh--hhhhHHHHH
Confidence 34779999999999999999999999999998875 4576544 34566777764 346788899
Q ss_pred HHHHh--cCCceEEEce
Q 023305 263 GHLQE--FATFLRVLGC 277 (284)
Q Consensus 263 ~~L~~--~~~~vkvLGs 277 (284)
++|++ ....|.++|+
T Consensus 133 ~kl~k~e~V~kVeivgs 149 (150)
T COG4492 133 EKLRKVEGVEKVEIVGS 149 (150)
T ss_pred HHHhcccceeEEEEeec
Confidence 98884 3556888875
No 68
>COG2061 ACT-domain-containing protein, predicted allosteric regulator of homoserine dehydrogenase [Amino acid transport and metabolism]
Probab=95.01 E-value=0.19 Score=42.41 Aligned_cols=74 Identities=22% Similarity=0.337 Sum_probs=53.0
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceee-eeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLT-KIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt-~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
+.++.+.++|+||-|.++|+.++..|.|+. =|.||-.+..| .--.-|-+++. ..+..++.++.
T Consensus 5 ritldIEL~D~PGQLl~vLqPls~~g~NiItIiH~r~kk~g~---------------r~pV~i~~~~d-~~~~~~~i~~~ 68 (170)
T COG2061 5 RITLDIELKDKPGQLLKVLQPLSKTGANIITIIHSRDKKYGP---------------RVPVQIVFEGD-REDKDAKIIRL 68 (170)
T ss_pred EEEEEEEecCCCcchhhhhcchhhcCccEEEEEeecCcccCC---------------ceeEEEEEEec-ccHHHHHHHHH
Confidence 578889999999999999999999999986 56788765432 22233444553 23667788888
Q ss_pred HHhcCCceEEE
Q 023305 265 LQEFATFLRVL 275 (284)
Q Consensus 265 L~~~~~~vkvL 275 (284)
+++.+..++-.
T Consensus 69 ~e~~Gi~I~~~ 79 (170)
T COG2061 69 LEEEGIIIIRF 79 (170)
T ss_pred HHhCCcEEEEe
Confidence 87666655444
No 69
>PRK07334 threonine dehydratase; Provisional
Probab=94.99 E-value=0.19 Score=48.85 Aligned_cols=76 Identities=13% Similarity=0.172 Sum_probs=56.3
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeC-CCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ-RKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 263 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~-~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~ 263 (284)
..+.|.+...|+||.|.++++.+++.++|+.++.++.. +..+. | .+...|-|++. +.+.+.++++
T Consensus 325 y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~--------~---~~~i~l~i~V~---d~~~L~~vi~ 390 (403)
T PRK07334 325 RLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPA--------K---GAELELVIETR---DAAHLQEVIA 390 (403)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCC--------C---eEEEEEEEEeC---CHHHHHHHHH
Confidence 46899999999999999999999999999999998864 11110 0 13344555553 4478899999
Q ss_pred HHHhcCCceEE
Q 023305 264 HLQEFATFLRV 274 (284)
Q Consensus 264 ~L~~~~~~vkv 274 (284)
.|++..-.+.+
T Consensus 391 ~Lr~~g~~~~~ 401 (403)
T PRK07334 391 ALRAAGFEARL 401 (403)
T ss_pred HHHHcCCeeEe
Confidence 99987655544
No 70
>PRK08526 threonine dehydratase; Provisional
Probab=94.75 E-value=0.24 Score=48.31 Aligned_cols=209 Identities=19% Similarity=0.156 Sum_probs=109.4
Q ss_pred CCCeEEEeeeecccceeeccccccc--cCCeEEEEEEEEeee---eEeeecCCCCcCCccEEE----e---cHHHHHHHH
Q 023305 40 LADKAVLPIENSSSGSIHRNYDLLL--RHRLHIVGEVQLAAN---FCLLALPGIKADQLKRVL----S---HPQALASSD 107 (284)
Q Consensus 40 ~~d~gvvPiENS~~G~V~~t~d~L~--~~~l~I~~E~~l~I~---~~L~~~~~~~l~~i~~V~----S---Hpqal~Qc~ 107 (284)
..|+-|+|+- ..|.+.-+...+. ..+.+|+|--.-.-. ..+-..+......+.++. . -|..+..|+
T Consensus 168 ~~D~vvvpvG--gGGl~aGia~~~k~~~p~~kvigVep~~~~~~~~s~~~g~~~~~~~~~tiadgiav~~~~~~~~~~~~ 245 (403)
T PRK08526 168 DLDMVVVPVG--GGGLISGIASAAKQINPNIKIIGVGAKGAPAMYESFHAKKIINSKSVRTIADGIAVRDASPINLAIIL 245 (403)
T ss_pred CCCEEEEecC--hHHHHHHHHHHHHHhCCCCEEEEEEECCCChHHHHHHcCCcccCCCCCceeccccCCCCCHHHHHHHH
Confidence 5899999985 4555544554443 245666654332110 011110001112222221 1 166677666
Q ss_pred HHHHhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeeccccCCCCCeeEEEEEeeCCCCCC-------
Q 023305 108 IVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDPIIPR------- 180 (284)
Q Consensus 108 ~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~~~------- 180 (284)
+++.+ +-.+.......|.+.+++.. + ..+.+..|+-+-+|.--...+ ..+.+=-++++- .+...
T Consensus 246 ~~vd~--~v~V~d~ei~~A~~~l~~~~--g-i~ve~aga~~lAall~~~~~~---~~~~~Vv~ilsG-Gnid~~~~~~i~ 316 (403)
T PRK08526 246 ECVDD--FVQVDDEEIANAILFLLEKQ--K-IVVEGAGAASVAALLHQKIDL---KKGKKIGVVLSG-GNIDVQMLNIII 316 (403)
T ss_pred HhCCE--EEEECHHHHHHHHHHHHHhc--C-cEeeHHHHHHHHHHHhCcccc---ccCCeEEEEECC-CCCCHHHHHHHH
Confidence 65542 22333344666666666542 1 223444444444443111111 122222223322 22110
Q ss_pred ----CCCCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeee-eeCCCCCCccccCCCCCCCccceeEEEEEeecCCCc
Q 023305 181 ----TDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIES-RPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMAD 255 (284)
Q Consensus 181 ----~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeS-RP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d 255 (284)
.....+..+.+.++|+||+|.++++.+...+.|++.|+= |.....+ ..+-...|.+|.. +.
T Consensus 317 ~~~l~~~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~~~~~-------------~~~~~~~~~~e~~-~~ 382 (403)
T PRK08526 317 EKGLIKSYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFSTKLD-------------YGDAMISITLETK-GK 382 (403)
T ss_pred HHHHHhcCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEeccCCCC-------------CccEEEEEEEEeC-CH
Confidence 012236788899999999999999999999999999977 5544322 1234455666653 44
Q ss_pred HHHHHHHHHHHhcCCceE
Q 023305 256 PRAQNALGHLQEFATFLR 273 (284)
Q Consensus 256 ~~~~~al~~L~~~~~~vk 273 (284)
+.++++++.|++..-.++
T Consensus 383 ~~~~~~~~~l~~~g~~~~ 400 (403)
T PRK08526 383 EHQEEIRKILTEKGFNFY 400 (403)
T ss_pred HHHHHHHHHHHHCCCCeE
Confidence 678888888877654443
No 71
>PRK08639 threonine dehydratase; Validated
Probab=94.24 E-value=0.27 Score=48.01 Aligned_cols=74 Identities=15% Similarity=0.246 Sum_probs=50.4
Q ss_pred ceEEEEEEecCCCchHHHHHH-HHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALA-VFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 263 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~-~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~ 263 (284)
.+..+.|.+||+||+|.++|+ +++... |++.|+-|.....+ .+ ...|.+|.. +.+.++++++
T Consensus 335 r~~~~~v~ipdrPGaL~~~l~~i~~~~~-NI~~~~~~~~~~~~-------------~~--~v~v~iE~~-~~~h~~~i~~ 397 (420)
T PRK08639 335 LKHYFIVNFPQRPGALREFLDDVLGPND-DITRFEYLKKNNRE-------------TG--PVLVGIELK-DAEDYDGLIE 397 (420)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCC-cEEEEEEeecCCCC-------------ce--EEEEEEEeC-CHHHHHHHHH
Confidence 477899999999999999999 555544 99999777543221 13 344455543 2356777888
Q ss_pred HHHhcCCceEEE
Q 023305 264 HLQEFATFLRVL 275 (284)
Q Consensus 264 ~L~~~~~~vkvL 275 (284)
.|++..-.++.+
T Consensus 398 ~L~~~Gy~~~~~ 409 (420)
T PRK08639 398 RMEAFGPSYIDI 409 (420)
T ss_pred HHHHCCCceEEC
Confidence 888766555544
No 72
>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=94.03 E-value=0.55 Score=34.65 Aligned_cols=69 Identities=16% Similarity=0.050 Sum_probs=44.6
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
|.+.-||+||-.+++-+.++++|.|+..+...-..+ .+-+..-++++. .+.+.+++.++.+.+.
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 345568999999999999999999999766554221 133334445442 2336677777776643
Q ss_pred -CCceE
Q 023305 269 -ATFLR 273 (284)
Q Consensus 269 -~~~vk 273 (284)
...++
T Consensus 68 ~~l~i~ 73 (77)
T cd04893 68 LDLTLM 73 (77)
T ss_pred cCCEEE
Confidence 43444
No 73
>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=94.02 E-value=0.45 Score=34.58 Aligned_cols=31 Identities=13% Similarity=0.288 Sum_probs=26.8
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceeeee
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLTKI 217 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt~I 217 (284)
+.+.+..+|+||-|+++-++|+.+|+|+..-
T Consensus 2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A 32 (73)
T cd04900 2 TEVFIYTPDRPGLFARIAGALDQLGLNILDA 32 (73)
T ss_pred EEEEEEecCCCCHHHHHHHHHHHCCCCeEEe
Confidence 3466777899999999999999999999843
No 74
>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=93.87 E-value=0.49 Score=46.11 Aligned_cols=74 Identities=15% Similarity=0.119 Sum_probs=48.9
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
.+..+.|.+|++||+|.++|+.....+-|+++++-|..... ..-...|.+|.. +...++++++.
T Consensus 324 r~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~y~~~~~~---------------~~~~v~v~iE~~-~~~h~~~i~~~ 387 (409)
T TIGR02079 324 LKHYFIVRFPQRPGALREFLNDVLGPNDDITRFEYTKKSNR---------------ETGPALIGIELN-DKEDFAGLLER 387 (409)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeecCCC---------------CeEEEEEEEEeC-CHHHHHHHHHH
Confidence 36788899999999999999944445559998888762211 122333444443 23566777888
Q ss_pred HHhcCCceEE
Q 023305 265 LQEFATFLRV 274 (284)
Q Consensus 265 L~~~~~~vkv 274 (284)
|++..-.+++
T Consensus 388 L~~~Gy~~~~ 397 (409)
T TIGR02079 388 MAAADIHYED 397 (409)
T ss_pred HHHCCCCeEE
Confidence 8876555543
No 75
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=93.79 E-value=0.33 Score=41.80 Aligned_cols=93 Identities=19% Similarity=0.261 Sum_probs=58.3
Q ss_pred EEEeeCCCCCCCCCCceEEEEE--EecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEE
Q 023305 170 LVLARDPIIPRTDKLFKTSIVF--TLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYI 247 (284)
Q Consensus 170 ~vl~~~~~~~~~~~~~ktsi~f--~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~i 247 (284)
+++.|....+.... -..+.+ ...|+||-+.++-..|..+||||-.++||-...- | -..-.|.+
T Consensus 76 v~m~rt~~~~~~a~--~~~v~v~v~a~DrpgIv~~~T~lf~~~~inie~L~~~~~~a~----------~---s~~~lfha 140 (176)
T COG2716 76 VVMKRTGAHPTPAN--PAPVWVYVDANDRPGIVEEFTALFDGHGINIENLVSRTYPAP----------G---SSAPLFHA 140 (176)
T ss_pred EEEeecCCCccCCC--CceEEEEEEecCCccHHHHHHHHHHhcCCchhhceeeeeecC----------C---CCccceeh
Confidence 55666554332221 133444 4479999999999999999999999999844321 1 13567999
Q ss_pred EeecCCCc-HHHHHHHHHHHhcCCceEEEce
Q 023305 248 DFEASMAD-PRAQNALGHLQEFATFLRVLGC 277 (284)
Q Consensus 248 d~eg~~~d-~~~~~al~~L~~~~~~vkvLGs 277 (284)
++..+..- -++..+.++++..|..+.+=|+
T Consensus 141 ~it~~lPa~~~i~~l~~~f~al~~~L~v~~~ 171 (176)
T COG2716 141 QITARLPANLSISALRDAFEALCDELNVDGS 171 (176)
T ss_pred hhhccCCCcCcHHHHHHHHHHHHHhhcceee
Confidence 98655321 2444455556666666655443
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=93.49 E-value=1.3 Score=44.42 Aligned_cols=214 Identities=17% Similarity=0.205 Sum_probs=108.3
Q ss_pred HHHHHHHhCCCCeEEEeeeecccceeeccccccc--cCCeEEEEEEEEeee---eEeeecCCCCcCCc---------cEE
Q 023305 31 DTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL--RHRLHIVGEVQLAAN---FCLLALPGIKADQL---------KRV 96 (284)
Q Consensus 31 ~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~--~~~l~I~~E~~l~I~---~~L~~~~~~~l~~i---------~~V 96 (284)
|+++.+. +..|+-|+|+= ..|.+.-+...+. ..+.+|+|--...-. ..+-+.....++.+ +.+
T Consensus 158 EI~~q~~-~~~D~vvvpvG--gGGliaGia~~lk~~~p~~kVIgVep~~~~~~~~s~~~g~~~~~~~~~t~adgiav~~~ 234 (499)
T TIGR01124 158 EILRQVA-NPLDAVFVPVG--GGGLAAGVAALIKQLMPEIKVIGVEPTDSDCMKQALDAGEPVDLDQVGLFADGVAVKRV 234 (499)
T ss_pred HHHHhCC-CCCCEEEEccC--ccHHHHHHHHHHHHhCCCCEEEEEEECCChHHHHHHhcCCceeCCCCCCccCcccCCCc
Confidence 4444432 36899999976 4555544443333 235666665442111 00100000011111 112
Q ss_pred EecHHHHHHHHHHHHhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeeccccCCCCCeeEEEEEeeCC
Q 023305 97 LSHPQALASSDIVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLARDP 176 (284)
Q Consensus 97 ~SHpqal~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~d~~~N~TRF~vl~~~~ 176 (284)
=+..+.-|++++.+ +-.+.......|.+.+.+.. + .-+.+..|+.+.+|.-+.+... .+ +.+=-+|++-..
T Consensus 235 --g~~~~~~~~~~vd~--vv~V~d~ei~~ai~~l~~~~-g--ii~EpagA~~lAal~~~~~~~~-~~-~~~vv~i~sG~n 305 (499)
T TIGR01124 235 --GDETFRLCQQYLDD--IVTVDTDEVCAAIKDLFEDT-R--AVAEPAGALALAGLKKYVALHG-IR-GQTLVAILSGAN 305 (499)
T ss_pred --cHHHHHHHHHhCCE--EEEECHHHHHHHHHHHHHhc-C--cEEechHHHHHHHHHHhhhhcC-CC-CCeEEEEECCCC
Confidence 13556655554432 12233334556666666542 1 2234445555556554433221 11 222222332221
Q ss_pred CCCC----------CCCCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEE
Q 023305 177 IIPR----------TDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFY 246 (284)
Q Consensus 177 ~~~~----------~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~ 246 (284)
.... -.......+.+++|++||+|.+.++.+.. -|+|.++=|-.... +=..|
T Consensus 306 ~~~~~l~~~~~r~~~~~~re~~l~V~iPerPGal~~f~~~i~~--~nItef~yr~~~~~----------------~a~v~ 367 (499)
T TIGR01124 306 MNFHRLRYVSERCELGEQREALLAVTIPEQPGSFLKFCELLGN--RNITEFNYRYADRK----------------DAHIF 367 (499)
T ss_pred CCHHHHHHHHHHHHHhcCCEEEEEEEeCCCCCHHHHHHHHhhh--cceEEEEEEecCCC----------------eEEEE
Confidence 1100 01224678889999999999999999997 48888888853321 22344
Q ss_pred EEeecCCCcHHHHHHHHHHHhcCCceEEE
Q 023305 247 IDFEASMADPRAQNALGHLQEFATFLRVL 275 (284)
Q Consensus 247 id~eg~~~d~~~~~al~~L~~~~~~vkvL 275 (284)
|.++.. +...++++++.|++..-.+..+
T Consensus 368 vgie~~-~~~~~~~l~~~L~~~Gy~~~dl 395 (499)
T TIGR01124 368 VGVQLS-NPQERQEILARLNDGGYSVVDL 395 (499)
T ss_pred EEEEeC-CHHHHHHHHHHHHHcCCCeEEC
Confidence 555543 4467888888888766555544
No 77
>cd04897 ACT_ACR_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products have been described (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) and are represented in this CD. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=93.45 E-value=0.71 Score=34.41 Aligned_cols=29 Identities=10% Similarity=0.256 Sum_probs=25.5
Q ss_pred EEEEEEecCCCchHHHHHHHHHhCCceee
Q 023305 187 TSIVFTLDEGPGVLFKALAVFALREINLT 215 (284)
Q Consensus 187 tsi~f~~~~~pGaL~~~L~~F~~~~INLt 215 (284)
|-|-+..+|+||-|+++...|.+.|+++.
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~ 30 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVF 30 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEE
Confidence 34556779999999999999999999987
No 78
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=93.41 E-value=0.44 Score=41.79 Aligned_cols=35 Identities=20% Similarity=0.407 Sum_probs=29.8
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCC
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQR 223 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~ 223 (284)
+.+.-+|+||-++++-+.|+.+|||+..+.++-..
T Consensus 98 v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~ 132 (190)
T PRK11589 98 VQVEVADSPHLIERFTALFDSHHMNIAELVSRTQP 132 (190)
T ss_pred EEEEECCCCCHHHHHHHHHHHcCCChhheEEeeec
Confidence 33444799999999999999999999999999543
No 79
>COG0440 IlvH Acetolactate synthase, small (regulatory) subunit [Amino acid transport and metabolism]
Probab=93.21 E-value=0.52 Score=40.31 Aligned_cols=73 Identities=18% Similarity=0.322 Sum_probs=52.4
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 265 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L 265 (284)
+-.+.+.+.|+||.|.++.+.|+.||.|+-.|---|..... .=.--+-..| ++..+.++.++|
T Consensus 4 ~rilsvlv~ne~GvLsRv~glfsrRG~NIeSltv~~tE~~~---------------~SRiTivv~g--~~~~~EQi~kQL 66 (163)
T COG0440 4 RRILSLLVENEPGVLSRVTGLFSRRGYNIESLTVGPTETPG---------------LSRITIVVSG--DEQVLEQIIKQL 66 (163)
T ss_pred eEEEEEEEECCCCeeehhhHHHHhcCcccceEEEEecCCCC---------------ceEEEEEEcC--CcchHHHHHHHH
Confidence 34556667899999999999999999999988888875432 1122223334 446788888888
Q ss_pred HhcCCceEEE
Q 023305 266 QEFATFLRVL 275 (284)
Q Consensus 266 ~~~~~~vkvL 275 (284)
.+.-.-+|++
T Consensus 67 ~kLidV~kV~ 76 (163)
T COG0440 67 NKLIDVLKVL 76 (163)
T ss_pred HhhccceeEE
Confidence 8876666665
No 80
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=93.00 E-value=0.72 Score=37.52 Aligned_cols=40 Identities=23% Similarity=0.301 Sum_probs=33.7
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCC
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR 225 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~ 225 (284)
+.-+.+..+|+||+|.+++.+|.+++||+--|.-.-.+.+
T Consensus 69 ~dVlaVEmeD~PG~l~~I~~vl~d~diNldYiYAFv~ek~ 108 (142)
T COG4747 69 TDVLAVEMEDVPGGLSRIAEVLGDADINLDYIYAFVTEKQ 108 (142)
T ss_pred eeEEEEEecCCCCcHHHHHHHHhhcCcCceeeeeeeecCc
Confidence 3446678899999999999999999999998887766543
No 81
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=92.64 E-value=0.38 Score=37.12 Aligned_cols=71 Identities=15% Similarity=0.269 Sum_probs=49.6
Q ss_pred EEEEe--cCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecC-CCcHHHHH-HHHH
Q 023305 189 IVFTL--DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEAS-MADPRAQN-ALGH 264 (284)
Q Consensus 189 i~f~~--~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~-~~d~~~~~-al~~ 264 (284)
.++++ +|+||-.+.+-++|+.+|+|+..|+---.++ .+...++||+... .+-..+++ +-++
T Consensus 4 avITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~---------------~ftm~~lV~~~~~~~d~~~lr~~l~~~ 68 (90)
T COG3830 4 AVITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDG---------------FFTMIMLVDISKEVVDFAALRDELAAE 68 (90)
T ss_pred EEEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhh---------------hceeeeEEcCChHhccHHHHHHHHHHH
Confidence 34444 7999999999999999999999998766544 3678899999532 23344554 3334
Q ss_pred HHhcCCceEE
Q 023305 265 LQEFATFLRV 274 (284)
Q Consensus 265 L~~~~~~vkv 274 (284)
.++....|++
T Consensus 69 ~~~lgv~V~v 78 (90)
T COG3830 69 GKKLGVDVRV 78 (90)
T ss_pred HHhcCcEEEE
Confidence 5566666654
No 82
>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=1.5 Score=32.24 Aligned_cols=26 Identities=15% Similarity=0.284 Sum_probs=23.5
Q ss_pred EEecCCCchHHHHHHHHHhCCceeee
Q 023305 191 FTLDEGPGVLFKALAVFALREINLTK 216 (284)
Q Consensus 191 f~~~~~pGaL~~~L~~F~~~~INLt~ 216 (284)
+..+|+||-|+++.++|+.+|+|+..
T Consensus 5 i~~~Dr~gLfa~i~~~l~~~~l~I~~ 30 (76)
T cd04927 5 LFCSDRKGLLHDVTEVLYELELTIER 30 (76)
T ss_pred EEECCCCCHHHHHHHHHHHCCCeEEE
Confidence 45589999999999999999999984
No 83
>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=92.18 E-value=1.3 Score=32.75 Aligned_cols=63 Identities=11% Similarity=0.231 Sum_probs=46.1
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecC-CCcHHHHHHHHHHHhcCCc
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEAS-MADPRAQNALGHLQEFATF 271 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~-~~d~~~~~al~~L~~~~~~ 271 (284)
.++.||.+.++++.|+++|||+-.|-+ +. ..+.|-|+-... ..+..+++++++|++.+ .
T Consensus 11 ~~~~~g~~~~IF~~La~~~I~vDmI~~-s~------------------~~isftv~~~~~~~~~~~~~~l~~el~~~~-~ 70 (75)
T cd04935 11 MWQQVGFLADVFAPFKKHGVSVDLVST-SE------------------TNVTVSLDPDPNGLDPDVLDALLDDLNQIC-R 70 (75)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEe-CC------------------CEEEEEEeCcccccchHHHHHHHHHHHhce-E
Confidence 357899999999999999999999965 11 257787775431 23348889999998854 3
Q ss_pred eEEE
Q 023305 272 LRVL 275 (284)
Q Consensus 272 vkvL 275 (284)
|.++
T Consensus 71 v~~~ 74 (75)
T cd04935 71 VKII 74 (75)
T ss_pred EEEe
Confidence 5443
No 84
>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=92.11 E-value=1.5 Score=33.03 Aligned_cols=65 Identities=20% Similarity=0.189 Sum_probs=44.8
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
.+.|+.|++||+|.+.|+.+.. +-|+|.++=|-..... +. -||-++-. ++.+..+++.|++
T Consensus 3 ~~~v~iPErpGal~~Fl~~l~p-~~~ITeF~YR~~~~~~--------------a~--vlvGi~~~--~~~~~~l~~~l~~ 63 (81)
T cd04907 3 LFRFEFPERPGALKKFLNELLP-KWNITLFHYRNQGSDY--------------GR--VLVGIQVP--DADLDELKERLDA 63 (81)
T ss_pred EEEEEcCCCCCHHHHHHHHhCC-CCeEeEEEEecCCCCc--------------ee--EEEEEEeC--hHHHHHHHHHHHH
Confidence 4678899999999999999943 8899999988754321 22 34444432 2367777788876
Q ss_pred cCCc
Q 023305 268 FATF 271 (284)
Q Consensus 268 ~~~~ 271 (284)
..-.
T Consensus 64 ~g~~ 67 (81)
T cd04907 64 LGYP 67 (81)
T ss_pred cCCC
Confidence 5433
No 85
>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=91.61 E-value=1.6 Score=31.88 Aligned_cols=56 Identities=14% Similarity=0.221 Sum_probs=43.4
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCC-cHHHHHHHHHHHh
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMA-DPRAQNALGHLQE 267 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~-d~~~~~al~~L~~ 267 (284)
+++.||.+.++++.|+++|||+-.+-+.+ -...|.|+-+.... +..++.++++|++
T Consensus 11 l~~~~g~~~~if~~L~~~~I~v~~i~~s~-------------------~~is~~v~~~~~~~~~~~~~~~~~~l~~ 67 (75)
T cd04912 11 MLGAHGFLAKVFEIFAKHGLSVDLISTSE-------------------VSVSLTLDPTKNLSDQLLLDALVKDLSQ 67 (75)
T ss_pred CCCCccHHHHHHHHHHHcCCeEEEEEcCC-------------------cEEEEEEEchhhccchHHHHHHHHHHHh
Confidence 46789999999999999999998886422 25788887644322 3588889999987
No 86
>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=91.44 E-value=1.9 Score=31.78 Aligned_cols=58 Identities=19% Similarity=0.288 Sum_probs=42.3
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHH-HHHHHHHhcC
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQ-NALGHLQEFA 269 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~-~al~~L~~~~ 269 (284)
+++.||.+.++++.|+++|||+-.|-+ +. ..+.|-|+-.-...+..++ .++++|++.+
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 2577877743222234565 7888888744
No 87
>PRK09224 threonine dehydratase; Reviewed
Probab=91.20 E-value=1.5 Score=44.04 Aligned_cols=73 Identities=15% Similarity=0.241 Sum_probs=49.9
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
.+..+.+++|++||+|.+.++.+. +-|+|.++=|-.... +=..+|.++....+..++++++.
T Consensus 327 re~~l~v~iPerPGaL~~f~~~l~--~~nItef~yr~~~~~----------------~a~V~vgie~~~~~~~~~~i~~~ 388 (504)
T PRK09224 327 REALLAVTIPEEPGSFLKFCELLG--GRNVTEFNYRYADAK----------------EAHIFVGVQLSRGQEERAEIIAQ 388 (504)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhc--cCcEEEEEEEecCCC----------------eEEEEEEEEeCChhhHHHHHHHH
Confidence 367888999999999999999999 688898887764321 22344555543222236778888
Q ss_pred HHhcCCceEEE
Q 023305 265 LQEFATFLRVL 275 (284)
Q Consensus 265 L~~~~~~vkvL 275 (284)
|++..-.++.+
T Consensus 389 L~~~gy~~~~l 399 (504)
T PRK09224 389 LRAHGYPVVDL 399 (504)
T ss_pred HHHcCCCeEEC
Confidence 87665544443
No 88
>COG1707 ACT domain-containing protein [General function prediction only]
Probab=91.17 E-value=0.74 Score=39.66 Aligned_cols=61 Identities=20% Similarity=0.256 Sum_probs=45.7
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
|.+...|+||.|.++-.+.+.+|.|+|.....-.+.. ..-..|.++||-.+ ...++++|+.
T Consensus 5 lsi~~enk~GvL~~ltgiiae~ggNIt~~q~~~~~~g---------------~~~~iYmEiEgi~d---~e~l~~~lks 65 (218)
T COG1707 5 LSIIAENKPGVLRDLTGIIAEEGGNITYAQQFLEKDG---------------EKALIYMEIEGIDD---FEKLLERLKS 65 (218)
T ss_pred eEEEeecCccHHHHHHHHHHhcCCceEeeehhhhccC---------------ceEEEEEEeeCCCC---HHHHHHHhhc
Confidence 4455679999999999999999999999888766543 13467889999643 3456666653
No 89
>PRK12483 threonine dehydratase; Reviewed
Probab=91.02 E-value=1.6 Score=44.12 Aligned_cols=72 Identities=17% Similarity=0.187 Sum_probs=51.2
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHH-HHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRA-QNALG 263 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~-~~al~ 263 (284)
.+..+.+.+|++||+|.++++++..+ |++.++=|-... .+-..+|.+|.. +.+.. +++++
T Consensus 344 r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v~v~ie~~-~~~~~~~~i~~ 404 (521)
T PRK12483 344 REAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYRYADA----------------REAHLFVGVQTH-PRHDPRAQLLA 404 (521)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEEecCC----------------CeeEEEEEEEeC-ChhhhHHHHHH
Confidence 47788899999999999999999988 999988875221 123455566553 22344 78888
Q ss_pred HHHhcCCceEEE
Q 023305 264 HLQEFATFLRVL 275 (284)
Q Consensus 264 ~L~~~~~~vkvL 275 (284)
.|++..-.++.+
T Consensus 405 ~l~~~g~~~~dl 416 (521)
T PRK12483 405 SLRAQGFPVLDL 416 (521)
T ss_pred HHHHCCCCeEEC
Confidence 888766555544
No 90
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=90.53 E-value=1.5 Score=40.90 Aligned_cols=64 Identities=8% Similarity=0.201 Sum_probs=45.8
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEee----cCCCcHHHHHHHHH
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFE----ASMADPRAQNALGH 264 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~e----g~~~d~~~~~al~~ 264 (284)
|.+.-+|+||-.+++=+.++++|+|+..+... .... ...|+..++++ ...+...++++|++
T Consensus 12 itv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~-~d~~--------------~~~ffm~i~~~~~~~~~~~~~~l~~~l~~ 76 (289)
T PRK13010 12 LTLACPSAPGIVAAVSGFLAEKGCYIVELTQF-DDDE--------------SGRFFMRVSFHAQSAEAASVDTFRQEFQP 76 (289)
T ss_pred EEEECCCCCCcHHHHHHHHHHCCCCEEecccc-cccc--------------cCcEEEEEEEEcCCCCCCCHHHHHHHHHH
Confidence 44445899999999999999999999998886 2111 13566666665 22334678888877
Q ss_pred HHh
Q 023305 265 LQE 267 (284)
Q Consensus 265 L~~ 267 (284)
+.+
T Consensus 77 l~~ 79 (289)
T PRK13010 77 VAE 79 (289)
T ss_pred HHH
Confidence 754
No 91
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=90.49 E-value=2.1 Score=39.88 Aligned_cols=65 Identities=9% Similarity=0.237 Sum_probs=45.5
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEee--cCCCcHHHHHHHHHH
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFE--ASMADPRAQNALGHL 265 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~e--g~~~d~~~~~al~~L 265 (284)
.+.+.-+|+||-..++-+.|+.+|+|+..+.+.-.... ..|...++++ ...+-..++++|+.+
T Consensus 9 vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~---------------~~F~m~~~~~~p~~~~~~~L~~~L~~l 73 (286)
T PRK13011 9 VLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLS---------------GRFFMRVEFHSEEGLDEDALRAGFAPI 73 (286)
T ss_pred EEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCC---------------CeEEEEEEEecCCCCCHHHHHHHHHHH
Confidence 44455589999999999999999999999999833322 1233344554 223357788888777
Q ss_pred Hh
Q 023305 266 QE 267 (284)
Q Consensus 266 ~~ 267 (284)
.+
T Consensus 74 ~~ 75 (286)
T PRK13011 74 AA 75 (286)
T ss_pred HH
Confidence 54
No 92
>PLN02550 threonine dehydratase
Probab=89.68 E-value=2.1 Score=43.87 Aligned_cols=208 Identities=13% Similarity=0.100 Sum_probs=106.3
Q ss_pred CCCeEEEeeeecccceeeccccccc--cCCeEEEEEEEEee---eeEeeecCCCCcCCccE----EEe---cHHHHHHHH
Q 023305 40 LADKAVLPIENSSSGSIHRNYDLLL--RHRLHIVGEVQLAA---NFCLLALPGIKADQLKR----VLS---HPQALASSD 107 (284)
Q Consensus 40 ~~d~gvvPiENS~~G~V~~t~d~L~--~~~l~I~~E~~l~I---~~~L~~~~~~~l~~i~~----V~S---Hpqal~Qc~ 107 (284)
..|+-|+|+- ..|.+.-....+. ..+++|+|--.-.- ...+...+-..++.+.+ +.. =++.+.-|+
T Consensus 258 ~~D~VvvpVG--gGGLiaGia~~lK~l~p~vkVIGVEp~~a~~~~~s~~~G~~v~~~~~~tiAdGiav~~~G~~t~~i~~ 335 (591)
T PLN02550 258 PLHAIFVPVG--GGGLIAGIAAYVKRVRPEVKIIGVEPSDANAMALSLHHGERVMLDQVGGFADGVAVKEVGEETFRLCR 335 (591)
T ss_pred CCCEEEEEeC--hhHHHHHHHHHHHHhCCCCEEEEEEECCChHHHHHHhcCCccccCCCCCccceeecCCCCHHHHHHHH
Confidence 5899999986 3454444444433 34677776544221 11111111111122211 111 134555555
Q ss_pred HHHHhcCCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeeccccCCCCCeeEEEEEee-CCCCC-------
Q 023305 108 IVLTQLGVARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLAR-DPIIP------- 179 (284)
Q Consensus 108 ~fl~~~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~d~~~N~TRF~vl~~-~~~~~------- 179 (284)
+++.. +-.+......+|.+.+.+.. + .-+-+..|+-+.+|.-..+... .+ +.+=-++++- .-...
T Consensus 336 ~~vD~--vV~Vsd~eI~~Ai~~l~e~~-g--ivvEpAGA~alAall~~~~~~~-~~-g~~Vv~vlsGgNid~~~l~~v~~ 408 (591)
T PLN02550 336 ELVDG--VVLVSRDAICASIKDMFEEK-R--SILEPAGALALAGAEAYCKYYG-LK-DENVVAITSGANMNFDRLRIVTE 408 (591)
T ss_pred hhCCE--EEEECHHHHHHHHHHHHHHC-C--CEEeHHHHHHHHHHHHHHHhcC-CC-CCeEEEEecCCCCCHHHHHHHHH
Confidence 54432 22334445677777777642 1 2233334444555443322111 11 2222223322 21110
Q ss_pred --CCCCCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHH
Q 023305 180 --RTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPR 257 (284)
Q Consensus 180 --~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~ 257 (284)
......+..+.+.++++||+|.++++++... |++.|+=|-... .+-..+|.+|.. +...
T Consensus 409 ~~~~~~~r~~~~~v~ipd~pG~l~~~~~~l~~~--ni~~~~~~~~~~----------------~~~~v~v~ie~~-~~~~ 469 (591)
T PLN02550 409 LADVGRQQEAVLATFMPEEPGSFKRFCELVGPM--NITEFKYRYSSE----------------KEALVLYSVGVH-TEQE 469 (591)
T ss_pred HHHhccCCEEEEEEEcCCCCCHHHHHHHHhhhh--cceEEEEEecCC----------------CceEEEEEEEeC-CHHH
Confidence 0011235678889999999999999999986 999998876321 233455566554 4567
Q ss_pred HHHHHHHHHhcCCceEEE
Q 023305 258 AQNALGHLQEFATFLRVL 275 (284)
Q Consensus 258 ~~~al~~L~~~~~~vkvL 275 (284)
++++++.|++..-.++.|
T Consensus 470 ~~~i~~~l~~~g~~~~~l 487 (591)
T PLN02550 470 LQALKKRMESAQLRTVNL 487 (591)
T ss_pred HHHHHHHHHHCCCCeEeC
Confidence 888899998765554443
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=89.31 E-value=4.2 Score=29.59 Aligned_cols=32 Identities=28% Similarity=0.351 Sum_probs=26.3
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeee
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESR 220 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSR 220 (284)
|-+..+|+||-|+++-.+|+.+|+|+..-...
T Consensus 3 ~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~ 34 (74)
T cd04925 3 IELTGTDRPGLLSEVFAVLADLHCNVVEARAW 34 (74)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCCcEEEEEEE
Confidence 44556899999999999999999999854333
No 94
>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=89.01 E-value=2.1 Score=31.42 Aligned_cols=55 Identities=16% Similarity=0.265 Sum_probs=43.1
Q ss_pred CCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcC
Q 023305 195 EGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFA 269 (284)
Q Consensus 195 ~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~ 269 (284)
..||.+.++++.|+++|||+-.|-+-. .++.|-|+-.. ..++.+++++++|++.+
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 479999999999999999999996611 35888887643 33358899999998843
No 95
>PRK06349 homoserine dehydrogenase; Provisional
Probab=88.96 E-value=1.8 Score=42.43 Aligned_cols=63 Identities=19% Similarity=0.286 Sum_probs=45.7
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
|.+.+.|+||.|.++-+.|++++||+..+...+.... ..+..+.++- ..+..+++++++|++.
T Consensus 351 lRl~v~d~pGvLa~I~~~f~~~~vsI~si~q~~~~~~--------------~~~ivivT~~---~~e~~l~~~i~~L~~l 413 (426)
T PRK06349 351 LRLLVADKPGVLAKIAAIFAENGISIESILQKGAGGE--------------GAEIVIVTHE---TSEAALRAALAAIEAL 413 (426)
T ss_pred EEEEecCCcchHHHHHHHHhhcCccEEEEEeccCCCC--------------ceeEEEEEEe---CCHHHHHHHHHHHhcC
Confidence 4455679999999999999999999998887764321 1234444442 2357899999998864
No 96
>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=88.60 E-value=3.4 Score=27.55 Aligned_cols=30 Identities=27% Similarity=0.335 Sum_probs=25.8
Q ss_pred EecCCCchHHHHHHHHHhCCceeeeeeeee
Q 023305 192 TLDEGPGVLFKALAVFALREINLTKIESRP 221 (284)
Q Consensus 192 ~~~~~pGaL~~~L~~F~~~~INLt~IeSRP 221 (284)
..++.||.+.++++.|+++|||+-.|..-+
T Consensus 7 ~~~~~~~~~~~i~~~L~~~~i~i~~i~~~~ 36 (61)
T cd04891 7 GVPDKPGVAAKIFSALAEAGINVDMIVQSV 36 (61)
T ss_pred cCCCCCcHHHHHHHHHHHcCCcEEEEEEcC
Confidence 357889999999999999999998876544
No 97
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=88.14 E-value=4.9 Score=42.11 Aligned_cols=70 Identities=11% Similarity=0.174 Sum_probs=51.3
Q ss_pred CceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHH
Q 023305 184 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 263 (284)
Q Consensus 184 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~ 263 (284)
...+.|.+...|++|.|.++...++..++|+.++.++..+.. ...-.|-|++. +-..+..++.
T Consensus 624 ~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~--------------~~~~~~~ieV~---~~~~L~~i~~ 686 (702)
T PRK11092 624 EFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGR--------------VYSAFIRLTAR---DRVHLANIMR 686 (702)
T ss_pred eeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCC--------------EEEEEEEEEEC---CHHHHHHHHH
Confidence 356788888899999999999999999999999998754321 12223334443 3368888999
Q ss_pred HHHhcCC
Q 023305 264 HLQEFAT 270 (284)
Q Consensus 264 ~L~~~~~ 270 (284)
.|+..-.
T Consensus 687 ~Lr~i~~ 693 (702)
T PRK11092 687 KIRVMPD 693 (702)
T ss_pred HHhCCCC
Confidence 9886543
No 98
>PRK11151 DNA-binding transcriptional regulator OxyR; Provisional
Probab=87.89 E-value=16 Score=33.14 Aligned_cols=122 Identities=13% Similarity=0.084 Sum_probs=66.7
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc-
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 94 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~- 94 (284)
.+|+.++.... +.+++++++.+|++|+||++......+-. ...|.+.++.++. +-+|-+...+..+++|+.
T Consensus 116 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~---~~~l~~~~~~~~~----~~~hpl~~~~~i~~~~L~~ 188 (305)
T PRK11151 116 TFPKLEMYLHEAQTHQLLAQLDSGKLDCAILALVKESEAFI---EVPLFDEPMLLAV----YEDHPWANRDRVPMSDLAG 188 (305)
T ss_pred HCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCeE---EEEeccCcEEEEe----cCCCCcccCCccCHHHhcC
Confidence 45777665443 68999999999999999987654433321 1223333444332 333434332222333332
Q ss_pred -EEEecHHH---HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 -RVLSHPQA---LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 -~V~SHpqa---l~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
..++++.. ..+...|+...+. . ...++|...+.++++.+ ...+|.+...+.
T Consensus 189 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~ilp~~~~~ 246 (305)
T PRK11151 189 EKLLMLEDGHCLRDQAMGFCFEAGADEDTHFRATSLETLRNMVAAG---SGITLLPALAVP 246 (305)
T ss_pred CCeEeecCCccHHHHHHHHHHHCCCCCCceEEeccHHHHHHHHHcC---CCEEEeeHHhhh
Confidence 12222221 2344455555432 2 35677777778888764 347788777664
No 99
>PRK06545 prephenate dehydrogenase; Validated
Probab=86.82 E-value=1.7 Score=41.54 Aligned_cols=40 Identities=15% Similarity=0.310 Sum_probs=35.1
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCC
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKR 225 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~ 225 (284)
-..+.+.++|+||.|.+++..+...|||+..|+-.-++..
T Consensus 290 ~~~~~v~v~d~pg~~~~~~~~~~~~~i~i~~~~i~~~~~~ 329 (359)
T PRK06545 290 FYDLYVDVPDEPGVIARVTAILGEEGISIENLRILEARED 329 (359)
T ss_pred ceEEEEeCCCCCCHHHHHHHHHHHcCCCeecceeeeccCC
Confidence 3568888999999999999999999999999988777654
No 100
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=86.81 E-value=7.9 Score=40.47 Aligned_cols=70 Identities=16% Similarity=0.245 Sum_probs=54.5
Q ss_pred CceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHH
Q 023305 184 LFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALG 263 (284)
Q Consensus 184 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~ 263 (284)
.....|.+...|++|.|.++++++++.++|+.++.++....+ .+.+.++++-+ +-..+..++.
T Consensus 625 ~f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~~----------------~~~~~~~i~v~-n~~~L~~i~~ 687 (701)
T COG0317 625 VYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQ----------------FATMQFTIEVK-NLNHLGRVLA 687 (701)
T ss_pred ceEEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCCc----------------eEEEEEEEEEC-cHHHHHHHHH
Confidence 457788888899999999999999999999999999987332 35555566543 3467888888
Q ss_pred HHHhcCC
Q 023305 264 HLQEFAT 270 (284)
Q Consensus 264 ~L~~~~~ 270 (284)
.|+....
T Consensus 688 ~l~~~~~ 694 (701)
T COG0317 688 RLKQLPD 694 (701)
T ss_pred HHhcCCC
Confidence 8876544
No 101
>PRK11790 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=86.81 E-value=2.1 Score=41.78 Aligned_cols=63 Identities=24% Similarity=0.336 Sum_probs=45.1
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCcccee-EEEEEeecCCCcHHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDY-LFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y-~F~id~eg~~~d~~~~~al~~ 264 (284)
.-+|++.-+|+||.+.+++++++++|||+-.+..+... ++ +..||+++... + +++++
T Consensus 338 ~~rlii~h~d~pG~ia~it~~l~~~~iNI~~m~~~~~~------------------~~A~~iie~D~~~~-~---~~~~~ 395 (409)
T PRK11790 338 GHRLLHIHENRPGVLAAINQIFAEQGINIAAQYLQTDG------------------EIGYVVIDVDADYA-E---EALDA 395 (409)
T ss_pred CceEEEEeCCCCCHHHHHHHHHHhcCCCHHHheeccCC------------------CEEEEEEEeCCCCc-H---HHHHH
Confidence 45677778899999999999999999999877664322 23 33449988543 3 45566
Q ss_pred HHhcCC
Q 023305 265 LQEFAT 270 (284)
Q Consensus 265 L~~~~~ 270 (284)
|++.-.
T Consensus 396 i~~i~~ 401 (409)
T PRK11790 396 LKAIPG 401 (409)
T ss_pred HHcCCC
Confidence 665433
No 102
>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=86.37 E-value=7 Score=32.83 Aligned_cols=43 Identities=23% Similarity=0.261 Sum_probs=35.6
Q ss_pred CCCcHHHHHHHhhCC-CCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKAYP-KCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~-~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
..|++......+.++ +.+++.+.|.++++++|.+|++|+.+++
T Consensus 116 ~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~i~~ 159 (225)
T PF00497_consen 116 VRGSSYADYLKQQYPSNINIVEVDSPEEALEALLSGRIDAFIVD 159 (225)
T ss_dssp ETTSHHHHHHHHHTHHTSEEEEESSHHHHHHHHHTTSSSEEEEE
T ss_pred ccchhHHHHhhhhccchhhhcccccHHHHHHHHhcCCeeeeecc
Confidence 457776666666665 7888999999999999999999999886
No 103
>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=86.28 E-value=2.2 Score=32.74 Aligned_cols=67 Identities=18% Similarity=0.229 Sum_probs=43.2
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
.+..+.|++|++||+|.+.|+.+..++ |+|.++=|-..... ..-..=|++. +....+.+++.
T Consensus 9 ~E~~~~v~~PE~pGal~~F~~~l~~~~-nITeF~YR~~~~~~--------------a~vlvgi~v~---~~~~~~~l~~~ 70 (91)
T PF00585_consen 9 REALFAVEFPERPGALKRFLDALGPRN-NITEFHYRYSGDDF--------------ARVLVGIEVP---DAEDLEELIER 70 (91)
T ss_dssp -EEEEEEE--BSTTHCHHHHHCCSSSE--EEEEEEE-TTTSC--------------SEEEEEEE-S---STHHHHHHHHH
T ss_pred CEEEEEEECCCCccHHHHHHHHhCCCc-eEEEEEEcCCCCCe--------------eeEEEEEEeC---CHHHHHHHHHH
Confidence 467788999999999999999997665 58988888765431 2333334443 23457788888
Q ss_pred HHhcC
Q 023305 265 LQEFA 269 (284)
Q Consensus 265 L~~~~ 269 (284)
|++..
T Consensus 71 L~~~g 75 (91)
T PF00585_consen 71 LKALG 75 (91)
T ss_dssp HTSSS
T ss_pred HHHcC
Confidence 87654
No 104
>cd08445 PBP2_BenM_CatM_CatR The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in benzoate catabolism; contains the type 2 periplasmic binding fold. This CD includes the C-terminal of LysR-type transcription regulators, BenM, CatM, and CatR, which are involved in the benzoate catabolism. The BenM and CatM are paralogs with overlapping functions. BenM responds synergistically to two effectors, benzoate and cis,cis-muconate, to activate expression of the benABCDE operon which is involved in benzoate catabolism, while CatM responses only to muconate. BenM and CatM share high protein sequence identity and bind to the operator-promoter regions that have similar DNA sequences. In Pseudomonas species, phenolic compounds are converted by different enzymes to central intermediates, such as protocatechuate and catechols. Generally, unsubstituted compounds, such as benzoate, are metabolized by an ortho-cleavage pathway. The catBCA operon encodes three enzymes
Probab=85.54 E-value=19 Score=29.53 Aligned_cols=121 Identities=16% Similarity=0.107 Sum_probs=60.7
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecC-CCCcCCc-
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALP-GIKADQL- 93 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~-~~~l~~i- 93 (284)
.+|+.++.... +-.++.+.+.+|++|+|+........+... ..|.+.++.++ .+-+|-|.... ..+++|+
T Consensus 26 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~---~~l~~~~~~~v----~~~~hpl~~~~~~i~~~dL~ 98 (203)
T cd08445 26 AAPDVEIELIEMTTVQQIEALKEGRIDVGFGRLRIEDPAIRR---IVLREEPLVVA----LPAGHPLAQEKAPLTLAQLA 98 (203)
T ss_pred HCCCeEEEEEeCChHHHHHHHHcCCCcEEEecCCCCCCCcee---EEEEeccEEEE----eeCCCCCccCCCCcCHHHhc
Confidence 35666654443 478999999999999999643211111111 11222233322 23334343322 2233333
Q ss_pred --cEEEecHH---H-HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHH
Q 023305 94 --KRVLSHPQ---A-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAA 147 (284)
Q Consensus 94 --~~V~SHpq---a-l~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 147 (284)
.-|.-... . ..+...|+.+.+. + ...++|...+.++++.+ ...++.+...+
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 158 (203)
T cd08445 99 DEPLILYPASPRPSFADQVLSLFRDHGLRPRVIQEVRELQTALGLVAAG---EGVTLVPASVQ 158 (203)
T ss_pred CCCEEecCcccChhHHHHHHHHHHHcCCCCceecccCCHHHHHHHHHcC---CCeEEehHHhh
Confidence 33331111 1 2345556666543 2 34566777777777765 24677776544
No 105
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=85.29 E-value=5.5 Score=37.03 Aligned_cols=35 Identities=17% Similarity=0.218 Sum_probs=29.2
Q ss_pred EEEEEEe--cCCCchHHHHHHHHHhCCceeeeeeeee
Q 023305 187 TSIVFTL--DEGPGVLFKALAVFALREINLTKIESRP 221 (284)
Q Consensus 187 tsi~f~~--~~~pGaL~~~L~~F~~~~INLt~IeSRP 221 (284)
+.+++++ +|+||-..++-+.|+.+|+|+..+.+.=
T Consensus 5 ~~~vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~ 41 (286)
T PRK06027 5 QRYVLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFV 41 (286)
T ss_pred ceEEEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEE
Confidence 3444444 8999999999999999999999888765
No 106
>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=84.55 E-value=20 Score=29.18 Aligned_cols=122 Identities=9% Similarity=0.005 Sum_probs=61.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcC---C
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD---Q 92 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~---~ 92 (284)
.+|+.++.-. .+..++.+.+.+|++|+|++.-.....|.. ...|.+.++.+ ..+-.|-+......+++ +
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~l----v~~~~hpl~~~~~~~~~~L~~ 97 (197)
T cd08452 25 KFPSVKVELRELSSPDQVEELLKGRIDIGFLHPPIQHTALH---IETVQSSPCVL----ALPKQHPLASKEEITIEDLRD 97 (197)
T ss_pred HCCCcEEEEEecChHHHHHHHHCCCccEEEeeCCCCCCCee---EEEeeeccEEE----EEeCCCccccCCCCCHHHhcC
Confidence 4677665433 467889999999999999985221111111 11122222222 22334444322212222 3
Q ss_pred ccEEEecHH----HHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 93 LKRVLSHPQ----ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 93 i~~V~SHpq----al~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
..-|...+. ...+...|+.+.+.. . ..+++...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 157 (197)
T cd08452 98 EPIITVAREAWPTLYDEIIQLCEQAGFRPKIVQEATEYQTVIGLVSAG---IGVTFVPSSAKK 157 (197)
T ss_pred CCEEeccCCcchhHHHHHHHHHHHcCCCccceeecccHHHHHHHHHcC---CCEEEchHHHhh
Confidence 333332211 233444566665432 2 3466677777777764 236677766543
No 107
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=83.97 E-value=6.4 Score=41.47 Aligned_cols=69 Identities=17% Similarity=0.259 Sum_probs=50.2
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
..+.|.+...|++|.|.++.++++..++|+..+.++..+... ...-.|-|++. +-..+..++..
T Consensus 665 ~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~~-------------~~~~~~~ieV~---~~~~L~~l~~~ 728 (743)
T PRK10872 665 YSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQQ-------------LATIDMTIEIY---NLQVLGRVLGK 728 (743)
T ss_pred eEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCC-------------EEEEEEEEEEC---CHHHHHHHHHH
Confidence 355677888999999999999999999999999987654221 12234445553 33678888888
Q ss_pred HHhcC
Q 023305 265 LQEFA 269 (284)
Q Consensus 265 L~~~~ 269 (284)
|+..-
T Consensus 729 L~~i~ 733 (743)
T PRK10872 729 LNQVP 733 (743)
T ss_pred HhcCC
Confidence 87643
No 108
>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=83.64 E-value=8.5 Score=40.20 Aligned_cols=68 Identities=15% Similarity=0.162 Sum_probs=50.0
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
..+.|.+...|++|.|.++.+.++..++|+..+.++-... ....+-++++-. +-..+..++..
T Consensus 609 f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~----------------~~~~~~~~ieV~-~~~~L~~ii~~ 671 (683)
T TIGR00691 609 FIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGK----------------REAILNITVEIK-NYKHLLKIMLK 671 (683)
T ss_pred eEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCC----------------CEEEEEEEEEEC-CHHHHHHHHHH
Confidence 4667888889999999999999999999999999865321 123333444332 34688888888
Q ss_pred HHhcC
Q 023305 265 LQEFA 269 (284)
Q Consensus 265 L~~~~ 269 (284)
|+...
T Consensus 672 L~~i~ 676 (683)
T TIGR00691 672 IKTKN 676 (683)
T ss_pred HhCCC
Confidence 88653
No 109
>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=83.27 E-value=7.3 Score=41.57 Aligned_cols=50 Identities=12% Similarity=0.161 Sum_probs=40.8
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEe
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDF 249 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~ 249 (284)
..|.+-+..+|+||-|+++.++|+.+|||+......-...+ ..-.|||..
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 46888889999999999999999999999996666654332 357899965
No 110
>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=82.84 E-value=6.4 Score=27.43 Aligned_cols=27 Identities=30% Similarity=0.407 Sum_probs=23.8
Q ss_pred EecCCCchHHHHHHHHHhCCceeeeee
Q 023305 192 TLDEGPGVLFKALAVFALREINLTKIE 218 (284)
Q Consensus 192 ~~~~~pGaL~~~L~~F~~~~INLt~Ie 218 (284)
.+++.||.+.++++.+++.|||+.-|-
T Consensus 8 ~~~~~~g~~~~i~~~L~~~~I~i~~i~ 34 (75)
T cd04913 8 GVPDKPGVAAKIFGALAEANINVDMIV 34 (75)
T ss_pred CCCCCCcHHHHHHHHHHHcCCeEEEEE
Confidence 457899999999999999999998664
No 111
>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=82.76 E-value=24 Score=28.62 Aligned_cols=122 Identities=12% Similarity=0.081 Sum_probs=62.1
Q ss_pred CCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeec--ccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc-
Q 023305 18 YPKCETVPCD-EFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 93 (284)
Q Consensus 18 f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS--~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i- 93 (284)
+|+.++.... +..+..+++.+|++|+|+..-... ....+ ....|.+.++.+ ..+-.|-+...+..+++++
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 5666654443 567889999999999999753211 01100 112223334433 2233343433222233333
Q ss_pred --cEEEec-H---HHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 --KRVLSH-P---QALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 --~~V~SH-p---qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|... . .....+..|+++.+.. . ..++|...+.++++.+ ...++.++..++
T Consensus 100 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08453 100 AEPLVIFPRRIAPAFHDAVTGYYRAAGQTPRIAQEAIQMQTIISLVSAG---MGVALVPASLRN 160 (200)
T ss_pred cCCEEeccCCcCCcHHHHHHHHHHHcCCCCceeeccccHHHHHHHHHcC---CcEEEeEhHHhh
Confidence 333322 1 1234567788776543 2 3455666666667664 246677765543
No 112
>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=82.22 E-value=6.4 Score=34.77 Aligned_cols=55 Identities=18% Similarity=0.270 Sum_probs=42.5
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIE-SRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADP 256 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~Ie-SRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~ 256 (284)
-..|++.-.|+||.+.++-+.|.+++||+..+. +|-.++ .+=+-.|.++....++
T Consensus 148 g~~L~~~~~D~PG~Ig~vg~~Lg~~~iNIa~m~v~r~~~g----------------~~Ai~vl~vD~~v~~~ 203 (208)
T TIGR00719 148 HPAILLEHNDKFGTIAGVANLLAGFEINIEHLETAKKDIG----------------NIALLTIEIDKNIDDH 203 (208)
T ss_pred ccEEEEEeCCCCChHHHHHHHHHhCCccEEEEEEEecCCC----------------CEEEEEEEeCCCCCHH
Confidence 456788889999999999999999999997664 443222 3567888998876654
No 113
>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=81.17 E-value=27 Score=28.20 Aligned_cols=123 Identities=15% Similarity=0.114 Sum_probs=63.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc--
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 93 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i-- 93 (284)
.+|+.++.-. .+..++++.+.+|++|+|+..-.....+. ....|.+.++.++. +-.|-+......+++++
T Consensus 26 ~~P~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~pl~~~~~~~~~~l~~ 98 (200)
T cd08411 26 AYPKLRLYLREDQTERLLEKLRSGELDAALLALPVDEPGL---EEEPLFDEPFLLAV----PKDHPLAKRKSVTPEDLAG 98 (200)
T ss_pred HCCCcEEEEEeCcHHHHHHHHHcCCccEEEEeccCCCCCc---eEEEeeccceEEEe----cCCCCccccCccCHHHHcC
Confidence 3566655443 46788999999999999997533221111 11222233333322 22232222111222222
Q ss_pred -cEEE-ec-HHHHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 94 -KRVL-SH-PQALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 94 -~~V~-SH-pqal~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
.-|. +. .....+...|+.+.+. . ...++|...+.++++.+ ...|+.+...++.
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 157 (200)
T cd08411 99 ERLLLLEEGHCLRDQALELCRLAGAREQTDFEATSLETLRQMVAAG---LGITLLPELAVPS 157 (200)
T ss_pred CceEecCCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CCEEEeCHHHhcc
Confidence 2222 11 1123344556655543 2 35667778888888875 2477888776664
No 114
>PRK05092 PII uridylyl-transferase; Provisional
Probab=81.03 E-value=8.9 Score=41.45 Aligned_cols=52 Identities=17% Similarity=0.228 Sum_probs=39.6
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEE-EeecC
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYI-DFEAS 252 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~i-d~eg~ 252 (284)
.|.|.+..+|+||-|+++.++|+..|||+..-...-... ...-.||| |-+|.
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 577778889999999999999999999999555543222 24568999 44554
No 115
>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=79.68 E-value=7.4 Score=26.78 Aligned_cols=51 Identities=18% Similarity=0.250 Sum_probs=37.5
Q ss_pred cCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHH
Q 023305 194 DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 265 (284)
Q Consensus 194 ~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L 265 (284)
.+.||...++++.|++++||+-.|.+ +. ....|+|+-.-. +..+++++++|
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 46799999999999999999999955 11 358888876321 24666666655
No 116
>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=79.64 E-value=12 Score=34.68 Aligned_cols=64 Identities=11% Similarity=0.244 Sum_probs=43.5
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecC---CCcHHHHHHHHH-
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEAS---MADPRAQNALGH- 264 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~---~~d~~~~~al~~- 264 (284)
|.+.-+|+||-.+++-+.++++|+|++.+...=.... ..|.-.++++.. .+...+++++++
T Consensus 3 itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~---------------~~F~mr~~v~~~~~~~~~~~l~~~l~~~ 67 (280)
T TIGR00655 3 LLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPET---------------GRFFMRVEFQLEGFRLEESSLLAAFKSA 67 (280)
T ss_pred EEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCC---------------CeEEEEEEEEeCCCCCCHHHHHHHHHHH
Confidence 4456699999999999999999999998877654221 122222344432 334678888877
Q ss_pred HHh
Q 023305 265 LQE 267 (284)
Q Consensus 265 L~~ 267 (284)
+.+
T Consensus 68 ~~~ 70 (280)
T TIGR00655 68 LAE 70 (280)
T ss_pred HHH
Confidence 654
No 117
>cd08417 PBP2_Nitroaromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators that involved in the catabolism of nitroaromatic/naphthalene compounds and that of related regulators; contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of dinitrotoluene and similar compounds, such as DntR, NahR, and LinR. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. Also included are related LysR-type regulators clustered together in phylogenetic trees, including NodD, ToxR, LeuO, SyrM, TdcA, and PnbR. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrate
Probab=79.26 E-value=31 Score=27.75 Aligned_cols=121 Identities=21% Similarity=0.135 Sum_probs=65.2
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCccE-
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR- 95 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~~- 95 (284)
+|+.++.. ..+-.++.+.+.+|++|+|+..-.+...+. ....|.+.++.++. +-.|-+.. +..+++++..
T Consensus 26 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~~~~~-~~~~~~~L~~~ 97 (200)
T cd08417 26 APGVRLRFVPLDRDDLEEALESGEIDLAIGVFPELPPGL---RSQPLFEDRFVCVA----RKDHPLAG-GPLTLEDYLAA 97 (200)
T ss_pred CCCeEEEeccCCHHHHHHHHHcCCCCEEEeecccCCCcc---chhhhhcCceEEEe----cCCCcccc-cccCHHHHhCC
Confidence 46655533 345678999999999999998644322111 11223344454443 33343332 2233444432
Q ss_pred --E-EecHH-HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 96 --V-LSHPQ-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 96 --V-~SHpq-al~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
| +.+.. .......|+++.+.. ...+++...+.+++..+ ...++.+...++.
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08417 98 PHVLVSPRGRGHGLVDDALAELGLSRRVALTVPHFLAAPALVAGT---DLIATVPRRLAEA 155 (200)
T ss_pred CeEEeccccchHHHHHHHHHHcCcccceEEeeCcHHHHHHHHhcC---CeeeeccHHHHHh
Confidence 2 33322 233456677766542 34566677777777765 3467777766653
No 118
>PRK13581 D-3-phosphoglycerate dehydrogenase; Provisional
Probab=78.80 E-value=7.9 Score=39.04 Aligned_cols=104 Identities=16% Similarity=0.216 Sum_probs=66.9
Q ss_pred hhHHHhcCCceeeccc--cCCCCCeeEEEEEeeCCCCC-----CCC---------------CCceEEEEEEecCCCchHH
Q 023305 144 ARAAEIYGLNILADRI--QDEPDNITRFLVLARDPIIP-----RTD---------------KLFKTSIVFTLDEGPGVLF 201 (284)
Q Consensus 144 ~~aa~~ygL~il~~~I--~d~~~N~TRF~vl~~~~~~~-----~~~---------------~~~ktsi~f~~~~~pGaL~ 201 (284)
..-|+..|+++-.... .+.-.|.-++.+-+...... ..+ .....++++...|+||.+.
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 4568888888755433 33346776776654332100 000 1234567777789999999
Q ss_pred HHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 202 KALAVFALREINLTKIE-SRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 202 ~~L~~F~~~~INLt~Ie-SRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
++.+.|..++||+.... +|-.++ .+....++++....+ +++++|++
T Consensus 468 ~v~~~L~~~~iNIa~m~~~r~~~g----------------~~al~~i~~D~~v~~----~~l~~i~~ 514 (526)
T PRK13581 468 KVGTLLGEAGINIAGMQLGRREAG----------------GEALMVLSVDDPVPE----EVLEELRA 514 (526)
T ss_pred HHHHHHhhcCCCchhcEeccCCCC----------------CeEEEEEECCCCCCH----HHHHHHhc
Confidence 99999999999998765 453222 467888899887653 35555554
No 119
>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=78.58 E-value=17 Score=26.54 Aligned_cols=34 Identities=15% Similarity=0.269 Sum_probs=27.7
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeC
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 222 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~ 222 (284)
+.+..+|+||-+.++-.+|+.+|+|+..=....+
T Consensus 4 I~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt 37 (68)
T cd04928 4 ITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFST 37 (68)
T ss_pred EEEEECCCcchHHHHHHHHHHCCCceEEEEEEEc
Confidence 5566689999999999999999999985444443
No 120
>KOG2663 consensus Acetolactate synthase, small subunit [Amino acid transport and metabolism]
Probab=78.21 E-value=8.1 Score=35.51 Aligned_cols=72 Identities=21% Similarity=0.278 Sum_probs=52.1
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEE--EEEeecCCCcHHHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLF--YIDFEASMADPRAQNALG 263 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F--~id~eg~~~d~~~~~al~ 263 (284)
+-.|-.-+.|+||.|.++=.+|+.||.|+-.+----... +-.| =|=+.| .|.-++++.+
T Consensus 77 rHvinclVqnEpGvlsRisGvlAaRGfNIdSLvVc~tev-----------------k~LsrmTIVl~G--td~VveQa~r 137 (309)
T KOG2663|consen 77 RHVINCLVQNEPGVLSRISGVLAARGFNIDSLVVCLTEV-----------------KALSRMTIVLQG--TDGVVEQARR 137 (309)
T ss_pred ceeEEEEecCCchHHHHHHHHHHhccCCchheeeechhh-----------------hhhhhceEEEec--cHHHHHHHHH
Confidence 455666678999999999999999999985443333222 2233 455566 5788999999
Q ss_pred HHHhcCCceEEEc
Q 023305 264 HLQEFATFLRVLG 276 (284)
Q Consensus 264 ~L~~~~~~vkvLG 276 (284)
+|++...-++++.
T Consensus 138 QiedlVnV~aVlD 150 (309)
T KOG2663|consen 138 QIEDLVNVYAVLD 150 (309)
T ss_pred HHHHhhhhheeee
Confidence 9998877666664
No 121
>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=77.99 E-value=10 Score=28.34 Aligned_cols=58 Identities=14% Similarity=0.170 Sum_probs=40.6
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCC----CcHHHHHHHHHHHhc
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASM----ADPRAQNALGHLQEF 268 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~----~d~~~~~al~~L~~~ 268 (284)
.++.||.+.++++.|+++|||+-.|.+-. ..+.|-|+-+... -+..++++.++|++.
T Consensus 11 ~~~~~g~~a~IF~~La~~~InVDmI~qs~-------------------~sISftV~~sd~~~~~~~~~~l~~~~~~~~~~ 71 (78)
T cd04933 11 MLGQYGFLAKVFSIFETLGISVDVVATSE-------------------VSISLTLDPSKLWSRELIQQELDHVVEELEKD 71 (78)
T ss_pred CCCccCHHHHHHHHHHHcCCcEEEEEecC-------------------CEEEEEEEhhhhhhhhhHHHHHHHHHHHHHHc
Confidence 36789999999999999999999996511 2577888753210 013566666777665
Q ss_pred C
Q 023305 269 A 269 (284)
Q Consensus 269 ~ 269 (284)
+
T Consensus 72 ~ 72 (78)
T cd04933 72 A 72 (78)
T ss_pred C
Confidence 4
No 122
>PRK05007 PII uridylyl-transferase; Provisional
Probab=77.91 E-value=6.2 Score=42.41 Aligned_cols=31 Identities=23% Similarity=0.296 Sum_probs=28.6
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceee
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLT 215 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt 215 (284)
..|.|-+..+|+||-|+++.++|...||++.
T Consensus 807 ~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~ 837 (884)
T PRK05007 807 RRSYMELIALDQPGLLARVGKIFADLGISLH 837 (884)
T ss_pred CeEEEEEEeCCchHHHHHHHHHHHHCCcEEE
Confidence 4678888899999999999999999999997
No 123
>PRK15007 putative ABC transporter arginine-biding protein; Provisional
Probab=77.82 E-value=4.7 Score=35.19 Aligned_cols=43 Identities=16% Similarity=0.198 Sum_probs=35.6
Q ss_pred CCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
+.|++......+.+++.+.+++++..+++.+|.+|++|..+.+
T Consensus 132 ~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~L~~grvDa~i~~ 174 (243)
T PRK15007 132 QNGTTHQKFIMDKHPEITTVPYDSYQNAKLDLQNGRIDAVFGD 174 (243)
T ss_pred ecCcHHHHHHHHhCCCCeEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 3577766666666778888999999999999999999999875
No 124
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=77.65 E-value=11 Score=32.91 Aligned_cols=37 Identities=19% Similarity=0.231 Sum_probs=31.1
Q ss_pred eEEEEEEe--cCCCchHHHHHHHHHhCCceeeeeeeeeCCC
Q 023305 186 KTSIVFTL--DEGPGVLFKALAVFALREINLTKIESRPQRK 224 (284)
Q Consensus 186 ktsi~f~~--~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~ 224 (284)
++.+++++ +|+||-.+++-+.++.+|.|+. +||-..-
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 46677776 8999999999999999999997 7777653
No 125
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=77.35 E-value=2.7 Score=46.02 Aligned_cols=43 Identities=9% Similarity=0.167 Sum_probs=39.5
Q ss_pred CCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
+.|++.+...++.+|+.+++.++|..+++++|.+|++|..|..
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 6788888888899999999999999999999999999988775
No 126
>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=76.96 E-value=38 Score=27.59 Aligned_cols=122 Identities=17% Similarity=0.105 Sum_probs=59.0
Q ss_pred hCCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc--
Q 023305 17 AYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK-- 94 (284)
Q Consensus 17 ~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~-- 94 (284)
.+|+.++.....-.+.++.+.+|++|+|+++-.....+.. ..-|.+.++.++ .+-+|-+.. ...+++++.
T Consensus 25 ~~P~i~l~i~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~hpl~~-~~~~~~~l~~~ 96 (200)
T cd08462 25 EAPGVRFELLPPDDQPHELLERGEVDLLIAPERFMSDGHP---SEPLFEEEFVCV----VWADNPLVG-GELTAEQYFSA 96 (200)
T ss_pred HCCCCEEEEecCChhHHHHHhcCCeeEEEecCCCCCCCce---eeeeeccceEEE----EcCCCCccC-CCCCHHHHhhC
Confidence 3576655444322399999999999999986332211110 111122222222 233444432 223334333
Q ss_pred -EEE-ecHHHH-HHHH-HHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 95 -RVL-SHPQAL-ASSD-IVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 95 -~V~-SHpqal-~Qc~-~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
-|. +.+... .... .++.+.+.. . ..++|.....++++.+ ...||.++..++.
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~giailp~~~~~~ 155 (200)
T cd08462 97 GHVVVRFGRNRRPSFEDWFLNEYGLKRRVEVVTPSFSSIPPLLVGT---NRIATLHRRLAEQ 155 (200)
T ss_pred CCEEEecCCCCCccHHHHHHHHcCCcceEEEEeChHHHHHHHHHcC---chhhhhHHHHHHh
Confidence 121 111111 1122 234444543 2 4566666667777764 3477888776653
No 127
>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=76.07 E-value=20 Score=31.19 Aligned_cols=140 Identities=21% Similarity=0.250 Sum_probs=80.0
Q ss_pred eeecCCHHHHHHHHHhCCCCeEEEeeeecccce--eeccccccccCCeEEEEEEEEeeeeEeeecCC-----CCcCCc--
Q 023305 23 TVPCDEFEDTFKAVELWLADKAVLPIENSSSGS--IHRNYDLLLRHRLHIVGEVQLAANFCLLALPG-----IKADQL-- 93 (284)
Q Consensus 23 ~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~--V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~-----~~l~~i-- 93 (284)
..+..|. ..+.++.+|++|.|.+-+-..-.|. +....++|...++.++.=.. =...|+.+++ .+++|+
T Consensus 15 ~~~~gS~-~gl~~L~~g~~~iAg~h~~~~~~~~~n~~~~~~~l~g~~~v~v~~~~--r~~Gl~v~~~np~~i~~~~dL~~ 91 (193)
T PF12727_consen 15 VQYTGSR-AGLSALARGEADIAGIHLPDPESGEYNIPFVRRLLPGIEVVLVRLAR--REQGLIVRPGNPKGITSLEDLAD 91 (193)
T ss_pred EEecCCH-HHHHHHHCCCceEEEecCCCCcccccchHHHHHhcCCCcEEEEeeeE--EeeeEEEeCCCCccCCCHHHhcc
Confidence 4444554 5578899999999998554332222 22222344444444433222 2356777777 345555
Q ss_pred -c-EEEecHHHHHHHHHHHHh----cCC-----e--EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh-cCCceeeccc
Q 023305 94 -K-RVLSHPQALASSDIVLTQ----LGV-----A--RENVDDTASAAQYVASNGLRDAGAVASARAAEI-YGLNILADRI 159 (284)
Q Consensus 94 -~-~V~SHpqal~Qc~~fl~~----~~~-----~--~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~-ygL~il~~~I 159 (284)
. +++.-+. =.=.+.+|.+ .++ . ...+.|..+.|..|+.+ ...++++.+.+|+. |||.++.=.-
T Consensus 92 ~~~r~vnR~~-GSGtR~l~d~~l~~~gi~~~~i~gy~~~~~th~~vA~aVa~G--~AD~G~g~~~~A~~~~gL~Fvpl~~ 168 (193)
T PF12727_consen 92 PGLRFVNRQP-GSGTRILFDQLLAEEGIDPEDIPGYAQEANTHLAVAAAVASG--KADAGIGIRAAAEEFYGLDFVPLAE 168 (193)
T ss_pred CCcEEEECCC-CCHHHHHHHHHHHHcCCChhhCCCccccccChHHHHHHHHcC--CCCEEeehHHHHHhhcCCCcEEccc
Confidence 2 2333333 3335555554 222 2 13566777788888876 45688999999975 7998875433
Q ss_pred cCCCCCeeEEEEEeeC
Q 023305 160 QDEPDNITRFLVLARD 175 (284)
Q Consensus 160 ~d~~~N~TRF~vl~~~ 175 (284)
=||.++-++
T Consensus 169 -------E~~dlv~~~ 177 (193)
T PF12727_consen 169 -------ERYDLVIRR 177 (193)
T ss_pred -------cceEEEEEh
Confidence 255555444
No 128
>cd08486 PBP2_CbnR The C-terminal substrate binding domain of LysR-type transcriptional regulator, CbnR, involved in the chlorocatechol catabolism, contains the type 2 periplasmic binding fold. This CD represents the substrate binding domain of LysR-type regulator CbnR which is involved in the regulation of chlorocatechol breakdown. The chlorocatechol-degradative pathway is often found in bacteria that can use chlorinated aromatic compounds as carbon and energy sources. CbnR is found in the 3-chlorobenzoate degradative bacterium Ralstonia eutropha NH9 and forms a tetramer. CbnR activates the expression of the cbnABCD genes, which are responsible for the degradation of chlorocatechol converted from 3-chlorobenzoate and are transcribed divergently from cbnR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccha
Probab=75.93 E-value=42 Score=27.47 Aligned_cols=120 Identities=10% Similarity=0.018 Sum_probs=62.0
Q ss_pred hCCCCcee-ecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc--
Q 023305 17 AYPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 93 (284)
Q Consensus 17 ~f~~~~~~-~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i-- 93 (284)
.+|+.++. -..+..++.+.+.+|++|+|++.-..-..|. ....+.+.++.+ .++-+|-+......+++|+
T Consensus 26 ~~P~v~i~i~~~~~~~l~~~l~~g~~D~~~~~~~~~~~~~---~~~~l~~~~~~l----v~~~~h~l~~~~~i~~~dL~~ 98 (198)
T cd08486 26 STPTATVSLTHMTKDEQVEGLLAGTIHVGFSRFFPRHPGI---EIVNIAQEDLYL----AVHRSQSGKFGKTCKLADLRA 98 (198)
T ss_pred hCCCeEEEEEECCHHHHHHHHHcCCceEEEecCCCCCCce---EEEEEeeccEEE----EecCCCccccCCcccHHHHcC
Confidence 35666553 2357789999999999999997422111110 011122233332 2344454433333334444
Q ss_pred -cEEEecH----HHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhH
Q 023305 94 -KRVLSHP----QALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARA 146 (284)
Q Consensus 94 -~~V~SHp----qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~a 146 (284)
.-|.-.+ ....+...++++.+.. . ..+++......+++.+ ...+|.+..+
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~ 156 (198)
T cd08486 99 VELTLFPRGGRPSFADEVIGLFKHAGIEPRIARVVEDATAALALTMAG---AASSIVPASV 156 (198)
T ss_pred CCeEeecCCcCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---ceEEEcchhh
Confidence 3343222 2345677777776533 2 3455666666666654 3466777653
No 129
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=75.75 E-value=18 Score=33.06 Aligned_cols=121 Identities=16% Similarity=0.019 Sum_probs=66.3
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCccE-
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR- 95 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~~- 95 (284)
+|+.++... .+-.++++.+.+|++|+|+++..-...+.. ...|.+.++.++ .+-+|-+. ....+++|+..
T Consensus 138 ~P~i~l~i~~~~~~~~~~~l~~g~~Di~i~~~~~~~~~l~---~~~l~~~~~~lv----~~~~hpl~-~~~~~~~~L~~~ 209 (314)
T PRK09508 138 APNIHVVFKSSLNQNIEHQLRYQETEFVISYEEFDRPEFT---SVPLFKDELVLV----ASKNHPRI-KGPITEEQLYNE 209 (314)
T ss_pred CCCcEEEEEeCcchhHHHHHhcCCccEEEecCCCCccccc---eeeeecCceEEE----EcCCCCcc-CCCCCHHHHhhC
Confidence 566665443 356888999999999999997542211111 112223333332 23344443 22233444431
Q ss_pred ---EEecHHHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 96 ---VLSHPQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 96 ---V~SHpqal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
+.+++....+...|+.+.+.. ...++|.....++|+.+ ...++.+...++.
T Consensus 210 ~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 266 (314)
T PRK09508 210 QHAVVSLDRFASFSQPWYDTVDKQASIAYQGTALSSVLNVVSQT---HLVAIAPRWLAEE 266 (314)
T ss_pred CCEEecCCCCccHHHHHHHhcCcCceEEEEcCcHHHHHHHHHhC---ChHHHHHHHHHHH
Confidence 233333334456777765542 34667777778888875 2367778776654
No 130
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=75.66 E-value=5.8 Score=34.67 Aligned_cols=43 Identities=12% Similarity=0.139 Sum_probs=35.9
Q ss_pred CCCcHHHHHHHhhCC-CCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKAYP-KCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~-~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
..|+..+....+.++ +.+++.+.+.++++++|.+|++|+.+..
T Consensus 137 ~~g~~~~~~l~~~~~~~~~~~~~~s~~~~~~~L~~g~vD~~v~~ 180 (250)
T TIGR01096 137 QSGTTHEQYLKDYFKPGVDIVEYDSYDNANMDLKAGRIDAVFTD 180 (250)
T ss_pred ecCchHHHHHHHhccCCcEEEEcCCHHHHHHHHHcCCCCEEEeC
Confidence 456776666666777 6788999999999999999999999884
No 131
>PRK11260 cystine transporter subunit; Provisional
Probab=74.71 E-value=5.8 Score=35.51 Aligned_cols=43 Identities=9% Similarity=0.043 Sum_probs=36.3
Q ss_pred CCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
..|+..+....+.++..++..+++..++++++.+|++|+.+.+
T Consensus 155 ~~G~~~~~~l~~~~~~~~i~~~~~~~~~l~~L~~GrvD~~i~d 197 (266)
T PRK11260 155 GLGTNYEQWLRQNVQGVDVRTYDDDPTKYQDLRVGRIDAILVD 197 (266)
T ss_pred ecCCcHHHHHHHhCCCCceEecCCHHHHHHHHHcCCCCEEEec
Confidence 4577666666677788889999999999999999999998885
No 132
>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=74.43 E-value=43 Score=26.81 Aligned_cols=122 Identities=14% Similarity=0.103 Sum_probs=61.1
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeec--ccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 93 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS--~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i 93 (284)
.+|+.++... .+..++.+.+.+|++|+|++..... ..|.. ...|.+.++.++ .+-+|-+...+..+++|+
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~---~~~l~~~~~~~~----~~~~~~l~~~~~~~~~dL 97 (201)
T cd08435 25 RHPRLTVRVVEGTSDELLEGLRAGELDLAIGRLADDEQPPDLA---SEELADEPLVVV----ARPGHPLARRARLTLADL 97 (201)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHcCCccEEEEecCcccCCCCcE---EEEcccCcEEEE----EeCCCcCcccCCcCHHHH
Confidence 3566655433 4678999999999999999753211 11211 112223333332 233333332222233333
Q ss_pred c---EEEec-HH-HHHHHHHHHHhcCCe----EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 K---RVLSH-PQ-ALASSDIVLTQLGVA----RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 ~---~V~SH-pq-al~Qc~~fl~~~~~~----~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
. -|..- .. -......|+++.+.. ...+++...+.+++..+ ...|+.+...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08435 98 ADYPWVLPPPGTPLRQRLEQLFAAAGLPLPRNVVETASISALLALLARS---DMLAVLPRSVAE 158 (201)
T ss_pred hcCCEEecCCCCcHHHHHHHHHHHcCCCCCCceEEEccHHHHHHHHhcC---CeEEEeEHHHhh
Confidence 2 22211 11 112345556654432 23456666666777764 246788877665
No 133
>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=74.43 E-value=7.5 Score=29.20 Aligned_cols=66 Identities=15% Similarity=0.050 Sum_probs=41.5
Q ss_pred cC-CCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCC-CcHHHHHHHHHHHh
Q 023305 194 DE-GPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASM-ADPRAQNALGHLQE 267 (284)
Q Consensus 194 ~~-~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~-~d~~~~~al~~L~~ 267 (284)
++ .+|.++++=+.++.+|+|+.+|...-... + ..+......|..-+++++.. +...++.+|.++.+
T Consensus 7 ~~~~a~~ia~Vs~~lA~~~~NI~~I~~l~~~~-~-------~~~~~~~~~~~~e~~v~~~~~~~~~lr~~L~~la~ 74 (84)
T cd04871 7 RPLTAEQLAAVTRVVADQGLNIDRIRRLSGRV-P-------LEEQDDSPKACVEFSVRGQPADLEALRAALLELAS 74 (84)
T ss_pred CcCCHHHHHHHHHHHHHcCCCHHHHHHhhccc-c-------ccccCCCCcEEEEEEEeCCCCCHHHHHHHHHHHhc
Confidence 45 78999999999999999999887641110 0 00001113466566666543 33577777777654
No 134
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=73.69 E-value=5.3 Score=32.61 Aligned_cols=28 Identities=25% Similarity=0.307 Sum_probs=23.8
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeee
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTK 216 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~ 216 (284)
|.+-+.|+||-|.++++.++.+|||+.-
T Consensus 6 ISvFlENk~GRL~~~~~~L~eagINiRA 33 (142)
T COG4747 6 ISVFLENKPGRLASVANKLKEAGINIRA 33 (142)
T ss_pred EEEEecCCcchHHHHHHHHHHcCCceEE
Confidence 3344679999999999999999999864
No 135
>PRK10341 DNA-binding transcriptional activator TdcA; Provisional
Probab=72.38 E-value=77 Score=28.87 Aligned_cols=119 Identities=14% Similarity=0.115 Sum_probs=58.9
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecc--cceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc-
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 93 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~--~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i- 93 (284)
+|+.++.- ..+-.++++++.+|++|+|+++..+.. .+. ....|.+.++.++. +-+|-+. . ..+++|+
T Consensus 123 ~p~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~l---~~~~l~~~~~~lv~----~~~~pl~-~-~i~~~dL~ 193 (312)
T PRK10341 123 FPKAQVSMYEAQLSSFLPAIRDGRLDFAIGTLSNEMKLQDL---HVEPLFESEFVLVA----SKSRTCT-G-TTTLESLK 193 (312)
T ss_pred CCCCEEEEEeCCHHHHHHHHHcCCCcEEEecCCcccccCCe---eEEEEecccEEEEE----cCCCchh-c-cCCHHHHh
Confidence 45655533 345689999999999999998754321 111 11122222332222 1122221 1 1122222
Q ss_pred --cEEEec--HHHHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 --KRVLSH--PQALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 --~~V~SH--pqal~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|.-- .....+...|+.++++ + ...++|.....+++..+ ...++.+...++
T Consensus 194 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 252 (312)
T PRK10341 194 NEQWVLPQTNMGYYSELLTTLQRNGISIENIVKTDSVVTIYNLVLNA---DFLTVIPCDMTS 252 (312)
T ss_pred CCCeEccCCCCcHHHHHHHHHHHcCcCCCceEEecCHHHHHHHHHhC---CcEEEeeHHhcC
Confidence 222211 1123344556666543 2 35566777777777765 246777766543
No 136
>PF12974 Phosphonate-bd: ABC transporter, phosphonate, periplasmic substrate-binding protein ; PDB: 3N5L_B 3QUJ_C 3P7I_A 3QK6_A 3S4U_A.
Probab=71.92 E-value=3.4 Score=36.55 Aligned_cols=74 Identities=20% Similarity=0.206 Sum_probs=49.3
Q ss_pred CCcHH-HHHHHhhC-CC--------CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccc------cCCeE
Q 023305 6 PGSFS-EDAALKAY-PK--------CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL------RHRLH 69 (284)
Q Consensus 6 ~GtfS-~~Aa~~~f-~~--------~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~------~~~l~ 69 (284)
.+|+| +.+...++ .+ .+.+...+.+.++.+|.+|++|.|+++-. +++.+. ..+++
T Consensus 113 ~~s~sg~l~~~~~L~~~~Gl~~~~~~~~~~~~~~~~~~~~l~~G~~Da~~~~~~---------~~~~~~~~~~~~~~~~r 183 (243)
T PF12974_consen 113 PSSTSGYLIPRYELLREAGLDPGDDFKQVFVGSHDAVLEALLNGKADAAAIPSD---------AFERLEAEGPDIPSQLR 183 (243)
T ss_dssp TT-TTTTHHHHHHTCCCCT--HHHHSSEEEEE-HHHHHHHHHTTSSSEEEEEHH---------HHHHHHHH-HHHHTTEE
T ss_pred CCccHHHHHHHHHHHHHcCCChhHceeEEEeCCHHHHHHHHHcCCccEEEEech---------hHHHHHHccCcccccEE
Confidence 33433 66666544 32 24567889999999999999999998742 444433 24699
Q ss_pred EEEEEEEeeeeEeeecCCC
Q 023305 70 IVGEVQLAANFCLLALPGI 88 (284)
Q Consensus 70 I~~E~~l~I~~~L~~~~~~ 88 (284)
|+++...-..+.++++++.
T Consensus 184 vl~~s~~~p~~~~~~~~~~ 202 (243)
T PF12974_consen 184 VLWTSPPYPNWPLVASPDL 202 (243)
T ss_dssp EEEEEEEEE--EEEEETTS
T ss_pred EEEEeCCCCCcEEEEeCCC
Confidence 9999877777788888763
No 137
>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=71.90 E-value=50 Score=26.44 Aligned_cols=32 Identities=13% Similarity=-0.077 Sum_probs=24.1
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEee
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPI 48 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPi 48 (284)
.+|+.++.-.. +-.++++.+.+|++|+|++.-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (196)
T cd08450 25 EHPDLDVELSSLFSPQLAEALMRGKLDVAFMRP 57 (196)
T ss_pred hCCCcEEEEEecChHHHHHHHhcCCccEEEEeC
Confidence 35676655443 567899999999999999753
No 138
>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=71.70 E-value=53 Score=26.67 Aligned_cols=115 Identities=20% Similarity=0.137 Sum_probs=66.9
Q ss_pred hCCCCcee-ecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCC--------
Q 023305 17 AYPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPG-------- 87 (284)
Q Consensus 17 ~f~~~~~~-~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~-------- 87 (284)
.+++.++. -..+..++.+.+.+|++|+|+........| +..+.....++++++.++
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 45665553 345558999999999999999975531111 122222233344444333
Q ss_pred CCcCCc---cEEEec--HHHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 88 IKADQL---KRVLSH--PQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 88 ~~l~~i---~~V~SH--pqal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
.+++|+ .-|.-. ..-..+..+++.+.+.. ...++|...+..+++.+ ...++.+...++.
T Consensus 96 i~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 162 (209)
T PF03466_consen 96 ITLEDLADYPLILLSPGSPYRDQLDRWLREHGFSPNIVIEVDSFESILSLVASG---DGIAILPDSLAQD 162 (209)
T ss_dssp SSGGGGTTSEEEEESTTTSHHHHHHHHHHHTTEEEEEEEEESSHHHHHHHHHTT---SEBEEEEHHHHHH
T ss_pred chhhhhhhccccccccccccccccccccccccccccccccccchhhhccccccc---cceeecCcccccc
Confidence 233333 334321 22456666677766653 24577788888888765 4677888777643
No 139
>PRK11242 DNA-binding transcriptional regulator CynR; Provisional
Probab=71.28 E-value=76 Score=28.31 Aligned_cols=121 Identities=16% Similarity=0.061 Sum_probs=61.5
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCC-CCcC---C
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPG-IKAD---Q 92 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~-~~l~---~ 92 (284)
|++.++... .+..++.+.+.+|++|+|+++......+... ..|.+.++.++ .+-+|-|...+. .+++ +
T Consensus 117 ~p~~~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~~----~~~~~pl~~~~~~i~~~~L~~ 189 (296)
T PRK11242 117 YPGITLTIREMSQERIEALLADDELDVGIAFAPVHSPEIEA---QPLFTETLALV----VGRHHPLAARRKALTLDELAD 189 (296)
T ss_pred CCCCEEEEEeCCHHHHHHHHHCCCCcEEEEecCCCCcceeE---EEeeeccEEEE----EcCCCcccccCCCcCHHHHhC
Confidence 466665554 4568899999999999999865433222111 12222333332 222232322211 2222 2
Q ss_pred ccEEEecHHHH--HHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 93 LKRVLSHPQAL--ASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 93 i~~V~SHpqal--~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
-.-|.-.+... ..-..|+.+.+.. . ..++|-..+.++++.+ ...++.++..++
T Consensus 190 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 247 (296)
T PRK11242 190 EPLVLLSAEFATREQIDRYFRRHGVTPRVAIEANSISAVLEIVRRG---RLATLLPAAIAR 247 (296)
T ss_pred CCcEeeCCCccHHHHHHHHHHHcCCCccEEEEeccHHHHHHHHHhC---CeEEEeehhhcc
Confidence 23344333322 2334566665543 2 4456666667777765 236677776554
No 140
>PRK09495 glnH glutamine ABC transporter periplasmic protein; Reviewed
Probab=71.02 E-value=7.7 Score=34.17 Aligned_cols=43 Identities=14% Similarity=0.058 Sum_probs=34.7
Q ss_pred CCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
..|+..+.-..+.+++.+++.+++.++++.+|.+|++|..+..
T Consensus 137 ~~g~~~~~~l~~~~~~~~i~~~~~~~~~~~~L~~grvDa~i~~ 179 (247)
T PRK09495 137 KSGTGSVDYAKANIKTKDLRQFPNIDNAYLELGTGRADAVLHD 179 (247)
T ss_pred ecCchHHHHHHhcCCCCceEEcCCHHHHHHHHHcCceeEEEeC
Confidence 3577666666666777788889999999999999999988753
No 141
>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=70.59 E-value=36 Score=28.36 Aligned_cols=122 Identities=19% Similarity=0.145 Sum_probs=69.9
Q ss_pred HHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCC---
Q 023305 12 DAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI--- 88 (284)
Q Consensus 12 ~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~--- 88 (284)
+++.+.--+.++++. ++..+++++.+|++|.++-++..+ .+. ...+.... -+....+.++.+++.
T Consensus 31 ~i~~~~g~~~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~--------~~r--~~~~~~s~-p~~~~~~~~~~~~~~~~~ 98 (225)
T PF00497_consen 31 AIAKRLGIKIEFVPM-PWSRLLEMLENGKADIIIGGLSIT--------PER--AKKFDFSD-PYYSSPYVLVVRKGDAPP 98 (225)
T ss_dssp HHHHHHTCEEEEEEE-EGGGHHHHHHTTSSSEEESSEB-B--------HHH--HTTEEEES-ESEEEEEEEEEETTSTCS
T ss_pred HHHhhcccccceeec-cccccccccccccccccccccccc--------ccc--cccccccc-cccchhheeeeccccccc
Confidence 344443224678888 999999999999999987555432 221 11122222 233334556665431
Q ss_pred --C---cCCc--cEEEecHHHHHHHHHHHHh-c--CCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 89 --K---ADQL--KRVLSHPQALASSDIVLTQ-L--GVARENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 89 --~---l~~i--~~V~SHpqal~Qc~~fl~~-~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
. +.++ ++|..-.-.. -..+|.+ . +++.+.+.|..++.+++..+ .-.++|+....+..
T Consensus 99 ~~~~~~~~dl~~~~i~~~~g~~--~~~~l~~~~~~~~~~~~~~~~~~~~~~l~~g--~~d~~i~~~~~~~~ 165 (225)
T PF00497_consen 99 IKTIKSLDDLKGKRIGVVRGSS--YADYLKQQYPSNINIVEVDSPEEALEALLSG--RIDAFIVDESTAEY 165 (225)
T ss_dssp TSSHSSGGGGTTSEEEEETTSH--HHHHHHHHTHHTSEEEEESSHHHHHHHHHTT--SSSEEEEEHHHHHH
T ss_pred cccccchhhhcCcccccccchh--HHHHhhhhccchhhhcccccHHHHHHHHhcC--Ceeeeeccchhhhh
Confidence 2 2244 2444433322 1223333 1 67788899999999999886 33477777765544
No 142
>PRK12683 transcriptional regulator CysB-like protein; Reviewed
Probab=70.54 E-value=86 Score=28.65 Aligned_cols=120 Identities=11% Similarity=0.019 Sum_probs=61.3
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeec-ccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc--
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENS-SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 93 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS-~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i-- 93 (284)
+|+.++.- ..+..++.+.|.+|++|+|+.+-... ..+. ...-|.+.++. ++.+.+|-|...+..+++++
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 56666543 35778999999999999999752211 1111 11122223332 23455555543333333333
Q ss_pred -cEEEecH--HHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHH
Q 023305 94 -KRVLSHP--QALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAA 147 (284)
Q Consensus 94 -~~V~SHp--qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 147 (284)
.-|.-.+ .--.+...|+.+.++. . ..++|.....++|..+ .+ .++.+...+
T Consensus 192 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~G-i~~lp~~~~ 248 (309)
T PRK12683 192 YPIITYDQGFTGRSRIDQAFAEAGLVPDIVLTALDADVIKTYVELG--MG-VGIVAAMAY 248 (309)
T ss_pred CCeEeccCCCcHHHHHHHHHHHCCCCceeEEEeccHHHHHHHHHhC--CC-eEEeehhhc
Confidence 3333211 1245567777776543 2 3455666666667664 23 445555433
No 143
>PRK04374 PII uridylyl-transferase; Provisional
Probab=70.41 E-value=23 Score=38.18 Aligned_cols=51 Identities=20% Similarity=0.305 Sum_probs=39.0
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceee--eeeeeeCCCCCCccccCCCCCCCccceeEEEE-EeecC
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLT--KIESRPQRKRPLRVVDDSNNGTAKYFDYLFYI-DFEAS 252 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt--~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~i-d~eg~ 252 (284)
..|.|-+..+|+||-|+++-.+|+.+|+|+. ||.+. .+ ...=.||| |-+|.
T Consensus 795 ~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~--g~---------------~a~D~F~V~d~~g~ 848 (869)
T PRK04374 795 RRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATF--GE---------------RAEDQFQITDEHDR 848 (869)
T ss_pred CeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEec--CC---------------EEEEEEEEECCCCC
Confidence 4677778889999999999999999999998 44444 22 23457888 55665
No 144
>PRK12684 transcriptional regulator CysB-like protein; Reviewed
Probab=70.01 E-value=89 Score=28.58 Aligned_cols=120 Identities=12% Similarity=0.031 Sum_probs=59.7
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeecccc--ccccCCeEEEEEEEEeeeeEeeecCCCCcCC--
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYD--LLLRHRLHIVGEVQLAANFCLLALPGIKADQ-- 92 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d--~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~-- 92 (284)
+|+.++.. ..+..++++.+.+|++|+++.+-.+.. ...++ -|.+..+.+ +.+..|-+......++++
T Consensus 119 ~p~i~l~~~~~~~~~~~~~L~~g~~D~~i~~~~~~~----~~~l~~~~l~~~~~~~----v~~~~~pl~~~~~i~~~dL~ 190 (313)
T PRK12684 119 YPKVRLSILQGSPTQIAEMVLHGQADLAIATEAIAD----YKELVSLPCYQWNHCV----VVPPDHPLLERKPLTLEDLA 190 (313)
T ss_pred CCCceEEEEeCChHHHHHHHHCCCcCEEEeecCCCC----CCCceEEEeccceEEE----EeCCCCccccCCCcCHHHHh
Confidence 46655543 346789999999999999998622111 11111 111222322 234444443322222222
Q ss_pred -ccEEEecH-H-HHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 93 -LKRVLSHP-Q-ALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 93 -i~~V~SHp-q-al~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
..-|.-.+ . --.+...|+...+. . ...++|......+|..+ .+ .++.+..+++
T Consensus 191 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~G-v~~lp~~~~~ 249 (313)
T PRK12684 191 QYPLITYDFAFAGRSKINKAFALRGLKPDIVLEAIDADVIKTYVELG--LG-VGIVADMAFD 249 (313)
T ss_pred cCCcEecCCCCcHHHHHHHHHHHcCCCCCeEEEeCCHHHHHHHHHhC--Cc-eEEeehhhcc
Confidence 23222111 1 12334556665443 3 35566777777777765 23 4555555443
No 145
>PRK12679 cbl transcriptional regulator Cbl; Reviewed
Probab=69.80 E-value=90 Score=28.57 Aligned_cols=120 Identities=10% Similarity=0.066 Sum_probs=59.3
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc---
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL--- 93 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i--- 93 (284)
+|+.++.. ..+-.++++++.+|++|+|+.+-.......+ ....|...++. ++.+.+|-|......+++++
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 3467789999999999999974221000000 01112222332 23455555543222233333
Q ss_pred cEEEecHH--HHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhH
Q 023305 94 KRVLSHPQ--ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARA 146 (284)
Q Consensus 94 ~~V~SHpq--al~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~a 146 (284)
+-|.-++. .-.....|+...+.. . ..++|+....+++..+ ...|+.+..+
T Consensus 193 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~v~~g---~Gi~~lp~~~ 247 (316)
T PRK12679 193 PLITYRQGITGRSRIDDAFARKGLLADIVLSAQDSDVIKTYVALG---LGIGLVAEQS 247 (316)
T ss_pred CeEEecCCCcHHHHHHHHHHHcCCCceEEEEeccHHHHHHHHHcC---CcEEEecccc
Confidence 23332221 222355666665543 2 4556666666777764 2356666643
No 146
>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=69.76 E-value=84 Score=28.20 Aligned_cols=121 Identities=18% Similarity=0.211 Sum_probs=61.3
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecc--cceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK 94 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~--~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~ 94 (284)
||+.++... .+-.++++++.+|++|+|++...+.. .+. ...-|.+.++.++ .+-.|-|...+..+++|+.
T Consensus 119 ~P~~~i~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~---~~~~l~~~~~~~~----~~~~hpl~~~~~i~~~dL~ 191 (300)
T TIGR02424 119 APRLRVRIMTGPNAYLLDQLRVGALDLVVGRLGAPETMQGL---SFEHLYNEPVVFV----VRAGHPLLAAPSLPVASLA 191 (300)
T ss_pred CCCcEEEEEeCchHHHHHHHHCCCCCEEEEecCCcccccce---eeeeecCCceEEE----EcCCCccccCCCCCHHHHh
Confidence 566655443 36678999999999999997543221 111 1111223333222 1223333332222333332
Q ss_pred E--EEecHHH---HHHHHHHHHhcCCe----EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 R--VLSHPQA---LASSDIVLTQLGVA----RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 ~--V~SHpqa---l~Qc~~fl~~~~~~----~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
. .+..+.. ......|+.+++.. ...+.+......++..+ ...++.+...++
T Consensus 192 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 251 (300)
T TIGR02424 192 DYPVLLPPEGSAIRPLAERLFIACGIPPPPQRIETVSGSFGRRYVQES---DAIWIISRGVVA 251 (300)
T ss_pred CCCEEecCCCCchHHHHHHHHHHCCCCCCCceEEeccHHHHHHHHHhC---CceEeCcHHHHh
Confidence 1 2232222 13345677665432 35566777777777765 236677776664
No 147
>PRK09959 hybrid sensory histidine kinase in two-component regulatory system with EvgA; Provisional
Probab=69.26 E-value=6 Score=43.32 Aligned_cols=44 Identities=18% Similarity=0.064 Sum_probs=38.6
Q ss_pred CCCcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEee
Q 023305 5 LPGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPI 48 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPi 48 (284)
+.|++.+....+.+++.+++.+++.++++.+|.+|++|.+|.+.
T Consensus 413 ~~g~~~~~~~~~~~p~~~~~~~~~~~~~l~av~~G~~Da~i~~~ 456 (1197)
T PRK09959 413 PYYYELHSQLKEMYPEVEWIKVDNASAAFHKVKEGELDALVATQ 456 (1197)
T ss_pred eCCcchHHHHHHHCCCcEEEEcCCHHHHHHHHHcCCCCEEehhh
Confidence 46777777778888999999999999999999999999988653
No 148
>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=68.95 E-value=24 Score=31.13 Aligned_cols=115 Identities=13% Similarity=-0.013 Sum_probs=62.3
Q ss_pred CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCC---CcCCcc--E
Q 023305 21 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI---KADQLK--R 95 (284)
Q Consensus 21 ~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~---~l~~i~--~ 95 (284)
+++++..+..++++++.+|++|+|++.....+. ..-...++.+++-..-.-..+++++++. +++|++ +
T Consensus 31 v~~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~~-------~~~~g~~~~~i~~~~~~~~~~~v~~~~~~i~s~~dL~Gk~ 103 (288)
T TIGR01728 31 VEWVEFPAGPPALEALGAGSLDFGYIGPGPALF-------AYAAGADIKAVGLVSDNKATAIVVIKGSPIRTVADLKGKR 103 (288)
T ss_pred EEEEecCCCcHHHHHHhcCCccccccCCcHHHH-------HHhcCCCEEEEEEecCCCceEEEECCCCCCCCHHHcCCCE
Confidence 567888888899999999999999765331110 0001235565554432224556665443 233442 5
Q ss_pred EEecHH--HHHHHHHHHHhcCCe---E-EecCCHHHHHHHHHhcCCCCeEEEcch
Q 023305 96 VLSHPQ--ALASSDIVLTQLGVA---R-ENVDDTASAAQYVASNGLRDAGAVASA 144 (284)
Q Consensus 96 V~SHpq--al~Qc~~fl~~~~~~---~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~ 144 (284)
|...+- .......+|++.++. . ....+.+.+.+.+..+. - .+++.++
T Consensus 104 i~~~~~~~~~~~~~~~l~~~G~~~~~v~~~~~~~~~~~~al~~g~-v-da~~~~~ 156 (288)
T TIGR01728 104 IAVPKGGSGHDLLLRALLKAGLSGDDVTILYLGPSDARAAFAAGQ-V-DAWAIWE 156 (288)
T ss_pred EEecCCccHHHHHHHHHHHcCCCccceeEEecCcHHHHHHHHCCC-C-CEEEecc
Confidence 553221 123444567665542 1 22245667777777653 3 3555544
No 149
>KOG3217 consensus Protein tyrosine phosphatase [Signal transduction mechanisms]
Probab=68.84 E-value=6.7 Score=33.10 Aligned_cols=62 Identities=19% Similarity=0.360 Sum_probs=40.4
Q ss_pred HHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH--HHhc--CCceEEEc
Q 023305 201 FKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH--LQEF--ATFLRVLG 276 (284)
Q Consensus 201 ~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~--L~~~--~~~vkvLG 276 (284)
.|.|+++++|||.+.|. +|+.+... =+.++|+| .+++.+++++++. .... -..|..||
T Consensus 58 ~R~~s~lK~hGI~~~H~-aRqit~~D-----------F~~FDYI~------~MDesN~~dL~~~a~~~~~~~kakV~Llg 119 (159)
T KOG3217|consen 58 PRTLSILKKHGIKIDHL-ARQITTSD-----------FREFDYIL------AMDESNLRDLLRKASNQPKGSKAKVLLLG 119 (159)
T ss_pred hHHHHHHHHcCCcchhh-cccccHhH-----------hhhcceeE------EecHHHHHHHHHHhccCCCCcceEEEEee
Confidence 67899999999997765 67776542 00133333 3667888887764 2222 23589999
Q ss_pred eeeC
Q 023305 277 CYPM 280 (284)
Q Consensus 277 sYp~ 280 (284)
+|-.
T Consensus 120 sy~~ 123 (159)
T KOG3217|consen 120 SYDK 123 (159)
T ss_pred ccCC
Confidence 9964
No 150
>PRK03381 PII uridylyl-transferase; Provisional
Probab=68.67 E-value=23 Score=37.63 Aligned_cols=37 Identities=11% Similarity=0.163 Sum_probs=30.5
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeC
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 222 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~ 222 (284)
.|-|.+..+|+||-|+++-.+|+.+|+|+..-...-.
T Consensus 707 ~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~ 743 (774)
T PRK03381 707 ATVLEVRAADRPGLLARLARALERAGVDVRWARVATL 743 (774)
T ss_pred eEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeec
Confidence 4667777899999999999999999999995544433
No 151
>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=68.43 E-value=28 Score=23.31 Aligned_cols=27 Identities=30% Similarity=0.428 Sum_probs=23.9
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
+++.||.+.++++.+++++|++-.|.+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04923 10 MRSHPGVAAKMFKALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEc
Confidence 557799999999999999999988864
No 152
>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=68.21 E-value=11 Score=37.95 Aligned_cols=105 Identities=13% Similarity=0.229 Sum_probs=66.1
Q ss_pred chhHHHhcCCceeeccccC--CCCCeeEEEEEeeCCCCC-----CCC---------------CCceEEEEEEecCCCchH
Q 023305 143 SARAAEIYGLNILADRIQD--EPDNITRFLVLARDPIIP-----RTD---------------KLFKTSIVFTLDEGPGVL 200 (284)
Q Consensus 143 s~~aa~~ygL~il~~~I~d--~~~N~TRF~vl~~~~~~~-----~~~---------------~~~ktsi~f~~~~~pGaL 200 (284)
+..-|+..|+++....... .-.|.-++-+-+...... -.+ ...-.++++...|+||.+
T Consensus 386 A~~iA~e~GI~v~~~~~~~~~~hpNtv~i~l~~~~~~~~v~G~s~gGg~~~I~~ing~~v~~~~~~~~li~~~~D~pG~I 465 (525)
T TIGR01327 386 APAVAKERGITVEESKSESSPDYKNYLSVTVTGDSGTVSVAGTVFGGFSPRIVEIDGFHVDLEPEGIMLIILHLDKPGVI 465 (525)
T ss_pred HHHHHHHcCCEEEEEEccCCCCCCCEEEEEEEeCCcEEEEEEEEecCCcEEEEEECCEEEEEecCccEEEEEecCcCCcc
Confidence 3466889999986654432 234665665543221100 000 012345677778999999
Q ss_pred HHHHHHHHhCCceeeeee-eeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 201 FKALAVFALREINLTKIE-SRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 201 ~~~L~~F~~~~INLt~Ie-SRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
.++.+.+..++||+..+. +|-.++ .+....++++....+ +++++|++
T Consensus 466 ~~v~~~L~~~~iNIa~m~~~R~~~g----------------~~al~~i~~D~~v~~----~~l~~i~~ 513 (525)
T TIGR01327 466 GKVGTLLGTAGINIASMQLGRKEKG----------------GEALMLLSLDQPVPD----EVLEEIKA 513 (525)
T ss_pred hHHHhHHhhcCCChHHcEeecCCCC----------------CeEEEEEEcCCCCCH----HHHHHHhc
Confidence 999999999999998764 554332 367888899886653 34555554
No 153
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=68.01 E-value=18 Score=38.81 Aligned_cols=31 Identities=23% Similarity=0.255 Sum_probs=28.5
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceee
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLT 215 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt 215 (284)
..|.|=+..+|+||-|+++.++|...|+++.
T Consensus 782 ~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~ 812 (854)
T PRK01759 782 EQTEMELFALDRAGLLAQVSQVFSELNLNLL 812 (854)
T ss_pred CeEEEEEEeCCchHHHHHHHHHHHHCCCEEE
Confidence 4688888899999999999999999999987
No 154
>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=67.63 E-value=64 Score=26.04 Aligned_cols=122 Identities=16% Similarity=0.154 Sum_probs=62.0
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc--
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 93 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i-- 93 (284)
.+|+.++.... +..++.+.+.+|++|+|+.+......+ + ....|.+.++.+ +.+-+|-+...+ .+++++
T Consensus 25 ~~P~v~v~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~-l--~~~~l~~~~~~~----v~~~~~~l~~~~-i~~~~L~~ 96 (201)
T cd08459 25 VAPGVRIETVRLPVDELEEALESGEIDLAIGYLPDLGAG-F--FQQRLFRERYVC----LVRKDHPRIGST-LTLEQFLA 96 (201)
T ss_pred HCCCCeEEEEecCccCHHHHhhCCCceEEEEcCCCCccc-c--eEEEeecCceEE----EEcCCCccccCC-cCHHHHhh
Confidence 35666554433 456888999999999999864321111 0 111222333322 233344433221 233332
Q ss_pred -cEEEecHH--HHHHHHHHHHhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 94 -KRVLSHPQ--ALASSDIVLTQLGV--AR-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 94 -~~V~SHpq--al~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
.-|...+. ...+..+|+.+++. .. ..++|.....++++.+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (201)
T cd08459 97 ARHVVVSASGTGHGLVEQALREAGIRRRIALRVPHFLALPLIVAQT---DLVATVPERLARL 155 (201)
T ss_pred CCcEEEccCCCCcchHHHHHHHhCccccEEEEcCcHHHHHHHHhcC---CEEEecHHHHHHH
Confidence 22332221 22345667776654 33 3455555555666654 3577888876664
No 155
>cd08412 PBP2_PAO1_like The C-terminal substrate-binding domain of putative LysR-type transcriptional regulator PAO1-like, a member of the type 2 periplasmic binding fold protein superfamily. This family includes the C-terminal substrate domain of a putative LysR-type transcriptional regulator from the plant pathogen Pseudomonas aeruginosa PAO1and its closely related homologs. The LysR-type transcriptional regulators (LTTRs) are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controll
Probab=67.61 E-value=62 Score=25.84 Aligned_cols=122 Identities=15% Similarity=0.070 Sum_probs=61.3
Q ss_pred hCCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCc---CC
Q 023305 17 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---DQ 92 (284)
Q Consensus 17 ~f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l---~~ 92 (284)
.+|+.++.- ..+-.++++.+.+|++|+|++.-.....|.. ...|.+..+.+ ..+-+|-|...+..++ .+
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08412 25 AYPGVEVRVVEGNQEELEEGLRSGELDLALTYDLDLPEDIA---FEPLARLPPYV----WLPADHPLAGKDEVSLADLAA 97 (198)
T ss_pred HCCCcEEEEEECCHHHHHHHHHcCCCcEEEEcCCCCCcccc---eeeeeccceEE----EecCCCCCCCCCcCCHHHHcC
Confidence 456665533 3467889999999999999985332111110 11122222221 2233444432222222 23
Q ss_pred ccEEE-ecHHHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 93 LKRVL-SHPQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 93 i~~V~-SHpqal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
..-|. .......+...|+.+.+.. ...+++...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (198)
T cd08412 98 EPLILLDLPHSREYFLSLFAAAGLTPRIAYRTSSFEAVRSLVANG---LGYSLLNDRPYR 154 (198)
T ss_pred CcEEecCchhHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CCEEEeeccccc
Confidence 33333 2222223344566655543 23466777777777764 246777776554
No 156
>cd00134 PBPb Bacterial periplasmic transport systems use membrane-bound complexes and substrate-bound, membrane-associated, periplasmic binding proteins (PBPs) to transport a wide variety of substrates, such as, amino acids, peptides, sugars, vitamins and inorganic ions. PBPs have two cell-membrane translocation functions: bind substrate, and interact with the membrane bound complex. A diverse group of periplasmic transport receptors for lysine/arginine/ornithine (LAO), glutamine, histidine, sulfate, phosphate, molybdate, and methanol are included in the PBPb CD.
Probab=66.97 E-value=12 Score=30.56 Aligned_cols=42 Identities=29% Similarity=0.350 Sum_probs=34.0
Q ss_pred CCcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 6 PGSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 6 ~GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
.|+..+....+.++..++.++.+.++++++|.+|++|.++++
T Consensus 112 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~ 153 (218)
T cd00134 112 KGSTAEKYLKKALPEAKVVSYDDNAEALAALENGRADAVIVD 153 (218)
T ss_pred cCchHHHHHHHhCCcccEEEeCCHHHHHHHHHcCCccEEEec
Confidence 455555566666666778999999999999999999988876
No 157
>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=66.96 E-value=64 Score=25.90 Aligned_cols=123 Identities=21% Similarity=0.188 Sum_probs=63.1
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc-
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 94 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~- 94 (284)
.+|+.++.-.. +-+++.+.+.+|++|+|++.......+.. ...|.+.++.++.. -+|-+.. +..+++++.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~~---~~~l~~~~~~lv~~----~~~p~~~-~~~~~~~L~~ 96 (198)
T cd08461 25 EAPGVRVAIRDLESDNLEAQLERGEVDLALTTPEYAPDGLR---SRPLFEERYVCVTR----RGHPLLQ-GPLSLDQFCA 96 (198)
T ss_pred HCCCcEEEEeeCCcccHHHHHhcCCCcEEEecCccCCccce---eeeeecCcEEEEEc----CCChhhc-CCCCHHHHhh
Confidence 45776654433 45678999999999999985332211111 11222333333322 2222221 112233222
Q ss_pred --EEEecHHH---HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhc
Q 023305 95 --RVLSHPQA---LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEIY 150 (284)
Q Consensus 95 --~V~SHpqa---l~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y 150 (284)
-|.-.+.. -.+...|+.+.+.. ...++|...+..+++.+ ...|+.+...++.+
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~ 157 (198)
T cd08461 97 LDHIVVSPSGGGFAGSTDEALAALGLTRNVVLSVPSFLVVPEILAAT---DMVAFVPSRLVPNL 157 (198)
T ss_pred CCcEEEecCCCCCCCHHHHHHHHcCCCCcEEEEcCchhhHHHHHhcC---CeEEEchHHHHHhh
Confidence 23322211 12355677665532 24566777777777764 35788888777654
No 158
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=66.24 E-value=12 Score=30.48 Aligned_cols=43 Identities=28% Similarity=0.355 Sum_probs=33.6
Q ss_pred CcHHHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEeee
Q 023305 7 GSFSEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIE 49 (284)
Q Consensus 7 GtfS~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiE 49 (284)
|+........+.++.+.....+..+++.++..|++|.++++-.
T Consensus 114 g~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~~d~~~~~~~ 156 (219)
T smart00062 114 GTTGEELLKKLYPEAKIVSYDSQAEALAALKAGRADAAVADAP 156 (219)
T ss_pred CccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCcccEEEeccH
Confidence 5555555554556678889999999999999999999988744
No 159
>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=65.50 E-value=34 Score=22.83 Aligned_cols=27 Identities=30% Similarity=0.433 Sum_probs=24.0
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
+++.||.+.++++.++++||++-.|.+
T Consensus 10 ~~~~~~~~~~i~~~L~~~~i~v~~i~~ 36 (63)
T cd04936 10 MRSHPGVAAKMFEALAEAGINIEMIST 36 (63)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 567799999999999999999988864
No 160
>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=64.86 E-value=51 Score=26.89 Aligned_cols=52 Identities=12% Similarity=0.167 Sum_probs=40.6
Q ss_pred CchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHH
Q 023305 197 PGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGH 264 (284)
Q Consensus 197 pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~ 264 (284)
+..+..+++.+.++||.+|-|..--...+| -.||+-++++-+...+.+.++.
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 445777899999999999999999887776 5799999998655555555543
No 161
>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=64.67 E-value=69 Score=25.32 Aligned_cols=121 Identities=19% Similarity=0.115 Sum_probs=59.3
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc---
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL--- 93 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i--- 93 (284)
+|+.++.-. .+..++.+.+.+|++|+|+..-.....+. ....|.+.++.++ .+-+|-+...+..+++++
T Consensus 26 ~p~v~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~~~----~~~~~pl~~~~~~~~~~l~~~ 98 (197)
T cd08440 26 HPGIRVRLRDVSAEQVIEAVRSGEVDFGIGSEPEADPDL---EFEPLLRDPFVLV----CPKDHPLARRRSVTWAELAGY 98 (197)
T ss_pred CCCcEEEEEeCChHHHHHHHHcCCccEEEEeCCCCCCCe---eEEEeecccEEEE----ecCCCCcccCCccCHHHHccC
Confidence 566655433 35688999999999999998532111110 0111222233222 222332322212223333
Q ss_pred cEEE-ecHHH-HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 KRVL-SHPQA-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 ~~V~-SHpqa-l~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|. .+... ......|+.+.+. + ...++|...+.++++.+ ...|+.++..++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (197)
T cd08440 99 PLIALGRGSGVRALIDRALAAAGLTLRPAYEVSHMSTALGMVAAG---LGVAVLPALALP 155 (197)
T ss_pred CEEecCCCccHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEcchhHHH
Confidence 2222 22211 2233455555543 2 34566777777777765 346777776554
No 162
>PRK09906 DNA-binding transcriptional regulator HcaR; Provisional
Probab=64.40 E-value=1.1e+02 Score=27.44 Aligned_cols=121 Identities=12% Similarity=0.007 Sum_probs=63.1
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCC---cCC
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIK---ADQ 92 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~---l~~ 92 (284)
.+|+.++... .+.+++++.+.+|++|+|++.-.....+ -....|.+.++.++ .+-.|-|......+ +.+
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 4566665443 3568899999999999999864321111 11223333444433 22333333222222 233
Q ss_pred ccEEEecH---H-HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHH
Q 023305 93 LKRVLSHP---Q-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAA 147 (284)
Q Consensus 93 i~~V~SHp---q-al~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 147 (284)
..-|.--+ . ...+...|++..++. ...++|......+++.+ ...++.+...+
T Consensus 188 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~g~~~~p~~~~ 246 (296)
T PRK09906 188 VNFISTDPAYSGSLAPIIKAWFAQHNSQPNIVQVATNILVTMNLVGMG---LGCTIIPGYMN 246 (296)
T ss_pred CCEEeccCCCCchHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcEEEeeHHHh
Confidence 33343221 1 134456677765543 34566777777777764 23556665544
No 163
>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=63.74 E-value=79 Score=25.68 Aligned_cols=122 Identities=15% Similarity=0.037 Sum_probs=61.0
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc--
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 93 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i-- 93 (284)
.+|+.++.... +-.++.+.+.+|++|+|+.+-.....+.+ ....|.+.++.+ +.+.+|-|......+++|+
T Consensus 25 ~~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~--~~~~l~~~~~~~----v~~~~hpl~~~~~i~~~~l~~ 98 (198)
T cd08413 25 RYPKVKLSLHQGTPSQIAEMVLKGEADIAIATEALDDHPDL--VTLPCYRWNHCV----IVPPGHPLADLGPLTLEDLAQ 98 (198)
T ss_pred hCCceEEEEEeCCHHHHHHHHHcCCCCEEEEccCCCCCCCc--EEEEeeeeeEEE----EecCCCcccccCCCCHHHHhc
Confidence 35666654433 45788999999999999985211000100 011122222222 2344454443322333333
Q ss_pred -cEEEecH-H-HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHH
Q 023305 94 -KRVLSHP-Q-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAA 147 (284)
Q Consensus 94 -~~V~SHp-q-al~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 147 (284)
.-|.-.+ . -..+.+.|+++.+.. ...++|......+++.+. ..|+.++..+
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~---Gi~~lp~~~~ 155 (198)
T cd08413 99 YPLITYDFGFTGRSSIDRAFARAGLEPNIVLTALDADVIKTYVRLGL---GVGIIAEMAY 155 (198)
T ss_pred CCEEECCCCccHHHHHHHHHHHcCCCcceEEEeCCHHHHHHHHHhCC---CEEEcccccc
Confidence 2333211 1 223455666665542 345667777777777652 3566666544
No 164
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=63.62 E-value=36 Score=36.81 Aligned_cols=36 Identities=22% Similarity=0.293 Sum_probs=30.5
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceee--eeeee
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLT--KIESR 220 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt--~IeSR 220 (284)
.-|-|.+..+|+||-|+++-++|+..|+|+. +|.+.
T Consensus 813 ~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~ 850 (895)
T PRK00275 813 PVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATL 850 (895)
T ss_pred CeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEec
Confidence 3577777889999999999999999999997 55544
No 165
>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=63.56 E-value=76 Score=25.44 Aligned_cols=122 Identities=14% Similarity=0.101 Sum_probs=60.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcC---C
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD---Q 92 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~---~ 92 (284)
.+|+.++.-. .+..++.+.+.+|++|+|+.+-.....+.. ...|.+.++.+ ..+-+|-+...+..+++ +
T Consensus 26 ~~P~v~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~----v~~~~~pl~~~~~~~~~~l~~ 98 (198)
T cd08446 26 ARPDVTVSLHNMTKDEQIEALRAGRIHIGFGRFYPVEPDIA---VENVAQERLYL----AVPKSHPLAARPAVSLADLRN 98 (198)
T ss_pred HCCCeEEEEeeCCHHHHHHHHHCCCccEEEEecCCCCCCce---eEEeeeccEEE----EEeCCCCcccCCccCHHHHcC
Confidence 4576655433 356778899999999999975321111110 01122223322 22233333222112222 3
Q ss_pred ccEEE-ecH---HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 93 LKRVL-SHP---QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 93 i~~V~-SHp---qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
..-|. ..+ ....+...|+.+.+.. ...++|...+.++++.+ ...++.++..++
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (198)
T cd08446 99 EPLILFPRGGRPSFADEVLGLFRRAGVEPRVAQEVEDVVAALALVAAG---FGVCIVPESVAA 158 (198)
T ss_pred CCEEEeccccChHHHHHHHHHHHHCCCCCCcceecCCHHHHHHHHHcC---CcEEEchhhhhc
Confidence 33343 111 1123345566665432 24566777777777764 346777766543
No 166
>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=63.29 E-value=1.4e+02 Score=28.26 Aligned_cols=130 Identities=14% Similarity=0.043 Sum_probs=68.4
Q ss_pred CCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEE-EeeeeEeeecCCCCcCCc--cEE
Q 023305 20 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQ-LAANFCLLALPGIKADQL--KRV 96 (284)
Q Consensus 20 ~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~-l~I~~~L~~~~~~~l~~i--~~V 96 (284)
+++++.+++..++++++.+|++|+|.+--.-++. .-.-...++.|+.-.. -.-...+++++..+++|+ |+|
T Consensus 36 ~Ve~~~f~~~~~~l~Al~aG~iD~~~~g~~~~~~------~~~a~g~~~~iv~v~~~~~g~~~ivv~~i~svaDLKGKkI 109 (328)
T TIGR03427 36 TIEVVQINDYVESINQYTAGKFDGCTMTNMDALT------IPAAGGVDTTALIVGDFSNGNDGIVLKGGKSLADLKGQKV 109 (328)
T ss_pred eEEEEECCChHHHHHHHHcCCCCEEeecCHHHHH------HHHhCCCCeEEEEEEccCCCceEEEECCCCCHHHcCCCEE
Confidence 4678999999999999999999998652110000 0000112333322111 111234556554567777 488
Q ss_pred EecHHHHHH--HHHHHHhcC-----CeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHH---hcCCceeec
Q 023305 97 LSHPQALAS--SDIVLTQLG-----VARENVDDTASAAQYVASNGLRDAGAVASARAAE---IYGLNILAD 157 (284)
Q Consensus 97 ~SHpqal~Q--c~~fl~~~~-----~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~---~ygL~il~~ 157 (284)
..++-...+ ..+.|++.+ ++.+.... +.+...+..+ .-+.+++-...... ..|..+|..
T Consensus 110 av~~gs~~~~ll~~aL~~aGL~~~DV~~v~~~~-~d~~aAl~~G-~VDAa~~~eP~~s~~~~~~g~~~l~~ 178 (328)
T TIGR03427 110 NLVELSVSHYLLARALESVGLSEKDVKVVNTSD-ADIVAAFITK-DVTAVVTWNPQLSEIKAQPGANEVFD 178 (328)
T ss_pred eccCCChHHHHHHHHHHHcCCCHHHeEEEeCCh-HHHHHHHhcC-CCcEEEEcCchHHHHHhCCCcEEecc
Confidence 765554443 334455544 44555543 5555555554 35555554444332 246666644
No 167
>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=63.16 E-value=78 Score=25.44 Aligned_cols=122 Identities=11% Similarity=0.007 Sum_probs=60.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecc-cceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSS-SGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK 94 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~-~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~ 94 (284)
.+|+.++.-. .+-.++.+.+.+|++|+|++.-.... .+. .....|.+.++.++ .+-+|-|......+++|+.
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~--l~~~~l~~~~~~~~----~~~~hpl~~~~~i~~~dL~ 98 (198)
T cd08437 25 TGLMIQIDTYEGGSAELLEQLLQGDLDIALLGSLTPLENSA--LHSKIIKTQHFMII----VSKDHPLAKAKKVNFADLK 98 (198)
T ss_pred hCCceEEEEEEcCHHHHHHHHHcCCCCEEEecCCCCCCccc--ceEEEeecceEEEE----ecCCCcccccCcccHHHHc
Confidence 3566665443 46788999999999999998532110 010 01122233333332 2233433322223333332
Q ss_pred ---EEEe-cHH-HHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHH
Q 023305 95 ---RVLS-HPQ-ALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAA 147 (284)
Q Consensus 95 ---~V~S-Hpq-al~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 147 (284)
-|.- ... --.+...++.+.+.. . ..++|.....++++.+ ...++.+...+
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~ 156 (198)
T cd08437 99 KENFILLNEHFVHPKAFDSLCQQANFQPNIVYRTNDIHILKSMVREN---VGIGFLTDIAV 156 (198)
T ss_pred CCCeEEecccchHHHHHHHHHHHcCCCccEEEEeCcHHHHHHHHHcC---CcEEEEEhhhc
Confidence 2321 111 123455666665432 3 4456666666777765 23667776544
No 168
>PRK03059 PII uridylyl-transferase; Provisional
Probab=62.88 E-value=41 Score=36.12 Aligned_cols=36 Identities=19% Similarity=0.360 Sum_probs=30.4
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceee--eeeee
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLT--KIESR 220 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt--~IeSR 220 (284)
..|.|.+..+|+||-|+++-++|+..|+|+. ||.+.
T Consensus 785 ~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~ 822 (856)
T PRK03059 785 QYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTL 822 (856)
T ss_pred CEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeec
Confidence 4677778889999999999999999999998 44443
No 169
>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=62.77 E-value=95 Score=26.30 Aligned_cols=105 Identities=17% Similarity=0.080 Sum_probs=67.4
Q ss_pred CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcC---Cc--cE
Q 023305 21 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD---QL--KR 95 (284)
Q Consensus 21 ~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~---~i--~~ 95 (284)
++++...+..++++++.+|++|+|+......+ ...-...++++++...-.-...|+++++..+. |+ |+
T Consensus 23 ve~~~~~~~~~~~~~l~~G~~D~~~~~~~~~~-------~~~~~g~~~~~i~~~~~~~~~~l~~~~~s~i~~~~DLkGK~ 95 (216)
T PF09084_consen 23 VEIVFFGGGGDVLEALASGKADIAVAGPDAVL-------FARAKGADIKIIAASYQSSPNALVVRKDSGIKSPADLKGKK 95 (216)
T ss_dssp EEEEEESSHHHHHHHHHTTSHSEEEEECHHHH-------HHHHTTSTEEEEEEEEEECCEEEEEETTTS-SSGGGGTTSE
T ss_pred EEEEEecChhHHHHHHhcCCceEEeccchHHH-------HHHhcCCeeEEEEEecCCCceEEEEeccCCCCCHHHhCCCE
Confidence 68899999999999999999999987654221 11112357888887775556778887765443 33 46
Q ss_pred EEecH--HHHHHHHHHHHhcCC-----eEEecCCHHHHHHHHHhc
Q 023305 96 VLSHP--QALASSDIVLTQLGV-----ARENVDDTASAAQYVASN 133 (284)
Q Consensus 96 V~SHp--qal~Qc~~fl~~~~~-----~~~~~~sTa~Aa~~v~~~ 133 (284)
|...+ .....-+.+|+++++ +.+.. +....+..+.++
T Consensus 96 i~v~~~s~~~~~~~~~l~~~g~~~~~v~~v~~-~~~~~~~al~~g 139 (216)
T PF09084_consen 96 IGVSRGSSSEYFLRALLKKNGIDPDDVKIVNL-GPPELAQALLSG 139 (216)
T ss_dssp EEESTTSHHHHHHHHHHHHTTT-GGGSEEEES--HHHHHHHHHTT
T ss_pred EEEecCcchhHHHHHHHHHhccccccceeeee-ehhhhhhhhhcC
Confidence 76666 344455677777654 33333 355555566655
No 170
>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=62.75 E-value=14 Score=33.34 Aligned_cols=43 Identities=21% Similarity=0.104 Sum_probs=34.5
Q ss_pred CCCcHHHHHHHhh-CCCCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKA-YPKCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~-f~~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
+.|++.+....+. ++..+++.+++.++++++|.+|++|+.+..
T Consensus 150 ~~g~~~~~~l~~~~~~~~~i~~~~~~~~~i~~L~~grvDa~i~d 193 (275)
T TIGR02995 150 PGGGTEEKLAREAGVKREQIIVVPDGQSGLKMVQDGRADAYSLT 193 (275)
T ss_pred eCCcHHHHHHHHcCCChhhEEEeCCHHHHHHHHHcCCCCEEecC
Confidence 5677777666653 355678899999999999999999988775
No 171
>smart00079 PBPe Eukaryotic homologues of bacterial periplasmic substrate binding proteins. Prokaryotic homologues are represented by a separate alignment: PBPb
Probab=62.48 E-value=15 Score=28.86 Aligned_cols=74 Identities=14% Similarity=0.053 Sum_probs=47.7
Q ss_pred CCCcHHHHHHHhhCCC-----------CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccc-cCCeEEEE
Q 023305 5 LPGSFSEDAALKAYPK-----------CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLL-RHRLHIVG 72 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~~-----------~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~-~~~l~I~~ 72 (284)
..||+.+..+++..+. .++..+++..+++.+|.+|+ |..+.. ++.... ++. ..++.+++
T Consensus 19 ~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-da~v~d--~~~~~~------~~~~~~~~~~~~ 89 (134)
T smart00079 19 IRGSSTLAFFKRSGNPEYSRMWNYMSASPSVFVKSYAEGVQRVRVSN-YAFLME--STYLDY------ELSQNCDLMTVG 89 (134)
T ss_pred ecCchHHHHHHhCCChHHHHHHHHHHhCCCCCCCCHHHHHHHHHcCC-CEEEee--hHhHHH------HHhCCCCeEEcC
Confidence 4689999888876543 25678999999999999999 865554 222211 111 23466776
Q ss_pred EEEEeeeeEeeecCC
Q 023305 73 EVQLAANFCLLALPG 87 (284)
Q Consensus 73 E~~l~I~~~L~~~~~ 87 (284)
+..-+-..+++.+++
T Consensus 90 ~~~~~~~~~ia~~k~ 104 (134)
T smart00079 90 ENFGRKGYGIAFPKG 104 (134)
T ss_pred cccCCCceEEEecCC
Confidence 654444555655554
No 172
>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=62.28 E-value=59 Score=26.39 Aligned_cols=121 Identities=20% Similarity=0.130 Sum_probs=62.2
Q ss_pred hCCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc--
Q 023305 17 AYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK-- 94 (284)
Q Consensus 17 ~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~-- 94 (284)
.+|+.++.......++.+.+.+|++|+|+........+ + ....|.+..+.++ .+-+|-|... ..+++|+.
T Consensus 25 ~~P~v~v~l~~~~~~~~~~l~~g~~D~~i~~~~~~~~~-~--~~~~l~~~~~~~v----~~~~hpl~~~-~~~l~dl~~~ 96 (200)
T cd08460 25 EAPGVRLRFVPESDKDVDALREGRIDLEIGVLGPTGPE-I--RVQTLFRDRFVGV----VRAGHPLARG-PITPERYAAA 96 (200)
T ss_pred HCCCCEEEEecCchhHHHHHHCCCccEEEecCCCCCcc-h--heeeeeccceEEE----EeCCCCCCCC-CCCHHHHhcC
Confidence 35766655443333889999999999999843211111 0 1122222333322 2334444322 12333333
Q ss_pred -EEE-ecHH-HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 -RVL-SHPQ-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 -~V~-SHpq-al~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
-|. +... .-.+..+|+++.+.. ...++|...+..+++.+ ...|+.+...++
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 124467777776543 24567777777888765 236677766554
No 173
>PRK11917 bifunctional adhesin/ABC transporter aspartate/glutamate-binding protein; Reviewed
Probab=61.78 E-value=23 Score=31.82 Aligned_cols=88 Identities=9% Similarity=0.047 Sum_probs=50.2
Q ss_pred CCcHHHHHHHhhC----CCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeE
Q 023305 6 PGSFSEDAALKAY----PKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFC 81 (284)
Q Consensus 6 ~GtfS~~Aa~~~f----~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~ 81 (284)
.||..+....++. ...+++..++..+++++|.+|++|..+..- ....+. ...+..++++..-+..++
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 234667899999999999999999775531 111111 112233444333334445
Q ss_pred eeecCCCCcCCccEEEecHHHHHHHHHHHHhc
Q 023305 82 LLALPGIKADQLKRVLSHPQALASSDIVLTQL 113 (284)
Q Consensus 82 L~~~~~~~l~~i~~V~SHpqal~Qc~~fl~~~ 113 (284)
++.+++ +++-..+...+|.++
T Consensus 226 ~a~~k~-----------~~~l~~~ln~~l~~~ 246 (259)
T PRK11917 226 IVTKKD-----------DPAFAKYVDDFVKEH 246 (259)
T ss_pred EEEeCC-----------CHHHHHHHHHHHHHH
Confidence 555544 466677777887653
No 174
>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=61.54 E-value=1.1e+02 Score=26.74 Aligned_cols=118 Identities=18% Similarity=0.180 Sum_probs=61.4
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc---
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL--- 93 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i--- 93 (284)
+|+.++.- ..+..++++.+.+|++|+|++.......+. ....|...++.++. +-+|-|...+..+++|+
T Consensus 110 ~p~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~lv~----s~~~pl~~~~~i~~~~L~~~ 182 (279)
T TIGR03339 110 YPGIEVSVRIGNSQEVLQALQSYRVDVAVSSEVVDDPRL---DRVVLGNDPLVAVV----HRQHPLAERESVTLEELAGQ 182 (279)
T ss_pred CCCcEEEEEECCHHHHHHHHHcCCCcEEEEecccCCCce---EEEEcCCceEEEEE----CCCCccccCCCcCHHHHhCC
Confidence 56666543 467889999999999999998533222211 11112222222221 22232322222233333
Q ss_pred cEEEecH--HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchh
Q 023305 94 KRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASAR 145 (284)
Q Consensus 94 ~~V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~ 145 (284)
.-|...+ ........|+.+.+.. ...++|...+.+++..+ . ..++.+..
T Consensus 183 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~-gi~~lp~~ 236 (279)
T TIGR03339 183 PLLMREPGSVTRQTTEEALAAAGVAPRPALEIGSREAIREAVLAG--L-GVSVVSAA 236 (279)
T ss_pred CeEEecCCCChHHHHHHHHHHcCCCccEEEEeCCHHHHHHHHHcC--C-CEEEcchh
Confidence 3343222 1234567777776532 34567777777777765 2 35666654
No 175
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=61.49 E-value=23 Score=35.62 Aligned_cols=59 Identities=19% Similarity=0.352 Sum_probs=44.3
Q ss_pred EEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 189 IVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 189 i~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
|-+...|+.|--.++|..|..++|||..||=-|.. ..|+++.. .+....+.+++++++.
T Consensus 3 l~~~~~dr~g~~~~~l~~~~~~~~~~~~~e~~~~~--------------------~~~~~~~~-~~~~~~~~~~~~~~~~ 61 (520)
T PRK10820 3 LEVFCEDRLGLTRELLDLLVLRSIDLRGIEIDPIG--------------------RIYLNFAE-LEFESFSSLMAEIRRI 61 (520)
T ss_pred EEEEeeccccHHHHHHHHHHhcCCCccEEEEcCCC--------------------eEEEeCCC-cChhhHHHHHHHHhcC
Confidence 44566799999999999999999999999975531 26777763 3444566777777643
No 176
>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=61.31 E-value=20 Score=23.23 Aligned_cols=27 Identities=30% Similarity=0.370 Sum_probs=23.6
Q ss_pred CCCchHHHHHHHHHhCCceeeeeeeee
Q 023305 195 EGPGVLFKALAVFALREINLTKIESRP 221 (284)
Q Consensus 195 ~~pGaL~~~L~~F~~~~INLt~IeSRP 221 (284)
+.||.+.++++.+++++|++..+..-.
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~~~~ 38 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMISQSE 38 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEEcCC
Confidence 579999999999999999998776554
No 177
>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=60.97 E-value=46 Score=22.55 Aligned_cols=27 Identities=22% Similarity=0.349 Sum_probs=23.5
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
+++.||.+.++++.+++.|||+--|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~q 37 (66)
T cd04924 11 MRGTPGVAGRVFGALGKAGINVIMISQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 467899999999999999999987754
No 178
>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=59.90 E-value=93 Score=25.26 Aligned_cols=122 Identities=16% Similarity=0.085 Sum_probs=60.4
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeec--ccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 93 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS--~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i 93 (284)
.+|+.++... .+-.++.+.+.+|++|+|++.-.+. ....+. ...|.+.++.++ .+-+|-+.. ..+++++
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~~~--~~~l~~~~~~~~----~~~~hpl~~--~~~~~~L 96 (202)
T cd08468 25 LAPSVRLNLVHAEQKLPLDALLAGEIDFALGYSHDDGAEPRLIE--ERDWWEDTYVVI----ASRDHPRLS--RLTLDAF 96 (202)
T ss_pred hCCCCEEEEEECChHhHHHHHHCCCccEEEecccccccCCCCEE--EEEEecCcEEEE----EeCCCCCcC--CCCHHHH
Confidence 3566666444 4678999999999999999853321 011110 011222232222 122222221 1223332
Q ss_pred ---cEEEec--HHHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 94 ---KRVLSH--PQALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 94 ---~~V~SH--pqal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
..|... ...-.+...++.+.+.. ...++|.....++++.+ +..++.++.+++.
T Consensus 97 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~---~~~~~~p~~~~~~ 157 (202)
T cd08468 97 LAERHLVVTPWNEDRGVVDQVLEKQGLEREIALQLPNVLNAPFIVASS---DLLMTLPRQAARA 157 (202)
T ss_pred hhCCCeEEecCCCCCchHHHHHHHcCCCceEEEEcChhHhHHHHHhcC---CeeeecHHHHHHH
Confidence 112111 11123455666665542 34566666666666543 4577888877664
No 179
>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=59.45 E-value=95 Score=25.24 Aligned_cols=122 Identities=14% Similarity=0.088 Sum_probs=60.6
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc-
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 94 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~- 94 (284)
.+|+.++.-. .+..++.+.+.+|++|+|+..-.-.....+. ...|.+.++.++ .+-+|-+......+++++.
T Consensus 25 ~~P~~~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~--~~~l~~~~~~~v----~~~~hpl~~~~~i~~~~l~~ 98 (198)
T cd08443 25 RYPRVSLQMHQGSPTQIAEMVSKGLVDFAIATEALHDYDDLI--TLPCYHWNRCVV----VKRDHPLADKQSISIEELAT 98 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEEeccccccCCce--EeeeeeceEEEE----EcCCCccccCCCCCHHHHhc
Confidence 4566665443 4678899999999999999742100011110 112222333332 2233444332222333333
Q ss_pred -EEEecHH--H-HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHH
Q 023305 95 -RVLSHPQ--A-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAA 147 (284)
Q Consensus 95 -~V~SHpq--a-l~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 147 (284)
...+++. . ......|+++.+.. ...+++.....++++.+ ...|+.+...+
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~~p~~~~ 155 (198)
T cd08443 99 YPIVTYTFGFTGRSELDTAFNRAGLTPNIVLTATDADVIKTYVRLG---LGVGVIASMAY 155 (198)
T ss_pred CCEEEecCCccHHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CcEEEeecccc
Confidence 2333332 1 22344556555543 34567777777777765 23556666544
No 180
>PRK11716 DNA-binding transcriptional regulator IlvY; Provisional
Probab=59.43 E-value=1.2e+02 Score=26.35 Aligned_cols=122 Identities=16% Similarity=0.121 Sum_probs=61.4
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecC----CCCcCC
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALP----GIKADQ 92 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~----~~~l~~ 92 (284)
+++.++.. ..+.+++.+.+.+|++|+|++...+...+.+. ...|...++.++. +-+|.+.... -.++.+
T Consensus 93 ~p~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~~~--~~~l~~~~~~~v~----~~~~~~~~~~~~~~~~~l~~ 166 (269)
T PRK11716 93 HPLVEIKLTTGDAADAVEKVQSGEADLAIAAKPETLPASVA--FSPIDEIPLVLIA----PALPCPVRQQLSQEKPDWSR 166 (269)
T ss_pred CCCeEEEEEECCHHHHHHHHHCCCccEEEEecCCCCCcceE--EEEcccceEEEEE----cCCcchhhhccccchhhHhh
Confidence 56665543 35778999999999999999864332222111 1223333444332 3333222111 112333
Q ss_pred ccEEEe-cHHHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 93 LKRVLS-HPQALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 93 i~~V~S-Hpqal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
..-|.. .......-..|+...+.. . ..++|......++..+ ...++.+...++
T Consensus 167 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 223 (269)
T PRK11716 167 IPFILPEHGPARRRIDLWFRRHKIKPNIYATVSGHEAIVSMVALG---CGVGLLPEVVLE 223 (269)
T ss_pred CCeeecCCCchHHHHHHHHHHcCCCCCeEEEechHHHHHHHHHcC---CCeEeccHHHhh
Confidence 333331 111122234566655432 2 3456666666677764 246788876664
No 181
>PRK12680 transcriptional regulator CysB-like protein; Reviewed
Probab=59.21 E-value=1.5e+02 Score=27.44 Aligned_cols=122 Identities=16% Similarity=0.085 Sum_probs=64.6
Q ss_pred CCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeec-CCCCcCCc--
Q 023305 18 YPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLAL-PGIKADQL-- 93 (284)
Q Consensus 18 f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~-~~~~l~~i-- 93 (284)
+|+.++.... +.+++++++.+|++|+||++--+...+... ...|.+..+. +.++..|-|... ...+++|+
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 5666665443 568999999999999999863211111111 1112233333 234556665432 12333333
Q ss_pred -cEEEecH-HHH-HHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 -KRVLSHP-QAL-ASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 -~~V~SHp-qal-~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|..-+ ... ....+|++..+.. ...+++.....++|+.+ . ..|+.+..++.
T Consensus 193 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~G--~-Gia~lp~~~~~ 250 (327)
T PRK12680 193 HPLISYESSTRPGSSLQRAFAQLGLEPSIALTALDADLIKTYVRAG--L-GVGLLAEMAVN 250 (327)
T ss_pred CCEEEecCCCchHHHHHHHHHHCCCCCcEEEEECCHHHHHHHHHcC--C-CEEEeechhcc
Confidence 3333222 122 4466677766532 34566777777777765 2 35666665443
No 182
>PRK09224 threonine dehydratase; Reviewed
Probab=58.86 E-value=25 Score=35.30 Aligned_cols=35 Identities=26% Similarity=0.381 Sum_probs=30.9
Q ss_pred ceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeee
Q 023305 185 FKTSIVFTLDEGPGVLFKALAVFALREINLTKIESR 220 (284)
Q Consensus 185 ~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSR 220 (284)
+..-+.|.+|.+||+|.+.|+.+. -+-|+|.+|=|
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 355678899999999999999887 78999999998
No 183
>TIGR00070 hisG ATP phosphoribosyltransferase. Members of this family from B. subtilis, Aquifex aeolicus, and Synechocystis PCC6803 (and related taxa) lack the C-terminal third of the sequence. The sole homolog from Archaeoglobus fulgidus lacks the N-terminal 50 residues (as reported) and is otherwise atypical of the rest of the family. This model excludes the C-terminal extension.
Probab=58.76 E-value=66 Score=28.01 Aligned_cols=107 Identities=21% Similarity=0.263 Sum_probs=61.6
Q ss_pred HHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeE---eeecCCCCc---CC--ccEEEe-cH
Q 023305 30 EDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFC---LLALPGIKA---DQ--LKRVLS-HP 100 (284)
Q Consensus 30 ~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~---L~~~~~~~l---~~--i~~V~S-Hp 100 (284)
.|+-.-|+.|.+|+||+= .|.|.+++-.+.--..|+..+| ++++++.+. ++ -++|.+ .|
T Consensus 50 ~Dip~yV~~G~aDlGI~G------------~D~l~E~~~~v~~~~dL~fg~crl~vA~p~~~~~~~~~~l~~~rIATkyp 117 (182)
T TIGR00070 50 QDIPTYVEHGAADLGITG------------YDVLLESGADVYELLDLGFGKCRLVLAVPQESDISSVEDLKGKRIATKYP 117 (182)
T ss_pred chhHHHHhCCCccEEEec------------chhhhhCCCCEEEEeecCcCceEEEEEEECCCCCCChHHhCCCEEEECCH
Confidence 578889999999999753 4555544433333333555544 445544322 22 146776 66
Q ss_pred HHHHHHHHHHHhcCCe--EEecCCHHHHHHHHHhcCCCCeEEE----cchhHHHhcCCceee
Q 023305 101 QALASSDIVLTQLGVA--RENVDDTASAAQYVASNGLRDAGAV----ASARAAEIYGLNILA 156 (284)
Q Consensus 101 qal~Qc~~fl~~~~~~--~~~~~sTa~Aa~~v~~~~~~~~aAI----~s~~aa~~ygL~il~ 156 (284)
. -.++||++++++ .+..+..-++|-. .+-+-|| .+-...+.+||++++
T Consensus 118 ~---i~~~~f~~~Gi~v~ii~l~GsvE~aP~-----~GlaD~IvDiv~TG~TL~~NgL~~ie 171 (182)
T TIGR00070 118 N---LARRYFEKKGIDVEIIKLNGSVELAPL-----LGLADAIVDIVSTGTTLRENGLRIIE 171 (182)
T ss_pred H---HHHHHHHHcCCeEEEEECcceeecccC-----CCceeEEEEEeCCHHHHHHCCCEEee
Confidence 6 456799998754 4555544443321 1112233 345567789999995
No 184
>cd04937 ACT_AKi-DapG-BS_2 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive AK isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The BS AKI is tetrameric consisting of two alpha and two beta subunits; th
Probab=58.31 E-value=43 Score=23.24 Aligned_cols=33 Identities=18% Similarity=0.334 Sum_probs=25.6
Q ss_pred EEEEE-EecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 187 TSIVF-TLDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 187 tsi~f-~~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
.+++- .+.+.||.+.++++.+++.|||+..+-+
T Consensus 4 isvvG~~~~~~~gi~~~if~aL~~~~I~v~~~~~ 37 (64)
T cd04937 4 VTIIGSRIRGVPGVMAKIVGALSKEGIEILQTAD 37 (64)
T ss_pred EEEECCCccCCcCHHHHHHHHHHHCCCCEEEEEc
Confidence 34443 3457899999999999999999975553
No 185
>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=57.88 E-value=52 Score=21.66 Aligned_cols=27 Identities=26% Similarity=0.408 Sum_probs=23.2
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
..+.+|.+.++++.|++++|++-.+..
T Consensus 10 ~~~~~~~~~~i~~~l~~~~i~v~~i~~ 36 (65)
T cd04892 10 MRGTPGVAARIFSALAEAGINIIMISQ 36 (65)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEc
Confidence 356799999999999999999987754
No 186
>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=57.86 E-value=16 Score=25.98 Aligned_cols=28 Identities=14% Similarity=0.144 Sum_probs=24.3
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIESRP 221 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeSRP 221 (284)
+++.||.+.++++.++++|||+-.| ++-
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 187
>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=57.71 E-value=1e+02 Score=25.00 Aligned_cols=122 Identities=11% Similarity=0.050 Sum_probs=62.5
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeee-ecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCc---C
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIE-NSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---D 91 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiE-NS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l---~ 91 (284)
.+|+.++.-. .+-+++.+.+.+|++|+|+..-. +...+. ....|...++. +..+.+|-|...+..++ .
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~~l~~~~~~----~~~~~~hpl~~~~~~~~~~l~ 97 (198)
T cd08444 25 QFPNVHLVLHQGSPEEIASMLANGQADIGIATEALENHPEL---VSFPYYDWHHH----IIVPVGHPLESITPLTIETIA 97 (198)
T ss_pred HCCCeEEEEEeCCHHHHHHHHHCCCccEEEeccccCCCcCc---EEeecccccee----EEecCCCccccCCCcCHHHHh
Confidence 3566665433 45678899999999999997411 000110 01111122221 23344455443222222 3
Q ss_pred CccEEEecHH-H-HHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 92 QLKRVLSHPQ-A-LASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 92 ~i~~V~SHpq-a-l~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
+..-|.-.+. . -.++..|+.+.+. + ...+++...+.++++.+ ...++.+...++
T Consensus 98 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~ 156 (198)
T cd08444 98 KWPIITYHGGFTGRSRIDRAFSRAELTPNIVLSALDADVIKTYVGLG---MGIGIVAEMAFE 156 (198)
T ss_pred CCCEEEecCCCchHHHHHHHHHHcCCCCceEEEeCCHHHHHHHHHcC---CcEEeccHHHHh
Confidence 3344443332 1 2346677776554 2 34566777777777765 236676765544
No 188
>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=57.68 E-value=52 Score=24.54 Aligned_cols=57 Identities=19% Similarity=0.223 Sum_probs=40.2
Q ss_pred cCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcCC
Q 023305 194 DEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFAT 270 (284)
Q Consensus 194 ~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~~ 270 (284)
....|-+.++|++|.++||+.-++ |+.- ......|+=. ...++..++++++|++.+.
T Consensus 12 n~evGF~rk~L~I~E~~~is~Eh~---PSGI----------------D~~Siii~~~-~~~~~~~~~i~~~i~~~~~ 68 (76)
T cd04911 12 NREVGFGRKLLSILEDNGISYEHM---PSGI----------------DDISIIIRDN-QLTDEKEQKILAEIKEELH 68 (76)
T ss_pred cchhcHHHHHHHHHHHcCCCEeee---cCCC----------------ccEEEEEEcc-ccchhhHHHHHHHHHHhcC
Confidence 457999999999999999998655 6542 2344444432 1334488899999988654
No 189
>PRK12682 transcriptional regulator CysB-like protein; Reviewed
Probab=57.55 E-value=1.5e+02 Score=26.87 Aligned_cols=120 Identities=15% Similarity=0.106 Sum_probs=58.5
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeecccc--ccccCCeEEEEEEEEeeeeEeeecCCCCcCCc-
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYD--LLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 93 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d--~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i- 93 (284)
+|+.++.- ..+.+++.+.+.+|++|+||.+-.... .+.++ .+...++ -+..+..|-|......+++++
T Consensus 119 ~P~i~i~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~----~~~l~~~~l~~~~~----~~~~~~~~pl~~~~~~~~~~L~ 190 (309)
T PRK12682 119 YPKVNLSLHQGSPDEIARMVISGEADIGIATESLAD----DPDLATLPCYDWQH----AVIVPPDHPLAQEERITLEDLA 190 (309)
T ss_pred CCCeEEEEecCCHHHHHHHHHcCCccEEEecCcccC----CCcceEEEeeeeeE----EEEecCCCccccCCCcCHHHHh
Confidence 46666544 345789999999999999997522100 00111 0111111 122333343332211222332
Q ss_pred --cEEEecHH-H-HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 --KRVLSHPQ-A-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 --~~V~SHpq-a-l~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|.-.+. . ..+-..|+.+.++. ...++|.....++|..+. ..++.+...++
T Consensus 191 ~~~~i~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~~~~~~~v~~g~---Gi~~lp~~~~~ 249 (309)
T PRK12682 191 EYPLITYHPGFTGRSRIDRAFAAAGLQPDIVLEAIDSDVIKTYVRLGL---GVGIVAEMAYR 249 (309)
T ss_pred cCCceeeCCCccHHHHHHHHHHHcCCCCcEEEEeCCHHHHHHHHHhCC---ceEEehhhhhh
Confidence 22321111 1 12344566655543 245678888888888752 35666665443
No 190
>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=56.41 E-value=1e+02 Score=24.57 Aligned_cols=122 Identities=21% Similarity=0.210 Sum_probs=59.2
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeec-ccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc-
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENS-SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 93 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS-~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i- 93 (284)
.+|+.++.... +-+++++.+.+|++|+|+++.... ..+. ....|.+.++.++ .+-+|-+......+++|+
T Consensus 26 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~~l~~~~~~~~~dL~ 98 (199)
T cd08451 26 AYPDVELTLEEANTAELLEALREGRLDAAFVRPPVARSDGL---VLELLLEEPMLVA----LPAGHPLARERSIPLAALA 98 (199)
T ss_pred HCCCcEEEEecCChHHHHHHHHCCCccEEEEecCCCCCCce---eEEEeecccEEEE----ecCCCCCcccCccCHHHhc
Confidence 45766654433 567889999999999999863321 1111 1111222333332 233344433222233333
Q ss_pred --cEEE-ecH---HHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 --KRVL-SHP---QALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 --~~V~-SHp---qal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|. +.. ....+-..|+.+.+.. . ..++|.....+++..+ ...++.+...++
T Consensus 99 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 159 (199)
T cd08451 99 DEPFILFPRPVGPGLYDAIIAACRRAGFTPRIGQEAPQMASAINLVAAG---LGVSIVPASMRQ 159 (199)
T ss_pred CCCEEEecCCcChhHHHHHHHHHHHcCCceeeEEehhhHHHHHHHHHcC---CCEEEechHHHh
Confidence 2332 111 1122334455554432 2 3455666666666664 236677776554
No 191
>cd08485 PBP2_ClcR The C-terminal substrate binding domain of LysR-type transcriptional regulator ClcR involved in the chlorocatechol catabolism, contains type 2 periplasmic binding fold. In soil bacterium Pseudomonas putida, the ortho-pathways of catechol and 3-chlorocatechol are central catabolic pathways that convert aromatic and chloroaromaric compounds to tricarboxylic acid (TCA) cycle intermediates. The 3-chlorocatechol-degradative pathway is encoded by clcABD operon, which requires the divergently transcribed clcR and an intermediate of the pathway, 2-chloromuconate, as an inducer for activation. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding th
Probab=56.03 E-value=1.1e+02 Score=24.87 Aligned_cols=122 Identities=11% Similarity=0.021 Sum_probs=60.9
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc--
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 93 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i-- 93 (284)
.+|+.++.... +.+++++++.+|++|+|+++-.....|... ..|.+.++.++ .+-.|.+......+++|+
T Consensus 26 ~~P~i~l~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~l~~---~~l~~~~~~~~----~~~~~~~~~~~~v~~~~L~~ 98 (198)
T cd08485 26 VAPSATVSLTQMSKNRQIEALDAGTIDIGFGRFYPYQEGVVV---RNVTNERLFLG----AQKSRARSFGEQVHCSALRN 98 (198)
T ss_pred hCCCcEEEEEECCHHHHHHHHHcCCccEEEecCCCCCCCeEE---EEeeccceEEE----eCCCCccccCCCcCHHHHhc
Confidence 45777665443 677899999999999999853211122111 11222333322 233333322222333333
Q ss_pred -cEEE-ecHH---HHHHHHHHHHhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 -KRVL-SHPQ---ALASSDIVLTQLGV--AR-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 -~~V~-SHpq---al~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|. .++. .-.+-..|+.+.+. +. ..++|.....++|+.+ ...++.++..++
T Consensus 99 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (198)
T cd08485 99 EPLILFPREGRPSFADEVIGVFKNARVEPKVVAIVEDVNAAMALALAG---VGVTIVPETVAM 158 (198)
T ss_pred CCeEecCCCCCccHHHHHHHHHHHcCCCcceEEEcCcHHHHHHHHHcC---CceEECcchhhc
Confidence 3332 2211 12233446665443 22 3456777777777765 236677765443
No 192
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=55.72 E-value=50 Score=32.72 Aligned_cols=43 Identities=16% Similarity=0.166 Sum_probs=31.7
Q ss_pred CCCcHHHHHHHh---hCCCCc--eeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALK---AYPKCE--TVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~---~f~~~~--~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
..||..+....+ .+++.. .+.+.+.++++++|.+|++|+.|+.
T Consensus 155 ~~gS~~~~~L~~l~~~~p~i~~~~~~~~s~~e~l~aL~~G~iDa~v~d 202 (482)
T PRK10859 155 AAGSSHVETLQELKKKYPELSWEESDDKDSEELLEQVAEGKIDYTIAD 202 (482)
T ss_pred ECCCcHHHHHHHHHHhCCCceEEecCCCCHHHHHHHHHCCCCCEEEEC
Confidence 457776665543 245543 3567899999999999999999874
No 193
>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=54.79 E-value=32 Score=23.40 Aligned_cols=27 Identities=22% Similarity=0.391 Sum_probs=23.8
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
+++.||.+.++++.|++.|||+--|..
T Consensus 11 ~~~~~~~~~~i~~~l~~~~I~v~~i~~ 37 (66)
T cd04922 11 MAGTPGVAATFFSALAKANVNIRAIAQ 37 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 467899999999999999999987753
No 194
>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=54.34 E-value=72 Score=22.23 Aligned_cols=34 Identities=18% Similarity=0.249 Sum_probs=27.3
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
+.|++-.+...+|.+.++++.|++.|||+.-|-.
T Consensus 3 ~VsvVG~~~~~~~~~~~i~~aL~~~~I~v~~i~~ 36 (65)
T cd04918 3 IISLIGNVQRSSLILERAFHVLYTKGVNVQMISQ 36 (65)
T ss_pred EEEEECCCCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 4566656556799999999999999999976653
No 195
>cd08436 PBP2_LTTR_like_3 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=53.22 E-value=1.1e+02 Score=24.12 Aligned_cols=33 Identities=18% Similarity=0.070 Sum_probs=24.6
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeee
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIE 49 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiE 49 (284)
.+|+.++.-. .+-.++.+.+.+|++|+|+..-.
T Consensus 25 ~~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (194)
T cd08436 25 RHPGVDIRLRQAGSDDLLAAVREGRLDLAFVGLP 58 (194)
T ss_pred HCCCcEEEEecCCHHHHHHHHHcCCccEEEEecC
Confidence 4676655433 35778999999999999998643
No 196
>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=53.02 E-value=38 Score=23.20 Aligned_cols=27 Identities=19% Similarity=0.260 Sum_probs=23.5
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
+++.||.+.++++.|++.|||+--|..
T Consensus 11 ~~~~~~~~~~if~~L~~~~I~v~~i~q 37 (66)
T cd04919 11 MKNMIGIAGRMFTTLADHRINIEMISQ 37 (66)
T ss_pred CCCCcCHHHHHHHHHHHCCCCEEEEEe
Confidence 356899999999999999999987754
No 197
>PRK09034 aspartate kinase; Reviewed
Probab=52.81 E-value=2.1e+02 Score=28.32 Aligned_cols=126 Identities=16% Similarity=0.086 Sum_probs=73.0
Q ss_pred CeEEecCCHHHHHHHHHhcCCCCeEEEcchhH---HHhcCCceeeccccCCCCCeeEEEEEeeCCCC---CCC---CCCc
Q 023305 115 VARENVDDTASAAQYVASNGLRDAGAVASARA---AEIYGLNILADRIQDEPDNITRFLVLARDPII---PRT---DKLF 185 (284)
Q Consensus 115 ~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~a---a~~ygL~il~~~I~d~~~N~TRF~vl~~~~~~---~~~---~~~~ 185 (284)
++.+..-|..+|.++..-+ |-+-.+.| |..++++|.-.+..+....-|..- ...... +-. ...+
T Consensus 235 A~~l~~lsy~Ea~ela~~G-----akvlhp~ai~~a~~~~Ipi~v~~~~~p~~~GT~I~--~~~~~~~~~~Vk~It~~~~ 307 (454)
T PRK09034 235 PKSIKEITYREMRELSYAG-----FSVFHDEALIPAYRGGIPINIKNTNNPEDPGTLIV--PDRDNKNKNPITGIAGDKG 307 (454)
T ss_pred CeECCccCHHHHHHHHhCC-----cccCCHHHHHHHHHcCCCEEEEcCCCCCCCccEEE--eccccCccccceEEEecCC
Confidence 4566677888888886543 22333333 356899999999877555556542 221111 000 0112
Q ss_pred eEEEEEE---ecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHH
Q 023305 186 KTSIVFT---LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNAL 262 (284)
Q Consensus 186 ktsi~f~---~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al 262 (284)
-+.|-+. .++.||.+.++++.|+++|||+-.| |+. . ....|+|+=+ ..+......++
T Consensus 308 i~~Itv~~~~~~~~~g~~a~if~~la~~~I~Vd~i---~ss-~---------------~sis~~v~~~-~~~~a~~~~l~ 367 (454)
T PRK09034 308 FTSIYISKYLMNREVGFGRKVLQILEDHGISYEHM---PSG-I---------------DDLSIIIRER-QLTPKKEDEIL 367 (454)
T ss_pred EEEEEEccCCCCCCccHHHHHHHHHHHcCCeEEEE---cCC-C---------------cEEEEEEeHH-HhhHHHHHHHH
Confidence 2233332 3457999999999999999999988 221 1 3577888732 22212225666
Q ss_pred HHHHh
Q 023305 263 GHLQE 267 (284)
Q Consensus 263 ~~L~~ 267 (284)
++|++
T Consensus 368 ~el~~ 372 (454)
T PRK09034 368 AEIKQ 372 (454)
T ss_pred HHHHH
Confidence 66653
No 198
>PRK11482 putative DNA-binding transcriptional regulator; Provisional
Probab=52.81 E-value=1.9e+02 Score=26.58 Aligned_cols=122 Identities=16% Similarity=0.156 Sum_probs=64.9
Q ss_pred hhCCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCccE
Q 023305 16 KAYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR 95 (284)
Q Consensus 16 ~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~~ 95 (284)
+.+|+.++... +..++++.+.+|++|+|+.+-.....+... ..|.+.++.+ ..+-+|-|... ..+++|+..
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 34577665433 345789999999999999875432232221 2233334433 23455555432 345555542
Q ss_pred ----E-EecHHHHHHHHHHHHhc--CCeE-EecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 96 ----V-LSHPQALASSDIVLTQL--GVAR-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 96 ----V-~SHpqal~Qc~~fl~~~--~~~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
+ ...+......+.++.+. .... ..+.+......+|+.+ ...+|.+...+..
T Consensus 212 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~ilp~~~~~~ 270 (317)
T PRK11482 212 AEHTLLLPEGQNFSGLRQRLQEMFPDRQISFSSYNILTIAALIASS---DMLGIMPSRFYNL 270 (317)
T ss_pred CCCEEEecCCCCcchHHHHHHHhCCCceEEEEcCcHHHHHHHHHcC---CeeEEeHHHHHHH
Confidence 2 22222212334555543 2232 3455666667777764 3567888776654
No 199
>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=52.70 E-value=2.2e+02 Score=27.36 Aligned_cols=96 Identities=19% Similarity=0.111 Sum_probs=58.4
Q ss_pred CeEEecCCHHHHHHHHHhcCCCCeEEEcchh---HHHhcCCceeeccccCCCCCeeEEEEEeeCCC-CCC-C---CCCce
Q 023305 115 VARENVDDTASAAQYVASNGLRDAGAVASAR---AAEIYGLNILADRIQDEPDNITRFLVLARDPI-IPR-T---DKLFK 186 (284)
Q Consensus 115 ~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~---aa~~ygL~il~~~I~d~~~N~TRF~vl~~~~~-~~~-~---~~~~k 186 (284)
.+.+..-|..+|.++...+ |-+-... -|..++.++.-.+..+.. --|.. .+... .+. . ...+.
T Consensus 190 a~~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~a~~~~i~i~i~~~~~~~-~gT~I---~~~~~~~~~v~~I~~~~~v 260 (401)
T TIGR00656 190 AKRIDKISYEEALELATFG-----AKVLHPRTVEPAMRSGVPIEVRSSFDPE-EGTLI---TNSMENPPLVKGIALRKNV 260 (401)
T ss_pred cEECCccCHHHHHHHHHcC-----CcccCHHHHHHHHHCCCeEEEEECCCCC-CCeEE---EeCcccCCceEEEEEECCE
Confidence 4456666788888877643 2233333 345689999888876543 23433 22211 111 0 01123
Q ss_pred EEEEEE---ecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 187 TSIVFT---LDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 187 tsi~f~---~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
+-+.+. +.++||.+.++++.|++++||+-.|..
T Consensus 261 a~vsv~g~~~~~~~g~~~~if~~L~~~~I~i~~i~~ 296 (401)
T TIGR00656 261 TRVTVHGLGMLGKRGFLARIFGALAERNINVDLISQ 296 (401)
T ss_pred EEEEEecCCCCCCccHHHHHHHHHHHcCCcEEEEEc
Confidence 333333 568899999999999999999987754
No 200
>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=52.62 E-value=1.2e+02 Score=24.21 Aligned_cols=122 Identities=17% Similarity=0.056 Sum_probs=60.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc-
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 94 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~- 94 (284)
.+|+.++... .+-.++.+.+.+|++|+|++.-.-...+. ....|.+.++.++. +-.|-+...+..+++++.
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~pl~~~~~~~~~~l~~ 97 (198)
T cd08421 25 AHPDVRIDLEERLSADIVRAVAEGRADLGIVAGNVDAAGL---ETRPYRTDRLVVVV----PRDHPLAGRASVAFADTLD 97 (198)
T ss_pred HCCCceEEEEecCcHHHHHHHhcCCceEEEEecCCCCCCc---EEEEeecCcEEEEe----CCCCCccccCCCCHHHhcC
Confidence 3566665433 46788999999999999998532111111 11222333333322 223333222222333332
Q ss_pred --EEEecHH--HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 --RVLSHPQ--ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 --~V~SHpq--al~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
-|.-.+. ...++..++.+.+.+ ...++|...+..+++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08421 98 HDFVGLPAGSALHTFLREAAARLGRRLRLRVQVSSFDAVCRMVAAG---LGIGIVPESAAR 155 (198)
T ss_pred CceEeecCCcchHHHHHHHHHHcCCCceEEEEECCHHHHHHHHHcC---CCeEEccchhhh
Confidence 2321111 122344555554433 24566777777777764 346777776555
No 201
>COG0725 ModA ABC-type molybdate transport system, periplasmic component [Inorganic ion transport and metabolism]
Probab=52.49 E-value=27 Score=31.93 Aligned_cols=46 Identities=17% Similarity=0.086 Sum_probs=37.4
Q ss_pred CCCCcHHHHHHHhhC--C--CCceeecCCHHHHHHHHHhCCCCeEEEeee
Q 023305 4 GLPGSFSEDAALKAY--P--KCETVPCDEFEDTFKAVELWLADKAVLPIE 49 (284)
Q Consensus 4 Gp~GtfS~~Aa~~~f--~--~~~~~~~~s~~~v~~av~~~~~d~gvvPiE 49 (284)
-|.|-|+.++-.+.- . ...++...+..+++..|++|++|+|+|=.-
T Consensus 146 ~P~G~ya~~~l~~~g~~~~~~~k~v~~~~v~~~l~~V~~G~ad~g~vy~s 195 (258)
T COG0725 146 VPAGKYAKEALELLGLWYTLKDKLVLATNVRQALAYVETGEADAGFVYVS 195 (258)
T ss_pred CCchHHHHHHHHHhchhhhccccEEecCcHHHHHHHHHcCCCCeEEEEEE
Confidence 589999999877531 1 246788999999999999999999999643
No 202
>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=51.99 E-value=1.2e+02 Score=24.25 Aligned_cols=119 Identities=13% Similarity=0.036 Sum_probs=59.4
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc--
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 93 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i-- 93 (284)
.+|+.++.... +-+++++.+.+|++|+|++.......+.. ...|.+..+.+ ..+-.|.+...+..+++|+
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08457 25 LRPNLHLSLMGLSSSQVLEAVASGRADLGIADGPLEERQGF---LIETRSLPAVV----AVPMGHPLAQLDVVSPQDLAG 97 (196)
T ss_pred HCCCeEEEEEecCcHHHHHHHHcCCccEEEeccCCCCCCcE---EEEeccCCeEE----EeeCCCccccCCccCHHHhCC
Confidence 35666554433 35788999999999999986432211111 11122223322 2233444433322233333
Q ss_pred -cEEE-ecHH-HHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchh
Q 023305 94 -KRVL-SHPQ-ALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASAR 145 (284)
Q Consensus 94 -~~V~-SHpq-al~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~ 145 (284)
.-|. ++.. .......++.+.+. . ...++|...+.++++.+ ...++.+..
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~ 152 (196)
T cd08457 98 ERIITLENGYLFRMRVEVALGKIGVKRRPIIEVNLSHTALSLVREG---LGIAIIDPA 152 (196)
T ss_pred CceEecCCCccHHHHHHHHHHHcCCCCceEEEeccHHHHHHHHHcC---CeEEEEChH
Confidence 3333 2222 22445666766543 2 34566666666666664 235566544
No 203
>COG0834 HisJ ABC-type amino acid transport/signal transduction systems, periplasmic component/domain [Amino acid transport and metabolism / Signal transduction mechanisms]
Probab=51.39 E-value=26 Score=30.66 Aligned_cols=42 Identities=26% Similarity=0.253 Sum_probs=33.5
Q ss_pred CCcH--HHHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 6 PGSF--SEDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 6 ~Gtf--S~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
.||. .+.......+..+++.+++..+++.++.+|++|..+..
T Consensus 153 ~gt~~~~~~~~~~~~~~~~~~~~~~~~~~~~al~~Gr~Da~~~d 196 (275)
T COG0834 153 LGTTDEAEEKAKKPGPNAKIVAYDSNAEALLALKNGRADAVVSD 196 (275)
T ss_pred cCcchhHHHHHhhccCCceEEeeCCHHHHHHHHHcCCccEEEcc
Confidence 4666 44555444566889999999999999999999999875
No 204
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=51.33 E-value=1.5e+02 Score=26.15 Aligned_cols=119 Identities=14% Similarity=0.053 Sum_probs=65.5
Q ss_pred CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecC------C-CCcCCc
Q 023305 21 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALP------G-IKADQL 93 (284)
Q Consensus 21 ~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~------~-~~l~~i 93 (284)
++++.+.+-.++.+++.+|++|++.+ ...++.+.-.-. .-...++.+++-...- ..+++++. + .+++|+
T Consensus 37 ve~~~~~~g~~~~~al~~G~iD~a~~-~~~~~~~~~~g~--~~~~~~~~~~~~~~~~-g~~lvv~~~~~~~~~~~~~~dl 112 (252)
T PF13379_consen 37 VEWVQFASGADILEALAAGEIDIAFV-LAPALIAIAKGA--GGPDVDIVVLAGLSQN-GNALVVRNDLKDASDIKSLADL 112 (252)
T ss_dssp EEEEEESSHHHHHHHHHCTSSSEEEE-CTHHHHHHHTTT--TT----EEEEEECSBS-SEEEEECGGGTTCSTTCCGHHH
T ss_pred EEEEEcCCHHHHHHHHHcCCCCEEEe-chHHHHHHHcCC--CCcccceEEeeccCCC-ceEEEEcCccccCCCccCHHHH
Confidence 67899999999999999999999999 443332211100 0011234444332221 13455553 2 245555
Q ss_pred ---------cEEEe-cHHH--HHHHHHHHHhcC------CeEEecCCHHHHHHHHHhcCCCCeEEEcchh
Q 023305 94 ---------KRVLS-HPQA--LASSDIVLTQLG------VARENVDDTASAAQYVASNGLRDAGAVASAR 145 (284)
Q Consensus 94 ---------~~V~S-Hpqa--l~Qc~~fl~~~~------~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~ 145 (284)
++|.. ++-. ....+.+|++.+ ++.+.... .++...++.+ .-+.+++..+.
T Consensus 113 ~~~~~~~kGk~i~~~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g-~iDa~~~~eP~ 180 (252)
T PF13379_consen 113 IKKRKAQKGKKIAVPFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAG-EIDAAVLWEPF 180 (252)
T ss_dssp HHTCCSCSTEEEEESSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTT-S-SEEEEETTH
T ss_pred HhhhcccCCcEEEEcCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCC-CcCEEEecCCH
Confidence 46666 5533 344678888754 34455555 7777777765 34555554444
No 205
>TIGR01096 3A0103s03R lysine-arginine-ornithine-binding periplasmic protein.
Probab=51.10 E-value=1.6e+02 Score=25.34 Aligned_cols=114 Identities=16% Similarity=0.179 Sum_probs=59.3
Q ss_pred CCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCC----CcCCc--
Q 023305 20 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI----KADQL-- 93 (284)
Q Consensus 20 ~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~----~l~~i-- 93 (284)
+.++++. +..++++++.+|++|.++.++..+.+-. ..+.. ..++ ......++.+.+. .++|+
T Consensus 64 ~~~~~~~-~~~~~~~~l~~G~~D~~~~~~~~~~~r~--~~~~~--s~p~-------~~~~~~~~~~~~~~~~~~~~dl~g 131 (250)
T TIGR01096 64 KCKFVEQ-NFDGLIPSLKAKKVDAIMATMSITPKRQ--KQIDF--SDPY-------YATGQGFVVKKGSDLAKTLEDLDG 131 (250)
T ss_pred eEEEEeC-CHHHHHHHHhCCCcCEEEecCccCHHHh--hcccc--ccch-------hcCCeEEEEECCCCcCCChHHcCC
Confidence 4677884 6899999999999999865432221110 00110 0011 1112233333321 12223
Q ss_pred cEEEecHHHHHHHHHHHHhc---CCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 94 KRVLSHPQALASSDIVLTQL---GVARENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 94 ~~V~SHpqal~Qc~~fl~~~---~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
++|.. .....+. .++.+. ++..+.+.|..++.+++..+ +-.++|++...+..
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 13322 2222222 344432 56677788999999998876 33466776665544
No 206
>PRK10216 DNA-binding transcriptional regulator YidZ; Provisional
Probab=51.09 E-value=1.9e+02 Score=26.28 Aligned_cols=125 Identities=14% Similarity=0.027 Sum_probs=61.4
Q ss_pred hCCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecc----cceee----ccccccccCCeEEEEEEEEeeeeEeeecCCC
Q 023305 17 AYPKCETVPCDEFEDTFKAVELWLADKAVLPIENSS----SGSIH----RNYDLLLRHRLHIVGEVQLAANFCLLALPGI 88 (284)
Q Consensus 17 ~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~----~G~V~----~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~ 88 (284)
.+|+.++.....-.++.+.+.+|++|+|++.- +.. .|... .....|...++.+ .++-+|-+.. ...
T Consensus 122 ~~P~v~v~i~~~~~~~~~~l~~g~~D~~i~~~-~~~~~~~~~~~~~~~~~~~~~l~~~~~~~----v~~~~hp~~~-~~~ 195 (319)
T PRK10216 122 RYPQATIKLRNWDYDSLDAITRGEVDIGFTGR-ESHPRSRELLSLLPLAIDFEVLFSDLPCV----WLRKDHPALH-EEW 195 (319)
T ss_pred HCCCCEEEEEeCCcchHHHHhcCCccEEEecC-CCCccccccccccccccceeeeeecceEE----EEeCCCCccC-CCC
Confidence 35665443332223578999999999999842 111 11100 0111111222222 2344454321 122
Q ss_pred CcCCc---cEEEecH--HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 89 KADQL---KRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 89 ~l~~i---~~V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.++|+ .-|..-+ ....+...++.+.+.. ...++|.....++|+.++ ....+|.++.+++
T Consensus 196 ~~~dL~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~~~-~~gi~ilp~~~~~ 262 (319)
T PRK10216 196 NLDTFLRYPHISICWEQSDTWALDDVLQELGRERTIALSLPEFEQSLFMAAQPD-HLLLATAPRYCQY 262 (319)
T ss_pred CHHHHhhCCCeEecCCCCCcchHHHHHHHhCCccceEEECCcHHHHHHHHHcCC-cceEeccHHHHHH
Confidence 23332 3333211 1233567777765542 356777887888888642 2247888876543
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=50.68 E-value=1.3e+02 Score=24.09 Aligned_cols=122 Identities=19% Similarity=0.115 Sum_probs=61.8
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc--
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 93 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i-- 93 (284)
.+|+.++... .+..++.+.+.+|++|+|++--.....+. ....|.+.++.++. +-.|-+... ..+++|+
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 3577666444 45678999999999999997421111111 11223333444332 223333221 2234444
Q ss_pred -cEEEecHHH-HHHHHHHHHhcCC---e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 94 -KRVLSHPQA-LASSDIVLTQLGV---A-RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 94 -~~V~SHpqa-l~Qc~~fl~~~~~---~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
..+.-.+.. ..+...|+.+.+. + ...++|.....++++.+ ...|+.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08466 97 EKHVVLSLRRGNLSALDLLTEEVLPQRNIAYEVSSLLSMLAVVSQT---DLIAIAPRWLADQ 155 (200)
T ss_pred CCcEEecCCCCcchHHHHHHHhcCCcccEEEEcCchhhHHHHHcCC---CeehhhHHHHHHH
Confidence 223222221 1234555655443 2 34556666666777664 3467778766654
No 208
>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=50.43 E-value=1.2e+02 Score=23.85 Aligned_cols=122 Identities=15% Similarity=0.116 Sum_probs=61.6
Q ss_pred hCCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCC---
Q 023305 17 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ--- 92 (284)
Q Consensus 17 ~f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~--- 92 (284)
.+++.++.. ..+..++.+++.+|++|+|++.......+.. ...|.+.++.++. +-+|-+......++++
T Consensus 25 ~~P~~~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v~----~~~~~~~~~~~i~~~~l~~ 97 (201)
T cd08420 25 RYPEVRVSLTIGNTEEIAERVLDGEIDLGLVEGPVDHPDLI---VEPFAEDELVLVV----PPDHPLAGRKEVTAEELAA 97 (201)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEecCCCCCcceE---EEeecCccEEEEe----cCCCCccccCccCHHHHhc
Confidence 356655433 3466789999999999999986443222211 1122233333322 2233332222222223
Q ss_pred ccEEEecHH--HHHHHHHHHHhcC-----Ce-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 93 LKRVLSHPQ--ALASSDIVLTQLG-----VA-RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 93 i~~V~SHpq--al~Qc~~fl~~~~-----~~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
..-|.-.+. -..+...|+...+ .. ...+.+...+.++++.+ ...|+.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 158 (201)
T cd08420 98 EPWILREPGSGTREVFERALAEAGLDGLDLNIVMELGSTEAIKEAVEAG---LGISILSRLAVR 158 (201)
T ss_pred CCEEEecCCCCHHHHHHHHHHHcCcccccCceEEEECCHHHHHHHHHcC---CCEEEeeHHHHH
Confidence 333332221 1234556666432 22 34566777777777764 347777776554
No 209
>smart00062 PBPb Bacterial periplasmic substrate-binding proteins. bacterial proteins, eukaryotic ones are in PBPe
Probab=49.93 E-value=1.3e+02 Score=24.02 Aligned_cols=109 Identities=17% Similarity=0.162 Sum_probs=60.8
Q ss_pred CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCC---CcCCc--cE
Q 023305 21 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI---KADQL--KR 95 (284)
Q Consensus 21 ~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~---~l~~i--~~ 95 (284)
.++++. +..++++++.+|++|+++.+.....+.. ..+ ............++.+++. +++|+ ++
T Consensus 41 ~~~~~~-~~~~~~~~l~~g~~D~~~~~~~~~~~~~-----~~~------~~~~~~~~~~~~~~~~~~~~~~~~~dL~g~~ 108 (219)
T smart00062 41 VEFVEV-SFDNLLTALKSGKIDVVAAGMTITPERA-----KQV------DFSDPYYKSGQVILVRKDSPIKSLEDLKGKK 108 (219)
T ss_pred EEEEec-cHHHHHHHHHCCcccEEeccccCCHHHH-----hhe------eeccceeeceeEEEEecCCCCCChHHhCCCE
Confidence 567888 8899999999999999987643211110 001 0111112223555555543 23333 24
Q ss_pred EEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcchh
Q 023305 96 VLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASAR 145 (284)
Q Consensus 96 V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~ 145 (284)
|..-+ . .-...++... +...+...+..++.+++..+. . .|++....
T Consensus 109 i~~~~-g-~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~-~-d~~~~~~~ 156 (219)
T smart00062 109 VAVVA-G-TTGEELLKKLYPEAKIVSYDSQAEALAALKAGR-A-DAAVADAP 156 (219)
T ss_pred EEEec-C-ccHHHHHHHhCCCceEEEcCCHHHHHHHhhcCc-c-cEEEeccH
Confidence 44332 1 2233455544 566777888888888887652 3 35555544
No 210
>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=49.44 E-value=1.3e+02 Score=23.91 Aligned_cols=121 Identities=18% Similarity=0.114 Sum_probs=61.0
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc---
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL--- 93 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i--- 93 (284)
+++.++... .+.+++.+.+.+|++|+|+..-.....+. ....|.+.++.++ .+-+|-+...+..+++++
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~hpl~~~~~~~~~~l~~~ 98 (199)
T cd08426 26 YPGVFFTVDVASTADVLEAVLSGEADIGLAFSPPPEPGI---RVHSRQPAPIGAV----VPPGHPLARQPSVTLAQLAGY 98 (199)
T ss_pred CCCeEEEEEeCCcHHHHHHHHCCCccEEEecCCCCCCCe---EEEeeccCcEEEE----ecCCCCcccCCccCHHHHhCC
Confidence 466555433 35688999999999999997533222221 1122222233322 233333332222222222
Q ss_pred cEEEecHH--HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 KRVLSHPQ--ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 ~~V~SHpq--al~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|.-.+. .......|+.+.+.. ...++|...+.+++..+ ...|+.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (199)
T cd08426 99 PLALPPPSFSLRQILDAAFARAGVQLEPVLISNSIETLKQLVAAG---GGISLLTELAVR 155 (199)
T ss_pred CeEecCCcchHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHcC---CCEEEEchHhhh
Confidence 23332211 123455666665432 34567777777888765 246777776543
No 211
>PRK05007 PII uridylyl-transferase; Provisional
Probab=49.27 E-value=66 Score=34.71 Aligned_cols=32 Identities=16% Similarity=0.168 Sum_probs=28.2
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeee
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKI 217 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~I 217 (284)
-|.+.+..+|+||-|+++.++|+.+|+|+..-
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 56777778999999999999999999999843
No 212
>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=49.22 E-value=61 Score=22.90 Aligned_cols=62 Identities=24% Similarity=0.293 Sum_probs=45.6
Q ss_pred EEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCc-HHHHHHHHHHHhc
Q 023305 190 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMAD-PRAQNALGHLQEF 268 (284)
Q Consensus 190 ~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d-~~~~~al~~L~~~ 268 (284)
-|.+++..-++..+|...-..++.-..|...|.. .++.|.|+-.|..+. ..+.+|++.|.+.
T Consensus 2 ~~~~~g~~~tl~N~LRr~ll~~vp~~ai~~~~~~-----------------~~~~~~IeT~g~~~p~~~l~~A~~~l~~~ 64 (66)
T PF01193_consen 2 EFLLKGEDHTLGNALRRILLSEVPGVAIDGHPNE-----------------DKFVFRIETDGSLTPKEALLKAIKILKEK 64 (66)
T ss_dssp EEEEESHHHHHHHHHHHHHHSSSEEEEEEESSEE-----------------EEEEEEEEEBSSS-HHHHHHHHHHHHHHH
T ss_pred EeEEcCCchHHHHHHHHHHHhcCCCceEEecCCC-----------------CEEEEEEEECCCCCHHHHHHHHHHHHHHh
Confidence 4556666678889999888889888888885432 468999999998643 4567777777654
No 213
>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=48.61 E-value=37 Score=23.97 Aligned_cols=33 Identities=36% Similarity=0.409 Sum_probs=26.0
Q ss_pred eEEEEEE-ec-CCCchHHHHHHHHHhCCceeeeee
Q 023305 186 KTSIVFT-LD-EGPGVLFKALAVFALREINLTKIE 218 (284)
Q Consensus 186 ktsi~f~-~~-~~pGaL~~~L~~F~~~~INLt~Ie 218 (284)
+.++.-. ++ +.||.+.++.+.+++.|||+--|-
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 3455555 44 489999999999999999998887
No 214
>COG3978 Acetolactate synthase (isozyme II), small (regulatory) subunit [Function unknown]
Probab=48.56 E-value=1e+02 Score=23.41 Aligned_cols=60 Identities=15% Similarity=0.144 Sum_probs=41.0
Q ss_pred EEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHH
Q 023305 191 FTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHL 265 (284)
Q Consensus 191 f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L 265 (284)
+..+.+|+.|.++|.+-..||.-...+.--+.... ..|+-.|-||=+.+. .-+.+-|++|
T Consensus 8 l~ar~~pe~leRVLrvtrhRGF~vcamnmt~~~da-------------~~~nie~tV~s~R~~--~lL~~QLeKl 67 (86)
T COG3978 8 LSARFNPETLERVLRVTRHRGFRVCAMNMTAAVDA-------------GNANIELTVDSDRSV--DLLTSQLEKL 67 (86)
T ss_pred eeccCChHHHHHHHHHhhhcCeEEEEeeccccccc-------------ccceEEEEEcCCCCh--HHHHHHHHHH
Confidence 45578999999999999999988887766565322 258877777755432 3344444444
No 215
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=48.12 E-value=2e+02 Score=25.52 Aligned_cols=124 Identities=11% Similarity=0.041 Sum_probs=62.1
Q ss_pred hCCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc-
Q 023305 17 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 94 (284)
Q Consensus 17 ~f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~- 94 (284)
.+|+.++.- ..+-+++++++.+|++|+|++.-....... .-....|.+.++.+ ..+-+|-+...+..+++|+.
T Consensus 122 ~~p~i~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~-~l~~~~l~~~~~~~----v~~~~~~l~~~~~~~~~dL~~ 196 (294)
T PRK09986 122 ENPNVEWLLRELSPSMQMAALERRELDAGIWRMADLEPNP-GFTSRRLHESAFAV----AVPEEHPLASRSSVPLKALRN 196 (294)
T ss_pred hCCCeEEEEEeCCHHHHHHHHHcCCCCEEEecCCccCCCC-CeEEEEeecccEEE----EEcCCCCcccCCccCHHHHcC
Confidence 356655433 345688999999999999997321000000 00011122222222 22333333333223344443
Q ss_pred --EEEecH--HHHH-HHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 --RVLSHP--QALA-SSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 --~V~SHp--qal~-Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
-|...+ ..+. +...++.+.+.. ...++|.....++|+.+ ...++.++..++
T Consensus 197 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~l~~~~~~ 255 (294)
T PRK09986 197 EYFITLPFVHSDWGKFLQRVCQQAGFSPQIIRQVNEPQTVLAMVSMG---IGITLLPDSYAQ 255 (294)
T ss_pred CCEEecCCCchhHHHHHHHHHHHCCCCCceeeecCCHHHHHHHHHcC---CeEEEccHHHhh
Confidence 344222 2233 555666555432 24566777777777765 346777876654
No 216
>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=46.74 E-value=50 Score=24.70 Aligned_cols=38 Identities=24% Similarity=0.409 Sum_probs=29.3
Q ss_pred cceeEEEEEeecCCCcHHHHHHHHHHHhcCC-----ceEEEce
Q 023305 240 YFDYLFYIDFEASMADPRAQNALGHLQEFAT-----FLRVLGC 277 (284)
Q Consensus 240 ~~~y~F~id~eg~~~d~~~~~al~~L~~~~~-----~vkvLGs 277 (284)
.+.|+|-||+.|+..-..=+++|..|+.... .|+|-|.
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 3689999999997666677889999986544 3777665
No 217
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=46.17 E-value=82 Score=33.72 Aligned_cols=32 Identities=28% Similarity=0.242 Sum_probs=29.0
Q ss_pred CceEEEEEEecCCCchHHHHHHHHHhCCceee
Q 023305 184 LFKTSIVFTLDEGPGVLFKALAVFALREINLT 215 (284)
Q Consensus 184 ~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt 215 (284)
+.+|.|-+.-.|+||.|+.+.++|+..++++.
T Consensus 789 ~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~ 820 (867)
T COG2844 789 NDKTVLEVRALDRPGLLAALAGVFADLGLSLH 820 (867)
T ss_pred CCceEEEEEeCCcccHHHHHHHHHHhccccee
Confidence 35788888889999999999999999999987
No 218
>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=45.69 E-value=30 Score=31.68 Aligned_cols=125 Identities=17% Similarity=0.140 Sum_probs=68.6
Q ss_pred CCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHhCCCCeEEEeeeec----ccceeeccc-------cccccCCeEE
Q 023305 6 PGSFSEDAALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLPIENS----SSGSIHRNY-------DLLLRHRLHI 70 (284)
Q Consensus 6 ~GtfS~~Aa~~~f~----~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS----~~G~V~~t~-------d~L~~~~l~I 70 (284)
.|+.+|.++..+.. +.+.+|+++-.+.+.++..|++|.++...-+. -.|.+.... +.|.+ +.-
T Consensus 114 ~g~~~hl~~~~l~~~~G~~~~~Vpy~G~~~~~~allgG~vd~~~~~~~~~~~~~~~G~~k~Lav~~~~r~~~~pd--vPT 191 (274)
T PF03401_consen 114 PGSSDHLAAALLAKAAGIKFTHVPYDGGAEALTALLGGHVDAAFGSPGEALPYVEAGDLKPLAVFSDERSPALPD--VPT 191 (274)
T ss_dssp TTSHHHHHHHHHHHHHT---EEEE-SSHHHHHHHHHTTSSSEEEEEHHHHHHHHHTTSEEEEEECSSS-BTTCTT--S-B
T ss_pred CCchHHHHHHHHHHHhCCceEEEEeCCccHHHHHHhCCeeeEEeecHHHHHHHHhCCCceEEEEecCccccccCC--CCC
Confidence 48899988876652 36789999999999999999999998875433 234443211 12211 000
Q ss_pred EE-----EEEEeeeeEeeecCCCCcCCccEEEecHHHH---HHHHHHHHhcCCeEEecCCHHHHHHHHHhc
Q 023305 71 VG-----EVQLAANFCLLALPGIKADQLKRVLSHPQAL---ASSDIVLTQLGVARENVDDTASAAQYVASN 133 (284)
Q Consensus 71 ~~-----E~~l~I~~~L~~~~~~~l~~i~~V~SHpqal---~Qc~~fl~~~~~~~~~~~sTa~Aa~~v~~~ 133 (284)
.. ++.+..-+.+++++|++.+-+.++..--+.- ...++|+++.+.... ..+..+..+.+.+.
T Consensus 192 ~~E~G~~d~~~~~~~g~~~p~gtp~~~~~~l~~a~~~~~~~pe~~~~~~~~g~~~~-~~~~~~~~~~l~~~ 261 (274)
T PF03401_consen 192 FKEQGYPDIVFGSWRGLFAPKGTPDEIVDKLADAIKKALEDPEFQEFLEKMGLEPV-YMDGEEFDAFLAEE 261 (274)
T ss_dssp TTTTT-TTG--EEEEEEEEETTS-HHHHHHHHHHHHHHHT-HHHHHHHHHHTEEEE-CESHHHHHHHHHHH
T ss_pred HHHhCccceeeeeeeeeecCCCCCHHHHHHHHHHHHHHhCCHHHHHHHHHCCCcCC-CCCHHHHHHHHHHH
Confidence 00 2234455678888887543333322222221 223345555554443 55666666666653
No 219
>cd08464 PBP2_DntR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to DntR, which is involved in the catabolism of dinitrotoluene; contains the type 2 periplasmic binding fold. This CD includes an uncharacterized LysR-type transcriptional regulator similar to DntR, NahR, and LinR, which are involved in the degradation of aromatic compounds. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytra
Probab=45.66 E-value=1.5e+02 Score=23.55 Aligned_cols=122 Identities=14% Similarity=0.047 Sum_probs=59.8
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc-
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 94 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~- 94 (284)
.+|+.++.-.. +-.++.+.+.+|++|+|+..-.....+. ....|.+.++.++ .+-+|-+.. ...+++++.
T Consensus 25 ~~P~v~l~i~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~~~~~-~~~~~~~l~~ 96 (200)
T cd08464 25 EAPGVRLVFRQVDPFNVGDMLDRGEIDLAIGVFGELPAWL---KREVLYTEGYACL----FDPQQLSLS-APLTLEDYVA 96 (200)
T ss_pred HCCCcEEEEecCCcccHHHHHhcCcccEEEecCCCCcccc---eeeeecccceEEE----EeCCCcccc-CCCCHHHHhc
Confidence 35776654443 4557789999999999997532111110 1112223333322 222232211 112333322
Q ss_pred --EE-EecHHH-HHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 95 --RV-LSHPQA-LASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 95 --~V-~SHpqa-l~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
.+ +..... ......|+.+.+.. . ..++|......+++.+ ...||.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 155 (200)
T cd08464 97 RPHVLVSYRGGLRGFVDDALAELGRSRRVVASTPHFAALPALLRGT---PLIATVPARLARA 155 (200)
T ss_pred CCcEEecCCCCCcchHHHHHHHcCCCcceEEEcCchhhHHHHHcCC---CceeecHHHHHHH
Confidence 22 222111 22345677666543 2 3455666555666654 3478888887764
No 220
>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=45.33 E-value=83 Score=33.70 Aligned_cols=31 Identities=16% Similarity=0.356 Sum_probs=27.9
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeee
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTK 216 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~ 216 (284)
-|-|.+..+|+||-|+++.++|+.+|+|+..
T Consensus 668 ~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~ 698 (850)
T TIGR01693 668 GTEVFIYAPDQPGLFAKVAGALAMLSLSVHD 698 (850)
T ss_pred eEEEEEEeCCCCcHHHHHHHHHHHCCCeEEE
Confidence 5677788899999999999999999999983
No 221
>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=45.24 E-value=1.1e+02 Score=24.68 Aligned_cols=113 Identities=15% Similarity=0.169 Sum_probs=60.9
Q ss_pred CCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCC---cCCcc--
Q 023305 20 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIK---ADQLK-- 94 (284)
Q Consensus 20 ~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~---l~~i~-- 94 (284)
+.++++.+ ..++.+++.+|++|+++.+...+-+.. ..+. ...........++++++.. ++|++
T Consensus 39 ~~~~~~~~-~~~~~~~l~~g~~D~~~~~~~~~~~~~--~~~~---------~~~~~~~~~~~~~~~~~~~~~~~~dl~g~ 106 (218)
T cd00134 39 KVKFVEVD-WDGLITALKSGKVDLIAAGMTITPERA--KQVD---------FSDPYYKSGQVILVKKGSPIKSVKDLKGK 106 (218)
T ss_pred eEEEEeCC-HHHHHHHHhcCCcCEEeecCcCCHHHH--hhcc---------CcccceeccEEEEEECCCCCCChHHhCCC
Confidence 35677877 889999999999999988762111110 0000 0011222334555554432 23332
Q ss_pred EEEecHHHHHHHHHHHHhc--CCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 RVLSHPQALASSDIVLTQL--GVARENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 ~V~SHpqal~Qc~~fl~~~--~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
+|..-+ .. -...++.+. ......+.+..++.+++..+. ..+++.....+.
T Consensus 107 ~i~~~~-~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~g~--~d~~~~~~~~~~ 158 (218)
T cd00134 107 KVAVQK-GS-TAEKYLKKALPEAKVVSYDDNAEALAALENGR--ADAVIVDEIALA 158 (218)
T ss_pred EEEEEc-Cc-hHHHHHHHhCCcccEEEeCCHHHHHHHHHcCC--ccEEEeccHHHH
Confidence 232211 11 122344443 355677888899999988763 346666555444
No 222
>PRK11139 DNA-binding transcriptional activator GcvA; Provisional
Probab=45.08 E-value=2.3e+02 Score=25.36 Aligned_cols=118 Identities=14% Similarity=-0.001 Sum_probs=57.9
Q ss_pred CCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc---c
Q 023305 18 YPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL---K 94 (284)
Q Consensus 18 f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i---~ 94 (284)
+|+.++....+ +..+.+.+|++|+|++..+....+... ..|.+.++.++ .+-.|.+......+++|+ .
T Consensus 120 ~p~i~i~l~~~--~~~~~l~~g~~Dl~i~~~~~~~~~l~~---~~l~~~~~~~~----~~~~~~~~~~~~i~~~dL~~~p 190 (297)
T PRK11139 120 HPDIDVRLKAV--DRLEDFLRDDVDVAIRYGRGNWPGLRV---EKLLDEYLLPV----CSPALLNGGKPLKTPEDLARHT 190 (297)
T ss_pred CCCceEEEEeC--CChhhhccCCCCEEEEeCCCCCCCceE---EEeccceeEEE----eCHHHhcccCCCCCHHHhhcCc
Confidence 46654433322 335778899999999876533333211 12222333322 333343332222333333 3
Q ss_pred EEEecHHHHHHHHHHHHhcCC-----e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 95 RVLSHPQALASSDIVLTQLGV-----A-RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 95 ~V~SHpqal~Qc~~fl~~~~~-----~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
-|...+ ......|+...+. . ...+++...+..+|..+ ...|+.+...++.
T Consensus 191 ~i~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 246 (297)
T PRK11139 191 LLHDDS--REDWRAWFRAAGLDDLNVQQGPIFSHSSMALQAAIHG---QGVALGNRVLAQP 246 (297)
T ss_pred eEeecC--cccHHHHHHHhCCCCcCcccceeeCCHHHHHHHHHhC---CCeEecchhhhHH
Confidence 343322 2345667776433 2 23455666566666654 2467777766653
No 223
>cd08418 PBP2_TdcA The C-terminal substrate binding domain of LysR-type transcriptional regulator TdcA, which is involved in the degradation of L-serine and L-threonine, contains the type 2 periplasmic binding fold. TdcA, a member of the LysR family, activates the expression of the anaerobically-regulated tdcABCDEFG operon which is involved in the degradation of L-serine and L-threonine to acetate and propionate, respectively. The tdc operon is comprised of one regulatory gene tdcA and six structural genes, tdcB to tdcG. The expression of the tdc operon is affected by several transcription factors including the cAMP receptor protein (CRP), integration host factor (IHF), histone-like protein (HU), and the operon specific regulators TdcA and TcdR. TcdR is divergently transcribed from the operon and encodes a small protein that is required for efficient expression of the Escherichia coli tdc operon. This substrate-binding domain shows significant homology to the type 2 periplasmic binding
Probab=45.03 E-value=1.6e+02 Score=23.45 Aligned_cols=120 Identities=14% Similarity=0.094 Sum_probs=61.4
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecc--cceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc-
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 93 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~--~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i- 93 (284)
+|+.++... .+..++.+.+.+|++|+|+....... .+. ....|.+.++.++..- +|-+.. + .+++++
T Consensus 26 ~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~~~l~~~~~~~v~~~----~~~~~~-~-~~~~~l~ 96 (201)
T cd08418 26 FPDVQISIYEGQLSSLLPELRDGRLDFAIGTLPDEMYLKEL---ISEPLFESDFVVVARK----DHPLQG-A-RSLEELL 96 (201)
T ss_pred CCCceEEEEeCcHHHHHHHHHcCCCcEEEEecCCCCCCcce---eEEeecCCceEEEeCC----CCcccc-C-CCHHHHc
Confidence 566655433 35678999999999999998532111 111 1112223333333221 222211 1 122332
Q ss_pred --cEEEec--HHHHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 94 --KRVLSH--PQALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 94 --~~V~SH--pqal~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
+.|... ......+..++.+.+. + ...++|...+..+++.+ ...|+.+...++.
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 156 (201)
T cd08418 97 DASWVLPGTRMGYYNNLLEALRRLGYNPRVAVRTDSIVSIINLVEKA---DFLTILSRDMGRG 156 (201)
T ss_pred CCCCEecCCCCCHHHHHHHHHHHcCCCCCceEEecCHHHHHHHHHhC---CEEEEeEHHHhhh
Confidence 223321 2233445666766543 2 34566777777888765 3577888766653
No 224
>cd08438 PBP2_CidR The C-terminal substrate binding domain of LysR-like transcriptional regulator CidR, contains the type 2 periplasmic binding fold. This CD includes the substrate binding domain of CidR which positively up-regulates the expression of cidABC operon in the presence of acetic acid produced by the metabolism of excess glucose. The CidR affects the control of murein hydrolase activity by enhancing cidABC expression in the presence of acetic acid. Thus, up-regulation of cidABC expression results in increased murein hydrolase activity. This substrate binding domain has significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they can interact with a cognate
Probab=44.62 E-value=1.6e+02 Score=23.31 Aligned_cols=30 Identities=20% Similarity=-0.006 Sum_probs=23.1
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEe
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvP 47 (284)
+|+.++.-. .+-.++.+.+.+|++|+|++.
T Consensus 26 ~p~v~i~i~~~~~~~~~~~L~~~~~Dl~i~~ 56 (197)
T cd08438 26 YPNIELELVEYGGKKVEQAVLNGELDVGITV 56 (197)
T ss_pred CcCeEEEEEEcCcHHHHHHHHcCCCCEEEEe
Confidence 566655433 467889999999999999975
No 225
>PHA03169 hypothetical protein; Provisional
Probab=43.53 E-value=1.2e+02 Score=29.38 Aligned_cols=70 Identities=7% Similarity=0.036 Sum_probs=50.0
Q ss_pred CCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHH
Q 023305 183 KLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNAL 262 (284)
Q Consensus 183 ~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al 262 (284)
..+|--++|.- .|-+||++-.+|.--||--+-+.--|..... ...|.|+.+|=|.-.....+|+.+-
T Consensus 320 ~~W~~~v~fWg--dP~~LyrLsraLqfpG~~ssgvq~lP~~p~~-----------p~~~~y~ItVyCqsk~TaK~V~kaq 386 (413)
T PHA03169 320 GPWCWVVFCWG--DPYSLYRLSRCLQFPGAVSSGVQTFPDAPGS-----------PVIWAYCITVFCQSRGTAKAVIKAQ 386 (413)
T ss_pred CceeEEEEecC--CcHHHHHHHHHhccCCeeccceeecCCCCCC-----------CCCceeEEEEEecCcccHHHHHHHH
Confidence 46788777775 7899999999999999987777777764332 2258888888886554445555554
Q ss_pred HHH
Q 023305 263 GHL 265 (284)
Q Consensus 263 ~~L 265 (284)
+.-
T Consensus 387 ~~y 389 (413)
T PHA03169 387 KKY 389 (413)
T ss_pred HHH
Confidence 443
No 226
>cd08423 PBP2_LTTR_like_6 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=43.46 E-value=1.6e+02 Score=23.24 Aligned_cols=124 Identities=19% Similarity=0.060 Sum_probs=58.7
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccc--cccccCCeEEEEEEEEeeeeEeeecCCCCcCCc-
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNY--DLLLRHRLHIVGEVQLAANFCLLALPGIKADQL- 93 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~--d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i- 93 (284)
+++.++.-. .+-.++.+.+.+|++|+|+++-..-........+ ..|.+.++.++ .+-+|-+...+..+++++
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~~~~~~~~~l~~~~~~~~----~~~~~p~~~~~~~~~~~l~ 101 (200)
T cd08423 26 HPGLEVRLREAEPPESLDALRAGELDLAVVFDYPVTPPPDDPGLTRVPLLDDPLDLV----LPADHPLAGREEVALADLA 101 (200)
T ss_pred CCCCeEEEEeCCHHHHHHHHhcCCccEEEEeccccccCCCCCCcEEEEeccCcEEEE----ecCCCCccccCCCCHHHhc
Confidence 466655433 3567889999999999999863210000000011 11222232222 122333322212223333
Q ss_pred --cEEE-ecHHHH-HHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 --KRVL-SHPQAL-ASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 --~~V~-SHpqal-~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|. +.+... .....|+.+++. + ...+++...+.++++.+ ...++.++..++
T Consensus 102 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 160 (200)
T cd08423 102 DEPWIAGCPGSPCHRWLVRACRAAGFTPRIAHEADDYATVLALVAAG---LGVALVPRLALG 160 (200)
T ss_pred CCceEEecCCchHHHHHHHHHHHcCCCCCeeeeeccHHHHHHHHHcC---CCHhhhhhHHHH
Confidence 2222 222222 334556666543 2 24566777777777764 246677766543
No 227
>PRK02047 hypothetical protein; Provisional
Probab=42.96 E-value=1.5e+02 Score=22.64 Aligned_cols=59 Identities=24% Similarity=0.333 Sum_probs=40.6
Q ss_pred ecCCCchHHHHHHHHHhC--CceeeeeeeeeCCCCCCccccCCCCCCCccceeE-EEEEeecCCCcHHHHHHHHHHHhc
Q 023305 193 LDEGPGVLFKALAVFALR--EINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYL-FYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~--~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~-F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
-++.++....+..++..+ +++...|.+||++++ .|. +=|.+... +.+.+.++.++|.+.
T Consensus 23 G~~~~~~~~~v~~iv~~~~~~~~~~~i~~k~Ss~G----------------kY~Svtv~v~v~-s~eq~~~iY~~L~~~ 84 (91)
T PRK02047 23 GKAHPEFADTIFKVVSVHDPEFDLEKIEERPSSGG----------------NYTGLTITVRAT-SREQLDNIYRALTGH 84 (91)
T ss_pred EeCcHhHHHHHHHHHHHhCCCCccCceEEccCCCC----------------eEEEEEEEEEEC-CHHHHHHHHHHHhhC
Confidence 356666777777777777 566788999999864 453 55555543 346777888888754
No 228
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=42.62 E-value=96 Score=33.37 Aligned_cols=35 Identities=11% Similarity=0.317 Sum_probs=29.8
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceee--eeeee
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLT--KIESR 220 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt--~IeSR 220 (284)
-|.|.+..+|+||-|+++-++|..+|+|+. +|.+.
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 577778889999999999999999999997 44443
No 229
>PRK13584 hisG ATP phosphoribosyltransferase catalytic subunit; Provisional
Probab=42.16 E-value=1.6e+02 Score=26.20 Aligned_cols=119 Identities=16% Similarity=0.201 Sum_probs=67.3
Q ss_pred HHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeE---eeecCCCCcCCccEEEecHHHHHH
Q 023305 29 FEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFC---LLALPGIKADQLKRVLSHPQALAS 105 (284)
Q Consensus 29 ~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~---L~~~~~~~l~~i~~V~SHpqal~Q 105 (284)
-.|+-.-|+.|.+|.||+= .|.|.+.+-.+..-..|....| ++++|+. .+.++|.+--.-+
T Consensus 52 ~~DIp~yV~~G~aDlGI~G------------~D~l~E~~~~v~el~dLgfG~crl~vA~p~~~--~~~~rVATkyp~i-- 115 (204)
T PRK13584 52 GSDVPIYVEQGMADIGIVG------------SDILDERQYNVNNLLNMPFGACHFAVAAKPET--TNYRKIATSYVHT-- 115 (204)
T ss_pred HHHHHHHHhCCCccEEEee------------eeEeeccCCCeEEEecCCCCcEEEEEEEEcCC--CCceEEEeCcHHH--
Confidence 3578899999999999874 4555544333333345555544 5555543 3557787765544
Q ss_pred HHHHHHhcCCe--EEecCCHHHHHHHHHhcCCCC-eEEE-cchhHHHhcCCceeeccccCCCCCeeEEE
Q 023305 106 SDIVLTQLGVA--RENVDDTASAAQYVASNGLRD-AGAV-ASARAAEIYGLNILADRIQDEPDNITRFL 170 (284)
Q Consensus 106 c~~fl~~~~~~--~~~~~sTa~Aa~~v~~~~~~~-~aAI-~s~~aa~~ygL~il~~~I~d~~~N~TRF~ 170 (284)
.++||.++++. .+..+..-+.|=.+ +.-+ .+=| .+-...+.+||.+++. |- +-.+|++
T Consensus 116 t~~yf~~~Gi~~~ii~l~GsvElaP~~---GlAD~IvDiv~TG~TLr~NgL~~~e~-I~---~ssa~LI 177 (204)
T PRK13584 116 AETYFKSKGIDVELIKLNGSVELACVV---DMVDGIVDIVQTGTTLKANGLVEKQH-IS---DINARLI 177 (204)
T ss_pred HHHHHHHcCCeEEEEECCCceeecccc---CCccEEEEEECccHHHHHCCCEEEEE-EE---eeEEEEE
Confidence 46799998764 44444333322211 0011 1112 3456778999988843 33 3455654
No 230
>PRK08961 bifunctional aspartate kinase/diaminopimelate decarboxylase protein; Provisional
Probab=42.10 E-value=4.7e+02 Score=28.14 Aligned_cols=127 Identities=12% Similarity=0.065 Sum_probs=74.5
Q ss_pred CeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHH---hcCCceeeccccCCCCCeeEEEEEeeCCCCCC----CCCCceE
Q 023305 115 VARENVDDTASAAQYVASNGLRDAGAVASARAAE---IYGLNILADRIQDEPDNITRFLVLARDPIIPR----TDKLFKT 187 (284)
Q Consensus 115 ~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~---~ygL~il~~~I~d~~~N~TRF~vl~~~~~~~~----~~~~~kt 187 (284)
.+.+..-|..+|.++...+ |.+-...|++ .+|.++.-.+..+....-|..- ......+. ....+-+
T Consensus 251 a~~i~~ls~~e~~el~~~g-----~~v~~~~a~~~a~~~~i~i~v~~~~~~~~~gT~I~--~~~~~~~~v~~It~~~~v~ 323 (861)
T PRK08961 251 ARLLTRLDYDEAQEIATTG-----AKVLHPRSIKPCRDAGIPMAILDTERPDLSGTSID--GDAEPVPGVKAISRKNGIV 323 (861)
T ss_pred ceEecccCHHHHHHHHHCC-----CeEECHHHHHHHHHCCCCEEEEeCCCCCCCccEEe--CCCCCCCcceeEEEECCEE
Confidence 4556666777877766543 4555555554 5799999888776544455442 21111111 0112233
Q ss_pred EEEEE---ecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCC-CcHHHHHHHH
Q 023305 188 SIVFT---LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASM-ADPRAQNALG 263 (284)
Q Consensus 188 si~f~---~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~-~d~~~~~al~ 263 (284)
.|.+. ..+.+|.+.++++.|+++|||+-.|.|-. ....|.|+-.... .+..++.+++
T Consensus 324 lItv~~~~~~~~~g~~a~if~~la~~~I~Vd~I~sse-------------------~sis~~i~~~~~~~~~~~~~~l~~ 384 (861)
T PRK08961 324 LVSMETIGMWQQVGFLADVFTLFKKHGLSVDLISSSE-------------------TNVTVSLDPSENLVNTDVLAALSA 384 (861)
T ss_pred EEEEecCCccccccHHHHHHHHHHHcCCeEEEEEcCC-------------------CEEEEEEccccccchHHHHHHHHH
Confidence 33342 24689999999999999999999994321 2466777653321 1234555566
Q ss_pred HHHh
Q 023305 264 HLQE 267 (284)
Q Consensus 264 ~L~~ 267 (284)
+|+.
T Consensus 385 ~l~~ 388 (861)
T PRK08961 385 DLSQ 388 (861)
T ss_pred HHhh
Confidence 6653
No 231
>COG2107 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=42.02 E-value=45 Score=30.80 Aligned_cols=45 Identities=36% Similarity=0.416 Sum_probs=33.1
Q ss_pred CCCCcHHHHH--HHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEeee
Q 023305 4 GLPGSFSEDA--ALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPIE 49 (284)
Q Consensus 4 Gp~GtfS~~A--a~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiE 49 (284)
+-+|-++-.+ .+-++++.++++. -|+++..||.+|++|-|++=.|
T Consensus 99 avpG~~TTA~lL~rl~~p~~~~V~m-~fdeI~~Avl~G~VDaGvlIHE 145 (272)
T COG2107 99 AVPGEMTTAALLFRLAYPKAEIVYM-PFDEIIPAVLEGKVDAGVLIHE 145 (272)
T ss_pred ecCCcccHHHHHHHHhCCCceEEEe-eHHHHHHHHHcCCCccceEEee
Confidence 3445444333 3445688877765 4999999999999999999777
No 232
>PRK11553 alkanesulfonate transporter substrate-binding subunit; Provisional
Probab=41.91 E-value=1.2e+02 Score=27.70 Aligned_cols=106 Identities=12% Similarity=-0.028 Sum_probs=54.7
Q ss_pred CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEE-EeeeeEeeecCCC---CcCCc--c
Q 023305 21 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQ-LAANFCLLALPGI---KADQL--K 94 (284)
Q Consensus 21 ~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~-l~I~~~L~~~~~~---~l~~i--~ 94 (284)
.+++...+-.++++++.+|++|+|+..-- ......-...++.+++... .+-..+++++++. +++|+ +
T Consensus 58 ie~~~~~~~~~~~~aL~~G~iDia~~~~~-------~~~~~~~~g~~~~~v~~~~~~~~~~~lvv~~~s~i~s~~dL~Gk 130 (314)
T PRK11553 58 ISWVEFPAGPQMLEALNVGSIDLGSTGDI-------PPIFAQAAGADLVYVGVEPPKPKAEVILVAENSPIKTVADLKGH 130 (314)
T ss_pred eEEEECCCcHHHHHHHHcCCCCEEccCCH-------HHHHHHhCCCCEEEEEEecCCCcceEEEEeCCCCCCCHHHhCCC
Confidence 45677777789999999999999985310 0000000122445554332 2223456666553 33344 2
Q ss_pred EEEecH--HHHHHHHHHHHhcCCe---E-EecCCHHHHHHHHHhc
Q 023305 95 RVLSHP--QALASSDIVLTQLGVA---R-ENVDDTASAAQYVASN 133 (284)
Q Consensus 95 ~V~SHp--qal~Qc~~fl~~~~~~---~-~~~~sTa~Aa~~v~~~ 133 (284)
+|...+ .....+..+|++.++. . ....+..++...+..+
T Consensus 131 ~I~~~~gs~~~~~l~~~l~~~g~~~~dv~~v~~~~~~~~~al~~G 175 (314)
T PRK11553 131 KVAFQKGSSSHNLLLRALRKAGLKFTDIQPTYLTPADARAAFQQG 175 (314)
T ss_pred EEeecCCCcHHHHHHHHHHHcCCCHHHeEEEecChHHHHHHHHcC
Confidence 444322 1234556677766542 1 1223555666666654
No 233
>PRK04998 hypothetical protein; Provisional
Probab=41.28 E-value=1.5e+02 Score=22.31 Aligned_cols=59 Identities=14% Similarity=0.129 Sum_probs=40.8
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeE-EEEEeecCCCcHHHHHHHHHHHhc
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYL-FYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~-F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
.+..++.+..+..+|.++--.-..+.+||++++ .|. +-|.+... +.+.+.++.++|.+.
T Consensus 22 g~~~~~~~~~v~~v~~~~~~~~~~~~~r~S~~G----------------kY~Svtv~v~v~-s~eq~~~iY~~L~~~ 81 (88)
T PRK04998 22 GLARPELVDQVVEVVQRHAPGDYTPTVKPSSKG----------------NYHSVSITITAT-SIEQVETLYEELAKI 81 (88)
T ss_pred EeCcHhHHHHHHHHHHHhCCCCCCceEccCCCC----------------EEEEEEEEEEEC-CHHHHHHHHHHHhcC
Confidence 345678888899999877444445889998763 563 66666654 446777788888754
No 234
>cd08414 PBP2_LTTR_aromatics_like The C-terminal substrate binding domain of LysR-type transcriptional regulators involved in the catabolism of aromatic compounds and that of other related regulators, contains type 2 periplasmic binding fold. This CD includes the C-terminal substrate binding domain of LTTRs involved in degradation of aromatic compounds, such as CbnR, BenM, CatM, ClcR and TfdR, as well as that of other transcriptional regulators clustered together in phylogenetic trees, including XapR, HcaR, MprR, IlvR, BudR, AlsR, LysR, and OccR. The structural topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their specific ligand with high affinity, they ca
Probab=40.93 E-value=1.8e+02 Score=22.94 Aligned_cols=32 Identities=16% Similarity=0.104 Sum_probs=23.7
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeee
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIE 49 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiE 49 (284)
+|+.++.-. .+..++.+.+.+|++|+|++.-.
T Consensus 26 ~p~i~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~ 58 (197)
T cd08414 26 YPDVELELREMTTAEQLEALRAGRLDVGFVRPP 58 (197)
T ss_pred CCCcEEEEecCChHHHHHHHHcCCccEEEEcCC
Confidence 466555433 35688999999999999998643
No 235
>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=40.66 E-value=1.9e+02 Score=23.04 Aligned_cols=122 Identities=17% Similarity=0.094 Sum_probs=61.1
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeec--ccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCc---
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA--- 90 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS--~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l--- 90 (284)
.+|+.++.-. .+-.++.+.+.+|++|+|+...... -.+.. ...|.+.++.+ ..+-.|-+...+..++
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~~l~---~~~l~~~~~~~----v~~~~hp~~~~~~~~~~~L 97 (199)
T cd08416 25 RRPELDIELTLGSNKDLLKKLKDGELDAILVATPEGLNDPDFE---VVPLFEDDIFL----AVPATSPLAASSEIDLRDL 97 (199)
T ss_pred hCCCeEEEEEEcCcHHHHHHHhCCCCCEEEEecCCcCCCCCeE---EEEeecceEEE----EECCCCcccccCccCHHHh
Confidence 3566655433 3556789999999999999864321 11110 11122223322 2334444433222222
Q ss_pred CCccEEE-ecHH-HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 91 DQLKRVL-SHPQ-ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 91 ~~i~~V~-SHpq-al~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.+..-|. +... .......++.+.++. ...++|...+.++++.+ ...++++...++
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (199)
T cd08416 98 KDEKFVTLSEGFATYRGFDEAFEIAGFEPNVVMRVNDIFSLMSMVSGG---VGYALLPGRIAD 157 (199)
T ss_pred cCCceEEecCCCcHHHHHHHHHHHcCCCCCceEEeCCHHHHHHHHHcC---CcEEEechhhhh
Confidence 3333333 2221 122355566655432 24566677777777764 236677766554
No 236
>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=40.56 E-value=45 Score=28.69 Aligned_cols=43 Identities=12% Similarity=-0.036 Sum_probs=28.7
Q ss_pred CCCcHHHHHHHhhCCCCcee---------ecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKAYPKCETV---------PCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~~~~~~---------~~~s~~~v~~av~~~~~d~gvvP 47 (284)
+.|+..+....+.....++. ...|..+++.+|.+|++|.+++.
T Consensus 110 ~~g~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~G~~Da~i~~ 161 (232)
T TIGR03871 110 FAGTPPAHWLARHGLVENVVGYSLFGDYRPESPPGRMVEDLAAGEIDVAIVW 161 (232)
T ss_pred EcCChHHHHHHhcCcccccccccccccccccCCHHHHHHHHHcCCcCEEEec
Confidence 45677766554432111211 23488999999999999999986
No 237
>PRK10797 glutamate and aspartate transporter subunit; Provisional
Probab=40.54 E-value=34 Score=31.54 Aligned_cols=43 Identities=19% Similarity=0.178 Sum_probs=34.5
Q ss_pred CCCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~----~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
..||.++...+++.+ +.+++.+++.++++++|.+|++|..+..
T Consensus 159 ~~gs~~~~~l~~~~~~~~~~~~i~~~~~~~~~l~~L~~GrvDa~i~d 205 (302)
T PRK10797 159 TSGTTSEVLLNKLNEEQKMNMRIISAKDHGDSFRTLESGRAVAFMMD 205 (302)
T ss_pred eCCCcHHHHHHHHhhhcCCceEEEEeCCHHHHHHHHHcCCceEEEcc
Confidence 578877776665543 3578999999999999999999988753
No 238
>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=39.88 E-value=1.9e+02 Score=22.97 Aligned_cols=121 Identities=17% Similarity=0.074 Sum_probs=59.9
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCC-CCcCCcc-
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPG-IKADQLK- 94 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~-~~l~~i~- 94 (284)
+++.++.-. .+..++++.+.+|++|+|+..-.....+.. ...|.+.++.++ .+-.|-+..... .+++|+.
T Consensus 27 ~P~v~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~dL~~ 99 (197)
T cd08425 27 YPGIALSLREMPQERIEAALADDRLDLGIAFAPVRSPDID---AQPLFDERLALV----VGATHPLAQRRTALTLDDLAA 99 (197)
T ss_pred CCCcEEEEEECcHHHHHHHHHcCCccEEEEecCCCCCCcE---EEEeccccEEEE----ecCCCchhHhcccCCHHHHhc
Confidence 566555433 456789999999999999975332111110 112222233222 222333322211 2333332
Q ss_pred --EEE-ec-HHHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 --RVL-SH-PQALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 --~V~-SH-pqal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
-|. .. .........|+++.+.. . ..++|...+.++++.+ ...|+.+...++
T Consensus 100 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08425 100 EPLALLSPDFATRQHIDRYFQKQGIKPRIAIEANSISAVLEVVRRG---RLATILPDAIAR 157 (197)
T ss_pred CCcEecCCCccHHHHHHHHHHHcCCCeeeEEeeCcHHHHHHHHhcC---CcEEeechhhhc
Confidence 222 11 11233456677765543 2 3456777777777765 246677765443
No 239
>PRK10859 membrane-bound lytic transglycosylase F; Provisional
Probab=39.80 E-value=1.5e+02 Score=29.39 Aligned_cols=27 Identities=30% Similarity=0.223 Sum_probs=23.1
Q ss_pred CCceeecCCHHHHHHHHHhCCCCeEEE
Q 023305 20 KCETVPCDEFEDTFKAVELWLADKAVL 46 (284)
Q Consensus 20 ~~~~~~~~s~~~v~~av~~~~~d~gvv 46 (284)
+.++++..+++++++++++|++|+++.
T Consensus 81 ~~e~v~~~~~~~ll~aL~~G~iDi~~~ 107 (482)
T PRK10859 81 KLEIKVRDNISQLFDALDKGKADLAAA 107 (482)
T ss_pred cEEEEecCCHHHHHHHHhCCCCCEEec
Confidence 357788899999999999999997653
No 240
>PRK05092 PII uridylyl-transferase; Provisional
Probab=39.75 E-value=1.7e+02 Score=31.78 Aligned_cols=32 Identities=16% Similarity=0.249 Sum_probs=28.3
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeee
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKI 217 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~I 217 (284)
-|.+.+..+|+||-+.++.++|+.+|+|+..-
T Consensus 732 ~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A 763 (931)
T PRK05092 732 VTEVTVLAADHPGLFSRIAGACAAAGANIVDA 763 (931)
T ss_pred eEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEE
Confidence 57777888999999999999999999999843
No 241
>PRK08210 aspartate kinase I; Reviewed
Probab=39.42 E-value=1.3e+02 Score=28.97 Aligned_cols=94 Identities=13% Similarity=-0.020 Sum_probs=53.4
Q ss_pred eEEecCCHHHHHHHHHhcCCCCeEEEcchhH---HHhcCCceeeccccCCCCCeeEEEEEeeCCC-------CCCC----
Q 023305 116 ARENVDDTASAAQYVASNGLRDAGAVASARA---AEIYGLNILADRIQDEPDNITRFLVLARDPI-------IPRT---- 181 (284)
Q Consensus 116 ~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~a---a~~ygL~il~~~I~d~~~N~TRF~vl~~~~~-------~~~~---- 181 (284)
+.++.-|..+|.++...+ +-+-.+.| |..++.++.-.+..+.+. -|..- ...+. .+.-
T Consensus 195 ~~i~~ls~~ea~~l~~~G-----~~v~~~~a~~~~~~~~i~i~i~~~~~~~~-gT~I~--~~~~~~~~~~~~~~~v~~It 266 (403)
T PRK08210 195 RLLDVVSYNEVFQMAYQG-----AKVIHPRAVEIAMQANIPLRIRSTYSDSP-GTLIT--SLGDAKGGIDVEERLITGIA 266 (403)
T ss_pred eECCccCHHHHHHHHHCC-----ccccCHHHHHHHHHCCCeEEEEecCCCcC-CcEEE--ecCccccccccccCceEEEE
Confidence 344455667777765543 22333333 456799998888776322 44431 11110 0000
Q ss_pred CCCceEEEEEE-ecCCCchHHHHHHHHHhCCceeeee
Q 023305 182 DKLFKTSIVFT-LDEGPGVLFKALAVFALREINLTKI 217 (284)
Q Consensus 182 ~~~~ktsi~f~-~~~~pGaL~~~L~~F~~~~INLt~I 217 (284)
...+-+.+.+. .++.||.+.++++.|+++|||+-.|
T Consensus 267 ~~~~i~~isv~~~~~~~g~la~If~~L~~~~I~i~~i 303 (403)
T PRK08210 267 HVSNVTQIKVKAKENAYDLQQEVFKALAEAGISVDFI 303 (403)
T ss_pred EcCCcEEEEEecCCCcchHHHHHHHHHHHcCCeEEEE
Confidence 01122333333 3445999999999999999999988
No 242
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=38.87 E-value=65 Score=28.50 Aligned_cols=43 Identities=19% Similarity=0.172 Sum_probs=31.7
Q ss_pred CCCcHHHHHHHhhCC--CCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 5 LPGSFSEDAALKAYP--KCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 5 p~GtfS~~Aa~~~f~--~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
+.|+..+.-..+.+. +.++++.++.++++++|..|++|+.+..
T Consensus 139 ~~gs~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~griDa~i~d 183 (260)
T PRK15010 139 LQGSTQEAYANETWRSKGVDVVAYANQDLVYSDLAAGRLDAALQD 183 (260)
T ss_pred ecCchHHHHHHHhcccCCceEEecCCHHHHHHHHHcCCccEEEeC
Confidence 456665544443332 3577889999999999999999998765
No 243
>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=38.21 E-value=2.2e+02 Score=23.09 Aligned_cols=107 Identities=18% Similarity=0.082 Sum_probs=53.9
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCccE-
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR- 95 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~~- 95 (284)
+|+.++.. ..+..++.+.+.+|++|+|+...+....+... ..|.+.++. +.++-+| +..+...+++++..
T Consensus 26 ~P~i~l~i~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~~~---~~l~~~~~~----lv~~~~h-~~~~~~i~~~~l~~~ 97 (200)
T cd08465 26 APGIDLAVSQASREAMLAQVADGEIDLALGVFPELPEELHA---ETLFEERFV----CLADRAT-LPASGGLSLDAWLAR 97 (200)
T ss_pred CCCcEEEEecCChHhHHHHHHCCCccEEEeccccCCcCeeE---EEeeeccEE----EEEeCCC-CccCCCcCHHHHhhC
Confidence 56666543 35778999999999999999754321111110 112222322 2233344 22222233444321
Q ss_pred --EEe--cHHHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHh
Q 023305 96 --VLS--HPQALASSDIVLTQLGVA--R-ENVDDTASAAQYVAS 132 (284)
Q Consensus 96 --V~S--Hpqal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~ 132 (284)
|.- ...-..+...++++.+++ . ..++|......+++.
T Consensus 98 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~ 141 (200)
T cd08465 98 PHVLVAMRGDAANEIDRALAARGLRRRVALTLPHWGVAPELIAG 141 (200)
T ss_pred CcEEEecCCCcCChHHHHHHHcCCceEEEEEcCcHHHHHHHHHc
Confidence 221 111123455666666654 2 346667777777775
No 244
>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=38.15 E-value=81 Score=25.06 Aligned_cols=116 Identities=12% Similarity=0.001 Sum_probs=57.6
Q ss_pred CCCCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc---c
Q 023305 18 YPKCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL---K 94 (284)
Q Consensus 18 f~~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i---~ 94 (284)
+|+.++....+ +..+.+.+|++|+|+....-...|. ....|.+.++.++. +-+| +......+++|+ +
T Consensus 26 ~P~i~l~~~~~--~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v~----~~~~-~~~~~~~~~~~L~~~~ 95 (190)
T cd08483 26 HPEIELSLLPS--ADLVDLRPDGIDVAIRYGNGDWPGL---ESEPLTAAPFVVVA----APGL-LGDRKVDSLADLAGLP 95 (190)
T ss_pred CCCceEEEEec--CCcCCCCCCCcCEEEEecCCCCCCc---EEEeecccceEeee----CHHH-HhhCCCCCHHHHhcCc
Confidence 56655443322 3457789999999998532111221 11233344444432 3334 322222333333 3
Q ss_pred EEEecHHHHHHHHHHHHhcCCe-----EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 RVLSHPQALASSDIVLTQLGVA-----RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 ~V~SHpqal~Qc~~fl~~~~~~-----~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
-|. +.. ......|+.+.+.. ...++|.....++++.+ ...++.++..++
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 12345677765532 24456677777777764 246677765444
No 245
>cd08449 PBP2_XapR The C-terminal substrate binding domain of LysR-type transcriptional regulator XapR involved in xanthosine catabolism, contains the type 2 periplasmic binding fold. In Escherichia coli, XapR is a positive regulator for the expression of xapA gene, encoding xanthosine phosphorylase, and xapB gene, encoding a polypeptide similar to the nucleotide transport protein NupG. As an operon, the expression of both xapA and xapB is fully dependent on the presence of both XapR and the inducer xanthosine. Expression of the xapR is constitutive but not auto-regulated, unlike many other LysR family proteins. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Venus flytrap. After binding their
Probab=38.03 E-value=2e+02 Score=22.70 Aligned_cols=32 Identities=16% Similarity=-0.011 Sum_probs=23.7
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEee
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPI 48 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPi 48 (284)
.+++.++.-. .+..+..+.+.+|++|+|++..
T Consensus 25 ~~P~i~i~~~~~~~~~~~~~l~~~~~Dl~i~~~ 57 (197)
T cd08449 25 QYPNVTVRFHELSPEAQKAALLSKRIDLGFVRF 57 (197)
T ss_pred HCCCeEEEEEECCHHHHHHHHhCCCccEEEecc
Confidence 3566655433 3578899999999999999754
No 246
>PRK06635 aspartate kinase; Reviewed
Probab=37.89 E-value=1.2e+02 Score=29.12 Aligned_cols=29 Identities=21% Similarity=0.354 Sum_probs=25.5
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIESRP 221 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeSRP 221 (284)
..++||.|.++++.|+++|||+-.|.+-.
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 247
>cd08469 PBP2_PnbR The C-terminal substrate binding domain of LysR-type transcriptional regulator PnbR, which is involved in regulating the pnb genes encoding enzymes for 4-nitrobenzoate catabolism, contains the type 2 periplasmic binding fold. PnbR is the regulator of one or both of the two pnb genes that encoding enzymes for 4-nitrobenzoate catabolism. In Pseudomonas putida strain, pnbA encodes a 4-nitrobenzoate reductase, which is responsible for catalyzing the direct reduction of 4-nitrobenzoate to 4-hydroxylaminobenzoate, and pnbB encodes a 4-hydroxylaminobenzoate lyase, which catalyzes the conversion of 4-hydroxylaminobenzoate to 3, 4-dihydroxybenzoic acid and ammonium. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft bet
Probab=37.73 E-value=2.3e+02 Score=23.25 Aligned_cols=31 Identities=13% Similarity=-0.091 Sum_probs=22.8
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEee
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPI 48 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPi 48 (284)
+++.++.- ..+-.++.+.+.+|++|+|+...
T Consensus 26 ~P~v~l~i~~~~~~~~~~~l~~g~~Di~i~~~ 57 (221)
T cd08469 26 APGIDLRIRPVTRLDLAEQLDLGRIDLVIGIF 57 (221)
T ss_pred CCCcEEEEeeCChhhHHHHHHCCCccEEEecC
Confidence 56655432 34566889999999999999853
No 248
>cd08427 PBP2_LTTR_like_2 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator, contains the type 2 periplasmic binding fold. LysR-transcriptional regulators comprise the largest family of prokaryotic transcription factor. Homologs of some of LTTRs with similar domain organizations are also found in the archaea and eukaryotic organisms. The LTTRs are composed of two functional domains joined by a linker helix involved in oligomerization: an N-terminal HTH (helix-turn-helix) domain, which is responsible for the DNA-binding specificity, and a C-terminal substrate-binding domain, which is structurally homologous to the type 2 periplasmic binding proteins. As also observed in the periplasmic binding proteins, the C-terminal domain of the bacterial transcriptional repressor undergoes a conformational change upon substrate binding which in turn changes the DNA binding affinity of the repressor. The genes controlled by the LTTRs have diverse functi
Probab=37.63 E-value=2e+02 Score=22.63 Aligned_cols=121 Identities=14% Similarity=0.032 Sum_probs=58.9
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecc--cceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSS--SGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL 93 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~--~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i 93 (284)
.+++.++... .+.+++.+.+.+|++|+|+.+-.... .+. ....|.+.++.++.-- +|-+.... ..+.+-
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~~---~~~~l~~~~~~~v~~~----~~p~~~~~-~~l~~~ 96 (195)
T cd08427 25 RHPDLEVHIVPGLSAELLARVDAGELDAAIVVEPPFPLPKDL---VWTPLVREPLVLIAPA----ELAGDDPR-ELLATQ 96 (195)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCCCEEEEcCCCCccccCc---eEEEcccCcEEEEECC----CCCcchHH-HHhcCC
Confidence 3566665443 35688999999999999998532111 111 1122223333322211 11111100 012222
Q ss_pred cEEEe-cHHH-HHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 KRVLS-HPQA-LASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 ~~V~S-Hpqa-l~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|.. +... -.+...|+.+.+.. . ..++|...+.++++.+ ...|+.+...++
T Consensus 97 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 153 (195)
T cd08427 97 PFIRYDRSAWGGRLVDRFLRRQGIRVREVMELDSLEAIAAMVAQG---LGVAIVPDIAVP 153 (195)
T ss_pred CeEEecCCchHHHHHHHHHHHcCCCCCeEEEeccHHHHHHHHHhC---CcEEEccHHHHh
Confidence 22221 1111 23345666665432 3 4556666666777764 346777776655
No 249
>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=37.26 E-value=2.1e+02 Score=22.58 Aligned_cols=122 Identities=20% Similarity=0.133 Sum_probs=59.3
Q ss_pred hCCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc-
Q 023305 17 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 94 (284)
Q Consensus 17 ~f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~- 94 (284)
.+|+.++.- ..+-.++.+.+.+|++|+|+..-.....+. ....|.+.++.++ .+-.|-|...+..+++++.
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~~~~Di~i~~~~~~~~~~---~~~~l~~~~~~~~----~~~~hpl~~~~~~~~~~L~~ 97 (197)
T cd08448 25 EYPGIEVALHEMSSAEQIEALLRGELDLGFVHSRRLPAGL---SARLLHREPFVCC----LPAGHPLAARRRIDLRELAG 97 (197)
T ss_pred HCCCCeEEEEeCCHHHHHHHHHcCCcceEEEeCCCCCcCc---eEEEEecCcEEEE----eeCCCCCcCCCCcCHHHhCC
Confidence 457766543 335788999999999999997432211111 1112233333332 2333433322222333332
Q ss_pred --EEE-ec---HHHHHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 --RVL-SH---PQALASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 --~V~-SH---pqal~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
-|. +. +....+-..|+.+.+.. . ..+++...+.+++..+ ...++.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 157 (197)
T cd08448 98 EPFVLFSREVSPDYYDQIIALCMDAGFHPKIRHEVRHWLTVVALVAAG---MGVALVPRSLAR 157 (197)
T ss_pred CcEEeeCcccChHHHHHHHHHHHHcCCceeeeeccccHHHHHHHHHcC---CceEecchhhhh
Confidence 232 11 11223334455554432 2 3455666666677654 246677766544
No 250
>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=36.47 E-value=45 Score=22.65 Aligned_cols=26 Identities=31% Similarity=0.360 Sum_probs=23.1
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIE 218 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~Ie 218 (284)
+++.||.+.++++.+++.|||+--|.
T Consensus 11 ~~~~~~~~~~i~~~L~~~~i~v~~i~ 36 (66)
T cd04916 11 MKNTVGVSARATAALAKAGINIRMIN 36 (66)
T ss_pred CCCCccHHHHHHHHHHHCCCCEEEEE
Confidence 45789999999999999999998774
No 251
>PRK03601 transcriptional regulator HdfR; Provisional
Probab=36.04 E-value=3.1e+02 Score=24.32 Aligned_cols=114 Identities=9% Similarity=-0.036 Sum_probs=57.4
Q ss_pred hCCCCcee-ecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCccE
Q 023305 17 AYPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR 95 (284)
Q Consensus 17 ~f~~~~~~-~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~~ 95 (284)
.+|+.++. -.....++++.+.+|++|+|+.+......+ +..+.....++++++.++-.+..-..
T Consensus 114 ~~P~v~v~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~---------------l~~~~l~~~~~~~v~~~~~~~~~~~~ 178 (275)
T PRK03601 114 NQEALQFEARIAQRQSLVKQLHERQLDLLITTEAPKMDE---------------FSSQLLGHFTLALYTSAPSKKKSELN 178 (275)
T ss_pred hCCCcEEEEEECChHHHHHHHHcCCCCEEEEcCCCccCC---------------ccEEEecceeEEEEecCchhhcccCC
Confidence 45676653 355677899999999999999753321111 11111122223444433321111111
Q ss_pred EE--ecHHHHHHHHHHHHhcCC-eEEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 96 VL--SHPQALASSDIVLTQLGV-ARENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 96 V~--SHpqal~Qc~~fl~~~~~-~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.+ ..+..+.+-..++...+. ....++|.....++|+.+ ...++.+...++
T Consensus 179 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gv~~~p~~~~~ 231 (275)
T PRK03601 179 YIRLEWGADFQQHEAGLIGADEVPILTTSSAELARQLLATL---NGCAFLPVHWAK 231 (275)
T ss_pred eEEccCCccHhHHHHHhcccCCcceEEeCcHHHHHHHHHhC---CCEEEEcHHHHh
Confidence 11 122223222222222222 245667777788888875 347788876664
No 252
>cd08430 PBP2_IlvY The C-terminal substrate binding of LysR-type transcriptional regulator IlvY, which activates the expression of ilvC gene that encoding acetohydroxy acid isomeroreductase for the biosynthesis of branched amino acids; contains the type 2 periplasmic binding fold. In Escherichia coli, IlvY is required for the regulation of ilvC gene expression that encodes acetohydroxy acid isomeroreductase (AHIR), a key enzyme in the biosynthesis of branched-chain amino acids (isoleucine, valine, and leucine). The ilvGMEDA operon genes encode remaining enzyme activities required for the biosynthesis of these amino acids. Activation of ilvC transcription by IlvY requires the additional binding of a co-inducer molecule (either alpha-acetolactate or alpha-acetohydoxybutyrate, the substrates for AHIR) to a preformed complex of IlvY protein-DNA. Like many other LysR-family members, IlvY negatively auto-regulates the transcription of its own divergently transcribed ilvY gene in an inducer-i
Probab=35.54 E-value=2.2e+02 Score=22.48 Aligned_cols=125 Identities=14% Similarity=0.079 Sum_probs=63.1
Q ss_pred hhCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecC-CC---Cc
Q 023305 16 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALP-GI---KA 90 (284)
Q Consensus 16 ~~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~-~~---~l 90 (284)
+.+|+.++.-. .+..++++.+.+|++|+|+..-.......+ ....|.+..+.+ ..+-+|-+...+ .. ++
T Consensus 24 ~~~P~v~l~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~l--~~~~l~~~~~~~----~~~~~~~~~~~~~~~~~~~l 97 (199)
T cd08430 24 AQHPQVEIKLHTGDPADAIDKVLNGEADIAIAARPDKLPARL--AFLPLATSPLVF----IAPNIACAVTQQLSQGEIDW 97 (199)
T ss_pred HHCCCceEEEEeCCHHHHHHHHHCCCCCEEEEecCCCCCccc--EEEeeccceEEE----EEeCCchhhhhhcccccccc
Confidence 34677665443 467789999999999999985321111111 112222333332 234444443221 11 23
Q ss_pred CCccEEEecHH-HHHHHHHHHHhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 91 DQLKRVLSHPQ-ALASSDIVLTQLGV--AR-ENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 91 ~~i~~V~SHpq-al~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
.+..-|...+. .......|+.+.+. +. ..+++.....++++.+ ...|+.+...++.
T Consensus 98 ~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~lp~~~~~~ 157 (199)
T cd08430 98 SRLPFILPERGLARERLDQWFRRRGIKPNIYAQVAGHEAIVSMVALG---CGVGIVPELVLDN 157 (199)
T ss_pred ccCCeEEccCChHHHHHHHHHHHcCCCCCeeEEEccHHHHHHHHHhC---CeEEEccHHHhhh
Confidence 33333432111 12334567766543 22 3455666666666664 3477888776653
No 253
>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=34.13 E-value=3.6e+02 Score=24.50 Aligned_cols=130 Identities=20% Similarity=0.154 Sum_probs=68.0
Q ss_pred HHHHhhCC----CCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccc-cc--cCCeEEEEEEEEeeeeEeee
Q 023305 12 DAALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDL-LL--RHRLHIVGEVQLAANFCLLA 84 (284)
Q Consensus 12 ~Aa~~~f~----~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~-L~--~~~l~I~~E~~l~I~~~L~~ 84 (284)
.|...++. +++++.+++..+..+|+.+|++|.+..=.+ . .+.. .. ..++.+++...+ ....+..
T Consensus 35 ~~~~~~~~~~G~~Ve~~~f~d~~~~~~Al~~G~ID~~~~q~~-------~-~l~~~~~~~g~~lv~v~~~~~-~p~~~ys 105 (258)
T TIGR00363 35 VAAKVAKEKYGLDVELVEFNDYALPNEAVSKGDLDANAFQHK-------P-YLDQDAKAKGYKLVAVGNTFV-YPLAGYS 105 (258)
T ss_pred HHHHHHHHhcCCEEEEEEeCCcHHHHHHHHcCCCCeEecCCH-------H-HHHHHHHhCCCcEEEEeeeEE-ecccccC
Confidence 44444443 367899999999999999999998743111 1 1111 11 235666664322 1123333
Q ss_pred cCCCCcCCcc---EEEec--HHHHHHHHHHHHhcC-----------------------CeEEecCCHHHHHHHHHhcCCC
Q 023305 85 LPGIKADQLK---RVLSH--PQALASSDIVLTQLG-----------------------VARENVDDTASAAQYVASNGLR 136 (284)
Q Consensus 85 ~~~~~l~~i~---~V~SH--pqal~Qc~~fl~~~~-----------------------~~~~~~~sTa~Aa~~v~~~~~~ 136 (284)
.+=.+++|++ +|.-. |.-.++.-..|.+.| ++.+... .+..++.+.++ .-
T Consensus 106 ~~~~sl~dlk~G~~IAip~d~~n~~raL~~L~~aGLi~l~~~~~~~~t~~DI~~n~~~v~~vel~-~~~~~~al~~g-~v 183 (258)
T TIGR00363 106 KKIKNVNELQDGAKVAVPNDPTNLGRALLLLQKQGLIKLKDGNGLLPTVLDIVENPKKLNITELE-TSQLPRALDDP-KV 183 (258)
T ss_pred cCCCCHHHcCCCCEEEEeCCcchHHHHHHHHHHcCCceecCCCCCcCChhhhhcCCCCCEEEEcC-HHHHHHHhhcc-cc
Confidence 3334566764 56443 433344444555533 3333333 34444444432 23
Q ss_pred CeEEEcchhHHHhcCCc
Q 023305 137 DAGAVASARAAEIYGLN 153 (284)
Q Consensus 137 ~~aAI~s~~aa~~ygL~ 153 (284)
+ ||+....-+...||.
T Consensus 184 D-aa~v~~~~~~~agl~ 199 (258)
T TIGR00363 184 D-LAVINTTYAGQVGLN 199 (258)
T ss_pred c-EEEEChHHHHHcCCC
Confidence 3 555555556666775
No 254
>PF06153 DUF970: Protein of unknown function (DUF970); InterPro: IPR010375 This is a family of uncharacterised bacterial proteins.; PDB: 3M05_A.
Probab=33.76 E-value=1.2e+02 Score=24.18 Aligned_cols=53 Identities=15% Similarity=0.052 Sum_probs=36.4
Q ss_pred HHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcCCc
Q 023305 201 FKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATF 271 (284)
Q Consensus 201 ~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~~~ 271 (284)
.++.+.|.++|+-.|||-|.=- +|. .++-.|.|-+| |++++++|+-+++.|..
T Consensus 14 ~~l~~~L~~~g~~~TkLsstGG-----------FLr---~GNtTlliGve----de~v~~vl~iIk~~c~~ 66 (109)
T PF06153_consen 14 DDLSDALNENGFRVTKLSSTGG-----------FLR---EGNTTLLIGVE----DEKVDEVLEIIKENCKK 66 (109)
T ss_dssp HHHHHHHHHTT--EEEEEEEET-----------TTT---EEEEEEEEEEE----GGGHHHHHHHHHHHH--
T ss_pred HHHHHHHHHCCceEEEEecccc-----------eec---cCCEEEEEEec----HHHHHHHHHHHHHhhcC
Confidence 3456668899999999998742 121 25678888885 46888999999887774
No 255
>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=33.67 E-value=2.5e+02 Score=22.40 Aligned_cols=122 Identities=22% Similarity=0.180 Sum_probs=61.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc-
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 94 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~- 94 (284)
.+|+.++.-. .+-.++.+.+.+|++|+|+..-.....+. ....|.+.++.++ .+.+|-+......+++++.
T Consensus 25 ~~P~i~i~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~~----~~~~~~l~~~~~~~~~~l~~ 97 (198)
T cd08441 25 RWPDVELDLSSGFHFDPLPALLRGELDLVITSDPLPLPGI---AYEPLFDYEVVLV----VAPDHPLAAKEFITPEDLAD 97 (198)
T ss_pred hCCCeEEEEEeCCchhHHHHHHcCCceEEEecCCcCCCCc---EEEEccCCcEEEE----EcCCCChHHcccCCHHHhcC
Confidence 3566665444 35578899999999999997422110110 1112223333322 2333433322222333332
Q ss_pred -EEEecHH---HHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 -RVLSHPQ---ALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 -~V~SHpq---al~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
....++. .......|+.+.+.. ...++|...+.++++.+ ...++.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 155 (198)
T cd08441 98 ETLITYPVERERLDVFRHFLQPAGIEPKRRRTVELTLMILQLVASG---RGVAALPNWAVR 155 (198)
T ss_pred CceEEecCCccHHHHHHHHHHhcCCCCCccEEeCCHHHHHHHHHhC---CcEEEeeHHHHH
Confidence 1222221 123345667665432 34567777777777765 235676766554
No 256
>PRK10837 putative DNA-binding transcriptional regulator; Provisional
Probab=33.66 E-value=3.4e+02 Score=23.97 Aligned_cols=32 Identities=19% Similarity=0.197 Sum_probs=24.3
Q ss_pred hCCCCceee-cCCHHHHHHHHHhCCCCeEEEee
Q 023305 17 AYPKCETVP-CDEFEDTFKAVELWLADKAVLPI 48 (284)
Q Consensus 17 ~f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPi 48 (284)
.+|+.++.- ..+..++++.+.+|++|+|+++-
T Consensus 114 ~~P~i~i~v~~~~~~~~~~~l~~g~~Di~i~~~ 146 (290)
T PRK10837 114 DYPQLPLELSVGNSQDVINAVLDFRVDIGLIEG 146 (290)
T ss_pred HCCCceEEEEECCHHHHHHHHHhCCceEEEecC
Confidence 357765543 35777899999999999999853
No 257
>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=33.54 E-value=2e+02 Score=21.44 Aligned_cols=74 Identities=15% Similarity=0.203 Sum_probs=39.3
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhC-Cceeeeeeee-eCCCCCCccccCCCCCCCccceeEEEEEeecCCCc-HHHHHHH
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALR-EINLTKIESR-PQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMAD-PRAQNAL 262 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~-~INLt~IeSR-P~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d-~~~~~al 262 (284)
+..+.|.+.+..-.|.++|..--.+ .|....-.-- |..+. ......+.|.|+-.|..+. ..+.+|+
T Consensus 8 ~~~~~~~~~~edhTl~n~L~~~l~~~pV~~a~Y~v~hp~~~~-----------~~~~d~~~~~VeT~Gs~~P~~al~~Ai 76 (86)
T cd00460 8 KNYVDFVLENEDHTLGNSLRRILLKSPVEFAAYYVEHPVKLQ-----------RTDEDKFILRIETVGSIPPEEALRRAV 76 (86)
T ss_pred CCEEEEEEeCCCchHHHHHHHHHhCCCceEEEEEeCCCccCC-----------CCCCCeEEEEEEECCCCCHHHHHHHHH
Confidence 4567777766666666666654443 1111111100 11111 0112367888888886543 4667888
Q ss_pred HHHHhcCC
Q 023305 263 GHLQEFAT 270 (284)
Q Consensus 263 ~~L~~~~~ 270 (284)
+.|.+.+.
T Consensus 77 ~~L~~~~~ 84 (86)
T cd00460 77 EILRKKLE 84 (86)
T ss_pred HHHHHHHh
Confidence 88876654
No 258
>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]
Probab=33.18 E-value=3e+02 Score=25.68 Aligned_cols=35 Identities=11% Similarity=0.187 Sum_probs=30.4
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeee
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESR 220 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSR 220 (284)
+..+.++.||+||-.+++-+.+..+|.|+.+-..-
T Consensus 7 ~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf 41 (287)
T COG0788 7 TFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQF 41 (287)
T ss_pred ceEEEEecCCCCCcHHHHHHHHHHcCCceeecccc
Confidence 46777888999999999999999999999866555
No 259
>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=33.06 E-value=3.2e+02 Score=23.61 Aligned_cols=29 Identities=10% Similarity=0.115 Sum_probs=25.2
Q ss_pred CceeecCCHHHHHHHHHhCCCCeEEEeee
Q 023305 21 CETVPCDEFEDTFKAVELWLADKAVLPIE 49 (284)
Q Consensus 21 ~~~~~~~s~~~v~~av~~~~~d~gvvPiE 49 (284)
.++++..++.+.++++.+|++|+++.+..
T Consensus 66 v~~~~~~~~~~~~~~l~~g~~Di~~~~~~ 94 (254)
T TIGR01098 66 VQLFVATDYSAVIEAMRFGRVDIAWFGPS 94 (254)
T ss_pred EEEEeCCCHHHHHHHHHcCCccEEEECcH
Confidence 56778899999999999999999987643
No 260
>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=33.04 E-value=1.8e+02 Score=20.60 Aligned_cols=27 Identities=22% Similarity=0.332 Sum_probs=23.5
Q ss_pred ecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 193 LDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 193 ~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
+.+.+|.+.++++.|++.+|++--|..
T Consensus 11 ~~~~~~~~~~i~~~L~~~~I~v~~i~~ 37 (80)
T cd04921 11 MVGVPGIAARIFSALARAGINVILISQ 37 (80)
T ss_pred CCCCccHHHHHHHHHHHCCCcEEEEEe
Confidence 457899999999999999999987754
No 261
>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=33.02 E-value=47 Score=29.39 Aligned_cols=63 Identities=27% Similarity=0.221 Sum_probs=34.0
Q ss_pred CCcHHHHHHHhhC---C-CCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccc-cccccCCeEEEE
Q 023305 6 PGSFSEDAALKAY---P-KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNY-DLLLRHRLHIVG 72 (284)
Q Consensus 6 ~GtfS~~Aa~~~f---~-~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~-d~L~~~~l~I~~ 72 (284)
+||=.+.-++.+. + ..|++..++..++++++++|++|-|||+.+ +.. .+++ |++.+.++++=|
T Consensus 76 kGsaADvl~Ral~d~~~~~~EvVytdD~~~i~~Ml~~g~vdsAVv~~~--~~~--G~~fEdl~~~~g~~~Pg 143 (201)
T PF12916_consen 76 KGSAADVLTRALLDLKGIKAEVVYTDDMSEIVKMLNEGEVDSAVVGSE--FSK--GETFEDLLGSLGLYAPG 143 (201)
T ss_dssp TTSHHHHHHHHHHHHH--T-EEEE---HHHHHHHHHTT-E--EEEETT--T-----EEHHHHHHHTT-----
T ss_pred cccHHHHHHHHHHhhccccceeEEecCHHHHHHHHhcCceeeeeecch--hcc--chhHHHHHhhcCCCCCh
Confidence 4555554444332 3 589999999999999999999999999944 322 4455 566677777644
No 262
>cd08433 PBP2_Nac The C-teminal substrate binding domain of LysR-like nitrogen assimilation control (NAC) protein, contains the type 2 periplasmic binding fold. The NAC is a LysR-type transcription regulator that activates expression of operons such as hut (histidine utilization) and ure (urea utilization), allowing use of non-preferred (poor) nitrogen sources, and represses expression of operons, such as glutamate dehydrogenase (gdh), allowing assimilation of the preferred nitrogen source. The expression of the nac gene is fully dependent on the nitrogen regulatory system (NTR) and the sigma54-containing RNA polymerase (sigma54-RNAP). In response to nitrogen starvation, NTR system activates the expression of nac, and NAC activates the expression of hut, ure, and put (proline utilization). NAC is not involved in the transcription of Sigma70-RNAP operons such as glnA, which directly respond by the NTR system, but activates the transcription of sigma70-RNAP dependent operons such as hut.
Probab=32.75 E-value=2.5e+02 Score=22.26 Aligned_cols=121 Identities=19% Similarity=0.101 Sum_probs=60.3
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcC---Cc
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKAD---QL 93 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~---~i 93 (284)
+|+.++... .+-.++.+.+.+|++|+|+..-.+...+. ....|.+.++.++ .+-+|-+...+..+++ +.
T Consensus 26 ~P~i~i~~~~~~~~~~~~~l~~~~~D~~i~~~~~~~~~~---~~~~l~~~~~~~~----~~~~~~~~~~~~~~~~~l~~~ 98 (198)
T cd08433 26 YPGIRLRIVEGLSGHLLEWLLNGRLDLALLYGPPPIPGL---STEPLLEEDLFLV----GPADAPLPRGAPVPLAELARL 98 (198)
T ss_pred CCCcEEEEEecCcHHHHHHHhCCCCcEEEEeCCCCCCCe---eEEEeccccEEEE----ecCCCccccCCCCCHHHhCCC
Confidence 566555443 45678899999999999997532221111 1111222233222 2333333222222222 22
Q ss_pred cEEE-ecHHH-HHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 KRVL-SHPQA-LASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 ~~V~-SHpqa-l~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|. .+... ...+..|+++++.. ...+++...+.++++.+ ...|+.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gia~~p~~~~~ 155 (198)
T cd08433 99 PLILPSRGHGLRRLVDEAAARAGLTLNVVVEIDSVATLKALVAAG---LGYTILPASAVA 155 (198)
T ss_pred ceEEcCCCCcHHHHHHHHHHHcCCCceeEEEeCcHHHHHHHHHcC---CcEEEcchhhhh
Confidence 2332 22222 23456666665433 34567777777777765 246666665443
No 263
>PRK01686 hisG ATP phosphoribosyltransferase catalytic subunit; Reviewed
Probab=32.74 E-value=2.8e+02 Score=24.78 Aligned_cols=112 Identities=21% Similarity=0.221 Sum_probs=60.3
Q ss_pred CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeE---eeecCCCCc------CCccEEEe
Q 023305 28 EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFC---LLALPGIKA------DQLKRVLS 98 (284)
Q Consensus 28 s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~---L~~~~~~~l------~~i~~V~S 98 (284)
--.|+-.-|+.|.+|+||+= .|.|.+.+-.+.-=..|...+| ++++++... ..-++|.+
T Consensus 53 r~~DIp~yV~~G~~DlGItG------------~D~l~E~~~~v~~l~dLgfG~crl~vAvp~~~~~~~~~~~~~~~rIAT 120 (215)
T PRK01686 53 RATDVPTYVEHGAADLGIVG------------KDVLLEHGKDLYEPLDLGIGKCRMSVAVPPGFDYAPAVKQGPRLRVAT 120 (215)
T ss_pred CHHHHHHHHhCCCccEEEee------------eeEeeecCCCeEEEecCCccCEEEEEEEECcccccchhhccCCCEEEe
Confidence 34688899999999999874 4555443322222233444444 444444221 12245655
Q ss_pred cHHHHHHHHHHHHhcCCe--EEecCCHHHHHHHHHhcCCCC-eEEE-cchhHHHhcCCceee
Q 023305 99 HPQALASSDIVLTQLGVA--RENVDDTASAAQYVASNGLRD-AGAV-ASARAAEIYGLNILA 156 (284)
Q Consensus 99 Hpqal~Qc~~fl~~~~~~--~~~~~sTa~Aa~~v~~~~~~~-~aAI-~s~~aa~~ygL~il~ 156 (284)
--.-+. ++||+++++. .+..+..-++|=.+ + .-+ .+=| .+-...+.+||++++
T Consensus 121 kYp~it--~~yf~~~gv~~~iv~l~GsvE~aP~~--G-lAD~IvDivsTG~TLr~NgL~~ie 177 (215)
T PRK01686 121 KYPNIA--RRYFAEKGEQVEIIKLYGSVELAPLV--G-LADAIVDIVETGNTLRANGLVEVE 177 (215)
T ss_pred CCHHHH--HHHHHHcCCeEEEEECcCceeecccc--C-CccEEEEeecChHHHHHCcCEEee
Confidence 544443 5699988754 44444333332211 0 011 1112 355677899999996
No 264
>PLN02550 threonine dehydratase
Probab=32.70 E-value=3.4e+02 Score=28.07 Aligned_cols=97 Identities=16% Similarity=0.166 Sum_probs=60.0
Q ss_pred cCCceeeccccCCCC--CeeEEEEEeeCCCCCCCCCCceEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCC
Q 023305 150 YGLNILADRIQDEPD--NITRFLVLARDPIIPRTDKLFKTSIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPL 227 (284)
Q Consensus 150 ygL~il~~~I~d~~~--N~TRF~vl~~~~~~~~~~~~~ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~ 227 (284)
.|++ ..+++|++. .+=||++=+|... ..-..+.|++|++||+|.+.|+.|.. .-|+|.++=|-....
T Consensus 480 ~g~~--~~~l~~~~~~~~~LR~v~g~ra~~------~~E~l~~v~fPErpGAl~~Fl~~lg~-~~nITeF~YR~~~~~-- 548 (591)
T PLN02550 480 AQLR--TVNLTSNDLVKDHLRYLMGGRAIV------KDELLYRFVFPERPGALMKFLDAFSP-RWNISLFHYRGQGET-- 548 (591)
T ss_pred CCCC--eEeCCCChHHhhhhhheecccccc------CceEEEEEEecCcCCHHHHHHHhhCC-CCceeeEEeecCCCC--
Confidence 3444 335666644 4447765445431 12456889999999999999998874 357788888854322
Q ss_pred ccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcCCceE
Q 023305 228 RVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATFLR 273 (284)
Q Consensus 228 ~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~~~vk 273 (284)
.- .-||-++-. +.++..+++.|++..-.+.
T Consensus 549 -------------~a-~vlvGi~v~--~~e~~~l~~~l~~~gy~~~ 578 (591)
T PLN02550 549 -------------GA-NVLVGIQVP--PEEMQEFKSRANALGYEYQ 578 (591)
T ss_pred -------------Cc-cEEEEEeeC--HHHHHHHHHHHHHcCCCeE
Confidence 11 244555432 3567777888877654433
No 265
>PRK11063 metQ DL-methionine transporter substrate-binding subunit; Provisional
Probab=32.43 E-value=3.1e+02 Score=25.07 Aligned_cols=85 Identities=19% Similarity=0.185 Sum_probs=49.7
Q ss_pred CCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeecccc-ccc--cCCeEEEEEEEE-eeeeEeeecCCCCcCCc--
Q 023305 20 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYD-LLL--RHRLHIVGEVQL-AANFCLLALPGIKADQL-- 93 (284)
Q Consensus 20 ~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d-~L~--~~~l~I~~E~~l-~I~~~L~~~~~~~l~~i-- 93 (284)
+++++.+++..+.++++.+|++|.... ..+. .+. .+. ..++.+++-... |+ .+....=.+++|+
T Consensus 60 ~Vel~~f~~~~~~~~ALa~GdID~~~~-----qh~~---~l~~~~~~~g~~l~~~~~~~vvp~--~~ys~~i~si~DL~~ 129 (271)
T PRK11063 60 DVELVTFNDYVLPNEALSKGDIDANAF-----QHKP---YLDQQIKDRGYKLVAVGNTFVYPI--AGYSKKIKSLDELQD 129 (271)
T ss_pred eEEEEEecCcHHHHHHHHcCCcceecc-----cCHH---HHHHHHHHcCCcEEEEeEEEEEEe--eccccCCCCHHHhcC
Confidence 468899999999999999999998751 1111 111 111 245666665443 43 2222211345666
Q ss_pred -cEEEec--HHHHHHHHHHHHhcC
Q 023305 94 -KRVLSH--PQALASSDIVLTQLG 114 (284)
Q Consensus 94 -~~V~SH--pqal~Qc~~fl~~~~ 114 (284)
++|.-. |.-.+.+-.+|.+.|
T Consensus 130 Gk~IAip~d~~n~~r~L~lL~~~G 153 (271)
T PRK11063 130 GSQVAVPNDPTNLGRSLLLLQKVG 153 (271)
T ss_pred CCEEEecCCCccHHHHHHHHHHCC
Confidence 466554 656666666777643
No 266
>PRK00341 hypothetical protein; Provisional
Probab=32.40 E-value=2.3e+02 Score=21.67 Aligned_cols=59 Identities=15% Similarity=0.299 Sum_probs=40.8
Q ss_pred cCCCchHHHHHHHHHhC-CceeeeeeeeeCCCCCCccccCCCCCCCccceeE-EEEEeecCCCcHHHHHHHHHHHhcC
Q 023305 194 DEGPGVLFKALAVFALR-EINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYL-FYIDFEASMADPRAQNALGHLQEFA 269 (284)
Q Consensus 194 ~~~pGaL~~~L~~F~~~-~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~-F~id~eg~~~d~~~~~al~~L~~~~ 269 (284)
.+.++....++.++.++ .++..+|.+||++++ .|. +=|.+... +.+.+.++.++|....
T Consensus 25 ~~~~~~~~~V~~iv~~~~~~~~~~~~~k~Ss~G----------------kY~S~tv~i~~~-s~~q~~~iy~~L~~~~ 85 (91)
T PRK00341 25 DTGVGFKDLVIEILQKHADVDLSTLAERQSSNG----------------KYTTVQLHIVAT-DEDQLQDINSALRATG 85 (91)
T ss_pred cCchhHHHHHHHHHHHhCCCcccceeeccCCCC----------------EEEEEEEEEEEC-CHHHHHHHHHHHhhCC
Confidence 46777778888888665 445678899999864 453 55555553 4467888888887653
No 267
>COG3181 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.37 E-value=35 Score=32.36 Aligned_cols=91 Identities=16% Similarity=0.061 Sum_probs=59.1
Q ss_pred CCcHHHHHHHhhCC----CCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeecccccccc---------CCeEEEE
Q 023305 6 PGSFSEDAALKAYP----KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLR---------HRLHIVG 72 (284)
Q Consensus 6 ~GtfS~~Aa~~~f~----~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~---------~~l~I~~ 72 (284)
.||..|.+..+++. +.+.+|++...++..++..|++|.++.=+-++....=.-++.+|.- .++.=..
T Consensus 158 ~Gs~dhl~~~~~~k~~Gi~~~~Vpy~g~gea~taLlgg~v~a~~~~~se~~~~vksG~lr~Lav~s~eRl~~~pdvPT~~ 237 (319)
T COG3181 158 LGSADHLAGALFAKAAGIKITYVPYKGGGEALTALLGGHVDAGSTNLSELLSQVKSGTLRLLAVFSEERLPGLPDVPTLK 237 (319)
T ss_pred CCcHHHHHHHHHHHHhCCceeEEeecCccHHHHHHhcCceeeeecChhhhhhhhccCceEEEEeechhhcCCCCCCCChH
Confidence 58899999887764 4678999999999999999999998876644433333334444431 1111122
Q ss_pred E----EEEeeeeEeeecCCCCcCCccEE
Q 023305 73 E----VQLAANFCLLALPGIKADQLKRV 96 (284)
Q Consensus 73 E----~~l~I~~~L~~~~~~~l~~i~~V 96 (284)
| +..++-+.+.+++|++-+.|.++
T Consensus 238 E~G~~~~~~~wrgvfap~g~~~e~~~~~ 265 (319)
T COG3181 238 EQGYDVVMSIWRGVFAPAGTPDEIIAKL 265 (319)
T ss_pred hcCCceeeeeeeEEEeCCCCCHHHHHHH
Confidence 2 12566677888888765544443
No 268
>PRK06635 aspartate kinase; Reviewed
Probab=31.95 E-value=1.4e+02 Score=28.65 Aligned_cols=28 Identities=29% Similarity=0.418 Sum_probs=25.0
Q ss_pred EecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 192 TLDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 192 ~~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
.+++.||.+.++++.|+++|||+..|.+
T Consensus 349 ~~~~~~g~~a~i~~~La~~~Ini~~i~s 376 (404)
T PRK06635 349 GMRSHPGVAAKMFEALAEEGINIQMIST 376 (404)
T ss_pred CCCCCchHHHHHHHHHHHCCCCEEEEEe
Confidence 3478999999999999999999998864
No 269
>PF01250 Ribosomal_S6: Ribosomal protein S6; InterPro: IPR000529 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein S6 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S6 is known to bind together with S18 to 16S ribosomal RNA. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities, groups bacterial, red algal chloroplast and cyanelle S6 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0019843 rRNA binding, 0006412 translation, 0005840 ribosome; PDB: 3BBN_F 3R3T_B 3F1E_F 2QNH_g 2OW8_g 3PYQ_F 3PYS_F 3PYU_F 3MR8_F 3PYN_F ....
Probab=31.87 E-value=2.2e+02 Score=21.23 Aligned_cols=60 Identities=17% Similarity=0.196 Sum_probs=39.1
Q ss_pred hHHHHHHHHHhCCceeeeeeee-------eCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhcCCc
Q 023305 199 VLFKALAVFALREINLTKIESR-------PQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEFATF 271 (284)
Q Consensus 199 aL~~~L~~F~~~~INLt~IeSR-------P~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~~~~ 271 (284)
.+.++-+.+...|-.+.++++. |.+... ..|+|++.++++. ..++++-+.|+..-.=
T Consensus 21 ~~~~~~~~i~~~gg~v~~~~~~G~r~LaY~i~k~~--------------~G~Y~~~~f~~~~--~~i~el~~~l~~~~~V 84 (92)
T PF01250_consen 21 LIERVKKIIEKNGGVVRSVENWGKRRLAYPIKKQK--------------EGHYFLFNFDASP--SAIKELERKLRLDEDV 84 (92)
T ss_dssp HHHHHHHHHHHTTEEEEEEEEEEEEEESSEETTEC--------------EEEEEEEEEEEST--THHHHHHHHHHTSTTE
T ss_pred HHHHHHHHHHHCCCEEEEEEEEeecccccCCCCCC--------------EEEEEEEEEEeCH--HHHHHHHHHhcCCCCe
Confidence 4566777789999999999985 554432 3477888888864 4555555566543333
Q ss_pred eEE
Q 023305 272 LRV 274 (284)
Q Consensus 272 vkv 274 (284)
+|+
T Consensus 85 lR~ 87 (92)
T PF01250_consen 85 LRY 87 (92)
T ss_dssp EEE
T ss_pred EEE
Confidence 443
No 270
>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=31.80 E-value=1.1e+02 Score=30.73 Aligned_cols=34 Identities=24% Similarity=0.342 Sum_probs=27.8
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeC
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQ 222 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~ 222 (284)
-+.|..|.+||+|.+.|+++.. +-|+|.+|=|-.
T Consensus 421 ~~~~~fperpgaL~~Fl~~l~~-~~~It~f~Yr~~ 454 (499)
T TIGR01124 421 LYSFEFPERPGALLRFLNTLQG-YWNISLFHYRNH 454 (499)
T ss_pred EEEEeCCCCccHHHHHHHhcCC-CCceeeEEEecC
Confidence 4667889999999999997755 668888888764
No 271
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=31.74 E-value=2.9e+02 Score=24.20 Aligned_cols=37 Identities=8% Similarity=0.175 Sum_probs=26.4
Q ss_pred HHHHHhhCCCCceeecCCHHHHHHHHHhCCCCeEEEee
Q 023305 11 EDAALKAYPKCETVPCDEFEDTFKAVELWLADKAVLPI 48 (284)
Q Consensus 11 ~~Aa~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPi 48 (284)
++++++.--+.++++. ++..+++++++|++|.++-++
T Consensus 57 ~~ia~~lg~~i~~~~~-pw~~~~~~l~~g~~D~~~~~~ 93 (259)
T PRK15437 57 KELCKRINTQCTFVEN-PLDALIPSLKAKKIDAIMSSL 93 (259)
T ss_pred HHHHHHcCCceEEEeC-CHHHHHHHHHCCCCCEEEecC
Confidence 3344443335677776 499999999999999776554
No 272
>PRK15385 magnesium transport protein MgtC; Provisional
Probab=31.19 E-value=3.8e+02 Score=24.18 Aligned_cols=66 Identities=11% Similarity=0.014 Sum_probs=43.1
Q ss_pred EEEEEecCCCc--hHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecC-CCcHHHHHHHHH
Q 023305 188 SIVFTLDEGPG--VLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEAS-MADPRAQNALGH 264 (284)
Q Consensus 188 si~f~~~~~pG--aL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~-~~d~~~~~al~~ 264 (284)
.+.+...++++ .+..+++.++..++.+..+++.+.+.. .+..-..++... .++..+.+++.+
T Consensus 144 ~~~v~~~~~~~~~vr~~L~~~l~~~~~~~~~l~~~~~~~~---------------~~~ei~a~l~~~~~~~~~le~iv~~ 208 (225)
T PRK15385 144 ILKVTCNKEDESAVRQWLLNIVKEAAICLQGLGSVPAQEQ---------------GYKEIRAELVGHADYRKTRELIISR 208 (225)
T ss_pred EEEEEEcCcchhHHHHHHHHHHHhCCCceEEeEeeecCCC---------------CeEEEEEEEEecCCchhhHHHHHHH
Confidence 34444555444 478888999999999999999987532 123333344332 256778888888
Q ss_pred HHhc
Q 023305 265 LQEF 268 (284)
Q Consensus 265 L~~~ 268 (284)
|...
T Consensus 209 L~~~ 212 (225)
T PRK15385 209 IGDN 212 (225)
T ss_pred HhCC
Confidence 8643
No 273
>TIGR00149 TIGR00149_YbjQ secondary thiamine-phosphate synthase enzyme. Members of this protein family have been studied extensively by crystallography. Members from several different species have been shown to have sufficient thiamin phosphate synthase activity (EC 2.5.1.3) to complement thiE mutants. However, it is presumed that this is a secondary activity, and the primary function of this enzyme remains unknown.
Probab=30.85 E-value=33 Score=28.27 Aligned_cols=18 Identities=22% Similarity=0.573 Sum_probs=14.5
Q ss_pred CCCCCCccceeEEEEEeecCC
Q 023305 233 SNNGTAKYFDYLFYIDFEASM 253 (284)
Q Consensus 233 ~~~g~~~~~~y~F~id~eg~~ 253 (284)
..+|+ |+.+||+|++|..
T Consensus 104 L~LGt---wQ~I~l~E~Dg~r 121 (132)
T TIGR00149 104 LQLGT---WQGIFFAEFDGPR 121 (132)
T ss_pred EcccC---ccEEEEEECCCCC
Confidence 45664 9999999999864
No 274
>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=30.83 E-value=1.8e+02 Score=22.93 Aligned_cols=105 Identities=11% Similarity=-0.011 Sum_probs=49.4
Q ss_pred HHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc---EEEecHHHHHHHHHHH
Q 023305 34 KAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK---RVLSHPQALASSDIVL 110 (284)
Q Consensus 34 ~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~---~V~SHpqal~Qc~~fl 110 (284)
+.+.+|++|+|++...+...+. ....|.+.++.++ .+-+| +...+..+++|+. -|. .......-..|+
T Consensus 40 ~~l~~~~~Dl~l~~~~~~~~~~---~~~~l~~~~~~~v----~~~~~-~~~~~~~~~~dl~~~~~i~-~~~~~~~~~~~~ 110 (194)
T cd08481 40 FDFSQGSFDAAIHFGDPVWPGA---ESEYLMDEEVVPV----CSPAL-LAGRALAAPADLAHLPLLQ-QTTRPEAWRDWF 110 (194)
T ss_pred cCcccCCCCEEEEcCCCCCCCc---cceecccCeeeec----CCHHH-HhcCCCCcHHHHhhCceEe-cCCCCcCHHHHH
Confidence 3688999999998644322221 1122333333332 22233 2222222333332 221 110011234566
Q ss_pred HhcCCe------EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhc
Q 023305 111 TQLGVA------RENVDDTASAAQYVASNGLRDAGAVASARAAEIY 150 (284)
Q Consensus 111 ~~~~~~------~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y 150 (284)
.+.+.. ...+++...+.++++.+ ...|+.++..++.+
T Consensus 111 ~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~~p~~~~~~~ 153 (194)
T cd08481 111 EEVGLEVPTAYRGMRFEQFSMLAQAAVAG---LGVALLPRFLIEEE 153 (194)
T ss_pred HHcCCCCCCccCceEeccHHHHHHHHHhC---CCeEEecHHHHHHH
Confidence 665432 13445666677777765 24778887766543
No 275
>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=30.47 E-value=2.9e+02 Score=22.25 Aligned_cols=122 Identities=20% Similarity=0.127 Sum_probs=61.3
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc-
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK- 94 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~- 94 (284)
.+|+.++.... +-.++.+.+.+|++|+|+.....- .+.+. ...|.+.++.++ .+-+|-|... ..+++|+.
T Consensus 25 ~~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~-~~~~~--~~~l~~~~~~~v----~~~~h~l~~~-~~~~~dL~~ 96 (200)
T cd08467 25 RAPGLDLRLCPIGDDLAERGLEQGTIDLAVGRFAVP-PDGLV--VRRLYDDGFACL----VRHGHPALAQ-EWTLDDFAT 96 (200)
T ss_pred hCCCCEEEEecCCcccHHHHhhCCCcCEEEecCCCC-Cccce--eEEeeeccEEEE----EcCCCccccC-CCCHHHHhC
Confidence 35777665544 445889999999999999742110 11111 112223333322 2334444322 12333322
Q ss_pred --EEEecH--HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 95 --RVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 95 --~V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
-|.-.. ....+...++++.++. ...++|.....++|+.+ ...++.+...++.
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~~ 155 (200)
T cd08467 97 LRHVAIAPPGRLFGGIYKRLENLGLKRNVAIAVSSFLTAAATVAAT---DLIATVPRRVATQ 155 (200)
T ss_pred CCCEEEcCCCCCCchHHHHHHhcCCcccEEEEecchHHHHHHHhcC---CeEEeeHHHHHHH
Confidence 222111 1112344566655543 34566777777777764 3467777766653
No 276
>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=30.14 E-value=2.7e+02 Score=21.87 Aligned_cols=123 Identities=15% Similarity=0.041 Sum_probs=60.5
Q ss_pred hhCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCc---C
Q 023305 16 KAYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKA---D 91 (284)
Q Consensus 16 ~~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l---~ 91 (284)
+.+|+.++.-. .+..+..+.+.+|++|+|++.-.....+ -....|.+.++.++ .+-+|-+...+..++ .
T Consensus 24 ~~~P~i~l~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~---~~~~~l~~~~~~~v----~~~~~~l~~~~~~~~~~l~ 96 (196)
T cd08415 24 ARHPDVRISLHTLSSSTVVEAVLSGQADLGLASLPLDHPG---LESEPLASGRAVCV----LPPGHPLARKDVVTPADLA 96 (196)
T ss_pred HHCCCcEEEEEecchHHHHHHHHcCCccEEEEeCCCCCCc---ceeeeecccceEEE----EcCCCChHhcCccCHHHhc
Confidence 34577665433 3667899999999999999863311111 01112222233222 122232222111222 2
Q ss_pred CccEEEe-cH-HHHHHHHHHHHhcCC--e-EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 92 QLKRVLS-HP-QALASSDIVLTQLGV--A-RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 92 ~i~~V~S-Hp-qal~Qc~~fl~~~~~--~-~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
+-.-|.- +. ....+...|+.+.+. + ...++|.....+++..+ ...++.+...++
T Consensus 97 ~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~lp~~~~~ 155 (196)
T cd08415 97 GEPLISLGRGDPLRQRVDAAFERAGVEPRIVIETQLSHTACALVAAG---LGVAIVDPLTAA 155 (196)
T ss_pred CCcEEEeCCCccHHHHHHHHHHHcCCCceEEEEEeHHHHHHHHHHcC---CCeEEechhhhh
Confidence 3333332 22 223455667766543 2 24566666667777764 236677765443
No 277
>PRK09791 putative DNA-binding transcriptional regulator; Provisional
Probab=29.60 E-value=4.1e+02 Score=23.74 Aligned_cols=31 Identities=6% Similarity=-0.015 Sum_probs=23.6
Q ss_pred CCCCcee-ecCCHHHHHHHHHhCCCCeEEEee
Q 023305 18 YPKCETV-PCDEFEDTFKAVELWLADKAVLPI 48 (284)
Q Consensus 18 f~~~~~~-~~~s~~~v~~av~~~~~d~gvvPi 48 (284)
+|+.++. -..+..++.+++.+|++|+|+++.
T Consensus 121 ~p~i~~~~~~~~~~~~~~~l~~g~~Di~i~~~ 152 (302)
T PRK09791 121 HPQVKVRIMEGQLVSMINELRQGELDFTINTY 152 (302)
T ss_pred CCCeEEEEEeCChHHHHHHHHCCCccEEEEec
Confidence 4665543 245778999999999999999853
No 278
>PRK15437 histidine ABC transporter substrate-binding protein HisJ; Provisional
Probab=29.56 E-value=1.1e+02 Score=26.95 Aligned_cols=42 Identities=14% Similarity=0.140 Sum_probs=30.3
Q ss_pred CCcHHHHHHHhhC--CCCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 6 PGSFSEDAALKAY--PKCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 6 ~GtfS~~Aa~~~f--~~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
.|++.++-...++ .+.+++...+.++++++|.+|++|+.+..
T Consensus 140 ~g~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~L~~grvD~~v~~ 183 (259)
T PRK15437 140 QGTTQETFGNEHWAPKGIEIVSYQGQDNIYSDLTAGRIDAAFQD 183 (259)
T ss_pred cCcHHHHHHHhhccccCceEEecCCHHHHHHHHHcCCccEEEec
Confidence 4565444333332 23567889999999999999999998764
No 279
>cd04920 ACT_AKiii-DAPDC_2 ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC). This CD includes the second of two ACT domains of a bifunctional AKIII (LysC)-like aspartokinase/meso-diaminopimelate decarboxylase (DAPDC) bacterial protein. Aspartokinase (AK) is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. The lysA gene encodes the enzyme DAPDC, a pyridoxal-5'-phosphate (PLP)-dependent enzyme which catalyzes the final step in the lysine biosynthetic pathway converting meso-diaminopimelic acid (DAP) to l-lysine. Tandem ACT domains are positioned centrally with the AK catalytic domain N-terminal and the DAPDC domains C-terminal. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=28.96 E-value=2e+02 Score=19.87 Aligned_cols=33 Identities=24% Similarity=0.186 Sum_probs=24.2
Q ss_pred EEEEE-EecCCCchHHHHHHHHHhCCceeeeeee
Q 023305 187 TSIVF-TLDEGPGVLFKALAVFALREINLTKIES 219 (284)
Q Consensus 187 tsi~f-~~~~~pGaL~~~L~~F~~~~INLt~IeS 219 (284)
.|++= .+.+.||.+.++++.|+..+|++-..-.
T Consensus 3 VsvVG~g~~~~~gv~~~~~~~L~~~~i~~i~~~~ 36 (63)
T cd04920 3 VSLVGRGIRSLLHKLGPALEVFGKKPVHLVSQAA 36 (63)
T ss_pred EEEECCCcccCccHHHHHHHHHhcCCceEEEEeC
Confidence 34443 3457899999999999998888854433
No 280
>COG2150 Predicted regulator of amino acid metabolism, contains ACT domain [General function prediction only]
Probab=28.90 E-value=3.1e+02 Score=23.62 Aligned_cols=36 Identities=25% Similarity=0.243 Sum_probs=30.6
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeeeeeeee
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTKIESRP 221 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP 221 (284)
-..+.-+..+.||-|..+.+.+++|||++..+-|+-
T Consensus 95 Viei~~~~~~~pgi~A~V~~~iak~gi~Irqi~~~d 130 (167)
T COG2150 95 VIEIYPEDARYPGILAGVASLIAKRGISIRQIISED 130 (167)
T ss_pred EEEEEeccCCCccHHHHHHHHHHHcCceEEEEecCC
Confidence 445555667899999999999999999999998884
No 281
>COG3283 TyrR Transcriptional regulator of aromatic amino acids metabolism [Transcription / Amino acid transport and metabolism]
Probab=28.21 E-value=2e+02 Score=28.37 Aligned_cols=70 Identities=20% Similarity=0.323 Sum_probs=51.9
Q ss_pred EEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHhc-
Q 023305 190 VFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQEF- 268 (284)
Q Consensus 190 ~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~~- 268 (284)
-+...|+-|-.-++|..+..++|||..||--|.. ..|++|-. ++....++++.+|+..
T Consensus 4 eV~cedRlGltrelLdlLv~r~idl~~iEid~~~--------------------~IYln~p~-l~~~~fs~L~aei~~I~ 62 (511)
T COG3283 4 EVFCEDRLGLTRELLDLLVLRGIDLRGIEIDPIG--------------------RIYLNFPE-LEFESFSSLMAEIRRIP 62 (511)
T ss_pred EEEehhhhchHHHHHHHHHhcccCccceeecCCC--------------------eEEEeccc-cCHHHHHHHHHHHhcCC
Confidence 3445789999999999999999999999986643 25667743 4456788888888754
Q ss_pred -CCceEEEceeeC
Q 023305 269 -ATFLRVLGCYPM 280 (284)
Q Consensus 269 -~~~vkvLGsYp~ 280 (284)
...||..+--|.
T Consensus 63 GV~~vr~V~~mPs 75 (511)
T COG3283 63 GVTDVRTVPWMPS 75 (511)
T ss_pred CccceeeecCCcc
Confidence 345777665554
No 282
>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=28.03 E-value=66 Score=29.12 Aligned_cols=45 Identities=22% Similarity=0.163 Sum_probs=34.2
Q ss_pred cCCCCcHHHHHHHhhCCC-------CceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 3 QGLPGSFSEDAALKAYPK-------CETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 3 lGp~GtfS~~Aa~~~f~~-------~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
.|+.|+.++....+++.. ...+++.+..+++.++.+|++|.++..
T Consensus 146 ~~~~~s~~~~~~~~~l~~~G~~~~~~~~v~~~~~~~~~~al~~G~vDa~~~~ 197 (320)
T TIGR02122 146 VGAPGSGTELNARAVLKAAGLTYDDVKKVEYLGYAEAADALKDGKIDAAFYT 197 (320)
T ss_pred cCCCCcchHHHHHHHHHHcCCCHHHccchhcCCHHHHHHHHHCCCccEEEEe
Confidence 366788788776665532 224678899999999999999999876
No 283
>PRK15010 ABC transporter lysine/arginine/ornithine binding periplasmic protein; Provisional
Probab=27.78 E-value=4.2e+02 Score=23.22 Aligned_cols=113 Identities=18% Similarity=0.180 Sum_probs=59.7
Q ss_pred CCceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCC----CcCCcc-
Q 023305 20 KCETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGI----KADQLK- 94 (284)
Q Consensus 20 ~~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~----~l~~i~- 94 (284)
+.++++. ++++++.+++.|++|.++-++.-+ -+. +..+....-+ +.....++++++. ++++++
T Consensus 66 ~~~~~~~-~~~~~~~~l~~g~~Di~~~~~~~t--------~eR--~~~~~fs~p~-~~~~~~~~~~~~~~~~~~~~dl~g 133 (260)
T PRK15010 66 KCTWVAS-DFDALIPSLKAKKIDAIISSLSIT--------DKR--QQEIAFSDKL-YAADSRLIAAKGSPIQPTLDSLKG 133 (260)
T ss_pred ceEEEeC-CHHHHHHHHHCCCCCEEEecCcCC--------HHH--Hhhcccccce-EeccEEEEEECCCCCCCChhHcCC
Confidence 3566664 699999999999999776443211 111 0111111111 2234455555542 223332
Q ss_pred -EEEecHHHHHHHHHHHHh----cCCeEEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 95 -RVLSHPQALASSDIVLTQ----LGVARENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 95 -~V~SHpqal~Qc~~fl~~----~~~~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
+|.-..-... ..|+.+ .++..+...+..++.+++..+. -.|.|++...+.
T Consensus 134 ~~Igv~~gs~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~gr--iDa~i~d~~~~~ 188 (260)
T PRK15010 134 KHVGVLQGSTQ--EAYANETWRSKGVDVVAYANQDLVYSDLAAGR--LDAALQDEVAAS 188 (260)
T ss_pred CEEEEecCchH--HHHHHHhcccCCceEEecCCHHHHHHHHHcCC--ccEEEeCcHHHH
Confidence 3433222211 123432 3566777778888888888763 346777765553
No 284
>PRK07431 aspartate kinase; Provisional
Probab=27.28 E-value=2.1e+02 Score=29.11 Aligned_cols=58 Identities=14% Similarity=0.182 Sum_probs=38.9
Q ss_pred EecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHH
Q 023305 192 TLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQ 266 (284)
Q Consensus 192 ~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~ 266 (284)
.+++.||.+.++++.|+++|||+-.|..-++... .....|.|+-+- -.+..++|+++.
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 135788885421 133445555554
No 285
>PRK15421 DNA-binding transcriptional regulator MetR; Provisional
Probab=27.18 E-value=4.9e+02 Score=23.79 Aligned_cols=120 Identities=23% Similarity=0.179 Sum_probs=59.0
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc--
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK-- 94 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~-- 94 (284)
+++.++.. ..+-.++.+.+.+|++|+|+++-.-...+. .+..|.+.++.+ +++-.|-+......+++++.
T Consensus 115 ~P~i~l~~~~~~~~~~~~~L~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~l----v~~~~hpl~~~~~i~~~~L~~~ 187 (317)
T PRK15421 115 WPQVEMDFKSGVTFDPQPALQQGELDLVMTSDILPRSGL---HYSPMFDYEVRL----VLAPDHPLAAKTRITPEDLASE 187 (317)
T ss_pred CCCceEEEEeCccHHHHHHHHCCCcCEEEecCcccCCCc---eEEEeccceEEE----EEcCCCCccccCcCCHHHhCCC
Confidence 46655533 345678899999999999998521001110 011222223332 23334434332223333332
Q ss_pred EEEecH---HHHHHHHHHHHhcCCe--EEecCCHHHHHHHHHhcCCCCeEEEcchhHH
Q 023305 95 RVLSHP---QALASSDIVLTQLGVA--RENVDDTASAAQYVASNGLRDAGAVASARAA 147 (284)
Q Consensus 95 ~V~SHp---qal~Qc~~fl~~~~~~--~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 147 (284)
..+..+ ........|+.+.+++ ...++|.....+++..+ . ..++.+...+
T Consensus 188 p~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g--~-Gi~i~p~~~~ 242 (317)
T PRK15421 188 TLLIYPVQRSRLDVWRHFLQPAGVSPSLKSVDNTLLLIQMVAAR--M-GIAALPHWVV 242 (317)
T ss_pred cEEecCCchhhHHHHHHHHHHhCCCCceeecCCHHHHHHHHHhC--C-cEEEecchhc
Confidence 122221 2233455566665543 33466777777777765 2 3556665543
No 286
>cd08442 PBP2_YofA_SoxR_like The C-terminal substrate binding domain of LysR-type transcriptional regulators, YofA and SoxR, contains the type 2 periplasmic binding fold. YofA is a LysR-like transcriptional regulator of cell growth in Bacillus subtillis. YofA controls cell viability and the formation of constrictions during cell division. YofaA positively regulates expression of the cell division gene ftsW, and thus is essential for cell viability during stationary-phase growth of Bacillus substilis. YofA shows significant homology to SoxR from Arthrobacter sp. TE1826. SoxR is a negative regulator for the sarcosine oxidase gene soxA. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine, which is involved in the metabolism of creatine and choline. The topology of this substrate-binding domain is most similar to that of the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides
Probab=26.73 E-value=3.1e+02 Score=21.44 Aligned_cols=122 Identities=12% Similarity=0.003 Sum_probs=61.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCccE
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLKR 95 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~~ 95 (284)
.+|+.++.-. .+-+++.+.+.+|++|+|++.-..-..+.. ...|.+.++.++. +-+|-+... -.++.+..-
T Consensus 25 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~v~----~~~~~~~~~-~~~l~~~~~ 96 (193)
T cd08442 25 RYPKVDLSLSTGTTGALIQAVLEGRLDGAFVAGPVEHPRLE---QEPVFQEELVLVS----PKGHPPVSR-AEDLAGSTL 96 (193)
T ss_pred HCCCceEEEEeCCcHHHHHHHHCCCccEEEEeCCCCCCCcE---EEEeecCcEEEEe----cCCCccccc-HHHhCCCce
Confidence 3567665433 356788999999999999975321111111 1112222322221 112222110 012223333
Q ss_pred EEecH--HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHHh
Q 023305 96 VLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAEI 149 (284)
Q Consensus 96 V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ 149 (284)
|.-.+ ....+...|+.+.+.. ...++|...+.+++.++ ...++.+...++.
T Consensus 97 i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~~ 152 (193)
T cd08442 97 LAFRAGCSYRRRLEDWLAEEGVSPGKIMEFGSYHAILGCVAAG---MGIALLPRSVLDS 152 (193)
T ss_pred EEecCCCcHHHHHHHHHHHcCCCcceEEecCCHHHHHHHHHhC---CcEEEcCHHHHhh
Confidence 32111 1234466777776533 24566777777777765 2467888776653
No 287
>PRK12483 threonine dehydratase; Reviewed
Probab=26.49 E-value=3.2e+02 Score=27.73 Aligned_cols=63 Identities=17% Similarity=0.230 Sum_probs=40.8
Q ss_pred EEEEEecCCCchHHHHHHHHHhCCceeeeeeeeeCCCCCCccccCCCCCCCccceeEEEEEeecCCCcHHHHHHHHHHHh
Q 023305 188 SIVFTLDEGPGVLFKALAVFALREINLTKIESRPQRKRPLRVVDDSNNGTAKYFDYLFYIDFEASMADPRAQNALGHLQE 267 (284)
Q Consensus 188 si~f~~~~~pGaL~~~L~~F~~~~INLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~F~id~eg~~~d~~~~~al~~L~~ 267 (284)
.+.|++|++||+|.+.|+.+.. .-|+|-..=|-.... .=.-||-++-. +...+.+++.|++
T Consensus 442 ~~~v~iPE~pGa~~~f~~~l~~-~~niTeF~YR~~~~~----------------~a~v~vgi~~~--~~~~~~~~~~l~~ 502 (521)
T PRK12483 442 LFRFEFPERPGALMKFLSRLGP-RWNISLFHYRNHGAA----------------DGRVLAGLQVP--EDERAALDAALAA 502 (521)
T ss_pred EEEEEcCCCCcHHHHHHHHhCC-CcceeeeeecCCCCC----------------ceEEEEEEeeC--hhHHHHHHHHHHH
Confidence 5778999999999999999985 245665666654322 12344555432 2455667777776
Q ss_pred cC
Q 023305 268 FA 269 (284)
Q Consensus 268 ~~ 269 (284)
..
T Consensus 503 ~g 504 (521)
T PRK12483 503 LG 504 (521)
T ss_pred CC
Confidence 53
No 288
>PRK11013 DNA-binding transcriptional regulator LysR; Provisional
Probab=26.32 E-value=4.8e+02 Score=23.49 Aligned_cols=120 Identities=15% Similarity=0.049 Sum_probs=58.4
Q ss_pred CCCCcee-ecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCC---cCCc
Q 023305 18 YPKCETV-PCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIK---ADQL 93 (284)
Q Consensus 18 f~~~~~~-~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~---l~~i 93 (284)
+|+.++. -..+-.++.+.+.+|++|+|+..-.=...|. ....+...+.. ..+|..|-+......+ +.+.
T Consensus 120 ~P~v~i~i~~~~~~~~~~~l~~~~~Dl~i~~~~~~~~~~---~~~~l~~~~~~----~~~~~~~pl~~~~~i~~~dL~~~ 192 (309)
T PRK11013 120 YPDVSLNIVPQESPLLEEWLSAQRHDLGLTETLHTPAGT---ERTELLTLDEV----CVLPAGHPLAAKKVLTPDDFAGE 192 (309)
T ss_pred CCCCeEEEEeCCHHHHHHHHHcCCCCEEEEcCCCCCCCc---eeeeecceeEE----EEEcCCCccccCCccCHHHHCCC
Confidence 4665543 2345677899999999999997421000110 01111111221 2355556554332223 3333
Q ss_pred cEEEecHH-HH-HHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHH
Q 023305 94 KRVLSHPQ-AL-ASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAA 147 (284)
Q Consensus 94 ~~V~SHpq-al-~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 147 (284)
+-|.-.+. .. ..+..|+...++. . ..++|...+.+++..+ ...++.+...+
T Consensus 193 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gv~~~p~~~~ 248 (309)
T PRK11013 193 NFISLSRTDSYRQLLDQLFAEHGVKRRMVVETHSAASVCAMVRAG---VGVSIVNPLTA 248 (309)
T ss_pred cEEeecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CeEEEeChhhh
Confidence 44443322 22 2356677776543 2 3444555555666654 23455655443
No 289
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=26.30 E-value=64 Score=26.01 Aligned_cols=25 Identities=20% Similarity=0.298 Sum_probs=21.3
Q ss_pred EEEEEeecCCCcHHHHHHHHHHHhc
Q 023305 244 LFYIDFEASMADPRAQNALGHLQEF 268 (284)
Q Consensus 244 ~F~id~eg~~~d~~~~~al~~L~~~ 268 (284)
.+.||..|+++++.+++.+.++...
T Consensus 2 ~vaiDtSGSis~~~l~~fl~ev~~i 26 (126)
T PF09967_consen 2 VVAIDTSGSISDEELRRFLSEVAGI 26 (126)
T ss_pred EEEEECCCCCCHHHHHHHHHHHHHH
Confidence 4789999999999999999887654
No 290
>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=25.99 E-value=1.3e+02 Score=21.51 Aligned_cols=30 Identities=20% Similarity=0.386 Sum_probs=23.3
Q ss_pred EEEEEeecCCCcHHHHHHHHHHHhcCCceEEE
Q 023305 244 LFYIDFEASMADPRAQNALGHLQEFATFLRVL 275 (284)
Q Consensus 244 ~F~id~eg~~~d~~~~~al~~L~~~~~~vkvL 275 (284)
.+++++.|. +..++++++.|++....+.+|
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 478899884 578999999999887766654
No 291
>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=25.73 E-value=1.7e+02 Score=28.10 Aligned_cols=27 Identities=22% Similarity=0.367 Sum_probs=23.7
Q ss_pred EecCCCchHHHHHHHHHhCCceeeeee
Q 023305 192 TLDEGPGVLFKALAVFALREINLTKIE 218 (284)
Q Consensus 192 ~~~~~pGaL~~~L~~F~~~~INLt~Ie 218 (284)
.+++.||.+.++++.++..|||+..+-
T Consensus 346 ~~~~~~g~~a~i~~~L~~~gIni~~i~ 372 (401)
T TIGR00656 346 GMVGAPGVASEIFSALEEKNINILMIG 372 (401)
T ss_pred CcccCccHHHHHHHHHHHCCCcEEEEE
Confidence 346899999999999999999998665
No 292
>CHL00180 rbcR LysR transcriptional regulator; Provisional
Probab=25.70 E-value=4.9e+02 Score=23.35 Aligned_cols=31 Identities=16% Similarity=0.010 Sum_probs=23.6
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEe
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvP 47 (284)
.+|+.++.... +..++.+.+.+|++|+|+.+
T Consensus 120 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~ 151 (305)
T CHL00180 120 RYPQINVQLQVHSTRRIAWNVANGQIDIAIVG 151 (305)
T ss_pred HCCCceEEEEeCCHHHHHHHHHcCCccEEEEc
Confidence 35666654433 57888999999999999984
No 293
>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=25.64 E-value=94 Score=27.11 Aligned_cols=64 Identities=14% Similarity=0.000 Sum_probs=38.1
Q ss_pred CceeecCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCC
Q 023305 21 CETVPCDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPG 87 (284)
Q Consensus 21 ~~~~~~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~ 87 (284)
.++....+..+++++|.+|++|.++.+-. ...+...+..+ ...++.+.++-.....+.++.+++
T Consensus 175 ~~i~~~~~~~~~~~al~~G~~Da~~~~~~-~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~ 238 (254)
T TIGR01098 175 SEVVFSGSHDASALAVANGKVDAATNNSS-AIGRLKKRGPS--DMKKVRVIWKSPLIPNDPIAVRKD 238 (254)
T ss_pred hheeecCchHHHHHHHHcCCCCeEEecHH-HHHHHHHhCcc--chhheEEEEecCCCCCCCEEEECC
Confidence 45667778999999999999999998733 22221111111 012567777644333445555554
No 294
>PF13379 NMT1_2: NMT1-like family; PDB: 2G29_A 3UN6_A 2I4C_A 2I49_A 2I4B_A 2I48_A 3QSL_A.
Probab=25.56 E-value=1.3e+02 Score=26.60 Aligned_cols=43 Identities=21% Similarity=0.096 Sum_probs=31.8
Q ss_pred CCCCcHHHHHHHhhC--------CCCceeecCCHHHHHHHHHhCCCCeEEEe
Q 023305 4 GLPGSFSEDAALKAY--------PKCETVPCDEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 4 Gp~GtfS~~Aa~~~f--------~~~~~~~~~s~~~v~~av~~~~~d~gvvP 47 (284)
.+.||-++...+.++ .+.+++..+. .+...++.+|++|.++++
T Consensus 127 ~~~gs~~~~~l~~~l~~~Gl~~~~dv~~~~~~~-~~~~~al~~g~iDa~~~~ 177 (252)
T PF13379_consen 127 PFPGSTHDMLLRYLLKKAGLDPKDDVTLVNVPP-PEMVAALRAGEIDAAVLW 177 (252)
T ss_dssp SSTTSHHHHHHHHHHHHTT--TTTSSEEEE--G-HHHHHHHHTTS-SEEEEE
T ss_pred cCCCCHHHHHHHHHHHhCCCCcccceEEEecCH-HHHHHHHhCCCcCEEEec
Confidence 467888887776554 2367888888 999999999999999985
No 295
>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=25.16 E-value=3.4e+02 Score=21.34 Aligned_cols=122 Identities=14% Similarity=0.053 Sum_probs=58.1
Q ss_pred hCCCCceeecC-CHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCC---
Q 023305 17 AYPKCETVPCD-EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ--- 92 (284)
Q Consensus 17 ~f~~~~~~~~~-s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~--- 92 (284)
.+|+.++.-.. +-.++.+.+.+|++|+|+..-.....+.. ...|.+..+.+ ..+-+|-+...+..++++
T Consensus 25 ~~P~i~~~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~~---~~~l~~~~~~~----~~~~~~~l~~~~~~~~~~l~~ 97 (196)
T cd08456 25 RHPDVTISIHTRDSPTVEQWLSAQQCDLGLVSTLHEPPGIE---RERLLRIDGVC----VLPPGHRLAVKKVLTPSDLEG 97 (196)
T ss_pred HCCCcEEEEEeCCHHHHHHHHHcCCccEEEEecCCCCCCee---EEEeeccCeEE----EecCCCchhccCccCHHHcCC
Confidence 35666554333 45678899999999999975322111111 11122223322 222233333222222333
Q ss_pred ccEEE-ecHHH-HHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 93 LKRVL-SHPQA-LASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 93 i~~V~-SHpqa-l~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
..-|. .+... ......|+.+.+.. . ..+++...+.+++..+ ...++.+...++
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 155 (196)
T cd08456 98 EPFISLARTDGTRQRVDALFEQAGVKRRIVVETSYAATICALVAAG---VGVSVVNPLTAL 155 (196)
T ss_pred CcEEEecCCcchHHHHHHHHHHCCCCcceEEEEccHHHHHHHHHcC---CeEEEeChhhhc
Confidence 23333 22222 22345566655432 2 3456666667777764 245666665443
No 296
>KOG4028 consensus Uncharacterized conserved protein [Function unknown]
Probab=25.07 E-value=65 Score=26.82 Aligned_cols=29 Identities=24% Similarity=0.189 Sum_probs=21.7
Q ss_pred cCCCCcHHHHHHHhhCCC-CceeecCCHHH
Q 023305 3 QGLPGSFSEDAALKAYPK-CETVPCDEFED 31 (284)
Q Consensus 3 lGp~GtfS~~Aa~~~f~~-~~~~~~~s~~~ 31 (284)
--|+||+-|+-|+++-+. .++..-+++++
T Consensus 113 wrp~gswreel~~~~vggg~ql~~~~ai~~ 142 (175)
T KOG4028|consen 113 WRPKGSWREELAHAFVGGGLQLLHGDAIED 142 (175)
T ss_pred cCCCCcHHHHHHHHHhcCCceeeccccccC
Confidence 359999999999988764 56666655544
No 297
>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=24.98 E-value=5.1e+02 Score=23.28 Aligned_cols=148 Identities=18% Similarity=0.122 Sum_probs=93.4
Q ss_pred CCCCcHHHHHHHhhCC--------C--CceeecC---CHHHHHHHHHhCCCCeEEEeeeecccceeecccc---------
Q 023305 4 GLPGSFSEDAALKAYP--------K--CETVPCD---EFEDTFKAVELWLADKAVLPIENSSSGSIHRNYD--------- 61 (284)
Q Consensus 4 Gp~GtfS~~Aa~~~f~--------~--~~~~~~~---s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d--------- 61 (284)
=|+|+...++..++.. + .++.|-. +-.+++++|..|.+|.++++.-+. .+. .+.+.
T Consensus 5 ~p~~~~~~~~~~~fa~~v~e~t~G~v~i~v~~~g~lg~~~e~~~~v~~G~vdm~~~~~~~~-~~~-~p~~~~~~lP~~~~ 82 (286)
T PF03480_consen 5 WPEGHPITQAVEKFAEEVEERTGGRVKIEVFPAGQLGKEAEVLEAVQDGAVDMAVVSPSYL-AGF-VPEFGVFDLPFLFR 82 (286)
T ss_dssp STTTSHHHHHHHHHHHHHHHHTTTSEEEEEEETTSSSSHHHHHHHHHTTSSSEEEEEGGGG-TTT-SGGGGGGGSTTTSS
T ss_pred CCCCCHHHHHHHHHHHHHHHHcCCeEEEEEecCcccCCHHHHHHHHhCCCccEEeecchhh-hhh-chhheeeeCCCCCC
Confidence 3889999998866542 2 2455544 467999999999999999987442 222 11111
Q ss_pred -------------------ccccCCeEEEEEEEEeeeeEeee-cCCCCcCCcc--EEEecHHHHHHHHHHHHhcCCeEEe
Q 023305 62 -------------------LLLRHRLHIVGEVQLAANFCLLA-LPGIKADQLK--RVLSHPQALASSDIVLTQLGVAREN 119 (284)
Q Consensus 62 -------------------~L~~~~l~I~~E~~l~I~~~L~~-~~~~~l~~i~--~V~SHpqal~Qc~~fl~~~~~~~~~ 119 (284)
.+.+.++++.+-...+-.+.... .|=.+++|++ +|.+-+.+ ....+++..|+..++
T Consensus 83 ~~~~~~~~~~~~~~~~l~~~~~~~g~~~L~~~~~g~~~~~~~~~pi~s~~DlkG~kiR~~~~~--~~~~~~~~lGa~pv~ 160 (286)
T PF03480_consen 83 DYEELDRVMDSGYGPELREELEEKGIKLLGWFPGGPRQFFSTKKPIRSPEDLKGLKIRVPGSP--VMSDFFEALGASPVP 160 (286)
T ss_dssp SHHHHHHHHHSHHHHHHHHHHHHTTEEEEEEEEEEEEEEEESSS--SSGGGGTTEEEEETSSH--HHHHHHHHCTSEEEE
T ss_pred CHHHHHHHHhCcHHHHHHHHHHhhceEEEEEecCCceEEEecccCCccHhhHhhCeEEecCCH--HHHHHHHHcCCeeec
Confidence 11124788888777777665553 4545778887 77776443 346688888887654
Q ss_pred --cCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeecccc
Q 023305 120 --VDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQ 160 (284)
Q Consensus 120 --~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~ 160 (284)
...+-.|.+ .+ .-.+++.+.....-+++.=+.+.+-
T Consensus 161 ip~~evy~aLq---~G--~vDg~~~~~~~~~~~~~~ev~~y~~ 198 (286)
T PF03480_consen 161 IPWSEVYQALQ---QG--VVDGAENSASSIYSLGLYEVAKYFT 198 (286)
T ss_dssp -TGGGHHHHHH---TT--SSSEEEEEHHHHHHTTGGGTSSEEE
T ss_pred CcHHHHHHHHh---cC--CcCeEecCHHHHHhcChhhhCCeeE
Confidence 445555444 33 2348888888888778764444443
No 298
>cd08447 PBP2_LTTR_aromatics_like_1 The C-terminal substrate binding domain of an uncharacterized LysR-type transcriptional regulator similar to regulators involved in the catabolism of aromatic compounds, contains type 2 periplasmic binding fold. This CD represents the substrate binding domain of an uncharacterized LysR-type regulator similar to CbnR which is involved in the regulation of chlorocatechol breakdown. The transcription of the genes encoding enzymes involved in such degradation is regulated and expression of these enzymes is enhanced by inducers, which are either an intermediate in the metabolic pathway or compounds to be degraded. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, and histidine. The PBP2 bind their ligand in the cleft between these domains in a manner resembling a Ve
Probab=24.89 E-value=3.5e+02 Score=21.34 Aligned_cols=121 Identities=17% Similarity=0.119 Sum_probs=58.7
Q ss_pred CCCCceee-cCCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCC---c
Q 023305 18 YPKCETVP-CDEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ---L 93 (284)
Q Consensus 18 f~~~~~~~-~~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~---i 93 (284)
+|+.++.. ..+..++.+.+.+|++|+|+..-.....+.. ...|.+.++.++ .+-.|-|...+..++++ .
T Consensus 26 ~P~i~v~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~---~~~l~~~~~~~v----~~~~~pl~~~~~~~~~~l~~~ 98 (198)
T cd08447 26 LPDVDLVLREMVTTDQIEALESGRIDLGLLRPPFARPGLE---TRPLVREPLVAA----VPAGHPLAGAERLTLEDLDGQ 98 (198)
T ss_pred CCCeEEEEEeCCHHHHHHHHHcCCceEEEecCCCCCCCee---EEEeecCceEEE----ecCCCchhhcCcccHHHhCCC
Confidence 46655543 2367889999999999999975321111111 111222232221 12223222221122222 2
Q ss_pred cEEE-ecH--HHHHH-HHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 94 KRVL-SHP--QALAS-SDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 94 ~~V~-SHp--qal~Q-c~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
.-|. .+. ....+ -..|+.+.+.. ...++|...+.++++.+. ..++.+...++
T Consensus 99 ~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g~---gi~~~p~~~~~ 157 (198)
T cd08447 99 PFIMYSPTEARYFHDLVVRLFASAGVQPRYVQYLSQIHTMLALVRAGL---GVALVPASASR 157 (198)
T ss_pred eEEEeCCCCCchHHHHHHHHHHHcCCCCCceeecCCHHHHHHHHHcCC---CeEEhhHHHhh
Confidence 3333 111 11222 24566665432 245667777777777752 36677776554
No 299
>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=24.88 E-value=81 Score=23.27 Aligned_cols=77 Identities=14% Similarity=0.170 Sum_probs=49.6
Q ss_pred EEecHHHHHHHHHHHHhcCC-eEEecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeeccccCCCCCeeEEEEEee
Q 023305 96 VLSHPQALASSDIVLTQLGV-ARENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILADRIQDEPDNITRFLVLAR 174 (284)
Q Consensus 96 V~SHpqal~Qc~~fl~~~~~-~~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~~I~d~~~N~TRF~vl~~ 174 (284)
|=.||.-..-.+.+|+..+. ....+.|..+|.+.+.... ++..-|--. -....|+.+++. |.... ..+++++++.
T Consensus 4 vd~~~~~~~~l~~~l~~~~~~~v~~~~~~~~~~~~~~~~~-~d~iiid~~-~~~~~~~~~~~~-i~~~~-~~~~ii~~t~ 79 (112)
T PF00072_consen 4 VDDDPEIRELLEKLLERAGYEEVTTASSGEEALELLKKHP-PDLIIIDLE-LPDGDGLELLEQ-IRQIN-PSIPIIVVTD 79 (112)
T ss_dssp EESSHHHHHHHHHHHHHTTEEEEEEESSHHHHHHHHHHST-ESEEEEESS-SSSSBHHHHHHH-HHHHT-TTSEEEEEES
T ss_pred EECCHHHHHHHHHHHHhCCCCEEEEECCHHHHHHHhcccC-ceEEEEEee-eccccccccccc-ccccc-ccccEEEecC
Confidence 44578888888899997788 6778888888888887653 544443322 222444444433 33323 7788888886
Q ss_pred CC
Q 023305 175 DP 176 (284)
Q Consensus 175 ~~ 176 (284)
..
T Consensus 80 ~~ 81 (112)
T PF00072_consen 80 ED 81 (112)
T ss_dssp ST
T ss_pred CC
Confidence 54
No 300
>cd08458 PBP2_NocR The C-terminal substrate-domain of LysR-type transcriptional regulator, NocR, involved in the catabolism of nopaline, contains the type 2 periplasmic binding fold. This CD includes the C-terminal substrate-domain of LysR-type transcriptional regulator NocR, which is involved in the catabolism of nopaline. Opines are low molecular weight compounds found in plant crown gall tumors produced by the parasitic bacterium Agrobacterium. There are at least 30 different opines identified so far. Opines are utilized by tumor-colonizing bacteria as a source of carbon, nitrogen, and energy. In Agrobacterium tumefaciens, NocR regulates expression of the divergently transcribed nocB and nocR genes of the nopaline catabolism (noc) region. This substrate-binding domain shows significant homology to the type 2 periplasmic binding proteins (PBP2), which are responsible for the uptake of a variety of substrates such as phosphate, sulfate, polysaccharides, lysine/arginine/ornithine, an
Probab=24.63 E-value=3.6e+02 Score=21.48 Aligned_cols=121 Identities=15% Similarity=0.087 Sum_probs=59.6
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCc--
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQL-- 93 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i-- 93 (284)
.+|+.++... .+..++.+.+.+|++|+|+..-.....|. ....|.+..+.++ .+-+|-+...+..+++|+
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~v----~~~~hpl~~~~~i~~~dL~~ 97 (196)
T cd08458 25 DRPDVSVYLDTVPSQTVLELVSLQHYDLGISILAGDYPGL---TTEPVPSFRAVCL----LPPGHRLEDKETVHATDLEG 97 (196)
T ss_pred HCCCcEEEEeccChHHHHHHHHcCCCCEEEEeccCCCCCc---eEEEeccCceEEE----ecCCCccccCCccCHHHhCC
Confidence 3566665443 46678999999999999998432111111 0112222233222 233343332222233333
Q ss_pred -cEEE-ecH-HHHHHHHHHHHhcCC--eE-EecCCHHHHHHHHHhcCCCCeEEEcchhHH
Q 023305 94 -KRVL-SHP-QALASSDIVLTQLGV--AR-ENVDDTASAAQYVASNGLRDAGAVASARAA 147 (284)
Q Consensus 94 -~~V~-SHp-qal~Qc~~fl~~~~~--~~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa 147 (284)
.-|. +.. ....+...|+++.+. +. ..++|.....+++..+ ...|+.+...+
T Consensus 98 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gia~l~~~~~ 154 (196)
T cd08458 98 ESLICLSPVSLLRMQTDAALDSCGVHCNRRIESSLALNLCDLVSRG---MGVGIVDPFTA 154 (196)
T ss_pred CccEEecCCCcHHHHHHHHHHHcCCCcceEEEeccHHHHHHHHHcC---CcEEEECchhh
Confidence 2232 111 123445667777553 32 3455666666677764 23556665544
No 301
>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=24.53 E-value=5e+02 Score=23.01 Aligned_cols=147 Identities=14% Similarity=0.075 Sum_probs=80.1
Q ss_pred cCCCCcHHHHHHHhhCC--------CC--ceeec---CCHHHHHHHHHhCCCCeEEEeeeeccccee-----------ec
Q 023305 3 QGLPGSFSEDAALKAYP--------KC--ETVPC---DEFEDTFKAVELWLADKAVLPIENSSSGSI-----------HR 58 (284)
Q Consensus 3 lGp~GtfS~~Aa~~~f~--------~~--~~~~~---~s~~~v~~av~~~~~d~gvvPiENS~~G~V-----------~~ 58 (284)
.-|+|+...++...+.. +. ++.|- -.-.+++++|..|.+|+++++.-+. .+.+ ..
T Consensus 4 ~~p~~~~~~~~~~~f~~~v~e~t~G~v~v~~~~~g~Lg~~~e~~~~v~~G~~d~~~~~~~~~-~~~~p~~~~~~lP~~~~ 82 (257)
T TIGR00787 4 NAARSSPKHKAAEKFAKLVNEKTNGEIKISVFPSSQLGSDRAMLEALQGGALDMTAPSSSKF-GPLVPELAVFDLPFLFR 82 (257)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHcCCeEEEEEcCCCCCCChHHHHHHHhCCCccEEecccccc-cccCcchhhccCCeecC
Confidence 45899988888876542 12 33332 2468999999999999998653221 1100 00
Q ss_pred c-------cc---------ccccCCeEEEEEEEEeeeeEeee---cCCCCcCCcc--EEEecHHHHHHHHHHHHhcCCeE
Q 023305 59 N-------YD---------LLLRHRLHIVGEVQLAANFCLLA---LPGIKADQLK--RVLSHPQALASSDIVLTQLGVAR 117 (284)
Q Consensus 59 t-------~d---------~L~~~~l~I~~E~~l~I~~~L~~---~~~~~l~~i~--~V~SHpqal~Qc~~fl~~~~~~~ 117 (284)
+ ++ .+.+.++++.+-.. ....++. .|-.+++|++ +|...+-.. -.++++..+...
T Consensus 83 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~l~~~~--~g~~~~~~~~~~i~s~~Dl~G~kir~~~~~~--~~~~~~~~Ga~~ 158 (257)
T TIGR00787 83 DYNHVHKVLDGEVGKALKKSLEKKGLKGLAYWD--NGFRQFTSSKKPITKPEDLKGLKIRIPNSPM--NEAQFKALGANP 158 (257)
T ss_pred CHHHHHHHHcCHHHHHHHHHHHHcCcEEEeecC--CceeEeeeCCCccCChHHhCCCEEecCCCHH--HHHHHHHcCCcc
Confidence 0 00 12234566665333 3333333 2323566665 566543222 355677777665
Q ss_pred EecCCHHHHHHHHHhcCCCCeEEEcchhHHHhcCCceeec
Q 023305 118 ENVDDTASAAQYVASNGLRDAGAVASARAAEIYGLNILAD 157 (284)
Q Consensus 118 ~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~ygL~il~~ 157 (284)
+ ..+.++.-..+..+. -.+++.+.....-++|.=+.+
T Consensus 159 v-~~~~~e~~~aL~~G~--vDg~~~~~~~~~~~~~~ev~~ 195 (257)
T TIGR00787 159 E-PMAFSEVYTALQTGV--VDGQENPLSNVYSSKFYEVQK 195 (257)
T ss_pred c-ccCHHHHHHHHHcCC--cccccCCHHHHhhcchhhhcc
Confidence 5 455666666666542 246677766655556643333
No 302
>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=24.50 E-value=39 Score=27.28 Aligned_cols=17 Identities=18% Similarity=0.559 Sum_probs=11.0
Q ss_pred CCCCCCccceeEEEEEeecC
Q 023305 233 SNNGTAKYFDYLFYIDFEAS 252 (284)
Q Consensus 233 ~~~g~~~~~~y~F~id~eg~ 252 (284)
..+|+ |+.+||+|++|.
T Consensus 92 L~LGt---wQ~I~l~E~dgp 108 (118)
T PF01894_consen 92 LALGT---WQGIYLVEFDGP 108 (118)
T ss_dssp E---T---TEEEEEEESS-S
T ss_pred EccCC---cCEEEEEECCCC
Confidence 34664 999999999983
No 303
>cd08419 PBP2_CbbR_RubisCO_like The C-terminal substrate binding of LysR-type transcriptional regulator (CbbR) of RubisCO operon, which is involved in the carbon dioxide fixation, contains the type 2 periplasmic binding fold. CbbR, a LysR-type transcriptional regulator, is required to activate expression of RubisCO, one of two unique enzymes in the Calvin-Benson-Bassham (CBB) cycle pathway. All plants, cyanobacteria, and many autotrophic bacteria use the CBB cycle to fix carbon dioxide. Thus, this cycle plays an essential role in assimilating CO2 into organic carbon on earth. The key CBB cycle enzyme is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the actual CO2 fixation reaction. The CO2 concentration affects the expression of RubisCO genes. It has also shown that NADPH enhances the DNA-binding ability of the CbbR. RubisCO is composed of eight large (CbbL) and eight small subunits (CbbS). The topology of this substrate-binding domain is most similar to t
Probab=24.42 E-value=3.5e+02 Score=21.18 Aligned_cols=122 Identities=15% Similarity=0.113 Sum_probs=60.0
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeecccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCC---
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLPIENSSSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQ--- 92 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~--- 92 (284)
.+|+.++.-. .+..++.+.+.+|++|+|+..-.....+. ....|.+.++.++. +-+|-+...+..++++
T Consensus 24 ~~P~i~l~i~~~~~~~~~~~l~~g~~Dl~i~~~~~~~~~~---~~~~l~~~~~~~~~----~~~~~l~~~~~~~~~~l~~ 96 (197)
T cd08419 24 RHPGVEVSLRVGNREQVLERLADNEDDLAIMGRPPEDLDL---VAEPFLDNPLVVIA----PPDHPLAGQKRIPLERLAR 96 (197)
T ss_pred HCCCceEEEEECCHHHHHHHHhcCCccEEEecCCCCCCCe---EEEEeccCCEEEEe----cCCCCCcCCCCcCHHHHhC
Confidence 3566655433 46778899999999999997432111111 01122222332221 1222222111122222
Q ss_pred ccEEEecH--HHHHHHHHHHHhcCCe---EEecCCHHHHHHHHHhcCCCCeEEEcchhHHH
Q 023305 93 LKRVLSHP--QALASSDIVLTQLGVA---RENVDDTASAAQYVASNGLRDAGAVASARAAE 148 (284)
Q Consensus 93 i~~V~SHp--qal~Qc~~fl~~~~~~---~~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~ 148 (284)
..-|.-.+ ....+...|+.+.+.. ...++|...+.++++.+ ...++.+...++
T Consensus 97 ~~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~gi~~~p~~~~~ 154 (197)
T cd08419 97 EPFLLREPGSGTRLAMERFFAEHGVTLRVRMELGSNEAIKQAVMAG---LGLSVLSLHTLA 154 (197)
T ss_pred CCcEEecCCCcHHHHHHHHHHHCCCCcceEEEECCHHHHHHHHHhC---CceEeecHHHHH
Confidence 22232111 1123355566665532 34567777777888875 236777776554
No 304
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=22.26 E-value=5.7e+02 Score=22.85 Aligned_cols=145 Identities=10% Similarity=-0.033 Sum_probs=69.4
Q ss_pred CCCCceeec-CCHHHHHHHHHhCCCCeEEEeeeec--ccceeeccccccccCCeEEEEEEEEeeeeEeeecCCCCcCCcc
Q 023305 18 YPKCETVPC-DEFEDTFKAVELWLADKAVLPIENS--SSGSIHRNYDLLLRHRLHIVGEVQLAANFCLLALPGIKADQLK 94 (284)
Q Consensus 18 f~~~~~~~~-~s~~~v~~av~~~~~d~gvvPiENS--~~G~V~~t~d~L~~~~l~I~~E~~l~I~~~L~~~~~~~l~~i~ 94 (284)
+|+.++.-. .+.+++.+.+.+|++|+|+...... ....+ ....|.+.++.++. +-.|-+.. .-..+.+..
T Consensus 119 ~P~i~l~~~~~~~~~~~~~l~~g~~D~~i~~~~~~~~~~~~l--~~~~l~~~~~~~~~----~~~~~~~~-~~~~l~~~~ 191 (296)
T PRK11062 119 DESIHLRCFESTHEMLLEQLSQHKLDMILSDCPVDSTQQEGL--FSKKLGECGVSFFC----TNPLPEKP-FPACLEERR 191 (296)
T ss_pred CCceEEEEEeCCHHHHHHHHHcCCCCEEEecCCCccccccch--hhhhhhccCcceEe----cCCCcccc-ChHHHhcCC
Confidence 456555433 5778999999999999999742211 01111 11122233332221 11221111 111223323
Q ss_pred EEEec-HHH-HHHHHHHHHhcCCe--E-EecCCHHHHHHHHHhcCCCCeEEEcchhHHHhc----CCceeeccccCCCCC
Q 023305 95 RVLSH-PQA-LASSDIVLTQLGVA--R-ENVDDTASAAQYVASNGLRDAGAVASARAAEIY----GLNILADRIQDEPDN 165 (284)
Q Consensus 95 ~V~SH-pqa-l~Qc~~fl~~~~~~--~-~~~~sTa~Aa~~v~~~~~~~~aAI~s~~aa~~y----gL~il~~~I~d~~~N 165 (284)
-|... ... ..+-..|+..++.. . ..++|.....+++..+ ...++.+...++.+ +|..+. +...-
T Consensus 192 ~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~g---~Gi~~lp~~~~~~~~~~~~l~~l~----~~~~~ 264 (296)
T PRK11062 192 LLIPGRRTMLGRKLLNWFNSQGLNVEILGEFDDAALMKAFGAYH---DAIFVAPSLYAQDFYADHSVVEIG----RVDNV 264 (296)
T ss_pred eeecCCCchHHHHHHHHHHHcCCCceeeeeeCcHHHHHHHHHcC---CceEECCHHHHHHHHHcCCeEEcC----Ccccc
Confidence 33211 111 22345566665543 2 3456666666666654 34778888777643 344432 11223
Q ss_pred eeEEEEEeeCC
Q 023305 166 ITRFLVLARDP 176 (284)
Q Consensus 166 ~TRF~vl~~~~ 176 (284)
...|+++.++.
T Consensus 265 ~~~~~lv~~~~ 275 (296)
T PRK11062 265 KEEYHVIFAER 275 (296)
T ss_pred ceEEEEEEecC
Confidence 44666666554
No 305
>PRK07377 hypothetical protein; Provisional
Probab=21.06 E-value=1.4e+02 Score=26.09 Aligned_cols=34 Identities=15% Similarity=-0.055 Sum_probs=28.0
Q ss_pred HhhCCCCceeecCCHHHHHHHHHhCCCCeEEEee
Q 023305 15 LKAYPKCETVPCDEFEDTFKAVELWLADKAVLPI 48 (284)
Q Consensus 15 ~~~f~~~~~~~~~s~~~v~~av~~~~~d~gvvPi 48 (284)
.+|+-+.+++++++.+++-+|+.+|++|..+.+-
T Consensus 104 ~~y~~rlElv~y~~~~~l~~aL~~~eVh~~c~~~ 137 (184)
T PRK07377 104 DKYHLRLELVVYPDLQALEQALRDKEVHAICLES 137 (184)
T ss_pred HHhCceeeEEecCCHHHHHHHHhcCCccEEecCC
Confidence 3444457899999999999999999999887643
No 306
>PRK00907 hypothetical protein; Provisional
Probab=20.99 E-value=3.9e+02 Score=20.53 Aligned_cols=62 Identities=15% Similarity=0.194 Sum_probs=43.0
Q ss_pred cCCCchHHHHHHHHHhCCc--eeeeeeeeeCCCCCCccccCCCCCCCccceeE-EEEEeecCCCcHHHHHHHHHHHhcCC
Q 023305 194 DEGPGVLFKALAVFALREI--NLTKIESRPQRKRPLRVVDDSNNGTAKYFDYL-FYIDFEASMADPRAQNALGHLQEFAT 270 (284)
Q Consensus 194 ~~~pGaL~~~L~~F~~~~I--NLt~IeSRP~~~~~~~~~~~~~~g~~~~~~y~-F~id~eg~~~d~~~~~al~~L~~~~~ 270 (284)
.++++-...++.++..+.- +..+++.||++++ .|. +=+.+... +.+.+.++.++|... .
T Consensus 25 ~a~~~l~~~V~~vv~~h~p~~~~~~i~~r~Ss~G----------------kY~Svtv~i~at-s~eQld~iY~~L~~~-~ 86 (92)
T PRK00907 25 TAERGLETELPRLLAATGVELLQERISWKHSSSG----------------KYVSVRIGFRAE-SREQYDAAHQALRDH-P 86 (92)
T ss_pred cCchhHHHHHHHHHHHhCCCCCcCcEEeccCCCC----------------EEEEEEEEEEEC-CHHHHHHHHHHHhhC-C
Confidence 4678888899999988854 6789999999864 453 33444333 347888888888754 3
Q ss_pred ceE
Q 023305 271 FLR 273 (284)
Q Consensus 271 ~vk 273 (284)
.||
T Consensus 87 ~Vk 89 (92)
T PRK00907 87 EVK 89 (92)
T ss_pred CEE
Confidence 344
No 307
>cd08439 PBP2_LrhA_like The C-terminal substrate domain of LysR-like regulator LrhA (LysR homologue A) and that of closely related homologs, contains the type 2 periplasmic binding fold. This CD represents the LrhA subfamily of LysR-like bacterial transcriptional regulators, including LrhA, HexA, PecT, and DgdR. LrhA is involved in control of the transcription of flagellar, motility, and chemotaxis genes by regulating the synthesis and concentration of FlhD(2)C(2), the master regulator for the expression of flagellar and chemotaxis genes. The LrhA protein has strong homology to HexA and PecT from plant pathogenic bacteria, in which HexA and PecT act as repressors of motility and of virulence factors, such as exoenzymes required for lytic reactions. DgdR also shares similar characteristics to those of LrhA, HexA and PecT. 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 vari
Probab=20.99 E-value=1.4e+02 Score=23.82 Aligned_cols=31 Identities=16% Similarity=0.188 Sum_probs=23.5
Q ss_pred hCCCCceeec-CCHHHHHHHHHhCCCCeEEEe
Q 023305 17 AYPKCETVPC-DEFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 17 ~f~~~~~~~~-~s~~~v~~av~~~~~d~gvvP 47 (284)
.+|+.++.-. .+-.++++.+.+|++|+|++.
T Consensus 25 ~~P~v~i~~~~~~~~~~~~~l~~~~~Dl~i~~ 56 (185)
T cd08439 25 VYPRLAIEVVCKRTPRLMEMLERGEVDLALIT 56 (185)
T ss_pred HCCCeEEEEEECChHHHHHHHHCCCCcEEEEe
Confidence 3566655443 356789999999999999985
No 308
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=20.92 E-value=4.9e+02 Score=28.29 Aligned_cols=31 Identities=13% Similarity=0.173 Sum_probs=27.9
Q ss_pred eEEEEEEecCCCchHHHHHHHHHhCCceeee
Q 023305 186 KTSIVFTLDEGPGVLFKALAVFALREINLTK 216 (284)
Q Consensus 186 ktsi~f~~~~~pGaL~~~L~~F~~~~INLt~ 216 (284)
-|-+.+..+|+||-+.++-++|+.+|+|+..
T Consensus 704 ~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~ 734 (895)
T PRK00275 704 GTQIFIYAPDQHDFFAATVAAMDQLNLNIHD 734 (895)
T ss_pred eEEEEEEeCCCCcHHHHHHHHHHHCCCeEEE
Confidence 4677778899999999999999999999984
No 309
>PF01522 Polysacc_deac_1: Polysaccharide deacetylase; InterPro: IPR002509 This domain is found in polysaccharide deacetylase. This family of polysaccharide deacetylases includes NodB (nodulation protein B from Rhizobium) which is a chitooligosaccharide deacetylase []. It also includes chitin deacetylase from yeast [], and endoxylanases which hydrolyses glucosidic bonds in xylan [].; GO: 0016810 hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, 0005975 carbohydrate metabolic process; PDB: 2IW0_A 2CC0_B 2VYO_A 2J13_A 2C71_A 2C79_A 1W1A_1 1W1B_1 1W17_A 1NY1_B ....
Probab=20.56 E-value=1.1e+02 Score=23.47 Aligned_cols=30 Identities=27% Similarity=0.317 Sum_probs=24.1
Q ss_pred eEEEEEEecCCC-chHHHHHHHHHhCCceee
Q 023305 186 KTSIVFTLDEGP-GVLFKALAVFALREINLT 215 (284)
Q Consensus 186 ktsi~f~~~~~p-GaL~~~L~~F~~~~INLt 215 (284)
+-+++++.++.+ ..+.+++..|+++|+..|
T Consensus 5 ~~~v~ltfDdg~~~~~~~~~~~l~~~~i~at 35 (123)
T PF01522_consen 5 KKSVALTFDDGYRDNYDRLLPLLKKYGIPAT 35 (123)
T ss_dssp SSEEEEEEESHCHTHHHHHHHHHHHTT--EE
T ss_pred CCEEEEEEecCchhhHHHHHHHHHhccccee
Confidence 567889998876 789999999999998776
No 310
>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=20.40 E-value=1.9e+02 Score=25.47 Aligned_cols=20 Identities=25% Similarity=0.011 Sum_probs=17.8
Q ss_pred CHHHHHHHHHhCCCCeEEEe
Q 023305 28 EFEDTFKAVELWLADKAVLP 47 (284)
Q Consensus 28 s~~~v~~av~~~~~d~gvvP 47 (284)
+..+++.+|.+|++|..+..
T Consensus 151 ~~~~~~~aL~~GrvDa~i~~ 170 (246)
T TIGR03870 151 DPRKLVSEVATGKADLAVAF 170 (246)
T ss_pred CHHHHHHHHHcCCCCEEEee
Confidence 46889999999999999885
Done!