Query 018897
Match_columns 349
No_of_seqs 185 out of 1238
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 04:57:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/018897.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/018897hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd00083 HLH Helix-loop-helix d 99.3 1.5E-12 3.2E-17 96.4 4.7 53 179-231 4-59 (60)
2 PF00010 HLH: Helix-loop-helix 99.3 2.7E-12 5.8E-17 94.5 3.7 49 180-228 2-55 (55)
3 smart00353 HLH helix loop heli 99.3 8E-12 1.7E-16 90.8 5.8 49 184-232 1-52 (53)
4 KOG1318 Helix loop helix trans 98.8 3E-09 6.6E-14 107.2 5.0 57 179-235 233-293 (411)
5 cd04897 ACT_ACR_3 ACT domain-c 98.6 4.2E-07 9.1E-12 72.0 10.2 69 275-343 2-73 (75)
6 KOG1319 bHLHZip transcription 98.6 4.1E-08 8.9E-13 89.6 4.0 63 179-241 62-131 (229)
7 cd04895 ACT_ACR_1 ACT domain-c 98.5 1.7E-06 3.7E-11 68.0 9.6 52 275-326 2-53 (72)
8 cd04896 ACT_ACR-like_3 ACT dom 98.4 2.3E-06 4.9E-11 67.9 9.6 67 276-343 2-73 (75)
9 cd04927 ACT_ACR-like_2 Second 98.4 2E-06 4.4E-11 67.5 9.1 68 275-343 1-72 (76)
10 KOG2588 Predicted DNA-binding 98.3 1.9E-06 4.1E-11 93.9 9.1 62 178-239 275-337 (953)
11 KOG4304 Transcriptional repres 98.2 5.5E-07 1.2E-11 86.1 2.7 56 178-233 31-94 (250)
12 cd04900 ACT_UUR-like_1 ACT dom 98.2 1.6E-05 3.5E-10 61.4 10.1 49 275-323 2-51 (73)
13 cd04925 ACT_ACR_2 ACT domain-c 98.0 6.4E-05 1.4E-09 58.5 10.4 67 276-342 2-72 (74)
14 KOG3561 Aryl-hydrocarbon recep 97.9 7.9E-06 1.7E-10 88.7 4.7 51 180-230 21-75 (803)
15 cd04926 ACT_ACR_4 C-terminal 97.9 0.00015 3.3E-09 56.0 10.2 71 275-349 2-72 (72)
16 KOG2483 Upstream transcription 97.8 5E-05 1.1E-09 72.0 7.8 65 176-240 56-123 (232)
17 cd04899 ACT_ACR-UUR-like_2 C-t 97.8 0.00027 5.9E-09 53.0 9.7 64 276-340 2-68 (70)
18 cd04928 ACT_TyrKc Uncharacteri 97.8 0.0003 6.5E-09 54.8 9.5 64 276-342 3-67 (68)
19 KOG3960 Myogenic helix-loop-he 97.7 0.0005 1.1E-08 65.7 11.2 56 182-237 121-178 (284)
20 PRK05007 PII uridylyl-transfer 97.4 0.00064 1.4E-08 75.4 10.3 70 272-342 806-878 (884)
21 PLN03217 transcription factor 97.3 0.00045 9.7E-09 56.1 5.7 51 191-241 19-75 (93)
22 KOG0561 bHLH transcription fac 97.3 0.00022 4.7E-09 69.7 3.5 53 181-233 62-116 (373)
23 PRK01759 glnD PII uridylyl-tra 97.2 0.0013 2.9E-08 72.6 9.9 70 272-342 781-853 (854)
24 PRK00275 glnD PII uridylyl-tra 97.2 0.0024 5.1E-08 71.0 11.1 71 272-342 812-885 (895)
25 PF01842 ACT: ACT domain; Int 97.2 0.004 8.6E-08 45.6 8.8 62 276-342 2-65 (66)
26 PRK04374 PII uridylyl-transfer 97.1 0.0037 8.1E-08 69.3 11.3 71 272-342 794-866 (869)
27 PRK05092 PII uridylyl-transfer 97.1 0.0041 8.8E-08 69.4 11.5 70 273-342 842-914 (931)
28 KOG4029 Transcription factor H 97.0 0.00063 1.4E-08 63.9 4.1 60 178-237 108-171 (228)
29 cd04873 ACT_UUR-ACR-like ACT d 97.0 0.0093 2E-07 44.1 9.5 48 276-323 2-49 (70)
30 PRK03059 PII uridylyl-transfer 96.9 0.0042 9.2E-08 68.8 9.6 71 272-342 784-854 (856)
31 TIGR01693 UTase_glnD [Protein- 96.6 0.011 2.3E-07 65.4 10.1 70 273-342 778-849 (850)
32 PRK03381 PII uridylyl-transfer 96.6 0.012 2.5E-07 64.7 10.1 51 273-323 706-756 (774)
33 cd04893 ACT_GcvR_1 ACT domains 96.4 0.035 7.6E-07 43.4 9.4 67 275-345 2-69 (77)
34 TIGR01693 UTase_glnD [Protein- 96.4 0.018 4E-07 63.5 10.7 72 272-343 666-741 (850)
35 PRK01759 glnD PII uridylyl-tra 96.4 0.02 4.4E-07 63.5 10.9 78 264-342 665-748 (854)
36 PRK03381 PII uridylyl-transfer 96.4 0.019 4.1E-07 63.1 10.5 71 272-343 597-667 (774)
37 PRK05007 PII uridylyl-transfer 96.4 0.021 4.6E-07 63.5 11.0 78 264-342 689-772 (884)
38 COG2844 GlnD UTP:GlnB (protein 96.4 0.011 2.3E-07 64.8 8.4 68 273-342 790-857 (867)
39 PF13740 ACT_6: ACT domain; PD 96.3 0.028 6E-07 43.8 8.2 65 274-342 2-66 (76)
40 cd04875 ACT_F4HF-DF N-terminal 95.9 0.077 1.7E-06 40.6 8.6 65 277-342 2-67 (74)
41 cd04869 ACT_GcvR_2 ACT domains 95.8 0.11 2.4E-06 40.0 9.4 65 277-345 2-74 (81)
42 PRK03059 PII uridylyl-transfer 95.8 0.051 1.1E-06 60.4 10.2 70 272-342 676-749 (856)
43 PRK05092 PII uridylyl-transfer 95.7 0.065 1.4E-06 60.0 10.9 71 272-342 730-804 (931)
44 PRK00275 glnD PII uridylyl-tra 95.7 0.059 1.3E-06 60.2 10.2 70 273-342 703-777 (895)
45 PRK00194 hypothetical protein; 95.7 0.069 1.5E-06 42.4 7.9 67 274-342 3-69 (90)
46 cd04872 ACT_1ZPV ACT domain pr 95.6 0.071 1.5E-06 42.3 7.7 66 275-342 2-67 (88)
47 PRK04374 PII uridylyl-transfer 95.3 0.086 1.9E-06 58.8 9.9 71 272-342 688-759 (869)
48 cd04894 ACT_ACR-like_1 ACT dom 95.0 0.14 3.1E-06 39.7 7.2 66 276-341 2-67 (69)
49 cd04870 ACT_PSP_1 CT domains f 94.7 0.32 7E-06 37.5 9.0 62 277-342 2-64 (75)
50 PF13291 ACT_4: ACT domain; PD 94.6 0.47 1E-05 36.6 9.6 61 274-340 6-68 (80)
51 cd04886 ACT_ThrD-II-like C-ter 93.2 0.99 2.2E-05 32.8 8.7 34 277-310 1-34 (73)
52 cd04887 ACT_MalLac-Enz ACT_Mal 92.8 1.5 3.3E-05 32.9 9.4 35 277-311 2-36 (74)
53 cd02116 ACT ACT domains are co 91.8 1 2.2E-05 29.6 6.6 35 277-311 1-35 (60)
54 KOG4447 Transcription factor T 91.7 0.11 2.3E-06 46.7 2.1 52 179-230 78-131 (173)
55 PRK13010 purU formyltetrahydro 91.5 0.99 2.1E-05 44.3 8.7 67 274-342 9-78 (289)
56 cd04876 ACT_RelA-SpoT ACT dom 91.3 0.92 2E-05 31.6 6.3 35 277-311 1-35 (71)
57 cd04881 ACT_HSDH-Hom ACT_HSDH_ 91.2 2.2 4.7E-05 31.4 8.6 35 276-310 2-36 (79)
58 cd04874 ACT_Af1403 N-terminal 90.8 2.3 5E-05 30.9 8.2 36 276-311 2-37 (72)
59 cd04888 ACT_PheB-BS C-terminal 90.6 1.4 2.9E-05 33.2 7.0 36 275-310 1-36 (76)
60 cd04883 ACT_AcuB C-terminal AC 90.3 2.4 5.2E-05 31.5 8.0 61 275-341 2-64 (72)
61 cd04877 ACT_TyrR N-terminal AC 89.6 3.2 7E-05 31.6 8.4 35 276-310 2-36 (74)
62 KOG3910 Helix loop helix trans 89.5 0.2 4.3E-06 52.4 2.0 56 179-234 526-585 (632)
63 TIGR00655 PurU formyltetrahydr 89.5 2.7 5.8E-05 41.0 9.7 62 276-340 2-66 (280)
64 cd04882 ACT_Bt0572_2 C-termina 89.4 2.2 4.8E-05 30.8 7.1 34 277-310 2-35 (65)
65 KOG3560 Aryl-hydrocarbon recep 89.3 0.3 6.5E-06 51.7 3.1 42 184-225 30-75 (712)
66 KOG3558 Hypoxia-inducible fact 89.3 0.23 5E-06 53.8 2.3 46 181-226 48-97 (768)
67 cd04908 ACT_Bt0572_1 N-termina 88.9 3.5 7.6E-05 30.7 8.0 37 276-312 3-39 (66)
68 PRK06027 purU formyltetrahydro 88.4 3.4 7.3E-05 40.4 9.6 66 274-342 6-74 (286)
69 KOG3559 Transcriptional regula 88.3 0.48 1E-05 48.7 3.7 44 184-227 6-53 (598)
70 PRK04435 hypothetical protein; 88.0 2.4 5.1E-05 37.5 7.5 70 270-341 65-135 (147)
71 cd04879 ACT_3PGDH-like ACT_3PG 87.7 3 6.5E-05 29.9 6.8 60 277-342 2-63 (71)
72 cd04884 ACT_CBS C-terminal ACT 87.3 3.2 6.9E-05 31.3 7.0 34 277-310 2-35 (72)
73 cd04903 ACT_LSD C-terminal ACT 86.9 4.3 9.4E-05 29.2 7.3 33 277-309 2-34 (71)
74 PRK13011 formyltetrahydrofolat 86.3 5.4 0.00012 39.0 9.7 65 274-342 7-74 (286)
75 cd04909 ACT_PDH-BS C-terminal 86.3 4.7 0.0001 29.9 7.4 35 276-310 3-37 (69)
76 cd04889 ACT_PDH-BS-like C-term 85.5 3.8 8.2E-05 29.3 6.3 43 277-319 1-44 (56)
77 PRK08577 hypothetical protein; 85.3 7.6 0.00016 33.4 9.1 66 274-341 56-123 (136)
78 cd04878 ACT_AHAS N-terminal AC 84.5 12 0.00027 26.7 8.8 35 276-310 2-36 (72)
79 cd04905 ACT_CM-PDT C-terminal 84.2 9.5 0.00021 29.4 8.4 63 277-342 4-67 (80)
80 COG2844 GlnD UTP:GlnB (protein 84.1 4.7 0.0001 44.9 8.8 55 269-323 679-734 (867)
81 PRK07334 threonine dehydratase 83.1 8.1 0.00018 39.2 9.6 37 274-310 326-362 (403)
82 cd04880 ACT_AAAH-PDT-like ACT 81.1 12 0.00027 28.3 7.9 34 278-311 3-36 (75)
83 KOG3898 Transcription factor N 80.5 1.6 3.4E-05 42.1 3.3 52 179-230 72-126 (254)
84 PRK11589 gcvR glycine cleavage 80.2 5.6 0.00012 36.8 6.6 65 273-342 7-72 (190)
85 cd04904 ACT_AAAH ACT domain of 77.6 13 0.00028 28.6 7.0 36 277-312 3-38 (74)
86 cd04901 ACT_3PGDH C-terminal A 76.8 2.8 6E-05 30.8 3.0 36 277-312 2-37 (69)
87 cd04902 ACT_3PGDH-xct C-termin 75.4 10 0.00023 27.9 5.8 60 277-342 2-63 (73)
88 COG0788 PurU Formyltetrahydrof 74.2 14 0.00029 36.5 7.6 70 273-345 6-79 (287)
89 KOG4395 Transcription factor A 73.3 5.7 0.00012 38.6 4.8 51 181-231 176-229 (285)
90 cd04931 ACT_PAH ACT domain of 71.7 24 0.00053 28.7 7.5 37 275-311 15-51 (90)
91 COG3830 ACT domain-containing 69.4 12 0.00026 31.0 5.2 65 275-342 4-69 (90)
92 cd04885 ACT_ThrD-I Tandem C-te 68.9 35 0.00075 25.5 7.4 32 278-310 2-33 (68)
93 PRK00227 glnD PII uridylyl-tra 68.3 27 0.00059 38.4 9.2 66 275-342 547-613 (693)
94 KOG4571 Activating transcripti 66.8 45 0.00097 33.1 9.4 9 31-39 61-69 (294)
95 KOG3582 Mlx interactors and re 65.3 1.9 4.1E-05 47.0 -0.3 61 178-238 650-715 (856)
96 TIGR00119 acolac_sm acetolacta 63.2 24 0.00053 31.7 6.4 36 276-311 3-38 (157)
97 PRK11895 ilvH acetolactate syn 59.5 34 0.00074 30.9 6.8 36 276-311 4-39 (161)
98 cd04922 ACT_AKi-HSDH-ThrA_2 AC 59.1 64 0.0014 23.1 7.8 32 276-307 3-37 (66)
99 PRK00227 glnD PII uridylyl-tra 58.9 15 0.00033 40.4 5.2 60 275-343 632-691 (693)
100 COG4747 ACT domain-containing 58.3 53 0.0011 28.9 7.3 40 276-315 5-44 (142)
101 PRK10872 relA (p)ppGpp synthet 58.3 32 0.00069 38.3 7.5 37 274-310 666-702 (743)
102 CHL00100 ilvH acetohydroxyacid 58.1 40 0.00088 30.8 7.0 63 276-342 4-68 (174)
103 cd04929 ACT_TPH ACT domain of 58.0 56 0.0012 25.5 7.0 33 278-310 4-36 (74)
104 PF13710 ACT_5: ACT domain; PD 55.7 25 0.00055 26.5 4.5 30 283-312 1-30 (63)
105 PRK11092 bifunctional (p)ppGpp 55.4 66 0.0014 35.6 9.3 39 274-312 626-664 (702)
106 PF05088 Bac_GDH: Bacterial NA 55.3 66 0.0014 38.7 9.8 69 273-342 488-561 (1528)
107 KOG4447 Transcription factor T 53.6 8 0.00017 35.0 1.7 42 186-227 29-72 (173)
108 KOG3582 Mlx interactors and re 53.4 5.1 0.00011 43.9 0.5 58 179-239 787-849 (856)
109 PRK11589 gcvR glycine cleavage 53.2 84 0.0018 29.0 8.4 64 275-342 96-166 (190)
110 PRK11152 ilvM acetolactate syn 52.8 87 0.0019 24.8 7.3 37 276-312 5-41 (76)
111 TIGR00691 spoT_relA (p)ppGpp s 51.6 90 0.002 34.3 9.6 38 274-311 610-647 (683)
112 PRK06737 acetolactate synthase 51.4 96 0.0021 24.7 7.3 37 276-312 4-40 (76)
113 PRK06382 threonine dehydratase 51.4 60 0.0013 33.0 7.8 37 272-308 328-364 (406)
114 PRK13562 acetolactate synthase 50.7 65 0.0014 26.3 6.3 37 276-312 4-40 (84)
115 cd04933 ACT_AK1-AT_1 ACT domai 46.7 1.4E+02 0.0031 23.6 7.7 31 276-306 3-36 (78)
116 TIGR01127 ilvA_1Cterm threonin 45.5 1E+02 0.0022 30.8 8.3 37 272-308 303-339 (380)
117 cd04892 ACT_AK-like_2 ACT doma 41.4 1.2E+02 0.0025 20.9 7.5 33 276-308 2-37 (65)
118 cd04937 ACT_AKi-DapG-BS_2 ACT 40.9 1.4E+02 0.0031 21.8 7.5 21 283-303 13-33 (64)
119 PRK08198 threonine dehydratase 40.9 1.3E+02 0.0028 30.4 8.3 38 272-309 325-362 (404)
120 cd04906 ACT_ThrD-I_1 First of 40.4 1.8E+02 0.0039 22.8 8.4 33 276-310 3-35 (85)
121 PF13840 ACT_7: ACT domain ; P 40.0 47 0.001 24.9 3.8 32 275-306 7-42 (65)
122 PF02120 Flg_hook: Flagellar h 39.8 1E+02 0.0023 23.6 5.9 44 266-309 29-78 (85)
123 cd04930 ACT_TH ACT domain of t 37.4 60 0.0013 27.6 4.5 35 276-310 43-77 (115)
124 COG4492 PheB ACT domain-contai 34.7 1.7E+02 0.0037 26.2 6.9 67 273-341 71-138 (150)
125 cd04890 ACT_AK-like_1 ACT doma 33.8 1.4E+02 0.0031 21.3 5.5 24 282-305 11-34 (62)
126 cd04919 ACT_AK-Hom3_2 ACT doma 32.9 1.8E+02 0.004 20.8 7.9 28 282-309 12-39 (66)
127 PRK11899 prephenate dehydratas 32.5 2.6E+02 0.0055 27.4 8.5 66 275-343 195-261 (279)
128 COG4747 ACT domain-containing 32.3 1.3E+02 0.0028 26.5 5.7 53 276-338 71-123 (142)
129 PRK08178 acetolactate synthase 31.9 2.5E+02 0.0054 23.5 7.1 38 275-312 9-46 (96)
130 PRK08526 threonine dehydratase 31.1 2.1E+02 0.0045 29.3 8.0 40 272-311 324-363 (403)
131 PF02344 Myc-LZ: Myc leucine z 27.2 65 0.0014 21.8 2.3 16 188-203 14-29 (32)
132 cd04868 ACT_AK-like ACT domain 27.1 1.7E+02 0.0037 19.5 4.7 24 283-306 12-35 (60)
133 COG3074 Uncharacterized protei 26.9 85 0.0018 25.0 3.3 24 217-240 13-36 (79)
134 PF06005 DUF904: Protein of un 26.6 1.1E+02 0.0023 24.2 3.9 23 217-239 13-35 (72)
135 cd04921 ACT_AKi-HSDH-ThrA-like 26.6 2.7E+02 0.006 20.7 6.4 27 282-308 12-38 (80)
136 PRK14627 hypothetical protein; 25.6 2.6E+02 0.0056 23.3 6.2 23 218-240 4-26 (100)
137 cd04932 ACT_AKiii-LysC-EC_1 AC 25.4 2.9E+02 0.0062 21.4 6.2 31 276-306 3-36 (75)
138 PRK14626 hypothetical protein; 25.2 2.7E+02 0.0058 23.7 6.4 24 217-240 7-30 (110)
139 COG0077 PheA Prephenate dehydr 25.0 3.6E+02 0.0079 26.6 8.1 69 274-345 194-263 (279)
140 cd04912 ACT_AKiii-LysC-EC-like 25.0 3.1E+02 0.0067 20.8 7.7 31 276-306 3-36 (75)
141 TIGR00103 DNA_YbaB_EbfC DNA-bi 23.7 2.8E+02 0.0061 23.0 6.1 24 217-240 7-30 (102)
142 PRK14623 hypothetical protein; 23.4 3E+02 0.0064 23.3 6.3 24 217-240 3-26 (106)
143 COG0317 SpoT Guanosine polypho 22.3 4.1E+02 0.009 29.6 8.7 39 274-312 627-665 (701)
144 PRK14625 hypothetical protein; 22.2 3.1E+02 0.0068 23.3 6.2 24 217-240 4-27 (109)
145 COG1591 Holliday junction reso 22.2 4.2E+02 0.0091 23.6 7.1 61 287-347 9-81 (137)
146 PF09849 DUF2076: Uncharacteri 22.2 2.3E+02 0.0049 27.5 6.0 26 213-240 48-73 (247)
147 PRK03762 hypothetical protein; 21.9 3.2E+02 0.007 22.9 6.2 24 217-240 7-30 (103)
148 COG1076 DjlA DnaJ-domain-conta 21.6 78 0.0017 28.5 2.6 57 182-239 115-171 (174)
149 PF02185 HR1: Hr1 repeat; Int 21.5 3.7E+02 0.0079 20.4 6.5 50 184-241 10-59 (70)
150 COG0013 AlaS Alanyl-tRNA synth 21.0 1.3E+03 0.028 26.6 13.9 58 283-342 785-843 (879)
151 PF11619 P53_C: Transcription 20.9 1.3E+02 0.0029 23.7 3.3 33 265-297 6-39 (71)
152 cd04916 ACT_AKiii-YclM-BS_2 AC 20.4 3.2E+02 0.0069 19.3 7.7 31 277-307 4-37 (66)
153 PRK00153 hypothetical protein; 20.4 3.6E+02 0.0078 22.2 6.2 25 217-241 5-29 (104)
154 PRK14622 hypothetical protein; 20.3 3.6E+02 0.0077 22.6 6.1 23 217-239 3-25 (103)
155 PRK14621 hypothetical protein; 20.3 3.6E+02 0.0078 22.9 6.2 24 217-240 6-29 (111)
156 PLN02705 beta-amylase 20.0 1.2E+02 0.0026 33.3 3.9 31 176-206 81-114 (681)
No 1
>cd00083 HLH Helix-loop-helix domain, found in specific DNA- binding proteins that act as transcription factors; 60-100 amino acids long. A DNA-binding basic region is followed by two alpha-helices separated by a variable loop region; HLH forms homo- and heterodimers, dimerization creates a parallel, left-handed, four helix bundle; the basic region N-terminal to the first amphipathic helix mediates high-affinity DNA-binding; there are several groups of HLH proteins: those (E12/E47) which bind specific hexanucleotide sequences such as E-box (5-CANNTG-3) or StRE 5-ATCACCCCAC-3), those lacking the basic domain (Emc, Id) function as negative regulators since they fail to bind DNA, those (hairy, E(spl), deadpan) which repress transcription although they can bind specific hexanucleotide sequences such as N-box (5-CACGc/aG-3), those which have a COE domain (Collier/Olf-1/EBF) which is involved in both in dimerization and in DNA binding, and those which bind pentanucleotides ACGTG or GCGTG and
Probab=99.33 E-value=1.5e-12 Score=96.40 Aligned_cols=53 Identities=36% Similarity=0.706 Sum_probs=50.0
Q ss_pred CCccchHHHHHHHHHHHHHHHHhHhcCCCC---CCCCchhhHHHHHHHHHHHHHHH
Q 018897 179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLDKI 231 (349)
Q Consensus 179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~---~K~dKaSIL~~AI~YIk~Lq~~v 231 (349)
.+..|+.+||+||.+||+.|..|+++||.. .|++|++||..||+||+.|+.++
T Consensus 4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~ 59 (60)
T cd00083 4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL 59 (60)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 457899999999999999999999999987 89999999999999999999876
No 2
>PF00010 HLH: Helix-loop-helix DNA-binding domain only nuclear translocator protein (Arnt).; InterPro: IPR011598 The helix-loop-helix (HLH) DNA-binding domain consists of a closed bundle of four helices in a left-handed twist with two crossover connections. The HLH domain directs dimerisation, and is juxtaposed to basic regions to create a DNA interaction interface surface that recognises specific DNA sequences. Basic region/HLH (bHLH) proteins regulate diverse biological pathways []. bHLH proteins include MyoD [], SREBPs (sterol regulatory element binding proteins) [], and yeast Pho4 (phosphatase system) []. In certain proteins the bHLH domain contains a leucine-zipper motif. The bHLH/leucine zipper (bHLHZip) domain specifies dimerisation within a network of proteins and determines sequence-specific DNA binding []. bHLHZip domains occur in the transcription factors Myc, Mad, Max and Usf [, ]. This entry is bHLHZip, which covers the bHLH domain and the leucine zipper motif, when present.; PDB: 1NLW_A 1NKP_D 1A93_A 2A93_A 1AM9_C 3U5V_A 1A0A_B 2QL2_C 1UKL_C 1AN4_B ....
Probab=99.28 E-value=2.7e-12 Score=94.53 Aligned_cols=49 Identities=43% Similarity=0.697 Sum_probs=46.1
Q ss_pred CccchHHHHHHHHHHHHHHHHhHhcCCCC-----CCCCchhhHHHHHHHHHHHH
Q 018897 180 PSKNLMAERRRRKRLNDRLSMLRSIVPKI-----SKMDRTSILADTIDYMKELL 228 (349)
Q Consensus 180 ~~~h~~aER~RR~kin~~~~~LrslvP~~-----~K~dKaSIL~~AI~YIk~Lq 228 (349)
+..|+.+||+||.+||+.|..|+.+||.. .|++|++||..||+||++||
T Consensus 2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 46899999999999999999999999975 68999999999999999997
No 3
>smart00353 HLH helix loop helix domain.
Probab=99.27 E-value=8e-12 Score=90.76 Aligned_cols=49 Identities=35% Similarity=0.659 Sum_probs=45.5
Q ss_pred hHHHHHHHHHHHHHHHHhHhcCCC---CCCCCchhhHHHHHHHHHHHHHHHH
Q 018897 184 LMAERRRRKRLNDRLSMLRSIVPK---ISKMDRTSILADTIDYMKELLDKIS 232 (349)
Q Consensus 184 ~~aER~RR~kin~~~~~LrslvP~---~~K~dKaSIL~~AI~YIk~Lq~~v~ 232 (349)
+.+||+||.+||+.|..|+++||. ..|++|++||..||+||+.|+++++
T Consensus 1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~ 52 (53)
T smart00353 1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ 52 (53)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 368999999999999999999994 6789999999999999999999875
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=98.83 E-value=3e-09 Score=107.16 Aligned_cols=57 Identities=32% Similarity=0.580 Sum_probs=52.0
Q ss_pred CCccchHHHHHHHHHHHHHHHHhHhcCCCC----CCCCchhhHHHHHHHHHHHHHHHHHHH
Q 018897 179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI----SKMDRTSILADTIDYMKELLDKISSLQ 235 (349)
Q Consensus 179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~----~K~dKaSIL~~AI~YIk~Lq~~v~~L~ 235 (349)
+|..|+++|||||++||++|..|..|||++ .|..|..||..+++||++||+..++..
T Consensus 233 Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~~~ 293 (411)
T KOG1318|consen 233 KRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQRAR 293 (411)
T ss_pred HHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999999999986 477899999999999999999877544
No 5
>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=98.61 E-value=4.2e-07 Score=72.03 Aligned_cols=69 Identities=19% Similarity=0.223 Sum_probs=58.7
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCH---HHHHHHHHHHhh
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSC---EDIKQALFRNAG 343 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~---edIkqaL~~~~g 343 (349)
..|+|.|.+|||||.+|..+|-.+|++|.+|.|+|.++.+.++|......+....+. +.|+++|..+++
T Consensus 2 TvveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~~g~kl~~~~~~~~l~~~L~~al~ 73 (75)
T cd04897 2 SVVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHKDGRTLSTEGERQRVIKCLEAAIE 73 (75)
T ss_pred EEEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcCCCCccCCHHHHHHHHHHHHHHHh
Confidence 368999999999999999999999999999999999999999999887655444443 567777777664
No 6
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=98.58 E-value=4.1e-08 Score=89.61 Aligned_cols=63 Identities=25% Similarity=0.426 Sum_probs=55.2
Q ss_pred CCccchHHHHHHHHHHHHHHHHhHhcCCCC-------CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897 179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI-------SKMDRTSILADTIDYMKELLDKISSLQQEIQAG 241 (349)
Q Consensus 179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~-------~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~ 241 (349)
+|..|.-+||+||+.||..+..|+.|||.+ .|+.||.||..+|+||..|++++.+.+++...+
T Consensus 62 rr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L 131 (229)
T KOG1319|consen 62 RRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTL 131 (229)
T ss_pred HHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999999999999953 378899999999999999999988877765443
No 7
>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=98.45 E-value=1.7e-06 Score=68.03 Aligned_cols=52 Identities=31% Similarity=0.323 Sum_probs=47.7
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCC
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQR 326 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~ 326 (349)
..|+|.+.+|||||.+|.++|..+||+|..|.|+|.++.+.++|......+.
T Consensus 2 Tviev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d~~g~ 53 (72)
T cd04895 2 TLVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTDQLGN 53 (72)
T ss_pred EEEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEECCCCC
Confidence 4689999999999999999999999999999999999999999998875333
No 8
>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=98.42 E-value=2.3e-06 Score=67.88 Aligned_cols=67 Identities=12% Similarity=0.129 Sum_probs=56.2
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe--eeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHhh
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS--CFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNAG 343 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS--t~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~g 343 (349)
.|+|.|.+|||||.+|.++|..+||+|..|.|+ |.|+.++++|.. ...+....+ .+.|+++|.+++-
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv-~~~g~kl~d~~~~~~L~~~L~~~l~ 73 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV-QSDGKKIMDPKKQAALCARLREEMV 73 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE-eCCCCccCCHHHHHHHHHHHHHHhc
Confidence 589999999999999999999999999999999 999999999999 433444223 3677888877653
No 9
>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=98.41 E-value=2e-06 Score=67.47 Aligned_cols=68 Identities=18% Similarity=0.192 Sum_probs=55.7
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee-eCCeEEEEEeeecccCCccC---CHHHHHHHHHHHhh
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC-FNDFAMQASCSEGVEQRETL---SCEDIKQALFRNAG 343 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt-~~d~vl~a~~se~~e~~~~i---s~edIkqaL~~~~g 343 (349)
+.++|.|.+++|||.+|..+|..+||+|+.|.|++ .++.+++++......+. .. ..+.|+++|.+++|
T Consensus 1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~~~~-~~~~~~~~~l~~~L~~~L~ 72 (76)
T cd04927 1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDAREL-LHTKKRREETYDYLRAVLG 72 (76)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCCCCC-CCCHHHHHHHHHHHHHHHc
Confidence 46899999999999999999999999999999997 89999999988654222 22 23557777777776
No 10
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=98.31 E-value=1.9e-06 Score=93.85 Aligned_cols=62 Identities=26% Similarity=0.497 Sum_probs=56.2
Q ss_pred CCCccchHHHHHHHHHHHHHHHHhHhcCCC-CCCCCchhhHHHHHHHHHHHHHHHHHHHHHHH
Q 018897 178 GQPSKNLMAERRRRKRLNDRLSMLRSIVPK-ISKMDRTSILADTIDYMKELLDKISSLQQEIQ 239 (349)
Q Consensus 178 ~~~~~h~~aER~RR~kin~~~~~LrslvP~-~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e 239 (349)
.+|..|++.|||.|..||+++..|+.+||+ ..|+.|..+|..||+||++|+...+.++.+.+
T Consensus 275 ~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~ 337 (953)
T KOG2588|consen 275 EKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENA 337 (953)
T ss_pred cccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhh
Confidence 578999999999999999999999999997 47999999999999999999988877776443
No 11
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=98.23 E-value=5.5e-07 Score=86.06 Aligned_cols=56 Identities=25% Similarity=0.482 Sum_probs=49.1
Q ss_pred CCCccchHHHHHHHHHHHHHHHHhHhcCCC--------CCCCCchhhHHHHHHHHHHHHHHHHH
Q 018897 178 GQPSKNLMAERRRRKRLNDRLSMLRSIVPK--------ISKMDRTSILADTIDYMKELLDKISS 233 (349)
Q Consensus 178 ~~~~~h~~aER~RR~kin~~~~~LrslvP~--------~~K~dKaSIL~~AI~YIk~Lq~~v~~ 233 (349)
.++..|-+.||+||.|||+-|..|+.|||. .+|++||.||.-|++|++.|+.....
T Consensus 31 ~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~ 94 (250)
T KOG4304|consen 31 YRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQA 94 (250)
T ss_pred HhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccc
Confidence 355678899999999999999999999993 37899999999999999999976544
No 12
>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=98.22 E-value=1.6e-05 Score=61.37 Aligned_cols=49 Identities=27% Similarity=0.375 Sum_probs=44.6
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecc
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGV 323 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~ 323 (349)
..|.|.|.+++|||.+|..+|..+||+|+.|.|.+. ++.+++++.....
T Consensus 2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~~ 51 (73)
T cd04900 2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLDP 51 (73)
T ss_pred EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEECC
Confidence 468999999999999999999999999999999988 6899999987653
No 13
>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=98.04 E-value=6.4e-05 Score=58.46 Aligned_cols=67 Identities=16% Similarity=0.115 Sum_probs=54.4
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeeccc-CCccCC---HHHHHHHHHHHh
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVE-QRETLS---CEDIKQALFRNA 342 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e-~~~~is---~edIkqaL~~~~ 342 (349)
.|+|.+.++||+|.+|..+|..+|++|+.|.+++.++.+++++.+.... +..... .+.|+++|.+++
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d~~~~~~~~~~~~~~~i~~~L~~~l 72 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRDEETGAPIDDPIRLASIEDRLDNVL 72 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEcCcCCCCCCCHHHHHHHHHHHHHHh
Confidence 5889999999999999999999999999999999999999999876543 222222 356777776655
No 14
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=97.94 E-value=7.9e-06 Score=88.68 Aligned_cols=51 Identities=24% Similarity=0.423 Sum_probs=47.9
Q ss_pred CccchHHHHHHHHHHHHHHHHhHhcCCCC----CCCCchhhHHHHHHHHHHHHHH
Q 018897 180 PSKNLMAERRRRKRLNDRLSMLRSIVPKI----SKMDRTSILADTIDYMKELLDK 230 (349)
Q Consensus 180 ~~~h~~aER~RR~kin~~~~~LrslvP~~----~K~dKaSIL~~AI~YIk~Lq~~ 230 (349)
|..|+.+|||||++||..|..|.+|||.+ -|+||..||.+||.+||.+++.
T Consensus 21 Re~~~~~EKrRRdq~N~yI~ELs~Mvp~~~~~~RK~DK~tVLr~aV~~lr~~k~~ 75 (803)
T KOG3561|consen 21 RENRSEIEKRRRDQMNKYIEELSEMVPTNASLSRKPDKLTVLRMAVDHLRLIKEQ 75 (803)
T ss_pred cccchhHHHHHHHHHHHHHHHHHHhhhcchhcccCchHHHHHHHHHHHHHHHhhh
Confidence 67999999999999999999999999975 5999999999999999999874
No 15
>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=97.91 E-value=0.00015 Score=55.99 Aligned_cols=71 Identities=21% Similarity=0.319 Sum_probs=56.7
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHhhcCCCCC
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAGYGGKCL 349 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~g~gg~cl 349 (349)
.+|.|.+++++|+|.+|..+|.++|++|++|.+.+.++.++.++.....++.. .+. +..++|.+.+| --||
T Consensus 2 tri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~~~~~~~-~~~-~~~~~l~~~l~--~~~~ 72 (72)
T cd04926 2 VRLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVTDANGNP-VDP-KTIEAVRQEIG--PACL 72 (72)
T ss_pred eEEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEECCCCCc-CCH-HHHHHHHHHhc--cccC
Confidence 46888999999999999999999999999999999988888888776543332 344 56667888887 5565
No 16
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=97.84 E-value=5e-05 Score=72.03 Aligned_cols=65 Identities=26% Similarity=0.389 Sum_probs=54.5
Q ss_pred CCCCCccchHHHHHHHHHHHHHHHHhHhcCCCC--CCCC-chhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 018897 176 LGGQPSKNLMAERRRRKRLNDRLSMLRSIVPKI--SKMD-RTSILADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 176 ~~~~~~~h~~aER~RR~kin~~~~~LrslvP~~--~K~d-KaSIL~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
....|..|+.-||+||..|++.|..|+.+||.. .+.. .++||..|+.||+.|+.+..+....+++
T Consensus 56 ~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~ 123 (232)
T KOG2483|consen 56 AASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIED 123 (232)
T ss_pred CCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHH
Confidence 345789999999999999999999999999974 2333 6899999999999999888777765544
No 17
>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=97.79 E-value=0.00027 Score=52.99 Aligned_cols=64 Identities=25% Similarity=0.365 Sum_probs=50.6
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHH---HHHHHHHH
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCE---DIKQALFR 340 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~e---dIkqaL~~ 340 (349)
+|.|.+.+++|+|.+|+.+|.++|++|.++.+.+.++.++..+......+.. .+.+ .|+++|.+
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~~~~~-~~~~~~~~i~~~l~~ 68 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDADGQP-LDPERQEALRAALGE 68 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECCCCCc-CCHHHHHHHHHHHHh
Confidence 6889999999999999999999999999999999988888888776643333 4442 34444443
No 18
>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=97.75 E-value=0.0003 Score=54.82 Aligned_cols=64 Identities=20% Similarity=0.266 Sum_probs=54.2
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.|-|.|+++||+|.+|..+|..+||+|+.|.|.+. ++++++++.+... ..-...++.++|++++
T Consensus 3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~---~~~~~~~~~~~~~~~~ 67 (68)
T cd04928 3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGW---KRGETAALGHALQKEI 67 (68)
T ss_pred EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecC---CccchHHHHHHHHHhh
Confidence 57889999999999999999999999999999875 6799998887763 3345678899998865
No 19
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=97.65 E-value=0.0005 Score=65.72 Aligned_cols=56 Identities=25% Similarity=0.430 Sum_probs=47.3
Q ss_pred cchHHHHHHHHHHHHHHHHhHhcC-CC-CCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 018897 182 KNLMAERRRRKRLNDRLSMLRSIV-PK-ISKMDRTSILADTIDYMKELLDKISSLQQE 237 (349)
Q Consensus 182 ~h~~aER~RR~kin~~~~~Lrslv-P~-~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~ 237 (349)
.-.|.||||=+|+|+.|.+|+.-. ++ ...+-|..||..||+||..||.=++++.+.
T Consensus 121 AATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~ 178 (284)
T KOG3960|consen 121 AATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQA 178 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 446899999999999999997543 33 467889999999999999999988888763
No 20
>PRK05007 PII uridylyl-transferase; Provisional
Probab=97.44 E-value=0.00064 Score=75.36 Aligned_cols=70 Identities=17% Similarity=0.282 Sum_probs=59.3
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNA 342 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~ 342 (349)
+....|+|.|.+|||||.+|.++|..+||+|++|.|+|.++.+.++|.+... ++..++ .+.|+++|..++
T Consensus 806 ~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~~-~g~~l~~~~~~~l~~~L~~~l 878 (884)
T PRK05007 806 DRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILATA-DRRALNEELQQELRQRLTEAL 878 (884)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEcC-CCCcCCHHHHHHHHHHHHHHH
Confidence 4467899999999999999999999999999999999999999999998764 333444 367777777766
No 21
>PLN03217 transcription factor ATBS1; Provisional
Probab=97.35 E-value=0.00045 Score=56.09 Aligned_cols=51 Identities=22% Similarity=0.522 Sum_probs=43.7
Q ss_pred HHHHHHHHHHhHhcCCCC------CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897 191 RKRLNDRLSMLRSIVPKI------SKMDRTSILADTIDYMKELLDKISSLQQEIQAG 241 (349)
Q Consensus 191 R~kin~~~~~LrslvP~~------~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~ 241 (349)
-++|++.+.+|+.|+|.. .|...+-+|+++.+||+.|+++|..|.+++...
T Consensus 19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~L 75 (93)
T PLN03217 19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSEL 75 (93)
T ss_pred HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 378999999999999953 455566799999999999999999999987554
No 22
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=97.26 E-value=0.00022 Score=69.73 Aligned_cols=53 Identities=28% Similarity=0.485 Sum_probs=46.1
Q ss_pred ccchHHHHHHHHHHHHHHHHhHhcCCC--CCCCCchhhHHHHHHHHHHHHHHHHH
Q 018897 181 SKNLMAERRRRKRLNDRLSMLRSIVPK--ISKMDRTSILADTIDYMKELLDKISS 233 (349)
Q Consensus 181 ~~h~~aER~RR~kin~~~~~LrslvP~--~~K~dKaSIL~~AI~YIk~Lq~~v~~ 233 (349)
.--+.-||+|=.-||..|..||+|+|. .-|.+||.||+.+.+||.+|+.+.-+
T Consensus 62 eIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~ 116 (373)
T KOG0561|consen 62 EIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTE 116 (373)
T ss_pred HhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcccc
Confidence 344567999999999999999999995 57999999999999999999876443
No 23
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=97.24 E-value=0.0013 Score=72.60 Aligned_cols=70 Identities=19% Similarity=0.256 Sum_probs=58.7
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNA 342 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~ 342 (349)
+....|+|.+.++||||.+|.++|.++|++|..|.|+|.++.+.++|.+....+. .++ .+.|+++|..++
T Consensus 781 ~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~~~g~-~l~~~~~~~l~~~L~~~l 853 (854)
T PRK01759 781 QEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTNQQGQ-ALDEEERKALKSRLLSNL 853 (854)
T ss_pred CCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEECCCCC-cCChHHHHHHHHHHHHHh
Confidence 3457999999999999999999999999999999999999999999998765333 333 267777777664
No 24
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=97.18 E-value=0.0024 Score=71.05 Aligned_cols=71 Identities=17% Similarity=0.262 Sum_probs=59.8
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNA 342 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~ 342 (349)
.....|.|.+.++||||.+|..+|..+||+|+.|.|+|.++.++++|.+....+....+ .+.|+++|.+++
T Consensus 812 ~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~~g~~l~~~~~~~~l~~~L~~~L 885 (895)
T PRK00275 812 RPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDADNQPLSDPQLCSRLQDAICEQL 885 (895)
T ss_pred CCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHH
Confidence 34678999999999999999999999999999999999999999999987754433323 256888888776
No 25
>PF01842 ACT: ACT domain; InterPro: IPR002912 The ACT domain is found in a variety of contexts and is proposed to be a conserved regulatory binding fold. ACT domains are linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. The archetypical ACT domain is the C-terminal regulatory domain of 3-phosphoglycerate dehydrogenase (3PGDH), which folds with a ferredoxin-like topology. A pair of ACT domains form an eight-stranded antiparallel sheet with two molecules of allosteric inhibitor serine bound in the interface. Biochemical exploration of a few other proteins containing ACT domains supports the suggestions that these domains contain the archetypical ACT structure [].; GO: 0016597 amino acid binding, 0008152 metabolic process; PDB: 3L76_B 2F06_B 3NRB_C 1Y7P_C 2QMX_A 2DT9_A 2ZHO_D 3K5P_A 3TVI_K 3C1M_C ....
Probab=97.17 E-value=0.004 Score=45.57 Aligned_cols=62 Identities=19% Similarity=0.205 Sum_probs=46.3
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC--eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND--FAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d--~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.|.|.|+++||+|.+|.++|.++|+.|.++.+.+..+ ..+..+... .....+.+.++|.+..
T Consensus 2 ~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~~-----~~~~~~~~~~~l~~~~ 65 (66)
T PF01842_consen 2 RVRVIVPDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIVIVV-----DEEDLEKLLEELEALP 65 (66)
T ss_dssp EEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEEE-----EGHGHHHHHHHHHHHT
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEEC-----CCCCHHHHHHHHHccc
Confidence 5788999999999999999999999999999999877 222222111 1334567777776654
No 26
>PRK04374 PII uridylyl-transferase; Provisional
Probab=97.07 E-value=0.0037 Score=69.33 Aligned_cols=71 Identities=20% Similarity=0.278 Sum_probs=59.0
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccC--CHHHHHHHHHHHh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETL--SCEDIKQALFRNA 342 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~i--s~edIkqaL~~~~ 342 (349)
+....|.|.+.++||||.+|..+|..+||+|+.|.|+|.++.+++++.+....+.... ..+.|+++|..++
T Consensus 794 ~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~~g~~~~~~~~~~l~~~L~~~l 866 (869)
T PRK04374 794 GRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDEHDRPLSESARQALRDALCACL 866 (869)
T ss_pred CCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCCCcCChHHHHHHHHHHHHHh
Confidence 3467999999999999999999999999999999999999999999988765333221 2267888887765
No 27
>PRK05092 PII uridylyl-transferase; Provisional
Probab=97.06 E-value=0.0041 Score=69.39 Aligned_cols=70 Identities=21% Similarity=0.275 Sum_probs=59.7
Q ss_pred CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHh
Q 018897 273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNA 342 (349)
Q Consensus 273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~ 342 (349)
....|.|.|.++||+|.+|..+|..+|++|..|.|+|.++.+++++.+....+....+ .+.|+++|..++
T Consensus 842 ~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~~g~~i~~~~~~~~l~~~L~~~L 914 (931)
T PRK05092 842 RFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDLFGLKITNEARQAAIRRALLAAL 914 (931)
T ss_pred CeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCCCCCcCCCHHHHHHHHHHHHHHh
Confidence 4578999999999999999999999999999999999999999999887654443333 367888888877
No 28
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=97.02 E-value=0.00063 Score=63.87 Aligned_cols=60 Identities=20% Similarity=0.356 Sum_probs=51.9
Q ss_pred CCCccchHHHHHHHHHHHHHHHHhHhcCCC----CCCCCchhhHHHHHHHHHHHHHHHHHHHHH
Q 018897 178 GQPSKNLMAERRRRKRLNDRLSMLRSIVPK----ISKMDRTSILADTIDYMKELLDKISSLQQE 237 (349)
Q Consensus 178 ~~~~~h~~aER~RR~kin~~~~~LrslvP~----~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~ 237 (349)
..+..++..||+|=+.+|..|..||.+||. .+|.+|..+|.-||.||+.|++-++.-+..
T Consensus 108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~ 171 (228)
T KOG4029|consen 108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAP 171 (228)
T ss_pred hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccC
Confidence 456677788999999999999999999995 468899999999999999999877766543
No 29
>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=96.99 E-value=0.0093 Score=44.10 Aligned_cols=48 Identities=29% Similarity=0.411 Sum_probs=42.1
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecc
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGV 323 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~ 323 (349)
.|.|.|.+++|+|.+|..+|.++|+.|.++.+.+.++.....+.....
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~~ 49 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTDS 49 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEECC
Confidence 578999999999999999999999999999999987777667766654
No 30
>PRK03059 PII uridylyl-transferase; Provisional
Probab=96.88 E-value=0.0042 Score=68.78 Aligned_cols=71 Identities=11% Similarity=0.174 Sum_probs=56.5
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.....|.|.|.++||||.+|..+|..+||+|+.|.|+|.++.+++++.+........-..+.|+++|.+++
T Consensus 784 ~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~~~~~~~~~~~~~l~~~L~~~L 854 (856)
T PRK03059 784 GQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLIDGSGLSDNRLQIQLETELLDAL 854 (856)
T ss_pred CCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEcCCCCCCHHHHHHHHHHHHHHh
Confidence 34678999999999999999999999999999999999999999999884321111112357777777665
No 31
>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=96.59 E-value=0.011 Score=65.41 Aligned_cols=70 Identities=24% Similarity=0.282 Sum_probs=56.8
Q ss_pred CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccC--CHHHHHHHHHHHh
Q 018897 273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETL--SCEDIKQALFRNA 342 (349)
Q Consensus 273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~i--s~edIkqaL~~~~ 342 (349)
....|.|.|.++||+|.+|.++|..+|++|.+|.|+|.++.+.+++......+...- ..+.|+++|..++
T Consensus 778 ~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~~~g~~~~~~~~~~l~~~L~~~l 849 (850)
T TIGR01693 778 KATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTDLFGLKLTDEEEQRLLEVLAASV 849 (850)
T ss_pred CeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEECCCCCCCCHHHHHHHHHHHHHHh
Confidence 457899999999999999999999999999999999999988888887654332221 2467777777654
No 32
>PRK03381 PII uridylyl-transferase; Provisional
Probab=96.57 E-value=0.012 Score=64.66 Aligned_cols=51 Identities=22% Similarity=0.350 Sum_probs=47.8
Q ss_pred CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecc
Q 018897 273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGV 323 (349)
Q Consensus 273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~ 323 (349)
....|.|.+.++||||.+|..+|..+|++|+.|.|+|.++.+++++.+...
T Consensus 706 ~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d~ 756 (774)
T PRK03381 706 DATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTGA 756 (774)
T ss_pred CeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEECC
Confidence 357999999999999999999999999999999999999999999988764
No 33
>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=96.44 E-value=0.035 Score=43.37 Aligned_cols=67 Identities=15% Similarity=0.119 Sum_probs=53.1
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh-hcC
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA-GYG 345 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~-g~g 345 (349)
+.|.+.|+++||+...|-+.|.++|..|+.++....++..+.....+.. ..+.++|+++|...+ .+|
T Consensus 2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~----~~~~~~l~~~l~~~~~~~~ 69 (77)
T cd04893 2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGS----WDAIAKLEAALPGLARRLD 69 (77)
T ss_pred EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEec----cccHHHHHHHHHHHHHHcC
Confidence 5789999999999999999999999999999999988744444344432 247789998888866 444
No 34
>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=96.43 E-value=0.018 Score=63.55 Aligned_cols=72 Identities=17% Similarity=0.247 Sum_probs=58.7
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe-eeCCeEEEEEeeecccCCccCC---HHHHHHHHHHHhh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS-CFNDFAMQASCSEGVEQRETLS---CEDIKQALFRNAG 343 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS-t~~d~vl~a~~se~~e~~~~is---~edIkqaL~~~~g 343 (349)
...+.|.|.+.+++|+|.+|..+|..+||+|+.|.|. +.++.+++++.+....+..... .+.|+++|..++.
T Consensus 666 ~~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~~g~~~~~~~~~~~i~~~L~~~L~ 741 (850)
T TIGR01693 666 SGGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDLFGSPPAAERVFQELLQGLVDVLA 741 (850)
T ss_pred CCeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECCCCCCCCcHHHHHHHHHHHHHHHc
Confidence 4567899999999999999999999999999999999 6788999999988754332222 3457778877774
No 35
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=96.41 E-value=0.02 Score=63.47 Aligned_cols=78 Identities=18% Similarity=0.300 Sum_probs=61.0
Q ss_pred Cceeeee--ecCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee-eCCeEEEEEeeecccCCccCCH---HHHHHH
Q 018897 264 PKFDVER--TNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC-FNDFAMQASCSEGVEQRETLSC---EDIKQA 337 (349)
Q Consensus 264 p~VeV~~--~~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt-~~d~vl~a~~se~~e~~~~is~---edIkqa 337 (349)
|.|.|+. ..+...|.|.|.+++|||.+|..+|..+||+|+.|.|.+ .++.+++++.+....+. .++. +.|+++
T Consensus 665 ~~V~i~~~~~~~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V~d~~g~-~~~~~~~~~l~~~ 743 (854)
T PRK01759 665 LLVKISNRFSRGGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTELNGK-LLEFDRRRQLEQA 743 (854)
T ss_pred CEEEEEecCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCCCCC-CCCHHHHHHHHHH
Confidence 4455543 245679999999999999999999999999999999987 78899999988775333 2343 356777
Q ss_pred HHHHh
Q 018897 338 LFRNA 342 (349)
Q Consensus 338 L~~~~ 342 (349)
|.+++
T Consensus 744 L~~aL 748 (854)
T PRK01759 744 LTKAL 748 (854)
T ss_pred HHHHH
Confidence 77766
No 36
>PRK03381 PII uridylyl-transferase; Provisional
Probab=96.41 E-value=0.019 Score=63.07 Aligned_cols=71 Identities=14% Similarity=0.127 Sum_probs=59.8
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHhh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAG 343 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~g 343 (349)
.+.+.|.|.|.++||++.+|..+|..+|++|+.|.|.+.++.+++++.+....+ .....+.|+++|.+++.
T Consensus 597 ~~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~~~~-~~~~~~~l~~~L~~~L~ 667 (774)
T PRK03381 597 PHMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSPRFG-SPPDAALLRQDLRRALD 667 (774)
T ss_pred CCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECCCC-CcchHHHHHHHHHHHHc
Confidence 466789999999999999999999999999999999998889999888776433 23345789999887763
No 37
>PRK05007 PII uridylyl-transferase; Provisional
Probab=96.41 E-value=0.021 Score=63.53 Aligned_cols=78 Identities=21% Similarity=0.223 Sum_probs=60.7
Q ss_pred Cceeeeee--cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCH---HHHHHH
Q 018897 264 PKFDVERT--NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSC---EDIKQA 337 (349)
Q Consensus 264 p~VeV~~~--~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~---edIkqa 337 (349)
|.|.|+.. .+.+.|.|.|.+++|+|..|..+|..+||+|+.|.|.|.++ .+++++.+....+. .++. +.|+++
T Consensus 689 p~V~i~~~~~~~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V~d~~g~-~~~~~~~~~I~~~ 767 (884)
T PRK05007 689 PLVLLSKQATRGGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLEPDGS-PLSQDRHQVIRKA 767 (884)
T ss_pred CeEEEEecCCCCeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEECCCCC-CCCHHHHHHHHHH
Confidence 44555432 45779999999999999999999999999999999988765 99999988765333 2343 347788
Q ss_pred HHHHh
Q 018897 338 LFRNA 342 (349)
Q Consensus 338 L~~~~ 342 (349)
|.+++
T Consensus 768 L~~aL 772 (884)
T PRK05007 768 LEQAL 772 (884)
T ss_pred HHHHH
Confidence 87776
No 38
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=96.40 E-value=0.011 Score=64.77 Aligned_cols=68 Identities=21% Similarity=0.372 Sum_probs=56.6
Q ss_pred CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
....|++.+.+|||||..|-.+|..++|+|++|.|+|+|..+.++++.-...+ ..+ ..+++|.|.+.+
T Consensus 790 ~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt~~~~-~~l-~~~~~q~l~~~l 857 (867)
T COG2844 790 DKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVTDADG-QAL-NAELRQSLLQRL 857 (867)
T ss_pred CceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEecccc-ccC-CHHHHHHHHHHH
Confidence 35689999999999999999999999999999999999999999999887533 333 445666666544
No 39
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=96.33 E-value=0.028 Score=43.78 Aligned_cols=65 Identities=15% Similarity=0.124 Sum_probs=49.8
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.+.|.+.+++|||++..|..+|.+.|.+|..++.++.++...-...++.. .-+.++|+.+|.+.+
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~----~~~~~~l~~~L~~l~ 66 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP----EDSLERLESALEELA 66 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES----HHHHHHHHHHHHHHH
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC----cccHHHHHHHHHHHH
Confidence 46799999999999999999999999999999999999944334444432 226688999988875
No 40
>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=95.86 E-value=0.077 Score=40.62 Aligned_cols=65 Identities=18% Similarity=0.148 Sum_probs=47.0
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
|.|.|++++|++.+|.+.|-++|+.|......+. ++..+.+.. +........+.++|+++|....
T Consensus 2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~-~~~~~~~~~~~~~l~~~l~~l~ 67 (74)
T cd04875 2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRV-EFELEGFDLSREALEAAFAPVA 67 (74)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEE-EEEeCCCCCCHHHHHHHHHHHH
Confidence 7899999999999999999999999999888763 222233221 1110111257899999998876
No 41
>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=95.81 E-value=0.11 Score=39.95 Aligned_cols=65 Identities=14% Similarity=0.236 Sum_probs=49.5
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC------C-eEEEEEeeecccCCccCCHHHHHHHHHHHh-hcC
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN------D-FAMQASCSEGVEQRETLSCEDIKQALFRNA-GYG 345 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~------d-~vl~a~~se~~e~~~~is~edIkqaL~~~~-g~g 345 (349)
|.|.|.+++|++.+|-+.|.++|++|...+..+.+ + +.+. ..... ....+..+|+.+|.... .+|
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~-~~v~~---p~~~~~~~l~~~l~~l~~~~~ 74 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQ-ATLAL---PAGTDLDALREELEELCDDLN 74 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEE-EEEec---CCCCCHHHHHHHHHHHHHHhc
Confidence 68999999999999999999999999999998876 2 2221 12222 23467889999998876 444
No 42
>PRK03059 PII uridylyl-transferase; Provisional
Probab=95.79 E-value=0.051 Score=60.42 Aligned_cols=70 Identities=11% Similarity=0.153 Sum_probs=55.9
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe-eeCCeEEEEEeeecccCCccC---CHHHHHHHHHHHh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS-CFNDFAMQASCSEGVEQRETL---SCEDIKQALFRNA 342 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS-t~~d~vl~a~~se~~e~~~~i---s~edIkqaL~~~~ 342 (349)
.+.+.|.|.|.+++|||.+|..+|..+||+|+.|.|. +-+|++++++.+....+. .. -.+.|+++|.+++
T Consensus 676 ~~~~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~~~~~-~~~~~~~~~i~~~l~~~l 749 (856)
T PRK03059 676 GEGLQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLDPEED-VHYRDIINLVEHELAERL 749 (856)
T ss_pred CCeEEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeCCCCC-CChHHHHHHHHHHHHHHH
Confidence 3567999999999999999999999999999999995 467899999988764333 11 2456777777665
No 43
>PRK05092 PII uridylyl-transferase; Provisional
Probab=95.75 E-value=0.065 Score=59.97 Aligned_cols=71 Identities=18% Similarity=0.148 Sum_probs=56.5
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee-eCCeEEEEEeeecccCCccC---CHHHHHHHHHHHh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC-FNDFAMQASCSEGVEQRETL---SCEDIKQALFRNA 342 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt-~~d~vl~a~~se~~e~~~~i---s~edIkqaL~~~~ 342 (349)
.+.+.|.|.|.+++|+|.+|..+|..+|++|+.|.|.+ .++++++++.+....+.... ..+.|+++|.+++
T Consensus 730 ~~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~~~g~~~~~~~~~~~l~~~L~~~l 804 (931)
T PRK05092 730 RGVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQDAFGRDEDEPRRLARLAKAIEDAL 804 (931)
T ss_pred CCeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEECCCCCCCCCHHHHHHHHHHHHHHH
Confidence 35789999999999999999999999999999999988 57799998877654332222 2456777777666
No 44
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=95.69 E-value=0.059 Score=60.19 Aligned_cols=70 Identities=17% Similarity=0.236 Sum_probs=56.1
Q ss_pred CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe-eeCCeEEEEEeeecccCCccCC----HHHHHHHHHHHh
Q 018897 273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS-CFNDFAMQASCSEGVEQRETLS----CEDIKQALFRNA 342 (349)
Q Consensus 273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS-t~~d~vl~a~~se~~e~~~~is----~edIkqaL~~~~ 342 (349)
+.+.|.|.|.++||+|.+|..+|..+||+|+.|.|. +-+|++++++.+....+..... .+.|+++|.+++
T Consensus 703 ~~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V~d~~g~~~~~~~~r~~~i~~~L~~~L 777 (895)
T PRK00275 703 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDDDGEPIGDNPARIEQIREGLTEAL 777 (895)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCCCCCCccchHHHHHHHHHHHHHHH
Confidence 567999999999999999999999999999999985 4577999999887654443222 245777777765
No 45
>PRK00194 hypothetical protein; Validated
Probab=95.67 E-value=0.069 Score=42.38 Aligned_cols=67 Identities=12% Similarity=0.150 Sum_probs=50.0
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.+.|.|.|+++||++.+|.+.|-++|++|...+..+.++...-.+..+.. ....+.++|++.|....
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~--~~~~~~~~l~~~l~~l~ 69 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDIS--ESKKDFAELKEELEELG 69 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEec--CCCCCHHHHHHHHHHHH
Confidence 45799999999999999999999999999998888776632222233321 11345788988888765
No 46
>cd04872 ACT_1ZPV ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein. This CD, ACT_1ZPV, includes those single ACT domain proteins similar to the yet uncharacterized Streptococcus pneumoniae ACT domain protein (pdb structure 1ZPV). Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=95.57 E-value=0.071 Score=42.35 Aligned_cols=66 Identities=11% Similarity=0.182 Sum_probs=50.3
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
..|.+.|+++||++..|.+.|-.+|++|...+..+.++...-....... ....+.++++.+|.+..
T Consensus 2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~~--~~~~~~~~L~~~l~~l~ 67 (88)
T cd04872 2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDIS--ESNLDFAELQEELEELG 67 (88)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEeC--CCCCCHHHHHHHHHHHH
Confidence 4689999999999999999999999999999888876632222223321 11456889999888876
No 47
>PRK04374 PII uridylyl-transferase; Provisional
Probab=95.31 E-value=0.086 Score=58.76 Aligned_cols=71 Identities=15% Similarity=0.106 Sum_probs=57.0
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee-eCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC-FNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt-~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.+.+.|.|.|.+++|||.+|..+|..+||+|+.|.|.+ .+|.+++++.+....+...-..+.|+++|.+++
T Consensus 688 ~~~~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~~~~~~~~~~~i~~~l~~~l 759 (869)
T PRK04374 688 NDALEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQDTYADGDPQRLAAALRQVL 759 (869)
T ss_pred CCeEEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCCCCCChHHHHHHHHHHHHHH
Confidence 35679999999999999999999999999999999998 577999999887654432223455777777665
No 48
>cd04894 ACT_ACR-like_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 (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=94.99 E-value=0.14 Score=39.73 Aligned_cols=66 Identities=17% Similarity=0.137 Sum_probs=50.5
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHH
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRN 341 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~ 341 (349)
.|.|.|+++.||-.+|..++-+.||.|..+.+++.|..-+-++-+......-.+.=+-+|+.|..+
T Consensus 2 vitvnCPDktGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~wVv~~~~~~~~rW~lLK~RL~~~ 67 (69)
T cd04894 2 VITINCPDKTGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVFWVVPRPPSIKVRWDLLKNRLMSA 67 (69)
T ss_pred EEEEeCCCccCcccHHHHHHHHhceEEEecccccCCcEEEEEEEEecCCCCCcccHHHHHHHHHhc
Confidence 589999999999999999999999999999999999954444443332223345557777777653
No 49
>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=94.75 E-value=0.32 Score=37.45 Aligned_cols=62 Identities=16% Similarity=0.253 Sum_probs=49.1
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
|.+.+.+|||++.++.++|.++|++|...+.++.++ |++.. ..... ...+.++++.+|....
T Consensus 2 vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~-~v~~p---~~~~~~~l~~~l~~l~ 64 (75)
T cd04870 2 ITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGI-LVQIP---DSADSEALLKDLLFKA 64 (75)
T ss_pred EEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEE-EEEcC---CCCCHHHHHHHHHHHH
Confidence 678899999999999999999999999998888877 44433 23332 2257889999988766
No 50
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=94.59 E-value=0.47 Score=36.64 Aligned_cols=61 Identities=20% Similarity=0.242 Sum_probs=41.9
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee--CCeEEEEEeeecccCCccCCHHHHHHHHHH
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF--NDFAMQASCSEGVEQRETLSCEDIKQALFR 340 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~--~d~vl~a~~se~~e~~~~is~edIkqaL~~ 340 (349)
.+.|+|.+.+++|+|.+|.++|.+.|+.|.+.++... ++...-.+..++ -+.+++.+.+.+
T Consensus 6 ~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V------~d~~~L~~ii~~ 68 (80)
T PF13291_consen 6 PVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEV------KDLEHLNQIIRK 68 (80)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEE------SSHHHHHHHHHH
T ss_pred EEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEE------CCHHHHHHHHHH
Confidence 4678999999999999999999999999999999995 343333333443 134455554444
No 51
>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=93.24 E-value=0.99 Score=32.77 Aligned_cols=34 Identities=15% Similarity=0.237 Sum_probs=29.2
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
+.|.++++||.|.+|+++|.+.|++|.+......
T Consensus 1 ~~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~ 34 (73)
T cd04886 1 LRVELPDRPGQLAKLLAVIAEAGANIIEVSHDRA 34 (73)
T ss_pred CEEEeCCCCChHHHHHHHHHHcCCCEEEEEEEec
Confidence 3577899999999999999999999997766543
No 52
>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=92.82 E-value=1.5 Score=32.87 Aligned_cols=35 Identities=17% Similarity=0.240 Sum_probs=31.9
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
|+|.+.+++|+|.+|+++|.+.|..|.+.++....
T Consensus 2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~ 36 (74)
T cd04887 2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQG 36 (74)
T ss_pred EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEec
Confidence 67889999999999999999999999988887764
No 53
>cd02116 ACT ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. Members of this CD belong to the superfamily of ACT regulatory domains. Pairs of ACT domains are commonly involved in specifically binding an amino acid or other small ligand leading to regulation of the enzyme. The ACT domain has been detected in a number of diverse proteins; some of these proteins are involved in amino acid and purine biosynthesis, phenylalanine hydroxylation, regulation of bacterial metabolism and transcription, and many remain to be characterized. ACT domain-containing enzymes involved in amino acid and purine synthesis are in many cases allosteric enzymes with complex regulation enforced by the binding of ligands. The ACT domain is commonly involved in the binding of a small regulatory molecule, such as the amino acids L-Ser and L-Phe in the case of D-3-phosphoglycerate dehydrogenase and the bifunctional chorismate mutase-p
Probab=91.76 E-value=1 Score=29.56 Aligned_cols=35 Identities=20% Similarity=0.370 Sum_probs=30.4
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
|.|.|.+++|.+.+|+.+|...|+.|.........
T Consensus 1 i~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~ 35 (60)
T cd02116 1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSG 35 (60)
T ss_pred CEEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence 46788899999999999999999999988776643
No 54
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=91.69 E-value=0.11 Score=46.74 Aligned_cols=52 Identities=27% Similarity=0.416 Sum_probs=46.2
Q ss_pred CCccchHHHHHHHHHHHHHHHHhHhcCCC--CCCCCchhhHHHHHHHHHHHHHH
Q 018897 179 QPSKNLMAERRRRKRLNDRLSMLRSIVPK--ISKMDRTSILADTIDYMKELLDK 230 (349)
Q Consensus 179 ~~~~h~~aER~RR~kin~~~~~LrslvP~--~~K~dKaSIL~~AI~YIk~Lq~~ 230 (349)
++.-|++-||+|=..+|+.|.+||.++|. +.|.+|.-.|.-|..||..|-+-
T Consensus 78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~v 131 (173)
T KOG4447|consen 78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQV 131 (173)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhc
Confidence 56789999999999999999999999996 57888888999999999988643
No 55
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=91.51 E-value=0.99 Score=44.28 Aligned_cols=67 Identities=19% Similarity=0.237 Sum_probs=49.8
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe---eeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS---CFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS---t~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.+.|.|.|++++|+...|-+.|-+.|++|+..+.. ..+.|.+.+..... ....++.++|+++|...+
T Consensus 9 ~~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~~~--~~~~~~~~~l~~~l~~l~ 78 (289)
T PRK13010 9 SYVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFHAQ--SAEAASVDTFRQEFQPVA 78 (289)
T ss_pred CEEEEEECCCCCCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEEcC--CCCCCCHHHHHHHHHHHH
Confidence 35799999999999999999999999999998885 23445443322211 123567889999998865
No 56
>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=91.28 E-value=0.92 Score=31.55 Aligned_cols=35 Identities=17% Similarity=0.267 Sum_probs=30.7
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
|+|.+.+++|.+.+|++.|...+++|.+..+...+
T Consensus 1 l~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~ 35 (71)
T cd04876 1 IRVEAIDRPGLLADITTVIAEEKINILSVNTRTDD 35 (71)
T ss_pred CEEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECC
Confidence 46778899999999999999999999988777654
No 57
>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=91.24 E-value=2.2 Score=31.42 Aligned_cols=35 Identities=20% Similarity=0.331 Sum_probs=31.5
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
.|.|.+.+++|+|.+|+..|.+.|..|.+......
T Consensus 2 yl~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~ 36 (79)
T cd04881 2 YLRLTVKDKPGVLAKITGILAEHGISIESVIQKEA 36 (79)
T ss_pred EEEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEccc
Confidence 58889999999999999999999999998877655
No 58
>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=90.79 E-value=2.3 Score=30.86 Aligned_cols=36 Identities=19% Similarity=0.168 Sum_probs=31.7
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
.|.|.+.+++|.|.+|++.|.+.++.|.+......+
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~ 37 (72)
T cd04874 2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIER 37 (72)
T ss_pred eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccC
Confidence 477889999999999999999999999987776653
No 59
>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=90.58 E-value=1.4 Score=33.17 Aligned_cols=36 Identities=8% Similarity=0.158 Sum_probs=31.3
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
+.|.|.+.+++|+|.+|+++|.+.|++|...+.+..
T Consensus 1 ~~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~ 36 (76)
T cd04888 1 VTLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIP 36 (76)
T ss_pred CEEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCC
Confidence 357888999999999999999999999998776543
No 60
>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=90.27 E-value=2.4 Score=31.52 Aligned_cols=61 Identities=16% Similarity=0.243 Sum_probs=41.4
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee--CCeEEEEEeeecccCCccCCHHHHHHHHHHH
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF--NDFAMQASCSEGVEQRETLSCEDIKQALFRN 341 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~--~d~vl~a~~se~~e~~~~is~edIkqaL~~~ 341 (349)
.+|.+..++++|.|.++++.|.+.|+.|.+...... .+...-.+..+. .+.++++++|.+.
T Consensus 2 ~~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~------~~~~~~~~~L~~~ 64 (72)
T cd04883 2 SQIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQT------MNPRPIIEDLRRA 64 (72)
T ss_pred cEEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEec------CCHHHHHHHHHHC
Confidence 467788899999999999999999999997654332 223332333322 2345777777553
No 61
>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=89.59 E-value=3.2 Score=31.65 Aligned_cols=35 Identities=20% Similarity=0.349 Sum_probs=32.2
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
.|+|.|.+++|+|.+|+.++.+.+..|...++.+.
T Consensus 2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~ 36 (74)
T cd04877 2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK 36 (74)
T ss_pred EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC
Confidence 58899999999999999999999999998888765
No 62
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=89.54 E-value=0.2 Score=52.44 Aligned_cols=56 Identities=16% Similarity=0.214 Sum_probs=46.9
Q ss_pred CCccchHHHHHHHHHHHHHHHHhHhcCCCC----CCCCchhhHHHHHHHHHHHHHHHHHH
Q 018897 179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI----SKMDRTSILADTIDYMKELLDKISSL 234 (349)
Q Consensus 179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~----~K~dKaSIL~~AI~YIk~Lq~~v~~L 234 (349)
+|+.++..||.|=..||+.|.+|-.+.--- ....|--||..|+.-|-.|++||.+-
T Consensus 526 RR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER 585 (632)
T KOG3910|consen 526 RRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER 585 (632)
T ss_pred HHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence 667888999999889999999998876532 23457889999999999999999864
No 63
>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=89.46 E-value=2.7 Score=41.04 Aligned_cols=62 Identities=16% Similarity=0.101 Sum_probs=48.0
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC--C-eEEEEEeeecccCCccCCHHHHHHHHHH
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN--D-FAMQASCSEGVEQRETLSCEDIKQALFR 340 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~--d-~vl~a~~se~~e~~~~is~edIkqaL~~ 340 (349)
.|.+.|++++|+...|-+.|-++|+.|+..+.+... + |.+ ....+. .....+.++|+++|..
T Consensus 2 ~itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~m-r~~v~~--~~~~~~~~~l~~~l~~ 66 (280)
T TIGR00655 2 ILLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPETGRFFM-RVEFQL--EGFRLEESSLLAAFKS 66 (280)
T ss_pred EEEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEEE-EEEEEe--CCCCCCHHHHHHHHHH
Confidence 578999999999999999999999999998888753 4 333 223332 1224678899999888
No 64
>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=89.38 E-value=2.2 Score=30.80 Aligned_cols=34 Identities=21% Similarity=0.229 Sum_probs=28.2
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
|.|.-+++||.|.++++.|.+.|+.|.+......
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~ 35 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVE 35 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEcc
Confidence 4566689999999999999999999986655443
No 65
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=89.33 E-value=0.3 Score=51.70 Aligned_cols=42 Identities=38% Similarity=0.644 Sum_probs=36.8
Q ss_pred hHHHHHHHHHHHHHHHHhHhcCCC----CCCCCchhhHHHHHHHHH
Q 018897 184 LMAERRRRKRLNDRLSMLRSIVPK----ISKMDRTSILADTIDYMK 225 (349)
Q Consensus 184 ~~aER~RR~kin~~~~~LrslvP~----~~K~dKaSIL~~AI~YIk 225 (349)
.---+|-|+|+|..|..|.+|+|- ++|.||-|||.-++.|++
T Consensus 30 SNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr 75 (712)
T KOG3560|consen 30 SNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLR 75 (712)
T ss_pred CCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHH
Confidence 334567799999999999999994 689999999999999975
No 66
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=89.32 E-value=0.23 Score=53.76 Aligned_cols=46 Identities=33% Similarity=0.491 Sum_probs=40.3
Q ss_pred ccchHHHHHHHHHHHHHHHHhHhcCCC----CCCCCchhhHHHHHHHHHH
Q 018897 181 SKNLMAERRRRKRLNDRLSMLRSIVPK----ISKMDRTSILADTIDYMKE 226 (349)
Q Consensus 181 ~~h~~aER~RR~kin~~~~~LrslvP~----~~K~dKaSIL~~AI~YIk~ 226 (349)
.+-.-|-|-||.|-|+-|..|..+||- .+.+|||||+.-||.|++-
T Consensus 48 EkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl 97 (768)
T KOG3558|consen 48 EKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL 97 (768)
T ss_pred hhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence 444568899999999999999999993 4689999999999999874
No 67
>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=88.94 E-value=3.5 Score=30.67 Aligned_cols=37 Identities=22% Similarity=0.373 Sum_probs=31.7
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
+|.|..+++||.|.+|++.|.+.|+.|.+..+...++
T Consensus 3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~ 39 (66)
T cd04908 3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTSE 39 (66)
T ss_pred EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCC
Confidence 5778889999999999999999999999777655544
No 68
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=88.43 E-value=3.4 Score=40.37 Aligned_cols=66 Identities=18% Similarity=0.260 Sum_probs=50.1
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee--eCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC--FND-FAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt--~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.+.|.+.|.+|||+...|-++|-++|++|...+.++ .++ |.+.... .. .....+.++|+++|....
T Consensus 6 ~~vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v-~~--~~~~~~~~~L~~~L~~l~ 74 (286)
T PRK06027 6 RYVLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEF-EG--DGLIFNLETLRADFAALA 74 (286)
T ss_pred eEEEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEE-Ee--CCCCCCHHHHHHHHHHHH
Confidence 467999999999999999999999999999999998 766 3333322 21 122345788998888755
No 69
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=88.27 E-value=0.48 Score=48.74 Aligned_cols=44 Identities=32% Similarity=0.429 Sum_probs=38.8
Q ss_pred hHHHHHHHHHHHHHHHHhHhcCCC----CCCCCchhhHHHHHHHHHHH
Q 018897 184 LMAERRRRKRLNDRLSMLRSIVPK----ISKMDRTSILADTIDYMKEL 227 (349)
Q Consensus 184 ~~aER~RR~kin~~~~~LrslvP~----~~K~dKaSIL~~AI~YIk~L 227 (349)
+-+-|.||++-|-.|..|..++|- .+..||++|+.-|..|||.-
T Consensus 6 KnaA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr 53 (598)
T KOG3559|consen 6 KNAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR 53 (598)
T ss_pred hhHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence 357799999999999999999995 35699999999999999853
No 70
>PRK04435 hypothetical protein; Provisional
Probab=87.97 E-value=2.4 Score=37.46 Aligned_cols=70 Identities=10% Similarity=-0.009 Sum_probs=47.0
Q ss_pred eecCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecccCCccCCHHHHHHHHHHH
Q 018897 270 RTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGVEQRETLSCEDIKQALFRN 341 (349)
Q Consensus 270 ~~~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~e~~~~is~edIkqaL~~~ 341 (349)
..+..+.|.+.+.+++|+|.+|+++|.+.|.+|...+.+.. ++...-.+..+.. +.....++|.++|.+.
T Consensus 65 ~~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs--~~~~~L~~Li~~L~~i 135 (147)
T PRK04435 65 VKGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTS--SMEGDIDELLEKLRNL 135 (147)
T ss_pred CCCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeC--ChHHHHHHHHHHHHcC
Confidence 35778899999999999999999999999999998776543 3422222233331 1122445666665543
No 71
>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=87.70 E-value=3 Score=29.90 Aligned_cols=60 Identities=17% Similarity=0.137 Sum_probs=42.5
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC--CeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN--DFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~--d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
+.|...+++|+|.+|++.|.+.|+.|.+..+..-. +...-.+..+. . ..++|.+.|...-
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v~~----~--~~~~l~~~l~~~~ 63 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVDS----P--VPEEVLEELKALP 63 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEcCC----C--CCHHHHHHHHcCC
Confidence 66788999999999999999999999988877654 43333332221 1 2457777776543
No 72
>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=87.29 E-value=3.2 Score=31.33 Aligned_cols=34 Identities=21% Similarity=0.258 Sum_probs=29.1
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
+.+.-+++||.|.++++.|.+.|..|++......
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~ 35 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFE 35 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccc
Confidence 5566789999999999999999999997765554
No 73
>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=86.90 E-value=4.3 Score=29.22 Aligned_cols=33 Identities=18% Similarity=0.255 Sum_probs=29.4
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISC 309 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt 309 (349)
|.+.+.+++|.|.+|...|.+.|+.|.+.....
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~ 34 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSR 34 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEe
Confidence 567889999999999999999999999877665
No 74
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=86.34 E-value=5.4 Score=39.03 Aligned_cols=65 Identities=15% Similarity=0.170 Sum_probs=48.5
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CC--eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-ND--FAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d--~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.+.|.|.|.++||+...|-+.|-++|++|...+..+- .+ |.+.+... . ....+.++|+++|...+
T Consensus 7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~-~---p~~~~~~~L~~~L~~l~ 74 (286)
T PRK13011 7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFH-S---EEGLDEDALRAGFAPIA 74 (286)
T ss_pred eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEe-c---CCCCCHHHHHHHHHHHH
Confidence 4678999999999999999999999999998887642 22 44433322 1 12356889998888765
No 75
>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=86.33 E-value=4.7 Score=29.85 Aligned_cols=35 Identities=17% Similarity=0.294 Sum_probs=30.2
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
-+.+.+++++|.|.+|++.|.+.|++|........
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~ 37 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEI 37 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEe
Confidence 36778899999999999999999999997765554
No 76
>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=85.53 E-value=3.8 Score=29.29 Aligned_cols=43 Identities=21% Similarity=0.349 Sum_probs=32.6
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC-CeEEEEEe
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN-DFAMQASC 319 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~-d~vl~a~~ 319 (349)
|.|...++||.|.++...|.+.|+.|....+.... +..+-.+.
T Consensus 1 ~~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~ 44 (56)
T cd04889 1 LSVFVENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLI 44 (56)
T ss_pred CEEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEE
Confidence 35678899999999999999999999877666544 44433333
No 77
>PRK08577 hypothetical protein; Provisional
Probab=85.27 E-value=7.6 Score=33.42 Aligned_cols=66 Identities=15% Similarity=0.249 Sum_probs=44.6
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC--CeEEEEEeeecccCCccCCHHHHHHHHHHH
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN--DFAMQASCSEGVEQRETLSCEDIKQALFRN 341 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~--d~vl~a~~se~~e~~~~is~edIkqaL~~~ 341 (349)
.+.|.|.+.+++|+|.+|++.|.+++.++.+.+..+.. +...-.+..+.. ......+++.+.|.+.
T Consensus 56 ~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~--~~~~~l~~l~~~L~~l 123 (136)
T PRK08577 56 LVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLS--KSDIDLEELEEELKKL 123 (136)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeC--CchhhHHHHHHHHHcC
Confidence 56799999999999999999999999999987776654 322112223331 1113345666666543
No 78
>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=84.50 E-value=12 Score=26.72 Aligned_cols=35 Identities=14% Similarity=0.271 Sum_probs=30.4
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
.|.|.+.+++|+|.+|+..|.+.++.|.+......
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~ 36 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPT 36 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeec
Confidence 36677889999999999999999999998877654
No 79
>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=84.22 E-value=9.5 Score=29.42 Aligned_cols=63 Identities=11% Similarity=0.081 Sum_probs=39.4
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
|.+...+++|.|.+|++.|.++|+.+.+.......+ .....+..+.. . ..+.+.++.+|...-
T Consensus 4 l~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~-~--~~~~~~~~~~l~~l~ 67 (80)
T cd04905 4 IVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFE-G--HIEDPNVAEALEELK 67 (80)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEE-C--CCCCHHHHHHHHHHH
Confidence 455567899999999999999999999776555432 22222223321 1 234456666665443
No 80
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=84.12 E-value=4.7 Score=44.91 Aligned_cols=55 Identities=18% Similarity=0.210 Sum_probs=47.6
Q ss_pred eeecCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee-CCeEEEEEeeecc
Q 018897 269 ERTNMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF-NDFAMQASCSEGV 323 (349)
Q Consensus 269 ~~~~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~-~d~vl~a~~se~~ 323 (349)
........|-|.|+++|.++..|..++...|++|+.|.|-+- +|+.++++.+...
T Consensus 679 r~~~~~teV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~~~ 734 (867)
T COG2844 679 RPHSGGTEVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVLEP 734 (867)
T ss_pred cccCCceEEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEecC
Confidence 334567899999999999999999999999999999998775 6679999977754
No 81
>PRK07334 threonine dehydratase; Provisional
Probab=83.11 E-value=8.1 Score=39.19 Aligned_cols=37 Identities=16% Similarity=0.239 Sum_probs=34.0
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
.+.|.|.+.+|+|+|.+|+++|.+.++.|.+.++.+.
T Consensus 326 ~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~ 362 (403)
T PRK07334 326 LARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRL 362 (403)
T ss_pred EEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEec
Confidence 4889999999999999999999999999998887654
No 82
>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=81.06 E-value=12 Score=28.29 Aligned_cols=34 Identities=15% Similarity=0.218 Sum_probs=27.7
Q ss_pred EEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 278 EICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 278 ~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
.+...++||.|.++++.|...|+.+.+.......
T Consensus 3 ~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~ 36 (75)
T cd04880 3 VFSLKNKPGALAKALKVFAERGINLTKIESRPSR 36 (75)
T ss_pred EEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecC
Confidence 3455789999999999999999999987555443
No 83
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]
Probab=80.53 E-value=1.6 Score=42.13 Aligned_cols=52 Identities=29% Similarity=0.435 Sum_probs=44.6
Q ss_pred CCccchHHHHHHHHHHHHHHHHhHhcCCC---CCCCCchhhHHHHHHHHHHHHHH
Q 018897 179 QPSKNLMAERRRRKRLNDRLSMLRSIVPK---ISKMDRTSILADTIDYMKELLDK 230 (349)
Q Consensus 179 ~~~~h~~aER~RR~kin~~~~~LrslvP~---~~K~dKaSIL~~AI~YIk~Lq~~ 230 (349)
+|.+=+..||+|=-.+|+.|..||.++|. ..|+.|...|.-|-+||..|++-
T Consensus 72 rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~ 126 (254)
T KOG3898|consen 72 RRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEV 126 (254)
T ss_pred hcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhccc
Confidence 45666788998889999999999999994 47889999999999999988753
No 84
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=80.21 E-value=5.6 Score=36.79 Aligned_cols=65 Identities=14% Similarity=0.190 Sum_probs=49.8
Q ss_pred CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
..+.|.+.+.+|||+...|-++|.++|..|..++.+.+++ |.+-..+ ... ......|+.+|....
T Consensus 7 ~~lviTviG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa~i~lv-s~~----~~~~~~le~~L~~l~ 72 (190)
T PRK11589 7 HYLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLL-SGS----WNAITLIESTLPLKG 72 (190)
T ss_pred cEEEEEEEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCCceEEEEEE-eCC----hhHHHHHHHHHHhhh
Confidence 4567899999999999999999999999999999999988 4443333 221 225667777776544
No 85
>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=77.57 E-value=13 Score=28.61 Aligned_cols=36 Identities=11% Similarity=0.144 Sum_probs=29.0
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
|-+...+++|-|.++++.+...|+.+.+-..-...+
T Consensus 3 l~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~ 38 (74)
T cd04904 3 LIFSLKEEVGALARALKLFEEFGVNLTHIESRPSRR 38 (74)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCC
Confidence 344557899999999999999999999776655543
No 86
>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=76.79 E-value=2.8 Score=30.82 Aligned_cols=36 Identities=17% Similarity=0.154 Sum_probs=28.7
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
|-+.+.+++|+|.+|+..|.+.|..|...+....++
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~ 37 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGE 37 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCC
Confidence 456778999999999999999999997665544334
No 87
>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=75.39 E-value=10 Score=27.86 Aligned_cols=60 Identities=13% Similarity=0.133 Sum_probs=40.6
Q ss_pred EEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee--eCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 277 VEICCAGKPGLLLSTVTSLEALGLEIQQCVISC--FNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 277 I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt--~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
+-+...+++|.+.+|.+.|.+.|+.|.+..... .++..+..+..+. ..+.++.+.|.+.-
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~------~~~~~~~~~l~~~~ 63 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDE------PVPDEVLEELRALP 63 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCC------CCCHHHHHHHHcCC
Confidence 345778999999999999999999998766544 2344444443332 12456666666543
No 88
>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]
Probab=74.25 E-value=14 Score=36.45 Aligned_cols=70 Identities=21% Similarity=0.297 Sum_probs=49.7
Q ss_pred CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC--C-eEEEEEeeecccCCccCCHHHHHHHHHHHh-hcC
Q 018897 273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN--D-FAMQASCSEGVEQRETLSCEDIKQALFRNA-GYG 345 (349)
Q Consensus 273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~--d-~vl~a~~se~~e~~~~is~edIkqaL~~~~-g~g 345 (349)
....+.++|++++|+...|-..|.+.|..|++++....- + |.+-+.- .. +....+.+.+.+++-..+ .+|
T Consensus 6 ~~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf~D~~~g~FFmR~~f-~~--~~~~~~~~~l~~~f~~~a~~f~ 79 (287)
T COG0788 6 DTFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQFDDPETGRFFMRVEF-EG--EGGPLDREALRAAFAPLAEEFG 79 (287)
T ss_pred cceEEEEecCCCCCcHHHHHHHHHHcCCceeecccccccccCeEEEEEEE-ec--CCCcccHHHHHHHHHHHHHhhC
Confidence 346799999999999999999999999999998887422 2 2222211 11 122377888888888765 344
No 89
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]
Probab=73.32 E-value=5.7 Score=38.64 Aligned_cols=51 Identities=27% Similarity=0.301 Sum_probs=43.7
Q ss_pred ccchHHHHHHHHHHHHHHHHhHhcCCCC---CCCCchhhHHHHHHHHHHHHHHH
Q 018897 181 SKNLMAERRRRKRLNDRLSMLRSIVPKI---SKMDRTSILADTIDYMKELLDKI 231 (349)
Q Consensus 181 ~~h~~aER~RR~kin~~~~~LrslvP~~---~K~dKaSIL~~AI~YIk~Lq~~v 231 (349)
..-+..||+|=..+|..|..||..||.. .|.+|-..|+.|-.||--|-..+
T Consensus 176 ~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l 229 (285)
T KOG4395|consen 176 LAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLL 229 (285)
T ss_pred cccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhh
Confidence 4556889999999999999999999964 67888889999999998887654
No 90
>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=71.72 E-value=24 Score=28.68 Aligned_cols=37 Identities=8% Similarity=0.044 Sum_probs=30.4
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
+-|-+...+++|.|.++++.|...|+.+.+-..-...
T Consensus 15 tslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~ 51 (90)
T cd04931 15 ISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSR 51 (90)
T ss_pred EEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCC
Confidence 4566666889999999999999999999977665543
No 91
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=69.41 E-value=12 Score=30.95 Aligned_cols=65 Identities=12% Similarity=0.249 Sum_probs=46.2
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
+.|.|.-.+|+|+...|-.+|-++|++|++.+.+-+.+ |++-.. ++- .....+...++..|...+
T Consensus 4 avITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ftm~~l-V~~--~~~~~d~~~lr~~l~~~~ 69 (90)
T COG3830 4 AVITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIML-VDI--SKEVVDFAALRDELAAEG 69 (90)
T ss_pred EEEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhhhceeeeE-EcC--ChHhccHHHHHHHHHHHH
Confidence 56888889999999999999999999999988888888 343322 221 112345556665555544
No 92
>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=68.85 E-value=35 Score=25.54 Aligned_cols=32 Identities=16% Similarity=0.154 Sum_probs=27.0
Q ss_pred EEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 278 EICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 278 ~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
.+.-+++||-|.++++.|.. |.+|+.......
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~ 33 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQ 33 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcC
Confidence 45668999999999999999 999997766654
No 93
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=68.30 E-value=27 Score=38.45 Aligned_cols=66 Identities=12% Similarity=0.064 Sum_probs=50.0
Q ss_pred eEEEEEc-CCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 275 TRVEICC-AGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 275 v~I~I~C-~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
..+.|.. ++++|+|.++..+|-.+|+.|.+|++.+ ++..+..+.+.. ..+...++..+.|.+...+
T Consensus 547 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~a~~~~-~~~~~~~~~v~~-~~~~~~~~~~~~~~~~~~~ 613 (693)
T PRK00227 547 GFFTVIWHGDYPRELVRVLALIAAKGWNILSARMVA-NGPWSAEFDVRA-NGPQDFDPQEFLQAYKSGV 613 (693)
T ss_pred CeEEEEecCCcccHHHHHHHHHHhcCceeeEeEEec-CCceEEEEEEec-CCCCCCChHHHHHHHHHhh
Confidence 4555555 9999999999999999999999999999 554444443333 2456678888888887544
No 94
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=66.81 E-value=45 Score=33.14 Aligned_cols=9 Identities=22% Similarity=0.161 Sum_probs=5.7
Q ss_pred ccccCCCCc
Q 018897 31 NQIFSDGNW 39 (349)
Q Consensus 31 ~~~~~~~~~ 39 (349)
.+.|+++.|
T Consensus 61 ~~~~s~~dn 69 (294)
T KOG4571|consen 61 EDAFSVPDN 69 (294)
T ss_pred ccccccccc
Confidence 456666667
No 95
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=65.30 E-value=1.9 Score=47.03 Aligned_cols=61 Identities=21% Similarity=0.364 Sum_probs=52.5
Q ss_pred CCCccchHHHHHHHHHHHHHHHHhHhcCCCC-----CCCCchhhHHHHHHHHHHHHHHHHHHHHHH
Q 018897 178 GQPSKNLMAERRRRKRLNDRLSMLRSIVPKI-----SKMDRTSILADTIDYMKELLDKISSLQQEI 238 (349)
Q Consensus 178 ~~~~~h~~aER~RR~kin~~~~~LrslvP~~-----~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~ 238 (349)
.++..|+-+|.+||.++.-.+..|.+++-+. .|+.++.-+...+.||..++++...+++|.
T Consensus 650 ~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~ 715 (856)
T KOG3582|consen 650 NRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEA 715 (856)
T ss_pred CCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhh
Confidence 5789999999999999999999999998864 467777789999999999988887777644
No 96
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=63.22 E-value=24 Score=31.71 Aligned_cols=36 Identities=14% Similarity=0.275 Sum_probs=31.8
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
.|.|.-.+++|.|.+|...|...|+.|.+..+..-+
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~ 38 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTE 38 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecC
Confidence 366777899999999999999999999988877765
No 97
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=59.51 E-value=34 Score=30.90 Aligned_cols=36 Identities=14% Similarity=0.279 Sum_probs=31.5
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
.|.|.-.++||.|.+|...|...|+.|.+..+....
T Consensus 4 ~IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te 39 (161)
T PRK11895 4 TLSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTE 39 (161)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecC
Confidence 467777899999999999999999999988777654
No 98
>cd04922 ACT_AKi-HSDH-ThrA_2 ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). This CD includes the second of two ACT domains of the bifunctional enzyme aspartokinase (AK) - homoserine dehydrogenase (HSDH). The ACT domains are positioned between the N-terminal catalytic domain of AK and the C-terminal HSDH domain found in bacteria (Escherichia coli (EC) ThrA) and higher plants (Zea mays AK-HSDH). AK and HSDH are the first and third enzymes in the biosynthetic pathway of the aspartate family of amino acids. AK catalyzes the phosphorylation of Asp to P-aspartyl phosphate. HSDH catalyzes the NADPH-dependent conversion of Asp 3-semialdehyde to homoserine. HSDH is the first committed reaction in the branch of the pathway that leads to Thr and Met. In E. coli, ThrA is subject to allosteric regulation by the end product L-threonine and the native enzyme is reported to be tetrameric. As with bacteria, plant AK and HSDH are feedback inhibited by pathwa
Probab=59.10 E-value=64 Score=23.08 Aligned_cols=32 Identities=19% Similarity=0.343 Sum_probs=24.8
Q ss_pred EEEEEc---CCCCchHHHHHHHHHhCCCeEEEEEE
Q 018897 276 RVEICC---AGKPGLLLSTVTSLEALGLEIQQCVI 307 (349)
Q Consensus 276 ~I~I~C---~~rpGLL~~Il~aLe~LgLeVv~A~I 307 (349)
.|.|.+ .+.+|++.+|+++|.+.|+.|.-.+.
T Consensus 3 ~isvvg~~~~~~~~~~~~i~~~l~~~~I~v~~i~~ 37 (66)
T cd04922 3 ILALVGDGMAGTPGVAATFFSALAKANVNIRAIAQ 37 (66)
T ss_pred EEEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 345555 45789999999999999999975444
No 99
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=58.94 E-value=15 Score=40.38 Aligned_cols=60 Identities=10% Similarity=0.081 Sum_probs=48.9
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHhh
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNAG 343 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~g 343 (349)
..++|...+|+|+|..|+.+|. +|..|.++|.|..++++++... ...-..+.++|.+++.
T Consensus 632 ~~~e~r~~dr~g~l~~~~~~l~----~~~~~~~~~~g~~~~~~~~~~~-----~~~r~~~~~~~~~~~~ 691 (693)
T PRK00227 632 NILEVRTEDRRGALGALLGVLP----DLLWITASTPGATMIVQAALKP-----GFDRATVERDVTRVLA 691 (693)
T ss_pred cEEEEEeCccccHHHHHHHHhh----hhhhHhhcCCCcceEEEEEecC-----cccHHHHHHHHHHHHh
Confidence 5789999999999999999999 9999999999999999888763 1234456666666553
No 100
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=58.33 E-value=53 Score=28.91 Aligned_cols=40 Identities=28% Similarity=0.505 Sum_probs=35.7
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEE
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAM 315 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl 315 (349)
.|.|..+++||-|..+.++|.+.|+.+...+|.-.++|-+
T Consensus 5 QISvFlENk~GRL~~~~~~L~eagINiRA~tiAdt~dFGI 44 (142)
T COG4747 5 QISVFLENKPGRLASVANKLKEAGINIRAFTIADTGDFGI 44 (142)
T ss_pred EEEEEecCCcchHHHHHHHHHHcCCceEEEEeccccCcce
Confidence 4788889999999999999999999999989888888644
No 101
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=58.31 E-value=32 Score=38.29 Aligned_cols=37 Identities=16% Similarity=0.153 Sum_probs=33.8
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
.+.|.|.+.+++|+|.+|..+|.+.++.|.+.++.+.
T Consensus 666 ~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~ 702 (743)
T PRK10872 666 SLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSD 702 (743)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEc
Confidence 3579999999999999999999999999999988765
No 102
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=58.10 E-value=40 Score=30.85 Aligned_cols=63 Identities=10% Similarity=0.194 Sum_probs=42.8
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee--CCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF--NDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~--~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
.|.|.-.++||+|.+|...|-..|++|.+.++... .+.. ..... .. ++ .-..+.|...|.+.+
T Consensus 4 ~isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~~~s-r~TIv-v~-~~-~~~ieqL~kQL~KLi 68 (174)
T CHL00100 4 TLSVLVEDESGVLTRIAGLFARRGFNIESLAVGPAEQKGIS-RITMV-VP-GD-DRTIEQLTKQLYKLV 68 (174)
T ss_pred EEEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCCCcc-EEEEE-EE-CC-HHHHHHHHHHHHHHh
Confidence 46777889999999999999999999998888663 2322 11111 11 11 112678888887765
No 103
>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=57.97 E-value=56 Score=25.47 Aligned_cols=33 Identities=12% Similarity=0.123 Sum_probs=27.3
Q ss_pred EEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 278 EICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 278 ~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
-+...+++|.|.++++.++..|+.+.+-..-..
T Consensus 4 ~~~l~~~~g~L~~iL~~f~~~~inl~~IeSRP~ 36 (74)
T cd04929 4 IFSLKNEVGGLAKALKLFQELGINVVHIESRKS 36 (74)
T ss_pred EEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccC
Confidence 344478999999999999999999997766554
No 104
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=55.68 E-value=25 Score=26.49 Aligned_cols=30 Identities=20% Similarity=0.360 Sum_probs=25.1
Q ss_pred CCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 283 GKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 283 ~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
+++|.|..|+..+..-|+.|.+-++...++
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~ 30 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTED 30 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-SS
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecCC
Confidence 479999999999999999999998888443
No 105
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=55.38 E-value=66 Score=35.57 Aligned_cols=39 Identities=13% Similarity=0.138 Sum_probs=34.9
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
.+.|.|.+.+++|+|.+|..+|-+.++.|.+.++.+..+
T Consensus 626 ~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~ 664 (702)
T PRK11092 626 IAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDG 664 (702)
T ss_pred EEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCC
Confidence 457999999999999999999999999999999877654
No 106
>PF05088 Bac_GDH: Bacterial NAD-glutamate dehydrogenase
Probab=55.28 E-value=66 Score=38.73 Aligned_cols=69 Identities=19% Similarity=0.175 Sum_probs=51.3
Q ss_pred CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC---C--eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN---D--FAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~---d--~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
..+.++|....++..|++|+-+|+++||.|+...--.+. + .-+|.+..... .....+.+++++.|.++.
T Consensus 488 ~~~~lkiy~~~~~~~Ls~vlPilenlGl~V~~e~~~~i~~~~~~~~~i~~F~l~~~-~~~~~~~~~~~~~~~~a~ 561 (1528)
T PF05088_consen 488 GRLRLKIYHPGEPLPLSDVLPILENLGLRVIDERPYEIRRADGRRVWIHDFGLQYP-DGDALDLDDIRERFEEAF 561 (1528)
T ss_pred CeEEEEEEcCCCCcCHHHHHHHHHhCCCEEEEEecceeecCCCceEEEEEEEEecC-CCccccHHHHHHHHHHHH
Confidence 468999999999999999999999999999987544443 2 55666665553 334467777777776654
No 107
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=53.60 E-value=8 Score=35.04 Aligned_cols=42 Identities=26% Similarity=0.373 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHHHHHhHhcCCCC--CCCCchhhHHHHHHHHHHH
Q 018897 186 AERRRRKRLNDRLSMLRSIVPKI--SKMDRTSILADTIDYMKEL 227 (349)
Q Consensus 186 aER~RR~kin~~~~~LrslvP~~--~K~dKaSIL~~AI~YIk~L 227 (349)
.||.|-.++++.+.-|++|+|+. .++.+.-.|.-+-+||.+|
T Consensus 29 ~e~~R~~~ls~~s~l~g~l~pgspa~gk~~~ktlr~~~~~~~~~ 72 (173)
T KOG4447|consen 29 KERGRKRRLSDASTLLGKLEPGSPADGKRGKKTLRIGTDSIQSL 72 (173)
T ss_pred HHHhHHhhhhhhhhhccccCCCCCCcccccccccccCCCchhhH
Confidence 68899999999999999999974 3333333355555555544
No 108
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=53.45 E-value=5.1 Score=43.88 Aligned_cols=58 Identities=24% Similarity=0.358 Sum_probs=50.4
Q ss_pred CCccchHHHHHHHHHHHHHHHHhHhcCCCC-----CCCCchhhHHHHHHHHHHHHHHHHHHHHHHH
Q 018897 179 QPSKNLMAERRRRKRLNDRLSMLRSIVPKI-----SKMDRTSILADTIDYMKELLDKISSLQQEIQ 239 (349)
Q Consensus 179 ~~~~h~~aER~RR~kin~~~~~LrslvP~~-----~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e 239 (349)
.+..|+-++|+||-.+-+++..|-.|.|.. .+..+++||. +.|+.+++.-+.+.+..+
T Consensus 787 v~a~sih~lrr~~~~~~dq~~sL~alrp~v~~~~~ql~S~tS~L~---dp~~~~eq~ska~~e~~~ 849 (856)
T KOG3582|consen 787 VSAGSIHALRRTRLNWLDQFCSLPALRPQVLLNLRQLLSSTSILT---DPIKQPEQASKAVTEKIE 849 (856)
T ss_pred eecchHHHHHHHHHHHhhccccHHHHHHHHHhhHHHhhhhhhccc---CcccchHHHHHHHHhhhh
Confidence 568899999999999999999999999953 5678999999 899999999888887554
No 109
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=53.23 E-value=84 Score=29.04 Aligned_cols=64 Identities=16% Similarity=0.194 Sum_probs=46.3
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-------eEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-------FAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-------~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
..|.+.-.++||++.++-+.|-+.|++|.+.+--+.+. |.++.. +.. -.....++|+.+|...+
T Consensus 96 ~~v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~a~~~~~~lf~~~~~-v~l---P~~~~~~~L~~~l~~l~ 166 (190)
T PRK11589 96 VWVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQIT-AHS---PASQDAANIEQAFKALC 166 (190)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHcCCChhheEEeeecCCCCCcccEEEEEE-EEc---CCCCCHHHHHHHHHHHH
Confidence 56788889999999999999999999998777766652 333322 111 22345778888887754
No 110
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=52.78 E-value=87 Score=24.84 Aligned_cols=37 Identities=14% Similarity=0.209 Sum_probs=31.8
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
.|.|.-.++||.|..|+..+..-|+.|.+-++....+
T Consensus 5 ~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~ 41 (76)
T PRK11152 5 QLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTD 41 (76)
T ss_pred EEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCC
Confidence 4666778999999999999999999999888887543
No 111
>TIGR00691 spoT_relA (p)ppGpp synthetase, RelA/SpoT family. (p)ppGpp is a regulatory metabolite of the stringent response, but appears also to be involved in antibiotic biosynthesis in some species.
Probab=51.59 E-value=90 Score=34.34 Aligned_cols=38 Identities=13% Similarity=0.184 Sum_probs=34.5
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
.+.|.|.+.+++|+|.+|..+|-+.+..|.+.++.+..
T Consensus 610 ~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~ 647 (683)
T TIGR00691 610 IVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYG 647 (683)
T ss_pred EEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcC
Confidence 45799999999999999999999999999999987764
No 112
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=51.40 E-value=96 Score=24.66 Aligned_cols=37 Identities=14% Similarity=0.169 Sum_probs=31.6
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
.|.+.-.++||+|.+|...+...|+.|.+-++...++
T Consensus 4 tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te~ 40 (76)
T PRK06737 4 TFSLVIHNDPSVLLRISGIFARRGYYISSLNLNERDT 40 (76)
T ss_pred EEEEEEecCCCHHHHHHHHHhccCcceEEEEecccCC
Confidence 4677778999999999999999999999887776543
No 113
>PRK06382 threonine dehydratase; Provisional
Probab=51.38 E-value=60 Score=33.02 Aligned_cols=37 Identities=19% Similarity=0.287 Sum_probs=32.2
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS 308 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS 308 (349)
+..+++.|.-+++||.|.+|++.|.+.|.+|++..+.
T Consensus 328 ~~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~~ 364 (406)
T PRK06382 328 GQLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEVD 364 (406)
T ss_pred CCEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEEe
Confidence 4566888888999999999999999999999976654
No 114
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=50.73 E-value=65 Score=26.30 Aligned_cols=37 Identities=11% Similarity=0.112 Sum_probs=32.1
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
.|.+.-.+++|+|.+|...|-..|+.|.+.+++.-.+
T Consensus 4 ~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~ 40 (84)
T PRK13562 4 ILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQ 40 (84)
T ss_pred EEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCC
Confidence 4667778999999999999999999999888877655
No 115
>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=46.68 E-value=1.4e+02 Score=23.56 Aligned_cols=31 Identities=23% Similarity=0.473 Sum_probs=24.8
Q ss_pred EEEEEc---CCCCchHHHHHHHHHhCCCeEEEEE
Q 018897 276 RVEICC---AGKPGLLLSTVTSLEALGLEIQQCV 306 (349)
Q Consensus 276 ~I~I~C---~~rpGLL~~Il~aLe~LgLeVv~A~ 306 (349)
.|.|.. .+.+|.+.+|+++|++.|+.|-.-.
T Consensus 3 ~i~i~~~~~~~~~g~~a~IF~~La~~~InVDmI~ 36 (78)
T cd04933 3 MLDITSTRMLGQYGFLAKVFSIFETLGISVDVVA 36 (78)
T ss_pred EEEEEcCCCCCccCHHHHHHHHHHHcCCcEEEEE
Confidence 345544 5678999999999999999998654
No 116
>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=45.49 E-value=1e+02 Score=30.82 Aligned_cols=37 Identities=19% Similarity=0.268 Sum_probs=32.3
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEe
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVIS 308 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~IS 308 (349)
+..+++.|.-+++||.|.++++.+.+.|.+|++....
T Consensus 303 gr~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~ 339 (380)
T TIGR01127 303 GRKVRIETVLPDRPGALYHLLESIAEARANIVKIDHD 339 (380)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEee
Confidence 4456888889999999999999999999999977655
No 117
>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=41.44 E-value=1.2e+02 Score=20.91 Aligned_cols=33 Identities=21% Similarity=0.352 Sum_probs=25.5
Q ss_pred EEEEEc---CCCCchHHHHHHHHHhCCCeEEEEEEe
Q 018897 276 RVEICC---AGKPGLLLSTVTSLEALGLEIQQCVIS 308 (349)
Q Consensus 276 ~I~I~C---~~rpGLL~~Il~aLe~LgLeVv~A~IS 308 (349)
.|.|.+ .+.+|.+.+++++|.+.++.|.....+
T Consensus 2 ~i~i~g~~~~~~~~~~~~i~~~l~~~~i~v~~i~~~ 37 (65)
T cd04892 2 LVSVVGAGMRGTPGVAARIFSALAEAGINIIMISQG 37 (65)
T ss_pred EEEEECCCCCCCccHHHHHHHHHHHCCCcEEEEEcC
Confidence 355544 367899999999999999999865543
No 118
>cd04937 ACT_AKi-DapG-BS_2 ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI. This CD includes the C-terminal of the two ACT domains of the diaminopimelate-sensitive aspartokinase (AK) isoenzyme AKI, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) strain 168), Clostridia, and Actinobacteria bacterial species. In B. subtilis, the regulation of the diaminopimelate-lysine biosynthetic pathway involves dual control by diaminopimelate and lysine, effected through separate diaminopimelate- and lysine-sensitive AK isoenzymes. AKI activity is invariant during the exponential and stationary phases of growth and is not altered by addition of amino acids to the growth medium. The role of this isoenzyme is most likely to provide a constant level of aspartyl-beta-phosphate for the biosynthesis of diaminopimelate for peptidoglycan synthesis and dipicolinate during sporulation. The BS AKI is tetrameric consisting of two alpha and two beta subunits; th
Probab=40.92 E-value=1.4e+02 Score=21.80 Aligned_cols=21 Identities=38% Similarity=0.664 Sum_probs=19.9
Q ss_pred CCCchHHHHHHHHHhCCCeEE
Q 018897 283 GKPGLLLSTVTSLEALGLEIQ 303 (349)
Q Consensus 283 ~rpGLL~~Il~aLe~LgLeVv 303 (349)
..+|++.+++++|.+.|+.|.
T Consensus 13 ~~~gi~~~if~aL~~~~I~v~ 33 (64)
T cd04937 13 GVPGVMAKIVGALSKEGIEIL 33 (64)
T ss_pred CCcCHHHHHHHHHHHCCCCEE
Confidence 689999999999999999997
No 119
>PRK08198 threonine dehydratase; Provisional
Probab=40.88 E-value=1.3e+02 Score=30.39 Aligned_cols=38 Identities=13% Similarity=0.231 Sum_probs=33.0
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC 309 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt 309 (349)
+..+.+.|.-+++||.|.++++.|-+.|..|...+...
T Consensus 325 gr~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~ 362 (404)
T PRK08198 325 GRYLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDR 362 (404)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEE
Confidence 45568889999999999999999999999998776654
No 120
>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=40.43 E-value=1.8e+02 Score=22.77 Aligned_cols=33 Identities=9% Similarity=0.094 Sum_probs=25.4
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
.+.+.-+++||-|.+++++|- +.+|........
T Consensus 3 vl~v~ipD~PG~L~~ll~~l~--~anI~~~~y~~~ 35 (85)
T cd04906 3 LLAVTIPERPGSFKKFCELIG--PRNITEFNYRYA 35 (85)
T ss_pred EEEEecCCCCcHHHHHHHHhC--CCceeEEEEEcc
Confidence 577778999999999999998 666665444443
No 121
>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=40.00 E-value=47 Score=24.92 Aligned_cols=32 Identities=16% Similarity=0.351 Sum_probs=24.7
Q ss_pred eEEEEEcC----CCCchHHHHHHHHHhCCCeEEEEE
Q 018897 275 TRVEICCA----GKPGLLLSTVTSLEALGLEIQQCV 306 (349)
Q Consensus 275 v~I~I~C~----~rpGLL~~Il~aLe~LgLeVv~A~ 306 (349)
..|.|..+ +.+|++.++..+|.+.|+.|...+
T Consensus 7 ~~i~v~g~g~~~~~~Gv~a~i~~~La~~~I~i~~is 42 (65)
T PF13840_consen 7 AKISVVGPGLRFDVPGVAAKIFSALAEAGINIFMIS 42 (65)
T ss_dssp EEEEEEEECGTTTSHHHHHHHHHHHHHTTS-ECEEE
T ss_pred EEEEEEccccCCCcccHHHHHHHHHHHCCCCEEEEE
Confidence 34555553 489999999999999999998555
No 122
>PF02120 Flg_hook: Flagellar hook-length control protein FliK; InterPro: IPR021136 This entry represents the C-terminal domain of the flagellar hook-length control protein FliK. This entry also includes YscP of the Yersinia type III secretion system, and equivalent proteins in other pathogenic bacterial type III secretion systems. During flagellar morphogenesis in Salmonella typhimurium and Escherichia coli, flagellar hook-length control protein (FliK) controls the length of the hook by directly measuring the hook length [, ]. It is considered unlikely that FliK functions as a molecular ruler for determining hook length, but that it is more likely to be employing a novel mechanism. The deduced amino acid sequences of FliK proteins from S. typhimurium and E. coli have molecular masses of 41,748 and 39,246 Da, respectively, and are fairly hydrophilic []. Sequence comparison reveals around 50% identity, with greatest conservation in the C-terminal region, with 71% identity in the last 154 amino acids - mutagenesis of this conserved region completely abolishes motility. The central and C-terminal regions are rich in proline and glutamine respectively; it is thought that they may constitute distinct domains [].; PDB: 2RRL_A.
Probab=39.79 E-value=1e+02 Score=23.61 Aligned_cols=44 Identities=18% Similarity=0.166 Sum_probs=30.4
Q ss_pred eeeeeecCeeEEEEEcCCCC------chHHHHHHHHHhCCCeEEEEEEee
Q 018897 266 FDVERTNMDTRVEICCAGKP------GLLLSTVTSLEALGLEIQQCVISC 309 (349)
Q Consensus 266 VeV~~~~~~v~I~I~C~~rp------GLL~~Il~aLe~LgLeVv~A~ISt 309 (349)
|.|...+..+.|.|.+.+.. .-+..+.+.|...|+.|.+.+++.
T Consensus 29 v~l~~~~~~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~~G~~~~~~~v~~ 78 (85)
T PF02120_consen 29 VKLRLQGGNLSVQFTAENPETKELLRQNLPELKERLQAQGLEVVNLSVSQ 78 (85)
T ss_dssp EEEEEETTEEEEEEE--SSHHHHHHHHTHHHHHHHHHTTT-EEEEEEEES
T ss_pred EEEEEeCCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCeEEEEEEE
Confidence 44555677888999886643 256788889999999999766654
No 123
>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=37.41 E-value=60 Score=27.61 Aligned_cols=35 Identities=9% Similarity=-0.044 Sum_probs=28.9
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeee
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCF 310 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~ 310 (349)
-|.+...+++|.|.++|+.|...|+.+.+-..-..
T Consensus 43 Slifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~ 77 (115)
T cd04930 43 TLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPS 77 (115)
T ss_pred EEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcC
Confidence 45555588999999999999999999998766555
No 124
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=34.74 E-value=1.7e+02 Score=26.22 Aligned_cols=67 Identities=7% Similarity=0.068 Sum_probs=42.2
Q ss_pred CeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEee-eCCeEEEEEeeecccCCccCCHHHHHHHHHHH
Q 018897 273 MDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISC-FNDFAMQASCSEGVEQRETLSCEDIKQALFRN 341 (349)
Q Consensus 273 ~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt-~~d~vl~a~~se~~e~~~~is~edIkqaL~~~ 341 (349)
..+.+.+.-.+|-|.|++++.++-..++.|...+.+- +++. -.+..+-.. -.-..++++|-.+|.+.
T Consensus 71 ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~-Anvtlsi~~-ssm~~~V~~ii~kl~k~ 138 (150)
T COG4492 71 RIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGR-ANVTLSIDT-SSMEKDVDKIIEKLRKV 138 (150)
T ss_pred eEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCce-eeEEEEEEc-hhhhhhHHHHHHHHhcc
Confidence 3556778889999999999999999999998655544 3331 111111100 02234566777776653
No 125
>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=33.76 E-value=1.4e+02 Score=21.28 Aligned_cols=24 Identities=25% Similarity=0.418 Sum_probs=21.3
Q ss_pred CCCCchHHHHHHHHHhCCCeEEEE
Q 018897 282 AGKPGLLLSTVTSLEALGLEIQQC 305 (349)
Q Consensus 282 ~~rpGLL~~Il~aLe~LgLeVv~A 305 (349)
...+|...+|+++|++.|+.|..-
T Consensus 11 ~~~~~~~~~if~~l~~~~i~v~~i 34 (62)
T cd04890 11 NGEVGFLRKIFEILEKHGISVDLI 34 (62)
T ss_pred CcccCHHHHHHHHHHHcCCeEEEE
Confidence 357899999999999999999965
No 126
>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=32.90 E-value=1.8e+02 Score=20.75 Aligned_cols=28 Identities=14% Similarity=0.112 Sum_probs=22.7
Q ss_pred CCCCchHHHHHHHHHhCCCeEEEEEEee
Q 018897 282 AGKPGLLLSTVTSLEALGLEIQQCVISC 309 (349)
Q Consensus 282 ~~rpGLL~~Il~aLe~LgLeVv~A~ISt 309 (349)
.+++|.+.+++++|.+.|++|.-...+.
T Consensus 12 ~~~~~~~~~if~~L~~~~I~v~~i~q~~ 39 (66)
T cd04919 12 KNMIGIAGRMFTTLADHRINIEMISQGA 39 (66)
T ss_pred CCCcCHHHHHHHHHHHCCCCEEEEEecC
Confidence 4578999999999999999997544433
No 127
>PRK11899 prephenate dehydratase; Provisional
Probab=32.49 E-value=2.6e+02 Score=27.42 Aligned_cols=66 Identities=11% Similarity=0.039 Sum_probs=42.5
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHhh
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNAG 343 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~g 343 (349)
+.|-+...++||.|.++|.+|...|+....-..-...+ .-=+.|..+.. + ......++++|.....
T Consensus 195 tsl~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~~~Y~F~id~e-g--~~~d~~v~~aL~~l~~ 261 (279)
T PRK11899 195 TTFVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSFTATQFYADIE-G--HPEDRNVALALEELRF 261 (279)
T ss_pred EEEEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCCceEEEEEEEE-C--CCCCHHHHHHHHHHHH
Confidence 44555557999999999999999999998766555533 11223334431 1 2334467777776554
No 128
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=32.31 E-value=1.3e+02 Score=26.52 Aligned_cols=53 Identities=19% Similarity=0.214 Sum_probs=34.8
Q ss_pred EEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHH
Q 018897 276 RVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQAL 338 (349)
Q Consensus 276 ~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL 338 (349)
.+-|.-+++||-|..|+++|-..++.+- -++++..++..--..+..+|+-.+.
T Consensus 71 VlaVEmeD~PG~l~~I~~vl~d~diNld----------YiYAFv~ek~KAlli~r~ed~d~~~ 123 (142)
T COG4747 71 VLAVEMEDVPGGLSRIAEVLGDADINLD----------YIYAFVTEKQKALLIVRVEDIDRAI 123 (142)
T ss_pred EEEEEecCCCCcHHHHHHHHhhcCcCce----------eeeeeeecCceEEEEEEhhHHHHHH
Confidence 3556678999999999999999888776 4466665552111223555554443
No 129
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=31.86 E-value=2.5e+02 Score=23.48 Aligned_cols=38 Identities=11% Similarity=0.232 Sum_probs=32.6
Q ss_pred eEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 275 TRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 275 v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
..|.+.-.++||+|.+|.-.+-.-|..|.+.++...++
T Consensus 9 ~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te~ 46 (96)
T PRK08178 9 VILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQD 46 (96)
T ss_pred EEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecCC
Confidence 45777788999999999999999999999877777654
No 130
>PRK08526 threonine dehydratase; Provisional
Probab=31.13 E-value=2.1e+02 Score=29.31 Aligned_cols=40 Identities=18% Similarity=0.276 Sum_probs=34.8
Q ss_pred cCeeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeC
Q 018897 272 NMDTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFN 311 (349)
Q Consensus 272 ~~~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~ 311 (349)
+..+.+.+.-+++||-|.++++.+-+.+.+|+........
T Consensus 324 ~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~ 363 (403)
T PRK08526 324 YRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFS 363 (403)
T ss_pred CCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEecc
Confidence 4567889999999999999999999999999988776543
No 131
>PF02344 Myc-LZ: Myc leucine zipper domain; InterPro: IPR003327 This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes. Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins is required for efficient DNA binding []. The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues every 7th position of the alpha helix. Like charge repulsion of adjacent residues in this region preturbs the formation of homodimers with heterodimers being promoted by opposing charge attractions. It has been demonstrated that in transgenic mice the balance between oncogene-induced proliferation and apoptosis in a given tissue can be a critical determinant in the initiation and maintenance of the tumor [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NKP_D 1A93_A 2A93_A.
Probab=27.15 E-value=65 Score=21.78 Aligned_cols=16 Identities=50% Similarity=0.879 Sum_probs=12.4
Q ss_pred HHHHHHHHHHHHHhHh
Q 018897 188 RRRRKRLNDRLSMLRS 203 (349)
Q Consensus 188 R~RR~kin~~~~~Lrs 203 (349)
|+||+.++.++..||.
T Consensus 14 rrr~eqLK~kLeqlrn 29 (32)
T PF02344_consen 14 RRRREQLKHKLEQLRN 29 (32)
T ss_dssp HHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHhc
Confidence 7788999999998875
No 132
>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=27.06 E-value=1.7e+02 Score=19.52 Aligned_cols=24 Identities=21% Similarity=0.508 Sum_probs=20.5
Q ss_pred CCCchHHHHHHHHHhCCCeEEEEE
Q 018897 283 GKPGLLLSTVTSLEALGLEIQQCV 306 (349)
Q Consensus 283 ~rpGLL~~Il~aLe~LgLeVv~A~ 306 (349)
+.+|.+.+++++|.+.++.|.-..
T Consensus 12 ~~~~~~~~i~~~l~~~~i~i~~i~ 35 (60)
T cd04868 12 GTPGVAAKIFSALAEAGINVDMIS 35 (60)
T ss_pred CCCCHHHHHHHHHHHCCCcEEEEE
Confidence 478999999999999999998443
No 133
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.94 E-value=85 Score=25.05 Aligned_cols=24 Identities=21% Similarity=0.308 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 018897 217 LADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
+..||+-|.-||-+|++|+++...
T Consensus 13 iqqAvdTI~LLQmEieELKEknn~ 36 (79)
T COG3074 13 VQQAIDTITLLQMEIEELKEKNNS 36 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhH
Confidence 677999999999999999986653
No 134
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=26.62 E-value=1.1e+02 Score=24.18 Aligned_cols=23 Identities=9% Similarity=0.173 Sum_probs=19.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 018897 217 LADTIDYMKELLDKISSLQQEIQ 239 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e 239 (349)
+..||+-|..||.++++|+++..
T Consensus 13 i~~aveti~~Lq~e~eeLke~n~ 35 (72)
T PF06005_consen 13 IQQAVETIALLQMENEELKEKNN 35 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999998643
No 135
>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=26.58 E-value=2.7e+02 Score=20.72 Aligned_cols=27 Identities=19% Similarity=0.380 Sum_probs=22.4
Q ss_pred CCCCchHHHHHHHHHhCCCeEEEEEEe
Q 018897 282 AGKPGLLLSTVTSLEALGLEIQQCVIS 308 (349)
Q Consensus 282 ~~rpGLL~~Il~aLe~LgLeVv~A~IS 308 (349)
.+.+|++.+++++|.+.++.|.-.+.+
T Consensus 12 ~~~~~~~~~i~~~L~~~~I~v~~i~~~ 38 (80)
T cd04921 12 VGVPGIAARIFSALARAGINVILISQA 38 (80)
T ss_pred CCCccHHHHHHHHHHHCCCcEEEEEec
Confidence 467899999999999999999755443
No 136
>PRK14627 hypothetical protein; Provisional
Probab=25.57 E-value=2.6e+02 Score=23.27 Aligned_cols=23 Identities=13% Similarity=0.359 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Q 018897 218 ADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 218 ~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
.+...-.+++|+++++++++++.
T Consensus 4 ~~~mkqaq~mQ~km~~~Q~el~~ 26 (100)
T PRK14627 4 RQLMQMAQQMQRQMQKVQEELAA 26 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 34556667788888888887753
No 137
>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=25.35 E-value=2.9e+02 Score=21.36 Aligned_cols=31 Identities=13% Similarity=0.132 Sum_probs=24.7
Q ss_pred EEEEE---cCCCCchHHHHHHHHHhCCCeEEEEE
Q 018897 276 RVEIC---CAGKPGLLLSTVTSLEALGLEIQQCV 306 (349)
Q Consensus 276 ~I~I~---C~~rpGLL~~Il~aLe~LgLeVv~A~ 306 (349)
.|.|. ....+|.+.+|+++|.+.|+.|-...
T Consensus 3 ~ItI~~~~~~~~~g~~~~IF~~La~~~I~VDmI~ 36 (75)
T cd04932 3 LVTLKSPNMLHAQGFLAKVFGILAKHNISVDLIT 36 (75)
T ss_pred EEEEecCCCCCCcCHHHHHHHHHHHcCCcEEEEe
Confidence 45553 35679999999999999999998654
No 138
>PRK14626 hypothetical protein; Provisional
Probab=25.22 E-value=2.7e+02 Score=23.65 Aligned_cols=24 Identities=17% Similarity=0.448 Sum_probs=18.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 018897 217 LADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
+.+.+.-.+++|+++++++++++.
T Consensus 7 ~~~mmkqaq~mQ~km~~~qeeL~~ 30 (110)
T PRK14626 7 LAELMKQMQSIKENVEKAKEELKK 30 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 456667778888999998888754
No 139
>COG0077 PheA Prephenate dehydratase [Amino acid transport and metabolism]
Probab=25.04 E-value=3.6e+02 Score=26.64 Aligned_cols=69 Identities=13% Similarity=0.114 Sum_probs=45.3
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC-eEEEEEeeecccCCccCCHHHHHHHHHHHhhcC
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND-FAMQASCSEGVEQRETLSCEDIKQALFRNAGYG 345 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d-~vl~a~~se~~e~~~~is~edIkqaL~~~~g~g 345 (349)
...|-+.-+++||-|.++|..|...|++...-..=.... .--+.|..+. ........+++||.+.-.++
T Consensus 194 kTsl~f~~~n~PGaL~~~L~~Fa~~gINlTkIESRP~k~~~~~Y~F~iD~---eg~~~~~~v~~AL~el~~~t 263 (279)
T COG0077 194 KTSLIFSVPNKPGALYKALGVFAKRGINLTKIESRPLKTGLGEYLFFIDI---EGHIDDPLVKEALEELKEIT 263 (279)
T ss_pred eEEEEEEcCCCCchHHHHHHHHHHcCcceeeEeecccCCCCeeEEEEEEE---ecCcCcHhHHHHHHHHHhhe
Confidence 344555557999999999999999999988665555443 2223344444 22344467888887765443
No 140
>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=24.97 E-value=3.1e+02 Score=20.75 Aligned_cols=31 Identities=19% Similarity=0.283 Sum_probs=24.4
Q ss_pred EEEEEc---CCCCchHHHHHHHHHhCCCeEEEEE
Q 018897 276 RVEICC---AGKPGLLLSTVTSLEALGLEIQQCV 306 (349)
Q Consensus 276 ~I~I~C---~~rpGLL~~Il~aLe~LgLeVv~A~ 306 (349)
.|.|.+ ...+|.+.+|+++|.+.|+.|....
T Consensus 3 ~Vsi~g~~l~~~~g~~~~if~~L~~~~I~v~~i~ 36 (75)
T cd04912 3 LLNIKSNRMLGAHGFLAKVFEIFAKHGLSVDLIS 36 (75)
T ss_pred EEEEEcCCCCCCccHHHHHHHHHHHcCCeEEEEE
Confidence 455533 5678999999999999999997543
No 141
>TIGR00103 DNA_YbaB_EbfC DNA-binding protein, YbaB/EbfC family. The function of this protein is unknown, but it has been expressed and crystallized. Its gene nearly always occurs next to recR and/or dnaX. It is restricted to Bacteria and the plant Arabidopsis. The plant form contains an additional N-terminal region that may serve as a transit peptide and shows a close relationship to the cyanobacterial member, suggesting that it is a chloroplast protein. Members of this family are found in a single copy per bacterial genome, but are broadly distributed. A member is present even in the minimal gene complement of Mycoplasm genitalium.
Probab=23.67 E-value=2.8e+02 Score=23.00 Aligned_cols=24 Identities=25% Similarity=0.488 Sum_probs=19.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 018897 217 LADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
+.+.+.-++++|+++++++++++.
T Consensus 7 ~~~m~kqaq~mQ~k~~~~q~eL~~ 30 (102)
T TIGR00103 7 LGELMKQAQQMQEKMKKLQEEIAQ 30 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 566677788888899999988754
No 142
>PRK14623 hypothetical protein; Provisional
Probab=23.43 E-value=3e+02 Score=23.32 Aligned_cols=24 Identities=13% Similarity=0.332 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 018897 217 LADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
+.+...-.+++|+++++++++++.
T Consensus 3 ~~~~mkqaqkmQ~km~~~Qeel~~ 26 (106)
T PRK14623 3 MMGMMGKLKEAQQKVEATKKRLDT 26 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 445566678888888888887754
No 143
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=22.34 E-value=4.1e+02 Score=29.65 Aligned_cols=39 Identities=18% Similarity=0.190 Sum_probs=34.5
Q ss_pred eeEEEEEcCCCCchHHHHHHHHHhCCCeEEEEEEeeeCC
Q 018897 274 DTRVEICCAGKPGLLLSTVTSLEALGLEIQQCVISCFND 312 (349)
Q Consensus 274 ~v~I~I~C~~rpGLL~~Il~aLe~LgLeVv~A~ISt~~d 312 (349)
.+.|.|...+++|+|.+|+++|-+.+..|...+..+..+
T Consensus 627 ~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~ 665 (701)
T COG0317 627 PVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKD 665 (701)
T ss_pred EEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCC
Confidence 467888889999999999999999999999888888643
No 144
>PRK14625 hypothetical protein; Provisional
Probab=22.23 E-value=3.1e+02 Score=23.29 Aligned_cols=24 Identities=13% Similarity=0.271 Sum_probs=17.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 018897 217 LADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
+.+.+.-.+++|+++++++++++.
T Consensus 4 m~~mmkqaq~mQ~km~~~Q~el~~ 27 (109)
T PRK14625 4 LGGLMKQAQAMQQKLADAQARLAE 27 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 455667778888888888887754
No 145
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=22.20 E-value=4.2e+02 Score=23.64 Aligned_cols=61 Identities=16% Similarity=0.094 Sum_probs=43.5
Q ss_pred hHHHHHHHHHhCCCeEEEEEEe-----------eeCCeEEEEEeeeccc-CCccCCHHHHHHHHHHHhhcCCC
Q 018897 287 LLLSTVTSLEALGLEIQQCVIS-----------CFNDFAMQASCSEGVE-QRETLSCEDIKQALFRNAGYGGK 347 (349)
Q Consensus 287 LL~~Il~aLe~LgLeVv~A~IS-----------t~~d~vl~a~~se~~e-~~~~is~edIkqaL~~~~g~gg~ 347 (349)
-=-+++..|++.|+-|+.+--| ..++.++.++.++... +.--++.++|.+-+.=+-.+||.
T Consensus 9 ~EReLv~~L~e~GfAvvR~paSG~sk~p~pDivA~~g~~~l~iE~K~~~~~kiYl~~e~ve~L~~FA~~fGg~ 81 (137)
T COG1591 9 FERELVRILWERGFAVVRAPASGGSKRPLPDIVAGNGGVYLAIEVKSRRETKIYLDKEQVEKLVEFARRFGGE 81 (137)
T ss_pred HHHHHHHHHHhcCceEEEcccCCCCCCCCCCEEecCCCEEEEEEEEeccCCcEEEcHHHHHHHHHHHHHcCCc
Confidence 4457889999999999987212 2234556666666643 34557999999988888888885
No 146
>PF09849 DUF2076: Uncharacterized protein conserved in bacteria (DUF2076); InterPro: IPR018648 This family of hypothetical prokaryotic proteins has no known function but includes putative perimplasmic ligand-binding sensor proteins.
Probab=22.19 E-value=2.3e+02 Score=27.52 Aligned_cols=26 Identities=19% Similarity=0.413 Sum_probs=17.8
Q ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 018897 213 RTSILADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 213 KaSIL~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
.+.||.++ =||.|++||++||.++..
T Consensus 48 Q~vlvQE~--AL~~a~~ri~eLe~ql~q 73 (247)
T PF09849_consen 48 QTVLVQEQ--ALKQAQARIQELEAQLQQ 73 (247)
T ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHh
Confidence 44444443 268899999999998743
No 147
>PRK03762 hypothetical protein; Provisional
Probab=21.86 E-value=3.2e+02 Score=22.95 Aligned_cols=24 Identities=13% Similarity=0.253 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 018897 217 LADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
++.-..-.+++|+++++++++++.
T Consensus 7 ~~~m~kqaqkmQ~km~~~Q~el~~ 30 (103)
T PRK03762 7 FSKLGEMLEQMQKKAKQLEEENAN 30 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344455678889999988887754
No 148
>COG1076 DjlA DnaJ-domain-containing proteins 1 [Posttranslational modification, protein turnover, chaperones]
Probab=21.58 E-value=78 Score=28.49 Aligned_cols=57 Identities=9% Similarity=0.190 Sum_probs=44.5
Q ss_pred cchHHHHHHHHHHHHHHHHhHhcCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHH
Q 018897 182 KNLMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQ 239 (349)
Q Consensus 182 ~h~~aER~RR~kin~~~~~LrslvP~~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e 239 (349)
....-++..+..+......++.++-.. ..|+++.++.=.+||+.|+++++++++.++
T Consensus 115 ~l~~l~~~~~~~~~~i~~~~r~l~~e~-~~d~a~~~~~~~e~~~~~~~~~~~i~~a~~ 171 (174)
T COG1076 115 ALKVLGVEIKADQDAIKKAYRKLLSEQ-HPDKAAAKGLKLEFIEKLKEKLQEIQEAYE 171 (174)
T ss_pred HHHHhcCchhhhHHHHHHHHHHHHHhc-CHHHHHHhcCCHHHHHHHHHHHHHHHHHHH
Confidence 344455556667777777788877544 489999999999999999999999998765
No 149
>PF02185 HR1: Hr1 repeat; InterPro: IPR000861 The HR1 repeat was first described as a three times repeated homology region of the N-terminal non-catalytic part of protein kinase PRK1(PKN) []. The first two of these repeats were later shown to bind the small G protein rho [, ] known to activate PKN in its GTP-bound form. Similar rho-binding domains also occur in a number of other protein kinases and in the rho-binding proteins rhophilin and rhotekin. Recently, the structure of the N-terminal HR1 repeat complexed with RhoA has been determined by X-ray crystallography []. It forms an antiparallel coiled-coil fold termed an ACC finger. This entry includes domains found within rho-associated protein kinases.; GO: 0007165 signal transduction, 0005622 intracellular; PDB: 1CXZ_B 3O0Z_C 2RMK_B 1URF_A.
Probab=21.51 E-value=3.7e+02 Score=20.36 Aligned_cols=50 Identities=16% Similarity=0.276 Sum_probs=29.3
Q ss_pred hHHHHHHHHHHHHHHHHhHhcCCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897 184 LMAERRRRKRLNDRLSMLRSIVPKISKMDRTSILADTIDYMKELLDKISSLQQEIQAG 241 (349)
Q Consensus 184 ~~aER~RR~kin~~~~~LrslvP~~~K~dKaSIL~~AI~YIk~Lq~~v~~L~~~~e~~ 241 (349)
+..|++=|......+..| ..|+..++.+|-.-+.+...+|+.|+.+++..
T Consensus 10 i~~E~ki~~Gae~m~~~~--------~t~~~~~~~~~~~~l~~s~~kI~~L~~~L~~l 59 (70)
T PF02185_consen 10 IDKELKIKEGAENMLQAY--------STDKKKVLSEAESQLRESNQKIELLREQLEKL 59 (70)
T ss_dssp HHHHHHHHHHHHHHHHHH--------CCHHCH-HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHH--------ccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555455554444444 34555577777777777777777777766543
No 150
>COG0013 AlaS Alanyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=20.95 E-value=1.3e+03 Score=26.59 Aligned_cols=58 Identities=9% Similarity=0.021 Sum_probs=33.3
Q ss_pred CCCchHHHHHHHHHhC-CCeEEEEEEeeeCCeEEEEEeeecccCCccCCHHHHHHHHHHHh
Q 018897 283 GKPGLLLSTVTSLEAL-GLEIQQCVISCFNDFAMQASCSEGVEQRETLSCEDIKQALFRNA 342 (349)
Q Consensus 283 ~rpGLL~~Il~aLe~L-gLeVv~A~ISt~~d~vl~a~~se~~e~~~~is~edIkqaL~~~~ 342 (349)
..++-|..++..|... +-.|+ +.++..++.+..+..+-.. -...+.+.+|...|...+
T Consensus 785 ~d~~~Lr~~a~~lk~k~~~~vi-vl~~~~~~Kv~~~~~v~~~-~~~~~~a~~lvk~la~~~ 843 (879)
T COG0013 785 ADMKELREIADDLKKKLGSAVI-VLASVADGKVSLVVAVSKD-LTDKVKAGELVKELAAIV 843 (879)
T ss_pred CCHHHHHHHHHHHHhhcCCcEE-EEEEecCCeEEEEEEechh-hhcccCHHHHHHHHHHhc
Confidence 3456778888888663 33333 4555555433333222221 122388999999888877
No 151
>PF11619 P53_C: Transcription factor P53 - C terminal domain; InterPro: IPR024631 The p53 tumour suppressor [, , , , ] is a protein found in increased amounts in a wide variety of transformed cells. It is also detectable in many proliferating non-transformed cells, but it is undetectable or present at low levels in resting cells. It is frequently mutated or inactivated in many types of cancer. p53 seems to act as a tumour suppressor in some, but probably not all, tumour types. p53 has been implicated in cell cycle regulation, particularly in the monitoring of genomic DNA integrity prior to replication; for this reason it has been dubbed `guardian of the genome'. p53 is a sequence-specific DNA-binding protein and transcription factor. The structure of p53 comprises 4 domains: an N-terminal transactivation domain; a central DNA-binding domain; an oligomerisation domain; and a C-terminal, basic, regulatory domain [, ]. The structure of the oligomerisation domain consists of a dimer of dimers, each dimer consisting of 2 anti-parallel alpha-helices and an anti-parallel beta-sheet. The sheets lie on opposite sides of the tetramer and the helices form an unusual 4-helix bundle [, ]. While the majority of p53 mutations found in human cancers are located in the DNA-binding domain, some are also found in the oligomerisation domain. This entry represents the C-terminal domain of Drosophila transcription factor p53. While the rest of the protein is quite conserved between the different transcription factors such as p53 and p73, the C-terminal domain is highly divergent. The Drosophila p53 structure is characterised by an additional N-terminal beta-strand and a C-terminal helix [].; PDB: 2RP4_B.
Probab=20.89 E-value=1.3e+02 Score=23.66 Aligned_cols=33 Identities=33% Similarity=0.448 Sum_probs=24.7
Q ss_pred ceeeeee-cCeeEEEEEcCCCCchHHHHHHHHHh
Q 018897 265 KFDVERT-NMDTRVEICCAGKPGLLLSTVTSLEA 297 (349)
Q Consensus 265 ~VeV~~~-~~~v~I~I~C~~rpGLL~~Il~aLe~ 297 (349)
.-+|.+. +++.++.|.|+++.-||-+|=-.+++
T Consensus 6 dW~Vsrt~dGdYrL~itcp~Ke~LlqSIEgmi~~ 39 (71)
T PF11619_consen 6 DWEVSRTLDGDYRLVITCPKKEWLLQSIEGMIKE 39 (71)
T ss_dssp S-EEEEETTTCEEEEEEESSHHHHHHHHHHHHHH
T ss_pred cceeeeccCCceEEEEecCcHHHHHHHHHHHHHH
Confidence 3567765 67899999999998888777665554
No 152
>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=20.43 E-value=3.2e+02 Score=19.27 Aligned_cols=31 Identities=13% Similarity=0.214 Sum_probs=23.9
Q ss_pred EEEEc---CCCCchHHHHHHHHHhCCCeEEEEEE
Q 018897 277 VEICC---AGKPGLLLSTVTSLEALGLEIQQCVI 307 (349)
Q Consensus 277 I~I~C---~~rpGLL~~Il~aLe~LgLeVv~A~I 307 (349)
|.|.+ .+.++++.+++.+|.+.|++|.-.+.
T Consensus 4 isivg~~~~~~~~~~~~i~~~L~~~~i~v~~i~~ 37 (66)
T cd04916 4 IMVVGEGMKNTVGVSARATAALAKAGINIRMINQ 37 (66)
T ss_pred EEEEcCCCCCCccHHHHHHHHHHHCCCCEEEEEe
Confidence 44444 35789999999999999999974443
No 153
>PRK00153 hypothetical protein; Validated
Probab=20.42 E-value=3.6e+02 Score=22.20 Aligned_cols=25 Identities=12% Similarity=0.360 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhC
Q 018897 217 LADTIDYMKELLDKISSLQQEIQAG 241 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e~~ 241 (349)
+.+-+.-++++|+++++++++++..
T Consensus 5 ~~~m~~qaq~~q~~~~~~q~~l~~~ 29 (104)
T PRK00153 5 MQNLMKQAQQMQEKMQKMQEELAQM 29 (104)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4556677888888998888877543
No 154
>PRK14622 hypothetical protein; Provisional
Probab=20.29 E-value=3.6e+02 Score=22.57 Aligned_cols=23 Identities=9% Similarity=0.203 Sum_probs=15.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 018897 217 LADTIDYMKELLDKISSLQQEIQ 239 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e 239 (349)
+.+...-.+++|++.++++++++
T Consensus 3 ~~~lmkqaq~mQ~~m~~~q~el~ 25 (103)
T PRK14622 3 IQYLMRQAKKLEKAMADAKEKLA 25 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 34455666777888887777765
No 155
>PRK14621 hypothetical protein; Provisional
Probab=20.25 E-value=3.6e+02 Score=22.94 Aligned_cols=24 Identities=17% Similarity=0.430 Sum_probs=17.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Q 018897 217 LADTIDYMKELLDKISSLQQEIQA 240 (349)
Q Consensus 217 L~~AI~YIk~Lq~~v~~L~~~~e~ 240 (349)
+.+.+.-.+++|+++++++++++.
T Consensus 6 m~~mmkqaq~mQ~km~~~Q~eL~~ 29 (111)
T PRK14621 6 LGDMMKQIQQAGEKMQDVQKQLEK 29 (111)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHc
Confidence 455667778888888888887753
No 156
>PLN02705 beta-amylase
Probab=20.02 E-value=1.2e+02 Score=33.32 Aligned_cols=31 Identities=19% Similarity=0.235 Sum_probs=21.4
Q ss_pred CCCCCccchHHHHHHH---HHHHHHHHHhHhcCC
Q 018897 176 LGGQPSKNLMAERRRR---KRLNDRLSMLRSIVP 206 (349)
Q Consensus 176 ~~~~~~~h~~aER~RR---~kin~~~~~LrslvP 206 (349)
+...|.+....||+|| .||-..++.++.+-+
T Consensus 81 ~~~e~e~~~~rer~rrai~~ki~aglr~~g~~~l 114 (681)
T PLN02705 81 REKEKERTKLRERHRRAITSRMLAGLRQYGNFPL 114 (681)
T ss_pred chhhhhhhHHHHHHHHHHHHHHHHHHHhccCCCC
Confidence 4457888899999999 566555555555433
Done!