Query 047004
Match_columns 497
No_of_seqs 252 out of 1254
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 06:38:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047004.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047004hhsearch_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 99.2 6.1E-12 1.3E-16 97.4 4.6 52 308-359 5-59 (60)
2 smart00353 HLH helix loop heli 99.2 2E-11 4.3E-16 92.9 5.7 49 312-360 1-52 (53)
3 PF00010 HLH: Helix-loop-helix 99.2 1.1E-11 2.4E-16 95.6 4.0 48 309-356 3-55 (55)
4 KOG1318 Helix loop helix trans 98.9 1.4E-09 3E-14 114.6 6.7 61 301-361 227-291 (411)
5 KOG1319 bHLHZip transcription 98.6 6.4E-08 1.4E-12 92.6 4.8 64 307-370 62-132 (229)
6 cd04927 ACT_ACR-like_2 Second 98.4 1.2E-06 2.6E-11 72.2 8.9 72 424-497 1-76 (76)
7 KOG4304 Transcriptional repres 98.3 4.3E-07 9.2E-12 91.0 2.9 52 309-360 34-93 (250)
8 cd04895 ACT_ACR_1 ACT domain-c 98.3 7.5E-06 1.6E-10 67.7 9.5 63 425-488 3-69 (72)
9 cd04897 ACT_ACR_3 ACT domain-c 98.2 1.3E-05 2.8E-10 66.9 9.3 66 425-491 3-72 (75)
10 cd04896 ACT_ACR-like_3 ACT dom 98.1 2.3E-05 4.9E-10 65.4 9.6 65 425-491 2-72 (75)
11 cd04900 ACT_UUR-like_1 ACT dom 98.1 4.2E-05 9.1E-10 62.0 10.2 65 424-489 2-71 (73)
12 KOG3561 Aryl-hydrocarbon recep 98.1 3.2E-06 6.9E-11 95.9 4.6 51 308-358 21-75 (803)
13 KOG2588 Predicted DNA-binding 97.9 3.4E-06 7.3E-11 96.2 2.2 64 307-370 276-340 (953)
14 KOG2483 Upstream transcription 97.9 1.9E-05 4.2E-10 78.5 7.1 57 305-361 57-116 (232)
15 cd04925 ACT_ACR_2 ACT domain-c 97.8 0.00018 3.9E-09 58.8 9.8 66 425-490 2-71 (74)
16 KOG3960 Myogenic helix-loop-he 97.7 6.8E-05 1.5E-09 75.0 5.9 59 309-367 120-180 (284)
17 cd04926 ACT_ACR_4 C-terminal 97.6 0.00068 1.5E-08 55.0 9.4 66 425-492 3-68 (72)
18 cd04899 ACT_ACR-UUR-like_2 C-t 97.4 0.002 4.2E-08 50.7 9.8 64 425-489 2-68 (70)
19 KOG0561 bHLH transcription fac 97.4 0.00013 2.7E-09 74.8 3.4 51 309-359 62-114 (373)
20 cd04928 ACT_TyrKc Uncharacteri 97.3 0.0019 4.1E-08 53.1 9.4 63 425-490 3-66 (68)
21 PRK05007 PII uridylyl-transfer 97.1 0.0025 5.3E-08 74.2 10.6 68 423-491 808-878 (884)
22 PLN03217 transcription factor 97.0 0.001 2.2E-08 56.9 4.7 52 319-370 19-76 (93)
23 KOG4029 Transcription factor H 97.0 0.00078 1.7E-08 66.3 4.4 59 306-364 108-170 (228)
24 PRK04374 PII uridylyl-transfer 96.9 0.0073 1.6E-07 70.3 12.1 80 411-491 783-866 (869)
25 PF13740 ACT_6: ACT domain; PD 96.9 0.0065 1.4E-07 49.8 8.3 70 423-496 2-71 (76)
26 PF01842 ACT: ACT domain; Int 96.8 0.017 3.6E-07 44.3 9.5 63 425-492 2-66 (66)
27 PRK00275 glnD PII uridylyl-tra 96.8 0.0094 2E-07 69.6 11.7 80 411-491 801-885 (895)
28 PRK01759 glnD PII uridylyl-tra 96.7 0.008 1.7E-07 69.8 10.4 68 423-491 783-853 (854)
29 PRK03059 PII uridylyl-transfer 96.7 0.009 2E-07 69.4 10.6 80 412-491 774-854 (856)
30 cd04873 ACT_UUR-ACR-like ACT d 96.6 0.025 5.4E-07 43.9 9.3 47 425-471 2-48 (70)
31 cd04893 ACT_GcvR_1 ACT domains 96.5 0.024 5.3E-07 46.6 9.5 65 424-492 2-66 (77)
32 PRK05092 PII uridylyl-transfer 96.4 0.024 5.1E-07 66.4 12.1 79 412-491 831-914 (931)
33 PRK03381 PII uridylyl-transfer 96.4 0.025 5.5E-07 65.1 11.9 79 412-491 588-666 (774)
34 PRK03381 PII uridylyl-transfer 96.2 0.034 7.4E-07 64.0 11.6 76 412-488 695-773 (774)
35 TIGR01693 UTase_glnD [Protein- 96.0 0.039 8.4E-07 64.0 11.0 68 423-491 779-849 (850)
36 cd04875 ACT_F4HF-DF N-terminal 96.0 0.055 1.2E-06 43.6 8.8 67 426-492 2-68 (74)
37 PRK00194 hypothetical protein; 95.8 0.05 1.1E-06 45.4 8.0 71 423-495 3-73 (90)
38 TIGR01693 UTase_glnD [Protein- 95.8 0.065 1.4E-06 62.2 11.4 69 422-491 667-740 (850)
39 PRK01759 glnD PII uridylyl-tra 95.6 0.1 2.2E-06 60.8 12.1 79 412-491 665-748 (854)
40 KOG3910 Helix loop helix trans 95.5 0.014 3E-07 63.5 4.4 58 304-361 523-584 (632)
41 PF13291 ACT_4: ACT domain; PD 95.5 0.21 4.6E-06 40.6 10.4 67 423-495 6-74 (80)
42 cd04869 ACT_GcvR_2 ACT domains 95.5 0.14 3E-06 41.4 9.2 64 426-492 2-71 (81)
43 cd04894 ACT_ACR-like_1 ACT dom 95.5 0.071 1.5E-06 43.7 7.2 66 425-490 2-67 (69)
44 cd04872 ACT_1ZPV ACT domain pr 95.4 0.08 1.7E-06 44.2 7.9 68 424-493 2-69 (88)
45 PRK05007 PII uridylyl-transfer 95.4 0.14 3E-06 60.0 12.4 79 412-491 689-772 (884)
46 cd04870 ACT_PSP_1 CT domains f 95.4 0.11 2.4E-06 42.1 8.4 67 426-495 2-68 (75)
47 COG2844 GlnD UTP:GlnB (protein 95.2 0.077 1.7E-06 61.1 9.1 70 411-481 778-848 (867)
48 PRK04374 PII uridylyl-transfer 94.8 0.19 4.1E-06 58.8 11.2 70 422-491 689-759 (869)
49 PRK05092 PII uridylyl-transfer 94.7 0.24 5.2E-06 58.3 11.9 80 411-491 719-804 (931)
50 PRK00275 glnD PII uridylyl-tra 94.7 0.25 5.3E-06 58.1 11.8 69 422-491 703-777 (895)
51 PRK03059 PII uridylyl-transfer 94.3 0.33 7.2E-06 56.8 11.7 69 422-491 677-749 (856)
52 cd04887 ACT_MalLac-Enz ACT_Mal 93.7 0.98 2.1E-05 35.7 9.9 62 426-490 2-64 (74)
53 cd04886 ACT_ThrD-II-like C-ter 93.2 0.58 1.3E-05 35.8 7.6 60 426-488 1-65 (73)
54 cd04876 ACT_RelA-SpoT ACT dom 93.0 0.47 1E-05 34.7 6.7 66 426-494 1-67 (71)
55 cd04888 ACT_PheB-BS C-terminal 92.7 0.57 1.2E-05 37.1 7.2 67 425-493 2-69 (76)
56 cd04881 ACT_HSDH-Hom ACT_HSDH_ 92.6 1.1 2.3E-05 34.8 8.5 46 425-470 2-49 (79)
57 cd04874 ACT_Af1403 N-terminal 91.7 1.4 3E-05 33.7 8.2 63 425-492 2-65 (72)
58 KOG4447 Transcription factor T 91.7 0.1 2.2E-06 49.4 2.0 49 309-357 80-130 (173)
59 PRK04435 hypothetical protein; 91.2 1.2 2.7E-05 41.3 8.6 71 420-492 66-137 (147)
60 cd02116 ACT ACT domains are co 91.1 1.5 3.2E-05 30.2 7.1 35 426-460 1-35 (60)
61 KOG3560 Aryl-hydrocarbon recep 90.1 0.25 5.5E-06 54.8 3.4 45 310-354 28-76 (712)
62 cd04878 ACT_AHAS N-terminal AC 89.7 1.9 4.2E-05 32.7 7.3 65 425-493 2-68 (72)
63 PRK06027 purU formyltetrahydro 89.6 2.3 4.9E-05 43.8 9.7 68 423-492 6-75 (286)
64 cd04882 ACT_Bt0572_2 C-termina 89.4 1.8 3.9E-05 33.0 6.8 59 426-493 2-62 (65)
65 cd04879 ACT_3PGDH-like ACT_3PG 89.2 2.6 5.7E-05 31.8 7.7 62 426-493 2-65 (71)
66 cd04877 ACT_TyrR N-terminal AC 89.2 3.6 7.8E-05 33.1 8.8 62 425-492 2-63 (74)
67 cd04903 ACT_LSD C-terminal ACT 89.1 2.2 4.8E-05 32.4 7.2 61 426-492 2-64 (71)
68 KOG3558 Hypoxia-inducible fact 88.9 0.24 5.3E-06 56.2 2.3 44 313-356 52-99 (768)
69 cd04883 ACT_AcuB C-terminal AC 88.7 4.7 0.0001 31.5 9.0 62 425-493 3-66 (72)
70 TIGR00655 PurU formyltetrahydr 88.1 2.9 6.4E-05 42.9 9.3 65 425-491 2-69 (280)
71 cd04908 ACT_Bt0572_1 N-termina 87.5 4.9 0.00011 31.6 8.4 60 425-493 3-62 (66)
72 PRK13011 formyltetrahydrofolat 87.4 3.7 7.9E-05 42.3 9.6 69 423-492 7-75 (286)
73 cd04909 ACT_PDH-BS C-terminal 87.3 4 8.7E-05 31.9 7.7 63 425-493 3-67 (69)
74 cd04880 ACT_AAAH-PDT-like ACT 86.8 5.7 0.00012 31.8 8.5 63 427-489 3-66 (75)
75 PRK13010 purU formyltetrahydro 86.7 2.9 6.4E-05 43.1 8.4 68 424-492 10-79 (289)
76 PRK11589 gcvR glycine cleavage 86.6 1.9 4.1E-05 42.0 6.6 65 423-491 8-72 (190)
77 PRK08577 hypothetical protein; 86.5 5.4 0.00012 36.2 9.1 69 422-492 55-125 (136)
78 KOG3898 Transcription factor N 85.8 0.46 9.9E-06 48.2 2.0 51 307-357 72-125 (254)
79 cd04884 ACT_CBS C-terminal ACT 85.5 5.4 0.00012 31.7 7.7 62 426-490 2-66 (72)
80 cd04905 ACT_CM-PDT C-terminal 84.5 9.3 0.0002 31.1 8.9 61 426-489 4-65 (80)
81 KOG3559 Transcriptional regula 83.6 1.1 2.4E-05 48.4 3.7 43 313-355 7-53 (598)
82 cd04889 ACT_PDH-BS-like C-term 83.5 4.7 0.0001 30.4 6.3 45 426-470 1-46 (56)
83 PRK07334 threonine dehydratase 82.6 6.6 0.00014 41.9 9.2 51 421-471 324-379 (403)
84 COG2844 GlnD UTP:GlnB (protein 81.3 7 0.00015 45.8 9.2 56 423-479 684-740 (867)
85 cd04902 ACT_3PGDH-xct C-termin 81.3 6.3 0.00014 30.7 6.4 62 427-494 3-66 (73)
86 KOG4395 Transcription factor A 78.9 2.7 5.9E-05 42.9 4.4 52 309-360 176-230 (285)
87 cd04901 ACT_3PGDH C-terminal A 78.6 1.8 4E-05 33.5 2.5 62 426-493 2-63 (69)
88 PRK10872 relA (p)ppGpp synthet 72.8 36 0.00078 39.9 11.8 77 413-492 652-734 (743)
89 PRK11092 bifunctional (p)ppGpp 70.5 50 0.0011 38.4 12.3 59 413-471 612-675 (702)
90 COG3830 ACT domain-containing 70.1 7.6 0.00016 34.0 4.4 67 424-492 4-70 (90)
91 cd04931 ACT_PAH ACT domain of 69.8 32 0.0007 29.6 8.2 47 424-470 15-62 (90)
92 cd04904 ACT_AAAH ACT domain of 69.3 26 0.00057 28.5 7.2 58 428-490 5-63 (74)
93 TIGR00691 spoT_relA (p)ppGpp s 68.7 49 0.0011 38.3 11.8 59 413-471 596-659 (683)
94 COG0788 PurU Formyltetrahydrof 66.4 27 0.00057 36.4 8.1 68 423-492 7-76 (287)
95 PRK06382 threonine dehydratase 65.3 27 0.00058 37.4 8.4 71 420-494 327-402 (406)
96 PF05088 Bac_GDH: Bacterial NA 62.4 38 0.00082 42.7 9.8 69 422-491 488-561 (1528)
97 cd04885 ACT_ThrD-I Tandem C-te 61.9 50 0.0011 26.1 7.4 62 427-493 2-64 (68)
98 TIGR00119 acolac_sm acetolacta 59.8 44 0.00096 31.7 7.8 63 425-491 3-67 (157)
99 TIGR01127 ilvA_1Cterm threonin 58.9 52 0.0011 34.6 9.0 67 420-489 302-373 (380)
100 PRK11589 gcvR glycine cleavage 58.5 54 0.0012 32.0 8.4 68 424-492 96-167 (190)
101 KOG3582 Mlx interactors and re 56.4 4.3 9.3E-05 46.6 0.5 65 306-370 650-719 (856)
102 PRK00227 glnD PII uridylyl-tra 54.4 61 0.0013 37.7 9.2 65 425-491 548-613 (693)
103 PRK11895 ilvH acetolactate syn 54.3 61 0.0013 31.0 7.8 62 425-490 4-67 (161)
104 PRK08526 threonine dehydratase 53.5 70 0.0015 34.5 9.1 71 420-494 323-398 (403)
105 PRK08198 threonine dehydratase 52.0 80 0.0017 33.6 9.1 70 420-493 324-398 (404)
106 CHL00100 ilvH acetohydroxyacid 49.4 87 0.0019 30.3 8.1 64 425-492 4-69 (174)
107 cd04929 ACT_TPH ACT domain of 47.6 1E+02 0.0022 25.5 7.2 55 431-490 8-63 (74)
108 COG4747 ACT domain-containing 44.9 1.1E+02 0.0025 28.5 7.6 38 425-462 5-42 (142)
109 PF02120 Flg_hook: Flagellar h 44.0 97 0.0021 25.2 6.6 46 412-458 27-78 (85)
110 KOG3582 Mlx interactors and re 44.0 9.4 0.0002 44.0 0.7 66 302-370 782-852 (856)
111 COG4492 PheB ACT domain-contai 43.6 1.2E+02 0.0025 28.8 7.6 69 420-490 69-138 (150)
112 cd04906 ACT_ThrD-I_1 First of 42.3 2E+02 0.0043 23.9 8.3 65 425-494 3-68 (85)
113 KOG4447 Transcription factor T 40.6 21 0.00045 34.3 2.3 42 314-355 29-72 (173)
114 PRK06737 acetolactate synthase 40.0 1.2E+02 0.0026 25.6 6.5 62 425-490 4-67 (76)
115 cd04892 ACT_AK-like_2 ACT doma 39.1 1E+02 0.0023 22.4 5.6 34 425-458 2-38 (65)
116 COG3074 Uncharacterized protei 38.1 40 0.00087 28.5 3.3 26 345-370 13-38 (79)
117 PF13710 ACT_5: ACT domain; PD 37.4 1.5E+02 0.0032 23.6 6.5 55 432-490 1-57 (63)
118 PRK13562 acetolactate synthase 36.7 1.2E+02 0.0027 26.2 6.2 63 425-490 4-68 (84)
119 PRK11152 ilvM acetolactate syn 36.2 2.4E+02 0.0053 23.7 7.8 62 425-491 5-68 (76)
120 cd04890 ACT_AK-like_1 ACT doma 32.9 62 0.0013 24.7 3.6 25 432-456 12-36 (62)
121 cd04868 ACT_AK-like ACT domain 32.7 1.8E+02 0.0039 20.6 5.9 25 433-457 13-37 (60)
122 PF06005 DUF904: Protein of un 30.8 53 0.0012 27.4 3.0 24 345-368 13-36 (72)
123 cd04930 ACT_TH ACT domain of t 28.6 2.2E+02 0.0048 25.6 6.8 43 428-470 46-89 (115)
124 PF02344 Myc-LZ: Myc leucine z 28.3 58 0.0013 23.5 2.4 17 315-331 13-29 (32)
125 PRK15385 magnesium transport p 28.3 2.9E+02 0.0064 27.9 8.3 67 423-492 142-214 (225)
126 PRK08639 threonine dehydratase 27.0 2.8E+02 0.0061 29.9 8.5 70 420-493 333-404 (420)
127 smart00338 BRLZ basic region l 26.2 2E+02 0.0042 22.8 5.4 21 349-369 25-45 (65)
128 cd04922 ACT_AKi-HSDH-ThrA_2 AC 26.1 2.8E+02 0.0062 20.8 6.3 33 425-457 3-38 (66)
129 COG2716 GcvR Glycine cleavage 25.6 66 0.0014 31.4 3.1 70 423-496 5-74 (176)
130 COG0317 SpoT Guanosine polypho 25.4 4.2E+02 0.0091 31.2 9.8 59 412-470 612-675 (701)
131 PRK11899 prephenate dehydratas 25.3 4.3E+02 0.0094 27.3 9.1 62 426-490 197-259 (279)
132 PF14689 SPOB_a: Sensor_kinase 24.8 2.1E+02 0.0045 22.8 5.3 40 316-362 17-56 (62)
133 PRK13702 replication protein; 24.3 1.7E+02 0.0037 25.5 5.0 27 309-335 22-50 (85)
134 PRK15422 septal ring assembly 24.2 84 0.0018 27.0 3.1 26 345-370 13-38 (79)
135 PF02185 HR1: Hr1 repeat; Int 23.7 2E+02 0.0042 23.2 5.1 52 311-370 9-60 (70)
136 PRK00227 glnD PII uridylyl-tra 23.6 1.1E+02 0.0024 35.6 4.9 43 424-470 632-674 (693)
137 PF09849 DUF2076: Uncharacteri 22.8 1.7E+02 0.0037 29.9 5.6 17 352-368 57-73 (247)
138 COG1591 Holliday junction reso 22.6 3.7E+02 0.0079 25.5 7.2 63 433-495 6-80 (137)
139 KOG2057 Predicted equilibrativ 22.3 1.4E+02 0.003 32.2 4.8 72 125-197 376-451 (499)
140 cd04937 ACT_AKi-DapG-BS_2 ACT 22.1 2.1E+02 0.0045 22.2 4.9 28 426-453 4-34 (64)
141 PF07106 TBPIP: Tat binding pr 22.0 2.4E+02 0.0052 26.4 6.1 45 317-371 93-137 (169)
142 PRK10820 DNA-binding transcrip 21.6 1.1E+02 0.0024 33.9 4.3 36 425-460 2-37 (520)
143 TIGR02079 THD1 threonine dehyd 21.2 4.5E+02 0.0097 28.4 8.7 70 420-493 322-393 (409)
144 PF14197 Cep57_CLD_2: Centroso 20.8 1.2E+02 0.0026 25.2 3.3 28 343-370 40-67 (69)
145 TIGR00986 3a0801s05tom22 mitoc 20.6 99 0.0022 29.4 3.1 36 320-355 49-84 (145)
146 PRK14626 hypothetical protein; 20.6 4.4E+02 0.0095 23.7 7.1 26 345-370 7-32 (110)
147 TIGR01124 ilvA_2Cterm threonin 20.2 5.1E+02 0.011 28.9 9.1 70 419-493 321-390 (499)
148 PRK14623 hypothetical protein; 20.2 4.5E+02 0.0097 23.6 7.0 26 345-370 3-28 (106)
149 PRK12483 threonine dehydratase 20.1 5.8E+02 0.013 28.8 9.5 68 420-493 342-411 (521)
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=99.25 E-value=6.1e-12 Score=97.39 Aligned_cols=52 Identities=37% Similarity=0.671 Sum_probs=49.1
Q ss_pred CccccHHHHHHHHHHHHHHHHHHhcCCCC---CcCCccchHHHHHHHHHHHHHHH
Q 047004 308 PAKNLMAERRRRKKLNDRLYMLRSVVPKI---SKMDRASILGDAIEYLKELLQRI 359 (497)
Q Consensus 308 ~~~H~~~ERrRR~kin~~~~~LrsLVP~~---~K~dKasIL~eAI~YIk~Lq~~v 359 (497)
+..|+..||+||++||+.|..|+++||.. .|++|++||..||+||+.|+.++
T Consensus 5 r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~ 59 (60)
T cd00083 5 REAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL 59 (60)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 46799999999999999999999999987 89999999999999999999875
No 2
>smart00353 HLH helix loop helix domain.
Probab=99.21 E-value=2e-11 Score=92.89 Aligned_cols=49 Identities=43% Similarity=0.655 Sum_probs=45.5
Q ss_pred cHHHHHHHHHHHHHHHHHHhcCCC---CCcCCccchHHHHHHHHHHHHHHHH
Q 047004 312 LMAERRRRKKLNDRLYMLRSVVPK---ISKMDRASILGDAIEYLKELLQRIN 360 (497)
Q Consensus 312 ~~~ERrRR~kin~~~~~LrsLVP~---~~K~dKasIL~eAI~YIk~Lq~~v~ 360 (497)
+..||+||++||+.|..|+++||. ..|++|++||.+||+||++|+.+++
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 468999999999999999999994 6799999999999999999999875
No 3
>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=99.21 E-value=1.1e-11 Score=95.60 Aligned_cols=48 Identities=44% Similarity=0.679 Sum_probs=45.5
Q ss_pred ccccHHHHHHHHHHHHHHHHHHhcCCCC-----CcCCccchHHHHHHHHHHHH
Q 047004 309 AKNLMAERRRRKKLNDRLYMLRSVVPKI-----SKMDRASILGDAIEYLKELL 356 (497)
Q Consensus 309 ~~H~~~ERrRR~kin~~~~~LrsLVP~~-----~K~dKasIL~eAI~YIk~Lq 356 (497)
..|+..||+||++||+.|..|+.+||.. .|++|++||..||+||++||
T Consensus 3 ~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 3 QKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 5799999999999999999999999976 68999999999999999997
No 4
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=98.92 E-value=1.4e-09 Score=114.64 Aligned_cols=61 Identities=30% Similarity=0.516 Sum_probs=53.3
Q ss_pred CCCCCCCCccccHHHHHHHHHHHHHHHHHHhcCCCC----CcCCccchHHHHHHHHHHHHHHHHH
Q 047004 301 KGKKKGLPAKNLMAERRRRKKLNDRLYMLRSVVPKI----SKMDRASILGDAIEYLKELLQRIND 361 (497)
Q Consensus 301 k~rk~~~~~~H~~~ERrRR~kin~~~~~LrsLVP~~----~K~dKasIL~eAI~YIk~Lq~~v~~ 361 (497)
..|.+.++..|+++|||||++||++|.+|..|||.+ .|..|..||..+++||++||+..++
T Consensus 227 ~~rdr~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~ 291 (411)
T KOG1318|consen 227 LERDRRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQR 291 (411)
T ss_pred hHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHH
Confidence 344556679999999999999999999999999987 4778999999999999999876653
No 5
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=98.55 E-value=6.4e-08 Score=92.63 Aligned_cols=64 Identities=23% Similarity=0.369 Sum_probs=56.3
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHhcCCCC-------CcCCccchHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 307 LPAKNLMAERRRRKKLNDRLYMLRSVVPKI-------SKMDRASILGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 307 ~~~~H~~~ERrRR~kin~~~~~LrsLVP~~-------~K~dKasIL~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
++..|.-+||+||+.||.-+..|+.|||.+ .|+.||.||.++|+||.+|++++.+-++|...+.
T Consensus 62 rr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~KlskA~ILqksidyi~~L~~~k~kqe~e~s~L~ 132 (229)
T KOG1319|consen 62 RRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQKLSKAIILQKTIDYIQFLHKEKKKQEEEVSTLR 132 (229)
T ss_pred HHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 348999999999999999999999999964 3888999999999999999998888777765554
No 6
>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=98.44 E-value=1.2e-06 Score=72.21 Aligned_cols=72 Identities=26% Similarity=0.385 Sum_probs=60.0
Q ss_pred EEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEeeecCCcc---cCHHHHHHHHHHhhcCCCCC
Q 047004 424 VNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISC-FNGFAMDVFRAEQCKEGQD---VHPEQIKAVLLDSAGFHGMM 497 (497)
Q Consensus 424 V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~-~ng~vl~~f~aeq~keg~~---v~~eqIk~~L~~~aG~~~~~ 497 (497)
+.|+|+|.+|+|+|.+|..+|..+||+|+.|.|++ .+|.++++|.+... ++.. -..++|+++|.+..| |.|+
T Consensus 1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V~d~-~~~~~~~~~~~~l~~~L~~~L~-~~~~ 76 (76)
T cd04927 1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFITDA-RELLHTKKRREETYDYLRAVLG-DSMI 76 (76)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEEeCC-CCCCCCHHHHHHHHHHHHHHHc-hhcC
Confidence 36899999999999999999999999999999996 89999999999532 3331 234679999999999 5553
No 7
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=98.27 E-value=4.3e-07 Score=91.01 Aligned_cols=52 Identities=27% Similarity=0.505 Sum_probs=46.0
Q ss_pred ccccHHHHHHHHHHHHHHHHHHhcCCC--------CCcCCccchHHHHHHHHHHHHHHHH
Q 047004 309 AKNLMAERRRRKKLNDRLYMLRSVVPK--------ISKMDRASILGDAIEYLKELLQRIN 360 (497)
Q Consensus 309 ~~H~~~ERrRR~kin~~~~~LrsLVP~--------~~K~dKasIL~eAI~YIk~Lq~~v~ 360 (497)
..|-+.||+||+|||+.|.+|+.|||. .+|++||.||.-|++|+++|+....
T Consensus 34 ~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~ 93 (250)
T KOG4304|consen 34 VRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQ 93 (250)
T ss_pred hcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhcccc
Confidence 455599999999999999999999994 2789999999999999999986543
No 8
>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=98.26 E-value=7.5e-06 Score=67.73 Aligned_cols=63 Identities=32% Similarity=0.494 Sum_probs=53.2
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCH----HHHHHHHH
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHP----EQIKAVLL 488 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~----eqIk~~L~ 488 (497)
.|+|.+.+|+|+|.+|.++|..+||+|..|.|++.++++.++|.+.. .+|..+.- ++|+++|.
T Consensus 3 viev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV~d-~~g~kl~d~~~~~~l~~~L~ 69 (72)
T cd04895 3 LVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHVTD-QLGNKLTDDSLIAYIEKSLG 69 (72)
T ss_pred EEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEEEC-CCCCCCCCHHHHHHHHHHhc
Confidence 58999999999999999999999999999999999999999999964 35665543 45555553
No 9
>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=98.17 E-value=1.3e-05 Score=66.87 Aligned_cols=66 Identities=17% Similarity=0.284 Sum_probs=56.4
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccC----HHHHHHHHHHhh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVH----PEQIKAVLLDSA 491 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~----~eqIk~~L~~~a 491 (497)
+|+|.|.+|||+|.+|.++|-.+|++|.+|.|++.++++.++|.+... +|..+. .+.|+.+|..++
T Consensus 3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV~d~-~g~kl~~~~~~~~l~~~L~~al 72 (75)
T cd04897 3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYIRHK-DGRTLSTEGERQRVIKCLEAAI 72 (75)
T ss_pred EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEEEcC-CCCccCCHHHHHHHHHHHHHHH
Confidence 489999999999999999999999999999999999999999999644 565554 346677776654
No 10
>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=98.12 E-value=2.3e-05 Score=65.39 Aligned_cols=65 Identities=20% Similarity=0.318 Sum_probs=54.8
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEE--eeCCeEEEEEEEeeecCCcccC----HHHHHHHHHHhh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVIS--CFNGFAMDVFRAEQCKEGQDVH----PEQIKAVLLDSA 491 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS--~~ng~vl~~f~aeq~keg~~v~----~eqIk~~L~~~a 491 (497)
.|+|.|.+|+|+|.+|.++|..+||+|..|.|+ +.+.++.++|.+ ..+ |..+. .+.|+++|++..
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv-~~~-g~kl~d~~~~~~L~~~L~~~l 72 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV-QSD-GKKIMDPKKQAALCARLREEM 72 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE-eCC-CCccCCHHHHHHHHHHHHHHh
Confidence 489999999999999999999999999999999 999999999999 543 43343 356777777654
No 11
>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=98.07 E-value=4.2e-05 Score=61.96 Aligned_cols=65 Identities=32% Similarity=0.591 Sum_probs=51.7
Q ss_pred EEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEeeecCCcccCH----HHHHHHHHH
Q 047004 424 VNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF-NGFAMDVFRAEQCKEGQDVHP----EQIKAVLLD 489 (497)
Q Consensus 424 V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~-ng~vl~~f~aeq~keg~~v~~----eqIk~~L~~ 489 (497)
..|.|+|.+++|+|.+|..+|..+||+|+.|.|.+. +|+++++|.+.. .++..... ++|+..|.+
T Consensus 2 ~~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v~~-~~~~~~~~~~~~~~l~~~L~~ 71 (73)
T cd04900 2 TEVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVVLD-PDGEPIGERERLARIREALED 71 (73)
T ss_pred EEEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEEEC-CCCCCCChHHHHHHHHHHHHh
Confidence 358899999999999999999999999999999877 799999999963 34444433 345555443
No 12
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=98.06 E-value=3.2e-06 Score=95.93 Aligned_cols=51 Identities=25% Similarity=0.395 Sum_probs=47.8
Q ss_pred CccccHHHHHHHHHHHHHHHHHHhcCCCC----CcCCccchHHHHHHHHHHHHHH
Q 047004 308 PAKNLMAERRRRKKLNDRLYMLRSVVPKI----SKMDRASILGDAIEYLKELLQR 358 (497)
Q Consensus 308 ~~~H~~~ERrRR~kin~~~~~LrsLVP~~----~K~dKasIL~eAI~YIk~Lq~~ 358 (497)
+..|+.+|||||+++|.-|.+|.+|||.+ .|+||..||.+||.+||.+++.
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 58899999999999999999999999975 5999999999999999999874
No 13
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=97.95 E-value=3.4e-06 Score=96.18 Aligned_cols=64 Identities=27% Similarity=0.449 Sum_probs=57.3
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHhcCCC-CCcCCccchHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 307 LPAKNLMAERRRRKKLNDRLYMLRSVVPK-ISKMDRASILGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 307 ~~~~H~~~ERrRR~kin~~~~~LrsLVP~-~~K~dKasIL~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
++.+||++|||+|..|||++.+|+.+||+ ..|+.|.++|..||+||++|+...+.++.+.++++
T Consensus 276 kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l~ 340 (953)
T KOG2588|consen 276 KRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASLR 340 (953)
T ss_pred ccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhhh
Confidence 46899999999999999999999999997 47999999999999999999988888777765554
No 14
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=97.94 E-value=1.9e-05 Score=78.48 Aligned_cols=57 Identities=28% Similarity=0.366 Sum_probs=47.2
Q ss_pred CCCCccccHHHHHHHHHHHHHHHHHHhcCCCC--CcC-CccchHHHHHHHHHHHHHHHHH
Q 047004 305 KGLPAKNLMAERRRRKKLNDRLYMLRSVVPKI--SKM-DRASILGDAIEYLKELLQRIND 361 (497)
Q Consensus 305 ~~~~~~H~~~ERrRR~kin~~~~~LrsLVP~~--~K~-dKasIL~eAI~YIk~Lq~~v~~ 361 (497)
.+.+..|+.-||+||+.|++.|..|+.+||.. .+. +.++||..|++||+.|+.+...
T Consensus 57 ~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~ 116 (232)
T KOG2483|consen 57 ASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSAT 116 (232)
T ss_pred CcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHH
Confidence 34567899999999999999999999999974 222 3689999999999999765433
No 15
>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=97.82 E-value=0.00018 Score=58.77 Aligned_cols=66 Identities=23% Similarity=0.272 Sum_probs=53.4
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCccc-C---HHHHHHHHHHh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDV-H---PEQIKAVLLDS 490 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v-~---~eqIk~~L~~~ 490 (497)
.|+|.+.+|+|+|.+|..+|..+|++|+.|.+.+.++.++++|.+.....+..+ . .+.|++.|.+.
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V~d~~~~~~~~~~~~~~~i~~~L~~~ 71 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYVRDEETGAPIDDPIRLASIEDRLDNV 71 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEEEcCcCCCCCCCHHHHHHHHHHHHHH
Confidence 489999999999999999999999999999999999999999998633213323 2 35666666654
No 16
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=97.67 E-value=6.8e-05 Score=74.99 Aligned_cols=59 Identities=27% Similarity=0.421 Sum_probs=49.6
Q ss_pred ccccHHHHHHHHHHHHHHHHH-HhcCCCC-CcCCccchHHHHHHHHHHHHHHHHHHHHhhh
Q 047004 309 AKNLMAERRRRKKLNDRLYML-RSVVPKI-SKMDRASILGDAIEYLKELLQRINDLHNELE 367 (497)
Q Consensus 309 ~~H~~~ERrRR~kin~~~~~L-rsLVP~~-~K~dKasIL~eAI~YIk~Lq~~v~~L~~e~e 367 (497)
.+-.|.||||=+|+|+.|.+| |.-+++. .++-|..||..||+||..||.-++++.....
T Consensus 120 KAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~ 180 (284)
T KOG3960|consen 120 KAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEK 180 (284)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccch
Confidence 345699999999999999999 6666654 6789999999999999999988887766544
No 17
>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=97.56 E-value=0.00068 Score=54.99 Aligned_cols=66 Identities=24% Similarity=0.378 Sum_probs=54.8
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
.|.|.++.++|+|.+|..+|.+++++|++|.+.+.++.++++|++.. .++.... .+..+.|.+..|
T Consensus 3 ri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v~~-~~~~~~~-~~~~~~l~~~l~ 68 (72)
T cd04926 3 RLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYVTD-ANGNPVD-PKTIEAVRQEIG 68 (72)
T ss_pred EEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEEEC-CCCCcCC-HHHHHHHHHHhc
Confidence 57788899999999999999999999999999999899999999964 3444453 356667777776
No 18
>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=97.39 E-value=0.002 Score=50.71 Aligned_cols=64 Identities=36% Similarity=0.576 Sum_probs=51.2
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCH---HHHHHHHHH
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHP---EQIKAVLLD 489 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~---eqIk~~L~~ 489 (497)
.|.|.|..++|+|.+|+.+|.+++++|.++.+.+.++.+++.|.+... ++..... ++|+++|.+
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i~~~-~~~~~~~~~~~~i~~~l~~ 68 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYVTDA-DGQPLDPERQEALRAALGE 68 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEEECC-CCCcCCHHHHHHHHHHHHh
Confidence 478899999999999999999999999999999998999999998643 3333333 345555544
No 19
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=97.37 E-value=0.00013 Score=74.78 Aligned_cols=51 Identities=27% Similarity=0.451 Sum_probs=45.7
Q ss_pred ccccHHHHHHHHHHHHHHHHHHhcCCC--CCcCCccchHHHHHHHHHHHHHHH
Q 047004 309 AKNLMAERRRRKKLNDRLYMLRSVVPK--ISKMDRASILGDAIEYLKELLQRI 359 (497)
Q Consensus 309 ~~H~~~ERrRR~kin~~~~~LrsLVP~--~~K~dKasIL~eAI~YIk~Lq~~v 359 (497)
.--+..||||=..||.-|..||+|+|- .-|+.||.||+.+.+||.+|+.+.
T Consensus 62 eIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~K 114 (373)
T KOG0561|consen 62 EIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHK 114 (373)
T ss_pred HhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhcc
Confidence 445688999999999999999999996 579999999999999999997653
No 20
>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=97.34 E-value=0.0019 Score=53.07 Aligned_cols=63 Identities=25% Similarity=0.355 Sum_probs=52.2
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEE-eeCCeEEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVIS-CFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS-~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
.|-|.|+.++|+|.+|.-+|..+||+|+.|.|. +.+|.++++|.+...+ .=...++..+|++.
T Consensus 3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V~d~~---~~~~~~~~~~~~~~ 66 (68)
T cd04928 3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVVTGWK---RGETAALGHALQKE 66 (68)
T ss_pred EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEEecCC---ccchHHHHHHHHHh
Confidence 477899999999999999999999999999988 4599999999996322 23456777777765
No 21
>PRK05007 PII uridylyl-transferase; Provisional
Probab=97.09 E-value=0.0025 Score=74.18 Aligned_cols=68 Identities=16% Similarity=0.350 Sum_probs=58.5
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCH---HHHHHHHHHhh
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHP---EQIKAVLLDSA 491 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~---eqIk~~L~~~a 491 (497)
--.|+|+|.+|+|+|.+|.++|.++||+|..|.|+|.++++.++|.+.. .+|..+.+ ++|+++|++.+
T Consensus 808 ~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~~-~~g~~l~~~~~~~l~~~L~~~l 878 (884)
T PRK05007 808 RSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILAT-ADRRALNEELQQELRQRLTEAL 878 (884)
T ss_pred eEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEEc-CCCCcCCHHHHHHHHHHHHHHH
Confidence 4569999999999999999999999999999999999999999999963 45655553 57777777765
No 22
>PLN03217 transcription factor ATBS1; Provisional
Probab=97.01 E-value=0.001 Score=56.95 Aligned_cols=52 Identities=25% Similarity=0.551 Sum_probs=44.8
Q ss_pred HHHHHHHHHHHHhcCCCC------CcCCccchHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 319 RKKLNDRLYMLRSVVPKI------SKMDRASILGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 319 R~kin~~~~~LrsLVP~~------~K~dKasIL~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
-+.|++.+..|+.|+|.. .|..-+-+|+|+..||+.|+.++.+|.+++.++-
T Consensus 19 ddqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL 76 (93)
T PLN03217 19 EDQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELL 76 (93)
T ss_pred HHHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 378999999999999963 3444555899999999999999999999998775
No 23
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=96.97 E-value=0.00078 Score=66.30 Aligned_cols=59 Identities=20% Similarity=0.305 Sum_probs=50.1
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHhcCCC----CCcCCccchHHHHHHHHHHHHHHHHHHHH
Q 047004 306 GLPAKNLMAERRRRKKLNDRLYMLRSVVPK----ISKMDRASILGDAIEYLKELLQRINDLHN 364 (497)
Q Consensus 306 ~~~~~H~~~ERrRR~kin~~~~~LrsLVP~----~~K~dKasIL~eAI~YIk~Lq~~v~~L~~ 364 (497)
.....++.+||+|=+.+|..|..||.+||. .+|+.|..+|.-||.||+.|+.-++.-..
T Consensus 108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~ 170 (228)
T KOG4029|consen 108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEA 170 (228)
T ss_pred hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhccccc
Confidence 344667788999999999999999999995 46889999999999999999986665443
No 24
>PRK04374 PII uridylyl-transferase; Provisional
Probab=96.90 E-value=0.0073 Score=70.30 Aligned_cols=80 Identities=25% Similarity=0.374 Sum_probs=63.5
Q ss_pred CceEEEEEec-CceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccC---HHHHHHH
Q 047004 411 PARVEVRVRE-GRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVH---PEQIKAV 486 (497)
Q Consensus 411 ~~~VEV~v~e-g~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~---~eqIk~~ 486 (497)
++.|.+.... .....|.|.+.+++|+|.+|..+|..+||+|+.|.|+|.+++++++|.+... +|..+. .++|+++
T Consensus 783 ~~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V~d~-~g~~~~~~~~~~l~~~ 861 (869)
T PRK04374 783 APRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQITDE-HDRPLSESARQALRDA 861 (869)
T ss_pred CCeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEECC-CCCcCChHHHHHHHHH
Confidence 3455554422 2457899999999999999999999999999999999999999999999643 443332 3688888
Q ss_pred HHHhh
Q 047004 487 LLDSA 491 (497)
Q Consensus 487 L~~~a 491 (497)
|++.+
T Consensus 862 L~~~l 866 (869)
T PRK04374 862 LCACL 866 (869)
T ss_pred HHHHh
Confidence 88765
No 25
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=96.87 E-value=0.0065 Score=49.78 Aligned_cols=70 Identities=17% Similarity=0.245 Sum_probs=57.1
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcCCCC
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFHGM 496 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~~~ 496 (497)
.+.|.+.+++|+|++..|.++|.+.|.+|..++.++.++.+..++.++.. .-..++|+++|...+.-.|+
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~~~----~~~~~~l~~~L~~l~~~~~l 71 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVSIP----EDSLERLESALEELAEELGL 71 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEEES----HHHHHHHHHHHHHHHHHTT-
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEEeC----cccHHHHHHHHHHHHHHCCc
Confidence 36799999999999999999999999999999999999999998888653 23778999999987654443
No 26
>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=96.78 E-value=0.017 Score=44.35 Aligned_cols=63 Identities=17% Similarity=0.223 Sum_probs=48.5
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCC--eEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNG--FAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng--~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
.|.|.|+.++|+|.+|.++|-++|++|.++.+....+ ..+..+... . ....+++.++|++..|
T Consensus 2 ~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~~~~~~~~~~~~-~----~~~~~~~~~~l~~~~~ 66 (66)
T PF01842_consen 2 RVRVIVPDRPGILADVTEILADHGINIDSISQSSDKDGVGIVFIVIVV-D----EEDLEKLLEELEALPG 66 (66)
T ss_dssp EEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESSTTEEEEEEEEE-E----GHGHHHHHHHHHHHTT
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCCCceEEEEEEEC-C----CCCHHHHHHHHHcccC
Confidence 5788999999999999999999999999999999987 333333222 1 3556777777776654
No 27
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=96.77 E-value=0.0094 Score=69.55 Aligned_cols=80 Identities=20% Similarity=0.336 Sum_probs=62.2
Q ss_pred CceEEEEEec-CceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccC----HHHHHH
Q 047004 411 PARVEVRVRE-GRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVH----PEQIKA 485 (497)
Q Consensus 411 ~~~VEV~v~e-g~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~----~eqIk~ 485 (497)
++.|.+.... .....|.|++.+++|+|.+|..+|..+||+|+.|.|+|.+++++++|.+... +|..+. .++|++
T Consensus 801 ~~~V~i~~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V~d~-~g~~l~~~~~~~~l~~ 879 (895)
T PRK00275 801 PTQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFITDA-DNQPLSDPQLCSRLQD 879 (895)
T ss_pred CCEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEEECC-CCCCCCCHHHHHHHHH
Confidence 3455554432 2456799999999999999999999999999999999999999999999643 444333 356777
Q ss_pred HHHHhh
Q 047004 486 VLLDSA 491 (497)
Q Consensus 486 ~L~~~a 491 (497)
+|.+..
T Consensus 880 ~L~~~L 885 (895)
T PRK00275 880 AICEQL 885 (895)
T ss_pred HHHHHH
Confidence 777654
No 28
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=96.69 E-value=0.008 Score=69.76 Aligned_cols=68 Identities=25% Similarity=0.424 Sum_probs=58.1
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccC---HHHHHHHHHHhh
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVH---PEQIKAVLLDSA 491 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~---~eqIk~~L~~~a 491 (497)
--.|+|.+.+|+|+|.+|.++|.++|++|..|.|+|.++++.++|.+.. .+|..+. .++|+++|+++.
T Consensus 783 ~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~~-~~g~~l~~~~~~~l~~~L~~~l 853 (854)
T PRK01759 783 QTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILTN-QQGQALDEEERKALKSRLLSNL 853 (854)
T ss_pred eEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEEC-CCCCcCChHHHHHHHHHHHHHh
Confidence 4579999999999999999999999999999999999999999999964 3455444 267888887654
No 29
>PRK03059 PII uridylyl-transferase; Provisional
Probab=96.67 E-value=0.009 Score=69.40 Aligned_cols=80 Identities=25% Similarity=0.361 Sum_probs=59.7
Q ss_pred ceEEEEEec-CceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 412 ARVEVRVRE-GRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 412 ~~VEV~v~e-g~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
+.|.+.... .....|.|.|.+++|+|.+|..+|..+||+|+.|.|+|.+++++++|.+...+....-..+.|+++|.+.
T Consensus 774 ~~V~~~~~~~~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V~~~~~~~~~~~~~l~~~L~~~ 853 (856)
T PRK03059 774 PRVDLRPDERGQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLIDGSGLSDNRLQIQLETELLDA 853 (856)
T ss_pred ceEEEEEcCCCCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEcCCCCCCHHHHHHHHHHHHHH
Confidence 345544322 2456799999999999999999999999999999999999999999999321111112245777777665
Q ss_pred h
Q 047004 491 A 491 (497)
Q Consensus 491 a 491 (497)
+
T Consensus 854 L 854 (856)
T PRK03059 854 L 854 (856)
T ss_pred h
Confidence 4
No 30
>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=96.57 E-value=0.025 Score=43.87 Aligned_cols=47 Identities=38% Similarity=0.617 Sum_probs=42.9
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEee
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQ 471 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq 471 (497)
.|.|.|..++|+|.+|+.+|.++++.|..+.+.+.++.....|++..
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v~~ 48 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYVTD 48 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEEEC
Confidence 47789999999999999999999999999999998788888888864
No 31
>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=96.53 E-value=0.024 Score=46.57 Aligned_cols=65 Identities=20% Similarity=0.184 Sum_probs=56.3
Q ss_pred EEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 424 VNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 424 V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
+.|.+.|++++|+...|-+.|.+.|.+|+.++....++.++..+.++.. ....++|++.|...+.
T Consensus 2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~~~----~~~~~~l~~~l~~~~~ 66 (77)
T cd04893 2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVEGS----WDAIAKLEAALPGLAR 66 (77)
T ss_pred EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEEec----cccHHHHHHHHHHHHH
Confidence 5689999999999999999999999999999999999998887777632 2467899988888764
No 32
>PRK05092 PII uridylyl-transferase; Provisional
Probab=96.42 E-value=0.024 Score=66.45 Aligned_cols=79 Identities=32% Similarity=0.445 Sum_probs=62.6
Q ss_pred ceEEEEEec-CceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccC----HHHHHHH
Q 047004 412 ARVEVRVRE-GRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVH----PEQIKAV 486 (497)
Q Consensus 412 ~~VEV~v~e-g~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~----~eqIk~~ 486 (497)
+.|.+.-.. .....|.|.|.+++|+|.+|..+|.++|++|..|.|.|.++++.++|.+... +|..+. .++|+++
T Consensus 831 ~~V~~~~~~s~~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v~d~-~g~~i~~~~~~~~l~~~ 909 (931)
T PRK05092 831 PRVTIDNEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYVTDL-FGLKITNEARQAAIRRA 909 (931)
T ss_pred CEEEEeeCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEEeCC-CCCcCCCHHHHHHHHHH
Confidence 455554432 2346899999999999999999999999999999999999999999999643 343332 3578888
Q ss_pred HHHhh
Q 047004 487 LLDSA 491 (497)
Q Consensus 487 L~~~a 491 (497)
|.+..
T Consensus 910 L~~~L 914 (931)
T PRK05092 910 LLAAL 914 (931)
T ss_pred HHHHh
Confidence 87765
No 33
>PRK03381 PII uridylyl-transferase; Provisional
Probab=96.40 E-value=0.025 Score=65.07 Aligned_cols=79 Identities=19% Similarity=0.265 Sum_probs=62.7
Q ss_pred ceEEEEEecCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhh
Q 047004 412 ARVEVRVREGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSA 491 (497)
Q Consensus 412 ~~VEV~v~eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~a 491 (497)
+.|.++......+.|.|+|.+|+|++.+|..+|..+|++|+.|.|.+.+|.++++|.+.. ..|.....++|++.|.+..
T Consensus 588 ~~v~~~~~~~~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V~~-~~~~~~~~~~l~~~L~~~L 666 (774)
T PRK03381 588 VHVEIAPADPHMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVVSP-RFGSPPDAALLRQDLRRAL 666 (774)
T ss_pred CEEEEeeCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEEEC-CCCCcchHHHHHHHHHHHH
Confidence 455554322346789999999999999999999999999999999999999999999963 3344344577888877654
No 34
>PRK03381 PII uridylyl-transferase; Provisional
Probab=96.20 E-value=0.034 Score=64.03 Aligned_cols=76 Identities=25% Similarity=0.363 Sum_probs=58.8
Q ss_pred ceEEEEEecC-ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccC--HHHHHHHHH
Q 047004 412 ARVEVRVREG-RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVH--PEQIKAVLL 488 (497)
Q Consensus 412 ~~VEV~v~eg-~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~--~eqIk~~L~ 488 (497)
+.|++....+ ....|.|.|.+++|+|.+|..+|..+|++|+.|.|+|.++.++++|.+.. .+|..+. .+.|+++|+
T Consensus 695 ~~v~~~~~~~~~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V~d-~~g~~~~~~~~~l~~~L~ 773 (774)
T PRK03381 695 PRVLWLDGASPDATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYVTG-AAGGPLADARAAVEQAVL 773 (774)
T ss_pred cEEEEEECCCCCeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEEEC-CCCCcCchHHHHHHHHhh
Confidence 3455544322 34789999999999999999999999999999999999999999999963 3454443 445555553
No 35
>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=96.02 E-value=0.039 Score=63.99 Aligned_cols=68 Identities=35% Similarity=0.452 Sum_probs=57.5
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccC---HHHHHHHHHHhh
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVH---PEQIKAVLLDSA 491 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~---~eqIk~~L~~~a 491 (497)
--.|+|.|.+|||+|.+|.++|..+|++|.+|.|+|.++.+.++|.+.. ..|..+. .+.|+++|++..
T Consensus 779 ~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v~~-~~g~~~~~~~~~~l~~~L~~~l 849 (850)
T TIGR01693 779 ATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYVTD-LFGLKLTDEEEQRLLEVLAASV 849 (850)
T ss_pred eEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEEEC-CCCCCCCHHHHHHHHHHHHHHh
Confidence 4679999999999999999999999999999999999999999999963 3444444 467777777654
No 36
>cd04875 ACT_F4HF-DF N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase). This CD includes the N-terminal ACT domain of formyltetrahydrofolate deformylase (F4HF-DF; formyltetrahydrofolate hydrolase) which catalyzes the hydrolysis of 10-formyltetrahydrofolate (formyl-FH4) to FH4 and formate. Formyl-FH4 hydrolase generates the formate that is used by purT-encoded 5'-phosphoribosylglycinamide transformylase for step three of de novo purine nucleotide synthesis. Formyl-FH4 hydrolase, a hexamer which is activated by methionine and inhibited by glycine, is proposed to regulate the balance FH4 and C1-FH4 in response to changing growth conditions. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=96.01 E-value=0.055 Score=43.60 Aligned_cols=67 Identities=22% Similarity=0.256 Sum_probs=49.1
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
|.|.|++++|++.+|.+.|-++|+.|...+..+..+......+++..-....+..++++++|...+.
T Consensus 2 i~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~l~~~l~~l~~ 68 (74)
T cd04875 2 LTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFVDPDSGRFFMRVEFELEGFDLSREALEAAFAPVAA 68 (74)
T ss_pred EEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeeecCCCCeEEEEEEEEeCCCCCCHHHHHHHHHHHHH
Confidence 7899999999999999999999999999988863222222233332212123678999999988774
No 37
>PRK00194 hypothetical protein; Validated
Probab=95.82 E-value=0.05 Score=45.38 Aligned_cols=71 Identities=13% Similarity=0.192 Sum_probs=55.5
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcCCC
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFHG 495 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~~ 495 (497)
.+.|.|.|.+++|++..|.+.|-+.|++|+..+..+.++.+.-.+.+... +.....++|++.|.....-.|
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v~~~--~~~~~~~~l~~~l~~l~~~~~ 73 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLVDIS--ESKKDFAELKEELEELGKELG 73 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEEEec--CCCCCHHHHHHHHHHHHHHcC
Confidence 36799999999999999999999999999999988888766665555422 223557889888887765433
No 38
>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=95.76 E-value=0.065 Score=62.17 Aligned_cols=69 Identities=22% Similarity=0.404 Sum_probs=56.2
Q ss_pred ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEE-eeCCeEEEEEEEeeecCCcccCH----HHHHHHHHHhh
Q 047004 422 RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVIS-CFNGFAMDVFRAEQCKEGQDVHP----EQIKAVLLDSA 491 (497)
Q Consensus 422 ~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS-~~ng~vl~~f~aeq~keg~~v~~----eqIk~~L~~~a 491 (497)
....|.|.+.+++|+|.+|..+|..+||+|+.|.|. +.+|.++++|.+... +|..+.. +.|++.|.+..
T Consensus 667 ~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V~~~-~g~~~~~~~~~~~i~~~L~~~L 740 (850)
T TIGR01693 667 GGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVVQDL-FGSPPAAERVFQELLQGLVDVL 740 (850)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEEECC-CCCCCCcHHHHHHHHHHHHHHH
Confidence 456799999999999999999999999999999999 889999999999643 4444433 34666666554
No 39
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=95.58 E-value=0.1 Score=60.81 Aligned_cols=79 Identities=20% Similarity=0.400 Sum_probs=60.1
Q ss_pred ceEEEEEe-cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEeeecCCcccCHH---HHHHH
Q 047004 412 ARVEVRVR-EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISC-FNGFAMDVFRAEQCKEGQDVHPE---QIKAV 486 (497)
Q Consensus 412 ~~VEV~v~-eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~-~ng~vl~~f~aeq~keg~~v~~e---qIk~~ 486 (497)
+.|.++-. ......|.|.|.+++|+|.+|..+|..+||+|+.|.|.+ .+|.++++|.+... +|..+..+ .|+++
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 LLVKISNRFSRGGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIVTEL-NGKLLEFDRRRQLEQA 743 (854)
T ss_pred CEEEEEecCCCCeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEEeCC-CCCCCCHHHHHHHHHH
Confidence 34555432 124567999999999999999999999999999999976 89999999999654 45444443 45666
Q ss_pred HHHhh
Q 047004 487 LLDSA 491 (497)
Q Consensus 487 L~~~a 491 (497)
|.+..
T Consensus 744 L~~aL 748 (854)
T PRK01759 744 LTKAL 748 (854)
T ss_pred HHHHH
Confidence 65544
No 40
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=95.52 E-value=0.014 Score=63.55 Aligned_cols=58 Identities=21% Similarity=0.242 Sum_probs=47.8
Q ss_pred CCCCCccccHHHHHHHHHHHHHHHHHHhcCCC----CCcCCccchHHHHHHHHHHHHHHHHH
Q 047004 304 KKGLPAKNLMAERRRRKKLNDRLYMLRSVVPK----ISKMDRASILGDAIEYLKELLQRIND 361 (497)
Q Consensus 304 k~~~~~~H~~~ERrRR~kin~~~~~LrsLVP~----~~K~dKasIL~eAI~YIk~Lq~~v~~ 361 (497)
.+.++.+++.+||-|=..||+.|++|-.+.-- -..-.|.-||..|+.-|-.|++||.+
T Consensus 523 EkERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRE 584 (632)
T KOG3910|consen 523 EKERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRE 584 (632)
T ss_pred HHHHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHH
Confidence 34456889999999999999999999776532 22346889999999999999999876
No 41
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=95.49 E-value=0.21 Score=40.60 Aligned_cols=67 Identities=19% Similarity=0.296 Sum_probs=49.6
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcCCC
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF--NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFHG 495 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~--ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~~ 495 (497)
.+.|+|.|.+++|+|.+|..+|-+.++.|.+.++... ++.+.-.|.++.. ..+++...+.+.-...|
T Consensus 6 ~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~V~------d~~~L~~ii~~L~~i~~ 74 (80)
T PF13291_consen 6 PVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVEVK------DLEHLNQIIRKLRQIPG 74 (80)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEEES------SHHHHHHHHHHHCTSTT
T ss_pred EEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEEEC------CHHHHHHHHHHHHCCCC
Confidence 4678999999999999999999999999999999985 6787777877752 34555555555444433
No 42
>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=95.46 E-value=0.14 Score=41.42 Aligned_cols=64 Identities=9% Similarity=0.181 Sum_probs=52.0
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC------CeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN------GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n------g~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
|.|.|.+++|++.+|-+.|.++|++|...+..+.+ +.+.-.+.+... ......+|++.|...+.
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~~~~~~~~~~~~~~~v~~p---~~~~~~~l~~~l~~l~~ 71 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYSAPMSGTPLFKAQATLALP---AGTDLDALREELEELCD 71 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeecCCCCCcceEEEEEEEecC---CCCCHHHHHHHHHHHHH
Confidence 78999999999999999999999999999998887 555555555422 24678999998888764
No 43
>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=95.46 E-value=0.071 Score=43.71 Aligned_cols=66 Identities=21% Similarity=0.241 Sum_probs=56.7
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
.|.|.|+++.|+-.++.+.+-+.||.|+.+.+++.+...+-+|-+........+.=+-+|.+|+..
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 489999999999999999999999999999999999998888877654433457778899988764
No 44
>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=95.43 E-value=0.08 Score=44.21 Aligned_cols=68 Identities=12% Similarity=0.197 Sum_probs=55.3
Q ss_pred EEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 424 VNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 424 V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
+.|.+.|++++|++..|.+.|-.+|++|...+..+.++.+.-.+.+.. .+.....+++++.|...+.-
T Consensus 2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v~~--~~~~~~~~~L~~~l~~l~~~ 69 (88)
T cd04872 2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIVDI--SESNLDFAELQEELEELGKE 69 (88)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEEEe--CCCCCCHHHHHHHHHHHHHH
Confidence 468999999999999999999999999999998888887766666642 22246688999888887643
No 45
>PRK05007 PII uridylyl-transferase; Provisional
Probab=95.41 E-value=0.14 Score=59.98 Aligned_cols=79 Identities=23% Similarity=0.346 Sum_probs=59.5
Q ss_pred ceEEEEEe-cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEeeecCCcccCH---HHHHHH
Q 047004 412 ARVEVRVR-EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF-NGFAMDVFRAEQCKEGQDVHP---EQIKAV 486 (497)
Q Consensus 412 ~~VEV~v~-eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~-ng~vl~~f~aeq~keg~~v~~---eqIk~~ 486 (497)
+.|.++.. ......|.|+|.+++|+|..|..+|..+||+|+.|.|.+. +|.++++|.+.. .+|..+.. +.|++.
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 PLVLLSKQATRGGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIVLE-PDGSPLSQDRHQVIRKA 767 (884)
T ss_pred CeEEEEecCCCCeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEEEC-CCCCCCCHHHHHHHHHH
Confidence 34555432 2246789999999999999999999999999999998766 669999999964 34444443 346777
Q ss_pred HHHhh
Q 047004 487 LLDSA 491 (497)
Q Consensus 487 L~~~a 491 (497)
|.+..
T Consensus 768 L~~aL 772 (884)
T PRK05007 768 LEQAL 772 (884)
T ss_pred HHHHH
Confidence 76655
No 46
>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=95.40 E-value=0.11 Score=42.13 Aligned_cols=67 Identities=21% Similarity=0.156 Sum_probs=55.4
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcCCC
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFHG 495 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~~ 495 (497)
|++.+.+|||++.+|.++|-++|++|...+.++..+.+.-.+.+... . .+..++++++|...+.-.|
T Consensus 2 vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v~~p-~--~~~~~~l~~~l~~l~~~l~ 68 (75)
T cd04870 2 ITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILVQIP-D--SADSEALLKDLLFKAHELG 68 (75)
T ss_pred EEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEEEcC-C--CCCHHHHHHHHHHHHHHcC
Confidence 78889999999999999999999999999999998887777666532 2 3678999999988774433
No 47
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=95.17 E-value=0.077 Score=61.14 Aligned_cols=70 Identities=29% Similarity=0.449 Sum_probs=56.7
Q ss_pred CceEEEEEecC-ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHH
Q 047004 411 PARVEVRVREG-RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPE 481 (497)
Q Consensus 411 ~~~VEV~v~eg-~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~e 481 (497)
+++|.+.-... +--.|++.+.+|+|+|..|-.+|..++|+|+.|.|+|++.++.++|.+. .-.++.+.++
T Consensus 778 ~p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~vt-~~~~~~l~~~ 848 (867)
T COG2844 778 PPRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIVT-DADGQALNAE 848 (867)
T ss_pred CCceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEEe-ccccccCCHH
Confidence 34555543322 3456999999999999999999999999999999999999999999995 4466766544
No 48
>PRK04374 PII uridylyl-transferase; Provisional
Probab=94.81 E-value=0.19 Score=58.84 Aligned_cols=70 Identities=23% Similarity=0.340 Sum_probs=55.0
Q ss_pred ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEeeecCCcccCHHHHHHHHHHhh
Q 047004 422 RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISC-FNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSA 491 (497)
Q Consensus 422 ~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~-~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~a 491 (497)
....|.|+|.+++|++.+|.-+|..+||+|+.|.|.+ .+|.++++|.+....+...-..++|++.|.+..
T Consensus 689 ~~~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V~~~~~~~~~~~~~i~~~l~~~l 759 (869)
T PRK04374 689 DALEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEVLPQDTYADGDPQRLAAALRQVL 759 (869)
T ss_pred CeEEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEEeCCCCCChHHHHHHHHHHHHHH
Confidence 4678999999999999999999999999999999986 699999999996433221222445666665543
No 49
>PRK05092 PII uridylyl-transferase; Provisional
Probab=94.75 E-value=0.24 Score=58.26 Aligned_cols=80 Identities=24% Similarity=0.346 Sum_probs=60.3
Q ss_pred CceEEEEEec-CceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEeeecCCccc----CHHHHH
Q 047004 411 PARVEVRVRE-GRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISC-FNGFAMDVFRAEQCKEGQDV----HPEQIK 484 (497)
Q Consensus 411 ~~~VEV~v~e-g~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~-~ng~vl~~f~aeq~keg~~v----~~eqIk 484 (497)
.+.|.++... .....|.|.|.+++|+|.+|..+|..+|++|+.|.|.+ .+|+++++|.+.. .+|... ..+.|+
T Consensus 719 ~~~v~~~~~~~~~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V~~-~~g~~~~~~~~~~~l~ 797 (931)
T PRK05092 719 PLATEVRPDPARGVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWIQD-AFGRDEDEPRRLARLA 797 (931)
T ss_pred CcEEEEEecCCCCeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEEEC-CCCCCCCCHHHHHHHH
Confidence 4456665432 24578999999999999999999999999999999887 7999999998853 233222 245566
Q ss_pred HHHHHhh
Q 047004 485 AVLLDSA 491 (497)
Q Consensus 485 ~~L~~~a 491 (497)
+.|....
T Consensus 798 ~~L~~~l 804 (931)
T PRK05092 798 KAIEDAL 804 (931)
T ss_pred HHHHHHH
Confidence 7776654
No 50
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=94.70 E-value=0.25 Score=58.06 Aligned_cols=69 Identities=23% Similarity=0.434 Sum_probs=54.6
Q ss_pred ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEE-EeeCCeEEEEEEEeeecCCccc-C----HHHHHHHHHHhh
Q 047004 422 RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVI-SCFNGFAMDVFRAEQCKEGQDV-H----PEQIKAVLLDSA 491 (497)
Q Consensus 422 ~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsI-S~~ng~vl~~f~aeq~keg~~v-~----~eqIk~~L~~~a 491 (497)
....|.|+|.+++|+|.+|..+|..+||+|+.|.| ++-+|.++++|.+... +|..+ . .+.|++.|....
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 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIVLDD-DGEPIGDNPARIEQIREGLTEAL 777 (895)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEEeCC-CCCCccchHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999999999998 5678999999999643 34332 1 234666666543
No 51
>PRK03059 PII uridylyl-transferase; Provisional
Probab=94.34 E-value=0.33 Score=56.76 Aligned_cols=69 Identities=17% Similarity=0.318 Sum_probs=54.2
Q ss_pred ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEE-EeeCCeEEEEEEEeeecCCccc---CHHHHHHHHHHhh
Q 047004 422 RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVI-SCFNGFAMDVFRAEQCKEGQDV---HPEQIKAVLLDSA 491 (497)
Q Consensus 422 ~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsI-S~~ng~vl~~f~aeq~keg~~v---~~eqIk~~L~~~a 491 (497)
....|.|+|.+++|++..|.-+|..+||+|+.|.| ++.+|.++++|.+... +|... ..++|++.|.+..
T Consensus 677 ~~~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V~~~-~~~~~~~~~~~~i~~~l~~~l 749 (856)
T PRK03059 677 EGLQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQVLDP-EEDVHYRDIINLVEHELAERL 749 (856)
T ss_pred CeEEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEEeCC-CCCCChHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999999999999 5679999999999643 33311 1345666665543
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=93.65 E-value=0.98 Score=35.73 Aligned_cols=62 Identities=19% Similarity=0.252 Sum_probs=44.6
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF-NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~-ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
|+|.+..++|+|.+|+.+|.+.|..|...++... ++.+...|.++... .-+..+|..+|...
T Consensus 2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~vev~~---~~~l~~i~~~L~~i 64 (74)
T cd04887 2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVDAPS---EEHAETIVAAVRAL 64 (74)
T ss_pred EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEEcCC---HHHHHHHHHHHhcC
Confidence 6788899999999999999999999999888776 36655556665321 22334455554443
No 53
>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=93.15 E-value=0.58 Score=35.81 Aligned_cols=60 Identities=22% Similarity=0.192 Sum_probs=41.8
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee-----CCeEEEEEEEeeecCCcccCHHHHHHHHH
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF-----NGFAMDVFRAEQCKEGQDVHPEQIKAVLL 488 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~-----ng~vl~~f~aeq~keg~~v~~eqIk~~L~ 488 (497)
+.|.++.++|.|.+|+++|.+.|++|.+...... .+...-.++++.. + ..+.++|.+.|.
T Consensus 1 ~~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v~~~-~--~~~l~~l~~~l~ 65 (73)
T cd04886 1 LRVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTLETR-G--AEHIEEIIAALR 65 (73)
T ss_pred CEEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEEEeC-C--HHHHHHHHHHHH
Confidence 3577889999999999999999999998887654 3555555555531 1 223345555554
No 54
>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=92.96 E-value=0.47 Score=34.74 Aligned_cols=66 Identities=21% Similarity=0.193 Sum_probs=45.0
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEeeecCCcccCHHHHHHHHHHhhcCC
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN-GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFH 494 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n-g~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~ 494 (497)
|+|.|.+++|.+.++++.|.+.+++|....+...+ +.....+.++... ......+.+.|...-|.+
T Consensus 1 l~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~---~~~~~~~~~~l~~~~~v~ 67 (71)
T cd04876 1 IRVEAIDRPGLLADITTVIAEEKINILSVNTRTDDDGLATIRLTLEVRD---LEHLARIMRKLRQIPGVI 67 (71)
T ss_pred CEEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECCCCEEEEEEEEEECC---HHHHHHHHHHHhCCCCcE
Confidence 46778899999999999999999999998887655 4444444444321 223455666665555543
No 55
>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=92.66 E-value=0.57 Score=37.10 Aligned_cols=67 Identities=12% Similarity=0.199 Sum_probs=48.8
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF-NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~-ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
.|.|.+..++|++.+|+++|.+.+++|...+.... ++.+.-.|.++. .+.+...++|.++|...-|.
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v~v--~~~~~~l~~l~~~L~~i~~V 69 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISIDT--STMNGDIDELLEELREIDGV 69 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEEEc--CchHHHHHHHHHHHhcCCCe
Confidence 57888999999999999999999999999877553 354444555553 22234567777777766553
No 56
>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=92.56 E-value=1.1 Score=34.83 Aligned_cols=46 Identities=17% Similarity=0.257 Sum_probs=36.6
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEe
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN--GFAMDVFRAE 470 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n--g~vl~~f~ae 470 (497)
+|+|.+.+++|++.+++..|.+.++.+.+....... +...-.+..+
T Consensus 2 yl~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~~~~~~~~~~i~~~ 49 (79)
T cd04881 2 YLRLTVKDKPGVLAKITGILAEHGISIESVIQKEADGGETAPVVIVTH 49 (79)
T ss_pred EEEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEcccCCCCceeEEEEEc
Confidence 688999999999999999999999999998876553 4444444443
No 57
>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=91.74 E-value=1.4 Score=33.74 Aligned_cols=63 Identities=16% Similarity=0.099 Sum_probs=45.6
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN-GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n-g~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
.|.|.|..++|.|.++++.|.+.++.|.+....... +...-++.+.. . ...+++.+.|...-|
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~i~~~~----~-~~~~~~~~~L~~~~~ 65 (72)
T cd04874 2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIEREGKARIYMELEG----V-GDIEELVEELRSLPI 65 (72)
T ss_pred eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEeccCCCeEEEEEEEec----c-ccHHHHHHHHhCCCC
Confidence 477889999999999999999999999988877653 44333333331 1 356677777766554
No 58
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=91.69 E-value=0.1 Score=49.35 Aligned_cols=49 Identities=29% Similarity=0.447 Sum_probs=44.5
Q ss_pred ccccHHHHHHHHHHHHHHHHHHhcCCC--CCcCCccchHHHHHHHHHHHHH
Q 047004 309 AKNLMAERRRRKKLNDRLYMLRSVVPK--ISKMDRASILGDAIEYLKELLQ 357 (497)
Q Consensus 309 ~~H~~~ERrRR~kin~~~~~LrsLVP~--~~K~dKasIL~eAI~YIk~Lq~ 357 (497)
.-|++.||+|=..||+.|.+||.++|. +.|..|.--|.-|..||..|-+
T Consensus 80 v~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~ 130 (173)
T KOG4447|consen 80 VMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQ 130 (173)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhh
Confidence 578999999999999999999999995 5788999999999999998854
No 59
>PRK04435 hypothetical protein; Provisional
Probab=91.18 E-value=1.2 Score=41.33 Aligned_cols=71 Identities=15% Similarity=0.257 Sum_probs=53.0
Q ss_pred cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEe-eCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 420 EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISC-FNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 420 eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~-~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
.|+.+.|.+.+.+++|+|.+|+++|.+.+++|...+.+. .+|.+.-.|.++.. +.....++|.+.|...-|
T Consensus 66 ~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVevs--~~~~~L~~Li~~L~~i~g 137 (147)
T PRK04435 66 KGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISIDTS--SMEGDIDELLEKLRNLDG 137 (147)
T ss_pred CCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEEeC--ChHHHHHHHHHHHHcCCC
Confidence 368899999999999999999999999999999887654 35666556666542 223356666666665544
No 60
>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=91.08 E-value=1.5 Score=30.21 Aligned_cols=35 Identities=23% Similarity=0.377 Sum_probs=30.8
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN 460 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n 460 (497)
|.|.|..++|.+.+++.+|...++.|.........
T Consensus 1 i~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~ 35 (60)
T cd02116 1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSG 35 (60)
T ss_pred CEEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence 46788899999999999999999999999876653
No 61
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=90.08 E-value=0.25 Score=54.75 Aligned_cols=45 Identities=36% Similarity=0.549 Sum_probs=38.9
Q ss_pred cccHHHHHHHHHHHHHHHHHHhcCCC----CCcCCccchHHHHHHHHHH
Q 047004 310 KNLMAERRRRKKLNDRLYMLRSVVPK----ISKMDRASILGDAIEYLKE 354 (497)
Q Consensus 310 ~H~~~ERrRR~kin~~~~~LrsLVP~----~~K~dKasIL~eAI~YIk~ 354 (497)
.+.---||-|+|||..+..|.+|+|- ++|+||.|||.-++.|++-
T Consensus 28 tkSNPSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~ 76 (712)
T KOG3560|consen 28 TKSNPSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV 76 (712)
T ss_pred ccCCcchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence 34445678899999999999999995 6899999999999999863
No 62
>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=89.72 E-value=1.9 Score=32.75 Aligned_cols=65 Identities=17% Similarity=0.178 Sum_probs=46.1
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF--NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~--ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
.|.|.+.+++|.|.+|+..|.+.++.|........ ++.....+.+... . ...+++.+.|++.-|.
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~---~-~~~~~l~~~l~~~~~v 68 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIVVEGD---D-DVIEQIVKQLNKLVDV 68 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEEEECC---H-HHHHHHHHHHhCCccE
Confidence 36778889999999999999999999999887764 4555555555421 1 3455666666655544
No 63
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=89.63 E-value=2.3 Score=43.75 Aligned_cols=68 Identities=21% Similarity=0.196 Sum_probs=53.9
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISC--FNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~--~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
.+.|.+.|.+|+|+...|-++|-++|++|.+.+.++ .+|.+.-.+.+.. +......++|+++|...+.
T Consensus 6 ~~vitv~G~DrpGIVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~--~~~~~~~~~L~~~L~~l~~ 75 (286)
T PRK06027 6 RYVLTLSCPDRPGIVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEG--DGLIFNLETLRADFAALAE 75 (286)
T ss_pred eEEEEEECCCCCcHHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEe--CCCCCCHHHHHHHHHHHHH
Confidence 367999999999999999999999999999999999 8885444444432 1224558899999887764
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=89.40 E-value=1.8 Score=33.01 Aligned_cols=59 Identities=25% Similarity=0.373 Sum_probs=41.9
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN--GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n--g~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
|.|.-+.++|.|.+++.+|.+.|+.|.+....... +....+++++. .+.+++.|.+ +||
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve~--------~~~~~~~L~~-~G~ 62 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTED--------IEKAIEVLQE-RGV 62 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeCC--------HHHHHHHHHH-CCc
Confidence 45566789999999999999999999877665443 45554555531 6677777655 354
No 65
>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=89.24 E-value=2.6 Score=31.82 Aligned_cols=62 Identities=19% Similarity=0.301 Sum_probs=47.6
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN--GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n--g~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
+.|.+..++|.+.+|++.|.+.++.|.+..+.... +.....|.++ + ...++|.+.|...-|.
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v~----~--~~~~~l~~~l~~~~~V 65 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDVD----S--PVPEEVLEELKALPGI 65 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEcC----C--CCCHHHHHHHHcCCCe
Confidence 56788899999999999999999999999887754 5655555552 1 2467888888776653
No 66
>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=89.16 E-value=3.6 Score=33.14 Aligned_cols=62 Identities=15% Similarity=0.193 Sum_probs=43.7
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
.|+|.|..++|+|.+|+.++.+.++.|...++... +. ++ +.++.. + ..+.++|...|...-|
T Consensus 2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~-i~-l~i~v~-~--~~~L~~li~~L~~i~g 63 (74)
T cd04877 2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-GR-IY-LNFPTI-E--FEKLQTLMPEIRRIDG 63 (74)
T ss_pred EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-Ce-EE-EEeEec-C--HHHHHHHHHHHhCCCC
Confidence 58899999999999999999999999999998775 54 22 334322 1 1224555555555444
No 67
>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=89.11 E-value=2.2 Score=32.45 Aligned_cols=61 Identities=15% Similarity=0.198 Sum_probs=43.5
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF--NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~--ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
|.|.+.+++|.+.+|+..|.+.+++|.+...... ++...-.+.++. . ...++.+.|...-|
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~v~~----~--~~~~~i~~l~~~~~ 64 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEVDQ----P--IDEEVIEEIKKIPN 64 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEEeCC----C--CCHHHHHHHHcCCC
Confidence 5678889999999999999999999998876652 344444444432 2 55567777766544
No 68
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=88.89 E-value=0.24 Score=56.16 Aligned_cols=44 Identities=39% Similarity=0.538 Sum_probs=38.8
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCC----CCcCCccchHHHHHHHHHHHH
Q 047004 313 MAERRRRKKLNDRLYMLRSVVPK----ISKMDRASILGDAIEYLKELL 356 (497)
Q Consensus 313 ~~ERrRR~kin~~~~~LrsLVP~----~~K~dKasIL~eAI~YIk~Lq 356 (497)
-+-|.||.|-|+-|++|..+||- .+.+|||+|+.-||-|++-=+
T Consensus 52 dAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRlrk 99 (768)
T KOG3558|consen 52 DAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRLRK 99 (768)
T ss_pred hhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHHHH
Confidence 57799999999999999999994 368999999999999987543
No 69
>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=88.67 E-value=4.7 Score=31.54 Aligned_cols=62 Identities=23% Similarity=0.385 Sum_probs=45.2
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF--NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~--ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
.|.+..++++|.|.++++.|.+.++.|.+...... .+...-+|+++. ..+++++++|.+. ||
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~~------~~~~~~~~~L~~~-G~ 66 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQT------MNPRPIIEDLRRA-GY 66 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEec------CCHHHHHHHHHHC-CC
Confidence 46778889999999999999999999987765433 345556666653 2345888887553 54
No 70
>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=88.14 E-value=2.9 Score=42.91 Aligned_cols=65 Identities=15% Similarity=0.146 Sum_probs=51.7
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEeeecCCcccCHHHHHHHHHH-hh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF--NGFAMDVFRAEQCKEGQDVHPEQIKAVLLD-SA 491 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~--ng~vl~~f~aeq~keg~~v~~eqIk~~L~~-~a 491 (497)
.|.+.|++++|+...|-..|-+.|++|+.++-+.. +++++-.+.+.. .+..+..++|+++|.. .+
T Consensus 2 ~itv~g~D~~GIVA~Vt~~La~~g~NI~d~sq~~~~~~~~F~mr~~v~~--~~~~~~~~~l~~~l~~~~~ 69 (280)
T TIGR00655 2 ILLVSCPDQKGLVAAISTFIAKHGANIISNDQHTDPETGRFFMRVEFQL--EGFRLEESSLLAAFKSALA 69 (280)
T ss_pred EEEEECCCCCChHHHHHHHHHHCCCCEEeeeEEEcCCCCeEEEEEEEEe--CCCCCCHHHHHHHHHHHHH
Confidence 47899999999999999999999999999998875 366665555542 2234678999999888 44
No 71
>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=87.50 E-value=4.9 Score=31.55 Aligned_cols=60 Identities=27% Similarity=0.523 Sum_probs=43.7
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
.|.|..++++|.|.+|+++|.+.|+.|.+..+....+. .+++... + .++.++++|.+ +||
T Consensus 3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~--~~~rl~~-~-----~~~~~~~~L~~-~G~ 62 (66)
T cd04908 3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTSEF--GILRLIV-S-----DPDKAKEALKE-AGF 62 (66)
T ss_pred EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCCC--CEEEEEE-C-----CHHHHHHHHHH-CCC
Confidence 46677889999999999999999999998887666553 4555543 2 15677766544 455
No 72
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=87.44 E-value=3.7 Score=42.30 Aligned_cols=69 Identities=13% Similarity=0.097 Sum_probs=50.7
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
.+.|.|.|.+++|+...|-+.|-+++++|...+..+..+.-+...+++.. -......++|+++|...+.
T Consensus 7 ~~vitv~G~DrpGIVa~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~-~p~~~~~~~L~~~L~~l~~ 75 (286)
T PRK13011 7 TFVLTLSCPSAAGIVAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFH-SEEGLDEDALRAGFAPIAA 75 (286)
T ss_pred eEEEEEEeCCCCCHHHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEe-cCCCCCHHHHHHHHHHHHH
Confidence 46799999999999999999999999999999987432222222344321 1124678999999988764
No 73
>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=87.30 E-value=4 Score=31.91 Aligned_cols=63 Identities=21% Similarity=0.362 Sum_probs=43.5
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC-C-eEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN-G-FAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n-g-~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
.+.+.+++++|.|.++++.|.+.|++|......... + .....+.++ ..+ +.+.+++.|.+ +||
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~~~~~~~~~~i~v~----~~~-~~~~~~~~L~~-~G~ 67 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEIREGIGGILRISFK----TQE-DRERAKEILKE-AGY 67 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEeecCCcEEEEEEEC----CHH-HHHHHHHHHHH-cCC
Confidence 467788899999999999999999999988766642 2 222233332 112 56777777654 455
No 74
>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=86.79 E-value=5.7 Score=31.84 Aligned_cols=63 Identities=11% Similarity=0.082 Sum_probs=40.6
Q ss_pred EEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCC-eEEEEEEEeeecCCcccCHHHHHHHHHH
Q 047004 427 HMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNG-FAMDVFRAEQCKEGQDVHPEQIKAVLLD 489 (497)
Q Consensus 427 ~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng-~vl~~f~aeq~keg~~v~~eqIk~~L~~ 489 (497)
.+...+++|.|.+|++.+.+.|+.+++.......+ ..-+.|.++....-.+...+++...|.+
T Consensus 3 ~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~~~~~~~f~id~~~~~~~~~~~~~l~~l~~ 66 (75)
T cd04880 3 VFSLKNKPGALAKALKVFAERGINLTKIESRPSRKGLWEYEFFVDFEGHIDDPDVKEALEELKR 66 (75)
T ss_pred EEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCCCCceEEEEEEEECCCCCHHHHHHHHHHHH
Confidence 34456799999999999999999999998777655 3444444543211023334444444444
No 75
>PRK13010 purU formyltetrahydrofolate deformylase; Reviewed
Probab=86.73 E-value=2.9 Score=43.12 Aligned_cols=68 Identities=12% Similarity=0.121 Sum_probs=49.6
Q ss_pred EEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEE--eeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 424 VNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVIS--CFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 424 V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS--~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
+.|.|.|++++|+...|-+.|-+.|++|++++-. +..+.++-.+... ......+..++|+++|...+-
T Consensus 10 ~iitv~G~Dr~GIVA~Vs~~Lae~g~NI~disq~~d~~~~~ffm~i~~~-~~~~~~~~~~~l~~~l~~l~~ 79 (289)
T PRK13010 10 YVLTLACPSAPGIVAAVSGFLAEKGCYIVELTQFDDDESGRFFMRVSFH-AQSAEAASVDTFRQEFQPVAE 79 (289)
T ss_pred EEEEEECCCCCCcHHHHHHHHHHCCCCEEecccccccccCcEEEEEEEE-cCCCCCCCHHHHHHHHHHHHH
Confidence 5699999999999999999999999999999985 3333333222222 111125778999999887653
No 76
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=86.58 E-value=1.9 Score=41.99 Aligned_cols=65 Identities=15% Similarity=0.178 Sum_probs=54.3
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhh
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSA 491 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~a 491 (497)
.+.|.+.+.+|+|++..|-++|.++|..|...+.+..+|.+--++.+. +......+|+.+|....
T Consensus 8 ~lviTviG~DrpGIVa~vs~~l~~~g~NI~ds~~t~lgg~Fa~i~lvs----~~~~~~~~le~~L~~l~ 72 (190)
T PRK11589 8 YLVITALGADRPGIVNTITRHVSSCGCNIEDSRLAMLGEEFTFIMLLS----GSWNAITLIESTLPLKG 72 (190)
T ss_pred EEEEEEEcCCCChHHHHHHHHHHHcCCCeeehhhHhhCCceEEEEEEe----CChhHHHHHHHHHHhhh
Confidence 467889999999999999999999999999999999999887777773 22346778888776655
No 77
>PRK08577 hypothetical protein; Provisional
Probab=86.46 E-value=5.4 Score=36.22 Aligned_cols=69 Identities=23% Similarity=0.324 Sum_probs=50.0
Q ss_pred ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 422 RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN--GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 422 ~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n--g~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
+.+.|.|.+.+++|+|.+|+++|.++++++.+.+..+.. +.+.-.+.++... ...+.++|.+.|...-|
T Consensus 55 ~~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~~~~~~~i~l~vev~~--~~~~l~~l~~~L~~l~~ 125 (136)
T PRK08577 55 KLVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELKRGELAECVIIVDLSK--SDIDLEELEEELKKLEE 125 (136)
T ss_pred cEEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEecCCCEEEEEEEEEeCC--chhhHHHHHHHHHcCCC
Confidence 367899999999999999999999999999988777653 4444444554321 12356777777766544
No 78
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]
Probab=85.83 E-value=0.46 Score=48.18 Aligned_cols=51 Identities=33% Similarity=0.417 Sum_probs=44.6
Q ss_pred CCccccHHHHHHHHHHHHHHHHHHhcCCC---CCcCCccchHHHHHHHHHHHHH
Q 047004 307 LPAKNLMAERRRRKKLNDRLYMLRSVVPK---ISKMDRASILGDAIEYLKELLQ 357 (497)
Q Consensus 307 ~~~~H~~~ERrRR~kin~~~~~LrsLVP~---~~K~dKasIL~eAI~YIk~Lq~ 357 (497)
++.+=+..||+|=-.+|+-|..||.++|. ..|+.|+..|.-|-+||..|++
T Consensus 72 rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~ 125 (254)
T KOG3898|consen 72 RRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSE 125 (254)
T ss_pred hcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcc
Confidence 34455789999999999999999999994 5789999999999999999875
No 79
>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=85.48 E-value=5.4 Score=31.70 Aligned_cols=62 Identities=13% Similarity=0.223 Sum_probs=42.7
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee---CCeEEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF---NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~---ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
+.+.-+.+||.|.++++.|.+.|+.|++...... .+.-.-.+++.. +..+ ..++|.++|.+.
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~~~~~~~~~~~v~v~~--e~~~-~~~~i~~~L~~~ 66 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFEDAPDGMRRVFIRVTP--MDRS-KENELIEELKAK 66 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccccCCCCccEEEEEEEE--ecch-HHHHHHHHHhCc
Confidence 4556678999999999999999999998877665 333344445433 2222 266788877543
No 80
>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=84.55 E-value=9.3 Score=31.12 Aligned_cols=61 Identities=16% Similarity=0.273 Sum_probs=41.8
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEeeecCCcccCHHHHHHHHHH
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN-GFAMDVFRAEQCKEGQDVHPEQIKAVLLD 489 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n-g~vl~~f~aeq~keg~~v~~eqIk~~L~~ 489 (497)
|.+...+++|.|.+|++.+.++|+.+++....... +.....|+++.. + ....++++++|..
T Consensus 4 l~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd~~--~-~~~~~~~~~~l~~ 65 (80)
T cd04905 4 IVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFIDFE--G-HIEDPNVAEALEE 65 (80)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEEEE--C-CCCCHHHHHHHHH
Confidence 44445678999999999999999999998766653 345566777542 2 2344555555543
No 81
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=83.64 E-value=1.1 Score=48.45 Aligned_cols=43 Identities=40% Similarity=0.529 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCC----CCcCCccchHHHHHHHHHHH
Q 047004 313 MAERRRRKKLNDRLYMLRSVVPK----ISKMDRASILGDAIEYLKEL 355 (497)
Q Consensus 313 ~~ERrRR~kin~~~~~LrsLVP~----~~K~dKasIL~eAI~YIk~L 355 (497)
-+-|.||++-|-.|.+|..++|- .+..||++|+.-|..|||.-
T Consensus 7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKmr 53 (598)
T KOG3559|consen 7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKMR 53 (598)
T ss_pred hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHHH
Confidence 46689999999999999999995 35799999999999999753
No 82
>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=83.52 E-value=4.7 Score=30.41 Aligned_cols=45 Identities=20% Similarity=0.355 Sum_probs=36.5
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEe
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN-GFAMDVFRAE 470 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n-g~vl~~f~ae 470 (497)
|.|.+..++|.|.++++.|.+.+++|....+.... +..+..|.++
T Consensus 1 ~~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~ 46 (56)
T cd04889 1 LSVFVENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIFS 46 (56)
T ss_pred CEEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEEC
Confidence 35677889999999999999999999888877655 6666666664
No 83
>PRK07334 threonine dehydratase; Provisional
Probab=82.65 E-value=6.6 Score=41.86 Aligned_cols=51 Identities=20% Similarity=0.191 Sum_probs=41.8
Q ss_pred CceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee-----CCeEEEEEEEee
Q 047004 421 GRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF-----NGFAMDVFRAEQ 471 (497)
Q Consensus 421 g~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~-----ng~vl~~f~aeq 471 (497)
+-.+.|+|.+.+|+|+|.+|+.+|.+.+++|.+.++... ++.+.-.|.+++
T Consensus 324 ~y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i~V 379 (403)
T PRK07334 324 GRLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVIET 379 (403)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEEEe
Confidence 445899999999999999999999999999999998764 456555555654
No 84
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=81.33 E-value=7 Score=45.81 Aligned_cols=56 Identities=29% Similarity=0.461 Sum_probs=47.2
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEE-eeCCeEEEEEEEeeecCCcccC
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVIS-CFNGFAMDVFRAEQCKEGQDVH 479 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS-~~ng~vl~~f~aeq~keg~~v~ 479 (497)
...|-|.|+.++.++..|.-++...|++|+.|+|- +-+|+++++|++... .|..+.
T Consensus 684 ~teV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv~~~-~g~~~~ 740 (867)
T COG2844 684 GTEVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIVLEP-DGFPVE 740 (867)
T ss_pred ceEEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEEecC-CCCccc
Confidence 35789999999999999999999999999999976 568889999988633 344444
No 85
>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=81.30 E-value=6.3 Score=30.66 Aligned_cols=62 Identities=19% Similarity=0.280 Sum_probs=47.0
Q ss_pred EEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcCC
Q 047004 427 HMFCSRRPGLLLSTMRALDNLGLDIQQAVISC--FNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFH 494 (497)
Q Consensus 427 ~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~--~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~ 494 (497)
-+....++|.+.+|.+.|.+.|+.|.+..+.. .++....+++++. ..+.++.+.|...-|.+
T Consensus 3 ~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~~------~~~~~~~~~l~~~~~v~ 66 (73)
T cd04902 3 VVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVDE------PVPDEVLEELRALPGIL 66 (73)
T ss_pred EEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeCC------CCCHHHHHHHHcCCCcc
Confidence 45677899999999999999999998877655 3567766666642 23568888888776654
No 86
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]
Probab=78.92 E-value=2.7 Score=42.93 Aligned_cols=52 Identities=31% Similarity=0.300 Sum_probs=44.8
Q ss_pred ccccHHHHHHHHHHHHHHHHHHhcCCCC---CcCCccchHHHHHHHHHHHHHHHH
Q 047004 309 AKNLMAERRRRKKLNDRLYMLRSVVPKI---SKMDRASILGDAIEYLKELLQRIN 360 (497)
Q Consensus 309 ~~H~~~ERrRR~kin~~~~~LrsLVP~~---~K~dKasIL~eAI~YIk~Lq~~v~ 360 (497)
.+-+..||+|=..||..|..||.+||.. .|+.|-..|..|-.||--|-..++
T Consensus 176 ~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~ 230 (285)
T KOG4395|consen 176 LAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD 230 (285)
T ss_pred cccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence 5667899999999999999999999974 677888999999999988865443
No 87
>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=78.58 E-value=1.8 Score=33.52 Aligned_cols=62 Identities=16% Similarity=0.192 Sum_probs=42.9
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
|-+.+..++|++.+|+..|.+.++.|........++...-.+..+. . ..+++.+.|.+.-|.
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~a~~~~~~~~----~--~l~~li~~l~~~~~V 63 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGEIGYVVIDIDS----E--VSEELLEALRAIPGT 63 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCCEEEEEEEcCC----C--CCHHHHHHHHcCCCe
Confidence 3457788999999999999999999977655544455555554432 1 556676776665443
No 88
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=72.82 E-value=36 Score=39.86 Aligned_cols=77 Identities=14% Similarity=0.065 Sum_probs=54.2
Q ss_pred eEEEEEecC----ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEeeecCCcccCHHHHHHH
Q 047004 413 RVEVRVREG----RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF--NGFAMDVFRAEQCKEGQDVHPEQIKAV 486 (497)
Q Consensus 413 ~VEV~v~eg----~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~--ng~vl~~f~aeq~keg~~v~~eqIk~~ 486 (497)
.|+|.+... -.+.|.|.+..|+|+|.+|..+|-+.++.|.++++... ++.+.-.|.+++.. .-....|...
T Consensus 652 ~I~V~W~~~~~~~~~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~~~~~~~~~ieV~~---~~~L~~l~~~ 728 (743)
T PRK10872 652 IVDAVWGESYSSGYSLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQQLATIDMTIEIYN---LQVLGRVLGK 728 (743)
T ss_pred EEEeEecCCCCceeEEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCCEEEEEEEEEECC---HHHHHHHHHH
Confidence 478888532 24689999999999999999999999999999998765 46655556665421 2234444555
Q ss_pred HHHhhc
Q 047004 487 LLDSAG 492 (497)
Q Consensus 487 L~~~aG 492 (497)
|...-|
T Consensus 729 L~~i~~ 734 (743)
T PRK10872 729 LNQVPD 734 (743)
T ss_pred HhcCCC
Confidence 544433
No 89
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=70.47 E-value=50 Score=38.41 Aligned_cols=59 Identities=15% Similarity=0.084 Sum_probs=46.6
Q ss_pred eEEEEEecC----ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEee
Q 047004 413 RVEVRVREG----RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN-GFAMDVFRAEQ 471 (497)
Q Consensus 413 ~VEV~v~eg----~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n-g~vl~~f~aeq 471 (497)
.|+|++... -.+.|.|.+.+++|+|.+|+.+|-+.++.|.++++.... +.+.-.|.+++
T Consensus 612 ~i~v~W~~~~~~~~~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~~~~~~~~ieV 675 (702)
T PRK11092 612 FMAVEWDKETEQEFIAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGRVYSAFIRLTA 675 (702)
T ss_pred eEEeEECCCCCceeEEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCCEEEEEEEEEE
Confidence 578888532 246899999999999999999999999999999987765 45444556654
No 90
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=70.13 E-value=7.6 Score=33.96 Aligned_cols=67 Identities=18% Similarity=0.280 Sum_probs=54.5
Q ss_pred EEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 424 VNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 424 V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
+.|.|.-.+|+|+...|..+|-++|++|...+=+...|++--.+.+...+ ..+....++..|...+-
T Consensus 4 avITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ftm~~lV~~~~--~~~d~~~lr~~l~~~~~ 70 (90)
T COG3830 4 AVITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIMLVDISK--EVVDFAALRDELAAEGK 70 (90)
T ss_pred EEEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhhhceeeeEEcCCh--HhccHHHHHHHHHHHHH
Confidence 56888888999999999999999999999999999999887777776432 35667777777766553
No 91
>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=69.83 E-value=32 Score=29.59 Aligned_cols=47 Identities=9% Similarity=0.054 Sum_probs=35.3
Q ss_pred EEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCe-EEEEEEEe
Q 047004 424 VNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGF-AMDVFRAE 470 (497)
Q Consensus 424 V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~-vl~~f~ae 470 (497)
..|-+...+++|.|.++|..+...|+.+.+-.+-..-+. --+.|.++
T Consensus 15 tslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfVD 62 (90)
T cd04931 15 ISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFIN 62 (90)
T ss_pred EEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEE
Confidence 344555577999999999999999999999888776433 33455555
No 92
>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=69.26 E-value=26 Score=28.45 Aligned_cols=58 Identities=7% Similarity=0.101 Sum_probs=40.5
Q ss_pred EEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCe-EEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 428 MFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGF-AMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 428 I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~-vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
+...+++|.|.++|..+...|+.+++-.+-...+. .-+.|.++. + | ..+.++++|.+.
T Consensus 5 f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffvd~-~-~---~~~~~~~~l~~L 63 (74)
T cd04904 5 FSLKEEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFVDC-E-V---DRGDLDQLISSL 63 (74)
T ss_pred EEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEEEE-E-c---ChHHHHHHHHHH
Confidence 34467999999999999999999999988877654 344555543 2 2 334455555543
No 93
>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=68.67 E-value=49 Score=38.25 Aligned_cols=59 Identities=19% Similarity=0.169 Sum_probs=47.0
Q ss_pred eEEEEEecC----ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee-CCeEEEEEEEee
Q 047004 413 RVEVRVREG----RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF-NGFAMDVFRAEQ 471 (497)
Q Consensus 413 ~VEV~v~eg----~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~-ng~vl~~f~aeq 471 (497)
.|.|.+... -.+.|.|.+.+++|+|.+|+.+|-+.+++|.++++... ++.+.-.|.+++
T Consensus 596 ~I~v~W~~~~~~~f~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~~~~~~~~~ieV 659 (683)
T TIGR00691 596 IIEVEWNASKPRRFIVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGKREAILNITVEI 659 (683)
T ss_pred EEEEEecCCCCceeEEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCEEEEEEEEEE
Confidence 578888532 25689999999999999999999999999999998876 355555566654
No 94
>COG0788 PurU Formyltetrahydrofolate hydrolase [Nucleotide transport and metabolism]
Probab=66.39 E-value=27 Score=36.35 Aligned_cols=68 Identities=21% Similarity=0.235 Sum_probs=50.5
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF--NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~--ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
...+.+.|+.++|+...|-..|-+.|..|++++-... .|+++- +++=..++....-+++++.+-..+.
T Consensus 7 ~~~LtvsCpd~~GiVaais~~l~~~g~NI~~~~qf~D~~~g~FFm--R~~f~~~~~~~~~~~l~~~f~~~a~ 76 (287)
T COG0788 7 TFILTVSCPDQPGIVAAISGFLAEHGCNIVDSDQFDDPETGRFFM--RVEFEGEGGPLDREALRAAFAPLAE 76 (287)
T ss_pred ceEEEEecCCCCCcHHHHHHHHHHcCCceeecccccccccCeEEE--EEEEecCCCcccHHHHHHHHHHHHH
Confidence 4678999999999999999999999999999887642 333332 3332234445778888888877654
No 95
>PRK06382 threonine dehydratase; Provisional
Probab=65.31 E-value=27 Score=37.37 Aligned_cols=71 Identities=25% Similarity=0.336 Sum_probs=50.9
Q ss_pred cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEE-----eeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcCC
Q 047004 420 EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVIS-----CFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFH 494 (497)
Q Consensus 420 eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS-----~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~ 494 (497)
.++.+.|.|.-++++|.|.+|++.|.+.+++|++.... .-.+...-+|+++... .-+.++|++.|.+ .||+
T Consensus 327 ~~~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~~~~~~~~~~~~~~v~i~vet~~---~~~~~~v~~~L~~-~Gy~ 402 (406)
T PRK06382 327 LGQLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEVDNLRKETPPGFQSVTFTVNVRG---QDHLDRILNALRE-MGYK 402 (406)
T ss_pred cCCEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEEeeccccCCCCcEEEEEEEEeCC---HHHHHHHHHHHHH-CCCC
Confidence 35677888888899999999999999999999987764 2244566667776531 2344577777654 4554
No 96
>PF05088 Bac_GDH: Bacterial NAD-glutamate dehydrogenase
Probab=62.38 E-value=38 Score=42.68 Aligned_cols=69 Identities=16% Similarity=0.288 Sum_probs=52.5
Q ss_pred ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC---C--eEEEEEEEeeecCCcccCHHHHHHHHHHhh
Q 047004 422 RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN---G--FAMDVFRAEQCKEGQDVHPEQIKAVLLDSA 491 (497)
Q Consensus 422 ~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n---g--~vl~~f~aeq~keg~~v~~eqIk~~L~~~a 491 (497)
..+.++|+...++..|++||-+|+++||.|+...-..+. + ..++-|.+.. ..+.....++++..+.++.
T Consensus 488 ~~~~lkiy~~~~~~~Ls~vlPilenlGl~V~~e~~~~i~~~~~~~~~i~~F~l~~-~~~~~~~~~~~~~~~~~a~ 561 (1528)
T PF05088_consen 488 GRLRLKIYHPGEPLPLSDVLPILENLGLRVIDERPYEIRRADGRRVWIHDFGLQY-PDGDALDLDDIRERFEEAF 561 (1528)
T ss_pred CeEEEEEEcCCCCcCHHHHHHHHHhCCCEEEEEecceeecCCCceEEEEEEEEec-CCCccccHHHHHHHHHHHH
Confidence 468899999999999999999999999999998744432 2 4666677753 3444567778887777654
No 97
>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=61.93 E-value=50 Score=26.13 Aligned_cols=62 Identities=18% Similarity=0.149 Sum_probs=39.7
Q ss_pred EEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCC-eEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 427 HMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNG-FAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 427 ~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng-~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
+|.-+.+||-|.+++++|.+ +.+|+.......+- ...-.+.++... .-+.++|.++|.+ .||
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~~~~~~~v~v~ie~~~---~~~~~~i~~~L~~-~G~ 64 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQGGDEARVLVGIQVPD---REDLAELKERLEA-LGY 64 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcCCCCceEEEEEEEeCC---HHHHHHHHHHHHH-cCC
Confidence 45567899999999999999 99999887765431 111112233221 2355677776655 555
No 98
>TIGR00119 acolac_sm acetolactate synthase, small subunit. acetohydroxyacid synthase is a synonym.
Probab=59.80 E-value=44 Score=31.73 Aligned_cols=63 Identities=16% Similarity=0.193 Sum_probs=47.8
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEeeecCCcccCHHHHHHHHHHhh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN--GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSA 491 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n--g~vl~~f~aeq~keg~~v~~eqIk~~L~~~a 491 (497)
.|.|.-.+++|.|.+|...|...|+.|.+..+...+ +...-++++.. .+...++|.+-|.+..
T Consensus 3 ~isI~ven~pGvL~rI~~lf~rrg~NI~Sl~v~~t~~~~~sriti~V~~----d~~~i~qi~kQl~Kli 67 (157)
T TIGR00119 3 ILSVLVENEPGVLSRVAGLFTRRGFNIESLTVGPTEDPDLSRMTIVVVG----DDKVLEQITKQLNKLV 67 (157)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCceEEEEEEeecCCCCEEEEEEEEEC----CHHHHHHHHHHHhcCc
Confidence 477788899999999999999999999998888665 55555566642 2455777777776543
No 99
>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=58.88 E-value=52 Score=34.64 Aligned_cols=67 Identities=27% Similarity=0.373 Sum_probs=48.5
Q ss_pred cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee-----CCeEEEEEEEeeecCCcccCHHHHHHHHHH
Q 047004 420 EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF-----NGFAMDVFRAEQCKEGQDVHPEQIKAVLLD 489 (497)
Q Consensus 420 eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~-----ng~vl~~f~aeq~keg~~v~~eqIk~~L~~ 489 (497)
+++.+.|.|.-++++|.|.++++.+.+.+.+|++...... .+.+.-.+.++... .-+.++|.+.|.+
T Consensus 302 ~gr~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~r~~~~~~~~~~~v~v~vet~~---~~~~~~i~~~L~~ 373 (380)
T TIGR01127 302 SGRKVRIETVLPDRPGALYHLLESIAEARANIVKIDHDRLSKEIPPGFAMVEITLETRG---KEHLDEILKILRD 373 (380)
T ss_pred CCCEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeccccCCCCceEEEEEEEEeCC---HHHHHHHHHHHHH
Confidence 4677889999999999999999999999999998876532 24444455555421 3445577777655
No 100
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=58.49 E-value=54 Score=31.97 Aligned_cols=68 Identities=12% Similarity=0.053 Sum_probs=49.1
Q ss_pred EEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC----CeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 424 VNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN----GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 424 V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n----g~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
+.|.+.-.++||++.+|-++|-+.|++|.+-+.-+.. +.-++..+++.. --.++..++++.+|.+.+.
T Consensus 96 ~~v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~a~~~~~~lf~~~~~v~-lP~~~~~~~L~~~l~~l~~ 167 (190)
T PRK11589 96 VWVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQPAEGERPAQLHIQITAH-SPASQDAANIEQAFKALCT 167 (190)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHcCCChhheEEeeecCCCCCcccEEEEEEEE-cCCCCCHHHHHHHHHHHHH
Confidence 4566777789999999999999999999888877664 333333333321 1124668899999888764
No 101
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=56.37 E-value=4.3 Score=46.60 Aligned_cols=65 Identities=20% Similarity=0.275 Sum_probs=54.0
Q ss_pred CCCccccHHHHHHHHHHHHHHHHHHhcCCC-----CCcCCccchHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 306 GLPAKNLMAERRRRKKLNDRLYMLRSVVPK-----ISKMDRASILGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 306 ~~~~~H~~~ERrRR~kin~~~~~LrsLVP~-----~~K~dKasIL~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
.+...|+-+|.+||.+++-.+..|.+++-+ ..|+.++.-+...++||..++++...+++|-..++
T Consensus 650 ~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~~lr 719 (856)
T KOG3582|consen 650 NRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAHSLR 719 (856)
T ss_pred CCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhhhhhh
Confidence 456889999999999999999999998865 35777888899999999999888777777655554
No 102
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=54.41 E-value=61 Score=37.68 Aligned_cols=65 Identities=17% Similarity=0.218 Sum_probs=54.4
Q ss_pred EEEEE-cCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhh
Q 047004 425 NIHMF-CSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSA 491 (497)
Q Consensus 425 ~I~I~-C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~a 491 (497)
.+.|. |++++|++.++.-+|--.++.|.+|++.+ +|.....|.+.. .-|....+..+.+.+....
T Consensus 548 ~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~a~~~~-~~~~~~~~~v~~-~~~~~~~~~~~~~~~~~~~ 613 (693)
T PRK00227 548 FFTVIWHGDYPRELVRVLALIAAKGWNILSARMVA-NGPWSAEFDVRA-NGPQDFDPQEFLQAYKSGV 613 (693)
T ss_pred eEEEEecCCcccHHHHHHHHHHhcCceeeEeEEec-CCceEEEEEEec-CCCCCCChHHHHHHHHHhh
Confidence 34444 48999999999999999999999999999 888888888865 4677888888888877544
No 103
>PRK11895 ilvH acetolactate synthase 3 regulatory subunit; Reviewed
Probab=54.31 E-value=61 Score=30.97 Aligned_cols=62 Identities=18% Similarity=0.283 Sum_probs=46.0
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN--GFAMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n--g~vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
.|.|.-..++|.|.+|...|...|+.|.+..+.... +...-++++. +.+-..+||..-|.+.
T Consensus 4 ~IsV~veN~pGvL~rI~~lf~rrg~NI~Sl~v~~te~~~~sriti~V~----~~~~~i~qi~kQl~KL 67 (161)
T PRK11895 4 TLSVLVENEPGVLSRVAGLFSRRGYNIESLTVGPTEDPGLSRMTIVTS----GDEQVIEQITKQLNKL 67 (161)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCcEEEEEeeecCCCCEEEEEEEEE----CCHHHHHHHHHHHhcc
Confidence 477778899999999999999999999998887654 5555556654 2345566666666543
No 104
>PRK08526 threonine dehydratase; Provisional
Probab=53.48 E-value=70 Score=34.45 Aligned_cols=71 Identities=24% Similarity=0.355 Sum_probs=50.9
Q ss_pred cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCe-----EEEEEEEeeecCCcccCHHHHHHHHHHhhcCC
Q 047004 420 EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGF-----AMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFH 494 (497)
Q Consensus 420 eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~-----vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~ 494 (497)
+++.+.+.+.-+++||-|.+++..+-+.+.+|+.......... +.-.+.+|.. ..-+.++|.+.|.. .||+
T Consensus 323 ~~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~~~~~~~~~~~~~~~~e~~---~~~~~~~~~~~l~~-~g~~ 398 (403)
T PRK08526 323 SYRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRFSTKLDYGDAMISITLETK---GKEHQEEIRKILTE-KGFN 398 (403)
T ss_pred cCCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEeccCCCCCccEEEEEEEEeC---CHHHHHHHHHHHHH-CCCC
Confidence 5788999999999999999999999999999999888665433 3333344432 13455667777644 5553
No 105
>PRK08198 threonine dehydratase; Provisional
Probab=51.98 E-value=80 Score=33.58 Aligned_cols=70 Identities=27% Similarity=0.407 Sum_probs=49.3
Q ss_pred cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee-----CCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 420 EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF-----NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 420 eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~-----ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
.++.+.+.|.-+++||.|.++++.|-+.|.+|+....... .+.+.-.+.++.. +.+ +.++|.+.|.+ .||
T Consensus 324 ~gr~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~~~~~~~~~~~~v~v~ie~~--~~~-~~~~l~~~L~~-~G~ 398 (404)
T PRK08198 324 AGRYLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDRFSPDLRLGEVEVELTLETR--GPE-HIEEILDALRD-AGY 398 (404)
T ss_pred cCCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEEccCCCCCceEEEEEEEEeC--CHH-HHHHHHHHHHH-CCC
Confidence 4677888899999999999999999999999998887653 2444444555531 112 45677777654 444
No 106
>CHL00100 ilvH acetohydroxyacid synthase small subunit
Probab=49.42 E-value=87 Score=30.33 Aligned_cols=64 Identities=13% Similarity=0.203 Sum_probs=46.4
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISC--FNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~--~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
.|.|.-.++||+|.+|...|-..|++|.+-++.. ..+...-++.+. .+... .++|++.|.+.+-
T Consensus 4 ~isvlv~n~PGVL~RIt~lFsrRg~NIesLsv~~t~~~~~sr~TIvv~---~~~~~-ieqL~kQL~KLid 69 (174)
T CHL00100 4 TLSVLVEDESGVLTRIAGLFARRGFNIESLAVGPAEQKGISRITMVVP---GDDRT-IEQLTKQLYKLVN 69 (174)
T ss_pred EEEEEEeCcCCHHHHHHHHHHhCCCCeeEEEeeEcCCCCccEEEEEEE---CCHHH-HHHHHHHHHHHhH
Confidence 4778888999999999999999999999988866 344442333332 22233 7899988887653
No 107
>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=47.57 E-value=1e+02 Score=25.45 Aligned_cols=55 Identities=9% Similarity=0.140 Sum_probs=38.0
Q ss_pred CCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCe-EEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 431 SRRPGLLLSTMRALDNLGLDIQQAVISCFNGF-AMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 431 ~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~-vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
.+++|.|.++|..++..|+.+.+-..-...+. .-+.|.++ ++ | +.+.|+++|...
T Consensus 8 ~~~~g~L~~iL~~f~~~~inl~~IeSRP~~~~~~~y~F~id-~e-~---~~~~i~~~l~~l 63 (74)
T cd04929 8 KNEVGGLAKALKLFQELGINVVHIESRKSKRRSSEFEIFVD-CE-C---DQRRLDELVQLL 63 (74)
T ss_pred CCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEEE-EE-c---CHHHHHHHHHHH
Confidence 57899999999999999999999887765333 33445554 32 2 223666666543
No 108
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=44.94 E-value=1.1e+02 Score=28.45 Aligned_cols=38 Identities=29% Similarity=0.501 Sum_probs=34.1
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCe
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGF 462 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~ 462 (497)
.|+|+.+.++|.|..+..+|.+.|+.+.--+|.-.++|
T Consensus 5 QISvFlENk~GRL~~~~~~L~eagINiRA~tiAdt~dF 42 (142)
T COG4747 5 QISVFLENKPGRLASVANKLKEAGINIRAFTIADTGDF 42 (142)
T ss_pred EEEEEecCCcchHHHHHHHHHHcCCceEEEEeccccCc
Confidence 58999999999999999999999999988887776665
No 109
>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=43.98 E-value=97 Score=25.22 Aligned_cols=46 Identities=15% Similarity=0.239 Sum_probs=32.6
Q ss_pred ceEEEEEecCceEEEEEEcCCC------CcHHHHHHHHHHhCCCeEEEEEEEe
Q 047004 412 ARVEVRVREGRAVNIHMFCSRR------PGLLLSTMRALDNLGLDIQQAVISC 458 (497)
Q Consensus 412 ~~VEV~v~eg~~V~I~I~C~kr------~GlL~~ILeALEeLgLdVvsAsIS~ 458 (497)
+.|.|++.+ +.+.|+|.+... ..-+..+-++|...|+.|.+.++..
T Consensus 27 v~v~l~~~~-~~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~~G~~~~~~~v~~ 78 (85)
T PF02120_consen 27 VEVKLRLQG-GNLSVQFTAENPETKELLRQNLPELKERLQAQGLEVVNLSVSQ 78 (85)
T ss_dssp EEEEEEEET-TEEEEEEE--SSHHHHHHHHTHHHHHHHHHTTT-EEEEEEEES
T ss_pred EEEEEEEeC-CEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCeEEEEEEE
Confidence 467776664 578999999864 4456778889999999999877654
No 110
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=43.96 E-value=9.4 Score=43.99 Aligned_cols=66 Identities=21% Similarity=0.263 Sum_probs=54.1
Q ss_pred CCCCCCCccccHHHHHHHHHHHHHHHHHHhcCCCC-----CcCCccchHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 302 GKKKGLPAKNLMAERRRRKKLNDRLYMLRSVVPKI-----SKMDRASILGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 302 ~rk~~~~~~H~~~ERrRR~kin~~~~~LrsLVP~~-----~K~dKasIL~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
...-...+.|+.+|||||-.+-+++..|..|.|.. .+..+++||. +.|+.+++.-+.+.+..+..+
T Consensus 782 p~n~~v~a~sih~lrr~~~~~~dq~~sL~alrp~v~~~~~ql~S~tS~L~---dp~~~~eq~ska~~e~~~~kr 852 (856)
T KOG3582|consen 782 PFNGMVSAGSIHALRRTRLNWLDQFCSLPALRPQVLLNLRQLLSSTSILT---DPIKQPEQASKAVTEKIEGKR 852 (856)
T ss_pred cccceeecchHHHHHHHHHHHhhccccHHHHHHHHHhhHHHhhhhhhccc---CcccchHHHHHHHHhhhhhhc
Confidence 33344567899999999999999999999999963 5678999999 889999998888888765543
No 111
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=43.62 E-value=1.2e+02 Score=28.81 Aligned_cols=69 Identities=12% Similarity=0.183 Sum_probs=49.9
Q ss_pred cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEE-eeCCeEEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 420 EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVIS-CFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 420 eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS-~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
+++.+.+.+.-.+|.|.|+++++++-..++.|.+.+=+ ..+|++--++-.... +-+-..+.|..+|...
T Consensus 69 k~ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~Anvtlsi~~s--sm~~~V~~ii~kl~k~ 138 (150)
T COG4492 69 KERIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGRANVTLSIDTS--SMEKDVDKIIEKLRKV 138 (150)
T ss_pred cceEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCceeeEEEEEEch--hhhhhHHHHHHHHhcc
Confidence 34667888889999999999999999999999887643 677776666555432 2234556666666543
No 112
>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=42.27 E-value=2e+02 Score=23.85 Aligned_cols=65 Identities=14% Similarity=0.110 Sum_probs=39.0
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC-CeEEEEEEEeeecCCcccCHHHHHHHHHHhhcCC
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN-GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFH 494 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n-g~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~ 494 (497)
++.|.-+.+||-|.+++++|- +.+|......... +...-.+..+. +++ .-+.+++.++|.+ .||.
T Consensus 3 vl~v~ipD~PG~L~~ll~~l~--~anI~~~~y~~~~~~~~~v~i~ie~-~~~-~~~~~~i~~~L~~-~G~~ 68 (85)
T cd04906 3 LLAVTIPERPGSFKKFCELIG--PRNITEFNYRYADEKDAHIFVGVSV-ANG-AEELAELLEDLKS-AGYE 68 (85)
T ss_pred EEEEecCCCCcHHHHHHHHhC--CCceeEEEEEccCCCeeEEEEEEEe-CCc-HHHHHHHHHHHHH-CCCC
Confidence 477778899999999999998 6666655554432 22222233332 111 2346677776644 5653
No 113
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=40.56 E-value=21 Score=34.26 Aligned_cols=42 Identities=21% Similarity=0.314 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCC--CcCCccchHHHHHHHHHHH
Q 047004 314 AERRRRKKLNDRLYMLRSVVPKI--SKMDRASILGDAIEYLKEL 355 (497)
Q Consensus 314 ~ERrRR~kin~~~~~LrsLVP~~--~K~dKasIL~eAI~YIk~L 355 (497)
.||.|..++++.+.-|+.|+|+. .++.+.--|.-+-.||+.|
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 68899999999999999999973 3333333355555555554
No 114
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=39.98 E-value=1.2e+02 Score=25.61 Aligned_cols=62 Identities=13% Similarity=0.125 Sum_probs=42.9
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN--GFAMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n--g~vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
.|.+.-.+++|+|.+|..++.-.|..|.+-++...+ +...-++.+. |.+-..++|.+-|.+.
T Consensus 4 tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te~~~~sriti~~~----~~~~~i~qi~kQL~KL 67 (76)
T PRK06737 4 TFSLVIHNDPSVLLRISGIFARRGYYISSLNLNERDTSGVSEMKLTAV----CTENEATLLVSQLKKL 67 (76)
T ss_pred EEEEEEecCCCHHHHHHHHHhccCcceEEEEecccCCCCeeEEEEEEE----CCHHHHHHHHHHHhCC
Confidence 577888899999999999999999999888877544 3333333332 2344556666665543
No 115
>cd04892 ACT_AK-like_2 ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the second of two ACT domains C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). The exception in this group, is the inclusion of the first ACT domain of the bifunctional aspartokinase - homoserine dehydrogenase-like enzyme group (ACT_AKi-HSDH-ThrA-like_1) which includes the monofunctional, threonine-sensitive, aspartokinase found in Methanococcus jannaschii and other related archaeal species. AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. AK is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids (lysine, threonine, methionine, and isoleucine) and the bacterial cell wall component, meso-diaminopimelate. One mechanism for the regulation of this pathway is by the production of several isoenzymes of AK with different repressors an
Probab=39.08 E-value=1e+02 Score=22.41 Aligned_cols=34 Identities=18% Similarity=0.286 Sum_probs=26.5
Q ss_pred EEEEEcC---CCCcHHHHHHHHHHhCCCeEEEEEEEe
Q 047004 425 NIHMFCS---RRPGLLLSTMRALDNLGLDIQQAVISC 458 (497)
Q Consensus 425 ~I~I~C~---kr~GlL~~ILeALEeLgLdVvsAsIS~ 458 (497)
.|+|.+. ..++.+.+++++|.+.++.|.....+.
T Consensus 2 ~i~i~g~~~~~~~~~~~~i~~~l~~~~i~v~~i~~~~ 38 (65)
T cd04892 2 LVSVVGAGMRGTPGVAARIFSALAEAGINIIMISQGS 38 (65)
T ss_pred EEEEECCCCCCCccHHHHHHHHHHHCCCcEEEEEcCC
Confidence 3566544 468899999999999999998776544
No 116
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.08 E-value=40 Score=28.47 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 345 LGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 345 L~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
+..||+-|.-||.+|++|+++..++.
T Consensus 13 iqqAvdTI~LLQmEieELKEknn~l~ 38 (79)
T COG3074 13 VQQAIDTITLLQMEIEELKEKNNSLS 38 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHhH
Confidence 67899999999999999999887664
No 117
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=37.44 E-value=1.5e+02 Score=23.62 Aligned_cols=55 Identities=20% Similarity=0.253 Sum_probs=38.4
Q ss_pred CCCcHHHHHHHHHHhCCCeEEEEEEEe--eCCeEEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 432 RRPGLLLSTMRALDNLGLDIQQAVISC--FNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 432 kr~GlL~~ILeALEeLgLdVvsAsIS~--~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
+++|.|.+|+..+.-.|..|.+-++.. .++...-++.+. +.+-..++|..-|.+.
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v~----~~~~~i~~l~~Ql~Kl 57 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDPGISRITIVVS----GDDREIEQLVKQLEKL 57 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEEE----S-CCHHHHHHHHHHCS
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEEe----eCchhHHHHHHHHhcc
Confidence 368999999999999999999988887 455544444442 3345667777766554
No 118
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=36.74 E-value=1.2e+02 Score=26.19 Aligned_cols=63 Identities=10% Similarity=0.023 Sum_probs=44.0
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCe--EEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGF--AMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~--vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
.|.+.-..++|+|.+|-.++--.|..|.+-++...... ..-++.++ .|.+-..+||.+-|.+.
T Consensus 4 ~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te~~~iSRmtivv~---~~d~~~ieqI~kQL~Kl 68 (84)
T PRK13562 4 ILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSEQPGISNMEIQVD---IQDDTSLHILIKKLKQQ 68 (84)
T ss_pred EEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccCCCCceEEEEEEe---CCCHHHHHHHHHHHhCC
Confidence 47778889999999999999999988888777755443 33333332 13455667777766543
No 119
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=36.23 E-value=2.4e+02 Score=23.68 Aligned_cols=62 Identities=10% Similarity=0.094 Sum_probs=44.5
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEee--CCeEEEEEEEeeecCCcccCHHHHHHHHHHhh
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCF--NGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSA 491 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~--ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~a 491 (497)
.|.|.-.+++|.|.+|+..+.-.|..|.+-++... .+...-++.+. .+...++|.+-|.+..
T Consensus 5 ~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t~~~~~sriti~v~-----~~~~i~ql~kQL~KL~ 68 (76)
T PRK11152 5 QLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQNTDAQNINIELTVA-----SERPIDLLSSQLNKLV 68 (76)
T ss_pred EEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeecCCCCEEEEEEEEC-----CCchHHHHHHHHhcCc
Confidence 46777788999999999999999999998888774 33333333331 2566777777665543
No 120
>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=32.92 E-value=62 Score=24.65 Aligned_cols=25 Identities=16% Similarity=0.314 Sum_probs=21.8
Q ss_pred CCCcHHHHHHHHHHhCCCeEEEEEE
Q 047004 432 RRPGLLLSTMRALDNLGLDIQQAVI 456 (497)
Q Consensus 432 kr~GlL~~ILeALEeLgLdVvsAsI 456 (497)
.++|...+|+++|++.+++|.....
T Consensus 12 ~~~~~~~~if~~l~~~~i~v~~i~t 36 (62)
T cd04890 12 GEVGFLRKIFEILEKHGISVDLIPT 36 (62)
T ss_pred cccCHHHHHHHHHHHcCCeEEEEec
Confidence 4689999999999999999987743
No 121
>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=32.73 E-value=1.8e+02 Score=20.56 Aligned_cols=25 Identities=24% Similarity=0.444 Sum_probs=21.2
Q ss_pred CCcHHHHHHHHHHhCCCeEEEEEEE
Q 047004 433 RPGLLLSTMRALDNLGLDIQQAVIS 457 (497)
Q Consensus 433 r~GlL~~ILeALEeLgLdVvsAsIS 457 (497)
.++.+.+++++|.+.++.|.....+
T Consensus 13 ~~~~~~~i~~~l~~~~i~i~~i~~~ 37 (60)
T cd04868 13 TPGVAAKIFSALAEAGINVDMISQS 37 (60)
T ss_pred CCCHHHHHHHHHHHCCCcEEEEEcC
Confidence 6799999999999999999765544
No 122
>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=30.76 E-value=53 Score=27.44 Aligned_cols=24 Identities=17% Similarity=0.237 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhc
Q 047004 345 LGDAIEYLKELLQRINDLHNELES 368 (497)
Q Consensus 345 L~eAI~YIk~Lq~~v~~L~~e~es 368 (497)
+..||+-|..||.++++|+.+..+
T Consensus 13 i~~aveti~~Lq~e~eeLke~n~~ 36 (72)
T PF06005_consen 13 IQQAVETIALLQMENEELKEKNNE 36 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 678999999999999999997543
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=28.62 E-value=2.2e+02 Score=25.60 Aligned_cols=43 Identities=5% Similarity=-0.118 Sum_probs=32.3
Q ss_pred EEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCe-EEEEEEEe
Q 047004 428 MFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGF-AMDVFRAE 470 (497)
Q Consensus 428 I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~-vl~~f~ae 470 (497)
+...+++|.|.+||..+...|+.+++-.+-...+. .-+.|.++
T Consensus 46 fsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~~~~~eY~FfId 89 (115)
T cd04930 46 FSLKEGFSSLSRILKVFETFEAKIHHLESRPSRKEGGDLEVLVR 89 (115)
T ss_pred EEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCCCCCceEEEEEE
Confidence 33467899999999999999999999887776333 23445554
No 124
>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=28.31 E-value=58 Score=23.48 Aligned_cols=17 Identities=47% Similarity=0.716 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHh
Q 047004 315 ERRRRKKLNDRLYMLRS 331 (497)
Q Consensus 315 ERrRR~kin~~~~~Lrs 331 (497)
=|+||+.++.++..||.
T Consensus 13 Lrrr~eqLK~kLeqlrn 29 (32)
T PF02344_consen 13 LRRRREQLKHKLEQLRN 29 (32)
T ss_dssp HHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 37889999999999985
No 125
>PRK15385 magnesium transport protein MgtC; Provisional
Probab=28.26 E-value=2.9e+02 Score=27.94 Aligned_cols=67 Identities=7% Similarity=0.029 Sum_probs=43.7
Q ss_pred eEEEEEEcCCCCc--HHHHHHHHHHhCCCeEEEEEEEeeCC--eEE--EEEEEeeecCCcccCHHHHHHHHHHhhc
Q 047004 423 AVNIHMFCSRRPG--LLLSTMRALDNLGLDIQQAVISCFNG--FAM--DVFRAEQCKEGQDVHPEQIKAVLLDSAG 492 (497)
Q Consensus 423 ~V~I~I~C~kr~G--lL~~ILeALEeLgLdVvsAsIS~~ng--~vl--~~f~aeq~keg~~v~~eqIk~~L~~~aG 492 (497)
.+.++|.|.+... +...+++.|++.++.+.+..+....+ .+. ..+.+.. ..+...++|.+.|...-|
T Consensus 142 ~~~~~v~~~~~~~~~vr~~L~~~l~~~~~~~~~l~~~~~~~~~~~ei~a~l~~~~---~~~~~le~iv~~L~~~pg 214 (225)
T PRK15385 142 RYILKVTCNKEDESAVRQWLLNIVKEAAICLQGLGSVPAQEQGYKEIRAELVGHA---DYRKTRELIISRIGDNDN 214 (225)
T ss_pred EEEEEEEEcCcchhHHHHHHHHHHHhCCCceEEeEeeecCCCCeEEEEEEEEecC---CchhhHHHHHHHHhCCCC
Confidence 4678899987654 57888899999999999999976632 222 2222221 134566666666655433
No 126
>PRK08639 threonine dehydratase; Validated
Probab=27.02 E-value=2.8e+02 Score=29.88 Aligned_cols=70 Identities=17% Similarity=0.042 Sum_probs=45.4
Q ss_pred cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCe-EEEE-EEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 420 EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGF-AMDV-FRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 420 eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~-vl~~-f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
+++.+.+++.-+.|||-|.++++.+-..+-+|+..+.-...+. .-.+ +.+|.. + .-+.++|++.|.+ .||
T Consensus 333 ~~r~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~~~~~~~~~~~~v~v~iE~~-~--~~h~~~i~~~L~~-~Gy 404 (420)
T PRK08639 333 EGLKHYFIVNFPQRPGALREFLDDVLGPNDDITRFEYLKKNNRETGPVLVGIELK-D--AEDYDGLIERMEA-FGP 404 (420)
T ss_pred cCCEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEEeecCCCCceEEEEEEEeC-C--HHHHHHHHHHHHH-CCC
Confidence 5788999999999999999999966555558887765532222 1122 222321 1 2356788887766 565
No 127
>smart00338 BRLZ basic region leucin zipper.
Probab=26.20 E-value=2e+02 Score=22.81 Aligned_cols=21 Identities=24% Similarity=0.317 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHhhhcC
Q 047004 349 IEYLKELLQRINDLHNELEST 369 (497)
Q Consensus 349 I~YIk~Lq~~v~~L~~e~esl 369 (497)
-.||..|+.+++.|+.+...+
T Consensus 25 k~~~~~Le~~~~~L~~en~~L 45 (65)
T smart00338 25 KAEIEELERKVEQLEAENERL 45 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 346666666666665555444
No 128
>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=26.14 E-value=2.8e+02 Score=20.76 Aligned_cols=33 Identities=15% Similarity=0.273 Sum_probs=25.5
Q ss_pred EEEEEcC---CCCcHHHHHHHHHHhCCCeEEEEEEE
Q 047004 425 NIHMFCS---RRPGLLLSTMRALDNLGLDIQQAVIS 457 (497)
Q Consensus 425 ~I~I~C~---kr~GlL~~ILeALEeLgLdVvsAsIS 457 (497)
.|.|.+. ..++++.+|+++|.+.++.|.-...+
T Consensus 3 ~isvvg~~~~~~~~~~~~i~~~l~~~~I~v~~i~~~ 38 (66)
T cd04922 3 ILALVGDGMAGTPGVAATFFSALAKANVNIRAIAQG 38 (66)
T ss_pred EEEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEec
Confidence 3555554 46899999999999999999665543
No 129
>COG2716 GcvR Glycine cleavage system regulatory protein [Amino acid transport and metabolism]
Probab=25.61 E-value=66 Score=31.43 Aligned_cols=70 Identities=14% Similarity=0.094 Sum_probs=56.4
Q ss_pred eEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcCCCC
Q 047004 423 AVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGFHGM 496 (497)
Q Consensus 423 ~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~~~~ 496 (497)
-++|.....++||+...|.++.-+.|..++.+.++.+++.+--++.+.- .-=....|++.|...-..||+
T Consensus 5 ~LvItavg~d~pgl~~~lar~v~s~Gcn~leSRla~~g~~~a~i~lisg----s~dav~~le~~l~~l~~~~~L 74 (176)
T COG2716 5 YLVITAVGADRPGLVNTLARAVASSGCNWLESRLAMLGEEFAGIMLISG----SWDAVTLLEATLPLLGAELDL 74 (176)
T ss_pred EEEEEEecCCCcHHHHHHHHHHHhcCCcchHHHHHHhhcceeEEEEEee----CHHHHHHHHHHhhcccccCCe
Confidence 3668888889999999999999999999999999999999888877752 223356788888776655554
No 130
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=25.44 E-value=4.2e+02 Score=31.22 Aligned_cols=59 Identities=19% Similarity=0.195 Sum_probs=45.6
Q ss_pred ceEEEEEecC----ceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEE-EEEe
Q 047004 412 ARVEVRVREG----RAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDV-FRAE 470 (497)
Q Consensus 412 ~~VEV~v~eg----~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~-f~ae 470 (497)
-.|+|.+... -.+.|.|...+++|+|.+|+++|-+.+..|..++.....+.+..+ |.++
T Consensus 612 r~i~v~W~~~~~~~f~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~~~~~~~~~i~ 675 (701)
T COG0317 612 RVIDVSWGPEYGQVYPVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQFATMQFTIE 675 (701)
T ss_pred eEEEEEecCCCCcceEEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCCceEEEEEEEE
Confidence 3577877543 347788999999999999999999999999999999874444443 3443
No 131
>PRK11899 prephenate dehydratase; Provisional
Probab=25.30 E-value=4.3e+02 Score=27.32 Aligned_cols=62 Identities=15% Similarity=0.213 Sum_probs=43.2
Q ss_pred EEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCe-EEEEEEEeeecCCcccCHHHHHHHHHHh
Q 047004 426 IHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGF-AMDVFRAEQCKEGQDVHPEQIKAVLLDS 490 (497)
Q Consensus 426 I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~-vl~~f~aeq~keg~~v~~eqIk~~L~~~ 490 (497)
|-+...+++|.|.++|.++-..|+..+.-.+=...+. .-++|.++. +| ......++++|...
T Consensus 197 l~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~~~Y~F~id~--eg-~~~d~~v~~aL~~l 259 (279)
T PRK11899 197 FVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSFTATQFYADI--EG-HPEDRNVALALEEL 259 (279)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCCceEEEEEEE--EC-CCCCHHHHHHHHHH
Confidence 3334468999999999999999999999888877544 556666664 23 23334556666554
No 132
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=24.78 E-value=2.1e+02 Score=22.82 Aligned_cols=40 Identities=23% Similarity=0.392 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHhcCCCCCcCCccchHHHHHHHHHHHHHHHHHH
Q 047004 316 RRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIEYLKELLQRINDL 362 (497)
Q Consensus 316 RrRR~kin~~~~~LrsLVP~~~K~dKasIL~eAI~YIk~Lq~~v~~L 362 (497)
|..|=.....+..+..++- ..-.++|.+||+++-..++.+
T Consensus 17 R~~RHD~~NhLqvI~gllq-------lg~~~~a~eYi~~~~~~~~~~ 56 (62)
T PF14689_consen 17 RAQRHDFLNHLQVIYGLLQ-------LGKYEEAKEYIKELSKDLQQE 56 (62)
T ss_dssp HHHHHHHHHHHHHHHHHHH-------TT-HHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHHH-------CCCHHHHHHHHHHHHHHHHHH
Confidence 5667778888888888883 122678999999999888876
No 133
>PRK13702 replication protein; Provisional
Probab=24.29 E-value=1.7e+02 Score=25.51 Aligned_cols=27 Identities=11% Similarity=0.124 Sum_probs=20.6
Q ss_pred ccccHHHHHHH--HHHHHHHHHHHhcCCC
Q 047004 309 AKNLMAERRRR--KKLNDRLYMLRSVVPK 335 (497)
Q Consensus 309 ~~H~~~ERrRR--~kin~~~~~LrsLVP~ 335 (497)
.-...+||+|+ .+..+.-.+|+-.||+
T Consensus 22 ~Pls~aErQr~svaRKr~THkei~vfi~n 50 (85)
T PRK13702 22 NPLSAAEKQRASVARKRATHKEIKVFIQN 50 (85)
T ss_pred CCCCHHHHHHHHHHHHHHhhhhhheeecH
Confidence 45668888884 6677777899999986
No 134
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=24.22 E-value=84 Score=27.04 Aligned_cols=26 Identities=23% Similarity=0.313 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 345 LGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 345 L~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
+..||+-|.-||.+|++|+.+...+.
T Consensus 13 IqqAvdtI~LLqmEieELKekn~~L~ 38 (79)
T PRK15422 13 VQQAIDTITLLQMEIEELKEKNNSLS 38 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999866553
No 135
>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=23.71 E-value=2e+02 Score=23.24 Aligned_cols=52 Identities=23% Similarity=0.299 Sum_probs=33.7
Q ss_pred ccHHHHHHHHHHHHHHHHHHhcCCCCCcCCccchHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 311 NLMAERRRRKKLNDRLYMLRSVVPKISKMDRASILGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 311 H~~~ERrRR~kin~~~~~LrsLVP~~~K~dKasIL~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
++..|++=|+.....+..| ..|+..++.+|-.-|.....+|+.|+.+++.+.
T Consensus 9 ~i~~E~ki~~Gae~m~~~~--------~t~~~~~~~~~~~~l~~s~~kI~~L~~~L~~l~ 60 (70)
T PF02185_consen 9 KIDKELKIKEGAENMLQAY--------STDKKKVLSEAESQLRESNQKIELLREQLEKLQ 60 (70)
T ss_dssp HHHHHHHHHHHHHHHHHHH--------CCHHCH-HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH--------ccCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666666665555555 345555777788888888888888887777654
No 136
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=23.57 E-value=1.1e+02 Score=35.64 Aligned_cols=43 Identities=14% Similarity=0.022 Sum_probs=39.9
Q ss_pred EEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEe
Q 047004 424 VNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAE 470 (497)
Q Consensus 424 V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~ae 470 (497)
..++|....|+|+|..|+.+|+ ||.-|.+++.+..++++|...
T Consensus 632 ~~~e~r~~dr~g~l~~~~~~l~----~~~~~~~~~~g~~~~~~~~~~ 674 (693)
T PRK00227 632 NILEVRTEDRRGALGALLGVLP----DLLWITASTPGATMIVQAALK 674 (693)
T ss_pred cEEEEEeCccccHHHHHHHHhh----hhhhHhhcCCCcceEEEEEec
Confidence 4688999999999999999999 999999999999999998885
No 137
>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=22.84 E-value=1.7e+02 Score=29.94 Aligned_cols=17 Identities=35% Similarity=0.583 Sum_probs=14.3
Q ss_pred HHHHHHHHHHHHHhhhc
Q 047004 352 LKELLQRINDLHNELES 368 (497)
Q Consensus 352 Ik~Lq~~v~~L~~e~es 368 (497)
||++++||++||.++..
T Consensus 57 L~~a~~ri~eLe~ql~q 73 (247)
T PF09849_consen 57 LKQAQARIQELEAQLQQ 73 (247)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 67899999999999744
No 138
>COG1591 Holliday junction resolvase - archaeal type [DNA replication, recombination, and repair]
Probab=22.65 E-value=3.7e+02 Score=25.46 Aligned_cols=63 Identities=19% Similarity=0.178 Sum_probs=46.1
Q ss_pred CCcHHHHHHHHHHhCCCeEEEEE-----------EEeeCCeEEEEEEEeeecCCc-ccCHHHHHHHHHHhhcCCC
Q 047004 433 RPGLLLSTMRALDNLGLDIQQAV-----------ISCFNGFAMDVFRAEQCKEGQ-DVHPEQIKAVLLDSAGFHG 495 (497)
Q Consensus 433 r~GlL~~ILeALEeLgLdVvsAs-----------IS~~ng~vl~~f~aeq~keg~-~v~~eqIk~~L~~~aG~~~ 495 (497)
....--+++..|++.|..|+.+- |...+|.++.+|.++...++. -+..+||...|.=+-.|+|
T Consensus 6 G~~~EReLv~~L~e~GfAvvR~paSG~sk~p~pDivA~~g~~~l~iE~K~~~~~kiYl~~e~ve~L~~FA~~fGg 80 (137)
T COG1591 6 GSRFERELVRILWERGFAVVRAPASGGSKRPLPDIVAGNGGVYLAIEVKSRRETKIYLDKEQVEKLVEFARRFGG 80 (137)
T ss_pred cchHHHHHHHHHHhcCceEEEcccCCCCCCCCCCEEecCCCEEEEEEEEeccCCcEEEcHHHHHHHHHHHHHcCC
Confidence 34455678999999999999982 344567778888888776554 4778999887765555544
No 139
>KOG2057 consensus Predicted equilibrative nucleoside transporter protein [Nucleotide transport and metabolism]
Probab=22.25 E-value=1.4e+02 Score=32.22 Aligned_cols=72 Identities=25% Similarity=0.393 Sum_probs=39.9
Q ss_pred cCCCccccccccccCCCCCCCCCCCcCCCCCCCCCCcccccCCC--CCCCCccc--ccccccCCCCCCCCCCCCCCh
Q 047004 125 FNDLSANNQMNATNLCSDPQFGTNRTLQFPENGSSSFTGFRGFD--ENNGNSLF--LNRSKLLRPLETFPSTGAQPT 197 (497)
Q Consensus 125 ~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~gf~~f~~f~--~~~~n~lf--~~~~~~~~pl~~~~~~~~~pt 197 (497)
|.||+.-.+-..--+.++-+|-.+...+..+-..|.|++|. |. .++.|-|| ...+..|-|...+-.-.++||
T Consensus 376 fgD~~AF~aAPsgpmAqSgef~g~aaaPa~e~~nGS~na~~-~~paa~nsndlfdlmG~aaa~m~~S~~mnfq~m~a 451 (499)
T KOG2057|consen 376 FGDLFAFGAAPSGPMAQSGEFAGPAAAPANEASNGSFNAFD-FGPAAGNSNDLFDLMGGAAALMPMSGLMNFQAMPA 451 (499)
T ss_pred chhhhhhcCCCCccccccccccCccccchhhhccCccccCC-CCcccCCcccccccccccccccccccccCcccccc
Confidence 44555333333333456667777766666666567776664 32 23455667 445566666665555555554
No 140
>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=22.12 E-value=2.1e+02 Score=22.17 Aligned_cols=28 Identities=29% Similarity=0.516 Sum_probs=22.9
Q ss_pred EEEEcC---CCCcHHHHHHHHHHhCCCeEEE
Q 047004 426 IHMFCS---RRPGLLLSTMRALDNLGLDIQQ 453 (497)
Q Consensus 426 I~I~C~---kr~GlL~~ILeALEeLgLdVvs 453 (497)
|.|.+. ..+|++.+++++|.+.++.|..
T Consensus 4 isvvG~~~~~~~gi~~~if~aL~~~~I~v~~ 34 (64)
T cd04937 4 VTIIGSRIRGVPGVMAKIVGALSKEGIEILQ 34 (64)
T ss_pred EEEECCCccCCcCHHHHHHHHHHHCCCCEEE
Confidence 444544 4799999999999999999973
No 141
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=21.95 E-value=2.4e+02 Score=26.41 Aligned_cols=45 Identities=27% Similarity=0.293 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHHHHhcCCCCCcCCccchHHHHHHHHHHHHHHHHHHHHhhhcCCC
Q 047004 317 RRRKKLNDRLYMLRSVVPKISKMDRASILGDAIEYLKELLQRINDLHNELESTPP 371 (497)
Q Consensus 317 rRR~kin~~~~~LrsLVP~~~K~dKasIL~eAI~YIk~Lq~~v~~L~~e~esl~~ 371 (497)
.....+...+..|++.++ ..+....|.+|+.+++.|+.+++.+..
T Consensus 93 ~~~k~l~~eL~~L~~~~t----------~~el~~~i~~l~~e~~~l~~kL~~l~~ 137 (169)
T PF07106_consen 93 KEVKSLEAELASLSSEPT----------NEELREEIEELEEEIEELEEKLEKLRS 137 (169)
T ss_pred HHHHHHHHHHHHHhcCCC----------HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 334555556666666555 788999999999999999999998874
No 142
>PRK10820 DNA-binding transcriptional regulator TyrR; Provisional
Probab=21.56 E-value=1.1e+02 Score=33.95 Aligned_cols=36 Identities=22% Similarity=0.375 Sum_probs=32.7
Q ss_pred EEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC
Q 047004 425 NIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN 460 (497)
Q Consensus 425 ~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n 460 (497)
.++|+|.+|-|+..+|+..|-..++++....|...+
T Consensus 2 rl~~~~~dr~g~~~~~l~~~~~~~~~~~~~e~~~~~ 37 (520)
T PRK10820 2 RLEVFCEDRLGLTRELLDLLVLRSIDLRGIEIDPIG 37 (520)
T ss_pred eEEEEeeccccHHHHHHHHHHhcCCCccEEEEcCCC
Confidence 579999999999999999999999999999886663
No 143
>TIGR02079 THD1 threonine dehydratase. This model represents threonine dehydratase, the first step in the pathway converting threonine into isoleucine. At least two other clades of biosynthetic threonine dehydratases have been characterized by models TIGR01124 and TIGR01127. Those sequences described by this model are exclusively found in species containg the rest of the isoleucine pathway and which are generally lacking in members of the those other two clades of threonine dehydratases. Members of this clade are also often gene clustered with other elements of the isoleucine pathway.
Probab=21.25 E-value=4.5e+02 Score=28.36 Aligned_cols=70 Identities=14% Similarity=0.054 Sum_probs=46.5
Q ss_pred cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeC--CeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 420 EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFN--GFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 420 eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~n--g~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
+++.+.+++.-+.|||-|.++++.+-..+.+|+....-... +...-.+.+|... .-+.++|.++|.+ .||
T Consensus 322 ~~r~~~~~v~ipdrPGaL~~~l~~i~~~~~NI~~~~y~~~~~~~~~~v~v~iE~~~---~~h~~~i~~~L~~-~Gy 393 (409)
T TIGR02079 322 EGLKHYFIVRFPQRPGALREFLNDVLGPNDDITRFEYTKKSNRETGPALIGIELND---KEDFAGLLERMAA-ADI 393 (409)
T ss_pred cCCEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEeeecCCCCeEEEEEEEEeCC---HHHHHHHHHHHHH-CCC
Confidence 57889999999999999999999776677688876665321 1222223344321 2355777777765 455
No 144
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=20.77 E-value=1.2e+02 Score=25.16 Aligned_cols=28 Identities=36% Similarity=0.373 Sum_probs=24.3
Q ss_pred chHHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 343 SILGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 343 sIL~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
.-|++|+.-+.+|+.+++.|+.+++...
T Consensus 40 ~~l~~a~~e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 40 RQLGDAYEENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3499999999999999999999987653
No 145
>TIGR00986 3a0801s05tom22 mitochondrial import receptor subunit Tom22. translocase (Tom) import receptor, five proteins of the Tom channel complex, five proteins of the inner membrane translocase (Tim) and three "motor" proteins. This family is specific for the Tom22 proteins.
Probab=20.65 E-value=99 Score=29.38 Aligned_cols=36 Identities=19% Similarity=0.391 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHhcCCCCCcCCccchHHHHHHHHHHH
Q 047004 320 KKLNDRLYMLRSVVPKISKMDRASILGDAIEYLKEL 355 (497)
Q Consensus 320 ~kin~~~~~LrsLVP~~~K~dKasIL~eAI~YIk~L 355 (497)
+-|-+|+..|+.++|+..+..-.+...-+..++|.+
T Consensus 49 ETl~ERi~ALkDm~Pp~~R~~i~~~~s~t~s~~ks~ 84 (145)
T TIGR00986 49 ETFTDRIYALKDIVPPTTRGWIYHKYSTTTNFVKST 84 (145)
T ss_pred CcHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHH
Confidence 346778999999999754443444455555555554
No 146
>PRK14626 hypothetical protein; Provisional
Probab=20.59 E-value=4.4e+02 Score=23.70 Aligned_cols=26 Identities=12% Similarity=0.364 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 345 LGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 345 L~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
+.+-+.-.+++|++.++++++++...
T Consensus 7 ~~~mmkqaq~mQ~km~~~qeeL~~~~ 32 (110)
T PRK14626 7 LAELMKQMQSIKENVEKAKEELKKEE 32 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccE
Confidence 55667778889999999999988764
No 147
>TIGR01124 ilvA_2Cterm threonine ammonia-lyase, biosynthetic, long form. Forms scoring between the trusted and noise cutoff tend to branch with this subgroup of threonine ammonia-lyase phylogenetically but have only a single copy of the C-terminal domain.
Probab=20.22 E-value=5.1e+02 Score=28.88 Aligned_cols=70 Identities=21% Similarity=0.252 Sum_probs=44.4
Q ss_pred ecCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEEEEEeeecCCcccCHHHHHHHHHHhhcC
Q 047004 419 REGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDVFRAEQCKEGQDVHPEQIKAVLLDSAGF 493 (497)
Q Consensus 419 ~eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~f~aeq~keg~~v~~eqIk~~L~~~aG~ 493 (497)
.+++.+.+.|.-+.|||-|.+++++|-. .+|+..+.-..+...-+++..-+.. ..-+.++|.+.|.+ .||
T Consensus 321 ~~~re~~l~V~iPerPGal~~f~~~i~~--~nItef~yr~~~~~~a~v~vgie~~--~~~~~~~l~~~L~~-~Gy 390 (499)
T TIGR01124 321 GEQREALLAVTIPEQPGSFLKFCELLGN--RNITEFNYRYADRKDAHIFVGVQLS--NPQERQEILARLND-GGY 390 (499)
T ss_pred hcCCEEEEEEEeCCCCCHHHHHHHHhhh--cceEEEEEEecCCCeEEEEEEEEeC--CHHHHHHHHHHHHH-cCC
Confidence 3578899999999999999999999987 4666666654333333333222221 12345566666654 344
No 148
>PRK14623 hypothetical protein; Provisional
Probab=20.18 E-value=4.5e+02 Score=23.60 Aligned_cols=26 Identities=19% Similarity=0.281 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhcCC
Q 047004 345 LGDAIEYLKELLQRINDLHNELESTP 370 (497)
Q Consensus 345 L~eAI~YIk~Lq~~v~~L~~e~esl~ 370 (497)
+.+.+.-.+++|+++++++++++...
T Consensus 3 ~~~~mkqaqkmQ~km~~~Qeel~~~~ 28 (106)
T PRK14623 3 MMGMMGKLKEAQQKVEATKKRLDTVL 28 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccE
Confidence 45667778889999999999987664
No 149
>PRK12483 threonine dehydratase; Reviewed
Probab=20.12 E-value=5.8e+02 Score=28.76 Aligned_cols=68 Identities=21% Similarity=0.231 Sum_probs=44.8
Q ss_pred cCceEEEEEEcCCCCcHHHHHHHHHHhCCCeEEEEEEEeeCCeEEEE-EEEeeecCCcccCH-HHHHHHHHHhhcC
Q 047004 420 EGRAVNIHMFCSRRPGLLLSTMRALDNLGLDIQQAVISCFNGFAMDV-FRAEQCKEGQDVHP-EQIKAVLLDSAGF 493 (497)
Q Consensus 420 eg~~V~I~I~C~kr~GlL~~ILeALEeLgLdVvsAsIS~~ng~vl~~-f~aeq~keg~~v~~-eqIk~~L~~~aG~ 493 (497)
+++.+.+.|.-+.+||-|.++++.|-+. +|+.......+..--.+ +.+|... .-+. ++|.++|.+ .||
T Consensus 342 ~~r~~~~~v~~~d~pG~l~~~~~~l~~~--ni~~~~~~~~~~~~~~v~v~ie~~~---~~~~~~~i~~~l~~-~g~ 411 (521)
T PRK12483 342 EQREAIIAVTIPEQPGSFKAFCAALGKR--QITEFNYRYADAREAHLFVGVQTHP---RHDPRAQLLASLRA-QGF 411 (521)
T ss_pred cCCEEEEEEEeCCCCCHHHHHHHHhhhc--CeEEEEEEecCCCeeEEEEEEEeCC---hhhhHHHHHHHHHH-CCC
Confidence 5788999999999999999999999877 77777666543332222 2233211 1233 577777664 344
Done!