Query 041101
Match_columns 433
No_of_seqs 305 out of 1263
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 03:49:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041101.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041101hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF14215 bHLH-MYC_N: bHLH-MYC 100.0 1.9E-42 4.1E-47 315.9 12.0 151 7-162 1-163 (163)
2 cd00083 HLH Helix-loop-helix d 99.3 4.4E-12 9.6E-17 96.3 5.3 53 266-318 4-59 (60)
3 smart00353 HLH helix loop heli 99.3 9.1E-12 2E-16 92.5 6.0 49 271-319 1-52 (53)
4 PF00010 HLH: Helix-loop-helix 99.3 5.8E-12 1.2E-16 94.6 4.7 49 267-315 2-55 (55)
5 KOG1319 bHLHZip transcription 99.1 6.4E-11 1.4E-15 108.0 5.7 94 228-329 29-132 (229)
6 KOG1318 Helix loop helix trans 98.6 4.8E-08 1E-12 100.3 5.0 57 264-320 231-291 (411)
7 KOG2483 Upstream transcription 98.1 6.1E-06 1.3E-10 79.4 7.5 67 262-328 55-124 (232)
8 cd04895 ACT_ACR_1 ACT domain-c 98.1 1.3E-05 2.8E-10 63.8 7.3 45 388-432 3-47 (72)
9 cd04897 ACT_ACR_3 ACT domain-c 98.0 1.8E-05 3.9E-10 63.4 7.2 45 388-432 3-47 (75)
10 KOG3561 Aryl-hydrocarbon recep 98.0 7.1E-06 1.5E-10 90.8 5.2 51 267-317 21-75 (803)
11 cd04927 ACT_ACR-like_2 Second 98.0 2.8E-05 6.1E-10 62.2 7.2 46 387-432 1-47 (76)
12 cd04896 ACT_ACR-like_3 ACT dom 97.9 4.1E-05 8.9E-10 61.4 7.0 45 388-432 2-48 (75)
13 KOG4304 Transcriptional repres 97.9 7.4E-06 1.6E-10 80.0 3.1 58 265-322 31-96 (250)
14 cd04900 ACT_UUR-like_1 ACT dom 97.8 8.6E-05 1.9E-09 58.6 7.5 45 388-432 3-48 (73)
15 cd04925 ACT_ACR_2 ACT domain-c 97.6 0.00026 5.5E-09 56.2 7.5 45 388-432 2-46 (74)
16 KOG3960 Myogenic helix-loop-he 97.5 0.00018 3.9E-09 69.2 6.6 62 265-326 117-180 (284)
17 KOG0561 bHLH transcription fac 97.4 0.00011 2.3E-09 72.3 3.8 55 267-321 61-117 (373)
18 KOG2588 Predicted DNA-binding 97.2 0.00017 3.8E-09 80.3 2.5 65 264-328 274-339 (953)
19 cd04928 ACT_TyrKc Uncharacteri 97.2 0.0016 3.4E-08 51.3 7.1 45 388-432 3-48 (68)
20 PLN03217 transcription factor 97.2 0.00094 2E-08 54.0 5.9 53 279-331 20-78 (93)
21 cd04899 ACT_ACR-UUR-like_2 C-t 97.2 0.0016 3.6E-08 50.1 7.1 45 388-432 2-46 (70)
22 cd04926 ACT_ACR_4 C-terminal 97.1 0.0027 5.8E-08 50.0 7.4 45 388-432 3-47 (72)
23 KOG4029 Transcription factor H 96.9 0.00079 1.7E-08 65.0 4.0 61 265-325 108-172 (228)
24 PRK05007 PII uridylyl-transfer 96.3 0.011 2.3E-07 67.8 8.3 59 375-433 796-855 (884)
25 PF13740 ACT_6: ACT domain; PD 96.2 0.023 4.9E-07 45.2 7.6 48 386-433 2-49 (76)
26 cd04873 ACT_UUR-ACR-like ACT d 96.2 0.026 5.5E-07 43.0 7.4 45 388-432 2-46 (70)
27 PF01842 ACT: ACT domain; Int 95.9 0.048 1E-06 40.9 7.7 37 388-424 2-38 (66)
28 PRK00275 glnD PII uridylyl-tra 95.8 0.036 7.7E-07 63.7 9.6 59 374-432 801-860 (895)
29 PRK01759 glnD PII uridylyl-tra 95.8 0.023 5E-07 64.9 7.9 60 374-433 770-830 (854)
30 PRK03059 PII uridylyl-transfer 95.7 0.045 9.8E-07 62.6 9.7 58 375-432 774-832 (856)
31 PRK04374 PII uridylyl-transfer 95.7 0.049 1.1E-06 62.3 9.8 59 374-432 783-842 (869)
32 cd04893 ACT_GcvR_1 ACT domains 95.6 0.047 1E-06 43.5 6.7 47 387-433 2-48 (77)
33 PRK03381 PII uridylyl-transfer 95.3 0.066 1.4E-06 60.6 9.2 48 385-432 706-753 (774)
34 PF13291 ACT_4: ACT domain; PD 95.2 0.11 2.4E-06 41.2 7.7 48 386-433 6-55 (80)
35 PRK05092 PII uridylyl-transfer 95.1 0.086 1.9E-06 60.9 9.4 59 374-432 830-889 (931)
36 COG2844 GlnD UTP:GlnB (protein 95.0 0.049 1.1E-06 60.8 6.6 60 373-432 777-837 (867)
37 PRK03381 PII uridylyl-transfer 94.5 0.15 3.2E-06 57.9 9.1 48 385-432 598-645 (774)
38 TIGR01693 UTase_glnD [Protein- 94.1 0.14 3E-06 58.7 8.0 48 385-432 667-715 (850)
39 TIGR01693 UTase_glnD [Protein- 94.1 0.14 3.1E-06 58.5 8.1 59 374-432 766-825 (850)
40 PRK01759 glnD PII uridylyl-tra 94.1 0.15 3.2E-06 58.5 8.1 48 385-432 676-724 (854)
41 KOG3910 Helix loop helix trans 93.8 0.031 6.8E-07 58.7 1.9 57 265-321 525-585 (632)
42 PRK00194 hypothetical protein; 93.7 0.12 2.6E-06 42.0 4.9 47 386-432 3-49 (90)
43 PRK05007 PII uridylyl-transfer 93.6 0.2 4.3E-06 57.6 8.2 48 385-432 700-748 (884)
44 cd04872 ACT_1ZPV ACT domain pr 93.6 0.13 2.7E-06 41.9 4.7 46 387-432 2-47 (88)
45 PRK00275 glnD PII uridylyl-tra 93.5 0.19 4.1E-06 57.9 7.7 48 385-432 703-751 (895)
46 cd04887 ACT_MalLac-Enz ACT_Mal 93.5 0.35 7.7E-06 37.4 7.0 45 389-433 2-47 (74)
47 PRK03059 PII uridylyl-transfer 93.1 0.23 5.1E-06 56.9 7.6 48 385-432 677-725 (856)
48 cd04886 ACT_ThrD-II-like C-ter 92.7 0.37 8.1E-06 36.3 6.0 44 389-432 1-49 (73)
49 cd04894 ACT_ACR-like_1 ACT dom 92.7 0.29 6.4E-06 37.8 5.1 45 388-432 2-46 (69)
50 cd04869 ACT_GcvR_2 ACT domains 92.6 0.5 1.1E-05 37.3 6.8 35 389-423 2-36 (81)
51 cd04870 ACT_PSP_1 CT domains f 92.1 0.44 9.5E-06 37.5 5.8 45 388-432 1-45 (75)
52 PRK05092 PII uridylyl-transfer 92.1 0.41 9E-06 55.4 7.9 48 385-432 731-779 (931)
53 cd04875 ACT_F4HF-DF N-terminal 92.1 0.38 8.3E-06 37.6 5.4 34 388-421 1-34 (74)
54 PRK04374 PII uridylyl-transfer 91.9 0.49 1.1E-05 54.4 8.1 48 385-432 689-737 (869)
55 cd04889 ACT_PDH-BS-like C-term 91.1 0.88 1.9E-05 33.3 6.2 45 389-433 1-46 (56)
56 cd04888 ACT_PheB-BS C-terminal 90.5 0.84 1.8E-05 35.3 6.0 45 388-432 2-47 (76)
57 cd02116 ACT ACT domains are co 90.4 1.3 2.8E-05 30.2 6.3 35 389-423 1-35 (60)
58 PRK04435 hypothetical protein; 89.8 1.3 2.7E-05 40.0 7.2 51 383-433 66-117 (147)
59 cd04876 ACT_RelA-SpoT ACT dom 89.6 1.2 2.6E-05 32.1 5.9 35 389-423 1-35 (71)
60 cd04877 ACT_TyrR N-terminal AC 89.6 1.3 2.7E-05 34.7 6.2 37 388-425 2-38 (74)
61 KOG4447 Transcription factor T 89.2 0.23 4.9E-06 44.8 1.8 52 266-317 78-131 (173)
62 cd04882 ACT_Bt0572_2 C-termina 89.2 1.1 2.3E-05 33.4 5.4 45 389-433 2-48 (65)
63 cd04874 ACT_Af1403 N-terminal 89.0 1.7 3.8E-05 32.5 6.6 35 388-422 2-36 (72)
64 cd04881 ACT_HSDH-Hom ACT_HSDH_ 88.5 1.6 3.4E-05 33.3 6.1 36 387-422 1-36 (79)
65 cd04879 ACT_3PGDH-like ACT_3PG 88.5 1.9 4.2E-05 31.9 6.5 44 389-432 2-47 (71)
66 KOG3560 Aryl-hydrocarbon recep 87.8 0.42 9.1E-06 51.1 3.1 41 273-313 32-76 (712)
67 cd04903 ACT_LSD C-terminal ACT 86.8 2.7 5.8E-05 31.3 6.4 44 389-432 2-47 (71)
68 cd04878 ACT_AHAS N-terminal AC 85.7 4 8.7E-05 30.3 6.9 44 388-431 2-47 (72)
69 cd04905 ACT_CM-PDT C-terminal 85.3 3.4 7.4E-05 32.7 6.5 45 389-433 4-49 (80)
70 KOG3558 Hypoxia-inducible fact 85.0 0.65 1.4E-05 51.1 2.8 48 266-313 46-97 (768)
71 cd04909 ACT_PDH-BS C-terminal 84.8 5.2 0.00011 30.4 7.2 35 388-422 3-37 (69)
72 KOG3559 Transcriptional regula 84.8 0.98 2.1E-05 46.8 3.8 42 272-313 7-52 (598)
73 cd04880 ACT_AAAH-PDT-like ACT 84.7 3.1 6.8E-05 32.4 6.0 35 390-424 3-37 (75)
74 PRK08577 hypothetical protein; 84.3 4.6 0.0001 35.6 7.5 40 384-423 54-93 (136)
75 cd04908 ACT_Bt0572_1 N-termina 83.5 4.6 0.0001 30.6 6.4 38 388-425 3-40 (66)
76 KOG3898 Transcription factor N 82.5 0.76 1.7E-05 45.3 1.9 54 265-318 71-127 (254)
77 cd04883 ACT_AcuB C-terminal AC 82.1 6.8 0.00015 29.8 6.9 46 388-433 3-50 (72)
78 PF13185 GAF_2: GAF domain; PD 80.0 6.9 0.00015 33.1 6.9 60 103-162 73-143 (148)
79 PRK11061 fused phosphoenolpyru 79.8 6.8 0.00015 44.5 8.5 108 5-152 20-137 (748)
80 cd04902 ACT_3PGDH-xct C-termin 79.3 5.1 0.00011 30.4 5.3 45 389-433 2-48 (73)
81 TIGR01817 nifA Nif-specific re 79.1 1.8 3.8E-05 46.9 3.5 73 93-165 69-155 (534)
82 PRK07334 threonine dehydratase 78.9 6.1 0.00013 41.3 7.3 48 385-432 325-377 (403)
83 cd04884 ACT_CBS C-terminal ACT 77.7 7.7 0.00017 29.9 5.9 34 389-422 2-35 (72)
84 cd04901 ACT_3PGDH C-terminal A 75.7 2.4 5.2E-05 32.0 2.4 45 389-433 2-46 (69)
85 KOG4395 Transcription factor A 75.3 4.8 0.0001 39.4 4.8 55 265-319 173-230 (285)
86 COG2844 GlnD UTP:GlnB (protein 70.8 9.1 0.0002 43.4 6.3 49 384-432 682-731 (867)
87 cd04931 ACT_PAH ACT domain of 69.2 17 0.00037 30.0 6.2 46 387-432 15-61 (90)
88 cd04904 ACT_AAAH ACT domain of 68.3 12 0.00026 29.3 5.0 43 390-432 4-47 (74)
89 COG3830 ACT domain-containing 65.8 6 0.00013 32.8 2.8 47 386-432 3-49 (90)
90 PRK10872 relA (p)ppGpp synthet 61.4 23 0.00049 40.2 7.3 48 386-433 666-715 (743)
91 PRK11152 ilvM acetolactate syn 58.6 50 0.0011 26.5 6.9 36 387-422 4-39 (76)
92 TIGR00691 spoT_relA (p)ppGpp s 58.1 27 0.00058 39.4 7.1 48 386-433 610-658 (683)
93 smart00065 GAF Domain present 57.9 39 0.00083 27.0 6.5 118 5-164 4-137 (149)
94 PRK11092 bifunctional (p)ppGpp 57.4 28 0.0006 39.4 7.1 48 386-433 626-674 (702)
95 KOG3582 Mlx interactors and re 56.3 3.2 6.9E-05 45.9 -0.5 62 265-326 650-716 (856)
96 PF13710 ACT_5: ACT domain; PD 53.3 45 0.00097 25.4 5.6 38 395-432 1-40 (63)
97 cd04929 ACT_TPH ACT domain of 53.1 41 0.00088 26.6 5.5 31 393-423 7-37 (74)
98 COG4492 PheB ACT domain-contai 52.7 45 0.00098 29.8 6.1 47 384-430 70-117 (150)
99 PF02344 Myc-LZ: Myc leucine z 51.7 15 0.00032 24.5 2.3 17 274-290 13-29 (32)
100 PF13492 GAF_3: GAF domain; PD 51.5 36 0.00079 27.8 5.4 112 5-162 4-123 (129)
101 PRK06737 acetolactate synthase 47.8 60 0.0013 26.0 5.7 37 387-423 3-39 (76)
102 COG4747 ACT domain-containing 46.7 60 0.0013 28.6 5.8 38 388-425 5-42 (142)
103 KOG4447 Transcription factor T 46.3 14 0.00031 33.5 2.1 42 273-314 29-72 (173)
104 cd04930 ACT_TH ACT domain of t 45.9 49 0.0011 28.5 5.4 36 388-423 43-78 (115)
105 PRK06382 threonine dehydratase 45.7 57 0.0012 34.1 6.8 50 384-433 328-382 (406)
106 PF02120 Flg_hook: Flagellar h 43.8 91 0.002 24.5 6.3 47 375-422 27-79 (85)
107 cd04906 ACT_ThrD-I_1 First of 43.6 91 0.002 24.9 6.3 32 387-420 2-33 (85)
108 PF01590 GAF: GAF domain; Int 42.8 19 0.00041 30.6 2.4 117 5-162 4-150 (154)
109 cd04868 ACT_AK-like ACT domain 41.2 1.1E+02 0.0023 21.2 5.9 25 396-420 13-37 (60)
110 cd04922 ACT_AKi-HSDH-ThrA_2 AC 41.1 1.3E+02 0.0029 21.8 6.6 34 388-421 3-39 (66)
111 cd04885 ACT_ThrD-I Tandem C-te 40.5 48 0.001 25.2 4.0 32 390-422 2-33 (68)
112 PF14689 SPOB_a: Sensor_kinase 39.8 73 0.0016 24.2 4.9 41 275-322 17-57 (62)
113 PRK00227 glnD PII uridylyl-tra 38.9 68 0.0015 36.2 6.5 46 387-433 547-593 (693)
114 TIGR01127 ilvA_1Cterm threonin 38.7 1E+02 0.0022 31.7 7.4 37 384-420 303-339 (380)
115 PRK08198 threonine dehydratase 38.3 1E+02 0.0022 32.1 7.3 38 384-421 325-362 (404)
116 cd04892 ACT_AK-like_2 ACT doma 37.4 1.4E+02 0.003 21.1 6.0 34 388-421 2-38 (65)
117 cd04919 ACT_AK-Hom3_2 ACT doma 36.1 1.7E+02 0.0037 21.4 6.7 27 395-421 13-39 (66)
118 PRK13562 acetolactate synthase 36.0 95 0.0021 25.5 5.2 36 388-423 4-39 (84)
119 cd04890 ACT_AK-like_1 ACT doma 34.0 1.7E+02 0.0036 21.4 6.1 25 395-419 12-36 (62)
120 KOG4005 Transcription factor X 31.2 2.3E+02 0.005 27.8 7.7 56 265-327 58-115 (292)
121 cd04937 ACT_AKi-DapG-BS_2 ACT 30.6 1.3E+02 0.0027 22.5 4.9 24 395-418 13-36 (64)
122 PF09849 DUF2076: Uncharacteri 30.0 1.4E+02 0.003 29.4 6.3 17 311-327 57-73 (247)
123 PF13840 ACT_7: ACT domain ; P 29.8 75 0.0016 24.2 3.6 34 385-418 5-42 (65)
124 cd04894 ACT_ACR-like_1 ACT dom 29.1 34 0.00073 26.7 1.4 22 18-39 37-58 (69)
125 PF06005 DUF904: Protein of un 28.7 94 0.002 24.7 4.0 25 304-328 13-37 (72)
126 PRK08178 acetolactate synthase 28.5 1.9E+02 0.0042 24.3 6.0 39 385-423 7-45 (96)
127 KOG3582 Mlx interactors and re 27.8 21 0.00045 39.8 0.1 58 266-326 787-849 (856)
128 PRK08526 threonine dehydratase 27.8 1.8E+02 0.004 30.4 7.2 39 384-422 324-362 (403)
129 PRK00227 glnD PII uridylyl-tra 26.5 50 0.0011 37.3 2.8 42 387-432 632-673 (693)
130 COG4747 ACT domain-containing 26.4 2E+02 0.0044 25.4 5.8 45 388-433 71-117 (142)
131 PRK11589 gcvR glycine cleavage 26.2 1.6E+02 0.0035 27.7 5.8 37 387-423 96-132 (190)
132 PRK11899 prephenate dehydratas 26.1 2E+02 0.0043 28.8 6.7 45 389-433 197-242 (279)
133 smart00338 BRLZ basic region l 25.8 2E+02 0.0042 21.8 5.3 43 274-329 4-46 (65)
134 PF05088 Bac_GDH: Bacterial NA 25.6 1.8E+02 0.0038 36.1 7.3 48 385-432 488-540 (1528)
135 cd04916 ACT_AKiii-YclM-BS_2 AC 24.8 2.7E+02 0.0059 20.1 6.5 26 395-420 13-38 (66)
136 COG0317 SpoT Guanosine polypho 24.3 1.8E+02 0.0038 33.0 6.5 41 386-426 627-667 (701)
137 PF14197 Cep57_CLD_2: Centroso 23.4 1.3E+02 0.0028 23.7 3.9 27 302-328 40-66 (69)
138 COG3074 Uncharacterized protei 23.2 1.3E+02 0.0029 23.9 3.8 25 304-328 13-37 (79)
139 cd04918 ACT_AK1-AT_2 ACT domai 22.9 2.3E+02 0.005 21.2 5.2 31 396-426 13-43 (65)
140 PRK11020 hypothetical protein; 22.6 1.6E+02 0.0034 25.6 4.5 53 274-326 3-55 (118)
141 PRK05022 anaerobic nitric oxid 22.0 1E+02 0.0022 33.2 4.1 72 92-164 65-154 (509)
142 PF04508 Pox_A_type_inc: Viral 21.9 1.2E+02 0.0026 18.9 2.6 17 311-327 3-19 (23)
143 PF14992 TMCO5: TMCO5 family 21.8 1.1E+02 0.0024 30.7 3.9 25 303-327 145-169 (280)
144 PF09006 Surfac_D-trimer: Lung 20.6 1.2E+02 0.0026 22.2 2.8 20 311-330 1-20 (46)
No 1
>PF14215 bHLH-MYC_N: bHLH-MYC and R2R3-MYB transcription factors N-terminal
Probab=100.00 E-value=1.9e-42 Score=315.87 Aligned_cols=151 Identities=25% Similarity=0.353 Sum_probs=114.2
Q ss_pred HHHHHHhccCCCCCeEEEEeeeCCCCCceEEEcCccccCCCCCCcceeecccccccccc--cc-ccccccccCcccchh-
Q 041101 7 AVEWLRPFVDSKAWDYCVVWKLGDDPSRFIEWLGCCCSGGVGGGFEYVKVKEESGEEQK--FS-FCRDAHLKHSARTKA- 82 (433)
Q Consensus 7 Lq~~Lr~l~~~~~W~YavFW~~~~~~~~~L~W~dg~c~~~~~~~~~~~~~~~~~~~~~~--~~-~~~d~~~~~~~~~~~- 82 (433)
|||+||+||++.+|+||||||+++++ ++|+||||||+|........ +..+..+.+++ ++ ++.+.. .++.++..
T Consensus 1 Lq~~Lr~lv~~~~W~YaVFWk~~~~~-~~L~W~DG~~~g~~~~~~~~-~~~~~~~~~~l~~l~~~~~~~~-~~~~~v~~~ 77 (163)
T PF14215_consen 1 LQQRLRSLVENSQWTYAVFWKLSPDN-SVLVWGDGYCNGPKETRKNG-EEEQEQRSKVLRELHSSFSSYA-LSPEEVTDT 77 (163)
T ss_pred ChHHHHHHhCCCCCcEEEEeEEcCCC-CeeeEcceeecCCcccccch-hhccchhhhHHHHHhhhccccc-cccchhHHH
Confidence 79999999999999999999999995 79999999999876521111 11111111111 11 111111 12213322
Q ss_pred -hhHhhccceeeecCCCcceeEeecCCceeeecCCCCccccc-------ccCCceEEEEeeCCceEeeccccccccChHH
Q 041101 83 -CEALAQLPSFMDLYSGIHGEVVITNQPKWISLANSSDSIAS-------HQSNSTRVLIPVFGGLIELFAAKHISKDQNI 154 (433)
Q Consensus 83 -~~~l~~m~~~f~~g~Gl~Gk~~~sg~h~Wi~~~~~~~~~~~-------~~gIqTiv~IPv~~GVveLGS~~~i~Ed~~~ 154 (433)
+||+.+|+++| |+|+|||||++|+|+||++++....+.+ .+||||||||||++|||||||+++|+||+++
T Consensus 78 e~f~~~s~~~sf--g~G~~G~a~~sg~~~Wi~~~~~~~~~~~~r~~~aq~~~~~Tiv~IPv~~GVvELGSt~~I~Ed~~~ 155 (163)
T PF14215_consen 78 EWFYLVSMSYSF--GEGIPGRAAASGQHIWISGANELDSSYCERAWLAQFAGIQTIVCIPVPNGVVELGSTEKIPEDSNL 155 (163)
T ss_pred HHHhhceeeEEe--cCCccEEEeecCccEEEeCCCccccccchhhhhhcccccceEEEEEecCCEEEeeeeeeeccCHHH
Confidence 67899998888 9999999999999999999985433332 2789999999999999999999999999999
Q ss_pred HHHHHHhc
Q 041101 155 IELVLAHC 162 (433)
Q Consensus 155 v~~vk~~f 162 (433)
|++||++|
T Consensus 156 v~~vk~~F 163 (163)
T PF14215_consen 156 VQRVKSLF 163 (163)
T ss_pred HHHHHhhC
Confidence 99999998
No 2
>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=99.28 E-value=4.4e-12 Score=96.26 Aligned_cols=53 Identities=34% Similarity=0.622 Sum_probs=50.1
Q ss_pred ccccchHHHHHHHHHHHHhHHHHHhcCCCC---CCCchhhHHHHHHHHHHHHHHHH
Q 041101 266 PKAKNLITERNRRNKLKDGLFALRALVPKI---SKMDRAAILGDAAEYIKELLQEV 318 (433)
Q Consensus 266 ~~~~h~~~Er~RR~~~n~~~~~LrslvP~~---~k~dkasil~~ai~YI~~Lq~~v 318 (433)
.+..|+..||+||++||..|..|+++||.. .|+||++||..||+||+.|+.++
T Consensus 4 ~r~~~~~~Er~RR~~~n~~~~~L~~llp~~~~~~k~~k~~iL~~a~~yI~~L~~~~ 59 (60)
T cd00083 4 RREAHNLRERRRRERINDAFDELRSLLPTLPPSKKLSKAEILRKAVDYIKSLQELL 59 (60)
T ss_pred HHHHHhHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 467899999999999999999999999987 89999999999999999999876
No 3
>smart00353 HLH helix loop helix domain.
Probab=99.26 E-value=9.1e-12 Score=92.47 Aligned_cols=49 Identities=41% Similarity=0.598 Sum_probs=45.7
Q ss_pred hHHHHHHHHHHHHhHHHHHhcCCC---CCCCchhhHHHHHHHHHHHHHHHHH
Q 041101 271 LITERNRRNKLKDGLFALRALVPK---ISKMDRAAILGDAAEYIKELLQEVD 319 (433)
Q Consensus 271 ~~~Er~RR~~~n~~~~~LrslvP~---~~k~dkasil~~ai~YI~~Lq~~v~ 319 (433)
+..||+||++||+.|..|+++||. ..|++|++||.+||+||+.|+++++
T Consensus 1 n~~Er~RR~~~n~~~~~L~~lip~~~~~~k~~k~~iL~~ai~yi~~L~~~~~ 52 (53)
T smart00353 1 NARERRRRRKINEAFDELRSLLPTLPNNKKLSKAEILRLAIEYIKSLQEELQ 52 (53)
T ss_pred CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHh
Confidence 368999999999999999999994 6799999999999999999999876
No 4
>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=99.26 E-value=5.8e-12 Score=94.58 Aligned_cols=49 Identities=39% Similarity=0.628 Sum_probs=46.3
Q ss_pred cccchHHHHHHHHHHHHhHHHHHhcCCCC-----CCCchhhHHHHHHHHHHHHH
Q 041101 267 KAKNLITERNRRNKLKDGLFALRALVPKI-----SKMDRAAILGDAAEYIKELL 315 (433)
Q Consensus 267 ~~~h~~~Er~RR~~~n~~~~~LrslvP~~-----~k~dkasil~~ai~YI~~Lq 315 (433)
+..|+..||+||++||+.|..|+.+||.. .|++|++||..||+||++||
T Consensus 2 R~~h~~~Er~RR~~i~~~~~~L~~llp~~~~~~~~k~~K~~iL~~ai~yI~~Lq 55 (55)
T PF00010_consen 2 RQKHNERERRRRDRINDCFDELRELLPSCSAGSSRKLSKASILQKAIDYIKQLQ 55 (55)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHCCSSHHCCTTSSSSHHHHHHHHHHHHHHHH
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHhccchhccccccCCHHHHHHHHHHHHHHhC
Confidence 56899999999999999999999999975 78999999999999999997
No 5
>KOG1319 consensus bHLHZip transcription factor BIGMAX [Transcription]
Probab=99.12 E-value=6.4e-11 Score=107.98 Aligned_cols=94 Identities=29% Similarity=0.411 Sum_probs=73.8
Q ss_pred CCCCCCCCCCCCCCCCcccccccCCCCCCC---CCCCCCCCccccchHHHHHHHHHHHHhHHHHHhcCCCC-------CC
Q 041101 228 SSRGSNPSIEHPSFDSNYGYIAQNAPLMQP---IGNSFAKRPKAKNLITERNRRNKLKDGLFALRALVPKI-------SK 297 (433)
Q Consensus 228 ss~~s~~~~~~~s~~s~~~~~~~~~~~~~~---r~~~~~~~~~~~h~~~Er~RR~~~n~~~~~LrslvP~~-------~k 297 (433)
|+.||+++++-+|++ ++++..+ ++.+..+.++..|..+||+||+.||..|+.|+.|||.. .|
T Consensus 29 Ss~GStsssSApNtd--------d~ds~~hS~a~k~syk~rrr~aHtqaEqkRRdAIk~GYddLq~LvP~cq~~ds~g~K 100 (229)
T KOG1319|consen 29 SSIGSTSASSAPNTD--------DEDSDYHSEAYKESYKDRRRRAHTQAEQKRRDAIKRGYDDLQTLVPTCQQQDSIGQK 100 (229)
T ss_pred CCCCCCCCCCCCCCC--------cccccchhHHHHhhHHHHHHHHHHHHHHHHHHHHHhchHHHHHhccccccccchhHH
Confidence 344555555555555 4444333 44566778999999999999999999999999999963 37
Q ss_pred CchhhHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 041101 298 MDRAAILGDAAEYIKELLQEVDKLQDELKENE 329 (433)
Q Consensus 298 ~dkasil~~ai~YI~~Lq~~v~~L~~~~~~~~ 329 (433)
..||-||..+|+||..|++++...+++...+.
T Consensus 101 lskA~ILqksidyi~~L~~~k~kqe~e~s~L~ 132 (229)
T KOG1319|consen 101 LSKAIILQKTIDYIQFLHKEKKKQEEEVSTLR 132 (229)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999988888776554
No 6
>KOG1318 consensus Helix loop helix transcription factor EB [Transcription]
Probab=98.58 E-value=4.8e-08 Score=100.28 Aligned_cols=57 Identities=32% Similarity=0.570 Sum_probs=51.6
Q ss_pred CCccccchHHHHHHHHHHHHhHHHHHhcCCCC----CCCchhhHHHHHHHHHHHHHHHHHH
Q 041101 264 KRPKAKNLITERNRRNKLKDGLFALRALVPKI----SKMDRAAILGDAAEYIKELLQEVDK 320 (433)
Q Consensus 264 ~~~~~~h~~~Er~RR~~~n~~~~~LrslvP~~----~k~dkasil~~ai~YI~~Lq~~v~~ 320 (433)
+.++..|+++|||||++||+++..|-.|||.. .|..|.+||..+.+||++||+..++
T Consensus 231 r~Krd~HNeVERRRR~nIN~~IkeLg~liP~~~~~~~~~nKgtILk~s~dYIr~Lqq~~q~ 291 (411)
T KOG1318|consen 231 RRKRDNHNEVERRRRENINDRIKELGQLIPKCNSEDMKSNKGTILKASCDYIRELQQTLQR 291 (411)
T ss_pred HHHHhhhhHHHHHHHHHHHHHHHHHHHhCCCCCcchhhcccchhhHHHHHHHHHHHHHHHH
Confidence 46888999999999999999999999999985 4667999999999999999987773
No 7
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=98.13 E-value=6.1e-06 Score=79.44 Aligned_cols=67 Identities=27% Similarity=0.344 Sum_probs=55.8
Q ss_pred CCCCccccchHHHHHHHHHHHHhHHHHHhcCCCC--CCC-chhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 041101 262 FAKRPKAKNLITERNRRNKLKDGLFALRALVPKI--SKM-DRAAILGDAAEYIKELLQEVDKLQDELKEN 328 (433)
Q Consensus 262 ~~~~~~~~h~~~Er~RR~~~n~~~~~LrslvP~~--~k~-dkasil~~ai~YI~~Lq~~v~~L~~~~~~~ 328 (433)
...+.+..|++.||+||..|++.|..|+.+||.. .+. +.++||..|.+||+.|+.+..+.+..++++
T Consensus 55 ~~~~~R~~HN~LEk~RRahlk~~~~~Lk~~vP~~~~~~~~t~lsiL~kA~~~i~~l~~~~~~~~~~~e~l 124 (232)
T KOG2483|consen 55 SAASSRAHHNALEKRRRAHLKDCFESLKDSVPLLNGETRSTTLSILDKALEHIQSLERKSATQQQDIEDL 124 (232)
T ss_pred CCCcchhhhhhhhHHHHHHHHHHHHHHHHhCCCCCCcchhhhhHhhhhHHHHHHHHHhHHHHHHHHHHHH
Confidence 3457889999999999999999999999999973 222 368999999999999998877776655543
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=98.09 E-value=1.3e-05 Score=63.76 Aligned_cols=45 Identities=20% Similarity=0.410 Sum_probs=43.7
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
+|+|.+.+|||+|.+|.++|..+||+|..|.|+|.|+++.++|.|
T Consensus 3 viev~a~DRpGLL~~i~~~l~~~gl~I~~AkIsT~Gerv~DvFyV 47 (72)
T cd04895 3 LVKVDSARKPGILLEAVQVLTDLDLCITKAYISSDGGWFMDVFHV 47 (72)
T ss_pred EEEEEECCcCCHHHHHHHHHHHCCcEEEEEEEeecCCeEEEEEEE
Confidence 689999999999999999999999999999999999999999987
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=98.03 E-value=1.8e-05 Score=63.43 Aligned_cols=45 Identities=9% Similarity=0.234 Sum_probs=43.6
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
+|.|.|.+|||+|.+|..+|-.+|++|.+|.|+|.++++.++|.|
T Consensus 3 vveV~~~DRpGLL~~i~~~l~~~~l~I~~A~I~T~gera~D~FyV 47 (75)
T cd04897 3 VVTVQCRDRPKLLFDVVCTLTDMDYVVFHATIDTDGDDAHQEYYI 47 (75)
T ss_pred EEEEEeCCcCcHHHHHHHHHHhCCeEEEEEEEeecCceEEEEEEE
Confidence 589999999999999999999999999999999999999999987
No 10
>KOG3561 consensus Aryl-hydrocarbon receptor nuclear translocator [Transcription]
Probab=97.97 E-value=7.1e-06 Score=90.79 Aligned_cols=51 Identities=20% Similarity=0.343 Sum_probs=48.2
Q ss_pred cccchHHHHHHHHHHHHhHHHHHhcCCCC----CCCchhhHHHHHHHHHHHHHHH
Q 041101 267 KAKNLITERNRRNKLKDGLFALRALVPKI----SKMDRAAILGDAAEYIKELLQE 317 (433)
Q Consensus 267 ~~~h~~~Er~RR~~~n~~~~~LrslvP~~----~k~dkasil~~ai~YI~~Lq~~ 317 (433)
+..|+.+||+||+|||..+..|.+|||.. .|+||.+||..||.+|+.+++.
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 88999999999999999999999999973 6999999999999999999884
No 11
>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=97.96 E-value=2.8e-05 Score=62.21 Aligned_cols=46 Identities=33% Similarity=0.643 Sum_probs=43.7
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEe-eCCEEEEEEEe
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVTT-FNGKVLNILRV 432 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist-~~~~vl~~f~v 432 (433)
++|+|.|.+++|+|.+|..+|..+||+|+.|.|++ .+++++++|.|
T Consensus 1 ~~~ei~~~Dr~gLfa~i~~~l~~~~l~I~~A~I~Tt~~~~v~D~F~V 47 (76)
T cd04927 1 FLLKLFCSDRKGLLHDVTEVLYELELTIERVKVSTTPDGRVLDLFFI 47 (76)
T ss_pred CEEEEEECCCCCHHHHHHHHHHHCCCeEEEEEEEECCCCEEEEEEEE
Confidence 46899999999999999999999999999999996 89999999987
No 12
>cd04896 ACT_ACR-like_3 ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). This CD includes the third ACT domain, of a novel type of ACT domain-containing protein which is composed almost entirely of four ACT domain repeats (the "ACR" protein). ACR proteins, found only in Arabidopsis and Oryza, as yet, are proposed to function as novel regulatory or sensor proteins in plants. Nine ACR gene products (ACR1-8 in Arabidopsis and OsARC1-9 in Oryza) have been described, however, the ACR-like sequences in this CD are distinct from those characterized. This CD includes the Oryza sativa ACR-like protein (Os05g0113000) encoded on chromosome 5 and the Arabidopsis thaliana predicted gene product, At2g39570. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=97.90 E-value=4.1e-05 Score=61.35 Aligned_cols=45 Identities=11% Similarity=0.318 Sum_probs=43.5
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEE--eeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVT--TFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~is--t~~~~vl~~f~v 432 (433)
+|.|.|.+|+|+|.+|.++|..+||+|..|.|+ |.|+++.++|.|
T Consensus 2 vlev~a~DRpGLL~~i~~~l~~~~l~i~~AkI~~~T~Gerv~D~Fyv 48 (75)
T cd04896 2 LLQIRCVDQKGLLYDILRTSKDCNIQISYGRFSSKVKGYREVDLFIV 48 (75)
T ss_pred EEEEEeCCcccHHHHHHHHHHHCCeEEEEEEEecCcccCEEEEEEEE
Confidence 589999999999999999999999999999999 999999999986
No 13
>KOG4304 consensus Transcriptional repressors of the hairy/E(spl) family (contains HLH) [Transcription]
Probab=97.89 E-value=7.4e-06 Score=79.97 Aligned_cols=58 Identities=24% Similarity=0.405 Sum_probs=50.7
Q ss_pred CccccchHHHHHHHHHHHHhHHHHHhcCCC--------CCCCchhhHHHHHHHHHHHHHHHHHHHH
Q 041101 265 RPKAKNLITERNRRNKLKDGLFALRALVPK--------ISKMDRAAILGDAAEYIKELLQEVDKLQ 322 (433)
Q Consensus 265 ~~~~~h~~~Er~RR~~~n~~~~~LrslvP~--------~~k~dkasil~~ai~YI~~Lq~~v~~L~ 322 (433)
.++..|-..||+||.+||+-|..|+.|||. .+|++||-||.-|++|++.|+.....-.
T Consensus 31 ~rk~~Kpl~EKkRRaRIN~~L~eLK~Li~e~~~~~~~~~sklEKAdILEltV~hL~~l~~~~~~~~ 96 (250)
T KOG4304|consen 31 YRKVRKPLLEKKRRARINRCLDELKDLIPEALKKDGQRHSKLEKADILELTVNHLRQLQRSQQAAA 96 (250)
T ss_pred HhhhcchhHHHHHHHHHHHHHHHHHHHHHHHHhhcchhhhhhHHHHHHHHHHHHHHHHhccccccc
Confidence 466777899999999999999999999994 3889999999999999999987655433
No 14
>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=97.81 E-value=8.6e-05 Score=58.60 Aligned_cols=45 Identities=27% Similarity=0.434 Sum_probs=42.4
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee-CCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF-NGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~-~~~vl~~f~v 432 (433)
.|.|.|.+++|+|.+|..+|..+||+|+.|.|.|. +++++++|.|
T Consensus 3 ~i~v~~~Dr~gLl~~i~~~l~~~~l~I~~A~i~T~~~~~v~D~F~v 48 (73)
T cd04900 3 EVFIYTPDRPGLFARIAGALDQLGLNILDARIFTTRDGYALDTFVV 48 (73)
T ss_pred EEEEEecCCCCHHHHHHHHHHHCCCCeEEeEEEEeCCCeEEEEEEE
Confidence 57889999999999999999999999999999888 6999999987
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=97.61 E-value=0.00026 Score=56.24 Aligned_cols=45 Identities=22% Similarity=0.352 Sum_probs=43.4
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
+|+|.+.+++|+|.+|..+|..+|++|+.|.+.+.++.++++|.|
T Consensus 2 ~~~v~~~Dr~gLl~~i~~~l~~~~lnI~~A~i~t~~~~~~d~f~V 46 (74)
T cd04925 2 AIELTGTDRPGLLSEVFAVLADLHCNVVEARAWTHNGRLACVIYV 46 (74)
T ss_pred EEEEEECCCCCHHHHHHHHHHHCCCcEEEEEEEEECCEEEEEEEE
Confidence 588999999999999999999999999999999999999999987
No 16
>KOG3960 consensus Myogenic helix-loop-helix transcription factor [Transcription]
Probab=97.54 E-value=0.00018 Score=69.18 Aligned_cols=62 Identities=21% Similarity=0.323 Sum_probs=52.8
Q ss_pred CccccchHHHHHHHHHHHHhHHHH-HhcCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 041101 265 RPKAKNLITERNRRNKLKDGLFAL-RALVPK-ISKMDRAAILGDAAEYIKELLQEVDKLQDELK 326 (433)
Q Consensus 265 ~~~~~h~~~Er~RR~~~n~~~~~L-rslvP~-~~k~dkasil~~ai~YI~~Lq~~v~~L~~~~~ 326 (433)
.++..-.+.||+|=+|+|+-|.+| |.-.++ ..+.-|+-||..||+||..||.-++++.+...
T Consensus 117 DRRKAATMRERRRLkKVNEAFE~LKRrT~~NPNQRLPKVEILRsAI~YIE~Lq~LL~~~~~~~~ 180 (284)
T KOG3960|consen 117 DRRKAATMRERRRLKKVNEAFETLKRRTSSNPNQRLPKVEILRSAIRYIERLQALLQEQDQAEK 180 (284)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCccccccHHHHHHHHHHHHHHHHHHHHHhhccch
Confidence 455566899999999999999999 666676 46779999999999999999999998877544
No 17
>KOG0561 consensus bHLH transcription factor [Transcription]
Probab=97.44 E-value=0.00011 Score=72.26 Aligned_cols=55 Identities=35% Similarity=0.531 Sum_probs=47.7
Q ss_pred cccchHHHHHHHHHHHHhHHHHHhcCCC--CCCCchhhHHHHHHHHHHHHHHHHHHH
Q 041101 267 KAKNLITERNRRNKLKDGLFALRALVPK--ISKMDRAAILGDAAEYIKELLQEVDKL 321 (433)
Q Consensus 267 ~~~h~~~Er~RR~~~n~~~~~LrslvP~--~~k~dkasil~~ai~YI~~Lq~~v~~L 321 (433)
+.--+--||+|-.-||..|..||+|+|. ..|..||.||..+.+||.+|+.+.-+|
T Consensus 61 ReIANsNERRRMQSINAGFqsLr~LlPr~eGEKLSKAAILQQTa~yI~~Le~~Kt~l 117 (373)
T KOG0561|consen 61 REIANSNERRRMQSINAGFQSLRALLPRKEGEKLSKAAILQQTADYIHQLEGHKTEL 117 (373)
T ss_pred HHhhcchHHHHHHhhhHHHHHHHHhcCcccchhhHHHHHHHHHHHHHHHHHhccccc
Confidence 3344567999999999999999999997 689999999999999999998765544
No 18
>KOG2588 consensus Predicted DNA-binding protein [Transcription]
Probab=97.20 E-value=0.00017 Score=80.33 Aligned_cols=65 Identities=28% Similarity=0.431 Sum_probs=58.4
Q ss_pred CCccccchHHHHHHHHHHHHhHHHHHhcCCC-CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 041101 264 KRPKAKNLITERNRRNKLKDGLFALRALVPK-ISKMDRAAILGDAAEYIKELLQEVDKLQDELKEN 328 (433)
Q Consensus 264 ~~~~~~h~~~Er~RR~~~n~~~~~LrslvP~-~~k~dkasil~~ai~YI~~Lq~~v~~L~~~~~~~ 328 (433)
..++.+|+.+||+-|-.||+++..|+.+||+ ..|+.|..+|..||+||++|+...+.+..+....
T Consensus 274 ~~kRtAHN~IEKRYRsSINDKI~eLk~lV~g~~aKl~kSavLr~ai~~i~dl~~~nq~lk~~~~~l 339 (953)
T KOG2588|consen 274 GEKRTAHNIIEKRYRSSINDKIIELKDLVPGTEAKLNKSAVLRKAIDYIEDLQGYNQKLKLENASL 339 (953)
T ss_pred CcccchhhHHHHHhhcchhHHHHHHHHhcCccHhhhhhhhhHHHHHHHHHHhhccccccchhhhhh
Confidence 4689999999999999999999999999997 5899999999999999999998887777665543
No 19
>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=97.19 E-value=0.0016 Score=51.27 Aligned_cols=45 Identities=22% Similarity=0.272 Sum_probs=41.3
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEE-eeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVT-TFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~is-t~~~~vl~~f~v 432 (433)
.|-|.|+.++|+|.+|..+|..+||+|+.|.+. +.+|.++++|.|
T Consensus 3 eI~V~~~Dr~gLFa~iag~L~~~~LnI~~A~i~tt~dG~~LDtF~V 48 (68)
T cd04928 3 EITFAAGDKPKLLSQLSSLLGDLGLNIAEAHAFSTDDGLALDIFVV 48 (68)
T ss_pred EEEEEECCCcchHHHHHHHHHHCCCceEEEEEEEcCCCeEEEEEEE
Confidence 467888999999999999999999999999998 558999999987
No 20
>PLN03217 transcription factor ATBS1; Provisional
Probab=97.19 E-value=0.00094 Score=54.05 Aligned_cols=53 Identities=30% Similarity=0.584 Sum_probs=44.6
Q ss_pred HHHHHhHHHHHhcCCCC---CCCchh---hHHHHHHHHHHHHHHHHHHHHHHHhhhhcc
Q 041101 279 NKLKDGLFALRALVPKI---SKMDRA---AILGDAAEYIKELLQEVDKLQDELKENEDC 331 (433)
Q Consensus 279 ~~~n~~~~~LrslvP~~---~k~dka---sil~~ai~YI~~Lq~~v~~L~~~~~~~~~~ 331 (433)
++|++....|+.|+|.. ...+|+ -||.++-+||+.|+++|..|.+++.++...
T Consensus 20 dqi~dLvsKLq~llPe~r~~r~s~k~saskvLqEtC~YIrsLhrEvDdLSerLs~LL~t 78 (93)
T PLN03217 20 DQINDLIIKLQQLLPELRDSRRSDKVSAARVLQDTCNYIRNLHREVDDLSERLSELLAN 78 (93)
T ss_pred HHHHHHHHHHHHHChHHHhhhccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 68999999999999974 223454 489999999999999999999999877643
No 21
>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=97.17 E-value=0.0016 Score=50.10 Aligned_cols=45 Identities=16% Similarity=0.316 Sum_probs=42.6
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.|.|.+.+++|+|.+|+.+|.+++++|.++.+.+.++.++.+|++
T Consensus 2 ~l~v~~~d~~gll~~i~~~l~~~~~~I~~~~~~~~~~~~~~~f~i 46 (70)
T cd04899 2 VLELTALDRPGLLADVTRVLAELGLNIHSAKIATLGERAEDVFYV 46 (70)
T ss_pred EEEEEEcCCccHHHHHHHHHHHCCCeEEEEEEEecCCEEEEEEEE
Confidence 578899999999999999999999999999999999999999987
No 22
>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=97.06 E-value=0.0027 Score=50.03 Aligned_cols=45 Identities=20% Similarity=0.242 Sum_probs=41.9
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.|.|.+++++|+|.+|..+|.++|++|++|.+.+.++.++.+|+|
T Consensus 3 ri~V~~~D~~Gll~~i~~~l~~~~lnI~sa~i~t~~~~~~d~f~v 47 (72)
T cd04926 3 RLELRTEDRVGLLSDVTRVFRENGLTVTRAEISTQGDMAVNVFYV 47 (72)
T ss_pred EEEEEECCccCHHHHHHHHHHHCCcEEEEEEEecCCCeEEEEEEE
Confidence 467788899999999999999999999999999999999999987
No 23
>KOG4029 consensus Transcription factor HAND2/Transcription factor TAL1/TAL2/LYL1 [Transcription]
Probab=96.93 E-value=0.00079 Score=64.96 Aligned_cols=61 Identities=25% Similarity=0.358 Sum_probs=53.4
Q ss_pred CccccchHHHHHHHHHHHHhHHHHHhcCCC----CCCCchhhHHHHHHHHHHHHHHHHHHHHHHH
Q 041101 265 RPKAKNLITERNRRNKLKDGLFALRALVPK----ISKMDRAAILGDAAEYIKELLQEVDKLQDEL 325 (433)
Q Consensus 265 ~~~~~h~~~Er~RR~~~n~~~~~LrslvP~----~~k~dkasil~~ai~YI~~Lq~~v~~L~~~~ 325 (433)
.++..++..||+|=+.+|..|..||.++|. .+|..|..+|.-||.||+.|++-++.-+...
T Consensus 108 ~~~~~~n~RER~Rv~~vN~~f~~Lr~~lP~~~~~~kklSKveTLr~A~~YI~~L~~lL~~~~~~~ 172 (228)
T KOG4029|consen 108 AQRQARNARERQRVQSVNSAFAELRALLPTEPPQSKKLSKVETLRLATSYIRYLTKLLATQEAPL 172 (228)
T ss_pred hhhhhhhhhhhhcccchhhhhHHHHhcCCCCCCcccccCcccchHHHHHHHHHHHHHhcccccCC
Confidence 466677888999999999999999999995 5688999999999999999999887766544
No 24
>PRK05007 PII uridylyl-transferase; Provisional
Probab=96.31 E-value=0.011 Score=67.82 Aligned_cols=59 Identities=19% Similarity=0.280 Sum_probs=50.4
Q ss_pred ceEEEEE-ecCceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEeC
Q 041101 375 VRVEVNQ-INDRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRVQ 433 (433)
Q Consensus 375 ~~VeV~~-i~~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~vE 433 (433)
+.|.+.. .++.-.+|+|.|.+|||+|.+|.++|.++||+|.+|.|+|.++++.++|-|.
T Consensus 796 ~~V~~d~~~s~~~TvlEV~a~DRpGLL~~I~~~l~~~~l~I~~AkI~T~gera~DvFyV~ 855 (884)
T PRK05007 796 TEVSFLPTHTDRRSYMELIALDQPGLLARVGKIFADLGISLHGARITTIGERVEDLFILA 855 (884)
T ss_pred CEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCcEEEEEEEeccCceEEEEEEEE
Confidence 4555532 1234578999999999999999999999999999999999999999999873
No 25
>PF13740 ACT_6: ACT domain; PDB: 1ZPV_A 3P96_A 1U8S_A.
Probab=96.24 E-value=0.023 Score=45.18 Aligned_cols=48 Identities=13% Similarity=0.218 Sum_probs=42.0
Q ss_pred eEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEeC
Q 041101 386 DFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRVQ 433 (433)
Q Consensus 386 ~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~vE 433 (433)
.++|.+.+++|||++..|..+|.+.|.+|..++.++.++.+..++.|+
T Consensus 2 ~~vItv~G~DrpGiv~~v~~~l~~~g~ni~d~~~~~~~~~f~~~~~v~ 49 (76)
T PF13740_consen 2 QLVITVVGPDRPGIVAAVTGVLAEHGCNIEDSRQAVLGGRFTLIMLVS 49 (76)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCTT-EEEEEEEEEETTEEEEEEEEE
T ss_pred EEEEEEEecCCCcHHHHHHHHHHHCCCcEEEEEEEEEcCeEEEEEEEE
Confidence 478999999999999999999999999999999999999998888764
No 26
>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=96.20 E-value=0.026 Score=42.98 Aligned_cols=45 Identities=18% Similarity=0.391 Sum_probs=41.2
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.|.|.|.+++|+|.+|+.+|.++++.|.++.+.+.++....+|++
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~~~v 46 (70)
T cd04873 2 VVEVYAPDRPGLLADITRVLADLGLNIHDARISTTGERALDVFYV 46 (70)
T ss_pred EEEEEeCCCCCHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE
Confidence 477899999999999999999999999999999988888888876
No 27
>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=95.91 E-value=0.048 Score=40.93 Aligned_cols=37 Identities=5% Similarity=0.144 Sum_probs=35.2
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCC
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNG 424 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~ 424 (433)
.|.|.|+++||.|.+|.++|.++|+.|.++.+.+.++
T Consensus 2 ~v~v~~~drpG~l~~v~~~la~~~inI~~~~~~~~~~ 38 (66)
T PF01842_consen 2 RVRVIVPDRPGILADVTEILADHGINIDSISQSSDKD 38 (66)
T ss_dssp EEEEEEETSTTHHHHHHHHHHHTTEEEEEEEEEEESS
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCHHHeEEEecCC
Confidence 5789999999999999999999999999999998887
No 28
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=95.84 E-value=0.036 Score=63.70 Aligned_cols=59 Identities=12% Similarity=0.268 Sum_probs=50.5
Q ss_pred cceEEEEEec-CceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 374 EVRVEVNQIN-DRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 374 ~~~VeV~~i~-~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.+.|.+..-. ++-..|.|.+.++||+|.+|..+|..+||+|+.|.|+|.+++++++|.|
T Consensus 801 ~~~V~i~~~~~~~~T~i~V~a~DrpGLLa~I~~~L~~~~l~I~~AkI~T~g~~v~D~F~V 860 (895)
T PRK00275 801 PTQVTISNDAQRPVTVLEIIAPDRPGLLARIGRIFLEFDLSLQNAKIATLGERVEDVFFI 860 (895)
T ss_pred CCEEEEEECCCCCeEEEEEEECCCCCHHHHHHHHHHHCCCEEEEeEEEecCCEEEEEEEE
Confidence 3455554322 3457799999999999999999999999999999999999999999987
No 29
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=95.82 E-value=0.023 Score=64.92 Aligned_cols=60 Identities=15% Similarity=0.270 Sum_probs=50.9
Q ss_pred cceEEEEE-ecCceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEeC
Q 041101 374 EVRVEVNQ-INDRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRVQ 433 (433)
Q Consensus 374 ~~~VeV~~-i~~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~vE 433 (433)
.++|.+.. .++.-.+|+|.+.+|||+|.+|.++|.++|++|..|.|+|.++++.++|-|.
T Consensus 770 ~~~V~~dn~~s~~~T~iev~a~DrpGLL~~I~~~l~~~~l~i~~AkI~T~gerv~D~Fyv~ 830 (854)
T PRK01759 770 KTEVRFLNEEKQEQTEMELFALDRAGLLAQVSQVFSELNLNLLNAKITTIGEKAEDFFILT 830 (854)
T ss_pred CCEEEEccCCCCCeEEEEEEeCCchHHHHHHHHHHHHCCCEEEEEEEcccCceEEEEEEEE
Confidence 34565532 1234578999999999999999999999999999999999999999999873
No 30
>PRK03059 PII uridylyl-transferase; Provisional
Probab=95.71 E-value=0.045 Score=62.58 Aligned_cols=58 Identities=12% Similarity=0.273 Sum_probs=49.9
Q ss_pred ceEEEEEe-cCceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 375 VRVEVNQI-NDRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 375 ~~VeV~~i-~~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
+.|.+... .++-..|.|.+.++||+|.+|..+|..+||+|+.|.|+|.++++.++|.|
T Consensus 774 ~~V~~~~~~~~~~T~i~V~a~DrpGLLa~Ia~~L~~~~l~I~~AkI~T~~~~v~DvF~V 832 (856)
T PRK03059 774 PRVDLRPDERGQYYILSVSANDRPGLLYAIARVLAEHRVSVHTAKINTLGERVEDTFLI 832 (856)
T ss_pred ceEEEEEcCCCCEEEEEEEeCCcchHHHHHHHHHHHCCCeEEEEEEeecCCEEEEEEEE
Confidence 34555432 23457899999999999999999999999999999999999999999987
No 31
>PRK04374 PII uridylyl-transferase; Provisional
Probab=95.67 E-value=0.049 Score=62.33 Aligned_cols=59 Identities=22% Similarity=0.339 Sum_probs=51.1
Q ss_pred cceEEEEEe-cCceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 374 EVRVEVNQI-NDRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 374 ~~~VeV~~i-~~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.+.|.+..- .++-..|.|.+.++||+|.+|..+|..+||+|+.|.|+|.++++.++|.|
T Consensus 783 ~~~V~~~~~~~~~~t~leI~a~DrpGLLa~Ia~~l~~~~l~I~~AkI~T~g~~a~D~F~V 842 (869)
T PRK04374 783 APRVEFSESAGGRRTRISLVAPDRPGLLADVAHVLRMQHLRVHDARIATFGERAEDQFQI 842 (869)
T ss_pred CCeEEEeecCCCCeEEEEEEeCCcCcHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEE
Confidence 356666542 23457899999999999999999999999999999999999999999987
No 32
>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=95.58 E-value=0.047 Score=43.53 Aligned_cols=47 Identities=15% Similarity=0.241 Sum_probs=42.9
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEeC
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRVQ 433 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~vE 433 (433)
+.|.+.|++++|+..+|-+.|.+.|..|+.++....++.++..+.++
T Consensus 2 ~iltv~g~Dr~GiVa~vs~~la~~g~nI~d~~q~~~~~~F~m~~~~~ 48 (77)
T cd04893 2 LVISALGTDRPGILNELTRAVSESGCNILDSRMAILGTEFALTMLVE 48 (77)
T ss_pred EEEEEEeCCCChHHHHHHHHHHHcCCCEEEceeeEEcCEEEEEEEEE
Confidence 67899999999999999999999999999999999999887776653
No 33
>PRK03381 PII uridylyl-transferase; Provisional
Probab=95.31 E-value=0.066 Score=60.60 Aligned_cols=48 Identities=21% Similarity=0.304 Sum_probs=45.9
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
+-..|.|.+.++||+|.+|..+|..+|++|++|.|+|.++.++++|.|
T Consensus 706 ~~t~i~V~a~DrpGLla~Ia~~L~~~~lnI~~AkI~T~g~~a~D~F~V 753 (774)
T PRK03381 706 DATVLEVRAADRPGLLARLARALERAGVDVRWARVATLGADVVDVFYV 753 (774)
T ss_pred CeEEEEEEeCCchhHHHHHHHHHHHCCCeEEEEEEeecCCeEEEEEEE
Confidence 358899999999999999999999999999999999999999999987
No 34
>PF13291 ACT_4: ACT domain; PDB: 2KO1_B 3IBW_A.
Probab=95.18 E-value=0.11 Score=41.19 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=39.2
Q ss_pred eEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee--CCEEEEEEEeC
Q 041101 386 DFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF--NGKVLNILRVQ 433 (433)
Q Consensus 386 ~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~--~~~vl~~f~vE 433 (433)
.+.|+|.+.+++|+|.+|..+|.+.++.|.++++... ++.+.-.|.+|
T Consensus 6 ~~~l~i~~~dr~GlL~dI~~~i~~~~~nI~~i~~~~~~~~~~~~~~l~v~ 55 (80)
T PF13291_consen 6 PVRLRIEAEDRPGLLADITSVISENGVNIRSINARTNKDDGTARITLTVE 55 (80)
T ss_dssp EEEEEEEEE--TTHHHHHHHHHHCSSSEEEEEEEEE--ETTEEEEEEEEE
T ss_pred EEEEEEEEEcCCCHHHHHHHHHHHCCCCeEEEEeEEeccCCEEEEEEEEE
Confidence 4678999999999999999999999999999999984 56776666654
No 35
>PRK05092 PII uridylyl-transferase; Provisional
Probab=95.09 E-value=0.086 Score=60.90 Aligned_cols=59 Identities=20% Similarity=0.390 Sum_probs=50.8
Q ss_pred cceEEEEEe-cCceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 374 EVRVEVNQI-NDRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 374 ~~~VeV~~i-~~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.+.|.+... .+....|.|.|.+++|+|.+|..+|.++|++|.+|.|.|.++++.++|.|
T Consensus 830 ~~~V~~~~~~s~~~t~i~I~~~DrpGLl~~I~~~l~~~gl~I~~A~I~T~~~~~~D~F~v 889 (931)
T PRK05092 830 PPRVTIDNEASNRFTVIEVNGRDRPGLLYDLTRALSDLNLNIASAHIATYGERAVDVFYV 889 (931)
T ss_pred CCEEEEeeCCCCCeEEEEEEECCcCcHHHHHHHHHHHCCceEEEEEEEEcCCEEEEEEEE
Confidence 345665542 23457899999999999999999999999999999999999999999987
No 36
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=94.97 E-value=0.049 Score=60.77 Aligned_cols=60 Identities=20% Similarity=0.275 Sum_probs=51.4
Q ss_pred ccceEEEEEec-CceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 373 SEVRVEVNQIN-DRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 373 ~~~~VeV~~i~-~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
..|+|++...- .+--+|+|.+.+|||+|..|-.+|..++|+|++|.|+|+|.++.++|.|
T Consensus 777 i~p~v~i~~t~~~~~t~lEv~alDRpGLLa~v~~v~~dl~l~i~~AkItT~GErveD~F~v 837 (867)
T COG2844 777 IPPRVTILPTASNDKTVLEVRALDRPGLLAALAGVFADLGLSLHSAKITTFGERVEDVFIV 837 (867)
T ss_pred cCCceeeccccCCCceEEEEEeCCcccHHHHHHHHHHhcccceeeeeeccccccceeEEEE
Confidence 44677765432 2357789999999999999999999999999999999999999999976
No 37
>PRK03381 PII uridylyl-transferase; Provisional
Probab=94.48 E-value=0.15 Score=57.89 Aligned_cols=48 Identities=17% Similarity=0.209 Sum_probs=45.6
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
+...|.|.|.++||+|++|..+|..+|++|+.|.|.+.+|.++.+|.|
T Consensus 598 ~~~~V~V~~~DrpGLfa~i~~vL~~~glnI~dA~i~t~dg~~ld~F~V 645 (774)
T PRK03381 598 HMVEVTVVAPDRRGLLSKAAGVLALHRLRVRSASVRSHDGVAVLEFVV 645 (774)
T ss_pred CeEEEEEEecCCccHHHHHHHHHHHCCCeEEEeEEEecCCEEEEEEEE
Confidence 457899999999999999999999999999999999999999999987
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=94.12 E-value=0.14 Score=58.67 Aligned_cols=48 Identities=27% Similarity=0.342 Sum_probs=45.2
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEE-eeCCEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVT-TFNGKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~is-t~~~~vl~~f~v 432 (433)
....|.|.+.+++|+|.+|..+|..+||+|+.|.|. +.++.++++|.|
T Consensus 667 ~~t~i~V~~~DrpgLla~i~~~L~~~~l~I~~A~I~tt~~g~~lD~F~V 715 (850)
T TIGR01693 667 GGTEVFIYAPDQPGLFAKVAGALAMLSLSVHDAQVNTTKDGVALDTFVV 715 (850)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEecCCEEEEEEEE
Confidence 456799999999999999999999999999999999 889999999987
No 39
>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=94.09 E-value=0.14 Score=58.48 Aligned_cols=59 Identities=20% Similarity=0.327 Sum_probs=50.5
Q ss_pred cceEEEEEe-cCceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 374 EVRVEVNQI-NDRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 374 ~~~VeV~~i-~~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.+.|.+... +++...|.|.|.++||+|.+|.++|.++|++|.+|.|+|.++++.++|.|
T Consensus 766 ~~~V~~d~~~s~~~t~~~v~~~DrpGll~~i~~~l~~~~~~i~~a~i~t~~~~~~d~F~v 825 (850)
T TIGR01693 766 PPRVTILNTASRKATIMEVRALDRPGLLARVGRTLEELGLSIQSAKITTFGEKAEDVFYV 825 (850)
T ss_pred CCeEEEccCCCCCeEEEEEEECCccHHHHHHHHHHHHCCCeEEEEEEEecCccceeEEEE
Confidence 345665432 23458899999999999999999999999999999999999999999987
No 40
>PRK01759 glnD PII uridylyl-transferase; Provisional
Probab=94.08 E-value=0.15 Score=58.50 Aligned_cols=48 Identities=27% Similarity=0.443 Sum_probs=45.0
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEe-eCCEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTT-FNGKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist-~~~~vl~~f~v 432 (433)
+...|.|.|.+++|+|.+|..+|..+||+|+.|.|.| .+|.++++|.|
T Consensus 676 ~~t~V~V~~~DrpGLfa~Ia~~L~~~~L~I~~A~I~T~~~g~alD~F~V 724 (854)
T PRK01759 676 GGTEIFIYCQDQANLFLKVVSTIGAKKLSIHDAQIITSQDGYVLDSFIV 724 (854)
T ss_pred CeEEEEEEecCCccHHHHHHHHHHHCCCeEEEEEEEEccCCEEEEEEEE
Confidence 4568999999999999999999999999999999976 89999999987
No 41
>KOG3910 consensus Helix loop helix transcription factor [Transcription]
Probab=93.83 E-value=0.031 Score=58.68 Aligned_cols=57 Identities=23% Similarity=0.218 Sum_probs=47.9
Q ss_pred CccccchHHHHHHHHHHHHhHHHHHhcCCCCCC----CchhhHHHHHHHHHHHHHHHHHHH
Q 041101 265 RPKAKNLITERNRRNKLKDGLFALRALVPKISK----MDRAAILGDAAEYIKELLQEVDKL 321 (433)
Q Consensus 265 ~~~~~h~~~Er~RR~~~n~~~~~LrslvP~~~k----~dkasil~~ai~YI~~Lq~~v~~L 321 (433)
.+|..++..||-|-+.||+-|..|-.+.----| -.|.-||..|+.-|-.|++||++-
T Consensus 525 ERR~aNNARERlRVRDINeAfKELGRMCqlHlkSeKpQTKLgILhqAVsVIlsLEQQVRER 585 (632)
T KOG3910|consen 525 ERRMANNARERLRVRDINEAFKELGRMCQLHLKSEKPQTKLGILHQAVSVILSLEQQVRER 585 (632)
T ss_pred HHHhhhhhhhheehhhHHHHHHHHHHHHHHhhcccCcchhhhHHHHHHHHHHHHHHHHHHc
Confidence 588899999999999999999999776543222 357889999999999999999764
No 42
>PRK00194 hypothetical protein; Validated
Probab=93.75 E-value=0.12 Score=42.01 Aligned_cols=47 Identities=17% Similarity=0.313 Sum_probs=40.7
Q ss_pred eEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 386 DFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 386 ~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.+.|.|.|+++||++.+|.+.|.+.|++|.+.+..+.++.+.-.+.+
T Consensus 3 ~~~ltv~g~DrpGiva~vt~~la~~g~nI~~~~~~~~~~~~~~~~~v 49 (90)
T PRK00194 3 KAIITVIGKDKVGIIAGVSTVLAELNVNILDISQTIMDGYFTMIMLV 49 (90)
T ss_pred eEEEEEEcCCCCCHHHHHHHHHHHcCCCEEehhhHhhCCeeEEEEEE
Confidence 47899999999999999999999999999999988877766554443
No 43
>PRK05007 PII uridylyl-transferase; Provisional
Probab=93.64 E-value=0.2 Score=57.61 Aligned_cols=48 Identities=19% Similarity=0.171 Sum_probs=43.8
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC-CEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN-GKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~-~~vl~~f~v 432 (433)
+...|.|.|.+++|+|.+|..+|..+||+|+.|.|.|.+ |.++++|.|
T Consensus 700 ~~t~V~V~a~DrpGLfa~Ia~~La~~~L~I~~A~I~T~~dg~alD~F~V 748 (884)
T PRK05007 700 GGTEIFIWSPDRPYLFAAVCAELDRRNLSVHDAQIFTSRDGMAMDTFIV 748 (884)
T ss_pred CeEEEEEEecCCcCHHHHHHHHHHHCCCEEEEEEEEEcCCCeEEEEEEE
Confidence 467899999999999999999999999999999988664 599999987
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=93.56 E-value=0.13 Score=41.88 Aligned_cols=46 Identities=17% Similarity=0.284 Sum_probs=40.8
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
+.|.+.|+++||++.+|.+.|-+.|++|.+.+..+.++.+.-.+.+
T Consensus 2 ~vl~i~g~D~pGiva~vt~~la~~g~nI~~~~~~~~~~~f~~~~~v 47 (88)
T cd04872 2 AVITVVGKDRVGIVAGVSTKLAELNVNILDISQTIMDGYFTMIMIV 47 (88)
T ss_pred EEEEEEcCCCCCHHHHHHHHHHHcCCCEEechhHhhCCccEEEEEE
Confidence 5789999999999999999999999999999998888876655554
No 45
>PRK00275 glnD PII uridylyl-transferase; Provisional
Probab=93.50 E-value=0.19 Score=57.88 Aligned_cols=48 Identities=21% Similarity=0.242 Sum_probs=44.4
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEE-EeeCCEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANV-TTFNGKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~i-st~~~~vl~~f~v 432 (433)
+...|.|.|.+++|+|++|..+|..+||+|+.|.| |+-+|.++++|.|
T Consensus 703 ~~t~V~V~~~DrpgLFa~i~g~L~~~~lnI~~A~I~Tt~dg~alD~F~V 751 (895)
T PRK00275 703 GGTQIFIYAPDQHDFFAATVAAMDQLNLNIHDARIITSSSQFTLDTYIV 751 (895)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCeEEEEEEEEcCCCeEEEEEEE
Confidence 45789999999999999999999999999999998 5778999999987
No 46
>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=93.48 E-value=0.35 Score=37.36 Aligned_cols=45 Identities=13% Similarity=0.119 Sum_probs=37.7
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC-CEEEEEEEeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN-GKVLNILRVQ 433 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~-~~vl~~f~vE 433 (433)
|+|.+.+++|.|.+|+.+|.+.|..|.+.++.... +.....|.+|
T Consensus 2 l~v~~~d~~g~L~~i~~~i~~~~~nI~~v~~~~~~~~~~~~~~~ve 47 (74)
T cd04887 2 LRLELPNRPGMLGRVTTAIGEAGGDIGAIDLVEQGRDYTVRDITVD 47 (74)
T ss_pred EEEEeCCCCchHHHHHHHHHHcCCcEEEEEEEEecCCEEEEEEEEE
Confidence 78889999999999999999999999999988764 5655555554
No 47
>PRK03059 PII uridylyl-transferase; Provisional
Probab=93.11 E-value=0.23 Score=56.85 Aligned_cols=48 Identities=21% Similarity=0.346 Sum_probs=44.8
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEE-EeeCCEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANV-TTFNGKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~i-st~~~~vl~~f~v 432 (433)
+...|.|.|.+++|+|++|..+|..+||+|+.|.| ++.+|.++++|.|
T Consensus 677 ~~~~v~i~~~d~~gLFa~i~g~l~~~~l~I~~A~i~t~~~g~~ld~f~V 725 (856)
T PRK03059 677 EGLQVMVYTPDQPDLFARICGYFDRAGFSILDARVHTTRHGYALDTFQV 725 (856)
T ss_pred CeEEEEEEecCCCcHHHHHHHHHHHCCCceeeeEEEEcCCCeEEEEEEE
Confidence 45789999999999999999999999999999999 5789999999997
No 48
>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=92.71 E-value=0.37 Score=36.25 Aligned_cols=44 Identities=16% Similarity=0.246 Sum_probs=34.4
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee-----CCEEEEEEEe
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTF-----NGKVLNILRV 432 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~-----~~~vl~~f~v 432 (433)
+.|.+++++|.|.+|+++|.+.|++|.+...... .+...-.|++
T Consensus 1 ~~v~~~d~~G~L~~i~~~i~~~~~nI~~i~~~~~~~~~~~~~~~~~i~v 49 (73)
T cd04886 1 LRVELPDRPGQLAKLLAVIAEAGANIIEVSHDRAFKTLPLGEVEVELTL 49 (73)
T ss_pred CEEEeCCCCChHHHHHHHHHHcCCCEEEEEEEeccCCCCCceEEEEEEE
Confidence 3578899999999999999999999998887654 3444444444
No 49
>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=92.67 E-value=0.29 Score=37.80 Aligned_cols=45 Identities=18% Similarity=0.184 Sum_probs=40.6
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.|.|.|+++.|+-.+|.+.+-+.||.|+...+++.|.-.+-+|.|
T Consensus 2 vitvnCPDktGLgcdlcr~il~fGl~i~rgd~sTDGkWCyiv~wV 46 (69)
T cd04894 2 VITINCPDKTGLGCDLCRIILEFGLNITRGDDSTDGRWCYIVFWV 46 (69)
T ss_pred EEEEeCCCccCcccHHHHHHHHhceEEEecccccCCcEEEEEEEE
Confidence 589999999999999999999999999999999998877666654
No 50
>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=92.63 E-value=0.5 Score=37.27 Aligned_cols=35 Identities=9% Similarity=0.250 Sum_probs=33.5
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
|.|.|++++|++.+|-+.|.+.|++|.+.+..+.+
T Consensus 2 l~v~g~D~~Giv~~it~~l~~~~~nI~~~~~~~~~ 36 (81)
T cd04869 2 VEVVGNDRPGIVHEVTQFLAQRNINIEDLSTETYS 36 (81)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCCCeEEeEeeeec
Confidence 78999999999999999999999999999998887
No 51
>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=92.10 E-value=0.44 Score=37.50 Aligned_cols=45 Identities=18% Similarity=0.242 Sum_probs=39.8
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
+|.|.+.+|||+..++.++|.++|++|...+.++.++.+.-.+.+
T Consensus 1 ~vtv~G~DrpGiv~~vt~~la~~~~nI~dl~~~~~~~~f~~~~~v 45 (75)
T cd04870 1 LITVTGPDRPGLTSALTEVLAAHGVRILDVGQAVIHGRLSLGILV 45 (75)
T ss_pred CEEEEcCCCCCHHHHHHHHHHHCCCCEEecccEEEcCeeEEEEEE
Confidence 378889999999999999999999999999999998876666654
No 52
>PRK05092 PII uridylyl-transferase; Provisional
Probab=92.08 E-value=0.41 Score=55.38 Aligned_cols=48 Identities=21% Similarity=0.340 Sum_probs=44.6
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEe-eCCEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTT-FNGKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist-~~~~vl~~f~v 432 (433)
+...|.|.|.+++|+|.+|..+|..+|++|+.|.|.+ .+++++++|.|
T Consensus 731 ~~t~v~I~~~Dr~GLfa~i~~~L~~~glnI~~A~I~t~~dg~alD~F~V 779 (931)
T PRK05092 731 GVTEVTVLAADHPGLFSRIAGACAAAGANIVDARIFTTTDGRALDTFWI 779 (931)
T ss_pred CeEEEEEEeCCCCcHHHHHHHHHHHCCCcEEEEEEEEecCCeEEEEEEE
Confidence 4678999999999999999999999999999999886 78999999987
No 53
>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=92.07 E-value=0.38 Score=37.57 Aligned_cols=34 Identities=9% Similarity=0.208 Sum_probs=31.8
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTT 421 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist 421 (433)
+|.|.|++++|++.+|.+.|.++|+.|...+..+
T Consensus 1 ii~v~g~D~~Giv~~it~~l~~~g~nI~~~~~~~ 34 (74)
T cd04875 1 ILTLSCPDRPGIVAAVSGFLAEHGGNIVESDQFV 34 (74)
T ss_pred CEEEEcCCCCCHHHHHHHHHHHcCCCEEeeeeee
Confidence 3789999999999999999999999999999885
No 54
>PRK04374 PII uridylyl-transferase; Provisional
Probab=91.85 E-value=0.49 Score=54.37 Aligned_cols=48 Identities=10% Similarity=0.226 Sum_probs=44.8
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEe-eCCEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTT-FNGKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist-~~~~vl~~f~v 432 (433)
+...|.|.|.+++|+|++|..+|..+||+|+.|.|.+ .+|.++++|.|
T Consensus 689 ~~~~v~v~~~d~~gLFa~i~g~l~~~~lnI~~A~i~t~~~g~~ld~f~V 737 (869)
T PRK04374 689 DALEVFVYSPDRDGLFAAIVATLDRKGYGIHRARVLDAPHDAIFDVFEV 737 (869)
T ss_pred CeEEEEEEeCCCccHHHHHHHHHHHCCCeEEEEEEEEcCCCEEEEEEEE
Confidence 4577899999999999999999999999999999986 78999999987
No 55
>cd04889 ACT_PDH-BS-like C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate. Included in this CD is the C-terminal ACT domain of the monofunctional, NAD dependent, prephenate dehydrogenase (PDH) enzyme that catalyzes the formation of 4-hydroxyphenylpyruvate from prephenate, found in Bacillus subtilis (BS) and other Firmicutes, Deinococci, and Bacteroidetes. PDH is the first enzyme in the aromatic amino acid pathway specific for the biosynthesis of tyrosine. This enzyme is feedback inhibited by tyrosine in B. subtilis and other microorganisms. Both phenylalanine and tryptophan have been shown to be inhibitors of this activity in B. subtilis. Bifunctional chorismate mutase-PDH (TyrA) enzymes such as those seen in Escherichia coli do not contain an ACT domain. Also included in this CD is the N-terminal ACT domain of a novel protein composed almost entirely of two tandem A
Probab=91.11 E-value=0.88 Score=33.35 Aligned_cols=45 Identities=9% Similarity=0.159 Sum_probs=37.1
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC-CEEEEEEEeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN-GKVLNILRVQ 433 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~-~~vl~~f~vE 433 (433)
|.|...+++|.|.+++++|.+.|+.|....+...+ +..+..|.++
T Consensus 1 ~~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~~v~ 46 (56)
T cd04889 1 LSVFVENKPGRLAEVTEILAEAGINIKAISIAETRGEFGILRLIFS 46 (56)
T ss_pred CEEEeCCCCChHHHHHHHHHHcCCCEeeEEEEEccCCcEEEEEEEC
Confidence 35678899999999999999999999888877655 6777776654
No 56
>cd04888 ACT_PheB-BS C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and related domains. This CD includes the C-terminal ACT domain of a small (~147 a.a.) putative phenylalanine biosynthetic pathway protein described in Bacillus subtilis (BS) PheB (PheB-BS) and other related ACT domains. In B. subtilis, the upstream gene of pheB, pheA encodes prephenate dehydratase (PDT). The presumed product of the pheB gene is chorismate mutase (CM). The deduced product of the B. subtilis pheB gene, however, has no significant homology to the CM portion of the bifunctional CM-PDT of Escherichia coli. The presence of an ACT domain lends support to the prediction that these proteins function as a phenylalanine-binding regulatory protein. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=90.55 E-value=0.84 Score=35.30 Aligned_cols=45 Identities=20% Similarity=0.341 Sum_probs=36.2
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee-CCEEEEEEEe
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF-NGKVLNILRV 432 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~-~~~vl~~f~v 432 (433)
.|.|.+.+++|.|.+|+++|.+.+.+|...+.... ++...-.|.+
T Consensus 2 ~l~i~~~d~~g~l~~I~~~la~~~inI~~i~~~~~~~~~~~i~~~v 47 (76)
T cd04888 2 TLSLLLEHRPGVLSKVLNTIAQVRGNVLTINQNIPIHGRANVTISI 47 (76)
T ss_pred EEEEEecCCCchHHHHHHHHHHcCCCEEEEEeCCCCCCeEEEEEEE
Confidence 47888999999999999999999999999987543 3554444544
No 57
>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=90.39 E-value=1.3 Score=30.25 Aligned_cols=35 Identities=6% Similarity=0.157 Sum_probs=30.8
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
|.+.|.+++|.+.+|+.+|...++.|...+.....
T Consensus 1 i~i~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~ 35 (60)
T cd02116 1 LTVSGPDRPGLLAKVLSVLAEAGINITSIEQRTSG 35 (60)
T ss_pred CEEEecCCCchHHHHHHHHHHCCCcEEEEEeEEcC
Confidence 46788889999999999999999999999876643
No 58
>PRK04435 hypothetical protein; Provisional
Probab=89.76 E-value=1.3 Score=39.99 Aligned_cols=51 Identities=14% Similarity=0.303 Sum_probs=42.6
Q ss_pred cCceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEe-eCCEEEEEEEeC
Q 041101 383 NDRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTT-FNGKVLNILRVQ 433 (433)
Q Consensus 383 ~~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist-~~~~vl~~f~vE 433 (433)
.|+.+.|.+.+.+++|.|.+|+++|.+.|.+|...+.+. .++...-+|.+|
T Consensus 66 ~~r~vtL~i~l~Dr~GlLs~Il~~IA~~~aNIltI~q~i~~~g~a~vs~tVe 117 (147)
T PRK04435 66 KGKIITLSLLLEDRSGTLSKVLNVIAEAGGNILTINQSIPLQGRANVTISID 117 (147)
T ss_pred CCcEEEEEEEEecCCCHHHHHHHHHHHcCCCeEEEEEEcCCCCEEEEEEEEE
Confidence 478899999999999999999999999999999998754 356655556553
No 59
>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=89.58 E-value=1.2 Score=32.13 Aligned_cols=35 Identities=14% Similarity=0.234 Sum_probs=31.2
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
|+|.+.+++|.+.+|++.|.+.++++.+..+...+
T Consensus 1 l~v~~~~~~~~l~~i~~~l~~~~~~i~~~~~~~~~ 35 (71)
T cd04876 1 IRVEAIDRPGLLADITTVIAEEKINILSVNTRTDD 35 (71)
T ss_pred CEEEEeccCcHHHHHHHHHHhCCCCEEEEEeEECC
Confidence 46778899999999999999999999999887655
No 60
>cd04877 ACT_TyrR N-terminal ACT domain of the TyrR protein. ACT_TyrR: N-terminal ACT domain of the TyrR protein. The TyrR protein of Escherichia coli controls the expression of a group of transcription units (TyrR regulon) whose gene products are involved in the biosynthesis or transport of the aromatic amino acids. Binding to specific DNA sequences known as TyrR boxes, the TyrR protein can either activate or repress transcription at different sigma70 promoters. Its regulatory activity occurs in response to intracellular levels of tyrosine, phenylalanine and tryptophan. The TyrR protein consists of an N-terminal region important for transcription activation with an ATP-independent aromatic amino acid binding site (contained within the ACT domain) and is involved in dimerization; a central region with an ATP binding site, an ATP-dependent aromatic amino acid binding site and is involved in hexamerization; and a helix turn helix DNA binding C-terminal region. In solution, in the absence
Probab=89.55 E-value=1.3 Score=34.71 Aligned_cols=37 Identities=11% Similarity=0.309 Sum_probs=33.3
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCE
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGK 425 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~ 425 (433)
.|+|.|.+++|+|.+|+.++.+.+..+...++.+- +.
T Consensus 2 ~l~I~~~dr~Gll~dI~~~i~~~~~nI~~~~~~~~-~~ 38 (74)
T cd04877 2 RLEITCEDRLGITQEVLDLLVEHNIDLRGIEIDPK-GR 38 (74)
T ss_pred EEEEEEEccchHHHHHHHHHHHCCCceEEEEEecC-Ce
Confidence 47899999999999999999999999999998764 44
No 61
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=89.17 E-value=0.23 Score=44.84 Aligned_cols=52 Identities=31% Similarity=0.454 Sum_probs=46.0
Q ss_pred ccccchHHHHHHHHHHHHhHHHHHhcCCC--CCCCchhhHHHHHHHHHHHHHHH
Q 041101 266 PKAKNLITERNRRNKLKDGLFALRALVPK--ISKMDRAAILGDAAEYIKELLQE 317 (433)
Q Consensus 266 ~~~~h~~~Er~RR~~~n~~~~~LrslvP~--~~k~dkasil~~ai~YI~~Lq~~ 317 (433)
++.-|++.||+|=..+|+-|.+||.++|. +.|..|.--|.-|..||-.|=+-
T Consensus 78 qrv~anvrerqRtqsLn~AF~~lr~iiptlPsdklSkiqtLklA~ryidfl~~v 131 (173)
T KOG4447|consen 78 QRVMANVRERQRTQSLNEAFAALRKIIPTLPSDKLSKIQTLKLAARYIDFLYQV 131 (173)
T ss_pred HHHHHHHHHHHhhhhHHHHHHHHHhhcCCCCccccccccchhhcccCCchhhhc
Confidence 67789999999999999999999999996 67788888899999999888543
No 62
>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=89.16 E-value=1.1 Score=33.44 Aligned_cols=45 Identities=16% Similarity=0.292 Sum_probs=35.6
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC--CEEEEEEEeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN--GKVLNILRVQ 433 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~--~~vl~~f~vE 433 (433)
|.|.-++++|.|.++++.|.+.|+.|.+....... +.....|++|
T Consensus 2 i~v~~~d~pG~L~~i~~~l~~~~~nI~~i~~~~~~~~~~~~v~~~ve 48 (65)
T cd04882 2 LAVEVPDKPGGLHEILQILSEEGINIEYMYAFVEKKGGKALLIFRTE 48 (65)
T ss_pred EEEEeCCCCcHHHHHHHHHHHCCCChhheEEEccCCCCeEEEEEEeC
Confidence 56677789999999999999999999877665443 5666677665
No 63
>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=88.99 E-value=1.7 Score=32.55 Aligned_cols=35 Identities=11% Similarity=0.078 Sum_probs=31.6
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF 422 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~ 422 (433)
.|.+.+.+++|.|.+++..|.+.+..|.+.+....
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~ 36 (72)
T cd04874 2 ALSIIAEDKPGVLRDLTGVIAEHGGNITYTQQFIE 36 (72)
T ss_pred eEEEEeCCCCChHHHHHHHHHhCCCCEEEEEEecc
Confidence 47788999999999999999999999998887765
No 64
>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=88.55 E-value=1.6 Score=33.28 Aligned_cols=36 Identities=6% Similarity=0.187 Sum_probs=32.6
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF 422 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~ 422 (433)
++|+|.+.+++|.+.+|+..|.+.+..+.+.+....
T Consensus 1 ~yl~i~~~d~~g~l~~i~~~l~~~~i~I~~~~~~~~ 36 (79)
T cd04881 1 YYLRLTVKDKPGVLAKITGILAEHGISIESVIQKEA 36 (79)
T ss_pred CEEEEEeCCCCcHHHHHHHHHHHcCCCeEEEEEccc
Confidence 468999999999999999999999999999987654
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=88.48 E-value=1.9 Score=31.94 Aligned_cols=44 Identities=11% Similarity=0.163 Sum_probs=36.8
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC--CEEEEEEEe
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN--GKVLNILRV 432 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~--~~vl~~f~v 432 (433)
+.|...+++|.+.+|++.|.+.++.|.+..+.... +.....|.+
T Consensus 2 l~v~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~~~~~~~~~v 47 (71)
T cd04879 2 LLIVHKDVPGVIGKVGTILGEHGINIAAMQVGRKEKGGIAYMVLDV 47 (71)
T ss_pred EEEEecCCCCHHHHHHHHHHhcCCCeeeEEEeccCCCCEEEEEEEc
Confidence 56788899999999999999999999999987654 666666654
No 66
>KOG3560 consensus Aryl-hydrocarbon receptor [Transcription]
Probab=87.82 E-value=0.42 Score=51.12 Aligned_cols=41 Identities=29% Similarity=0.528 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHhHHHHHhcCCC----CCCCchhhHHHHHHHHHHH
Q 041101 273 TERNRRNKLKDGLFALRALVPK----ISKMDRAAILGDAAEYIKE 313 (433)
Q Consensus 273 ~Er~RR~~~n~~~~~LrslvP~----~~k~dkasil~~ai~YI~~ 313 (433)
.-++-|+++|..++.|.+|+|. ++|.||.|||.=++.|++-
T Consensus 32 PSKRHRdRLNaELD~lAsLLPfpqdiisKLDkLSVLRLSVSyLr~ 76 (712)
T KOG3560|consen 32 PSKRHRDRLNAELDHLASLLPFPQDIISKLDKLSVLRLSVSYLRV 76 (712)
T ss_pred cchhHHHHhhhHHHHHHHhcCCCHHHHhhhhhhhhhhhhHHHHHH
Confidence 3456899999999999999997 7999999999999999863
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=86.82 E-value=2.7 Score=31.29 Aligned_cols=44 Identities=11% Similarity=0.279 Sum_probs=34.6
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee--CCEEEEEEEe
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTF--NGKVLNILRV 432 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~--~~~vl~~f~v 432 (433)
|.+.+.+++|.+.+|+..|.+.++.|.+...... ++.....|.+
T Consensus 2 l~i~~~d~~g~l~~i~~~l~~~~~~I~~~~~~~~~~~~~~~i~i~v 47 (71)
T cd04903 2 LIVVHKDKPGAIAKVTSVLADHEINIAFMRVSRKEKGDQALMVIEV 47 (71)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCcCeeeeEEEeccCCCeEEEEEEe
Confidence 6778899999999999999999999998887652 3444333544
No 68
>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=85.68 E-value=4 Score=30.34 Aligned_cols=44 Identities=16% Similarity=0.151 Sum_probs=35.3
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee--CCEEEEEEE
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF--NGKVLNILR 431 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~--~~~vl~~f~ 431 (433)
.|.+...+++|.|.+|+..|.+.++.+...+.... ++.....|.
T Consensus 2 ~l~i~~~d~~g~l~~i~~~l~~~~~~i~~~~~~~~~~~~~~~~~~~ 47 (72)
T cd04878 2 TLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDPGISRITIV 47 (72)
T ss_pred EEEEEEcCCCcHHHHHHHHHHhCCCCEEEEEeeecCCCCeEEEEEE
Confidence 46778889999999999999999999999987764 354444444
No 69
>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=85.35 E-value=3.4 Score=32.68 Aligned_cols=45 Identities=7% Similarity=0.142 Sum_probs=34.7
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC-CEEEEEEEeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN-GKVLNILRVQ 433 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~-~~vl~~f~vE 433 (433)
|.+.-++++|.|.+|++.+.++|+.+++....... +.-.++|+|+
T Consensus 4 l~~~~~d~~G~L~~il~~f~~~~ini~~i~s~p~~~~~~~~~f~vd 49 (80)
T cd04905 4 IVFTLPNKPGALYDVLGVFAERGINLTKIESRPSKGGLWEYVFFID 49 (80)
T ss_pred EEEEECCCCCHHHHHHHHHHHCCcCEEEEEEEEcCCCCceEEEEEE
Confidence 44555678999999999999999999999876653 3455666653
No 70
>KOG3558 consensus Hypoxia-inducible factor 1/Neuronal PAS domain protein NPAS1 [Signal transduction mechanisms; Transcription]
Probab=84.99 E-value=0.65 Score=51.07 Aligned_cols=48 Identities=29% Similarity=0.476 Sum_probs=41.4
Q ss_pred ccccchHHHHHHHHHHHHhHHHHHhcCCC----CCCCchhhHHHHHHHHHHH
Q 041101 266 PKAKNLITERNRRNKLKDGLFALRALVPK----ISKMDRAAILGDAAEYIKE 313 (433)
Q Consensus 266 ~~~~h~~~Er~RR~~~n~~~~~LrslvP~----~~k~dkasil~~ai~YI~~ 313 (433)
++.+-.-+-|-||.|-|+-|+.|..+||- .+..|||||+.=||.|++-
T Consensus 46 rkEkSRdAARsRRsKEn~~FyeLa~~lPlp~aisshLDkaSimRLtISyLRl 97 (768)
T KOG3558|consen 46 RKEKSRDAARSRRSKENEEFYELAKLLPLPAAISSHLDKASIMRLTISYLRL 97 (768)
T ss_pred HhhhhhhhhhhhcccchHHHHHHHHhCCCcchhhhhhhhHHHHHHHHHHHHH
Confidence 34555678899999999999999999995 4778999999999999863
No 71
>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=84.84 E-value=5.2 Score=30.36 Aligned_cols=35 Identities=6% Similarity=0.130 Sum_probs=30.8
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF 422 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~ 422 (433)
.+.+.+++++|.|.+|++.|.+.|++|........
T Consensus 3 ~~~v~~~d~~G~L~~l~~~l~~~~i~i~~~~~~~~ 37 (69)
T cd04909 3 DLYVDVPDEPGVIAEVTQILGDAGISIKNIEILEI 37 (69)
T ss_pred EEEEEcCCCCCHHHHHHHHHHHcCCCceeeEeEEe
Confidence 46788899999999999999999999998876654
No 72
>KOG3559 consensus Transcriptional regulator SIM1 [Transcription]
Probab=84.83 E-value=0.98 Score=46.85 Aligned_cols=42 Identities=31% Similarity=0.510 Sum_probs=37.8
Q ss_pred HHHHHHHHHHHHhHHHHHhcCCC----CCCCchhhHHHHHHHHHHH
Q 041101 272 ITERNRRNKLKDGLFALRALVPK----ISKMDRAAILGDAAEYIKE 313 (433)
Q Consensus 272 ~~Er~RR~~~n~~~~~LrslvP~----~~k~dkasil~~ai~YI~~ 313 (433)
-+-|.||++-|-.|..|..++|- ....||++|+.=|..|||-
T Consensus 7 naA~tRRekEN~EF~eLAklLPLa~AItsQlDKasiiRLtTsYlKm 52 (598)
T KOG3559|consen 7 NAARTRREKENYEFYELAKLLPLASAITSQLDKASIIRLTTSYLKM 52 (598)
T ss_pred hHHHHHHHhhcchHHHHHhhccchhhhhhccchhhhhhHHHHHHHH
Confidence 46689999999999999999996 4679999999999999984
No 73
>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=84.67 E-value=3.1 Score=32.37 Aligned_cols=35 Identities=3% Similarity=0.111 Sum_probs=29.4
Q ss_pred EEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCC
Q 041101 390 KLLCEHERGGFLRLMEAINSLELQVIDANVTTFNG 424 (433)
Q Consensus 390 ~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~ 424 (433)
-+..++++|.|.+|++.+.+.|+.+++.......+
T Consensus 3 ~~~l~d~pG~L~~vL~~f~~~~vni~~I~Srp~~~ 37 (75)
T cd04880 3 VFSLKNKPGALAKALKVFAERGINLTKIESRPSRK 37 (75)
T ss_pred EEEeCCcCCHHHHHHHHHHHCCCCEEEEEeeecCC
Confidence 34456789999999999999999999997776554
No 74
>PRK08577 hypothetical protein; Provisional
Probab=84.28 E-value=4.6 Score=35.60 Aligned_cols=40 Identities=10% Similarity=0.255 Sum_probs=35.6
Q ss_pred CceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 384 DRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 384 ~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
++.+.|.|.+.+++|.|.+|++.|.+.+.++.+.+..+..
T Consensus 54 k~~~~I~V~~~Dr~GvLa~I~~~l~~~~inI~~i~~~~~~ 93 (136)
T PRK08577 54 KKLVEIELVVEDRPGVLAKITGLLAEHGVDILATECEELK 93 (136)
T ss_pred ccEEEEEEEEcCCCCHHHHHHHHHHHCCCCEEEEEEEEec
Confidence 3478899999999999999999999999999998877653
No 75
>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=83.55 E-value=4.6 Score=30.64 Aligned_cols=38 Identities=8% Similarity=0.197 Sum_probs=32.2
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCE
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGK 425 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~ 425 (433)
.|.|..++++|.|.+|+++|.+.|+.|.+.-+...++.
T Consensus 3 ri~v~v~d~pG~La~v~~~l~~~~inI~~i~~~~~~~~ 40 (66)
T cd04908 3 QLSVFLENKPGRLAAVTEILSEAGINIRALSIADTSEF 40 (66)
T ss_pred EEEEEEcCCCChHHHHHHHHHHCCCCEEEEEEEecCCC
Confidence 36677889999999999999999999998887665553
No 76
>KOG3898 consensus Transcription factor NeuroD and related HTH proteins [Transcription]
Probab=82.51 E-value=0.76 Score=45.26 Aligned_cols=54 Identities=33% Similarity=0.431 Sum_probs=46.6
Q ss_pred CccccchHHHHHHHHHHHHhHHHHHhcCCC---CCCCchhhHHHHHHHHHHHHHHHH
Q 041101 265 RPKAKNLITERNRRNKLKDGLFALRALVPK---ISKMDRAAILGDAAEYIKELLQEV 318 (433)
Q Consensus 265 ~~~~~h~~~Er~RR~~~n~~~~~LrslvP~---~~k~dkasil~~ai~YI~~Lq~~v 318 (433)
.++.+=+..||+|--.+|+-|+.||.++|. ..|+.|.-.|.-|-+||..|++-.
T Consensus 71 ~rR~kaNaRER~RMH~LNdAld~LReviP~~~~~~klskIetl~~a~~yi~als~~~ 127 (254)
T KOG3898|consen 71 LRRLKANARERTRMHDLNDALDALREVIPHGLHPPKLSKIETLRLAANYIAALSEVL 127 (254)
T ss_pred hhcccccchhhccccchhHHHHHhHhhccCcCCCCCCCcchhHHhhhcchhhhcccc
Confidence 466677889999999999999999999995 578888888999999999987543
No 77
>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=82.08 E-value=6.8 Score=29.75 Aligned_cols=46 Identities=13% Similarity=0.221 Sum_probs=35.7
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee--CCEEEEEEEeC
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF--NGKVLNILRVQ 433 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~--~~~vl~~f~vE 433 (433)
.|.+..++++|.|.++++.|.+.|+.|.+...... ++....+|++|
T Consensus 3 ~~~v~~~d~pG~l~~i~~~l~~~~inI~~i~~~~~~~~~~~~v~i~v~ 50 (72)
T cd04883 3 QIEVRVPDRPGQLADIAAIFKDRGVNIVSVLVYPSKEEDNKILVFRVQ 50 (72)
T ss_pred EEEEEECCCCCHHHHHHHHHHHcCCCEEEEEEeccCCCCeEEEEEEEe
Confidence 46777889999999999999999999988765432 35655666653
No 78
>PF13185 GAF_2: GAF domain; PDB: 2QYB_A 3KSG_B 3KSF_C 3KSI_A 3KSH_A 3MMH_A 3RFB_B 1F5M_A 3KO6_B 3HCY_A ....
Probab=79.99 E-value=6.9 Score=33.14 Aligned_cols=60 Identities=22% Similarity=0.348 Sum_probs=35.6
Q ss_pred EeecCCceeee-cCCC--CcccccccCCceEEEEeeC--C---ceEeecccccccc---ChHHHHHHHHhc
Q 041101 103 VVITNQPKWIS-LANS--SDSIASHQSNSTRVLIPVF--G---GLIELFAAKHISK---DQNIIELVLAHC 162 (433)
Q Consensus 103 ~~~sg~h~Wi~-~~~~--~~~~~~~~gIqTiv~IPv~--~---GVveLGS~~~i~E---d~~~v~~vk~~f 162 (433)
++.+|+++|+. .... ........||+.+++||+. + |||.|++.+.-.= |..+++.+-.+.
T Consensus 73 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPl~~~~~~~Gvl~l~~~~~~~f~~~~~~~l~~la~~~ 143 (148)
T PF13185_consen 73 VLRTGEPIIINDDDSSFPPWELARHPGIRSILCVPLRSGGEVIGVLSLYSKEPNAFSEEDLELLEALADQI 143 (148)
T ss_dssp HHHHTS-EEESCCCGGGSTTHHHCCTT-SEEEEEEEEETTEEEEEEEEEESSTT---HHHHHHHHHHHHHH
T ss_pred HHhcCceEEEeCccccccchhhhccccCCEEEEEEEeECCEEEEEEEEeeCCCCCcCHHHHHHHHHHHHHH
Confidence 38899999998 1111 1111234789999999983 3 9999999766444 444444444433
No 79
>PRK11061 fused phosphoenolpyruvate-protein phosphotransferase PtsP/GAF domain; Provisional
Probab=79.78 E-value=6.8 Score=44.49 Aligned_cols=108 Identities=15% Similarity=0.108 Sum_probs=67.7
Q ss_pred HHHHHHHHhccCCCCCeEEEEeeeCCCCCceEEEcCccccCCCCCCcceeeccccccccccccccccccccCcccchhhh
Q 041101 5 EKAVEWLRPFVDSKAWDYCVVWKLGDDPSRFIEWLGCCCSGGVGGGFEYVKVKEESGEEQKFSFCRDAHLKHSARTKACE 84 (433)
Q Consensus 5 ~~Lq~~Lr~l~~~~~W~YavFW~~~~~~~~~L~W~dg~c~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~ 84 (433)
+.|+..++.++..-+..+|..|-+.++. ..|...- -.|... + . ..
T Consensus 20 e~L~~Iv~~~~~~l~~d~~sI~L~D~~~-~~L~~~a--s~Gl~~--------------~---------~-~~-------- 64 (748)
T PRK11061 20 EALDILVTETCLAMDTEVCSVYLADHDR-RCYYLMA--TRGLKK--------------P---------R-GR-------- 64 (748)
T ss_pred HHHHHHHHHHHHHhCCCEEEEEEEECCC-CEEEEEE--eeCCCh--------------H---------h-cc--------
Confidence 4577777777788899999999887763 2222210 001000 0 0 00
Q ss_pred HhhccceeeecCCCcceeEeecCCceeeecCCCCcc-----cccccCCceEEEEeeCC-----ceEeeccccccccCh
Q 041101 85 ALAQLPSFMDLYSGIHGEVVITNQPKWISLANSSDS-----IASHQSNSTRVLIPVFG-----GLIELFAAKHISKDQ 152 (433)
Q Consensus 85 ~l~~m~~~f~~g~Gl~Gk~~~sg~h~Wi~~~~~~~~-----~~~~~gIqTiv~IPv~~-----GVveLGS~~~i~Ed~ 152 (433)
...+++|+|+.|+++.+|++++|.+.....+ .....++...++||+.. |||.+...+.-.-+.
T Consensus 65 -----~~~l~~geGi~G~Va~tg~pV~V~Dv~~dprf~~~~~~~~~~~~S~L~VPL~~~geVIGVL~v~~~~~~~Fs~ 137 (748)
T PRK11061 65 -----TVTLAFDEGIVGLVGRLAEPINLADAQKHPSFKYIPSVKEERFRAFLGVPIIYRRQLLGVLVVQQRELRQFDE 137 (748)
T ss_pred -----ceeccCCcchHHHHhccCceEEECCcccCcccccCccccCccceEEEEEEEeeCCEEEEEEEEeeCCCCCCCH
Confidence 0236789999999999999999986653211 11235688999999842 777776665433333
No 80
>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=79.32 E-value=5.1 Score=30.40 Aligned_cols=45 Identities=13% Similarity=0.192 Sum_probs=36.0
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEe--eCCEEEEEEEeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTT--FNGKVLNILRVQ 433 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist--~~~~vl~~f~vE 433 (433)
+-+...+++|.+.+|.+.|.+.|+.|.+..... .++....+|+++
T Consensus 2 l~v~~~d~~G~l~~i~~~l~~~~inI~~~~~~~~~~~~~~~~~i~v~ 48 (73)
T cd04902 2 LVVRNTDRPGVIGKVGTILGEAGINIAGMQVGRDEPGGEALMVLSVD 48 (73)
T ss_pred EEEEeCCCCCHHHHHHHHHHHcCcChhheEeeccCCCCEEEEEEEeC
Confidence 345778899999999999999999998887654 456777777664
No 81
>TIGR01817 nifA Nif-specific regulatory protein. This model represents NifA, a DNA-binding regulatory protein for nitrogen fixation. The model produces scores between the trusted and noise cutoffs for a well-described NifA homolog in Aquifex aeolicus (which lacks nitrogenase), for transcriptional activators of alternative nitrogenases (VFe or FeFe instead of MoFe), and truncated forms.
Probab=79.12 E-value=1.8 Score=46.92 Aligned_cols=73 Identities=11% Similarity=0.143 Sum_probs=54.8
Q ss_pred eecCCCcceeEeecCCceeeecCCCCcc-----cccccCCceEEEEeeC-C----ceEeeccccc----cccChHHHHHH
Q 041101 93 MDLYSGIHGEVVITNQPKWISLANSSDS-----IASHQSNSTRVLIPVF-G----GLIELFAAKH----ISKDQNIIELV 158 (433)
Q Consensus 93 f~~g~Gl~Gk~~~sg~h~Wi~~~~~~~~-----~~~~~gIqTiv~IPv~-~----GVveLGS~~~----i~Ed~~~v~~v 158 (433)
+.+|+|+.|+|+.+|+++++.+.....+ .....++++++|||+. + |||.+.+... -.+|.+++..+
T Consensus 69 ~~~~~gi~g~v~~~~~pvii~Dv~~d~~~~~~~~~~~~~~~S~l~VPL~~~g~viGvL~v~s~~~~~~ft~~d~~lL~~l 148 (534)
T TIGR01817 69 YRVGEGAIGQIVATGNSLVVPDVAAEPLFLDRLSLYDPGPVPFIGVPIKADSETIGVLAADRDFRSRERLEEEVRFLEMV 148 (534)
T ss_pred ccCCccHHHHHHhcCCeEEecccccCchhhhccccccCCcceEEEEEEcCCCEEEEEEEEEeccccccccHHHHHHHHHH
Confidence 5679999999999999999987642111 1223578899999983 2 8999998753 45788888888
Q ss_pred HHhcccc
Q 041101 159 LAHCNTS 165 (433)
Q Consensus 159 k~~f~~~ 165 (433)
-...+..
T Consensus 149 A~~ia~a 155 (534)
T TIGR01817 149 ANLIGQT 155 (534)
T ss_pred HHHHHHH
Confidence 7776543
No 82
>PRK07334 threonine dehydratase; Provisional
Probab=78.93 E-value=6.1 Score=41.31 Aligned_cols=48 Identities=13% Similarity=0.129 Sum_probs=39.9
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee-----CCEEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF-----NGKVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~-----~~~vl~~f~v 432 (433)
-.+.|+|.+.+|+|+|.+|+.+|.+.+++|.++++.+. ++...-.|.+
T Consensus 325 y~v~l~I~~~dr~GlL~dI~~~is~~~~nI~~v~~~~~~~~~~~~~~~i~l~i 377 (403)
T PRK07334 325 RLARLRVDIRDRPGALARVTALIGEAGANIIEVSHQRLFTDLPAKGAELELVI 377 (403)
T ss_pred CEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEecccCCCCCeEEEEEEE
Confidence 35889999999999999999999999999999998764 4565444544
No 83
>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=77.66 E-value=7.7 Score=29.86 Aligned_cols=34 Identities=12% Similarity=0.256 Sum_probs=29.2
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTF 422 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~ 422 (433)
+.|.-+++||.|.+|++.|.+.|..|++......
T Consensus 2 l~v~~~d~pG~L~~l~~~i~~~g~nI~~i~~~~~ 35 (72)
T cd04884 2 FTFLLEDKPGTLKPVVDTLREFNARIISILTAFE 35 (72)
T ss_pred EEEEecCCCccHHHHHHHHHHCCCeEEEEEeccc
Confidence 4566678999999999999999999998876654
No 84
>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=75.68 E-value=2.4 Score=32.01 Aligned_cols=45 Identities=7% Similarity=0.087 Sum_probs=34.2
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRVQ 433 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~vE 433 (433)
|-+.+.+++|++.+|+..|.+.+..+...+....++...-.|.+|
T Consensus 2 ~~~~~~d~~g~l~~i~~~l~~~~~nI~~~~~~~~~~~a~~~~~~~ 46 (69)
T cd04901 2 ILHIHKNVPGVLGQINTILAEHNINIAAQYLQTRGEIGYVVIDID 46 (69)
T ss_pred EEEEecCCCcHHHHHHHHHHHcCCCHHHHhccCCCCEEEEEEEcC
Confidence 345778999999999999999999997776655446655555543
No 85
>KOG4395 consensus Transcription factor Atonal, contains HTH domain [Transcription]
Probab=75.31 E-value=4.8 Score=39.41 Aligned_cols=55 Identities=29% Similarity=0.294 Sum_probs=45.1
Q ss_pred CccccchHHHHHHHHHHHHhHHHHHhcCCCC---CCCchhhHHHHHHHHHHHHHHHHH
Q 041101 265 RPKAKNLITERNRRNKLKDGLFALRALVPKI---SKMDRAAILGDAAEYIKELLQEVD 319 (433)
Q Consensus 265 ~~~~~h~~~Er~RR~~~n~~~~~LrslvP~~---~k~dkasil~~ai~YI~~Lq~~v~ 319 (433)
.++..-+..||+|-..+|.-|+.||.+||.. .|..|---|.-|-.||--|-..+.
T Consensus 173 ~rr~aanarErrrm~gLN~AfD~Lr~v~p~~~~d~~LSkyetLqmaq~yi~~l~~~l~ 230 (285)
T KOG4395|consen 173 HRRLAANARERRRMNGLNSAFDRLRLVVPDGDSDKKLSKYETLQMAQGYILALGCLLD 230 (285)
T ss_pred hhhcccchHHHHHhhhHHHHHHHHHHhcCCCCccchhhhhhHHHHHHHHHhhhHHhhc
Confidence 3445557899999999999999999999974 566677789999999988876654
No 86
>COG2844 GlnD UTP:GlnB (protein PII) uridylyltransferase [Posttranslational modification, protein turnover, chaperones]
Probab=70.85 E-value=9.1 Score=43.45 Aligned_cols=49 Identities=18% Similarity=0.220 Sum_probs=44.7
Q ss_pred CceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEE-eeCCEEEEEEEe
Q 041101 384 DRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVT-TFNGKVLNILRV 432 (433)
Q Consensus 384 ~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~is-t~~~~vl~~f~v 432 (433)
.+..-|-|.|+.+|++|+.+..++...|++|+.|.|- +.+|+++++|.|
T Consensus 682 ~~~teV~V~a~d~p~Lfa~v~~~~~~~g~~i~dAqi~tt~dG~alDtfiv 731 (867)
T COG2844 682 SGGTEVFVYAPDRPRLFAVVCAALSRRGLSIVDAQIFTTRDGYALDTFIV 731 (867)
T ss_pred CCceEEEEEcCCCccHHHHHHHHHccCCCceeeeEEEEccCCceeeeEEE
Confidence 4567899999999999999999999999999999987 778899999976
No 87
>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=69.17 E-value=17 Score=30.03 Aligned_cols=46 Identities=4% Similarity=0.063 Sum_probs=34.7
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCE-EEEEEEe
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGK-VLNILRV 432 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~-vl~~f~v 432 (433)
..|-+..++++|.|.++|..+...|+.+.+...-...+. --|.|.|
T Consensus 15 tslif~l~~~pGsL~~vL~~Fa~~~INLt~IeSRP~~~~~~~Y~FfV 61 (90)
T cd04931 15 ISLIFSLKEEVGALAKVLRLFEEKDINLTHIESRPSRLNKDEYEFFI 61 (90)
T ss_pred EEEEEEcCCCCcHHHHHHHHHHHCCCCEEEEEeccCCCCCceEEEEE
Confidence 445555578899999999999999999999988765432 3355544
No 88
>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=68.35 E-value=12 Score=29.33 Aligned_cols=43 Identities=9% Similarity=0.093 Sum_probs=32.9
Q ss_pred EEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCE-EEEEEEe
Q 041101 390 KLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGK-VLNILRV 432 (433)
Q Consensus 390 ~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~-vl~~f~v 432 (433)
-+..++++|.|.++|+.+...|+.+++..+-...+. --|.|.|
T Consensus 4 ~f~l~~~pG~L~~vL~~f~~~~iNlt~IeSRP~~~~~~~y~Ffv 47 (74)
T cd04904 4 IFSLKEEVGALARALKLFEEFGVNLTHIESRPSRRNGSEYEFFV 47 (74)
T ss_pred EEEeCCCCcHHHHHHHHHHHCCCcEEEEECCCCCCCCceEEEEE
Confidence 344467899999999999999999999987766543 3355444
No 89
>COG3830 ACT domain-containing protein [Signal transduction mechanisms]
Probab=65.81 E-value=6 Score=32.85 Aligned_cols=47 Identities=15% Similarity=0.237 Sum_probs=40.3
Q ss_pred eEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 386 DFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 386 ~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
-++|.|.-.+|+|.-..|..+|-++|++|++.+=+-.++++.-.+.|
T Consensus 3 ~avITV~GkDr~GIva~is~vLAe~~vNIldisQtvm~~~ftm~~lV 49 (90)
T COG3830 3 RAVITVIGKDRVGIVAAVSRVLAEHGVNILDISQTVMDGFFTMIMLV 49 (90)
T ss_pred eEEEEEEcCCCCchhHHHHHHHHHcCCcEEEHHHHHHhhhceeeeEE
Confidence 36788899999999999999999999999999888888776555554
No 90
>PRK10872 relA (p)ppGpp synthetase I/GTP pyrophosphokinase; Provisional
Probab=61.44 E-value=23 Score=40.24 Aligned_cols=48 Identities=4% Similarity=0.134 Sum_probs=39.7
Q ss_pred eEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee--CCEEEEEEEeC
Q 041101 386 DFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF--NGKVLNILRVQ 433 (433)
Q Consensus 386 ~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~--~~~vl~~f~vE 433 (433)
.+.|.|.+.+++|+|.+|..+|.+.++.|.++++.+. ++...-.|.+|
T Consensus 666 ~v~I~I~~~Dr~GlL~dIt~~is~~~~nI~~v~~~~~~~~~~~~~~~~ie 715 (743)
T PRK10872 666 SLVVRVTANDRSGLLRDITTILANEKVNVLGVASRSDTKQQLATIDMTIE 715 (743)
T ss_pred EEEEEEEEcCCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCCEEEEEEEEE
Confidence 3578999999999999999999999999999998765 46554455553
No 91
>PRK11152 ilvM acetolactate synthase 2 regulatory subunit; Provisional
Probab=58.62 E-value=50 Score=26.47 Aligned_cols=36 Identities=14% Similarity=0.177 Sum_probs=31.9
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF 422 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~ 422 (433)
..|.+.-.++||.|.+|+..+..-|+.|.+.++...
T Consensus 4 ~~lsi~v~n~pGVL~Ri~~lf~rRGfnI~sl~v~~t 39 (76)
T PRK11152 4 HQLTIKARFRPEVLERVLRVVRHRGFQVCSMNMTQN 39 (76)
T ss_pred EEEEEEEECCccHHHHHHHHHhcCCeeeeeEEeeec
Confidence 357778889999999999999999999999998863
No 92
>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=58.08 E-value=27 Score=39.36 Aligned_cols=48 Identities=15% Similarity=0.218 Sum_probs=39.9
Q ss_pred eEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC-CEEEEEEEeC
Q 041101 386 DFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN-GKVLNILRVQ 433 (433)
Q Consensus 386 ~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~-~~vl~~f~vE 433 (433)
.+.|.|.+.+++|+|.+|+.+|.+.+..|.++++.+.+ +...-.|.+|
T Consensus 610 ~v~I~I~~~dr~GlLadI~~~ia~~~~nI~~v~~~~~~~~~~~~~~~ie 658 (683)
T TIGR00691 610 IVDINIEAVDRKGVLSDLTTAISENDSNIVSISTKTYGKREAILNITVE 658 (683)
T ss_pred EEEEEEEEecCCCHHHHHHHHHHHCCCCeEEEEeEEcCCCEEEEEEEEE
Confidence 46789999999999999999999999999999998764 5554445543
No 93
>smart00065 GAF Domain present in phytochromes and cGMP-specific phosphodiesterases. Mutations within these domains in PDE6B result in autosomal recessive inheritance of retinitis pigmentosa.
Probab=57.89 E-value=39 Score=27.02 Aligned_cols=118 Identities=15% Similarity=0.154 Sum_probs=68.3
Q ss_pred HHHHHHHHhccCCCCCeEEEEeeeCCCCCc-eEEE-cCccccCCCCCCcceeeccccccccccccccccccccCcccchh
Q 041101 5 EKAVEWLRPFVDSKAWDYCVVWKLGDDPSR-FIEW-LGCCCSGGVGGGFEYVKVKEESGEEQKFSFCRDAHLKHSARTKA 82 (433)
Q Consensus 5 ~~Lq~~Lr~l~~~~~W~YavFW~~~~~~~~-~L~W-~dg~c~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~ 82 (433)
+.+...++.++...+++++.+|.+..+... +..+ .. +.... .
T Consensus 4 ~~~~~~~~~l~~~~~~~~~~i~~~~~~~~~~~~~~~~~----~~~~~-------~------------------------- 47 (149)
T smart00065 4 ELLQTILEELRQLLGADRVLIYLVDEDDRGELVLVAAD----GLTLP-------L------------------------- 47 (149)
T ss_pred HHHHHHHHHHHHHhCCceEEEEEEecCCCCcEEEEEec----CCCcc-------c-------------------------
Confidence 557788888888899999999999884232 2221 11 10000 0
Q ss_pred hhHhhccceeeecCCCcceeEeecCCceeeecCCCCc---ccc-c-ccCCceEEEEeeC-----CceEeeccccc----c
Q 041101 83 CEALAQLPSFMDLYSGIHGEVVITNQPKWISLANSSD---SIA-S-HQSNSTRVLIPVF-----GGLIELFAAKH----I 148 (433)
Q Consensus 83 ~~~l~~m~~~f~~g~Gl~Gk~~~sg~h~Wi~~~~~~~---~~~-~-~~gIqTiv~IPv~-----~GVveLGS~~~----i 148 (433)
....++.+.++.++++.+++++.+.+..... ... . ..|++.++++|+. -|++.+.+.+. -
T Consensus 48 ------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~Pl~~~~~~~G~l~~~~~~~~~~~~ 121 (149)
T smart00065 48 ------LGLRYPLGEGLAGRVAETGRPLNIPDVEADPVFALDLLGRYQGVRSFLAVPLVADGELVGVLALHNKDSPRPFT 121 (149)
T ss_pred ------ceEEecCCCChHHHHHHcCCeEEeechhhCCccccccccceeceeeEEEeeeeecCEEEEEEEEEecCCCCCCC
Confidence 0011345556666676677666665432111 001 1 1348999999973 27888887622 2
Q ss_pred ccChHHHHHHHHhccc
Q 041101 149 SKDQNIIELVLAHCNT 164 (433)
Q Consensus 149 ~Ed~~~v~~vk~~f~~ 164 (433)
.+|..+++.+..+++.
T Consensus 122 ~~~~~~l~~~~~~i~~ 137 (149)
T smart00065 122 EEDEELLQALANQLAI 137 (149)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 4466777777666644
No 94
>PRK11092 bifunctional (p)ppGpp synthetase II/ guanosine-3',5'-bis pyrophosphate 3'-pyrophosphohydrolase; Provisional
Probab=57.44 E-value=28 Score=39.35 Aligned_cols=48 Identities=19% Similarity=0.158 Sum_probs=39.4
Q ss_pred eEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC-CEEEEEEEeC
Q 041101 386 DFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN-GKVLNILRVQ 433 (433)
Q Consensus 386 ~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~-~~vl~~f~vE 433 (433)
.+.|+|.+.+++|+|.+|+.+|.+.++.|.++++.+.+ +.+.-.|.+|
T Consensus 626 ~v~i~I~~~dr~GlL~dI~~~i~~~~~nI~~v~~~~~~~~~~~~~~~ie 674 (702)
T PRK11092 626 IAEIKVEMFNHQGALANLTAAINTTGSNIQSLNTEEKDGRVYSAFIRLT 674 (702)
T ss_pred EEEEEEEEeCCCCHHHHHHHHHHHCCCCeEEEEEEEcCCCEEEEEEEEE
Confidence 46789999999999999999999999999999987765 4444445443
No 95
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=56.33 E-value=3.2 Score=45.89 Aligned_cols=62 Identities=23% Similarity=0.237 Sum_probs=52.0
Q ss_pred CccccchHHHHHHHHHHHHhHHHHHhcCCC-----CCCCchhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 041101 265 RPKAKNLITERNRRNKLKDGLFALRALVPK-----ISKMDRAAILGDAAEYIKELLQEVDKLQDELK 326 (433)
Q Consensus 265 ~~~~~h~~~Er~RR~~~n~~~~~LrslvP~-----~~k~dkasil~~ai~YI~~Lq~~v~~L~~~~~ 326 (433)
.++..|+-+|.+||..++-.|..|.+++-+ ..|+.++.-+...++||..++.....+.+|-.
T Consensus 650 ~r~it~~Sa~qkrr~n~kl~~~~~Ns~~Sn~~~l~s~k~t~~~~~q~~vhYi~~t~~e~~~v~~e~~ 716 (856)
T KOG3582|consen 650 NRPITHISAEQKRRFNIKLQFDVLNSLSSNSSSLSSIKTTNSNSLQKTVHYINVTQQERVPVQEEAH 716 (856)
T ss_pred CCcccCccHHHHHHhhHHhhhHhhhhhccCcccccchhhhccccccCceeeeeccchhccccchhhh
Confidence 678899999999999999999999999875 35667777799999999998887776665544
No 96
>PF13710 ACT_5: ACT domain; PDB: 2FGC_A 2PC6_A 2F1F_B.
Probab=53.32 E-value=45 Score=25.45 Aligned_cols=38 Identities=13% Similarity=0.099 Sum_probs=29.9
Q ss_pred CCCChHHHHHHHHHcCCCeEEEEEEEe--eCCEEEEEEEe
Q 041101 395 HERGGFLRLMEAINSLELQVIDANVTT--FNGKVLNILRV 432 (433)
Q Consensus 395 ~r~g~L~~Il~aLe~LgL~V~~a~ist--~~~~vl~~f~v 432 (433)
+++|.|.+|+..+..-|+.|.+.++.. .++..--++.+
T Consensus 1 n~~GvL~Ri~~vf~rRg~nI~sl~v~~~~~~~~~riti~v 40 (63)
T PF13710_consen 1 NQPGVLNRITGVFRRRGFNIESLSVGPTEDPGISRITIVV 40 (63)
T ss_dssp SSTTHHHHHHHHHHTTT-EECEEEEEE-SSTTEEEEEEEE
T ss_pred CCcHHHHHHHHHHhcCCeEEeeEEeeecCCCCEEEEEEEE
Confidence 469999999999999999999999987 55555555543
No 97
>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=53.14 E-value=41 Score=26.62 Aligned_cols=31 Identities=16% Similarity=0.359 Sum_probs=27.2
Q ss_pred ccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 393 CEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 393 c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
-++++|.|.+++..++..|+.+.+...-...
T Consensus 7 l~~~~g~L~~iL~~f~~~~inl~~IeSRP~~ 37 (74)
T cd04929 7 LKNEVGGLAKALKLFQELGINVVHIESRKSK 37 (74)
T ss_pred cCCCCcHHHHHHHHHHHCCCCEEEEEeccCC
Confidence 3678999999999999999999999877554
No 98
>COG4492 PheB ACT domain-containing protein [General function prediction only]
Probab=52.67 E-value=45 Score=29.82 Aligned_cols=47 Identities=21% Similarity=0.313 Sum_probs=38.9
Q ss_pred CceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEE-eeCCEEEEEE
Q 041101 384 DRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVT-TFNGKVLNIL 430 (433)
Q Consensus 384 ~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~is-t~~~~vl~~f 430 (433)
+..+.+.+.-++|-|.|+++++++...++.|++.+=+ ..+|+.--++
T Consensus 70 ~ri~TL~l~ledr~G~LS~vLd~iA~~~~nvLTI~Q~ipl~g~Anvtl 117 (150)
T COG4492 70 ERIITLSLSLEDRVGILSDVLDVIAREEINVLTIHQTIPLQGRANVTL 117 (150)
T ss_pred ceEEEEEEEEhhhhhhHHHHHHHHHHhCCcEEEEecccccCceeeEEE
Confidence 5678889999999999999999999999999988766 6666654433
No 99
>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=51.73 E-value=15 Score=24.51 Aligned_cols=17 Identities=47% Similarity=0.565 Sum_probs=13.5
Q ss_pred HHHHHHHHHHhHHHHHh
Q 041101 274 ERNRRNKLKDGLFALRA 290 (433)
Q Consensus 274 Er~RR~~~n~~~~~Lrs 290 (433)
=|+||++++.++..||.
T Consensus 13 Lrrr~eqLK~kLeqlrn 29 (32)
T PF02344_consen 13 LRRRREQLKHKLEQLRN 29 (32)
T ss_dssp HHHHHHHHHHHHHHH--
T ss_pred HHHHHHHHHHHHHHHhc
Confidence 37899999999999985
No 100
>PF13492 GAF_3: GAF domain; PDB: 3EEA_A 4DMZ_A 4DN0_A 1VHM_A.
Probab=51.53 E-value=36 Score=27.82 Aligned_cols=112 Identities=13% Similarity=0.104 Sum_probs=63.7
Q ss_pred HHHHHHHHhccCCCCCeEEEEeeeCCCCCceEEEcCccccCCCCCCcceeeccccccccccccccccccccCcccchhhh
Q 041101 5 EKAVEWLRPFVDSKAWDYCVVWKLGDDPSRFIEWLGCCCSGGVGGGFEYVKVKEESGEEQKFSFCRDAHLKHSARTKACE 84 (433)
Q Consensus 5 ~~Lq~~Lr~l~~~~~W~YavFW~~~~~~~~~L~W~dg~c~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~~ 84 (433)
|-++..++.+++.-+.+.+.+|.+.++ ...+...-++ .+... +
T Consensus 4 ~l~~~i~~~l~~~~~~~~~~l~~~d~~-~~~~~~~~~~-~~~~~----------------------------~------- 46 (129)
T PF13492_consen 4 ELLERILELLRELLGADRAALFLLDED-GNRLRVVAGW-GGDPR----------------------------L------- 46 (129)
T ss_dssp HHHHHHHHHHHHHST-SEEEEEEEETT-CECEEEEEEE-SS-GC----------------------------G-------
T ss_pred HHHHHHHHHHHHHhCCCEEEEEEEECC-CCEEEEEEEe-CCCcc----------------------------c-------
Confidence 557888888888899999999999766 3222222111 01000 0
Q ss_pred HhhccceeeecCCCcceeEeecCCceeeecCCCCcccccccCCceEEEEeeC-----CceEeeccccccc---cChHHHH
Q 041101 85 ALAQLPSFMDLYSGIHGEVVITNQPKWISLANSSDSIASHQSNSTRVLIPVF-----GGLIELFAAKHIS---KDQNIIE 156 (433)
Q Consensus 85 ~l~~m~~~f~~g~Gl~Gk~~~sg~h~Wi~~~~~~~~~~~~~gIqTiv~IPv~-----~GVveLGS~~~i~---Ed~~~v~ 156 (433)
...++.+.++.++++.+++. +...+.. ... ..+++.+++||+. -|||.+++.+.-. +|..+++
T Consensus 47 -----~~~l~~~~~~~~~~~~~~~~-~~~~~~~-~~~--~~~~~s~~~vPl~~~~~~~Gvl~~~~~~~~~~~~~d~~~l~ 117 (129)
T PF13492_consen 47 -----SESLPEDDPLIGRALETGEP-VSVPDID-ERD--FLGIRSLLVVPLRSRDRVIGVLCLDSREPEEFSDEDLQLLE 117 (129)
T ss_dssp -----HHCEETTSHHHHHHHHHTS--EEESTCC-C-T--TTTTCEEEEEEEEETTEEEEEEEEEECTTCG-SHHHHHHHH
T ss_pred -----cccCCCCccHHHHHHhhCCe-EEecccc-ccc--CCCCCEEEEEEEeECCEEEEEEEEEECCCCCCCHHHHHHHH
Confidence 00244666777777777765 3332211 111 1667899999983 3999998876543 3455555
Q ss_pred HHHHhc
Q 041101 157 LVLAHC 162 (433)
Q Consensus 157 ~vk~~f 162 (433)
.+-..+
T Consensus 118 ~~a~~~ 123 (129)
T PF13492_consen 118 SLANQL 123 (129)
T ss_dssp HHHHHH
T ss_pred HHHHHH
Confidence 554444
No 101
>PRK06737 acetolactate synthase 1 regulatory subunit; Validated
Probab=47.79 E-value=60 Score=26.04 Aligned_cols=37 Identities=11% Similarity=0.153 Sum_probs=32.3
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
..|.+.-+++||.|.+|..++...|..|.+.++...+
T Consensus 3 ~tisi~v~n~pGVL~Ri~~lf~rRgfNI~Sl~vg~te 39 (76)
T PRK06737 3 HTFSLVIHNDPSVLLRISGIFARRGYYISSLNLNERD 39 (76)
T ss_pred EEEEEEEecCCCHHHHHHHHHhccCcceEEEEecccC
Confidence 3578888899999999999999999999998888444
No 102
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=46.75 E-value=60 Score=28.56 Aligned_cols=38 Identities=8% Similarity=0.180 Sum_probs=34.7
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCE
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGK 425 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~ 425 (433)
.|.|+-+++||.|..+..+|.+.|+.+.-.++.-.+++
T Consensus 5 QISvFlENk~GRL~~~~~~L~eagINiRA~tiAdt~dF 42 (142)
T COG4747 5 QISVFLENKPGRLASVANKLKEAGINIRAFTIADTGDF 42 (142)
T ss_pred EEEEEecCCcchHHHHHHHHHHcCCceEEEEeccccCc
Confidence 47899999999999999999999999999998877765
No 103
>KOG4447 consensus Transcription factor TWIST [Transcription]
Probab=46.34 E-value=14 Score=33.53 Aligned_cols=42 Identities=26% Similarity=0.306 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhHHHHHhcCCCCC--CCchhhHHHHHHHHHHHH
Q 041101 273 TERNRRNKLKDGLFALRALVPKIS--KMDRAAILGDAAEYIKEL 314 (433)
Q Consensus 273 ~Er~RR~~~n~~~~~LrslvP~~~--k~dkasil~~ai~YI~~L 314 (433)
.||.|.+++++.+.-|++|+|+.. ++.+.--|.-+-+||..|
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 699999999999999999999842 222222244444555444
No 104
>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=45.88 E-value=49 Score=28.54 Aligned_cols=36 Identities=6% Similarity=0.135 Sum_probs=29.7
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
.|-+..++++|.|.++|..+...|+.+++..+-...
T Consensus 43 Slifsl~~~pGsL~~iL~~Fa~~gINLt~IESRP~~ 78 (115)
T cd04930 43 TLLFSLKEGFSSLSRILKVFETFEAKIHHLESRPSR 78 (115)
T ss_pred EEEEEeCCCCcHHHHHHHHHHHCCCCEEEEECCcCC
Confidence 344444778999999999999999999999877653
No 105
>PRK06382 threonine dehydratase; Provisional
Probab=45.70 E-value=57 Score=34.13 Aligned_cols=50 Identities=22% Similarity=0.149 Sum_probs=39.4
Q ss_pred CceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEE-----eeCCEEEEEEEeC
Q 041101 384 DRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVT-----TFNGKVLNILRVQ 433 (433)
Q Consensus 384 ~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~is-----t~~~~vl~~f~vE 433 (433)
+..+.|.|.-+++||.|.+|++.|.+.+.+|++.... .-.+...-+|+||
T Consensus 328 ~~~~rl~v~v~D~pG~L~~l~~ii~~~~~nI~~v~~~~~~~~~~~~~~~v~i~ve 382 (406)
T PRK06382 328 GQLVRIECNIPDRPGNLYRIANAIASNGGNIYHAEVDNLRKETPPGFQSVTFTVN 382 (406)
T ss_pred CCEEEEEEEcCCCCCHHHHHHHHHhcCCCcEEEEEEeeccccCCCCcEEEEEEEE
Confidence 5667888888999999999999999999999987764 2234555666664
No 106
>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=43.76 E-value=91 Score=24.51 Aligned_cols=47 Identities=19% Similarity=0.314 Sum_probs=34.6
Q ss_pred ceEEEEEecCceEEEEEEccCC------CChHHHHHHHHHcCCCeEEEEEEEee
Q 041101 375 VRVEVNQINDRDFLIKLLCEHE------RGGFLRLMEAINSLELQVIDANVTTF 422 (433)
Q Consensus 375 ~~VeV~~i~~~~~~I~I~c~~r------~g~L~~Il~aLe~LgL~V~~a~ist~ 422 (433)
+.|.+... ++.+.|++.+.+. ..-+..|-++|...|+.+.+.++..-
T Consensus 27 v~v~l~~~-~~~l~v~~~~~~~~~~~~L~~~~~~L~~~L~~~G~~~~~~~v~~~ 79 (85)
T PF02120_consen 27 VEVKLRLQ-GGNLSVQFTAENPETKELLRQNLPELKERLQAQGLEVVNLSVSQG 79 (85)
T ss_dssp EEEEEEEE-TTEEEEEEE--SSHHHHHHHHTHHHHHHHHHTTT-EEEEEEEESS
T ss_pred EEEEEEEe-CCEEEEEEEECCHHHHHHHHHHHHHHHHHHHHCCCCeEEEEEEEC
Confidence 56777654 6789999999775 33578899999999999999888743
No 107
>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=43.56 E-value=91 Score=24.90 Aligned_cols=32 Identities=19% Similarity=0.301 Sum_probs=25.8
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEE
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVT 420 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~is 420 (433)
.++.|.-+.+||.|.+++++|- +.+|......
T Consensus 2 ~vl~v~ipD~PG~L~~ll~~l~--~anI~~~~y~ 33 (85)
T cd04906 2 ALLAVTIPERPGSFKKFCELIG--PRNITEFNYR 33 (85)
T ss_pred eEEEEecCCCCcHHHHHHHHhC--CCceeEEEEE
Confidence 5688888999999999999999 6666655544
No 108
>PF01590 GAF: GAF domain; InterPro: IPR003018 This domain is present in phytochromes and cGMP-specific phosphodiesterases. cGMP-dependent 3',5'-cyclic phosphodiesterase (3.1.4.17 from EC) catalyses the conversion of guanosine 3',5'-cyclic phosphate to guanosine 5'-phosphate. A phytochrome is a regulatory photoreceptor which exists in 2 forms that are reversibly interconvertible by light, the PR form that absorbs maximally in the red region of the spectrum, and the PFR form that absorbs maximally in the far-red region. This domain is also found in NifA, a transcriptional activator which is required for activation of most Nif operons which are directly involved in nitrogen fixation. NifA interacts with sigma-54.; GO: 0005515 protein binding; PDB: 2Y8H_A 3DBA_B 3CI6_A 3E0Y_B 2W3G_B 2W3D_A 2W3E_A 2Y79_B 2W3H_A 2W3F_A ....
Probab=42.79 E-value=19 Score=30.60 Aligned_cols=117 Identities=17% Similarity=0.218 Sum_probs=73.9
Q ss_pred HHHHHHHHhccCCCCCeEEEEeeeCCCCCce-EEEcCccccCCCCCCcceeeccccccccccccccccccccCcccchhh
Q 041101 5 EKAVEWLRPFVDSKAWDYCVVWKLGDDPSRF-IEWLGCCCSGGVGGGFEYVKVKEESGEEQKFSFCRDAHLKHSARTKAC 83 (433)
Q Consensus 5 ~~Lq~~Lr~l~~~~~W~YavFW~~~~~~~~~-L~W~dg~c~~~~~~~~~~~~~~~~~~~~~~~~~~~d~~~~~~~~~~~~ 83 (433)
+.|+..|+.+++.-+.+++.++.+..+...+ +.+.. +... .+
T Consensus 4 ~~l~~~~~~l~~~l~~~~~~i~~~d~~~~~~~~~~~~----~~~~---------------------------~~------ 46 (154)
T PF01590_consen 4 ELLQRILRELAELLGADRASIFLLDPDGNRLYSVAGV----GLPD---------------------------PP------ 46 (154)
T ss_dssp HHHHHHHHHHHHHHTESEEEEEEEETTTTEEEEEEEE----EGGG---------------------------SE------
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEEecCCCeEEEEEee----cccc---------------------------cc------
Confidence 4588888888888888888887777763322 33332 1000 00
Q ss_pred hHhhccceeeecCCCcceeEeecCCceeeecCCCCccc-------------------c-cccCCceEEEEeeC-C----c
Q 041101 84 EALAQLPSFMDLYSGIHGEVVITNQPKWISLANSSDSI-------------------A-SHQSNSTRVLIPVF-G----G 138 (433)
Q Consensus 84 ~~l~~m~~~f~~g~Gl~Gk~~~sg~h~Wi~~~~~~~~~-------------------~-~~~gIqTiv~IPv~-~----G 138 (433)
.-...+..+.++.|+++.++++..|.+....++- + ...|+++++++|+. + |
T Consensus 47 ----~~~~~~~~~~~~~~~~~~~~~~~~i~d~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~l~vPi~~~g~~~G 122 (154)
T PF01590_consen 47 ----PGGRRLSMDESICGQVLQSREPIVISDVAADPRFAPQIAAQSALRALSSAERPFLAEYGVRSYLCVPIISGGRLIG 122 (154)
T ss_dssp ----HHHEEEETTSSHHHHHHHHTSCEEESSSGGSTTSSCHHHHHHTTBTTTHHHHHHHHTTTESEEEEEEEEETTEEEE
T ss_pred ----cccccccccccHHHHHHhCCCeEeeccccccccccccccccccccccccccccccccccCceeeEeeeecccCcEE
Confidence 0001345678889999999999998866421110 0 03589999999983 2 8
Q ss_pred eEeeccccc----cccChHHHHHHHHhc
Q 041101 139 LIELFAAKH----ISKDQNIIELVLAHC 162 (433)
Q Consensus 139 VveLGS~~~----i~Ed~~~v~~vk~~f 162 (433)
||.|..+.. =.+|..+++.+-...
T Consensus 123 ~l~l~~~~~~~~~~~~d~~ll~~~a~~~ 150 (154)
T PF01590_consen 123 VLSLYRTRPGRPFTEEDLALLESFAQQL 150 (154)
T ss_dssp EEEEEEESSSSS--HHHHHHHHHHHHHH
T ss_pred EEEEEECCCCCCcCHHHHHHHHHHHHHH
Confidence 999988877 234566666555443
No 109
>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=41.23 E-value=1.1e+02 Score=21.15 Aligned_cols=25 Identities=12% Similarity=0.128 Sum_probs=21.6
Q ss_pred CCChHHHHHHHHHcCCCeEEEEEEE
Q 041101 396 ERGGFLRLMEAINSLELQVIDANVT 420 (433)
Q Consensus 396 r~g~L~~Il~aLe~LgL~V~~a~is 420 (433)
.+|.+.+++++|.+.++.|...+.+
T Consensus 13 ~~~~~~~i~~~l~~~~i~i~~i~~~ 37 (60)
T cd04868 13 TPGVAAKIFSALAEAGINVDMISQS 37 (60)
T ss_pred CCCHHHHHHHHHHHCCCcEEEEEcC
Confidence 5889999999999999999777654
No 110
>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=41.13 E-value=1.3e+02 Score=21.83 Aligned_cols=34 Identities=9% Similarity=0.179 Sum_probs=25.6
Q ss_pred EEEEEcc---CCCChHHHHHHHHHcCCCeEEEEEEEe
Q 041101 388 LIKLLCE---HERGGFLRLMEAINSLELQVIDANVTT 421 (433)
Q Consensus 388 ~I~I~c~---~r~g~L~~Il~aLe~LgL~V~~a~ist 421 (433)
.|.|.+. ..+|.+.+|+++|.+.|+.|.-.+.+.
T Consensus 3 ~isvvg~~~~~~~~~~~~i~~~l~~~~I~v~~i~~~~ 39 (66)
T cd04922 3 ILALVGDGMAGTPGVAATFFSALAKANVNIRAIAQGS 39 (66)
T ss_pred EEEEECCCCCCCccHHHHHHHHHHHCCCCEEEEEecC
Confidence 3455553 458999999999999999997665433
No 111
>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=40.46 E-value=48 Score=25.23 Aligned_cols=32 Identities=6% Similarity=0.188 Sum_probs=27.1
Q ss_pred EEEccCCCChHHHHHHHHHcCCCeEEEEEEEee
Q 041101 390 KLLCEHERGGFLRLMEAINSLELQVIDANVTTF 422 (433)
Q Consensus 390 ~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~ 422 (433)
+|.-+.+||-|.+++++|.+ |.+|+..+....
T Consensus 2 ~v~ipdkPG~l~~~~~~i~~-~~nI~~~~~~~~ 33 (68)
T cd04885 2 AVTFPERPGALKKFLELLGP-PRNITEFHYRNQ 33 (68)
T ss_pred EEECCCCCCHHHHHHHHhCC-CCcEEEEEEEcC
Confidence 46667899999999999999 999998876643
No 112
>PF14689 SPOB_a: Sensor_kinase_SpoOB-type, alpha-helical domain; PDB: 1F51_C 2FTK_B 1IXM_B.
Probab=39.82 E-value=73 Score=24.23 Aligned_cols=41 Identities=29% Similarity=0.517 Sum_probs=31.4
Q ss_pred HHHHHHHHHhHHHHHhcCCCCCCCchhhHHHHHHHHHHHHHHHHHHHH
Q 041101 275 RNRRNKLKDGLFALRALVPKISKMDRAAILGDAAEYIKELLQEVDKLQ 322 (433)
Q Consensus 275 r~RR~~~n~~~~~LrslvP~~~k~dkasil~~ai~YI~~Lq~~v~~L~ 322 (433)
|.-|-.+...+..+..++ ...+ .++|.+||+++-+.++.+.
T Consensus 17 R~~RHD~~NhLqvI~gll-qlg~------~~~a~eYi~~~~~~~~~~s 57 (62)
T PF14689_consen 17 RAQRHDFLNHLQVIYGLL-QLGK------YEEAKEYIKELSKDLQQES 57 (62)
T ss_dssp HHHHHHHHHHHHHHHHHH-HTT-------HHHHHHHHHHHHHHHHHHH
T ss_pred HHHhHHHHHHHHHHHHHH-HCCC------HHHHHHHHHHHHHHHHHHH
Confidence 666777777888888887 3333 6788999999999888773
No 113
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=38.94 E-value=68 Score=36.24 Aligned_cols=46 Identities=13% Similarity=0.213 Sum_probs=39.6
Q ss_pred EEEEEE-ccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEeC
Q 041101 387 FLIKLL-CEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRVQ 433 (433)
Q Consensus 387 ~~I~I~-c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~vE 433 (433)
..+.|. +++++|.|+++..+|--.++.|.+|++.+ +|.....|.|.
T Consensus 547 ~~~~~~~~~~~~~~~~~~~~~~a~~~~~~~~a~~~~-~~~~~~~~~v~ 593 (693)
T PRK00227 547 GFFTVIWHGDYPRELVRVLALIAAKGWNILSARMVA-NGPWSAEFDVR 593 (693)
T ss_pred CeEEEEecCCcccHHHHHHHHHHhcCceeeEeEEec-CCceEEEEEEe
Confidence 445554 59999999999999999999999999999 88888888773
No 114
>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=38.65 E-value=1e+02 Score=31.69 Aligned_cols=37 Identities=16% Similarity=0.332 Sum_probs=33.3
Q ss_pred CceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEE
Q 041101 384 DRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVT 420 (433)
Q Consensus 384 ~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~is 420 (433)
+..+.|.|.-+++||.|.++++.+.+.+.+|++....
T Consensus 303 gr~~~l~v~l~D~pG~L~~v~~~i~~~~~NI~~i~~~ 339 (380)
T TIGR01127 303 GRKVRIETVLPDRPGALYHLLESIAEARANIVKIDHD 339 (380)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHHhcCCCcEEEEEee
Confidence 5677899999999999999999999999999988655
No 115
>PRK08198 threonine dehydratase; Provisional
Probab=38.35 E-value=1e+02 Score=32.09 Aligned_cols=38 Identities=21% Similarity=0.343 Sum_probs=34.1
Q ss_pred CceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEe
Q 041101 384 DRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTT 421 (433)
Q Consensus 384 ~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist 421 (433)
++.+.+.|.-+++||.|.+|++.|.+.|.+|+..+...
T Consensus 325 gr~~~l~v~l~D~PG~L~~ll~~i~~~g~NI~~i~~~~ 362 (404)
T PRK08198 325 GRYLKLRVRLPDRPGQLAKLLSIIAELGANVIDVDHDR 362 (404)
T ss_pred CCEEEEEEEeCCCCCHHHHHHHHHhhCCCceEEEEEEE
Confidence 56788999999999999999999999999999888764
No 116
>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=37.40 E-value=1.4e+02 Score=21.10 Aligned_cols=34 Identities=15% Similarity=0.249 Sum_probs=26.2
Q ss_pred EEEEEcc---CCCChHHHHHHHHHcCCCeEEEEEEEe
Q 041101 388 LIKLLCE---HERGGFLRLMEAINSLELQVIDANVTT 421 (433)
Q Consensus 388 ~I~I~c~---~r~g~L~~Il~aLe~LgL~V~~a~ist 421 (433)
.|.|.+. ..++.+.+++++|.+.++.|...+.+.
T Consensus 2 ~i~i~g~~~~~~~~~~~~i~~~l~~~~i~v~~i~~~~ 38 (65)
T cd04892 2 LVSVVGAGMRGTPGVAARIFSALAEAGINIIMISQGS 38 (65)
T ss_pred EEEEECCCCCCCccHHHHHHHHHHHCCCcEEEEEcCC
Confidence 3555543 558899999999999999998876543
No 117
>cd04919 ACT_AK-Hom3_2 ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the aspartokinase (AK) HOM3, a monofunctional class enzyme found in Saccharomyces cerevisiae, and other related ACT domains. AK is the first enzyme in the aspartate metabolic pathway, catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and in fungi, is responsible for the production of threonine, isoleucine and methionine. S. cerevisiae has a single AK, which is regulated by feedback, allosteric inhibition by L-threonine. Recent studies shown that the allosteric transition triggered by binding of threonine to AK involves a large change in the conformation of the native hexameric enzyme that is converted to an inactive one of different shape and substantially smaller hydrodynamic size. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=36.12 E-value=1.7e+02 Score=21.38 Aligned_cols=27 Identities=7% Similarity=0.031 Sum_probs=22.3
Q ss_pred CCCChHHHHHHHHHcCCCeEEEEEEEe
Q 041101 395 HERGGFLRLMEAINSLELQVIDANVTT 421 (433)
Q Consensus 395 ~r~g~L~~Il~aLe~LgL~V~~a~ist 421 (433)
.++|.+.+++++|.+.|++|.-.+.++
T Consensus 13 ~~~~~~~~if~~L~~~~I~v~~i~q~~ 39 (66)
T cd04919 13 NMIGIAGRMFTTLADHRINIEMISQGA 39 (66)
T ss_pred CCcCHHHHHHHHHHHCCCCEEEEEecC
Confidence 458999999999999999996665443
No 118
>PRK13562 acetolactate synthase 1 regulatory subunit; Provisional
Probab=35.99 E-value=95 Score=25.50 Aligned_cols=36 Identities=19% Similarity=0.253 Sum_probs=31.6
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
.|.+.-++++|.|.+|..++...|..|.+.++....
T Consensus 4 ~isvlVeN~~GVL~Rit~lFsRRg~NI~SLtvg~Te 39 (84)
T PRK13562 4 ILKLQVADQVSTLNRITSAFVRLQYNIDTLHVTHSE 39 (84)
T ss_pred EEEEEEECCCCHHHHHHHHHhccCcCeeeEEecccC
Confidence 578888999999999999999999999988887544
No 119
>cd04890 ACT_AK-like_1 ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). This CD includes the first of two ACT domains found C-terminal to the catalytic domain of aspartokinase (AK; 4-L-aspartate-4-phosphotransferase). AK catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP, and is the first enzyme in the pathway of the biosynthesis of the aspartate family of amino acids, lysine, threonine, methionine, and isoleucine. This CD, includes the first ACT domain of the Escherichia coli (EC) isoenzyme, AKIII (LysC) and the Arabidopsis isoenzyme, asparate kinase 1, both enzymes monofunctional and involved in lysine synthesis, as well as the the first ACT domain of Bacillus subtilis (BS) isoenzyme, AKIII (YclM), and of the Saccharomyces cerevisiae AK (Hom3). Also included are the first ACT domains of the Methylomicrobium alcaliphilum AK, the first enzyme of the ectoine biosynthetic pathway. Members of this CD bel
Probab=33.96 E-value=1.7e+02 Score=21.36 Aligned_cols=25 Identities=16% Similarity=0.126 Sum_probs=22.0
Q ss_pred CCCChHHHHHHHHHcCCCeEEEEEE
Q 041101 395 HERGGFLRLMEAINSLELQVIDANV 419 (433)
Q Consensus 395 ~r~g~L~~Il~aLe~LgL~V~~a~i 419 (433)
.++|...+|+++|++.++.|.....
T Consensus 12 ~~~~~~~~if~~l~~~~i~v~~i~t 36 (62)
T cd04890 12 GEVGFLRKIFEILEKHGISVDLIPT 36 (62)
T ss_pred cccCHHHHHHHHHHHcCCeEEEEec
Confidence 4588999999999999999998853
No 120
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=31.23 E-value=2.3e+02 Score=27.82 Aligned_cols=56 Identities=34% Similarity=0.395 Sum_probs=29.9
Q ss_pred Cccccch-HHHHHHHHHHHHhHHHHHhcCCCCCCCchh-hHHHHHHHHHHHHHHHHHHHHHHHhh
Q 041101 265 RPKAKNL-ITERNRRNKLKDGLFALRALVPKISKMDRA-AILGDAAEYIKELLQEVDKLQDELKE 327 (433)
Q Consensus 265 ~~~~~h~-~~Er~RR~~~n~~~~~LrslvP~~~k~dka-sil~~ai~YI~~Lq~~v~~L~~~~~~ 327 (433)
.++..|. +-|+--|+|++.|..+=-+ .||- .-..+-=.-|++|.++-+.|..+.+.
T Consensus 58 r~RL~HLS~EEK~~RrKLKNRVAAQta-------RDrKKaRm~eme~~i~dL~een~~L~~en~~ 115 (292)
T KOG4005|consen 58 RRRLDHLSWEEKVQRRKLKNRVAAQTA-------RDRKKARMEEMEYEIKDLTEENEILQNENDS 115 (292)
T ss_pred HHhhcccCHHHHHHHHHHHHHHHHhhh-------hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555664 4677788888888765432 2321 12222223355666666655554443
No 121
>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=30.55 E-value=1.3e+02 Score=22.50 Aligned_cols=24 Identities=8% Similarity=0.279 Sum_probs=20.8
Q ss_pred CCCChHHHHHHHHHcCCCeEEEEE
Q 041101 395 HERGGFLRLMEAINSLELQVIDAN 418 (433)
Q Consensus 395 ~r~g~L~~Il~aLe~LgL~V~~a~ 418 (433)
..+|.+.+++++|.+.++.|....
T Consensus 13 ~~~gi~~~if~aL~~~~I~v~~~~ 36 (64)
T cd04937 13 GVPGVMAKIVGALSKEGIEILQTA 36 (64)
T ss_pred CCcCHHHHHHHHHHHCCCCEEEEE
Confidence 469999999999999999997433
No 122
>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=29.99 E-value=1.4e+02 Score=29.42 Aligned_cols=17 Identities=18% Similarity=0.483 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHHHHhh
Q 041101 311 IKELLQEVDKLQDELKE 327 (433)
Q Consensus 311 I~~Lq~~v~~L~~~~~~ 327 (433)
||+|++||++||.++..
T Consensus 57 L~~a~~ri~eLe~ql~q 73 (247)
T PF09849_consen 57 LKQAQARIQELEAQLQQ 73 (247)
T ss_pred HHHHHHHHHHHHHHHHh
Confidence 68899999999998855
No 123
>PF13840 ACT_7: ACT domain ; PDB: 3S1T_A 1ZHV_A 3AB4_K 3AB2_O 2DTJ_A 3AAW_A 2RE1_B 3MAH_A 1ZVP_D.
Probab=29.75 E-value=75 Score=24.16 Aligned_cols=34 Identities=9% Similarity=0.079 Sum_probs=27.2
Q ss_pred ceEEEEEEcc----CCCChHHHHHHHHHcCCCeEEEEE
Q 041101 385 RDFLIKLLCE----HERGGFLRLMEAINSLELQVIDAN 418 (433)
Q Consensus 385 ~~~~I~I~c~----~r~g~L~~Il~aLe~LgL~V~~a~ 418 (433)
+-..|.|... ..+|.+.++..+|.+.|+.|...+
T Consensus 5 ~~~~i~v~g~g~~~~~~Gv~a~i~~~La~~~I~i~~is 42 (65)
T PF13840_consen 5 DWAKISVVGPGLRFDVPGVAAKIFSALAEAGINIFMIS 42 (65)
T ss_dssp EEEEEEEEEECGTTTSHHHHHHHHHHHHHTTS-ECEEE
T ss_pred CEEEEEEEccccCCCcccHHHHHHHHHHHCCCCEEEEE
Confidence 4455667666 369999999999999999998888
No 124
>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=29.05 E-value=34 Score=26.70 Aligned_cols=22 Identities=32% Similarity=0.742 Sum_probs=15.2
Q ss_pred CCCeEEEEeeeCCCCCceEEEc
Q 041101 18 KAWDYCVVWKLGDDPSRFIEWL 39 (433)
Q Consensus 18 ~~W~YavFW~~~~~~~~~L~W~ 39 (433)
..|.|.|||-+...++.-.-|.
T Consensus 37 GkWCyiv~wVv~~~~~~~~rW~ 58 (69)
T cd04894 37 GRWCYIVFWVVPRPPSIKVRWD 58 (69)
T ss_pred CcEEEEEEEEecCCCCCcccHH
Confidence 3499999999865533345564
No 125
>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=28.75 E-value=94 Score=24.67 Aligned_cols=25 Identities=28% Similarity=0.298 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh
Q 041101 304 LGDAAEYIKELLQEVDKLQDELKEN 328 (433)
Q Consensus 304 l~~ai~YI~~Lq~~v~~L~~~~~~~ 328 (433)
+..||+-|..||.++++|+.+...+
T Consensus 13 i~~aveti~~Lq~e~eeLke~n~~L 37 (72)
T PF06005_consen 13 IQQAVETIALLQMENEELKEKNNEL 37 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhH
Confidence 6789999999999999999875543
No 126
>PRK08178 acetolactate synthase 1 regulatory subunit; Reviewed
Probab=28.53 E-value=1.9e+02 Score=24.31 Aligned_cols=39 Identities=8% Similarity=0.117 Sum_probs=33.1
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
+...|.+.-++++|.|.+|.-.+..-|..|.+.++...+
T Consensus 7 ~~~tisvlv~N~pGVL~RIaglFsRRgyNIeSLtvg~te 45 (96)
T PRK08178 7 DNVILELTVRNHPGVMSHVCGLFARRAFNVEGILCLPIQ 45 (96)
T ss_pred CCEEEEEEEECCcCHHHHHHHHHhcCCcCeeeEEEeecC
Confidence 346688888999999999999999999998888777544
No 127
>KOG3582 consensus Mlx interactors and related transcription factors [Transcription]
Probab=27.77 E-value=21 Score=39.82 Aligned_cols=58 Identities=22% Similarity=0.311 Sum_probs=48.5
Q ss_pred ccccchHHHHHHHHHHHHhHHHHHhcCCCC-----CCCchhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 041101 266 PKAKNLITERNRRNKLKDGLFALRALVPKI-----SKMDRAAILGDAAEYIKELLQEVDKLQDELK 326 (433)
Q Consensus 266 ~~~~h~~~Er~RR~~~n~~~~~LrslvP~~-----~k~dkasil~~ai~YI~~Lq~~v~~L~~~~~ 326 (433)
....|+.++|+||-.+.++|..|-.|.|.+ .+..++|||. +.|+.+++.-+.+.+..+
T Consensus 787 v~a~sih~lrr~~~~~~dq~~sL~alrp~v~~~~~ql~S~tS~L~---dp~~~~eq~ska~~e~~~ 849 (856)
T KOG3582|consen 787 VSAGSIHALRRTRLNWLDQFCSLPALRPQVLLNLRQLLSSTSILT---DPIKQPEQASKAVTEKIE 849 (856)
T ss_pred eecchHHHHHHHHHHHhhccccHHHHHHHHHhhHHHhhhhhhccc---CcccchHHHHHHHHhhhh
Confidence 667899999999999999999999999963 5567889998 788888887777766544
No 128
>PRK08526 threonine dehydratase; Provisional
Probab=27.75 E-value=1.8e+02 Score=30.44 Aligned_cols=39 Identities=10% Similarity=0.310 Sum_probs=35.3
Q ss_pred CceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEee
Q 041101 384 DRDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTF 422 (433)
Q Consensus 384 ~~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~ 422 (433)
++.+.+.|.-+++||.|.++++.+-+.+.+|+.......
T Consensus 324 ~r~~~~~~~~~d~pg~l~~~~~~~~~~~~~i~~~~~~r~ 362 (403)
T PRK08526 324 YRKMKLHVTLVDKPGALMGLTDILKEANANIVKIDYDRF 362 (403)
T ss_pred CCEEEEEEEcCCCCCHHHHHHHHHccCCCcEEEEEEEec
Confidence 678899999999999999999999999999999888653
No 129
>PRK00227 glnD PII uridylyl-transferase; Provisional
Probab=26.50 E-value=50 Score=37.27 Aligned_cols=42 Identities=12% Similarity=0.205 Sum_probs=38.9
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEEEEEEEe
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKVLNILRV 432 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~vl~~f~v 432 (433)
.+++|....|+|+|..|+.+|. +|.-|.++|.|..+...|-+
T Consensus 632 ~~~e~r~~dr~g~l~~~~~~l~----~~~~~~~~~~g~~~~~~~~~ 673 (693)
T PRK00227 632 NILEVRTEDRRGALGALLGVLP----DLLWITASTPGATMIVQAAL 673 (693)
T ss_pred cEEEEEeCccccHHHHHHHHhh----hhhhHhhcCCCcceEEEEEe
Confidence 6789999999999999999999 99999999999999888854
No 130
>COG4747 ACT domain-containing protein [General function prediction only]
Probab=26.42 E-value=2e+02 Score=25.37 Aligned_cols=45 Identities=31% Similarity=0.422 Sum_probs=32.6
Q ss_pred EEEEEccCCCChHHHHHHHHHcCCC--eEEEEEEEeeCCEEEEEEEeC
Q 041101 388 LIKLLCEHERGGFLRLMEAINSLEL--QVIDANVTTFNGKVLNILRVQ 433 (433)
Q Consensus 388 ~I~I~c~~r~g~L~~Il~aLe~LgL--~V~~a~ist~~~~vl~~f~vE 433 (433)
++-|.-+++||.|.+|+++|-..++ +-+-|-++-- +..+-++++|
T Consensus 71 VlaVEmeD~PG~l~~I~~vl~d~diNldYiYAFv~ek-~KAlli~r~e 117 (142)
T COG4747 71 VLAVEMEDVPGGLSRIAEVLGDADINLDYIYAFVTEK-QKALLIVRVE 117 (142)
T ss_pred EEEEEecCCCCcHHHHHHHHhhcCcCceeeeeeeecC-ceEEEEEEhh
Confidence 3567778999999999999997765 4455554433 6677777765
No 131
>PRK11589 gcvR glycine cleavage system transcriptional repressor; Provisional
Probab=26.25 E-value=1.6e+02 Score=27.71 Aligned_cols=37 Identities=8% Similarity=0.064 Sum_probs=33.1
Q ss_pred EEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC
Q 041101 387 FLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN 423 (433)
Q Consensus 387 ~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~ 423 (433)
+.|.|.-.++||+..+|-++|-+.|++|.+.+.-+.+
T Consensus 96 ~~v~v~G~DrPGIV~~vT~~la~~~iNI~~L~T~~~~ 132 (190)
T PRK11589 96 VWVQVEVADSPHLIERFTALFDSHHMNIAELVSRTQP 132 (190)
T ss_pred EEEEEEECCCCCHHHHHHHHHHHcCCChhheEEeeec
Confidence 5677778899999999999999999999999887765
No 132
>PRK11899 prephenate dehydratase; Provisional
Probab=26.14 E-value=2e+02 Score=28.77 Aligned_cols=45 Identities=0% Similarity=-0.006 Sum_probs=34.9
Q ss_pred EEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeC-CEEEEEEEeC
Q 041101 389 IKLLCEHERGGFLRLMEAINSLELQVIDANVTTFN-GKVLNILRVQ 433 (433)
Q Consensus 389 I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~-~~vl~~f~vE 433 (433)
|-+..+++||.|.++|.++...|+.++...+-... ..--|+|-+|
T Consensus 197 l~~~~~~~pGaL~~vL~~Fa~~gINLtkIeSRP~~~~~~~Y~F~id 242 (279)
T PRK11899 197 FVFRVRNIPAALYKALGGFATNGVNMTKLESYMVGGSFTATQFYAD 242 (279)
T ss_pred EEEEeCCCCChHHHHHHHHHHcCCCeeeEEeeecCCCCceEEEEEE
Confidence 33444689999999999999999999999988664 3455666553
No 133
>smart00338 BRLZ basic region leucin zipper.
Probab=25.79 E-value=2e+02 Score=21.79 Aligned_cols=43 Identities=26% Similarity=0.314 Sum_probs=27.0
Q ss_pred HHHHHHHHHHhHHHHHhcCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 041101 274 ERNRRNKLKDGLFALRALVPKISKMDRAAILGDAAEYIKELLQEVDKLQDELKENE 329 (433)
Q Consensus 274 Er~RR~~~n~~~~~LrslvP~~~k~dkasil~~ai~YI~~Lq~~v~~L~~~~~~~~ 329 (433)
++.+|.++..+-.+-++= ..--.||..|+.+++.|+.+...+.
T Consensus 4 ~k~~rR~~rNR~aA~~~R-------------~rKk~~~~~Le~~~~~L~~en~~L~ 46 (65)
T smart00338 4 EKRRRRRERNREAARRSR-------------ERKKAEIEELERKVEQLEAENERLK 46 (65)
T ss_pred HHHHHHHHHhHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555556666665541 1334588888888888887776654
No 134
>PF05088 Bac_GDH: Bacterial NAD-glutamate dehydrogenase
Probab=25.63 E-value=1.8e+02 Score=36.05 Aligned_cols=48 Identities=15% Similarity=0.173 Sum_probs=38.0
Q ss_pred ceEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCC-----EEEEEEEe
Q 041101 385 RDFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNG-----KVLNILRV 432 (433)
Q Consensus 385 ~~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~-----~vl~~f~v 432 (433)
+.+.++|....++..|+++|-+|+++||.|+...-..+.. ..+|-|.+
T Consensus 488 ~~~~lkiy~~~~~~~Ls~vlPilenlGl~V~~e~~~~i~~~~~~~~~i~~F~l 540 (1528)
T PF05088_consen 488 GRLRLKIYHPGEPLPLSDVLPILENLGLRVIDERPYEIRRADGRRVWIHDFGL 540 (1528)
T ss_pred CeEEEEEEcCCCCcCHHHHHHHHHhCCCEEEEEecceeecCCCceEEEEEEEE
Confidence 4688999999999999999999999999999886554332 35555544
No 135
>cd04916 ACT_AKiii-YclM-BS_2 ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII. This CD includes the second of two ACT domains located C-terminal to the catalytic domain of the lysine plus threonine-sensitive aspartokinase isoenzyme AKIII, a monofunctional class enzyme found in Bacilli (Bacillus subtilis (BS) YclM) and Clostridia species. Aspartokinase is the first enzyme in the aspartate metabolic pathway and catalyzes the conversion of aspartate and ATP to aspartylphosphate and ADP. B. subtilis YclM is reported to be a single polypeptide of 50 kD. AKIII from B. subtilis strain 168 is induced by lysine and repressed by threonine and it is synergistically inhibited by lysine and threonine. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=24.83 E-value=2.7e+02 Score=20.10 Aligned_cols=26 Identities=15% Similarity=0.078 Sum_probs=21.9
Q ss_pred CCCChHHHHHHHHHcCCCeEEEEEEE
Q 041101 395 HERGGFLRLMEAINSLELQVIDANVT 420 (433)
Q Consensus 395 ~r~g~L~~Il~aLe~LgL~V~~a~is 420 (433)
..++.+.+++.+|.+.+++|.-.+.+
T Consensus 13 ~~~~~~~~i~~~L~~~~i~v~~i~~~ 38 (66)
T cd04916 13 NTVGVSARATAALAKAGINIRMINQG 38 (66)
T ss_pred CCccHHHHHHHHHHHCCCCEEEEEec
Confidence 46899999999999999999766543
No 136
>COG0317 SpoT Guanosine polyphosphate pyrophosphohydrolases/synthetases [Signal transduction mechanisms / Transcription]
Probab=24.27 E-value=1.8e+02 Score=33.05 Aligned_cols=41 Identities=10% Similarity=0.151 Sum_probs=36.1
Q ss_pred eEEEEEEccCCCChHHHHHHHHHcCCCeEEEEEEEeeCCEE
Q 041101 386 DFLIKLLCEHERGGFLRLMEAINSLELQVIDANVTTFNGKV 426 (433)
Q Consensus 386 ~~~I~I~c~~r~g~L~~Il~aLe~LgL~V~~a~ist~~~~v 426 (433)
.+.|.|.-.+++|+|.+|+++|-+.+..|.++++.+.++.+
T Consensus 627 ~~~i~v~~~~r~glL~~i~~~i~~~~~ni~~v~~~~~~~~~ 667 (701)
T COG0317 627 PVDIEIRAYDRSGLLRDVSQVLANEKINVLGVNTRSDKDQF 667 (701)
T ss_pred EEEEEEEEccccchHHHHHHHHHhCCCceEEeeccccCCce
Confidence 46678889999999999999999999999999998865443
No 137
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=23.40 E-value=1.3e+02 Score=23.66 Aligned_cols=27 Identities=41% Similarity=0.443 Sum_probs=23.7
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 041101 302 AILGDAAEYIKELLQEVDKLQDELKEN 328 (433)
Q Consensus 302 sil~~ai~YI~~Lq~~v~~L~~~~~~~ 328 (433)
+-|++|+.-|.+|+.+++.|.++++..
T Consensus 40 ~~l~~a~~e~~~Lk~E~e~L~~el~~~ 66 (69)
T PF14197_consen 40 RQLGDAYEENNKLKEENEALRKELEEL 66 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 349999999999999999999987754
No 138
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.20 E-value=1.3e+02 Score=23.86 Aligned_cols=25 Identities=20% Similarity=0.292 Sum_probs=21.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhh
Q 041101 304 LGDAAEYIKELLQEVDKLQDELKEN 328 (433)
Q Consensus 304 l~~ai~YI~~Lq~~v~~L~~~~~~~ 328 (433)
+..||+-|.-||-.|++|+.+...+
T Consensus 13 iqqAvdTI~LLQmEieELKEknn~l 37 (79)
T COG3074 13 VQQAIDTITLLQMEIEELKEKNNSL 37 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhHh
Confidence 6789999999999999999877643
No 139
>cd04918 ACT_AK1-AT_2 ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1). This CD includes the second of two ACT domains located C-terminal to the catalytic domain of a monofunctional, lysine-sensitive, plant aspartate kinase 1 (AK1), which can be synergistically inhibited by S-adenosylmethionine (SAM). This isoenzyme is found in higher plants, Arabidopsis thaliana (AT) and Zea mays, and also in Chlorophyta. In its inactive state, Arabidopsis AK1 binds the effectors lysine and SAM (two molecules each) at the interface of two ACT1 domain subunits. The second ACT domain (ACT2), this CD, does not interact with an effector. Members of this CD belong to the superfamily of ACT regulatory domains.
Probab=22.94 E-value=2.3e+02 Score=21.18 Aligned_cols=31 Identities=6% Similarity=-0.066 Sum_probs=24.1
Q ss_pred CCChHHHHHHHHHcCCCeEEEEEEEeeCCEE
Q 041101 396 ERGGFLRLMEAINSLELQVIDANVTTFNGKV 426 (433)
Q Consensus 396 r~g~L~~Il~aLe~LgL~V~~a~ist~~~~v 426 (433)
.+|.+.+++++|.+.|+.|.-.+.++.+-.+
T Consensus 13 ~~~~~~~i~~aL~~~~I~v~~i~~g~s~~si 43 (65)
T cd04918 13 SSLILERAFHVLYTKGVNVQMISQGASKVNI 43 (65)
T ss_pred CccHHHHHHHHHHHCCCCEEEEEecCccceE
Confidence 4789999999999999999766655444333
No 140
>PRK11020 hypothetical protein; Provisional
Probab=22.61 E-value=1.6e+02 Score=25.61 Aligned_cols=53 Identities=23% Similarity=0.223 Sum_probs=40.6
Q ss_pred HHHHHHHHHHhHHHHHhcCCCCCCCchhhHHHHHHHHHHHHHHHHHHHHHHHh
Q 041101 274 ERNRRNKLKDGLFALRALVPKISKMDRAAILGDAAEYIKELLQEVDKLQDELK 326 (433)
Q Consensus 274 Er~RR~~~n~~~~~LrslvP~~~k~dkasil~~ai~YI~~Lq~~v~~L~~~~~ 326 (433)
+++-=.++|++++.+|-=++.....+.+.++..--+-|..|..++..|.....
T Consensus 3 ~K~Eiq~L~drLD~~~~Klaaa~~rgd~~~i~qf~~E~~~l~k~I~~lk~~~~ 55 (118)
T PRK11020 3 EKNEIKRLSDRLDAIRHKLAAASLRGDAEKYAQFEKEKATLEAEIARLKEVQS 55 (118)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555789999999988777777777777888888888888888888776544
No 141
>PRK05022 anaerobic nitric oxide reductase transcription regulator; Provisional
Probab=22.00 E-value=1e+02 Score=33.23 Aligned_cols=72 Identities=11% Similarity=0.027 Sum_probs=49.4
Q ss_pred eeecCCC-cceeEeecCCceeeecCCCCccccc---------ccCCceEEEEeeC-----CceEeeccccc---cccChH
Q 041101 92 FMDLYSG-IHGEVVITNQPKWISLANSSDSIAS---------HQSNSTRVLIPVF-----GGLIELFAAKH---ISKDQN 153 (433)
Q Consensus 92 ~f~~g~G-l~Gk~~~sg~h~Wi~~~~~~~~~~~---------~~gIqTiv~IPv~-----~GVveLGS~~~---i~Ed~~ 153 (433)
.|.+|+| ..|.++.+|.++.+.+... ++.++ ..||..++|||+. -|||.+.+... -.+|..
T Consensus 65 ~~~~geGP~l~av~~~g~~v~v~~~~~-~p~~~~~~~~~~~~~~gi~S~l~vPL~~~~~~~GvL~l~~~~~~~f~~~~~~ 143 (509)
T PRK05022 65 RFALEEHPRLEAILRAGDPVRFPADSE-LPDPYDGLIPGVQESLPVHDCMGLPLFVDGRLIGALTLDALDPGQFDAFSDE 143 (509)
T ss_pred ccCCCcchHHHHHHhcCCeEEEecCCC-CCcccccccccccccCCcceEEEEEEEECCEEEEEEEEeeCCCCcCCHHHHH
Confidence 3668898 7788888899987765432 22222 2478889999982 38899987653 455678
Q ss_pred HHHHHHHhccc
Q 041101 154 IIELVLAHCNT 164 (433)
Q Consensus 154 ~v~~vk~~f~~ 164 (433)
++..+-.++..
T Consensus 144 ~l~~~a~~~a~ 154 (509)
T PRK05022 144 ELRALAALAAA 154 (509)
T ss_pred HHHHHHHHHHH
Confidence 88777766653
No 142
>PF04508 Pox_A_type_inc: Viral A-type inclusion protein repeat ; InterPro: IPR007596 The repeat is found in the A-type inclusion protein of the Poxvirus family [].; GO: 0016032 viral reproduction
Probab=21.94 E-value=1.2e+02 Score=18.94 Aligned_cols=17 Identities=24% Similarity=0.501 Sum_probs=13.1
Q ss_pred HHHHHHHHHHHHHHHhh
Q 041101 311 IKELLQEVDKLQDELKE 327 (433)
Q Consensus 311 I~~Lq~~v~~L~~~~~~ 327 (433)
|..|+.+|..|++++.+
T Consensus 3 ~~rlr~rI~dLer~L~~ 19 (23)
T PF04508_consen 3 MNRLRNRISDLERQLSE 19 (23)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 56788888888887753
No 143
>PF14992 TMCO5: TMCO5 family
Probab=21.76 E-value=1.1e+02 Score=30.66 Aligned_cols=25 Identities=24% Similarity=0.413 Sum_probs=22.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 041101 303 ILGDAAEYIKELLQEVDKLQDELKE 327 (433)
Q Consensus 303 il~~ai~YI~~Lq~~v~~L~~~~~~ 327 (433)
+..|+++||++||++++.++.+++.
T Consensus 145 l~eDq~~~i~klkE~L~rmE~ekE~ 169 (280)
T PF14992_consen 145 LCEDQANEIKKLKEKLRRMEEEKEM 169 (280)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4889999999999999999998774
No 144
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=20.58 E-value=1.2e+02 Score=22.15 Aligned_cols=20 Identities=30% Similarity=0.456 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHHhhhhc
Q 041101 311 IKELLQEVDKLQDELKENED 330 (433)
Q Consensus 311 I~~Lq~~v~~L~~~~~~~~~ 330 (433)
|..|+++|+.|+.++..++.
T Consensus 1 i~aLrqQv~aL~~qv~~Lq~ 20 (46)
T PF09006_consen 1 INALRQQVEALQGQVQRLQA 20 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHHHHHHHHH
Confidence 56788888888888776654
Done!